US20110239315A1 - Modular dna-binding domains and methods of use - Google Patents

Modular dna-binding domains and methods of use Download PDF

Info

Publication number
US20110239315A1
US20110239315A1 US13/019,526 US201113019526A US2011239315A1 US 20110239315 A1 US20110239315 A1 US 20110239315A1 US 201113019526 A US201113019526 A US 201113019526A US 2011239315 A1 US2011239315 A1 US 2011239315A1
Authority
US
United States
Prior art keywords
recognition
repeat
dna
polypeptide
dna sequence
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
US13/019,526
Inventor
Ulla Bonas
Jens Boch
Jana Streubel
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Individual
Original Assignee
Individual
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from EP09165328A external-priority patent/EP2206723A1/en
Priority to US13/019,526 priority Critical patent/US20110239315A1/en
Application filed by Individual filed Critical Individual
Priority to US13/218,050 priority patent/US8470973B2/en
Publication of US20110239315A1 publication Critical patent/US20110239315A1/en
Priority to PCT/IB2012/000373 priority patent/WO2012104729A1/en
Priority to US13/755,826 priority patent/US20130217119A1/en
Priority to US14/153,241 priority patent/US9017967B2/en
Priority to US14/625,698 priority patent/US9453054B2/en
Priority to US15/222,498 priority patent/US9809628B2/en
Priority to US15/724,420 priority patent/US10590175B2/en
Priority to US16/781,646 priority patent/US11827676B2/en
Abandoned legal-status Critical Current

Links

Images

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/001—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof by chemical synthesis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • C12N15/8217—Gene switch
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • C12N15/8237—Externally regulated expression systems
    • C12N15/8238—Externally regulated expression systems chemically inducible, e.g. tetracycline
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • C12N15/8237—Externally regulated expression systems
    • C12N15/8239—Externally regulated expression systems pathogen inducible
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • C12N15/825—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine involving pigment biosynthesis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/04—Plant cells or tissues
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06—Animal cells or tissues; Human cells or tissues
    • C12N5/0602—Vertebrate cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/09—Fusion polypeptide containing a localisation/targetting motif containing a nuclear localisation signal
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/60—Fusion polypeptide containing spectroscopic/fluorescent detection, e.g. green fluorescent protein [GFP]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/80—Fusion polypeptide containing a DNA binding domain, e.g. Lacl or Tet-repressor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2501/00—Active agents used in cell culture processes, e.g. differentation
    • C12N2501/998—Proteins not provided for elsewhere
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/119—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being proteinic

Definitions

  • the present invention refers to methods for selectively recognizing a base pair in a target DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a target DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.
  • Phytopathogenic bacteria of the genus Xanthomonas cause severe diseases on many important crop plants.
  • the bacteria translocate an arsenal of effectors including members of the large transcription activator-like (TAL)/AvrBs3-like effector family via the type III secretion system into plant cells (Kay & Bonas (2009) Curr. Opin. Microbiol. 12:37-43, White & Yang (2009) Plant Physiol . doi:10.1104/pp. 1109.139360; Schornack et al. (2006) J. Plant Physiol. 163:256-272).
  • TAL large transcription activator-like
  • TAL effectors key virulence factors of Xanthomonas , contain a central domain of tandem repeats, nuclear localization signals (NLSs), and an activation domain (AD) and act as transcription factors in plant cells (Kay et al. (2007) Science 318:648-651; Römer et al. (2007) Science 318:645-648; Gu et al. (2005) Nature 435, 1122-1125; FIG. 1 a ).
  • vesicatoria contains 17.5 repeats and induces expression of UPA (upregulated by AvrBs3) genes including the Bs3 resistance gene in pepper plants (Kay et al. (2007) Science 318:648-651; Römer et al. (2007) Science 318:645-648; Marois et al. (2002) Mol. Plant - Microbe Interact. 15:637-646).
  • the number and order of repeats in a TAL effector determine its specific activity (Herbers et al. (1992) Nature 356:172-174).
  • the repeats were shown to be essential for DNA-binding of AvrBs3 and constitute a novel DNA-binding domain (Kay et al. (2007) Science 318:648-651). How this domain contacts DNA and what determines specificity has remained enigmatic.
  • the ability to specifically design and generate DNA-binding domains that recognize a desired DNA target is highly desirable in biotechnology. Such ability can be useful for the development of custom transcription factors with the ability to modulate gene expression upon target DNA binding. Examples include the extensive work done with the design of custom zinc finger DNA-binding proteins specific for a desired target DNA sequence (Choo et al. (1994) Nature 372:645; Pomerantz et al., (1995) Science 267:93-96; Liu et al., Proc. Natl. Acad. Sci. USA 94:5525-5530 (1997); Guan et al. (2002) Proc. Natl. Acad. Sci. USA 99:13296-13301; U.S. Pat. No.
  • polypeptides containing designer DNA-binding domains can be utilized to modify the actual target DNA sequence by the inclusion of DNA modifying domains, such as a nuclease catalytic domain, within the polypeptide.
  • DNA modifying domains such as a nuclease catalytic domain
  • examples of such include the DNA binding domain of a meganuclease/homing endonuclease DNA recognition site in combination with a non-specific nuclease domain (see US Pat. Appl. 2007/0141038), modified meganuclease DNA recognition site and/or nuclease domains from the same or different meganucleases (see U.S. Pat. App. Pub.
  • a domain with nuclease activity typically from a type IIS restriction endonuclease such as FokI (Bibikova et al. (2003) Science 300:764; Urnov et al. (2005) Nature 435, 646; Skukla, et al. (2009) Nature 459, 437-441; Townsend et al. (2009) Nature 459:442445; Kim et al. (1996) Proc. Natl. Acad. Sci. USA 93:1156-1160; U.S. Pat. No. 7,163,824).
  • FokI Bibikova et al. (2003) Science 300:764; Urnov et al. (2005) Nature 435, 646; Skukla, et al. (2009) Nature 459, 437-441; Townsend et al. (2009) Nature 459:442445; Kim et al. (1996) Proc. Natl. Acad. Sci. USA 93:1156-1160; U.S
  • the current methods utilized for identifying custom zinc finger DNA-binding domains employ combinatorial selection-based methods utilizing large randomized libraries (typically >10 8 in size) to generate multi-finger domains with desired DNA specificity (Greisman & Pabo (1997) Science 275:657-661; Hurt et al. (2003) Proc Natl Acad Sci USA 100:12271-12276; Isalan et al. (2001) Nat Biotechnol 19:656-660.
  • Such methods are time intensive, technically demanding and potentially quite costly.
  • the identification of a simple recognition code for the engineering of DNA-binding polypeptides would represent a significant advancement over the current methods for designing DNA-binding domains that recognize a desired nucleotide target.
  • the present invention provides a method for producing a polypeptide that selectively recognizes a base pair in a DNA sequence, the method comprising synthesizing a polypeptide comprising a repeat domain, wherein the repeat domain comprises at least one repeat unit derived from a transcription activator-like (TAL) effector, wherein the repeat unit comprises a hypervariable region which determines recognition of a base pair in the DNA sequence, wherein the repeat unit is responsible for the recognition of one base pair in the DNA sequence.
  • TAL transcription activator-like
  • These polypeptides of the invention comprise repeat units of the present invention and can be constructed by a modular approach by preassembling repeat units in target vectors that can subsequently be assembled into a final destination vector.
  • the invention provides the polypeptide produced the this method as well as DNA sequences encoding the polypeptides and host organisms and cells comprising such DNA sequences.
  • the present invention provides a method for selectively recognizing a base pair in a target DNA sequence by a polypeptide wherein said polypeptide comprises at least a repeat domain comprising repeat units wherein in said repeat units each comprise a hypervariable region which determines recognition of a base pair in said target DNA sequence.
  • the inventors have determined those amino acids in a DNA-binding polypeptide responsible for selective recognition of base pairs in a target DNA sequence. With elucidation of the recognition code, a general principle for recognizing specific base pairs in a target DNA sequence by selected amino acids in a polypeptide has been determined. The inventors have found that distinct types of repeat units that are part of a repeat unit array of varying length have the capacity to recognize one defined/specific base pair. Within each repeat unit forming a repeat domain, a hypervariable region is responsible for the specific recognition of a base pair in a target DNA sequence.
  • the present invention provides not only a method for selectively recognizing a base pair in a target DNA sequence by a polypeptide comprising at least a repeat domain comprising repeat units but also methods wherein target DNA sequences can be generated which are selectively recognized by repeat domains in a polypeptide.
  • the invention also provides for a method for constructing polypeptides that recognize specific DNA sequences.
  • These polypeptides of the invention comprise repeat units of the present invention and can be constructed by a modular approach by preassembling repeat units in target vectors that can subsequently be assembled into a final destination vector.
  • the invention also provides a method for targeted modulation of gene expression by constructing modular repeat units specific for a target DNA sequence of interest, modifying a polypeptide by the addition of said repeat units so as to enable said polypeptide to now recognize the target DNA, introducing or expressing said modified polypeptide in a prokaryotic or eurkaryotic cell so as to enable said modified polypeptide to recognize the target DNA sequence, and modulation of the expression of said target gene in said cell as a result of such recognition.
  • the invention also provides a method for directed modification of a target DNA sequence by the construction of a polypeptide including at least a repeat domain of the present invention that recognizes said target DNA sequence and that said polypeptide also contains a functional domain capable of modifying the target DNA (such as via site specific recombination, restriction or integration of donor target sequences) thereby enabling targeted DNA modifications in complex genomes.
  • the invention further provides for the production of modified polypeptides including at least a repeat domain comprising repeat units wherein a hypervariable region within each of the repeat units determines selective recognition of a base pair in a target DNA sequence.
  • DNA is provided which encodes for a polypeptide containing a repeat domain as described above.
  • DNA is provided which is modified to include one or more base pairs located in a target DNA sequence so that said each of the base pairs can be specifically recognized by a polypeptide including a repeat domain having corresponding repeat units, each repeat unit comprising a hypervariable region which determines recognition of the corresponding base pair in said DNA.
  • polypeptides and DNAs are provided. Additionally provided are plants, plant parts, seeds, plant cells and other non-human host cells transformed with the isolated nucleic acid molecules of the present invention and the proteins or polypeptides encoded by the coding sequences of the present invention. Still further, the polypeptides and DNA described herein can be introduced into animal and human cells as well as cells of other organisms like fungi or plants.
  • the invention focuses on a method for selectively recognizing base pairs in a target DNA sequence by a polypeptide wherein said polypeptide comprises at least a repeat domain comprising repeat units wherein each repeat unit contains a hypervariable region which determines recognition of a base pair in said target DNA sequence wherein consecutive repeat units correspond to consecutive base pairs in said target DNA sequence.
  • FIG. 1 Model for DNA-target specificity of TAL effectors.
  • TAL effectors contain central tandem repeat units (red), nuclear localization signals (NLS) and an activation domain (AD). Amino acid sequence of the first repeat of AvrBs3. Hypervariable amino acids 12 and 13 are shaded in gray.
  • B Hypervariable amino acids at position 12 and 13 of the 17.5 AvrBs3 repeat units are aligned to the UPA-box consensus (21).
  • C Repeat units of TAL effectors and predicted target sequences in promoters of induced genes were aligned manually.
  • Nucleotides in the upper DNA strand that correspond to the hypervariable amino acids in each repeat were counted based on the following combinations of eight effectors and experimentally identified target genes: AvrBs3/Bs3, UPA10, UPA12, UPA14, UPA19, UPA20, UPA21, UPA23, UPA25, AvrBs3 ⁇ rep16/Bs3-E, AvrBs3 ⁇ rep109/Bs3, AvrHah1/Bs3, AvrXa27/Xa27, PthXo1/Xa13, PthXo6/OsTFX1, PthXo7/OsTFIIA ⁇ 1 (see FIG. 5 ).
  • Predominant combinations are shaded in gray. An asterisk indicates that amino acid 13 is missing in this repeat type.
  • FIG. 2 Target DNA sequences of Hax2, Hax3, and Hax4.
  • (C) Specific inducibility of the Hax-boxes by Hax effectors. GUS reporter constructs were codelivered via A. tumefaciens into N. benthamiana with 35S-driven hax2, hax3, hax4, and empty T-DNA ( ⁇ ), respectively (error bars indicate SD; n 3 samples; 4-MU, 4-methyl-umbelliferone). 35S::uidA (+) served as control. Leaf discs were stained with X-Gluc (5-bromo-4-chloro-3-indolyl- ⁇ -D-glucuronide).
  • FIG. 3 DNA base pair recognition specificities of repeat types.
  • A Hax4- and ArtX-box-derivatives were cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
  • B Specificity of NG-, HD-, NI-, and NS-repeat units. Hax4-inducibility of Hax4-box derivatives permutated in repeat type target bases (gray background).
  • C Specificity of NN-repeat units. Artificial effector ArtX1 and predicted target DNA sequences. ArtX1-inducibility of ArtX1 box derivatives permutated in NN-repeat target bases (gray background).
  • D Artificial effectors ArtX2 and ArtX3 and derived DNA target sequences.
  • (E) Specific inducibility of ArtX-boxes by artificial effectors.
  • (A)-(E) GUS reporter constructs were co-delivered via A. tumefaciens into N. benthamiana with 35S-driven hax4, artX1, artX2, or artX3 genes, and empty T-DNA ( ⁇ ), respectively.
  • 35S::uidA (+) served as control.
  • Leaf discs were stained with X-Gluc. For quantitative data see FIG. 11 .
  • FIG. 4 A minimal number of repeat units is required for transcriptional activation.
  • A Artificial ArtHD effectors with different numbers (0.5-15.5) of HD-repeat units (total 1.5 to 16.5 repeat units).
  • B An ArtHD target box consisting of TA and 17 C was cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
  • FIG. 5 Alignment of DNA target sequences in promoters of induced genes with the hypervariable amino acids 12 and 13 of TAL effector repeat units.
  • AvrBs3, AvrBs3 ⁇ rep16, AvrBs3 ⁇ rep109, and AvrHah1 were aligned to the UPA-box in the promoter of the pepper ECW-30R Bs3 gene (accession: EU078684).
  • AvrBs3 ⁇ rep16 and AvrBs3 ⁇ rep109 are deletion derivatives of AvrBs3 in which repeat units 11-14 and repeat units 12-14 were deleted, respectively.
  • AvrBs3, AvrBs3 ⁇ rep109, and AvrHah1, but not AvrBs3 ⁇ rep16 induce the HR in ECW-30R plants.
  • Xa27 (accession: AY986492) is induced by AvrXa27 in rice cultivar IRBB27 leading to an HR, but not xa27 (accession: AY986491) in rice cultivar IR24.
  • D Repeat units of PthXo1 were aligned to a putative target sequence in the promoter of the rice Xa13/Os8N3 gene.
  • Xa13 (accession: DQ421396) is induced by PthXo1 in rice cultivar IR24 leading to susceptibility, but not xal3 (accession: DQ421394) in rice cultivar IRBB13.
  • FIG. 6 The DNA region protected by AvrBs3 ⁇ rep16 is 4 bp shorter than with AvrBs3.
  • DNaseI footprinting revealed that AvrBs3 protected 37 nucleotides of the sense strand and 36 nucleotides of the antisense strand of the Bs3 promoter, and AvrBs3 ⁇ rep16 protected 30 nucleotides of the sense strand and 32 nucleotides of the antisense strand of the Bs3-E promoter.
  • the UPA-box and the predicted AvrBs3 ⁇ rep16-box are underlined.
  • UPA20-ubm-r16 (lower part) promoter sequences protected by AvrBs3 and AvrBs3 ⁇ rep16.
  • the UPA20-ubmr16 promoter is a UPA20 promoter derivative with a 2 bp substitution (GA to CT, bold italic) that results in recognition by both, AvrBs3 and AvrBs3 ⁇ rep16.
  • DNaseI footprinting revealed that 35 nucleotides of the sense strand and 34 nucleotides of the antisense strand are protected by AvrBs3 (UPA-box is underlined), and 31 nucleotides of the sense strand and 32 nucleotides of the antisense strand are protected by AvrBs3 ⁇ rep16 (AvrBs3 ⁇ rep16-box is underlined).
  • DNA regions shaded in green (AvrBs3) or red (AvrBs3 ⁇ rep16) refer to the core footprints which were protected by AvrBs3 and AvrBs3 ⁇ rep16, respectively, in every experiment, even with low protein amounts (equal molarity of DNA and protein dimers).
  • DNA regions shaded in gray refer to nucleotides which were not protected in all of the 4 experiments at all protein concentrations by the given proteins. Please note that the 5′ ends of the AvrBs3- and AvrBs3 ⁇ rep16-protected regions are identical. Dashed vertical lines indicate the differences between the 3′ ends of the AvrBs3- and AvrBs3 ⁇ rep16-protected promoter regions which corroborates our model that one repeat contacts one base pair in the DNA.
  • FIG. 7 Bs3 and Bs3-E promoter sequences protected by AvrBs3 and AvrBs3 ⁇ rep16, respectively.
  • AvrBs3 DNaseI footprint on the Bs3 promoter sequence (A, upper/sense DNA strand; B, lower/antisense DNA strand).
  • AvrBs3 ⁇ rep16 DNaseI footprint on the Bs3-E promoter sequence (C, upper, sense DNA strand; D, lower antisense DNA strand).
  • Nucleotides covered are marked by a green (AvrBs3) or red (AvrBs3 ⁇ rep16) box. Numbers below refer to nucleotide positions relative to the transcription start (+1) in the presence of AvrBs3 (a, b) or AvrBs3 ⁇ rep16 (c, d), respectively. (bottom) DNA PCR product used for DNaseI footprinting, amplified from the Bs3 (a, b) or Bs3-E (c, d) promoters, respectively. The protected regions on the single DNA strands are indicated by gray boxes. Numbers below refer to nucleotide positions relative to the transcription start (+1) in the presence of AvrBs3 (a, b) or AvrBs3 ⁇ rep16 (c, d), respectively. The experiments were repeated three times with similar results.
  • FIG. 8 UPA20-ubm-r16 promoter sequence protected by AvrBs3 and AvrBs3 ⁇ rep16.
  • a representative DNaseI footprint experiment AvrBs3 and AvrBs3 ⁇ rep16 DNaseI footprint on the UPA20-ubm-r16 promoter sequence (A), upper, sense DNA strand; (B) lower, antisense DNA strand). (top Fluorescently labelled PCR product was incubated with a 5 ⁇ molar excess of His6::AvrBs3, His6::AvrBs3 ⁇ rep16 and BSA (calculated for protein dimers), respectively, treated with DNaseI and analyzed on a capillary sequencer.
  • the y axis of the electropherogram shows the relative fluorescence intensity corresponding to the 5′-6-FAM-labelled sense strand (a) or the 5′-HEX-labelled antisense strand (b) of the PCR product on an arbitrary scale.
  • the traces for the reactions with His6::AvrBs3 (green), His6::AvrBs3 ⁇ rep16 (red) and the negative control BSA (black) were superimposed.
  • a reduction of peak height in the presence of AvrBs3 and AvrBs3 ⁇ rep16 in comparison to the negative control corresponds to protection.
  • the protected regions are indicated by green (AvrBs3) and red (AvrBs3 ⁇ rep16) vertical lines.
  • FIG. 9 GUS reporter constructs.
  • Target DNA sequences (TAL effector-box) were inserted 5′ of the minimal tomato Bs4 promoter (41) (pBs4; ⁇ 50 to +25) sequence and transferred by GATEWAY recombination into the A.
  • tumefaciens T-DNA vector pGWB330 constructing a fusion to a promoterles uidA ( ⁇ -glucuronidase, GUS) gene. attB1, attB2; GATEWAY recombination sites.
  • FIG. 10 Recognition specificity of the putative repeat 0 in Hax3.
  • (A) Amino acids 12 and 13 of Hax3-repeat units and four possible target Hax3-boxes with permutations in the position corresponding to repeat 0. (B) The target boxes were cloned in front of the minimal tomato Bs4 promoter into a GUS reporter vector. (C) GUS activities with 35S-driven hax3 or empty T-DNA ( ⁇ ) codelivered via A. tumefaciens with the GUS reporter constructs into N. benthamiana leaf cells (4-MU, 4-methyl-umbelliferone; n 3; error bars indicate SD). For qualitative assays, leaf discs were stained with X-Gluc. The experiment was performed twice with similar results.
  • FIG. 11 DNA base pair recognition specificities of repeat types.
  • Hax4- and ArtX-box-derivatives were cloned in front of the minimal Bs4 promoter into a GUS reporter vector. Quantitative data to FIG. 3 .
  • A Specificity of NG-, HD-, NI-, and NS-repeat units. Hax4-inducibility of Hax4-box derivatives permutated in repeat type target bases.
  • B Specificity of NN-repeat units. ArtX1-inducibility of ArtX1-box derivatives permutated in NN-repeat target bases.
  • C Specific inducibility of ArtX-boxes by artificial effectors ArtX1, ArtX2, and ArtX3, respectively.
  • FIG. 12 Predicted target DNA sequences for AvrXa10.
  • A Amino acids 12 and 13 of the AvrXa10-repeat units and two possible target boxes with predicted NN type repeat-specificity A or G.
  • B AvrXa10 target boxes were cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
  • FIG. 13 Recognition specificity of the repeat type IG in Hax2.
  • A Amino acids 12 and 13 of Hax2 repeat units and four possible target Hax2-boxes for repeat type IG.
  • B The Hax2 target boxes were cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
  • FIG. 14 Hax2 induces expression of PAP1 in A. thaliana.
  • A Leaves of A. thaliana were inoculated with A. tumefaciens strains delivering T-DNA constructs for 35S-driven expression of hax2, hax3, and hax4, respectively. Expression of hax2, but not of hax3 and hax4 induced purple pigmentation suggestive of anthocyanin production. The photograph was taken 7 days post inoculation.
  • B Transgenic A. thaliana line carrying hax2 under control of an ethanol-inducible promoter. Plants of a segregating T2 population were sprayed with 10% ethanol to induce expression of the transgene. Only hax2-transgenic plants accumulated anthocyanin. The photograph was taken 6 days post treatment.
  • C Semiquantitative RT-PCR of hax2 (29 cycles), PAP1 (32 cycles), and elongation factor Tu (EF-Tu, 32 cycles) with cDNA from hax2-transgenic plants of three independent A. thaliana lines before ( ⁇ ) and 24 h after (+) spraying with 10% ethanol.
  • D Amino acids 12 and 13 of Hax2 repeat units and target DNA sequence of Hax2.
  • E The promoter of PAP1 from A. thaliana Col-0 contains an imperfect Hax2-box. Mismatches to the predicted Hax2-box are coloured in red. A putative TATA-box, the natural transcription start site (+1), and the first codon of the PAP1 coding sequence are indicated.
  • FIG. 15 Table I. Predicted DNA target sequences of TAL effectors
  • the table shows repeat sequences of TAL effectors and the predicted DNA target sequences used from amino acids 12 and 13 of the repeat units.
  • FIG. 16 Protein sequences of AvrBs3, Hax2, Hax3, Hax4
  • FIG. 17 The effector ARTBs4 induces expression of the minimal Bs4 promoter
  • the Hax4(mut) box contains four base pair exchanges in comparison to the Hax4 box.
  • GUS reporter constructs were codelivered via Agrobacterium tumefaciens into N. benthamiana with 35S-driven hax4 (grey bars), ARTBs4 (white bars) and empty T-DNA (ev, black bars), respectively (error bars indicate SD). 4-MU, 4-methyl-umbelliferone. 35S::uidA (GUS, grey bar) served as control. Leaf disks were stained with X-Gluc (5-bromo-4-chloro-3-indolyl- ⁇ -D-glucuronide).
  • FIG. 18 Diagram for “Golden gate” cloning of repeat domains and effectors
  • B The building blocks are assembled into a target vector by ligation of matching overhangs using “Golden gate” cloning (restriction-ligation). In general, the resulting assembly product does not contain any of the target sites used for cloning.
  • FIG. 19 Alternative method for generation of designer effectors via Golden Gate cloning
  • FIGS. 19 A-D depict various vectors described in the methods disclosed in Example 3 below as well as provide a schematic of the method.
  • FIG. 20 Experiments to analyze novel repeat specificities
  • FIG. 21 TAL repeat specificities
  • Agrobacterium -mediated expression of artificial TALs and corresponding reporter constructs in Nicotiana benthamiana Leaf disks were sampled two days post transformation, stained for GUS reporter activity and destained with ethanol. A blue colour indicates expression of the reporter construct and therefore, an activity of the TAL. Empty vector (ev) and constitutively expressed GUS were used as negative control, respectively. Novel repeat specificities are colored in red. Repeat types with strong DNA recognition properties are: NH, NP, NT, and HN. Repeat types with weak DNA recognition properties are: NG, N*, NK, SH, SN, IS.
  • FIG. 22 Quantitative analysis of known repeat specificities.
  • FIG. 23 Quantitative analysis of novel repeats with multiple specificities
  • FIG. 24 Quantitative analysis of novel repeats with only one specificity
  • FIG. 25 Quantitative analysis of novel repeats with novel specificities
  • FIG. 26 Experimental setup to study specificity of repeat types with low DNA recognition potential
  • the artificial effectors were assembled to contain 6, 4, 3, or 2 repeats, respectively, with unknown specificity (designated XX) in addition to Hax3 repeats.
  • Target boxes in the reporter constructs contain A, C, G, or T, respectively, at positions corresponding to the “XX” repeats. The rest of the target DNA boxes is equivalent to the Hax3 box.
  • FIG. 27A-C Experimental setup to study specificity of repeat types with low DNA recognition potential
  • the artificial effectors were assembled to contain 4, 3, or 2 repeats, respectively, as “test repeats” with unknown specificity (designated X) in addition to Hax3 repeats (see, FIG. 26 for details).
  • Target boxes in the reporter constructs contain A, C, G, or T, respectively, at positions corresponding to the test repeats. The rest of the target DNA boxes is equivalent to the Hax3 box.
  • TALs with four or more combined N* repeats do not show a specificity, a combination of three or two N* repeats indicates a specificity for T, or T and C, respectively.
  • N* and NI are obviously repeat types with weak DNA recognition properties.
  • FIG. 27A HD
  • FIG. 27B N*
  • FIG. 27C NI.
  • nucleotide and amino acid sequences listed in the accompanying figures and the sequence listing are shown using standard letter abbreviations for nucleotide bases, and one-letter code for amino acids.
  • the nucleotide sequences follow the standard convention of beginning at the 5′ end of the sequence and proceeding forward (i.e., from left to right in each line) to the 3′ end. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood to be included by any reference to the displayed strand.
  • the amino acid sequences follow the standard convention of beginning at the amino terminus of the sequence and proceeding forward (i.e., from left to right in each line) to the carboxy terminus.
  • repeat domain is used to describe the DNA recognition domain from a TAL effector, or artificial version thereof that is made using the methods disclosed, consisting of modular repeat units that when present in a polypeptide confer target DNA specificity.
  • a repeat domain comprised of repeat units can be added to any polypeptide in which DNA sequence targeting is desired and are not limited to use in TAL effectors.
  • repeat unit is used to describe the modular portion of a repeat domain from a TAL effector, or an artificial version thereof, that contains one amino acid or two adjacent amino acids that determine recognition of a base pair in a target DNA sequence. Repeat units taken together recognize a defined target DNA sequence and constitute a repeat domain. Repeat units can be added to any polypeptide in which DNA sequence targeting is desired and are not limited to use in TAL effectors.
  • recognition code is used to describe the relationship between the amino acids in positions 12 and 13 of a repeat unit and the corresponding DNA base pair in a target DNA sequence that such amino acids confer recognition of, as follows: HD for recognition of C/G; NI for recognition of A/T; NG for recognition of T/A; NS for recognition of C/G or A/T or T/A or G/C; NN for recognition of G/C or A/T; IG for recognition of T/A; N for recognition of C/G or T/A; HG for recognition of C/G or T/A; H for recognition of T/A; NK for recognition of G/C; NH for recognition of G/C; NP for recognition of A/T, C/G, or T/A; NT for recognition of A/T or G/C; NH for recognition of A/T or G/C; SH for recognition of G/C; SN for recognition of G/C; and IS for recognition of A/T.
  • effector refers to constructs or their encoded polypeptide products in which said polypeptide is able to recognize a target DNA sequence.
  • the effector protein includes a repeat domain comprised of 1.5 or more repeat units and also may include one or more functional domains such as a regulatory domain.
  • the “effector” is additionally capable of exerting an effect, such as regulation of gene expression.
  • naturally occurring is used to describe an object that can be found in nature as distinct from being produced by man.
  • a polypeptide or polynucleotide sequence that is present in an organism (including viruses) that can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory is naturally occurring.
  • the term naturally occurring refers to an object as-present in a wild-type individual, such as would be typical for the species.
  • modulating expression “inhibiting expression” and “activating expression” of a gene refer to the ability of a polypeptide of the present invention to activate or inhibit transcription of a gene. Activation includes prevention of subsequent transcriptional inhibition (i.e., prevention of repression of gene expression) and inhibition includes prevention of subsequent transcriptional activation (i.e., prevention of gene activation). Modulation can be assayed by determining any parameter that is indirectly or directly affected by the expression of the target gene.
  • Such parameters include, e.g., changes in RNA or protein levels, changes in protein activity, changes in product levels, changes in downstream gene expression, changes in reporter gene transcription (luciferase, CAT, beta-galactosidase, GFP (see, e.g., Mistili & Spector (1997) Nature Biotechnology 15:961-964); changes in signal transduction, phosphorylation and dephosphorylation, receptor-ligand interactions, second messenger concentrations (e.g., cGMP, cAMP, IP3, and Ca2+), cell growth, neovascularization, in vitro, in vivo, and ex vivo.
  • reporter gene transcription luciferase, CAT, beta-galactosidase, GFP (see, e.g., Mistili & Spector (1997) Nature Biotechnology 15:961-964
  • changes in signal transduction, phosphorylation and dephosphorylation, receptor-ligand interactions e.g., cGMP, cAMP,
  • Such functional effects can be measured by any means known to those skilled in the art, e.g., measurement of RNA or protein levels, measurement of RNA stability, identification of downstream or reporter gene expression, e.g., via chemiluminescence, fluorescence, calorimetric reactions, antibody binding, inducible markers, ligand binding assays; changes in intracellular second messengers such as cGMP and inositol triphosphate (IP3); changes in intracellular calcium levels; cytokine release, and the like.
  • chemiluminescence, fluorescence, calorimetric reactions, antibody binding, inducible markers, ligand binding assays e.g., via chemiluminescence, fluorescence, calorimetric reactions, antibody binding, inducible markers, ligand binding assays
  • changes in intracellular second messengers such as cGMP and inositol triphosphate (IP3)
  • changes in intracellular calcium levels cytokine release, and the like.
  • a “regulatory domain” refers to a protein or a protein subsequence that has transcriptional modulation activity.
  • a regulatory domain is covalently or non-covalently linked to a polypeptide of the present invention to modulate transcription.
  • a polypeptide of the present invention can act alone, without a regulatory domain, or with multiple regulatory domains to modulate transcription.
  • Transcription factor polypeptides from which one can obtain a regulatory domain include those that are involved in regulated and basal transcription.
  • Such polypeptides include transcription factors, their effector domains, coactivators, silencers, nuclear hormone receptors (see, e.g., Goodrich et al.
  • Coactivators and co-repressors that mediate transcription regulation by nuclear hormone receptors are reviewed in, for example, Meier (1996) Eur. J. Endocrinol. 134(2):158 9; Kaiser et al. (1996) Trends Biochem. Sci. 21:342 5; and Utley et al. (1998) Nature 394:498 502).
  • GATA transcription factors, which are involved in regulation of hematopoiesis are described in, for example, Simon (1995) Nat. Genet. 11:9 11; Weiss et al. (1995) Exp. Hematol. 23:99-107.
  • TATA box binding protein TBP
  • TAF polypeptides which include TAF30, TAF55, TAF80, TAF110, TAF150, and TAF250
  • TAF30, TAF55, TAF80, TAF110, TAF150, and TAF250 are described in Goodrich & Tjian (1994) Curr. Opin. Cell Biol. 6:403 9 and Hurley (1996) Curr. Opin. Struct. Biol. 6:69 75.
  • the STAT family of transcription factors are reviewed in, for example, Barahmand-Pour et al. (1996) Curr. Top. Microbiol. Immunol. 211:121 8. Transcription factors involved in disease are reviewed in Aso et al. (1996) J. Clin. Invest. 97:1561 9.
  • Kinases, phosphatases, and other proteins that modify polypeptides involved in gene regulation are also useful as regulatory domains for polypeptides of the present invention. Such modifiers are often involved in switching on or off transcription mediated by, for example, hormones.
  • Kinases involved in transcription regulation are reviewed in Davis (1995) Mol. Reprod. Dev. 42:459 67, Jackson et al. (1993) Adv. Second Messenger Phosphoprotein Res. 28:279 86, and Boulikas (1995) Crit. Rev. Eukaryot. Gene Expr. 5:1 77, while phosphatases are reviewed in, for example, Schonthal & Semin (1995) Cancer Biol. 6:239 48.
  • Nuclear tyrosine kinases are described in Wang (1994) Trends Biochem. Sci. 19:373 6. Useful domains can also be obtained from the gene products of oncogenes (e.g., myc, jun, fos, myb, max, mad, rel, ets, bcl, myb, mos family members) and their associated factors and modifiers.
  • oncogenes e.g., myc, jun, fos, myb, max, mad, rel, ets, bcl, myb, mos family members
  • Oncogenes are described in, for example, Cooper, Oncogenes, 2nd ed., The Jones and Bartlett Series in Biology, Boston, Mass., Jones and Bartlett Publishers, 1995.
  • the ets transcription factors are reviewed in Waslylk et al. (1993) Eur. J. Biochem.
  • Polypeptides of the present invention can include regulatory domains obtained from DNA repair enzymes and their associated factors and modifiers.
  • DNA repair systems are reviewed in, for example, Vos (1992) Curr. Opin. Cell Biol. 4:385 95; Sancar (1995) Ann. Rev. Genet. 29:69 105; Lehmann (1995) Genet. Eng. 17:1 19; and Wood (1996) Ann. Rev. Biochem. 65:135 67.
  • DNA rearrangement enzymes and their associated factors and modifiers can also be used as regulatory domains (see, e.g., Gangloff et al. (1994) Experientia 50:261 9; Sadowski (1993) FASEB J. 7:760 7).
  • regulatory domains can be derived from DNA modifying enzymes (e.g., DNA methyltransferases, topoisomerases, helicases, ligases, kinases, phosphatases, polymerases) and their associated factors and modifiers.
  • DNA modifying enzymes e.g., DNA methyltransferases, topoisomerases, helicases, ligases, kinases, phosphatases, polymerases
  • Helicases are reviewed in Matson et al. (1994) Bioessays 16:13 22, and methyltransferases are described in Cheng (1995) Curr. Opin. Struct. Biol. 5:4 10.
  • Chromatin associated proteins and their modifiers are also useful as domains for addition to the effector of choice.
  • the regulatory domain is a DNA methyl transferase that acts as a transcriptional repressor (see, e.g., Van den Wyngaert et al. FEBS Lett. 426:283 289 (1998); Flynn et al. J. Mol. Biol. 279:101 116 (1998); Okano et al. Nucleic Acids Res.
  • endonucleases such as FokI are used as transcriptional repressors, which act via gene cleavage (see, e.g., WO95/09233; and PCT/US94/01201).
  • Factors that control chromatin and DNA structure, movement and localization and their associated factors and modifiers; factors derived from microbes (e.g., prokaryotes, eukaryotes and virus) and factors that associate with or modify them can also be used to obtain chimeric proteins.
  • recombinases and integrases are used as regulatory domains.
  • histone acetyltransferase is used as a transcriptional activator (see, e.g., Jin & Scotto (1998) Mol. Cell. Biol. 18:4377 4384; Wolffe (1996) Science 272:371 372; Taunton et al. Science 272:408 411 (1996); and Hassig et al. PNAS 95:3519 3524 (1998)).
  • histone deacetylase is used as a transcriptional repressor (see, e.g., Jin & Scotto (1998) Mol. Cell. Biol.
  • gene refers to a nucleic acid molecule or portion thereof which comprises a coding sequence, optionally containing introns, and control regions which regulate the expression of the coding sequence and the transcription of untranslated portions of the transcript.
  • the term “gene” includes, besides coding sequence, regulatory sequence such as the promoter, enhancer, 5′ untranslated regions, 3′ untranslated region, termination signals, poly adenylation region and the like. Regulatory sequence of a gene may be located proximal to, within, or distal to the coding region.
  • target gene refers to a gene whose expression is to be modulated by a polypeptide of the present invention.
  • plant refers to any of various photosynthetic, eucaryotic multi-cellular organisms of the kingdom Plantae, characteristically producing embryos, containing chloroplasts, having cellulose cell walls and lacking locomotion.
  • plant includes any plant or part of a plant at any stage of development, including seeds, suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, microspores, and progeny thereof. Also included are cuttings, and cell or tissue cultures.
  • plant tissue includes, but is not limited to, whole plants, plant cells, plant organs, e.g., leafs, stems, roots, meristems, plant seeds, protoplasts, callus, cell cultures, and any groups of plant cells organized into structural and/or functional units.
  • modulate the expression of a target gene in plant cells refers to increasing (activation) or decreasing (repression) the expression of the target gene in plant cells with a polypeptide of the present invention, alone or in combination with other transcription and/or translational regulatory factors, or nucleic acids encoding such polypeptide, in plant cells.
  • a “target DNA sequence” refers to a portion of double-stranded DNA to which recognition by a protein is desired.
  • a “target DNA sequence” is all or part of a transcriptional control element for a gene for which a desired phenotypic result can be attained by altering the degree of its expression.
  • a transcriptional control element includes positive and negative control elements such as a promoter, an enhancer, other response elements, e.g., steroid response element, heat shock response element, metal response element, a repressor binding site, operator, and/or a silencer.
  • the transcriptional control element can be viral, eukaryotic, or prokaryotic.
  • a “target DNA sequence” also includes a downstream or an upstream sequence which can bind a protein and thereby modulate, typically prevent, transcription.
  • DNA or “DNA sequence” herein is not intended to limit the present invention to polynucleotide molecules comprising DNA.
  • RNA ribonucleotides
  • the methods and compositions of the invention encompass polynucleotide molecules comprised of deoxyribonucleotides (i.e., DNA), ribonucleotides (i.e., RNA) or combinations of ribonucleotides and deoxyribonucleotides.
  • deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues including, but not limited to, nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides.
  • Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).
  • polynucleotide molecules of the invention also encompass all forms of polynucleotide molecules including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like. Furthermore, it is understood by those of ordinary skill in the art that the DNA sequences disclosed herein also encompasses the complement of that exemplified nucleotide sequence.
  • “specifically binds to a target DNA sequence” means that the binding affinity of a polypeptide of the present invention to a specified target DNA sequence is statistically higher than the binding affinity of the same polypeptide to a generally comparable, but non-target DNA sequence. It also refers to binding of a repeat domain of the present invention to a specified target DNA sequence to a detectably greater degree, e.g., at least 1.5-fold over background, than its binding to non-target DNA sequences and to the substantial exclusion of non-target DNA sequences.
  • a polypeptide of the present invention's Kd to each DNA sequence can be compared to assess the binding specificity of the polypeptide to a particular target DNA sequence.
  • a “target DNA sequence within a target gene” refers to a functional relationship between the target DNA sequence and the target gene in that recognition of a polypeptide of the present invention to the target DNA sequence will modulate the expression of the target gene.
  • the target DNA sequence can be physically located anywhere inside the boundaries of the target gene, e.g., 5′ ends, coding region, 3′ ends, upstream and downstream regions outside of cDNA encoded region, or inside enhancer or other regulatory region, and can be proximal or distal to the target gene.
  • endogenous refers to nucleic acid or protein sequence naturally associated with a target gene or a host cell into which it is introduced.
  • exogenous refers to nucleic acid or protein sequence not naturally associated with a target gene or a host cell into which it is introduced, including non-naturally occurring multiple copies of a naturally occurring nucleic acid, e.g., DNA sequence, or naturally occurring nucleic acid sequence located in a non-naturally occurring genome location.
  • transgenic plant refers to a plant which comprises within its genome an exogenous polynucleotide. Generally, and preferably, the exogenous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations. The exogenous polynucleotide may be integrated into the genome alone or as part of a recombinant expression cassette.
  • Transgenic is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of exogenous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic.
  • transgenic does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation.
  • minimal promoter refers to a promoter element, particularly a TATA element, that is inactive or that has greatly reduced promoter activity in the absence of upstream activation. In the presence of a suitable transcription factor, the minimal promoter functions to permit transcription.
  • repressor protein or “repressor” refers to a protein that binds to operator of DNA or to RNA to prevent transcription or translation, respectively.
  • repression refers to inhibition of transcription or translation by binding of repressor protein to specific site on DNA or mRNA.
  • repression includes a significant change in transcription or translation level of at least 1.5 fold, more preferably at least two fold, and even more preferably at least five fold.
  • activator protein or “activator” refers to a protein that binds to operator of DNA or to RNA to enhance transcription or translation, respectively.
  • activation refers to enhancement of transcription or translation by binding of activator protein to specific site on DNA or mRNA.
  • activation includes a significant change in transcription or translation level of at least 1.5 fold, more preferably at least two fold, and even more preferably at least five fold.
  • derivative or “analog” of a molecule refers to a portion derived from or a modified version of the molecule.
  • a “repeat unit derived from a transcription activator-like (TAL) effector” refers to a repeat unit from a TAL effector or a modified or artificial version of one or more TAL effectors that is produced by any of the methods disclosed herein.
  • the invention is specifically described with respect to the transcription activator-like (TAL) effector family which are translocated via the type III secretion system into plant cells.
  • the type member of this effector family is AvrBs3.
  • the TAL effector family is also named AvrBs3-like family of proteins. Both expressions are used synonymously and can be interchanged.
  • Non-limiting examples of the AvrBs3-like family are as follows: AvrBs4 and the members of the Hax sub-family Hax2, Hax3, and Hax4 as well as Brg11.
  • AvrBs3 and the other members of its family are characterized by their binding capability to specific DNA sequences in promoter regions of target genes and induction of expression of these genes.
  • AvrBs3-like family and homologous effectors typically have in their C-terminal region nuclear localisation sequences (NLS) and a transcriptional activation domain (AD).
  • the central region contains repeat units of typically 34 or 35 amino acids. The repeat units are nearly identical, but variable at certain positions and it has now been found how these positions determine the nucleotide sequence binding specificity of the proteins.
  • AvrBs3 the repeat units are responsible for binding to DNA.
  • This repeat domain consists in AvrBs3 of 17.5 repeat units and in homologous proteins is comprised of 1.5 to 33.5 repeat units which are typically 34 amino acids each. Other repeat unit lengths are also known (e.g. 30, 33, 35, 39, 40, 42 amino acids).
  • the last repeat in the repeat domain is usually only a half repeat of 19 or 20 amino acids length.
  • the individual repeat units are generally not identical.
  • AvrBs3-like proteins from Xanthomonas reveals 80 to 97% overall sequence identity with most differences confined to the repeat domain.
  • AvrBs3 and the AvrBs3-like family member AvrBs4 differ exclusively in their repeat domain region, with the exception of a four amino acid deletion in the C-terminus of AvrBs4 with respect to AvrBs3.
  • FIG. 16 the amino acid sequences of AvrBs3 as well as the amino acid sequences of the members of the Hax-sub family are shown.
  • the repeat units which are identical except for the hypervariable amino acids at positions 12 and 13 and the variable amino acids at positions 4 and 24. Hence, each repeat unit of these proteins is given separately.
  • the inventors have discovered that one repeat unit within a repeat domain is responsible for the recognition of one specific DNA base pair in a target DNA sequence. This finding is, however, only one element of the invention.
  • the inventors additionally discovered that a hypervariable region within each repeat unit of a repeat domain is responsible for recognition of one specific DNA base pair in a target DNA sequence.
  • the hypervariable region (corresponds to amino acid positions 12 and 13) are typically responsible for this recognition specificity.
  • each variation in these amino acids reflects a corresponding variation in target DNA recognition and preferably also recognition capacity.
  • hypervariable region is intended to mean positions 12 and 13 or equivalent position in a repeat unit of the present invention. It is recognized that positions 12 and 13 of the invention correspond to positions 12 and 13 in the full-length repeat units of AvrBs3 and other TAL effectors as disclosed herein. It is further recognized that by “equivalent positions” is intended positions that corresponds to positions 12 and 13, respectively, in a repeat unit of the present. One can readily determine such equivalent positions by aligning any repeat unit with a full-length repeat unit of AvrBs3.
  • one repeat unit in a repeat domain of a DNA-binding protein recognizes one base pair in the target DNA, and that one amino acid or two adjacent amino acid residues in a repeat unit, typically within the hypervariable regions of a repeat unit, determine which base pair in the target DNA is recognized.
  • a person skilled in the art would be able to specifically target base pairs in a target DNA sequence of interest by modifying a polypeptide within its repeat units of the repeat domain to specifically target base pairs in the desired target DNA sequence.
  • the inventors have identified a recognition code for DNA-target specificities of different repeat types and were able to predict target DNA sequences of several TAL effectors which could be confirmed experimentally.
  • the linear array of repeat units which recognizes a linear sequence of bases in the target DNA is a novel DNA-protein interaction.
  • the modular architecture of the repeat domain and the recognition code identified by the inventors for targeting DNA with high specificity allows the efficient design of specific DNA-binding domains for use in a variety of technological fields.
  • the repeat domains are included in a transcription factor, for instance in transcription factors active in plants, particularly preferred in type III effector proteins, e.g. in effectors of the AvrBs3-like family.
  • a transcription factor for instance in transcription factors active in plants, particularly preferred in type III effector proteins, e.g. in effectors of the AvrBs3-like family.
  • the modular architecture of the repeat domain can be used in any protein which shall be used for targeting specific target DNA sequences.
  • repeat domains comprising repeat units into a polypeptide wherein the repeat units are modified in order to comprise one hypervariable region per repeat unit and wherein the hypervariable region determines recognition of a base pair in a target DNA sequence
  • the recognition of a large variety of proteins to pre-determined target DNA sequences will be available.
  • each repeat unit within a repeat domain has been found to be responsible for the specific recognition of one base pair in a DNA
  • several repeat units can be combined with each other wherein each repeat unit includes a hypervariable region that is responsible for the recognition of each repeat unit to a particular base pair in a target DNA sequence.
  • the following examples provide methods for constructing new repeat units and testing the specific binding activities of artificially constructed repeat units specifically recognizing base pairs in a target DNA sequence.
  • repeat units to be used in a repeat domain can be ascertained by one skilled in the art by routine experimentation. Generally, at least 1.5 repeat units are considered as a minimum, although typically at least about 8 repeat units will be used. The repeat units do not have to be complete repeat units, as repeat units of half the size can be used. Moreover, the methods and polypeptides disclosed herein do depend on repeat domains with a particular number of repeat units.
  • a polypeptide of the invention can comprise, for example, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5, 12, 12.5, 13, 13.5, 14, 14.5, 15, 15.5, 16, 16.5, 17, 17.5, 18, 18.5, 19, 19.5, 20, 20.5, 21, 21.5, 22, 22.5, 23, 23.5, 24, 24.5, 25, 25.5, 26, 26.5, 27, 27.5, 28, 28.5, 29, 29.5, 30, 30.5, 31, 31.5, 32, 32.5, 33, 33.5, 34, 34.5, 35, 35.5, 36, 36.5, 37, 37.5, 38, 38.5, 39, 39.5, 40, 40.5, 41, 41.5, 42, 42.5, 43, 43.5, 44, 44.5, 46, 46.5, 47, 47.5, 48, 48.5, 49, 49.5, 50, 50.5 or more repeat units.
  • AvrBs3 contains 17.5 repeat units and induces expression of UPA (up-regulated by AvrBs3) genes. The number and order of repeat units will determine the corresponding activity and DNA recognition specificity.
  • the AvrBs3 family members Hax2 includes 21.5 repeat units, Hax3 11.5 repeat units and Hax4 14.5 repeat units.
  • a polypeptide of the invention comprises about 8 and to about 39 repeat units. More preferably, a polypeptide of the invention comprises about 11.5 to about 33.5 repeat units.
  • the repeat units which can be used in one embodiment of the invention have an identity with the consensus sequences described above of at least 35%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95%.
  • the repeat sequences of AvrBs3, Hax2, Hax3 and Hax4 and further members of the AvrBs3-family are used.
  • the repeat unit sequences of these members are indicated in FIG. 16 .
  • These repeat unit sequences can be modified by exchanging one or more of the amino acids.
  • the modified repeat unit sequences have an identity with the original repeat sequence of the original member of the AvrBs3-family sequence of at least 35%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95%.
  • amino acids in positions 4, 11, 24, and 32 are altered.
  • the number of amino acids per repeat are in a range between 20-45 amino acids, furthermore 32-40 amino acids, still further 32-39 amino acid, and further optionally 32, 34, 35 or 39 amino acids per repeat unit.
  • the hypervariable region in a repeat unit determines the specific recognition of one base pair in a target DNA sequence. More specifically, the inventors have found the following correlation of recognition specificity between amino acids found at positions 12 and 13 in a repeat unit and base pairs in the target DNA sequence:
  • amino acids are represented in the single letter code.
  • the nucleotides are given as base pairs, wherein the first base is located in the upper strand and the second base in the lower strand; for example C/G means that C is located in the upper strand, G in the lower strand.
  • the methods of the present invention can further comprise making a repeat unit in which one or more of the hypervariable regions is selected from the following group in order to determine recognition of one of the following base pairs: HA for recognition of C/G; ND for recognition of C/G; HI for recognition of C/G; HN for recognition of G/C; and NA for recognition of G/C.
  • amino acid 13 of AvrBs3 appears to be missing from the repeat unit when compared by multiple amino acid sequence alignments with the other repeat units.
  • the N-terminal domain of AvrBs3-like proteins confers recognition specificity for a T, 5′ of the recognition specificity of said repeat.
  • repeat units of the protein family AvrBs3 are used.
  • the members of this protein family have been specified above.
  • the members of the protein family have an amino acid homology of at least 95%, at least 90%, at least 80%, at least 85%, at least 70%, at least 75%, at least 60%, at least 50%, at least 40% or at least 35% to the amino acid sequence of AvrBs3, particularly to the amino acid sequence of the repeat unit of AvrBs3.
  • the hypervariable region in a repeat unit can be deduced by an amino acid comparison between the members of the AvrBs3 family.
  • the amino acids are in positions 12 and 13 of a repeat unit of AvrBs3.
  • variable regions may also be located in different amino acid positions. Examples for variable positions are amino acids numbers 4, 11, 24, and 32.
  • the amino acids responsible for the specific recognition of a base pair in a DNA sequence are located in positions which typically do not vary between the members of the AvrBs3 family or in positions which are variable but not hypervariable.
  • repeat units determine the recognition of one base pair on a DNA sequence and that the hypervariable region within a repeat unit determines the recognition specificity of the corresponding repeat unit.
  • sequence of repeat units correlates with a specific linear order of base pairs in a target DNA sequence.
  • the inventors have found this correlation with respect to AvrBs3 and verified it with respect to a representative number of members of the AvrBs3-like family of proteins. With respect to AvrBs3-like family members, amino acid residues in positions 12 and 13 in a repeat unit of 34 or other amino acids length correlate with defined binding specificities of AvrBs3-like proteins.
  • the discovery of this core principle provides a powerful tool to customize a polypeptide with its cognate target DNA template for a variety of applications including, but not limited to, modulation of gene expression and targeted genome engineering.
  • polypeptides can be designed which comprise a repeat domain with repeat units wherein in the repeat units hypervariable regions are included which determine recognition of a base pair in a target DNA sequence.
  • each repeat unit includes a hypervariable region which determine recognition of one base pair in a target DNA sequence.
  • 1 or 2 repeat units in a repeat domain are included which do not specifically recognize a base pair in a target DNA sequence.
  • a modular arrangement of repeat units is feasible wherein each repeat unit is responsible for the specific recognition of one base pair in a target DNA sequence. Consequently, a sequence of repeat units corresponds to a sequence of base pairs in a target DNA sequence so that 1 repeat unit matches to one base pair.
  • a target DNA sequence is known and to which recognition by a protein is desired, the person skilled in the art is able to specifically construct a modular series of repeat units, including specific recognition amino acid sequences, and assemble these repeat units into a polypeptide in the appropriate order to enable recognition of and binding to the desired target DNA sequence.
  • Any polypeptide can be modified by being combined with a modular repeat unit DNA-binding domain of the present invention.
  • Such examples include polypeptides that are transcription activator and repressor proteins, resistance-mediating proteins, nucleases, topoisomerases, ligases, integrases, recombinases, resolvases, methylases, acetylases, demethylases, deacetylases, and any other polypeptide capable of modifying DNA, RNA, or proteins.
  • the modular repeat unit DNA-binding domain of the present invention can be combined with cell compartment localisation signals such as nuclear localisation signals, to function at any other regulatory regions, including but not limited to, transcriptional regulatory regions and translational termination regions.
  • cell compartment localisation signals such as nuclear localisation signals
  • these modularly designed repeat units are combined with an endoneclease domain capable of cleaving DNA when brought into proximity with DNA as a result of binding by the repeat domain.
  • endonucleolytic breaks are known to stimulate the rate of homologous recombination in eukaryotes, including fungi, plants, and animals.
  • the ability to simulate homologous recombination at a specific site as a result of a site-specific endonucleolytic break allows the recovery of transformed cells that have integrated a DNA sequence of interest at the specific site, at a much higher frequency than is possible without having made the site-specific break.
  • endonucleolytic breaks such as those caused by polypeptides formed from a repeat domain and an endonuclease domain are sometimes repaired by the cellular DNA metabolic machinery in a way that alters the sequence at the site of the break, for instance by causing a short insertion or deletion at the site of the break compared to the unaltered sequence.
  • sequence alterations can cause inactivation of the function of a gene or protein, for instance by altering a protein-coding sequence to make a non-functional protein, modifying a splice site so that a gene transcript is not properly cleaved, making a non-functional transcript, changing the promoter sequence of a gene so that it can no longer by appropriately transcribed, etc.
  • Breaking DNA using site specific endonucleases can increase the rate of homologous recombination in the region of the breakage.
  • the Fok I (Flavobacterium okeanokoites) endonuclease may be utilized in an effector to induce DNA breaks.
  • the Fok I endonuclease domain functions independently of the DNA binding domain and cuts a double stranded DNA typically as a dimer (Li et al. (1992) Proc. Natl. Acad. Sci. U.S.A 89 (10):4275-4279, and Kim et al. (1996) Proc. Natl. Acad. Sci.
  • the FokI endonuclease domain can be cloned by PCR from the genomic DNA of the marine bacteria Flavobacterium okeanokoites (ATCC) prepared by standard methods.
  • the sequence of the FokI endonuclease is available on Pubmed (Acc. No. M28828 and Acc. No J04623, the disclosures of which are incorporated herein by reference in their entireties).
  • the I-Sce I endonuclease from the yeast Saccharomyces cerevisiae has been used to produce DNA breaks that increase the rate of homologous recombination.
  • I-Sce I is an endonuclease encoded by a mitochondrial intron which has an 18 bp recognition sequence, and therefore a very low frequency of recognition sites within a given DNA, even within large genomes (Gold et al. (1991) Nucleic Acids Res. 19 (1):189-190; the disclosure of which is incorporated herein by reference in its entirety).
  • the infrequency of cleavage sites recognized by I-SceI makes it suitable to use for enhancing homologous recombination. Additional description regarding the use of I-Sce Ito induce said DNA breaks can be found in U.S. Pat. Appl. 20090305402, which is incorporated herein by reference in its entirety.
  • I-Sce I The recognition site for I-Sce I has been introduced into a range of different systems. Subsequent cutting of this site with I-Sce I increases homologous recombination at the position where the site has been introduced. Enhanced frequencies of homologous recombination have been obtained with I-Sce I sites introduced into the extra-chromosomal DNA in Xenopus oocytes , the mouse genome, and the genomic DNA of the tobacco plant Nicotiana plumbaginifolia. See, for example, Segal et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92 (3):806-810; Choulika et al. (1995) Mol. Cell. Biol.
  • endonucleases that have a DNA recognition and binding domain such as I-Sce I
  • the recognition site has to be introduced by standard methods of homologous recombination at the desired location prior to the use of said endonuclease to enhance homologous recombination at that site, if such site is not already present in the desired location.
  • endonuclease domains could be similarly engineered so as to render the DNA-binding activity non-functional but leaving the DNA cleaving function active and to utilize said similarly engineered endonuclease cleavage domain in an effector to induce DNA breaks similar to the use of FokI above.
  • target DNA sequence recognition would preferably be provided by the repeat domain of the effector but DNA cleavage would be accomplished by the engineered endonuclease domain.
  • an effector includes a repeat domain with specific recognition for a desired specific target sequence.
  • the effector specifically binds to an endogenous chromosomal DNA sequence.
  • the specific nucleic acid sequence or more preferably specific endogenous chromosomal sequence can be any sequence in a nucleic acid region where it is desired to enhance homologous recombination.
  • the nucleic acid region may be a region which contains a gene in which it is desired to introduce a mutation, such as a point mutation or deletion, or a region into which it is desired to introduce a gene conferring a desired phenotype.
  • inventions relate to methods of generating a modified plant in which a desired addition has been introduced.
  • the methods can include obtaining a plant cell that includes an endogenous target DNA sequence into which it is desired to introduce a modification; generating a double-stranded cut within the endogenous target DNA sequence with an effector that includes a repeat domain that binds to an endogenous target DNA sequence and an endonuclease domain;
  • an exogenous nucleic acid that includes a sequence homologous to at least a portion of the endogenous target DNA into the plant cell under conditions which permit homologous recombination to occur between the exogenous nucleic acid and the endogenous target DNA sequence; and generating a plant from the plant cell in which homologous recombination has occurred.
  • Other embodiments relate to genetically modified cells and plants made according to the method described above and herein. It should be noted that the target DNA sequence could be artificial or naturally occurring. It will be appreciated that such methods could be used in any organism (such non-limiting organisms to include animals, humans, fungi, oomycetes bacteria and viruses) using techniques and methods known in the art and utilized for such purposes in such organisms.
  • these modularly designed repeat domains are combined with one or more domains responsible for the modulation or control of the expression of a gene, for instance of plant genes, animal genes, fungal genes, oomycete genes, viral genes, or human genes.
  • Methods for modulating gene expression by generating DNA-binding polypeptides containing zinc finger domains is known in the art (U.S. Pat. Nos. 7,285,416, 7,521,241, 7,361,635, 7,273,923, 7,262,054, 7,220,719, 7,070,934, 7,013,219, 6,979,539, 6,933,113, 6,824,978, each of which is hereby herein incorporated by reference in its entirety).
  • these effectors of the AvrBs3-like family are modified in order to bind to specific target DNA sequences.
  • Such polypeptides might for instance be transcription activators or repressor proteins of transcription which are modified by the method of the present invention to specifically bind to genetic control regions in a promoter of or other regulatory region for a gene of interest in order to activate, repress or otherwise modulate transcription of said gene.
  • the target DNA sequences are modified in order to be specifically recognized by a naturally occurring repeat domain or by a modified repeat domain.
  • the target DNA sequences for members of the AvrBs3-like family can be inserted into promoters to generate novel controllable promoters that can be induced by the corresponding AvrBs3 effector.
  • Secondary inducible systems can be constructed using a trans-activator and a target gene, wherein the trans-activator is a polypeptide wherein said polypeptide comprises at least a repeat domain comprising repeat units of the present invention that bind to said target gene and induce expression.
  • trans-activator and the target gene can be introduced into one cell line but may also be present in different cell lines and later be introgressed.
  • disease-resistant plants can be constructed by inserting the target DNA sequence of a repeat domain containing polypeptide of the present invention in front of a gene which after expression leads to a defence reaction of the plant by activating a resistance-mediating gene.
  • custom DNA-binding polypeptides can be constructed by rearranging repeat unit types thus allowing the generation of repeat domains with novel target DNA binding specificity. Individual repeat units are nearly identical at the DNA level which precludes classical cloning strategies.
  • the present invention provides a quick and inexpensive strategy to assemble custom polypeptides with repeat domains of the present invention. To improve cloning versatility such polypeptides, a two-step assembly method was designed. This method was used to assemble polypeptides with novel repeat types to study their target DNA recognition and binding specificity.
  • any DNA sequence can be modified to enable binding by a repeat domain containing polypeptide of the present invention by introducing base pairs into any DNA region or specific regions of a gene or a genetic control element to specifically target a polypeptide having a repeat domain comprised of repeat units that will bind said modified DNA sequence in order to facilitate specific recognition and binding to each other.
  • the inventors have demonstrated that a truly modular DNA recognizing and preferably binding polypeptide can be efficiently produced, wherein the binding motif of said polypeptide is a repeat domain comprised of repeat units which are selected on the basis of their recognition capability of a combination of particular base pairs. Accordingly, it should be well within the capability of one of normal skill in the art to design a polypeptide capable of binding to any desired target DNA sequence simply by considering the sequence of base pairs present in the target DNA and combining in the appropriate order repeat units as binding motifs having the necessary characteristics to bind thereto. The greater the length of known sequence of the target DNA, the greater the number of modular repeat units that can be included in the polypeptide.
  • the known sequence is only 9 bases long, then nine repeat units as defined above can be included in the polypeptide. If the known sequence is 27 bases long, then up to 27 repeat units could be included in the polypeptide. The longer the target DNA sequence, the lower the probability of its occurrence in any other given portion of DNA elsewhere in the genome.
  • those repeat units selected for inclusion in the polypeptide could be artificially modified in order to modify their binding characteristics.
  • the length and amino acid sequence of the repeat unit could be varied as long as its binding characteristic is not affected.
  • effectors can be designed to recognize any suitable target site, for regulation of expression of any endogenous gene of choice.
  • endogenous genes suitable for regulation include VEGF, CCR5, ER.alpha., Her2/Neu, Tat, Rev, HBV C, S, X, and P, LDL-R, PEPCK, CYP7, Fibrinogen, ApoB, Apo E, Apo(a), renin, NF-.kappa.B, I-.kappa.B, TNF-.alpha., FAS ligand, amyloid precursor protein, atrial naturetic factor, ob-leptin, ucp-1, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-12, G-CSF, GM-CSF, Epo, PDGF, PAF, p53, Rb, fetal hemoglobin, dystrophin, eutrophin, GDNF, NGF, IGF-1,
  • suitable genes to be regulated include cytokines, lymphokines, growth factors, mitogenic factors, chemotactic factors, onco-active factors, receptors, potassium channels, G-proteins, signal transduction molecules, disease resistance genes, and other disease-related genes.
  • a method of modulating expression of a target gene in a cell is provided.
  • the cell may be preferably a plant cell, a human cell, animal cell, fungal cell or any other living cell.
  • the cells contain a polypeptide wherein said polypeptide comprises at least a repeat domain comprising repeat units, and these repeat units contain a hypervariable region and each repeat unit is responsible for the recognition of 1 base pair in said target DNA sequence.
  • Said polypeptide is introduced either as DNA encoding for the polypeptide or the polypeptide is introduced per se into the cell by methods known in the art. Regardless of how introduced, the polypeptide should include at least one repeat domain that specifically recognizes and preferably binds to a target DNA sequence of base pairs and modulates the expression of a target gene.
  • all repeat units contain a hypervariable region which determines recognition of base pairs in a target DNA sequence.
  • Examples of peptide sequences which can be linked to an effector of the present invention, for facilitating uptake of effectors into cells include, but are not limited to: an 11 animo acid peptide of the tat protein of HIV; a 20 residue peptide sequence which corresponds to amino acids 84 103 of the p16 protein (see Fahraeus et al. (1996) Current Biology 6:84); the third helix of the 60-amino acid long homeodomain of Antennapedia (Derossi et al. (1994) J. Biol. Chem.
  • K-FGF Kaposi fibroblast growth factor
  • VP22 translocation domain from HSV (Elliot & O'Hare (1997) Cell 88:223 233).
  • Other suitable chemical moieties that provide enhanced cellular uptake may also be chemically linked to effectors.
  • Toxin molecules also have the ability to transport polypeptides across cell membranes. Often, such molecules are composed of at least two parts (called “binary toxins”): a translocation or binding domain or polypeptide and a separate toxin domain or polypeptide. Typically, the translocation domain or polypeptide binds to a cellular receptor, and then the toxin is transported into the cell.
  • Clostridium perfringens iota toxin diphtheria toxin (DT), Pseudomonas exotoxin A (PE), pertussis toxin (PT), Bacillus anthracis toxin, and pertussis adenylate cyclase (CYA)
  • DT diphtheria toxin
  • PE Pseudomonas exotoxin A
  • PT pertussis toxin
  • Bacillus anthracis toxin Bacillus anthracis toxin
  • pertussis adenylate cyclase CYA
  • Effectors can also be introduced into an animal cell, preferably a mammalian cell, via liposomes and liposome derivatives such as immunoliposomes.
  • liposome refers to vesicles comprised of one or more concentrically ordered lipid bilayers, which encapsulate an aqueous phase.
  • the aqueous phase typically contains the compound to be delivered to the cell, in this case an effector.
  • the liposome fuses with the plasma membrane, thereby releasing the effector into the cytosol.
  • the liposome is phagocytosed or taken up by the cell in a transport vesicle. Once in the endosome or phagosome, the liposome either degrades or fuses with the membrane of the transport vesicle and releases its contents.
  • the present invention is directed to a method to modulate the expression of a target gene in plant cells, which method comprises providing plant cells with a polypeptide modified according to the invention, said polypeptide being capable of specifically recognizing a target nucleotide sequence, or a complementary strand thereof, within a target gene, and allowing said polypeptide to recognize and particularly bind to said target nucleotide sequence, whereby the expression of said target gene in said plant cells is modulated.
  • the polypeptide can be provided to the plant cells via any suitable methods known in the art.
  • the protein can be exogenously added to the plant cells and the plant cells are maintained under conditions such that the polypeptide is introduced into the plant cell, binds to the target nucleotide sequence and regulates the expression of the target gene in the plant cells.
  • a nucleotide sequence e.g., DNA or RNA
  • encoding the polypeptide can be expressed in the plant cells and the plant cells are maintained under conditions such that the expressed polypeptide binds to the target nucleotide sequence and regulates the expression of the target gene in the plant cells.
  • a preferred method to modulate the expression of a target gene in plant cells comprises the following steps: a) providing plant cells with an expression system for a polypeptide modified according to the invention, said polypeptide being capable of specifically recognizing, and preferably binding, to a target nucleotide sequence, or a complementary strand thereof, within an expression control element of a target gene, preferably a promoter; and b) culturing said plant cells under conditions wherein said polypeptide is produced and binds to said target nucleotide sequence, whereby expression of said target gene in said plant cells is modulated.
  • any target nucleotide sequence can be modulated by the present method.
  • the target nucleotide sequence can be endogenous or exogenous to the target gene.
  • the target nucleotide sequence can be present in a living cell or present in vitro.
  • the target nucleotide sequence is endogenous to the plant.
  • the target nucleotide sequence can be located in any suitable place in relation to the target gene.
  • the target nucleotide sequence can be upstream or downstream of the coding region of the target gene.
  • the target nucleotide sequence is within the coding region of the target gene.
  • the target nucleotide sequence is a promoter of a gene.
  • any target gene can be modulated by the present method.
  • the target gene can encode a product that affects biosynthesis, modification, cellular trafficking, metabolism and degradation of a peptide, a protein, an oligonucleotide, a nucleic acid, a vitamin, an oligosaccharide, a carbohydrate, a lipid, or a small molecule.
  • effectors can be used to engineer plants for traits such as increased disease resistance, modification of structural and storage polysaccharides, flavors, proteins, and fatty acids, fruit ripening, yield, color, nutritional characteristics, improved storage capability, and the like.
  • the invention provides a method of altering the expression of a gene of interest in a target cell, comprising: determining (if necessary) at least part of the DNA sequence of the structural region and/or a regulatory region of the gene of interest; designing a polypeptide including the repeat units modified in accordance with the invention to recognize specific base pairs on the DNA of known sequence, and causing said modified polypeptide to be present in the target cell, (preferably in the nucleus thereof). (It will be apparent that the DNA sequence need not be determined if it is already known.)
  • the regulatory region could be quite remote from the structural region of the gene of interest (e.g. a distant enhancer sequence or similar).
  • polypeptide may advantageously comprise functional domains from other proteins (e.g. catalytic domains from restriction endonucleases, recombinases, replicases, integrases and the like) or even “synthetic” effector domains.
  • the polypeptide may also comprise activation or processing signals, such as nuclear localisation signals. These are of particular usefulness in targeting the polypeptide to the nucleus of the cell in order to enhance the binding of the polypeptide to an intranuclear target (such as genomic DNA).
  • the modified polypeptide may be synthesised in situ in the cell as a result of delivery to the cell of DNA directing expression of the polypeptide.
  • Methods of facilitating delivery of DNA include, for example, recombinant viral vectors (e.g. retroviruses, adenoviruses), liposomes and the like.
  • the modified polypeptide could be made outside the cell and then delivered thereto. Delivery could be facilitated by incorporating the polypeptide into liposomes etc.
  • one significant advantage of the modified proteins of the invention in controlling gene expression would be the vector-free delivery of protein to target cells.
  • effector polypeptides are designed for therapeutic and/or prophylactic use in regulating the expression of disease-associated genes.
  • said polypeptides could be used to inhibit the expression of foreign genes (e.g., the genes of bacterial or viral pathogens) in humans, other animals, or plants, or to modify the expression of mutated host genes (such as oncogenes).
  • the invention therefore also provides an effector polypeptide capable of inhibiting the expression of a disease-associated gene.
  • the polypeptide will not be a naturally occurring polypeptide but will be specifically designed to inhibit the expression of the disease-associated gene.
  • the effector polypeptide will be designed by any of the methods of the invention.
  • the invention also relates to the field of genome engineering.
  • An effector polypeptide can be generated according to the invention to target a specific DNA sequence in a genome.
  • Said polypeptide can be modified to contain an activity that directs modification of the target DNA sequence (e.g. site specific recombination or integration of target sequences). This method enables targeted DNA modifications in complex genomes.
  • a polypeptide is provided which is modified to include at least a repeat domain comprising repeat units, the repeat units having hypervariable region for determining selective recognition of a base pair in a DNA sequence.
  • the polypeptide comprises within said repeat unit a hypervariable region which is selected from the following group in order to determine recognition of one of the following base pairs:
  • the polypeptides of the present invention can further comprise within a repeat unit a hypervariable region which is selected from the following group in order to determine recognition of one of the following base pairs: HA for recognition of C/G; ND for recognition of C/G; HI for recognition of C/G; FIN for recognition of G/C; and NA for recognition of G/C.
  • a hypervariable region which is selected from the following group in order to determine recognition of one of the following base pairs: HA for recognition of C/G; ND for recognition of C/G; HI for recognition of C/G; FIN for recognition of G/C; and NA for recognition of G/C.
  • the invention also comprises DNA which encodes for any one of the polypeptides described before.
  • DNA is provided which is modified to include a base pair located in a target DNA sequence so that said base pair can be specifically recognized by a polypeptide which includes at least a repeat domain comprising repeat units, the repeat units having a hypervariable region which determine recognition of said base pair in said DNA.
  • said base pair is located in a gene expression control sequence. Due to the modular assembly of the repeat domain, a sequence of base pairs can be specifically targeted by said repeat domain.
  • said DNA is modified by a base pair selected from the following group in order to receive a selective and determined recognition by one of the following hypervariable regions:
  • the invention provides a method of modifying a nucleic acid sequence of interest present in a sample mixture by binding thereto a polypeptide according to the invention, comprising contacting the sample mixture with said polypeptide having affinity for at least a portion of the sequence of interest, so as to allow the polypeptide to recognize and preferably bind specifically to the sequence of interest.
  • modifying as used herein is intended to mean that the sequence is considered modified simply by the binding of the polypeptide. It is not intended to suggest that the sequence of nucleotides is changed, although such changes (and others) could ensue following binding of the polypeptide to the nucleic acid of interest. Conveniently the nucleic acid sequence is DNA.
  • Modification of the nucleic acid of interest could be detected in any of a number of methods (e.g. gel mobility shift assays, use of labelled polypeptides—labels could include radioactive, fluorescent, enzyme or biotin/streptavidin labels).
  • Modification of the nucleic acid sequence of interest may be all that is required (e.g. in diagnosis of disease). Desirably, however, further processing of the sample is performed. Conveniently the polypeptide (and nucleic acid sequences specifically bound thereto) is separated from the rest of the sample.
  • the polypeptide-DNA complex is bound to a solid phase support, to facilitate such separation.
  • the polypeptide may be present in an acrylamide or agarose gel matrix or, more preferably, is immobilised on the surface of a membrane or in the wells of a microtitre plate.
  • said repeat domain comprising repeat units is inserted in a bacterial, viral, fungal, oomycete, human, animal or plant polypeptide to achieve a targeted recognition and preferably binding of one or more specified base pairs in a DNA sequence, and optionally wherein said repeat units are taken from the repeat domains of AvrBs3-like family of proteins which are further optionally modified in order to obtain a pre-selected specific binding activity to one or more base pairs in a DNA sequence.
  • the invention encompasses isolated or substantially purified polynucleotide or protein compositions.
  • An “isolated” or “purified” polynucleotide or protein, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or protein as found in its naturally occurring environment.
  • an isolated or purified polynucleotide or protein is substantially free of other cellular material or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived.
  • the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived.
  • Fragments and variants of the disclosed DNA sequences and proteins encoded thereby are also encompassed by the present invention.
  • fragment is intended a portion of the DNA sequence or a portion of the amino acid sequence and hence protein encoded thereby.
  • Fragments of a DNA sequence comprising coding sequences may encode protein fragments that retain biological activity of the native protein and hence DNA recognition or binding activity to a target DNA sequence as herein described.
  • fragments of a DNA sequence that are useful as hybridization probes generally do not encode proteins that retain biological activity or do not retain promoter activity.
  • fragments of a DNA sequence may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full-length polynucleotide of the invention.
  • a variant comprises a DNA sequence having deletions (i.e., truncations) at the 5′ and/or 3′ end; deletion and/or addition of one or more nucleotides at one or more internal sites in the native polynucleotide; and/or substitution of one or more nucleotides at one or more sites in the native polynucleotide.
  • a “native” DNA sequence or polypeptide comprises a naturally occurring DNA sequence or amino acid sequence, respectively.
  • conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the polypeptides of the invention.
  • Variant DNA sequences also include synthetically derived DNA sequences, such as those generated, for example, by using site-directed mutagenesis but which still encode a protein of the invention.
  • variants of a particular DNA sequence of the invention will have at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters as described elsewhere herein.
  • Variants of a particular DNA sequence of the invention can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant DNA sequence and the polypeptide encoded by the reference DNA sequence. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides of the invention is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
  • “Variant” protein is intended to mean a protein derived from the native protein by deletion (so-called truncation) of one or more amino acids at the N-terminal and/or C-terminal end of the native protein; deletion and/or addition of one or more amino acids at one or more internal sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein.
  • Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein as described herein. Such variants may result from, for example, genetic polymorphism or from human manipulation.
  • Biologically active variants of a protein of the invention will have at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native protein as determined by sequence alignment programs and parameters described elsewhere herein.
  • a biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
  • the proteins of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants and fragments of the proteins can be prepared by mutations in the DNA. Methods for mutagenesis and polynucleotide alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds.
  • deletions, insertions, and substitutions of the protein sequences encompassed herein are not expected to produce radical changes in the characteristics of the protein. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays as described elsewhere herein or known in the art.
  • Variant DNA sequences and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling.
  • Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.
  • oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any organism of interest.
  • Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds.
  • PCR PCR Strategies
  • nested primers single specific primers
  • degenerate primers gene-specific primers
  • vector-specific primers partially-mismatched primers
  • hybridization techniques all or part of a known polynucleotide is used as a probe that selectively hybridizes to other corresponding polynucleotides present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen organism.
  • the hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32 P, or any other detectable marker.
  • probes for hybridization can be made by labeling synthetic oligonucleotides based on the DNA sequences of the invention.
  • Hybridization of such sequences may be carried out under stringent conditions.
  • stringent conditions or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background).
  • Stringent conditions are sequence-dependent and will be different in different circumstances.
  • target sequences that are 100% complementary to the probe can be identified (homologous probing).
  • stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing).
  • a probe is less than about 1000 nucleotides in length, optimally less than 500 nucleotides in length.
  • stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides).
  • Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
  • Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5 ⁇ to 1 ⁇ SSC at 55 to 60° C.
  • Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1 ⁇ SSC at 60 to 65° C.
  • wash buffers may comprise about 0.1% to about 1% SDS.
  • Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.
  • T m 81.5° C.+16.6 (log M)+0.41 (% GC) ⁇ 0.61 (% form)-500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs.
  • the T m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. T m is reduced by about 1° C. for each 1% of mismatching; thus, T m , hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ⁇ 90% identity are sought, the T m can be decreased 10° C.
  • stringent conditions are selected to be about 5° C. lower than the thermal melting point (T m ) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C.
  • T m thermal melting point
  • moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (T m ); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (T m ).
  • T m thermal melting point
  • DNA sequences and proteins of the invention encompass polynucleotide molecules and proteins comprising a nucleotide or an amino acid sequence that is sufficiently identical to the DNA sequences or to the amino acid sequence disclosed herein.
  • the term “sufficiently identical” is used herein to refer to a first amino acid or nucleotide sequence that contains a sufficient or minimum number of identical or equivalent (e.g., with a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have a common structural domain and/or common functional activity.
  • amino acid or nucleotide sequences that contain a common structural domain having at least about 70% identity, preferably 75% identity, more preferably 85%, 90%, 95%, 96%, 97%, 98% or 99% identity are defined herein as sufficiently identical.
  • the sequences are aligned for optimal comparison purposes.
  • the two sequences are the same length.
  • the percent identity between two sequences can be determined using techniques similar to those described below, with or without allowing gaps. In calculating percent identity, typically exact matches are counted.
  • the determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • a preferred, nonlimiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (1990) J. Mol. Biol. 215:403.
  • Gapped BLAST can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389.
  • PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra.
  • sequence identity/similarity values provided herein refer to the value obtained using the full-length sequences of the invention and using multiple alignment by mean of the algorithm Clustal W (Nucleic Acid Research, 22(22):4673-4680, 1994) using the program AlignX included in the software package Vector NTI Suite Version 7 (InforMax, Inc., Bethesda, Md., USA) using the default parameters; or any equivalent program thereof.
  • equivalent program any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by CLUSTALW (Version 1.83) using default parameters (available at the European Bioinformatics Institute website: http://www.ebi.ac.uk/Tools/clustalw/html).
  • the DNA sequences of the invention can be provided in expression cassettes for expression in any prokaryotic or eukaryotic cell and/or organism of interest including, but not limited to, bacteria, fungi, algae, plants, and animals.
  • the cassette will include 5′ and 3′ regulatory sequences operably linked to a DNA sequence of the invention.
  • “Operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a polynucleotide or gene of interest and a regulatory sequence (i.e., a promoter) is functional link that allows for expression of the polynucleotide of interest. Operably linked elements may be contiguous or non-contiguous.
  • the cassette may additionally contain at least one additional gene to be cotransformed into the organism.
  • the additional gene(s) can be provided on multiple expression cassettes.
  • Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the DNA sequence to be under the transcriptional regulation of the regulatory regions.
  • the expression cassette may additionally contain selectable marker genes.
  • the expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a DNA sequence of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants or other organism or non-human host cell.
  • the regulatory regions i.e., promoters, transcriptional regulatory regions, and translational termination regions
  • the DNA sequence of the invention may be native/analogous to the host cell or to each other.
  • the regulatory regions and/or DNA sequence of the invention may be heterologous to the host cell or to each other.
  • heterologous in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.
  • a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide.
  • a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.
  • the termination region may be native with the transcriptional initiation region, may be native with the operably linked DNA sequence of interest, may be native with the host, or may be derived from another source (i.e., foreign or heterologous) to the promoter, the DNA sequence of interest, the plant host, or any combination thereof.
  • Convenient termination regions for use in plants are available from the Ti-plasmid of A. tumefaciens , such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev.
  • the polynucleotides may be optimized for increased expression in a transformed organism. That is, the polynucleotides can be synthesized using codons preferred by the host for improved expression. See, for example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for a discussion of host-preferred codon usage. Methods are available in the art for synthesizing host-preferred gene, particularly plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.
  • Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression.
  • the G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
  • the expression cassettes may additionally contain 5′ leader sequences.
  • leader sequences can act to enhance translation.
  • Translation leaders are known in the art and include: picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein et al. (1989) Proc. Natl. Acad. Sci. USA 86:6126-6130); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Gallie et al. (1995) Gene 165(2):233-238), MDMV leader (Maize Dwarf Mosaic Virus) ( Virology 154:9-20), and human immunoglobulin heavy-chain binding protein (BiP) (Macejak et al.
  • EMCV leader Engelphalomyocarditis 5′ noncoding region
  • potyvirus leaders for example, TEV leader (Tobacco Etch Virus) (Gallie et al. (1995) Gene 165(2):233-238), MD
  • the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame.
  • adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like.
  • in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions may be involved.
  • a number of promoters can be used in the practice of the invention.
  • the promoters can be selected based on the host of interest and the desired outcome.
  • the nucleic acids can be combined with constitutive, tissue-preferred, or other promoters for expression in plants.
  • constitutive promoters include, for example, the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol.
  • pEMU Last et al. (1991) Theon. Appl. Genet. 81:581-588
  • MAS Velten et al. (1984) EMBO J. 3:2723-2730
  • ALS promoter U.S. Pat. No. 5,659,026), and the like.
  • Other constitutive promoters include, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611.
  • Tissue-preferred promoters can be utilized to target enhanced expression within a particular host tissue.
  • tissue-preferred promoters for use in plants include, but are not limited to, leaf-preferred promoters, root-preferred promoters, seed-preferred promoters, and stem-preferred promoters.
  • Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen. Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol.
  • an inducible promoter particularly from a pathogen-inducible promoter.
  • promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-1,3-glucanase, chitinase, etc.
  • PR proteins pathogenesis-related proteins
  • SAR proteins beta-1,3-glucanase
  • chitinase etc.
  • PR proteins pathogenesis-related proteins
  • promoters that are expressed locally at or near the site of pathogen infection. See, for example, Marineau et al. (1987) Plant Mol. Biol. 9:335-342; Matton et al. (1989) Molecular Plant - Microbe Interactions 2:325-331; Somsisch et al. (1986) Proc. Natl. Acad. Sci. USA 83:2427-2430; Somsisch et al. (1988) Mol. Gen. Genet. 2:93-98; and Yang (1996) Proc. Natl. Acad. Sci. USA 93:14972-14977. See also, Chen et al. (1996) Plant J. 10:955-966; Zhang et al. (1994) Proc.
  • Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator.
  • the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression.
  • Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-1a promoter, which is activated by salicylic acid.
  • promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
  • the expression cassette can also comprise a selectable marker gene for the selection of transformed cells.
  • Selectable marker genes are utilized for the selection of transformed cells or tissues.
  • Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D).
  • Additional selectable markers include phenotypic markers such as ⁇ -galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al.
  • selectable marker genes are not meant to be limiting. Any selectable marker gene can be used in the present invention.
  • the methods of the invention involve introducing a polynucleotide construct comprising a DNA sequence into a host cell.
  • introducing is intended presenting to the plant the polynucleotide construct in such a manner that the construct gains access to the interior of the host cell.
  • the methods of the invention do not depend on a particular method for introducing a polynucleotide construct into a host cell, only that the polynucleotide construct gains access to the interior of one cell of the host.
  • Methods for introducing polynucleotide constructs into bacteria, plants, fungi and animals are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.
  • stable transformation is intended that the polynucleotide construct introduced into a plant integrates into the genome of the host and is capable of being inherited by progeny thereof.
  • transient transformation is intended that a polynucleotide construct introduced into the host does not integrate into the genome of the host.
  • the DNA sequences of the invention are inserted using standard techniques into any vector known in the art that is suitable for expression of the DNA sequences in a host cell or organism of interest.
  • the selection of the vector depends on the preferred transformation technique and the target host species to be transformed.
  • the DNA sequences of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids. Generally, such methods involve incorporating a polynucleotide construct of the invention within a viral DNA or RNA molecule. It is recognized that the a protein of the invention may be initially synthesized as part of a viral polyprotein, which later may be processed by proteolysis in vivo or in vitro to produce the desired recombinant protein. Further, it is recognized that promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotide constructs into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367 and 5,316,931; herein incorporated by reference.
  • the DNA sequences of the invention can be provided to a plant using a variety of transient transformation methods.
  • transient transformation methods include, but are not limited to, the introduction of the protein or variants and fragments thereof directly into the plant or the introduction of a transcript encoding the protein into the plant.
  • Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986) Mol. Gen. Genet. 202:179-185; Nomura et al. (1986) Plant Sci. 44:53-58; Hepler et al. (1994) Proc. Natl. Acad. Sci. 91: 2176-2180 and Hush et al.
  • polynucleotide can be transiently transformed into the plant using techniques known in the art. Such techniques include Agrobacterium tumefaciens -mediated transient expression as described below.
  • the cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a polynucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • the present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots.
  • Plants of particular interest include, but are not limited to, and grain plants that provide seeds of interest, oil-seed plants, leguminous plants, and Arabidopsis thaliana .
  • Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc.
  • Oil-seed plants include cotton, soybean, safflower, sunflower, Brassica , maize, alfalfa, palm, coconut, etc.
  • Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
  • the term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruits, roots, root tips, anthers, and the like. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
  • the present invention further encompasses the introduction of the DNA sequences of the invention into non-plant host cells, including, but not limited to, bacterial cells, yeast cells other fungal cells, human cells, and other animal cells.
  • the invention encompasses the introduction of the DNA sequences into animals and other organisms by both stable and transient transformation methods.
  • a DNA sequence of the present invention can be expressed in these eukaryotic systems.
  • Synthesis of heterologous polynucleotides in yeast is well known (Sherman et al. (1982) Methods in Yeast Genetics, Cold Spring Harbor Laboratory).
  • yeasts for production of eukaryotic proteins are Saccharomyces cerevisiae and Pichia pastoris .
  • Vectors, strains, and protocols for expression in Saccharomyces and Pichia are known in the art and available from commercial suppliers (e.g., Invitrogen).
  • Suitable vectors usually have expression control sequences, such as promoters, including 3-phosphoglycerate kinase or alcohol oxidase, and an origin of replication, termination sequences and the like as desired.
  • sequences of the present invention can also be ligated to various expression vectors for use in transfecting cell cultures of mammalian or insect origin.
  • Illustrative cell cultures useful for the production of the peptides are mammalian cells.
  • a number of suitable host cell lines capable of expressing intact proteins have been developed in the art, and include the HEK293, BHK21, and CHO cell lines.
  • Expression vectors for these cells can include expression control sequences, such as an origin of replication, a promoter (e.g. the CMV promoter, a HSV tk promoter or pgk (phosphoglycerate kinase) promoter), an enhancer (Queen et al. (1986) Immunol. Rev.
  • ribosome binding sites such as ribosome binding sites, RNA splice sites, polyadenylation sites (e.g., an SV40 large T Ag poly A addition site), and transcriptional terminator sequences.
  • polyadenylation sites e.g., an SV40 large T Ag poly A addition site
  • transcriptional terminator sequences e.g., an SV40 large T Ag poly A addition site
  • Appropriate vectors for expressing proteins of the present invention in insect cells are usually derived from the SF9 baculovirus.
  • suitable insect cell lines include mosquito larvae, silkworm, armyworm, moth and Drosophila cell lines such as a Schneider cell line (See, Schneider (1987) J. Embyol. Exp. Morphol. 27:353-365).
  • polyadenylation or transcription terminator sequences are typically incorporated into the vector.
  • An example of a terminator sequence is the polyadenylation sequence from the bovine growth hormone gene. Sequences for accurate splicing of the transcript may also be included.
  • An example of a splicing sequence is the VP 1 intron from SV40 (Sprague et al. (1983) J. Virol. 45:773-781).
  • gene sequences to control replication in the host cell may be incorporated into the vector such as those found in bovine papilloma virus type-vectors (Saveria-Campo (1985) DNA Cloning Vol. II a Practical Approach, D. M. Glover, Ed., IRL Press, Arlington, Va., pp. 213-238).
  • Animal and lower eukaryotic (e.g., yeast) host cells are competent or rendered competent for transfection by various means.
  • eukaryotic (e.g., yeast) host cells are competent or rendered competent for transfection by various means.
  • methods of introducing DNA into animal cells include: calcium phosphate precipitation, fusion of the recipient cells with bacterial protoplasts containing the DNA, treatment of the recipient cells with liposomes containing the DNA, DEAE dextrin, electroporation, biolistics, and micro-injection of the DNA directly into the cells.
  • the transfected cells are cultured by means well known in the art (Kuchler (1997) Biochemical Methods in Cell Culture and Virology, Dowden, Hutchinson and Ross, Inc.).
  • Prokaryotes most frequently are represented by various strains of E. coli ; however, other microbial strains may also be used in the method of the invention.
  • Commonly used prokaryotic control sequences which are defined herein to include promoters for transcription initiation, optionally with an operator, along with ribosome binding sequences, include such commonly used promoters as the beta lactamase (penicillinase) and lactose (lac) promoter systems (Chang et al. (1977) Nature 198:1056), the tryptophan (trp) promoter system (Goeddel et al. (1980) Nucleic Acids Res.
  • Bacterial vectors are typically of plasmid or phage origin. Appropriate bacterial cells are infected with phage vector particles or transfected with naked phage vector DNA. If a plasmid vector is used, the bacterial cells are transfected with the plasmid vector DNA. Expression systems for expressing a protein of the present invention are available using Bacillus sp. and Salmonella (Palva et al. (1983) Gene 22:229-235); Mosbach et al. (1983) Nature 302:543-545).
  • “operably linked” is intended to mean a functional linkage between two or more elements or domains. If it recognized that a linker of one or more amino acids may be inserted in between each of the two or more elements to maintain the desired function of the two or more elements.
  • fusion proteins comprise a repeat domain of the invention operably linked to at least one protein or part or domain thereof.
  • the protein or part or domain thereof comprises a protein or functional part or domain thereof, that is capable of modifying DNA or RNA.
  • protein or functional part or domain thereof is capable of functioning as a transcriptional activator or a transcriptional repressor.
  • Preferred proteins include, but are not limited to, transcription activators, a transcription repressors, a resistance-mediating proteins, nucleases, topoisomerases, ligases, integrases, recombinases, resolvases, methylases, acetylases, demethylases, and deacetylases.
  • AvrBs3 directly binds the UPA-box, a promoter element in induced target genes (Kay et al. (2007) Science 318, 648-651; Römer et al. (2007) Science 318:645-648), prompted us to investigate the basis for DNA-sequence specificity.
  • Each repeat region generally consists of 34 amino acid, and the repeat units are nearly identical; however, amino acids 12 and 13 are hypervariable (Schornack et al. (2006) J. Plant Physiol. 163:256-272; FIG. 1A ).
  • the most C-terminal repeat of AvrBs3 shows sequence similarity to other repeat units only in its first 20 amino acids and is therefore referred to as half repeat.
  • the repeat units can be classified into different repeat types based on their hypervariable 12th and 13th amino acids ( FIG. 1B ). Because the size of the UPA-box (18 (20)/19 (21) bp) almost corresponds to the number of repeat units (17.5) in AvrBs3, we considered the possibility that one repeat unit of AvrBs3 contacts one specific DNA base pair. When the repeat types of AvrBs3 (amino acid 12 and 13 of each repeat) are projected onto the UPA box, it becomes evident that certain repeat types correlate with specific base pairs in the target DNA. For example, HD and NI repeat units have a strong preference for C and A, respectively ( FIG. 1B ). For simplicity, we designate only bases in the upper (sense) DNA strand.
  • AvrBs3 repeat deletion derivative AvrBs3 ⁇ rep16 which lacks four repeat units ( ⁇ 11-14; FIG. 5A , B) recognizes a shorter and different target DNA sequence ( FIGS. 5 to 8 ).
  • the target DNA box of AvrBs3 appears to be 1 bp longer than the number of repeat units in AvrBs3.
  • a T is conserved at the 5′ end of the UPA box immediately preceding the predicted recognition specificity of the first repeat ( FIG. 1 ).
  • secondary structure predictions of the protein region preceding the first repeat and the repeat region show similarities, despite lack of amino acid-sequence conservation. This suggests an additional repeat, termed repeat 0 ( FIG. 1B ).
  • FIG. 1B To further substantiate and extend our model ( FIG. 1B ), we predicted the yet unknown target DNA sequences of Xanthomonas TAL effectors based on the sequence of their repeat units, and inspected the promoters of known TAL target genes and their alleles for the presence of putative binding sites. We identified sequences matching the predicted specificity in promoters of alleles that are induced in response to the corresponding TAL effector, but not in non-induced alleles
  • FIGS. 5C-F The presence of these boxes suggests that the induced genes are direct targets of the corresponding TAL effectors. Based on the DNA base frequency for different repeat types in the target DNA sequences using eight TAL effectors we deduced a code for the DNA target specificity of certain repeat types ( FIG. 1C , D; FIG. 5 ).
  • the Hax3 and Hax4 target boxes were placed in front of the minimal ( ⁇ 55 to +25) tomato Bs4 promoter, which has very weak basal activity (Schornack et al. (2005) Mol. Plant - Microbe Interact. 18:1215-1225; FIG. 2B ; FIG. 9 ), driving a promoterless uidA ( ⁇ -glucuronidase, GUS) reporter gene.
  • uidA ⁇ -glucuronidase, GUS
  • Hax2 An exceptional TAL effector is Hax2 because it contains 35 amino acids per repeat instead of the typical 34 amino acid-repeat units (Kay et al. (2005) Mol. Plant - Microbe Interact. 18:838-848).
  • Hax2 contains a rare amino acid combination in its second repeat (amino acids 12/13: IG; FIG. 2A ).
  • IG amino acids 12/13
  • FIG. 2A We permutated the corresponding third base of the Hax2-box and analyzed reporter gene activation with the effector Hax2 using the transient assay. This showed that an IG repeat confers specificity for T ( FIG. 13 ).
  • the Hax2-box only leads to promoter activation by Hax2, but not by Hax3 or Hax4 ( FIG. 2C ).
  • FIGS. 14A , B To identify Hax2 target genes we analyzed promoter regions of the A. thaliana genome using pattern search (Patmatch, TAIR; www.arabidopsis.org) with degenerated Hax2-box sequences.
  • One of the putative Hax2 target genes encodes the MYB transcription factor PAP1 (At1G56650) which controls anthocyanin biosynthesis (Borevitz et al. (2000) Plant Cell 12:2383-2394).
  • PAP1 MYB transcription factor
  • FIGS. 14D , E Visual inspection of the PAP1 promoter region revealed the presence of a suboptimal Hax2-box ( FIGS. 14D , E). Based on the code for TAL effector repeat types ( FIG. 1D ) and the data described above we predicted putative target DNA sequences for additional TAL effectors some of which are important virulence factors ( FIG. 15 , Table 1).
  • FIGS. 4C While at least 6.5 repeat units were needed for gene induction, 10.5 or more repeat units led to strong reporter gene activation ( FIG. 4C ). These data demonstrate that a minimal number of repeat units is required to recognize the artificial target DNA-box and activate gene expression. The results also suggest that effectors with fewer repeat numbers are largely inactive. We have shown that the repeat region of TAL effectors has a sequential nature that corresponds to a consecutive target DNA sequence. Hence, it should be feasible to generate effectors with novel DNA-binding specificities. Three artificial effectors were generated (ArtX1, ArtX2, ArtX3), each with randomly assembled 12.5 repeat units ( FIGS.
  • TAL effectors have a linear DNA-binding specificity that can easily be rearranged. It has not escaped our notice that the postulated right-handed superhelical structure of the repeat regions in TAL effectors immediately suggests a possible mechanism for interaction with the right-handed helix of the genetic material. It will be important to determine the structure of the novel DNA-binding domain of TAL effectors complexed with target DNA.
  • the repeat units of the repeat domain of naturally occurring effectors of the AvrBs3-family encode a corresponding DNA-binding specificity. These recognition sequences can be predicted with the recognition code.
  • the artificial insertion of the predicted recognition sequences in front of a gene in transgenic plants leads to expression of the gene if the corresponding AvrBs3-like effector is translocated into the plant cell (e.g. during a bacterial infection).
  • the recognition sequence is inserted in front of a gene whose expression leads to a defence reaction (resistance-mediating gene) of the plant, such constructed transgenic plants are resistant against an infection of plant pathogenic bacteria which translocate the corresponding effector.
  • the prediction of DNA target sequences of a corresponding effector of the AvrBs3-family in the promoter region of plant genes is an indication for the inducible expression of these genes by the effector.
  • Using the method according to the invention it is possible to predict inducible plant genes. Predictions are particularly straightforward in sequenced genomes.
  • the predicted DNA binding sequences of other members of the AvrBs3-family can be inserted into promoters to generate new controllable promoters which can be induced by the corresponding effector.
  • Two constructs are introduced into plants. First, a hax3 gene whose expression is under control of an inducible promoter. Secondly, a target gene that contains the Hax3-box in the promoter.
  • Hax3 Induction of the expression of hax3 leads to production of the Hax3 protein that then induces the expression of the target gene.
  • the described two-component construction leads to a twofold expression switch which allows a variable expression of the target gene.
  • the trans-activator and the target gene can also be present first in different plant lines and can be introgressed at will. Analogous to this, Hax4 and the corresponding Hax4-box can be used.
  • This system can also be used with other members of the AvrBs3-family or artificial derivatives and predicted DNA-target sequences. The functionality of the system could already be verified.
  • Transgenic Arabidopsis thaliana plants were constructed, which contain an inducible avrBs3 gene as well as a Bs3 gene under control of its native promoter, whose expression can be induced by AvrBs3.
  • the induction of expression of avrBs3 leads to expression of Bs3 and therefore to cell death. See, WO 2009/042753, herein incorporated by reference.
  • the DNA target sequence of an AvrBs3-similar effector is inserted in front of a gene whose expression leads to a defence reaction (resistance-mediating gene) of the plant, correspondingly constructed transgenic plants will be resistant against infection of plant pathogenic organisms, which make this effector available.
  • a resistance-mediating gene can for example lead to a local cell death which prevents spreading of the organisms/pathogens, or induce the basal or systemic resistance of the plant cell.
  • the modular architecture of the central repeat domain enables the targeted construction of definite DNA binding specificities and with this the induction of transcription of selected plant genes.
  • the DNA binding specificities can either be artificially inserted in front of target genes so that novel effector-DNA-box variants are generated for the inducible expression of target genes.
  • repeat domains can be constructed that recognize a naturally occurring DNA sequence in organisms. The advantage of this approach is that the expression of any gene in non-transgenic organisms can be induced if a corresponding effector of the invention is present in the cells of this organism.
  • the central repeat domain of effectors of the AvrBs3-family is a new type of DNA binding domain (Kay et al., 2007).
  • the decryption of the specificity of the single repeat units now allows the targeted adaptation of the DNA-binding specificity of this region.
  • the DNA binding region can be translationally fused to other functional domains to generate sequence-specific effects. Below, four examples of such protein fusions are given.
  • the effectors of the AvrBs3-like family induce the expression of genes in plant cells.
  • the C-terminus of the protein is essential, which contains a transcriptional activation domain and nuclear localization sequences that mediate the import of the protein into the plant nucleus.
  • the C-terminus of the AvrBs3-homologous protein can be modified in such a way that it mediates the expression of genes in fungal, animal, or human systems. Thereby, effectors can constructed that function as transcriptional activators in humans, other animals, or fungi.
  • the methods according to the invention can be applied not only to plants, but also to other living organisms.
  • the DNA binding specificity of the repeat domain can be used together with other domains in protein fusions to construct effectors that act as specific repressors. These effectors exhibit a DNA binding specificity that has been generated in such a way that they bind to promoters of target genes. In contrast to the TAL effectors which are transcription activators, these effectors are constructed to block the expression of target genes. Like classical repressors, these effectors are expected to cover promoter sequences by their recognition of, or binding to, a target DNA sequence and make them inaccessible for factors that otherwise control the expression of the target genes.
  • the repeat domains can be fused to a transcription-repressing domain, such as an EAR motif (Ohta et al. Plant Cell 13:1959-1968 (2001)).
  • a repeat domain to recognize a specific target DNA sequence an be used together with other domains to label specific DNA sequences.
  • C-terminally a GFP (“green-fluorescent-protein”) can for example be fused to an artificial repeat domain that detects a desired DNA sequence.
  • This fusion protein binds in vivo and in vitro to a corresponding DNA sequence.
  • the position of this sequence on the chromosome can be localized using the fused GFP-protein.
  • other protein domains that enable a cellular localization of the protein e.g. by FISH
  • the DNA recognition specificity of repeat domains of the invention can be used to isolate specific DNA sequences.
  • the AvrBs3-like protein can be immobilized to a matrix and interacts with corresponding DNA molecules that contain a matching sequence. Therefore, specific DNA sequences can be isolated from a mixture of DNA molecules.
  • the DNA recognition specificity of the repeat domain can be fused to a suitable restriction endonuclease to specifically cleave DNA. Therefore, the sequence-specific binding of the repeat domain leads to localization of the fusion protein to few specific sequences, so that the endonuclease specifically cleaves the DNA at the desired location.
  • unspecific nucleases such as FokI can be changed into specific endonucleases analogous to work done with zinc finger nucleases. For example, the optimal distance between the two effector DNA target sites would be determined to that would be required to support dimerization of two FokI domains. This would be accomplished by analysis of a collection of constructs in which the two DNA binding sites are separated by differently sized spacer sequences.
  • these methods enable very specific cuts at only a few positions in complex DNA-molecules. These methods can amongst other things be used to introduce double-strand breaks in vivo and selectively incorporate donor DNA at these positions. These methods can also be used to specifically insert transgenes.
  • a repeat domain with a repeat unit order that matches a desired DNA-sequence in a promoter of interest is determined based on the recognition code of the present invention.
  • Generation of a specific 11.5 repeat unit order was accomplished using “Golden gate” cloning (Engler et al. (2008) PLoS ONE 3:e3647).
  • Each building block contained individual flanking BsaI sites ( FIG. 18 ) that allowed an ordered assembly of the fragments into a custom effector polypeptide.
  • the effector (ARTBs4) was correctly assembled from the total of 14 fragments into a BsaI-compatible binary vector that allows Agrobacterium -mediated expression of the custom effector polypeptide as an N-terminally tagged GFP fusion in plant cells ( FIG. 18 ).
  • the nucleotide binding specificity of the repeat domain can be used to design effectors that disrupt viral replication in cells. These effectors will exhibit a nucleotide binding specificity targeted to nucleotide sequence in viral origins of replication and other sequences critical to viral function. No additional protein domains need to be fused to these repeat domain proteins in order to block viral function. They act like classical repressors by covering origins of replication or other key sequences, including promoters, enhancers, long terminal repeat units, and internal ribosome entry sites, by binding and making them inaccessible for host or viral factors, including viral encoded RNA-dependent RNA polymerase, nucleocapsid proteins and integrases, which participate in viral replication and function. This type of strategy has been used successfully with zinc-finger proteins (Sera (2005) J. Vir. 79:2614-2619; Takenaka et al. (2007) Nucl Acids Symposium Series 51:429-430).
  • the present invention additionally covers isolated nucleic acid molecules to be used in any of the methods of the present invention, transformed plants comprising a heterologous polynucleotide stably incorporated in their genome and comprising the nucleotide molecule described above, preferably operably linked to a promoter element and/or operably linked to a gene of interest.
  • the transformed plant is preferably a monocot or a dicot.
  • the invention covers also seeds of the transformed plants.
  • the invention covers human and non-human host cells transformed with any of the polynucleotides of the invention or the polypeptides of the invention.
  • the promoters used in combination with any of the nucleotides and polypeptides of the invention are preferably tissue specific promoters, chemical-inducible promoters and promoters inducible by pathogens.
  • plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seed, leaves, flowers, branches, fruits, roots, root tips, anthers and the like. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
  • Escherichia coli Bacterial strains and growth conditions. Escherichia coli were cultivated at 37° C. in lysogeny broth (LB) and Agrobacterium tumefaciens GV3101 at 30° C. in yeast extract broth (YEB) supplemented with appropriate antibiotics.
  • LB lysogeny broth
  • YEB yeast extract broth
  • Nicotiana benthamiana plants were grown in the greenhouse (day and night temperatures of 23° C. and 19° C., respectively) with 16 h light and 40 to 60% humidity. Mature leaves of five- to seven-week-old plants were inoculated with Agrobacterium using a needleless syringe as described previously (S1). Inoculated plants were transferred to a Percival growth chamber (Percival Scientific) with 16 h light, 22° C. and 18° C. night temperature.
  • Percival Scientific Percival Scientific
  • effectors The construction of effectors with modified repeat region was based on ligation of Esp3I (Fermentas) restriction fragments. Esp3I cuts outside of its recognition sequence and typically once per repeat.
  • Esp3I Fermentas
  • proof reading polymerase HotStar HiFidelity Polymerase Kit
  • SOE splicing by overlap extension
  • a 1 bp frame-shift preceding the start codon was inserted by site-directed mutagenesis to allow in frame N-terminal fusions using GATEWAY recombination (Invitrogen) resulting in pC3SEIF.
  • Single repeat units were amplified from TAL effectors using a forward primer binding to most repeat units and repeat-specific reverse primers. Both primers included the naturally present Esp3I sites. To avoid amplification of more than one repeat, template DNA was digested with Esp3I prior to the PCR reaction.
  • the ArtHD effector backbone construct consists of the N- and C-terminus of Hax3 with the last half repeat mutated into a HD-repeat. The resulting construct was restricted by Esp3I and dephosphorylated.
  • DNA fragments encoding repeat units were excised with Esp3I from pC3SE26-derivatives containing a single HD-repeat and purified via agarose gels. Ligation was performed using a molar excess of insert to vector to facilitate concatemer ligation and transformed into E. coli . The number of repeat units was determined in recombinant plasmids using StuI and HincII. ArtX1-3 effectors with a random combination of repeat types were generated by isolating DNA fragments encoding repeat units as described above from cloned single NI-, HD-, NN-, and NG-repeat units (specificities for A, C, G/A, and T, respectively).
  • the fragments were added in equal molar amounts each to the concatemer ligation reaction with vector pC3SEIF. Plasmids containing effectors of the invention with 12.5 repeat units were chosen for subsequent analysis. Effectors were cloned by GATEWAY-recombination (Invitrogen) into pGWB6 (S2) for expression of N-terminal GFP-effector fusions. Oligonucleotide sequences are available upon request. All constructs were sequenced.
  • GUS reporter constructs The minimal Bs4 promoter was amplified by PCR and inserted into pENTR/D-TOPO (Invitrogen) with target DNA boxes at the 5′ end (S3; FIG. S5). Promoter derivatives were cloned into pGWB3 (S2) containing a promoterless uidA gene.
  • hax2-transgenic A. thaliana . hax2 was cloned under control of the inducible alcA promoter from Aspergillus nidulans into a GATEWAY-compatible derivative of the binary T-DNA vector binSRNACatN (Zeneca Agrochemicals) containing the 35S-driven alcR ethanol-dependent regulator gene and a nptII selection marker. AlcR drives ethanol-dependent induction of the alcA promoter (S4). T-DNA containing these genes was transformed into A. thaliana Col-0 via A. tumefaciens using floral dip inoculation (S5). Transformants were selected as kanamycin-resistant plants on sterile medium.
  • ARTBs4 an artificial effector.
  • Golden gate cloning (Engler et al. (2008) PLoS ONE 3:e3647) was used to assemble effectors with 11.5 specifically ordered repeat units. The N- and C-terminus of Hax3 and 12 individual repeat units resembling the 11.5 repeat units were subcloned. Each building block contained individual flanking BsaI sites that allowed an ordered assembly of the fragments into an artificial effector. For the targeted assembly of effectors with any desired repeat composition, the building block repertoire of repeat units was expanded. To allow for target specificity to any of the four natural bases (A, C, G, and T) in DNA, four different repeat types were chosen, based on the amino acids 12 and 13 per repeat unit.
  • GUS ⁇ -Glucuronidase assays.
  • Agrobacterium strains delivering effector constructs and GUS reporter constructs were mixed 1:1, and inoculated into Nicotiana benthamiana leaves with an OD 600 of 0.8.
  • Two leaf discs (0.9 cm diameter) were sampled two days post infiltration (dpi) and quantitative GUS activity was determined using 4-methyl-umbelliferyl- ⁇ -D-glucuronide (MUG), as described previously (Si). Proteins were quantified using Bradford assays (BioRad). Data correspond to triplicate samples from different plants.
  • leaf discs were sampled 2 dpi, incubated in X-Gluc (5-bromo-4-chloro-3-indolyl- ⁇ -D-glucuronide) staining solution (S3), destained in ethanol, and dried. Experiments were performed at least twice with similar results.
  • X-Gluc 5-bromo-4-chloro-3-indolyl- ⁇ -D-glucuronide staining solution
  • hax2, hax3, and hax4 were expressed in planta under control of the constitutive cauliflower mosaic virus 35S promoter using pAGH2, pAGH3, and pAGH4 (S6).
  • DNaseI footprinting was performed as described (S7) with the following modifications: Fluorescently labeled PCR products of Bs3 and Bs3-E promoter DNA were generated using plasmids pCRBluntII-TOPO::FPBs3 (Bs3 promoter fragment from ⁇ 211 to +108) and pCRBluntII-TOPO::FPBs3-E (Bs3-E promoter fragment from ⁇ 224 to +108), respectively, as template and Phusion DNA polymerase (Finnzymes).
  • Fluorescently labeled PCR product of UPA20-ubm-r16 promoter DNA was generated using plasmid pCRBluntII-TOPO::FPU20-ubm-r16 (UPA20 promoter fragment from ⁇ 213 to +86 containing the ubm-r16 mutation (S7) as template and Phusion DNA polymerase (Finnzymes).
  • Plasmids pCRBluntII-TOPO::FPBs3, pCRBluntII-TOPO::FPBs3-E and pCRBluntII-TOPO::FPU20-ubm-r16 were sequenced, using the Thermo Sequenase Dye Primer Manual Cycle Sequencing Kit (USB) according to the manufacturer's instructions. An internal Gene Scan-500 LIZ Size Standard (Applied Biosystems) was used to determine the DNA fragment size.
  • the DNA binding domain of TAL effectors is composed of tandem-arranged 34-amino acid repeat units.
  • the amino acid sequences of the repeat units are mostly conserved, except for two adjacent highly variable residues (HVRs) at positions 12 and 13 that define DNA target specificity (Boch et al. (2009) Science 326:1509-1512; Moscou & Bogdanove (2009) Science 326:1501).
  • HVRs highly variable residues
  • Functional analysis identified HVR motifs that bind preferentially to A (NI), C(HD), T (NG, IG) or equally well to G and A (NN) (Boch et al. (2009) Science 326:1509-1512).
  • HVRs that in the given promoter-TAL effector interactions match specifically to G (Moscou & Bogdanove (2009) Science 326:1501).
  • HN & NA single or two (NK) interaction sites.
  • NK two interaction sites.
  • these HVRs can be considered as suitable candidates that may mediate specific binding to G.
  • the wildtype Bs3 promoter and the three promoter mutants were fused to an uidA reporter gene and tested via Agrobacterium tumefaciens transient expression in combination with either wildtype AvrBs3 or AvrBs3-NK 5/6 in Nicotiana benthamiana leaves.
  • GUS assays revealed that AvrBs3-NK 5/6 activated the GUS reporter only in combination with the “GG” Bs3 promoter mutant while AvrBs3 activated only the Bs3 wildtype promoter construct.
  • the DNA binding domain of TAL effectors is composed of tandem-arranged 34-amino acid repeat units.
  • the amino acid sequences of the repeat units are mostly conserved, except for two adjacent highly variable residues (HVRs) at positions 12 and 13 that define DNA target specificity (Boch et al. (2009) Science 326:1509-1512; Moscou & Bogdanove (2009) Science 326:1501).
  • HVRs highly variable residues
  • Different HVR motifs bind with different levels of specificity to individual A, C, G or T nucleotides.
  • tandem arranged repeat units do not to interfere with the specificity of adjacent units (Moscou & Bogdanove (2009) Science 326:1501).
  • modular assembly of repeat units with pre-characterized specificities is likely to provide an efficient way for generation of DNA-recognition modules with desired DNA specificity.
  • the recently developed “Golden-Gate cloning” provides an alternative approach for generation of repeat unit arrays of desired composition.
  • the strategy is based on the use of type IIS restriction enzymes, which cut outside of their recognition sequence.
  • BsaI the type IIS enzyme
  • BsaI restriction in principle 256 (4 4 ) different sticky ends which provides the basis for multi fragment ligations.
  • two or more fragments cut by type IIS restriction enzymes can be ligated into a product lacking the original restriction site (Engler et al. (2008) PLoS ONE 3:e3647; Engler et al. (2009) PLoS ONE 4:e5553).
  • repeat-array building kit The basis for our “repeat-array building kit” is a set of “insert plasmids” that contain individual repeat units (one repeat unit per plasmid), “intermediate vectors” that contain repeat domains consisting of sets of 10 repeat units, and one “acceptor vector” that contains the N- and C-terminal non-repeat region of a TAL effector. All repeat units are designed in such a way that the BsaI recognition sites flank the insert in the insert plasmids.
  • the insert plasmid containing the 1 st repeat unit gene is designed in such a way that BsaI treatment creates A[N] and B[C] termini.
  • the 2 nd repeatunit gene has B[N] and C[C] termini upon BsaI cleavage, while BsaI cleavage of the insert plasmid with the 3 rd repeat unit gene results in C[N] and D[C] termini, and so on.
  • the B[C] terminus of the 1 st repeat unit gene will fuse specifically to the B[N] terminus of the 2 nd repeat unit gene.
  • the C[C] terminus of the 2 nd repeat unit gene will ligate specifically to the C[N] terminus of the 3 rd repeat unit gene and so on.
  • BsaI digestion releases the repeat units with 4-bp sticky overhangs that are compatible only with the designed adjacent repeat units.
  • the BsaI recognition site itself remains in the cleaved insert plasmid vector and the released insert has no BsaI recognition site.
  • the repeat units are joined together in the order specified by the overhanging ends in a cut-ligation reaction (cleavage and ligation running simultaneously). Due to the simultaneous action of BsaI and ligase the religation of repeat units into the insert donor vector is avoided since this restores the BsaI recognition site. By contrast the desired ligation products lack the BsaI recognition sites. This experimental design makes this cloning procedure highly efficient.
  • each repeat unit position is made with individual repeat units with specific nucleotide recognition specificity, (e.g. HD residues at position 12 and 13 for recognition of a C base, NI for A, and so on).
  • the variant for each position is made with the appropriate sticky ends for each repeat unit, for example A[N] and B[C] termini for repeat unit 1, such that there are four possible insert plasmids for repeat unit one, chosen based on the desired DNA recognition.
  • Ligations are carried out in two stages. In the first stage, 10 repeat units are combined into an intermediate vector. Different sets of 10 repeat units can be combined in intermediate vectors. Intermediate vector 1 contains repeat units 1-10, intermediate vector 2 contains repeat units 11-20 and so on. In the second stage, separately assembled 10 repeat units are combined into acceptor vectors. The acceptor vector also contains the N- and C-terminal non-repeat areas of the effector, such that a complete effector comprised of 10, 20, 30 40 or other multiples of 10 repeat units is assembled in the final construct.
  • the intermediate vector has BsaI sites in the insert for introducing the 10 repeat unit fragments and also has flanking BpiI sites in the flanking vector sequence. BpiI is another type IIS enzyme with a recognition site distinct from BsaI.
  • the 10 repeat units are first assembled into the “intermediate vector” and using BpiI the assembled 10 mers are released as one fragment. This fragment is ligated in a BpiI cut-ligase reaction with the acceptor vector, which contains BpiI sites between the N- and C-terminal non-repeat areas of the TAL effector. In this case only 2-4 inserts are ligated into the acceptor vector. This allows to make each ligation highly specific and to assemble easily 40 and more repeat units.
  • the acceptor vector in which the repeat unit array is finally cloned represents a GATEWAY Entry clone and thus allows recombination-based transfer of the effector into any desired expression construct.
  • the acceptor vector is designed to generate a TAL-type transcription factor.
  • the acceptor vector allows also fusions of the repeat array to the FokI endonuclease or other desired functional domains.
  • FIG. 19A-D A schematic of this method is provided in FIG. 19A-D .
  • Fusion proteins comprising a repeat domain of the invention that recognizes a target DNA sequence and a FokI nuclease (“TAL-type-nucleases”) are produced as described by any of the method disclosed herein or known in the art.
  • the fusion proteins are tested for nuclease activity by incubation with corresponding target DNA.
  • the repeat domain DNA target site is cloned into the multiple cloning site of a plasmid vector (e.g., bluescript).
  • a plasmid vector e.g., bluescript
  • the vector Before treatment of the DNA substrate with the TAL-type nuclease, the vector is linearized by treatment with a suitable standard endonuclease that cleaves in the vector backbone. This linearized vector is incubated with in vitro generated repeat domain-FokI nuclease fusion proteins and the products analyzed by agarose gel electrophoresis. The detection of two DNA fragments in gel electrophoresis is indicative for specific nuclease mediated cleavage. By contrast, the negative controls that do not contain a target site that is recognized by repeat domain are unaffected by treatment with the repeat domain-FokI nuclease fusion protein.
  • DNA-driven, cell-free systems for in vitro gene expression and protein synthesis are used to generate repeat domain-FokI nuclease fusion proteins (e.g. T7 High-Yield Protein Expression System; Promega).
  • repeat domain-FokI nuclease fusion protein nucleotide sequences are cloned in front of a T7 RNA polymerase.
  • Such fusion proteins that are produced via in vitro transcription and translation are used in DNA cleavage assays without further purification.
  • the recognition specificities set forth in this Example can be used in the methods of the present invention. It is further recognized that the recognition specificities set forth in this Example can be used to produce compositions of the present invention, such as, for example, polypeptides and DNA. Preferably, the recognition specificities set forth in this Example are used in such methods or to produce such compositions in combination with any of the other recognition specificities disclosed herein.

Abstract

The present invention refers to methods for selectively recognizing a base pair in a DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.

Description

    CROSS-REFERENCE TO RELATED APPLICATIONS
  • This application is a continuation-in-part of U.S. Ser. No. 13/016,297, filed Jan. 28, 2011 which is a continuation of International Application PCT/IB2010/000154, filed Jan. 12, 2010, which designates the U.S and was published by the International Bureau in English on Jul. 15, 2010, and which claims the benefit of U.S. Provisional Patent Application No. 61/225,043, filed Jul. 12, 2009, European (EP) Patent Applicaiton No. 09165328.7, filed Jul. 13, 2009, German (DE) Patent Application No. 102009004659.3, filed Jan. 12, 2009; all of which are hereby incorporated herein in their entirety by reference.
    • TECHNICAL FIELD OF THE INVENTION
  • The present invention refers to methods for selectively recognizing a base pair in a target DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a target DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.
    • BACKGROUND OF THE INVENTION
  • Phytopathogenic bacteria of the genus Xanthomonas cause severe diseases on many important crop plants. The bacteria translocate an arsenal of effectors including members of the large transcription activator-like (TAL)/AvrBs3-like effector family via the type III secretion system into plant cells (Kay & Bonas (2009)Curr. Opin. Microbiol. 12:37-43, White & Yang (2009) Plant Physiol. doi:10.1104/pp. 1109.139360; Schornack et al. (2006) J. Plant Physiol. 163:256-272). TAL effectors, key virulence factors of Xanthomonas, contain a central domain of tandem repeats, nuclear localization signals (NLSs), and an activation domain (AD) and act as transcription factors in plant cells (Kay et al. (2007)Science 318:648-651; Römer et al. (2007) Science 318:645-648; Gu et al. (2005)Nature 435, 1122-1125; FIG. 1 a). The type member of this effector family, AvrBs3 from Xanthomonas campestris pv. vesicatoria, contains 17.5 repeats and induces expression of UPA (upregulated by AvrBs3) genes including the Bs3 resistance gene in pepper plants (Kay et al. (2007)Science 318:648-651; Römer et al. (2007)Science 318:645-648; Marois et al. (2002)Mol. Plant-Microbe Interact. 15:637-646). The number and order of repeats in a TAL effector determine its specific activity (Herbers et al. (1992) Nature 356:172-174). The repeats were shown to be essential for DNA-binding of AvrBs3 and constitute a novel DNA-binding domain (Kay et al. (2007)Science 318:648-651). How this domain contacts DNA and what determines specificity has remained enigmatic.
  • Selective gene expression is mediated via the interaction of protein transcription factors with specific nucleotide sequences within the regulatory region of the gene. The manner in which DNA-binding protein domains are able to discriminate between different DNA sequences is an important question in understanding crucial processes such as the control of gene expression in differentiation and development.
  • The ability to specifically design and generate DNA-binding domains that recognize a desired DNA target is highly desirable in biotechnology. Such ability can be useful for the development of custom transcription factors with the ability to modulate gene expression upon target DNA binding. Examples include the extensive work done with the design of custom zinc finger DNA-binding proteins specific for a desired target DNA sequence (Choo et al. (1994) Nature 372:645; Pomerantz et al., (1995) Science 267:93-96; Liu et al., Proc. Natl. Acad. Sci. USA 94:5525-5530 (1997); Guan et al. (2002)Proc. Natl. Acad. Sci. USA 99:13296-13301; U.S. Pat. No. 7,273,923; U.S. Pat. No. 7,220,719). Furthermore, polypeptides containing designer DNA-binding domains can be utilized to modify the actual target DNA sequence by the inclusion of DNA modifying domains, such as a nuclease catalytic domain, within the polypeptide. Examples of such include the DNA binding domain of a meganuclease/homing endonuclease DNA recognition site in combination with a non-specific nuclease domain (see US Pat. Appl. 2007/0141038), modified meganuclease DNA recognition site and/or nuclease domains from the same or different meganucleases (see U.S. Pat. App. Pub. 20090271881), and zinc finger domains in combination with a domain with nuclease activity, typically from a type IIS restriction endonuclease such as FokI (Bibikova et al. (2003)Science 300:764; Urnov et al. (2005)Nature 435, 646; Skukla, et al. (2009) Nature 459, 437-441; Townsend et al. (2009)Nature 459:442445; Kim et al. (1996) Proc. Natl. Acad. Sci. USA 93:1156-1160; U.S. Pat. No. 7,163,824). The current methods utilized for identifying custom zinc finger DNA-binding domains employ combinatorial selection-based methods utilizing large randomized libraries (typically >108 in size) to generate multi-finger domains with desired DNA specificity (Greisman & Pabo (1997) Science 275:657-661; Hurt et al. (2003)Proc Natl Acad Sci USA 100:12271-12276; Isalan et al. (2001)Nat Biotechnol 19:656-660. Such methods are time intensive, technically demanding and potentially quite costly. The identification of a simple recognition code for the engineering of DNA-binding polypeptides would represent a significant advancement over the current methods for designing DNA-binding domains that recognize a desired nucleotide target.
    • BRIEF SUMMARY OF THE INVENTION
  • The present invention provides a method for producing a polypeptide that selectively recognizes a base pair in a DNA sequence, the method comprising synthesizing a polypeptide comprising a repeat domain, wherein the repeat domain comprises at least one repeat unit derived from a transcription activator-like (TAL) effector, wherein the repeat unit comprises a hypervariable region which determines recognition of a base pair in the DNA sequence, wherein the repeat unit is responsible for the recognition of one base pair in the DNA sequence. These polypeptides of the invention comprise repeat units of the present invention and can be constructed by a modular approach by preassembling repeat units in target vectors that can subsequently be assembled into a final destination vector. The invention provides the polypeptide produced the this method as well as DNA sequences encoding the polypeptides and host organisms and cells comprising such DNA sequences.
  • The present invention provides a method for selectively recognizing a base pair in a target DNA sequence by a polypeptide wherein said polypeptide comprises at least a repeat domain comprising repeat units wherein in said repeat units each comprise a hypervariable region which determines recognition of a base pair in said target DNA sequence.
  • More specifically, the inventors have determined those amino acids in a DNA-binding polypeptide responsible for selective recognition of base pairs in a target DNA sequence. With elucidation of the recognition code, a general principle for recognizing specific base pairs in a target DNA sequence by selected amino acids in a polypeptide has been determined. The inventors have found that distinct types of repeat units that are part of a repeat unit array of varying length have the capacity to recognize one defined/specific base pair. Within each repeat unit forming a repeat domain, a hypervariable region is responsible for the specific recognition of a base pair in a target DNA sequence.
  • Thus, the present invention provides not only a method for selectively recognizing a base pair in a target DNA sequence by a polypeptide comprising at least a repeat domain comprising repeat units but also methods wherein target DNA sequences can be generated which are selectively recognized by repeat domains in a polypeptide.
  • The invention also provides for a method for constructing polypeptides that recognize specific DNA sequences. These polypeptides of the invention comprise repeat units of the present invention and can be constructed by a modular approach by preassembling repeat units in target vectors that can subsequently be assembled into a final destination vector.
  • The invention also provides a method for targeted modulation of gene expression by constructing modular repeat units specific for a target DNA sequence of interest, modifying a polypeptide by the addition of said repeat units so as to enable said polypeptide to now recognize the target DNA, introducing or expressing said modified polypeptide in a prokaryotic or eurkaryotic cell so as to enable said modified polypeptide to recognize the target DNA sequence, and modulation of the expression of said target gene in said cell as a result of such recognition.
  • The invention also provides a method for directed modification of a target DNA sequence by the construction of a polypeptide including at least a repeat domain of the present invention that recognizes said target DNA sequence and that said polypeptide also contains a functional domain capable of modifying the target DNA (such as via site specific recombination, restriction or integration of donor target sequences) thereby enabling targeted DNA modifications in complex genomes.
  • The invention further provides for the production of modified polypeptides including at least a repeat domain comprising repeat units wherein a hypervariable region within each of the repeat units determines selective recognition of a base pair in a target DNA sequence.
  • In a further embodiment of the invention, DNA is provided which encodes for a polypeptide containing a repeat domain as described above.
  • In a still further embodiment of the invention, DNA is provided which is modified to include one or more base pairs located in a target DNA sequence so that said each of the base pairs can be specifically recognized by a polypeptide including a repeat domain having corresponding repeat units, each repeat unit comprising a hypervariable region which determines recognition of the corresponding base pair in said DNA.
  • In a still further embodiment of the invention, uses of those polypeptides and DNAs are provided. Additionally provided are plants, plant parts, seeds, plant cells and other non-human host cells transformed with the isolated nucleic acid molecules of the present invention and the proteins or polypeptides encoded by the coding sequences of the present invention. Still further, the polypeptides and DNA described herein can be introduced into animal and human cells as well as cells of other organisms like fungi or plants.
  • In summary, the invention focuses on a method for selectively recognizing base pairs in a target DNA sequence by a polypeptide wherein said polypeptide comprises at least a repeat domain comprising repeat units wherein each repeat unit contains a hypervariable region which determines recognition of a base pair in said target DNA sequence wherein consecutive repeat units correspond to consecutive base pairs in said target DNA sequence.
    • BRIEF DESCRIPTION OF THE FIGURES
  • FIG. 1. Model for DNA-target specificity of TAL effectors.
  • (A) TAL effectors contain central tandem repeat units (red), nuclear localization signals (NLS) and an activation domain (AD). Amino acid sequence of the first repeat of AvrBs3. Hypervariable amino acids 12 and 13 are shaded in gray.
    (B) Hypervariable amino acids at position 12 and 13 of the 17.5 AvrBs3 repeat units are aligned to the UPA-box consensus (21).
    (C) Repeat units of TAL effectors and predicted target sequences in promoters of induced genes were aligned manually. Nucleotides in the upper DNA strand that correspond to the hypervariable amino acids in each repeat were counted based on the following combinations of eight effectors and experimentally identified target genes: AvrBs3/Bs3, UPA10, UPA12, UPA14, UPA19, UPA20, UPA21, UPA23, UPA25, AvrBs3Δrep16/Bs3-E, AvrBs3Δrep109/Bs3, AvrHah1/Bs3, AvrXa27/Xa27, PthXo1/Xa13, PthXo6/OsTFX1, PthXo7/OsTFIIAγ1 (see FIG. 5). Predominant combinations (n>4) are shaded in gray. An asterisk indicates that amino acid 13 is missing in this repeat type.
    (D) DNA target specificity code (R=A/G; N=A/C/G/T) of repeat types based on the hypervariable amino acids 12 and 13 (experimentally proven in this study).
  • FIG. 2. Target DNA sequences of Hax2, Hax3, and Hax4.
  • (A) Amino acids 12 and 13 of the Hax2, Hax3, and Hax4 repeat units and predicted target DNA specificities (Hax-box).
    (B) Hax-boxes were cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
    (C) Specific inducibility of the Hax-boxes by Hax effectors. GUS reporter constructs were codelivered via A. tumefaciens into N. benthamiana with 35S-driven hax2, hax3, hax4, and empty T-DNA (−), respectively (error bars indicate SD; n=3 samples; 4-MU, 4-methyl-umbelliferone). 35S::uidA (+) served as control. Leaf discs were stained with X-Gluc (5-bromo-4-chloro-3-indolyl-β-D-glucuronide).
  • FIG. 3. DNA base pair recognition specificities of repeat types.
  • (A) Hax4- and ArtX-box-derivatives were cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
    (B) Specificity of NG-, HD-, NI-, and NS-repeat units. Hax4-inducibility of Hax4-box derivatives permutated in repeat type target bases (gray background).
    (C) Specificity of NN-repeat units. Artificial effector ArtX1 and predicted target DNA sequences. ArtX1-inducibility of ArtX1 box derivatives permutated in NN-repeat target bases (gray background).
    (D) Artificial effectors ArtX2 and ArtX3 and derived DNA target sequences.
    (E) Specific inducibility of ArtX-boxes by artificial effectors.
    (A)-(E) GUS reporter constructs were co-delivered via A. tumefaciens into N. benthamiana with 35S-driven hax4, artX1, artX2, or artX3 genes, and empty T-DNA (−), respectively. 35S::uidA (+) served as control. Leaf discs were stained with X-Gluc. For quantitative data see FIG. 11.
  • FIG. 4. A minimal number of repeat units is required for transcriptional activation.
  • (A) Artificial ArtHD effectors with different numbers (0.5-15.5) of HD-repeat units (total 1.5 to 16.5 repeat units).
    (B) An ArtHD target box consisting of TA and 17 C was cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
    (C) Promoter activation by ArtHD effectors with different number of repeat units. 35S-driven effector gene or empty T-DNA (−) were codelivered via A. tumefaciens with the GUS-reporter construct into N. benthamiana (error bars indicate SD; n=3 samples; 4-MU). 35S::uidA (+) served as control. Leaf discs were stained with X-Gluc.
  • FIG. 5. Alignment of DNA target sequences in promoters of induced genes with the hypervariable amino acids 12 and 13 of TAL effector repeat units.
  • (A) Repeat units of AvrBs3, AvrBs3Δrep16, AvrBs3Δrep109, and AvrHah1 were aligned to the UPA-box in the promoter of the pepper ECW-30R Bs3 gene (accession: EU078684). AvrBs3Δrep16 and AvrBs3Δrep109 are deletion derivatives of AvrBs3 in which repeat units 11-14 and repeat units 12-14 were deleted, respectively. AvrBs3, AvrBs3Δrep109, and AvrHah1, but not AvrBs3Δrep16 induce the HR in ECW-30R plants.
    (B) Repeat units of AvrBs3, AvrBs3Δrep16, AvrBs3Δrep109, and AvrHah1 were aligned to the non-functional UPA-box in the promoter of the pepper ECW Bs3-E gene (accession: EU078683). AvrBs3Δrep16, but not AvrBs3, AvrBs3Δrep109, or AvrHah1 induce the HR in pepper ECW plants.
    (C) Repeat units of AvrXa27 were aligned to a putative target sequence in the promoter of the rice Xa27 gene. Xa27 (accession: AY986492) is induced by AvrXa27 in rice cultivar IRBB27 leading to an HR, but not xa27 (accession: AY986491) in rice cultivar IR24.
    (D) Repeat units of PthXo1 were aligned to a putative target sequence in the promoter of the rice Xa13/Os8N3 gene. Xa13 (accession: DQ421396) is induced by PthXo1 in rice cultivar IR24 leading to susceptibility, but not xal3 (accession: DQ421394) in rice cultivar IRBB13.
    (E) Repeat units of PthXo6 were aligned to a putative target sequence in the promoter of the rice OsTFX1 gene (accession: AK108319). OsTFX1 is induced by PthXo6 in rice cultivar IR24.
    (F) Repeat units of PthXo7 were aligned to a putative target sequence in the promoter of the rice OsTFIIAγ1 gene (CB097192). OsTFIIAγ1 is induced by PthXo7 in rice cultivar IR24.
    (A)-(F) Numbers above the DNA sequences indicate nucleotide distance to the first ATG in the coding region. Repeat/base combinations not matching our predicted target specificity (amino acids 12/13: NI=A; HD=C; NG=T; NS=A/C/G/T; NN=A/G; IG=T) are coloured in red. Repeat units with unknown target DNA specificity are coloured in green.
  • FIG. 6. The DNA region protected by AvrBs3Δrep16 is 4 bp shorter than with AvrBs3.
  • Summary of DNaseI footprint analyses with AvrBs3 and AvrBs3Δrep16 (see FIGS. 7, 8).
  • (A) Bs3 (top) and Bs3-E (middle) promoter sequences protected by AvrBs3 and AvrBs3Δrep16, respectively. DNaseI footprinting revealed that AvrBs3 protected 37 nucleotides of the sense strand and 36 nucleotides of the antisense strand of the Bs3 promoter, and AvrBs3Δrep16 protected 30 nucleotides of the sense strand and 32 nucleotides of the antisense strand of the Bs3-E promoter. The UPA-box and the predicted AvrBs3Δrep16-box are underlined. UPA20-ubm-r16 (lower part) promoter sequences protected by AvrBs3 and AvrBs3Δrep16. The UPA20-ubmr16 promoter is a UPA20 promoter derivative with a 2 bp substitution (GA to CT, bold italic) that results in recognition by both, AvrBs3 and AvrBs3Δrep16. DNaseI footprinting revealed that 35 nucleotides of the sense strand and 34 nucleotides of the antisense strand are protected by AvrBs3 (UPA-box is underlined), and 31 nucleotides of the sense strand and 32 nucleotides of the antisense strand are protected by AvrBs3Δrep16 (AvrBs3Δrep16-box is underlined). DNA regions shaded in green (AvrBs3) or red (AvrBs3Δrep16) refer to the core footprints which were protected by AvrBs3 and AvrBs3Δrep16, respectively, in every experiment, even with low protein amounts (equal molarity of DNA and protein dimers). DNA regions shaded in gray refer to nucleotides which were not protected in all of the 4 experiments at all protein concentrations by the given proteins. Please note that the 5′ ends of the AvrBs3- and AvrBs3Δrep16-protected regions are identical. Dashed vertical lines indicate the differences between the 3′ ends of the AvrBs3- and AvrBs3Δrep16-protected promoter regions which corroborates our model that one repeat contacts one base pair in the DNA.
    (B) Alignment of AvrBs3 and AvrBs3Δrep16 target DNA sequences in the UPA20-ubm-r16 promoter with AvrBs3 and AvrBs3Δrep16 repeat regions (hypervariable amino acids at position 12 and 13). Repeat/base combinations not matching our predicted target specificity (amino acids 12/13: NI=A; HD=C; NG=T; NS=A/C/G/T) are coloured in red.
  • FIG. 7. Bs3 and Bs3-E promoter sequences protected by AvrBs3 and AvrBs3Δrep16, respectively.
  • A representative DNaseI footprint experiment is shown. AvrBs3 DNaseI footprint on the Bs3 promoter sequence (A, upper/sense DNA strand; B, lower/antisense DNA strand). AvrBs3Δrep16 DNaseI footprint on the Bs3-E promoter sequence (C, upper, sense DNA strand; D, lower antisense DNA strand).
  • (A)-(D) (top) Fluorescently labelled PCR product was incubated with a 5× molar excess (calculated for protein dimers) of His6::AvrBs3, His6::AvrBs3Δrep16, and BSA, respectively, treated with DNaseI and analyzed on a capillary sequencer. The y axis of the electropherogram shows the relative fluorescence intensity corresponding to the 5′-6-FAM-labelled sense strand (a, c) or the 5′-HEX-labelled antisense strand (b, d) of the PCR product on an arbitrary scale. The traces for the reactions with His6::AvrBs3 (green) or His 6::AvrBs3Δrep16 (red), respectively, and BSA (black, negative control) were superimposed. A reduction of peak height in the presence of AvrBs3 or AvrBs3Δrep16, respectively, in comparison to the negative control corresponds to protection. The protected region is indicated by green (AvrBs3) or red (AvrBs3Δrep16) vertical lines, (middle) Electropherogram of the DNA sequence. Orange coloured peaks with numbers correspond to the DNA nucleotide size standard. The predicted target boxes of the effectors in the DNA sequence are underlined. Nucleotides covered are marked by a green (AvrBs3) or red (AvrBs3Δrep16) box. Numbers below refer to nucleotide positions relative to the transcription start (+1) in the presence of AvrBs3 (a, b) or AvrBs3Δrep16 (c, d), respectively. (bottom) DNA PCR product used for DNaseI footprinting, amplified from the Bs3 (a, b) or Bs3-E (c, d) promoters, respectively. The protected regions on the single DNA strands are indicated by gray boxes. Numbers below refer to nucleotide positions relative to the transcription start (+1) in the presence of AvrBs3 (a, b) or AvrBs3Δrep16 (c, d), respectively. The experiments were repeated three times with similar results.
  • FIG. 8. UPA20-ubm-r16 promoter sequence protected by AvrBs3 and AvrBs3Δrep16.
  • A representative DNaseI footprint experiment. AvrBs3 and AvrBs3Δrep16 DNaseI footprint on the UPA20-ubm-r16 promoter sequence (A), upper, sense DNA strand; (B) lower, antisense DNA strand). (top Fluorescently labelled PCR product was incubated with a 5× molar excess of His6::AvrBs3, His6::AvrBs3Δrep16 and BSA (calculated for protein dimers), respectively, treated with DNaseI and analyzed on a capillary sequencer. The y axis of the electropherogram shows the relative fluorescence intensity corresponding to the 5′-6-FAM-labelled sense strand (a) or the 5′-HEX-labelled antisense strand (b) of the PCR product on an arbitrary scale. The traces for the reactions with His6::AvrBs3 (green), His6::AvrBs3Δrep16 (red) and the negative control BSA (black) were superimposed. A reduction of peak height in the presence of AvrBs3 and AvrBs3Δrep16 in comparison to the negative control corresponds to protection. The protected regions are indicated by green (AvrBs3) and red (AvrBs3Δrep16) vertical lines. (middle) Electropherogram of the DNA sequence. Orange coloured peaks with numbers correspond to the DNA nucleotide size standard. Nucleotides covered by AvrBs3 are marked by green lines and a green box (with the UPA box underlined), nucleotides covered by AvrBs3Δrep16 are marked by red lines and a red box (with the AvrBs3Δrep16-box underlined). The UPA20-ubm-r16 mutation (GA to CT) is indicated in italics. (bottom) DNA PCR product used for DNaseI footprinting, amplified from the UPA20-ubm-r16 promoter. The protected regions on the single DNA strands are indicated by gray boxes. Numbers below refer to nucleotide positions relative to the transcription start (+1) of the UPA20 wildtype promoter in the presence of AvrBs3. The experiment was repeated three times with similar results.
  • FIG. 9. GUS reporter constructs.
  • Target DNA sequences (TAL effector-box) were inserted 5′ of the minimal tomato Bs4 promoter (41) (pBs4; −50 to +25) sequence and transferred by GATEWAY recombination into the A. tumefaciens T-DNA vector pGWB330 constructing a fusion to a promoterles uidA (β-glucuronidase, GUS) gene. attB1, attB2; GATEWAY recombination sites.
  • FIG. 10. Recognition specificity of the putative repeat 0 in Hax3.
  • (A) Amino acids 12 and 13 of Hax3-repeat units and four possible target Hax3-boxes with permutations in the position corresponding to repeat 0.
    (B) The target boxes were cloned in front of the minimal tomato Bs4 promoter into a GUS reporter vector.
    (C) GUS activities with 35S-driven hax3 or empty T-DNA (−) codelivered via A. tumefaciens with the GUS reporter constructs into N. benthamiana leaf cells (4-MU, 4-methyl-umbelliferone; n=3; error bars indicate SD). For qualitative assays, leaf discs were stained with X-Gluc. The experiment was performed twice with similar results.
  • FIG. 11. DNA base pair recognition specificities of repeat types.
  • Hax4- and ArtX-box-derivatives were cloned in front of the minimal Bs4 promoter into a GUS reporter vector. Quantitative data to FIG. 3.
  • (A) Specificity of NG-, HD-, NI-, and NS-repeat units. Hax4-inducibility of Hax4-box derivatives permutated in repeat type target bases.
    (B) Specificity of NN-repeat units. ArtX1-inducibility of ArtX1-box derivatives permutated in NN-repeat target bases.
    (C) Specific inducibility of ArtX-boxes by artificial effectors ArtX1, ArtX2, and ArtX3, respectively.
  • (A)-(C) GUS reporter constructs were codelivered via A. tumefaciens into N. benthamiana leaf cells together with 35S-driven hax4, artX1, artX2, artX3 genes (gray bars), and empty T-DNA (a, b, white bars; c, -), respectively (n=3; error bars indicate SD). 35S::uidA (+) served as control. The experiments were performed three times with similar results.
  • FIG. 12. Predicted target DNA sequences for AvrXa10.
  • (A) Amino acids 12 and 13 of the AvrXa10-repeat units and two possible target boxes with predicted NN type repeat-specificity A or G.
    (B) AvrXa10 target boxes were cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
    (C) GUS assay of 35S-driven avrXa10, hax3 (specificity control), or empty T-DNA (−) codelivered via A. tumefaciens with GUS reporter constructs into N. benthamiana leaf cells. 35S::uidA (+) served as constitutive control (n=3; error bars indicate SD). For qualitative assays, leaf discs were stained with X-Gluc. The experiment was performed three times with similar results.
  • FIG. 13. Recognition specificity of the repeat type IG in Hax2.
  • (A) Amino acids 12 and 13 of Hax2 repeat units and four possible target Hax2-boxes for repeat type IG.
    (B) The Hax2 target boxes were cloned in front of the minimal Bs4 promoter into a GUS reporter vector.
    (C) GUS assay of 35S promoter-driven hax2 or empty T-DNA (−) codelivered via A. tumefaciens with the GUS reporter constructs into N. benthamiana leaf cells. 35S::uidA (+) served as constitutive control (n=3; error bars indicate SD. For qualitative assays, leaf discs were stained with X-Gluc. The experiment was performed three times with similar results.
  • FIG. 14. Hax2 induces expression of PAP1 in A. thaliana.
  • (A) Leaves of A. thaliana were inoculated with A. tumefaciens strains delivering T-DNA constructs for 35S-driven expression of hax2, hax3, and hax4, respectively. Expression of hax2, but not of hax3 and hax4 induced purple pigmentation suggestive of anthocyanin production. The photograph was taken 7 days post inoculation.
    (B) Transgenic A. thaliana line carrying hax2 under control of an ethanol-inducible promoter. Plants of a segregating T2 population were sprayed with 10% ethanol to induce expression of the transgene. Only hax2-transgenic plants accumulated anthocyanin. The photograph was taken 6 days post treatment.
    (C) Semiquantitative RT-PCR of hax2 (29 cycles), PAP1 (32 cycles), and elongation factor Tu (EF-Tu, 32 cycles) with cDNA from hax2-transgenic plants of three independent A. thaliana lines before (−) and 24 h after (+) spraying with 10% ethanol.
    (D) Amino acids 12 and 13 of Hax2 repeat units and target DNA sequence of Hax2.
    (E) The promoter of PAP1 from A. thaliana Col-0 contains an imperfect Hax2-box. Mismatches to the predicted Hax2-box are coloured in red. A putative TATA-box, the natural transcription start site (+1), and the first codon of the PAP1 coding sequence are indicated.
  • FIG. 15. Table I. Predicted DNA target sequences of TAL effectors
  • The table shows repeat sequences of TAL effectors and the predicted DNA target sequences used from amino acids 12 and 13 of the repeat units.
  • The annotations show:
  • (A) Xcv, Xanthomonas campestris pv. vesicatoria; Xg, Xanthomonas gardneri; Xca, Xanthomonas campestris pv. armoraciae; Xoo, Xanthomonas oryzae pv. oryzae; Xac, Xanthomonas axonopodis pv. citri; Xau, Xanthomonas citri pv. aurantifolii; Xcm, Xanthomonas campestris pv. malvacearum; Xam, Xanthomonas axonopodis pv. manihotis; Xoc, Xanthomonas oryzae pv. oryzicola
    (B) A star (*) indicates a deletion of amino acid 13
    (C) Target DNA specificity deduced from amino acids 12 and 13 of the repeat units. A thymidine nucleotide is added at the 5′ end due to the specificity of the putative repeat 0. The sequence of the upper (sense) strand of the double stranded DNA is given in ambiguous code (R=A/G; N=A/C/G/T; •=unknown specificity)
  • FIG. 16. Protein sequences of AvrBs3, Hax2, Hax3, Hax4
  • For each of the protein sequences, the N-terminus, C-terminus as well as the single repeat sequences are shown.
  • FIG. 17. The effector ARTBs4 induces expression of the minimal Bs4 promoter
  • (A) Amino acids 12 and 13 of the Hax4 repeat units and predicted target DNA specificity (Hax4 box). The Hax4(mut) box contains four base pair exchanges in comparison to the Hax4 box.
    (B) Amino acids 12 and 13 of the artificial effector ARTBs4 repeat units and predicted target DNA specificity (ARTBs4 box).
    (C) The Hax4 box was cloned in front of the minimal Bs4 promoter into a GUS reporter vector. The ARTBs4 box is naturally present in the minimal Bs4 promoter.
    (D) Specific inducibility of the Hax4 and ARTBs4 boxes by Hax4 and ARTBs4, respectively. GUS reporter constructs were codelivered via Agrobacterium tumefaciens into N. benthamiana with 35S-driven hax4 (grey bars), ARTBs4 (white bars) and empty T-DNA (ev, black bars), respectively (error bars indicate SD). 4-MU, 4-methyl-umbelliferone. 35S::uidA (GUS, grey bar) served as control. Leaf disks were stained with X-Gluc (5-bromo-4-chloro-3-indolyl-β-D-glucuronide).
  • FIG. 18. Diagram for “Golden gate” cloning of repeat domains and effectors
  • (A) Building blocks consisting of individual repeat units (or other protein domains) are subcloned with flanking type II restriction enzyme target sites (e.g. BsaI) that generate specific overhangs. Matching overhangs are indicated with identical letters (A to O). Different repeat types are cloned as building blocks for each position (e.g. repeat 1, repeat 2, etc.). The repeat specificities are: NI=A, HD=C, NG=T, NN=G or A.
    (B) The building blocks are assembled into a target vector by ligation of matching overhangs using “Golden gate” cloning (restriction-ligation). In general, the resulting assembly product does not contain any of the target sites used for cloning.
  • FIG. 19. Alternative method for generation of designer effectors via Golden Gate cloning
  • FIGS. 19 A-D depict various vectors described in the methods disclosed in Example 3 below as well as provide a schematic of the method.
  • FIG. 20. Experiments to analyze novel repeat specificities
  • Artificial TALs were assembled with the first six repeats of the TAL Hax3. Repeat 7 to 11.5 were assembled using one repeat type with unknown specificity. Four possible target DNA boxes were used containing six A, C, G, or T, respectively. Similarly, artificial TALs and reporter were constructed with 2, 3, or 4 repeats to test. The target DNA boxes were inserted into the Bs4 minimal promoter upstream of a promoterless uidA reporter gene.
  • FIG. 21. TAL repeat specificities
  • Agrobacterium-mediated expression of artificial TALs and corresponding reporter constructs in Nicotiana benthamiana. Leaf disks were sampled two days post transformation, stained for GUS reporter activity and destained with ethanol. A blue colour indicates expression of the reporter construct and therefore, an activity of the TAL. Empty vector (ev) and constitutively expressed GUS were used as negative control, respectively. Novel repeat specificities are colored in red. Repeat types with strong DNA recognition properties are: NH, NP, NT, and HN. Repeat types with weak DNA recognition properties are: NG, N*, NK, SH, SN, IS.
  • FIG. 22. Quantitative analysis of known repeat specificities.
  • Artificial TALs were assembled with the first six repeats of the TAL Hax3. Repeat 7 to 11.5 were assembled using one repeat type. Four possible target DNA boxes were used containing six A, C, G, or T, respectively upstream of the Bs4 minimal promoter and a promoterless uidA reporter gene. The data show that repeat type NN has much stronger DNA-recognition properties than the other repeat types. Repeat type NI is very weak and does not show a preference in this setup. Repeat type NS was shown to recognice all four DNA bases, before, but does show a preference for A and G, here. EV: empty vector control.
  • FIG. 23. Quantitative analysis of novel repeats with multiple specificities
  • Quantitative analysis of novel repeats with multiple specificities. Artificial TALs were assembled with the first six repeats of the TAL Hax3. Repeat 7 to 11.5 were assembled using one repeat type. Four possible target DNA boxes were used containing six A, C, G, or T, respectively upstream of the Bs4 minimal promoter and a promoterless uidA reporter gene (see, FIG. 20).
  • FIG. 24. Quantitative analysis of novel repeats with only one specificity
  • Artificial TALs were assembled with the first six repeats of the TAL Hax3. Repeat 7 to 11.5 were assembled using one repeat type. Four possible target DNA boxes were used containing six A, C, G, or T, respectively upstream of the Bs4 minimal promoter and a promoterless uidA reporter gene. The data show that repeat type NH is much stronger than repeat type NK, but also recognizes only one specific base (G).
  • FIG. 25. Quantitative analysis of novel repeats with novel specificities
  • Artificial TALs were assembled with the first six repeats of the TAL Hax3. Repeat 7 to 11.5 were assembled using one repeat type. Four possible target DNA boxes were used containing six A, C, G, or T, respectively upstream of the Bs4 minimal promoter and a promoterless uidA reporter gene. These repeat types show only very low activity in the reporter assay, likely due to their weak DNA interaction potential.
  • FIG. 26. Experimental setup to study specificity of repeat types with low DNA recognition potential
  • The artificial effectors were assembled to contain 6, 4, 3, or 2 repeats, respectively, with unknown specificity (designated XX) in addition to Hax3 repeats. Target boxes in the reporter constructs contain A, C, G, or T, respectively, at positions corresponding to the “XX” repeats. The rest of the target DNA boxes is equivalent to the Hax3 box.
  • FIG. 27A-C. Experimental setup to study specificity of repeat types with low DNA recognition potential
  • The artificial effectors were assembled to contain 4, 3, or 2 repeats, respectively, as “test repeats” with unknown specificity (designated X) in addition to Hax3 repeats (see, FIG. 26 for details). Target boxes in the reporter constructs contain A, C, G, or T, respectively, at positions corresponding to the test repeats. The rest of the target DNA boxes is equivalent to the Hax3 box. Although TALs with four or more combined N* repeats do not show a specificity, a combination of three or two N* repeats indicates a specificity for T, or T and C, respectively. N* and NI are obviously repeat types with weak DNA recognition properties. FIG. 27A: HD; FIG. 27B: N*; and FIG. 27C: NI.
    • SEQUENCE LISTING
  • The nucleotide and amino acid sequences listed in the accompanying figures and the sequence listing are shown using standard letter abbreviations for nucleotide bases, and one-letter code for amino acids. The nucleotide sequences follow the standard convention of beginning at the 5′ end of the sequence and proceeding forward (i.e., from left to right in each line) to the 3′ end. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood to be included by any reference to the displayed strand. The amino acid sequences follow the standard convention of beginning at the amino terminus of the sequence and proceeding forward (i.e., from left to right in each line) to the carboxy terminus.
    •  DETAILED DESCRIPTION OF THE INVENTION
  • The present invention now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the inventions are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Like numbers refer to like elements throughout.
  • Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
  • A number of terms that are used throughout this disclosure are defined hereinbelow.
  • The term “repeat domain” is used to describe the DNA recognition domain from a TAL effector, or artificial version thereof that is made using the methods disclosed, consisting of modular repeat units that when present in a polypeptide confer target DNA specificity. A repeat domain comprised of repeat units can be added to any polypeptide in which DNA sequence targeting is desired and are not limited to use in TAL effectors.
  • The term “repeat unit” is used to describe the modular portion of a repeat domain from a TAL effector, or an artificial version thereof, that contains one amino acid or two adjacent amino acids that determine recognition of a base pair in a target DNA sequence. Repeat units taken together recognize a defined target DNA sequence and constitute a repeat domain. Repeat units can be added to any polypeptide in which DNA sequence targeting is desired and are not limited to use in TAL effectors.
  • The term “recognition code” is used to describe the relationship between the amino acids in positions 12 and 13 of a repeat unit and the corresponding DNA base pair in a target DNA sequence that such amino acids confer recognition of, as follows: HD for recognition of C/G; NI for recognition of A/T; NG for recognition of T/A; NS for recognition of C/G or A/T or T/A or G/C; NN for recognition of G/C or A/T; IG for recognition of T/A; N for recognition of C/G or T/A; HG for recognition of C/G or T/A; H for recognition of T/A; NK for recognition of G/C; NH for recognition of G/C; NP for recognition of A/T, C/G, or T/A; NT for recognition of A/T or G/C; NH for recognition of A/T or G/C; SH for recognition of G/C; SN for recognition of G/C; and IS for recognition of A/T. Additional specificities for the amino acids in positions in positions 12 and 13 of a repeat unit and the corresponding DNA base pair in a target DNA sequence have been reported: HA for recognition of C/G; ND for recognition of C/G; HI for recognition of C/G; HN for recognition of G/C; and NA for recognition of G/C (Moscou & Bogdanove (2009) Science 326:1501).
  • As used herein, “effector” (or “effector protein” or “effector polypeptide”) refers to constructs or their encoded polypeptide products in which said polypeptide is able to recognize a target DNA sequence. The effector protein includes a repeat domain comprised of 1.5 or more repeat units and also may include one or more functional domains such as a regulatory domain. In preferred embodiments of the invention, the “effector” is additionally capable of exerting an effect, such as regulation of gene expression. Although the present invention is not dependent on a particularly biological mechanism, it is believe that the proteins or polypeptides of the invention that recognize a target DNA sequence bind to the target DNA sequence.
  • The term “naturally occurring” is used to describe an object that can be found in nature as distinct from being produced by man. For example, a polypeptide or polynucleotide sequence that is present in an organism (including viruses) that can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory is naturally occurring. Generally, the term naturally occurring refers to an object as-present in a wild-type individual, such as would be typical for the species.
  • The terms “modulating expression” “inhibiting expression” and “activating expression” of a gene refer to the ability of a polypeptide of the present invention to activate or inhibit transcription of a gene. Activation includes prevention of subsequent transcriptional inhibition (i.e., prevention of repression of gene expression) and inhibition includes prevention of subsequent transcriptional activation (i.e., prevention of gene activation). Modulation can be assayed by determining any parameter that is indirectly or directly affected by the expression of the target gene. Such parameters include, e.g., changes in RNA or protein levels, changes in protein activity, changes in product levels, changes in downstream gene expression, changes in reporter gene transcription (luciferase, CAT, beta-galactosidase, GFP (see, e.g., Mistili & Spector (1997) Nature Biotechnology 15:961-964); changes in signal transduction, phosphorylation and dephosphorylation, receptor-ligand interactions, second messenger concentrations (e.g., cGMP, cAMP, IP3, and Ca2+), cell growth, neovascularization, in vitro, in vivo, and ex vivo. Such functional effects can be measured by any means known to those skilled in the art, e.g., measurement of RNA or protein levels, measurement of RNA stability, identification of downstream or reporter gene expression, e.g., via chemiluminescence, fluorescence, calorimetric reactions, antibody binding, inducible markers, ligand binding assays; changes in intracellular second messengers such as cGMP and inositol triphosphate (IP3); changes in intracellular calcium levels; cytokine release, and the like.
  • A “regulatory domain” refers to a protein or a protein subsequence that has transcriptional modulation activity. Typically, a regulatory domain is covalently or non-covalently linked to a polypeptide of the present invention to modulate transcription. Alternatively, a polypeptide of the present invention can act alone, without a regulatory domain, or with multiple regulatory domains to modulate transcription. Transcription factor polypeptides from which one can obtain a regulatory domain include those that are involved in regulated and basal transcription. Such polypeptides include transcription factors, their effector domains, coactivators, silencers, nuclear hormone receptors (see, e.g., Goodrich et al. (1996) Cell 84:825 30 for a review of proteins and nucleic acid elements involved in transcription; transcription factors in general are reviewed in Barnes & Adcock (1995) Clin. Exp. Allergy 25 Suppl. 2:46 9 and Roeder (1996) Methods Enzymol. 273:165 71). Databases dedicated to transcription factors are known (see, e.g., Science (1995) 269:630). Nuclear hormone receptor transcription factors are described in, for example, Rosen et al. (1995) J. Med. Chem. 38:4855 74. The C/EBP family of transcription factors are reviewed in Wedel et al. (1995) Immunobiology 193:171 85. Coactivators and co-repressors that mediate transcription regulation by nuclear hormone receptors are reviewed in, for example, Meier (1996) Eur. J. Endocrinol. 134(2):158 9; Kaiser et al. (1996) Trends Biochem. Sci. 21:342 5; and Utley et al. (1998) Nature 394:498 502). GATA transcription factors, which are involved in regulation of hematopoiesis, are described in, for example, Simon (1995) Nat. Genet. 11:9 11; Weiss et al. (1995) Exp. Hematol. 23:99-107. TATA box binding protein (TBP) and its associated TAF polypeptides (which include TAF30, TAF55, TAF80, TAF110, TAF150, and TAF250) are described in Goodrich & Tjian (1994) Curr. Opin. Cell Biol. 6:403 9 and Hurley (1996) Curr. Opin. Struct. Biol. 6:69 75. The STAT family of transcription factors are reviewed in, for example, Barahmand-Pour et al. (1996) Curr. Top. Microbiol. Immunol. 211:121 8. Transcription factors involved in disease are reviewed in Aso et al. (1996) J. Clin. Invest. 97:1561 9. Kinases, phosphatases, and other proteins that modify polypeptides involved in gene regulation are also useful as regulatory domains for polypeptides of the present invention. Such modifiers are often involved in switching on or off transcription mediated by, for example, hormones. Kinases involved in transcription regulation are reviewed in Davis (1995) Mol. Reprod. Dev. 42:459 67, Jackson et al. (1993) Adv. Second Messenger Phosphoprotein Res. 28:279 86, and Boulikas (1995) Crit. Rev. Eukaryot. Gene Expr. 5:1 77, while phosphatases are reviewed in, for example, Schonthal & Semin (1995) Cancer Biol. 6:239 48. Nuclear tyrosine kinases are described in Wang (1994) Trends Biochem. Sci. 19:373 6. Useful domains can also be obtained from the gene products of oncogenes (e.g., myc, jun, fos, myb, max, mad, rel, ets, bcl, myb, mos family members) and their associated factors and modifiers. Oncogenes are described in, for example, Cooper, Oncogenes, 2nd ed., The Jones and Bartlett Series in Biology, Boston, Mass., Jones and Bartlett Publishers, 1995. The ets transcription factors are reviewed in Waslylk et al. (1993) Eur. J. Biochem. 211:7 18 and Crepieux et al. (1994) Crit. Rev. Oncog. 5:615 38. Myc oncogenes are reviewed in, for example, Ryan et al. (1996) Biochem. J. 314:713 21. The jun and fos transcription factors are described in, for example, The Fos and Jun Families of Transcription Factors, Angel & Herrlich, eds. (1994). The max oncogene is reviewed in Hurlin et al. Cold Spring Harb. Symp. Quant. Biol. 59:109 16. The myb gene family is reviewed in Kanei-Ishii et al. (1996) Curr. Top. Microbiol. Immunol. 211:89 98. The mos family is reviewed in Yew et al. (1993) Curr. Opin. Genet. Dev. 3:19 25. Polypeptides of the present invention can include regulatory domains obtained from DNA repair enzymes and their associated factors and modifiers. DNA repair systems are reviewed in, for example, Vos (1992) Curr. Opin. Cell Biol. 4:385 95; Sancar (1995) Ann. Rev. Genet. 29:69 105; Lehmann (1995) Genet. Eng. 17:1 19; and Wood (1996) Ann. Rev. Biochem. 65:135 67. DNA rearrangement enzymes and their associated factors and modifiers can also be used as regulatory domains (see, e.g., Gangloff et al. (1994) Experientia 50:261 9; Sadowski (1993) FASEB J. 7:760 7).
  • Similarly, regulatory domains can be derived from DNA modifying enzymes (e.g., DNA methyltransferases, topoisomerases, helicases, ligases, kinases, phosphatases, polymerases) and their associated factors and modifiers. Helicases are reviewed in Matson et al. (1994) Bioessays 16:13 22, and methyltransferases are described in Cheng (1995) Curr. Opin. Struct. Biol. 5:4 10. Chromatin associated proteins and their modifiers (e.g., kinases, acetylases and deacetylases), such as histone deacetylase (Wolffe Science 272:371 2 (1996)) are also useful as domains for addition to the effector of choice. In one preferred embodiment, the regulatory domain is a DNA methyl transferase that acts as a transcriptional repressor (see, e.g., Van den Wyngaert et al. FEBS Lett. 426:283 289 (1998); Flynn et al. J. Mol. Biol. 279:101 116 (1998); Okano et al. Nucleic Acids Res. 26:2536 2540 (1998); and Zardo & Caiafa, J. Biol. Chem. 273:16517 16520 (1998)). In another preferred embodiment, endonucleases such as FokI are used as transcriptional repressors, which act via gene cleavage (see, e.g., WO95/09233; and PCT/US94/01201). Factors that control chromatin and DNA structure, movement and localization and their associated factors and modifiers; factors derived from microbes (e.g., prokaryotes, eukaryotes and virus) and factors that associate with or modify them can also be used to obtain chimeric proteins. In one embodiment, recombinases and integrases are used as regulatory domains. In one embodiment, histone acetyltransferase is used as a transcriptional activator (see, e.g., Jin & Scotto (1998) Mol. Cell. Biol. 18:4377 4384; Wolffe (1996) Science 272:371 372; Taunton et al. Science 272:408 411 (1996); and Hassig et al. PNAS 95:3519 3524 (1998)). In another embodiment, histone deacetylase is used as a transcriptional repressor (see, e.g., Jin & Scotto (1998) Mol. Cell. Biol. 18:4377 4384; Syntichaki & Thireos (1998) J. Biol. Chem. 273:24414 24419; Sakaguchi et al. (1998) Genes Dev. 12:2831 2841; and Martinez et al. (1998) J. Biol. Chem. 273:23781 23785).
  • As used herein, “gene” refers to a nucleic acid molecule or portion thereof which comprises a coding sequence, optionally containing introns, and control regions which regulate the expression of the coding sequence and the transcription of untranslated portions of the transcript.
  • Thus, the term “gene” includes, besides coding sequence, regulatory sequence such as the promoter, enhancer, 5′ untranslated regions, 3′ untranslated region, termination signals, poly adenylation region and the like. Regulatory sequence of a gene may be located proximal to, within, or distal to the coding region.
  • As used herein, “target gene” refers to a gene whose expression is to be modulated by a polypeptide of the present invention.
  • As used herein, “plant” refers to any of various photosynthetic, eucaryotic multi-cellular organisms of the kingdom Plantae, characteristically producing embryos, containing chloroplasts, having cellulose cell walls and lacking locomotion. As used herein, “plant” includes any plant or part of a plant at any stage of development, including seeds, suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, microspores, and progeny thereof. Also included are cuttings, and cell or tissue cultures. As used in conjunction with the present invention, the term “plant tissue” includes, but is not limited to, whole plants, plant cells, plant organs, e.g., leafs, stems, roots, meristems, plant seeds, protoplasts, callus, cell cultures, and any groups of plant cells organized into structural and/or functional units.
  • As used herein, “modulate the expression of a target gene in plant cells” refers to increasing (activation) or decreasing (repression) the expression of the target gene in plant cells with a polypeptide of the present invention, alone or in combination with other transcription and/or translational regulatory factors, or nucleic acids encoding such polypeptide, in plant cells.
  • As used herein, a “target DNA sequence” refers to a portion of double-stranded DNA to which recognition by a protein is desired. In one embodiment, a “target DNA sequence” is all or part of a transcriptional control element for a gene for which a desired phenotypic result can be attained by altering the degree of its expression. A transcriptional control element includes positive and negative control elements such as a promoter, an enhancer, other response elements, e.g., steroid response element, heat shock response element, metal response element, a repressor binding site, operator, and/or a silencer. The transcriptional control element can be viral, eukaryotic, or prokaryotic. A “target DNA sequence” also includes a downstream or an upstream sequence which can bind a protein and thereby modulate, typically prevent, transcription.
  • The use of the term “DNA” or “DNA sequence” herein is not intended to limit the present invention to polynucleotide molecules comprising DNA. Those of ordinary skill in the art will recognize that the methods and compositions of the invention encompass polynucleotide molecules comprised of deoxyribonucleotides (i.e., DNA), ribonucleotides (i.e., RNA) or combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues including, but not limited to, nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs). The polynucleotide molecules of the invention also encompass all forms of polynucleotide molecules including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like. Furthermore, it is understood by those of ordinary skill in the art that the DNA sequences disclosed herein also encompasses the complement of that exemplified nucleotide sequence.
  • As used herein, “specifically binds to a target DNA sequence” means that the binding affinity of a polypeptide of the present invention to a specified target DNA sequence is statistically higher than the binding affinity of the same polypeptide to a generally comparable, but non-target DNA sequence. It also refers to binding of a repeat domain of the present invention to a specified target DNA sequence to a detectably greater degree, e.g., at least 1.5-fold over background, than its binding to non-target DNA sequences and to the substantial exclusion of non-target DNA sequences. A polypeptide of the present invention's Kd to each DNA sequence can be compared to assess the binding specificity of the polypeptide to a particular target DNA sequence.
  • As used herein, a “target DNA sequence within a target gene” refers to a functional relationship between the target DNA sequence and the target gene in that recognition of a polypeptide of the present invention to the target DNA sequence will modulate the expression of the target gene. The target DNA sequence can be physically located anywhere inside the boundaries of the target gene, e.g., 5′ ends, coding region, 3′ ends, upstream and downstream regions outside of cDNA encoded region, or inside enhancer or other regulatory region, and can be proximal or distal to the target gene.
  • As used herein, “endogenous” refers to nucleic acid or protein sequence naturally associated with a target gene or a host cell into which it is introduced.
  • As used herein, “exogenous” refers to nucleic acid or protein sequence not naturally associated with a target gene or a host cell into which it is introduced, including non-naturally occurring multiple copies of a naturally occurring nucleic acid, e.g., DNA sequence, or naturally occurring nucleic acid sequence located in a non-naturally occurring genome location.
  • As used herein, “genetically modified plant (or transgenic plant)” refers to a plant which comprises within its genome an exogenous polynucleotide. Generally, and preferably, the exogenous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations. The exogenous polynucleotide may be integrated into the genome alone or as part of a recombinant expression cassette. “Transgenic” is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of exogenous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic. The term “transgenic” as used herein does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation.
  • As used herein, “minimal promoter” or substantially similar term refers to a promoter element, particularly a TATA element, that is inactive or that has greatly reduced promoter activity in the absence of upstream activation. In the presence of a suitable transcription factor, the minimal promoter functions to permit transcription.
  • As used herein, “repressor protein” or “repressor” refers to a protein that binds to operator of DNA or to RNA to prevent transcription or translation, respectively.
  • As used herein, “repression” refers to inhibition of transcription or translation by binding of repressor protein to specific site on DNA or mRNA. Preferably, repression includes a significant change in transcription or translation level of at least 1.5 fold, more preferably at least two fold, and even more preferably at least five fold.
  • As used herein, “activator protein” or “activator” refers to a protein that binds to operator of DNA or to RNA to enhance transcription or translation, respectively.
  • As used herein, “activation” refers to enhancement of transcription or translation by binding of activator protein to specific site on DNA or mRNA. Preferably, activation includes a significant change in transcription or translation level of at least 1.5 fold, more preferably at least two fold, and even more preferably at least five fold.
  • As used herein, “derivative” or “analog” of a molecule refers to a portion derived from or a modified version of the molecule.
  • As used herein, a “repeat unit derived from a transcription activator-like (TAL) effector” refers to a repeat unit from a TAL effector or a modified or artificial version of one or more TAL effectors that is produced by any of the methods disclosed herein.
  • In the following, the invention is specifically described with respect to the transcription activator-like (TAL) effector family which are translocated via the type III secretion system into plant cells. The type member of this effector family is AvrBs3. Hence, the TAL effector family is also named AvrBs3-like family of proteins. Both expressions are used synonymously and can be interchanged. Non-limiting examples of the AvrBs3-like family are as follows: AvrBs4 and the members of the Hax sub-family Hax2, Hax3, and Hax4 as well as Brg11. AvrBs3 and the other members of its family are characterized by their binding capability to specific DNA sequences in promoter regions of target genes and induction of expression of these genes. They have conserved structural features that enable them to act as transcriptional activators of plant genes. AvrBs3-like family and homologous effectors typically have in their C-terminal region nuclear localisation sequences (NLS) and a transcriptional activation domain (AD). The central region contains repeat units of typically 34 or 35 amino acids. The repeat units are nearly identical, but variable at certain positions and it has now been found how these positions determine the nucleotide sequence binding specificity of the proteins.
  • It was shown for AvrBs3 that the repeat units are responsible for binding to DNA. The DNA-binding specificity of AvrBs3 and probably other members of the AvrBs3-family seems to be mediated by the central repeat domain of the proteins. This repeat domain consists in AvrBs3 of 17.5 repeat units and in homologous proteins is comprised of 1.5 to 33.5 repeat units which are typically 34 amino acids each. Other repeat unit lengths are also known (e.g. 30, 33, 35, 39, 40, 42 amino acids). The last repeat in the repeat domain is usually only a half repeat of 19 or 20 amino acids length. The individual repeat units are generally not identical. They vary at certain variable amino acid positions, among these positions 12 and 13 are hypervariable while positions 4, 11, 24, and 32 vary with high frequency but at a lower frequency than 12 and 13 (variations at other positions occur also, but at lower frequency). The comparison of different AvrBs3-like proteins from Xanthomonas reveals 80 to 97% overall sequence identity with most differences confined to the repeat domain. For example, AvrBs3 and the AvrBs3-like family member AvrBs4 differ exclusively in their repeat domain region, with the exception of a four amino acid deletion in the C-terminus of AvrBs4 with respect to AvrBs3.
  • In FIG. 16, the amino acid sequences of AvrBs3 as well as the amino acid sequences of the members of the Hax-sub family are shown. Of particular importance for the present invention is the repeat units, which are identical except for the hypervariable amino acids at positions 12 and 13 and the variable amino acids at positions 4 and 24. Hence, each repeat unit of these proteins is given separately.
  • As stated above, it has already been described that the repeat units within the repeat domains determine recognition or binding capability and specificity of type III effector proteins of AvrBs3-family. However, the principle underlying was not known until the present invention.
  • The inventors have discovered that one repeat unit within a repeat domain is responsible for the recognition of one specific DNA base pair in a target DNA sequence. This finding is, however, only one element of the invention. The inventors additionally discovered that a hypervariable region within each repeat unit of a repeat domain is responsible for recognition of one specific DNA base pair in a target DNA sequence. Within a repeat unit, the hypervariable region (corresponds to amino acid positions 12 and 13) are typically responsible for this recognition specificity. Hence each variation in these amino acids reflects a corresponding variation in target DNA recognition and preferably also recognition capacity.
  • As used herein, “hypervariable region” is intended to mean positions 12 and 13 or equivalent position in a repeat unit of the present invention. It is recognized that positions 12 and 13 of the invention correspond to positions 12 and 13 in the full-length repeat units of AvrBs3 and other TAL effectors as disclosed herein. It is further recognized that by “equivalent positions” is intended positions that corresponds to positions 12 and 13, respectively, in a repeat unit of the present. One can readily determine such equivalent positions by aligning any repeat unit with a full-length repeat unit of AvrBs3.
  • It has, therefore, been shown for the first time that one repeat unit in a repeat domain of a DNA-binding protein recognizes one base pair in the target DNA, and that one amino acid or two adjacent amino acid residues in a repeat unit, typically within the hypervariable regions of a repeat unit, determine which base pair in the target DNA is recognized. Based on this finding, a person skilled in the art would be able to specifically target base pairs in a target DNA sequence of interest by modifying a polypeptide within its repeat units of the repeat domain to specifically target base pairs in the desired target DNA sequence. Based on this finding, the inventors have identified a recognition code for DNA-target specificities of different repeat types and were able to predict target DNA sequences of several TAL effectors which could be confirmed experimentally. This will additionally facilitate the identification of host genes that are regulated by TAL effectors. The linear array of repeat units which recognizes a linear sequence of bases in the target DNA is a novel DNA-protein interaction. The modular architecture of the repeat domain and the recognition code identified by the inventors for targeting DNA with high specificity allows the efficient design of specific DNA-binding domains for use in a variety of technological fields.
  • In one embodiment of the present invention, the repeat domains are included in a transcription factor, for instance in transcription factors active in plants, particularly preferred in type III effector proteins, e.g. in effectors of the AvrBs3-like family. However, after having uncovered the correlation between the repeat units in a repeat domain on the one hand and the base sequence in the target DNA on the other hand, the modular architecture of the repeat domain can be used in any protein which shall be used for targeting specific target DNA sequences. By introducing repeat domains comprising repeat units into a polypeptide wherein the repeat units are modified in order to comprise one hypervariable region per repeat unit and wherein the hypervariable region determines recognition of a base pair in a target DNA sequence, the recognition of a large variety of proteins to pre-determined target DNA sequences will be available.
  • As one repeat unit within a repeat domain has been found to be responsible for the specific recognition of one base pair in a DNA, several repeat units can be combined with each other wherein each repeat unit includes a hypervariable region that is responsible for the recognition of each repeat unit to a particular base pair in a target DNA sequence.
  • Techniques to specifically modify DNA sequences in order to obtain a specified codon for a specific amino acid are known in the art.
  • Methods for mutagenesis and polynucleotide alterations have been widely described. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York) and the references cited therein. All these publications are herein incorporated by reference.
  • The following examples provide methods for constructing new repeat units and testing the specific binding activities of artificially constructed repeat units specifically recognizing base pairs in a target DNA sequence.
  • The number of repeat units to be used in a repeat domain can be ascertained by one skilled in the art by routine experimentation. Generally, at least 1.5 repeat units are considered as a minimum, although typically at least about 8 repeat units will be used. The repeat units do not have to be complete repeat units, as repeat units of half the size can be used. Moreover, the methods and polypeptides disclosed herein do depend on repeat domains with a particular number of repeat units. Thus, a polypeptide of the invention can comprise, for example, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5, 12, 12.5, 13, 13.5, 14, 14.5, 15, 15.5, 16, 16.5, 17, 17.5, 18, 18.5, 19, 19.5, 20, 20.5, 21, 21.5, 22, 22.5, 23, 23.5, 24, 24.5, 25, 25.5, 26, 26.5, 27, 27.5, 28, 28.5, 29, 29.5, 30, 30.5, 31, 31.5, 32, 32.5, 33, 33.5, 34, 34.5, 35, 35.5, 36, 36.5, 37, 37.5, 38, 38.5, 39, 39.5, 40, 40.5, 41, 41.5, 42, 42.5, 43, 43.5, 44, 44.5, 46, 46.5, 47, 47.5, 48, 48.5, 49, 49.5, 50, 50.5 or more repeat units. Typically, AvrBs3 contains 17.5 repeat units and induces expression of UPA (up-regulated by AvrBs3) genes. The number and order of repeat units will determine the corresponding activity and DNA recognition specificity. As further examples, the AvrBs3 family members Hax2 includes 21.5 repeat units, Hax3 11.5 repeat units and Hax4 14.5 repeat units. Preferably, a polypeptide of the invention comprises about 8 and to about 39 repeat units. More preferably, a polypeptide of the invention comprises about 11.5 to about 33.5 repeat units.
  • A typical consensus sequence of a repeat with 34 amino acids (in one-letter code) is shown below:
  • LTPEQVVAIASNGGGKQALETVQRLLPVLCQAHG
  • A further consensus sequence for a repeat unit with 35 amino acids (in one-letter code) is as follows:
  • LTPEQVVAIASNGGGKQALETVQRLLPVLCQAPHD
  • The repeat units which can be used in one embodiment of the invention have an identity with the consensus sequences described above of at least 35%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95%. In preferred embodiments, the repeat sequences of AvrBs3, Hax2, Hax3 and Hax4 and further members of the AvrBs3-family are used. The repeat unit sequences of these members are indicated in FIG. 16. These repeat unit sequences can be modified by exchanging one or more of the amino acids. The modified repeat unit sequences have an identity with the original repeat sequence of the original member of the AvrBs3-family sequence of at least 35%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95%. In preferred embodiments, the amino acids in positions
  • 12 and 13 are altered. In still further embodiments, amino acids in positions 4, 11, 24, and 32 are altered. Preferably, the number of amino acids per repeat are in a range between 20-45 amino acids, furthermore 32-40 amino acids, still further 32-39 amino acid, and further optionally 32, 34, 35 or 39 amino acids per repeat unit.
  • Specifically, the hypervariable region in a repeat unit determines the specific recognition of one base pair in a target DNA sequence. More specifically, the inventors have found the following correlation of recognition specificity between amino acids found at positions 12 and 13 in a repeat unit and base pairs in the target DNA sequence:
      • HD for recognition of C/G
      • NI for recognition of A/T
      • NG for recognition of T/A
      • NS for recognition of C/G or A/T or T/A or G/C
      • NN for recognition of G/C or A/T
      • IG for recognition of T/A
      • N for recognition of C/G or T/A
      • HG for recognition of T/A
      • H for recognition of T/A
      • NK for recognition of G/C
      • NH for recognition of G/C
      • NP for recognition of A/T or C/G or T/A
      • NT for recognition of A/T or G/C
      • HN for recognition of A/T or G/C
      • SH for recognition of G/C
      • SN for recognition of G/C and
      • IS for recognition of A/T.
  • It has to be noted that the amino acids are represented in the single letter code. The nucleotides are given as base pairs, wherein the first base is located in the upper strand and the second base in the lower strand; for example C/G means that C is located in the upper strand, G in the lower strand.
  • The methods of the present invention can further comprise making a repeat unit in which one or more of the hypervariable regions is selected from the following group in order to determine recognition of one of the following base pairs: HA for recognition of C/G; ND for recognition of C/G; HI for recognition of C/G; HN for recognition of G/C; and NA for recognition of G/C.
  • With respect to the single amino acids N and H, respectively, amino acid 13 of AvrBs3 appears to be missing from the repeat unit when compared by multiple amino acid sequence alignments with the other repeat units.
  • In one embodiment of the invention, the N-terminal domain of AvrBs3-like proteins confers recognition specificity for a T, 5′ of the recognition specificity of said repeat.
  • In a particularly preferred embodiment of the invention, repeat units of the protein family AvrBs3 are used. Examples for the members of this protein family have been specified above. Particularly, the members of the protein family have an amino acid homology of at least 95%, at least 90%, at least 80%, at least 85%, at least 70%, at least 75%, at least 60%, at least 50%, at least 40% or at least 35% to the amino acid sequence of AvrBs3, particularly to the amino acid sequence of the repeat unit of AvrBs3. Having this in mind, the hypervariable region in a repeat unit can be deduced by an amino acid comparison between the members of the AvrBs3 family. In particularly preferred embodiments, the amino acids are in positions 12 and 13 of a repeat unit of AvrBs3. However, variable regions may also be located in different amino acid positions. Examples for variable positions are amino acids numbers 4, 11, 24, and 32. In a further embodiment of the invention, the amino acids responsible for the specific recognition of a base pair in a DNA sequence are located in positions which typically do not vary between the members of the AvrBs3 family or in positions which are variable but not hypervariable.
  • To summarize, the inventors have found that repeat units determine the recognition of one base pair on a DNA sequence and that the hypervariable region within a repeat unit determines the recognition specificity of the corresponding repeat unit. Hence, the sequence of repeat units correlates with a specific linear order of base pairs in a target DNA sequence. The inventors have found this correlation with respect to AvrBs3 and verified it with respect to a representative number of members of the AvrBs3-like family of proteins. With respect to AvrBs3-like family members, amino acid residues in positions 12 and 13 in a repeat unit of 34 or other amino acids length correlate with defined binding specificities of AvrBs3-like proteins. The discovery of this core principle provides a powerful tool to customize a polypeptide with its cognate target DNA template for a variety of applications including, but not limited to, modulation of gene expression and targeted genome engineering.
  • In the present invention, polypeptides can be designed which comprise a repeat domain with repeat units wherein in the repeat units hypervariable regions are included which determine recognition of a base pair in a target DNA sequence. In one embodiment of the invention, each repeat unit includes a hypervariable region which determine recognition of one base pair in a target DNA sequence. In a further embodiment, 1 or 2 repeat units in a repeat domain are included which do not specifically recognize a base pair in a target DNA sequence. Considering the recognition code found by the inventors, a modular arrangement of repeat units is feasible wherein each repeat unit is responsible for the specific recognition of one base pair in a target DNA sequence. Consequently, a sequence of repeat units corresponds to a sequence of base pairs in a target DNA sequence so that 1 repeat unit matches to one base pair.
  • Provided that a target DNA sequence is known and to which recognition by a protein is desired, the person skilled in the art is able to specifically construct a modular series of repeat units, including specific recognition amino acid sequences, and assemble these repeat units into a polypeptide in the appropriate order to enable recognition of and binding to the desired target DNA sequence. Any polypeptide can be modified by being combined with a modular repeat unit DNA-binding domain of the present invention. Such examples include polypeptides that are transcription activator and repressor proteins, resistance-mediating proteins, nucleases, topoisomerases, ligases, integrases, recombinases, resolvases, methylases, acetylases, demethylases, deacetylases, and any other polypeptide capable of modifying DNA, RNA, or proteins.
  • The modular repeat unit DNA-binding domain of the present invention can be combined with cell compartment localisation signals such as nuclear localisation signals, to function at any other regulatory regions, including but not limited to, transcriptional regulatory regions and translational termination regions.
  • In a further embodiment of the invention, these modularly designed repeat units are combined with an endoneclease domain capable of cleaving DNA when brought into proximity with DNA as a result of binding by the repeat domain. Such endonucleolytic breaks are known to stimulate the rate of homologous recombination in eukaryotes, including fungi, plants, and animals. The ability to simulate homologous recombination at a specific site as a result of a site-specific endonucleolytic break allows the recovery of transformed cells that have integrated a DNA sequence of interest at the specific site, at a much higher frequency than is possible without having made the site-specific break. In addition, endonucleolytic breaks such as those caused by polypeptides formed from a repeat domain and an endonuclease domain are sometimes repaired by the cellular DNA metabolic machinery in a way that alters the sequence at the site of the break, for instance by causing a short insertion or deletion at the site of the break compared to the unaltered sequence. These sequence alterations can cause inactivation of the function of a gene or protein, for instance by altering a protein-coding sequence to make a non-functional protein, modifying a splice site so that a gene transcript is not properly cleaved, making a non-functional transcript, changing the promoter sequence of a gene so that it can no longer by appropriately transcribed, etc.
  • Breaking DNA using site specific endonucleases can increase the rate of homologous recombination in the region of the breakage. In some embodiments, the Fok I (Flavobacterium okeanokoites) endonuclease may be utilized in an effector to induce DNA breaks. The Fok I endonuclease domain functions independently of the DNA binding domain and cuts a double stranded DNA typically as a dimer (Li et al. (1992) Proc. Natl. Acad. Sci. U.S.A 89 (10):4275-4279, and Kim et al. (1996) Proc. Natl. Acad. Sci. U.S.A 93 (3):1156-1160; the disclosures of which are incorporated herein by reference in their entireties). A single-chain FokI dimer has also been developed and could also be utilized (Mino et al. (2009) J. Biotechnol. 140:156-161). An effector could be constructed that contains a repeat domain for recognition of a desired target DNA sequence as well as a FokI endonuclease domain to induce DNA breakage at or near the target DNA sequence similar to previous work done employing zinc finger nucleases (Townsend et al. (2009) Nature 459:442-445; Shukla et al. (2009) Nature 459, 437-441, all of which are herein incorporated by reference in their entireties). Utilization of such effectors could enable the generation of targeted changes in genomes which include additions, deletions and other modifications, analogous to those uses reported for zinc finger nucleases as per Bibikova et al. (2003) Science 300, 764; Urnov et al. (2005) Nature 435, 646; Wright et al. (2005) The Plant Journal 44:693-705; and U.S. Pat. Nos. 7,163,824 and 7,001,768, all of which are herein incorporated by reference in their entireties.
  • The FokI endonuclease domain can be cloned by PCR from the genomic DNA of the marine bacteria Flavobacterium okeanokoites (ATCC) prepared by standard methods. The sequence of the FokI endonuclease is available on Pubmed (Acc. No. M28828 and Acc. No J04623, the disclosures of which are incorporated herein by reference in their entireties). The I-Sce I endonuclease from the yeast Saccharomyces cerevisiae has been used to produce DNA breaks that increase the rate of homologous recombination. I-Sce I is an endonuclease encoded by a mitochondrial intron which has an 18 bp recognition sequence, and therefore a very low frequency of recognition sites within a given DNA, even within large genomes (Thierry et al. (1991) Nucleic Acids Res. 19 (1):189-190; the disclosure of which is incorporated herein by reference in its entirety). The infrequency of cleavage sites recognized by I-SceI makes it suitable to use for enhancing homologous recombination. Additional description regarding the use of I-Sce Ito induce said DNA breaks can be found in U.S. Pat. Appl. 20090305402, which is incorporated herein by reference in its entirety.
  • The recognition site for I-Sce I has been introduced into a range of different systems. Subsequent cutting of this site with I-Sce I increases homologous recombination at the position where the site has been introduced. Enhanced frequencies of homologous recombination have been obtained with I-Sce I sites introduced into the extra-chromosomal DNA in Xenopus oocytes, the mouse genome, and the genomic DNA of the tobacco plant Nicotiana plumbaginifolia. See, for example, Segal et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92 (3):806-810; Choulika et al. (1995) Mol. Cell. Biol. 15 (4):1968-1973; and Puchta et al. (1993) Nucleic Acids Res. 21 (22):5034-5040; the disclosures of which are incorporated herein by reference in their entireties. It will be appreciated that any other endonuclease domain that works with heterologous DNA binding domains can be utilized in an effector and that the I-Sce I endonuclease is one such non-limiting example. The limitation of the use of endonucleases that have a DNA recognition and binding domain such as I-Sce I is that the recognition site has to be introduced by standard methods of homologous recombination at the desired location prior to the use of said endonuclease to enhance homologous recombination at that site, if such site is not already present in the desired location. Methods have been reported that enable the design and synthesis of novel endonucleases, such as by modifying known endonucleases or making chimeric versions of one or more such endonucleases, that recognize novel target DNA sequences, thus paving the way for generation of such engineered endonuclease domains to cleave endogenous target DNA sequences of interest (Chevalier et al. (2002) Molecular Cell 10:895-905; WO2007/060495; WO2009/095793; Fajardo-Sanchez et al. (2008) Nucleic Acids Res. 36:2163-2173, both of which are incorporated by reference in their entireties). As such, it could be envisioned that such endonuclease domains could be similarly engineered so as to render the DNA-binding activity non-functional but leaving the DNA cleaving function active and to utilize said similarly engineered endonuclease cleavage domain in an effector to induce DNA breaks similar to the use of FokI above. In such applications, target DNA sequence recognition would preferably be provided by the repeat domain of the effector but DNA cleavage would be accomplished by the engineered endonuclease domain.
  • As mentioned above, an effector includes a repeat domain with specific recognition for a desired specific target sequence. In preferred embodiments, the effector specifically binds to an endogenous chromosomal DNA sequence. The specific nucleic acid sequence or more preferably specific endogenous chromosomal sequence can be any sequence in a nucleic acid region where it is desired to enhance homologous recombination. For example, the nucleic acid region may be a region which contains a gene in which it is desired to introduce a mutation, such as a point mutation or deletion, or a region into which it is desired to introduce a gene conferring a desired phenotype.
  • Further embodiments relate to methods of generating a modified plant in which a desired addition has been introduced. The methods can include obtaining a plant cell that includes an endogenous target DNA sequence into which it is desired to introduce a modification; generating a double-stranded cut within the endogenous target DNA sequence with an effector that includes a repeat domain that binds to an endogenous target DNA sequence and an endonuclease domain;
  • introducing an exogenous nucleic acid that includes a sequence homologous to at least a portion of the endogenous target DNA into the plant cell under conditions which permit homologous recombination to occur between the exogenous nucleic acid and the endogenous target DNA sequence; and generating a plant from the plant cell in which homologous recombination has occurred. Other embodiments relate to genetically modified cells and plants made according to the method described above and herein. It should be noted that the target DNA sequence could be artificial or naturally occurring. It will be appreciated that such methods could be used in any organism (such non-limiting organisms to include animals, humans, fungi, oomycetes bacteria and viruses) using techniques and methods known in the art and utilized for such purposes in such organisms.
  • In a further embodiment of the invention, these modularly designed repeat domains are combined with one or more domains responsible for the modulation or control of the expression of a gene, for instance of plant genes, animal genes, fungal genes, oomycete genes, viral genes, or human genes. Methods for modulating gene expression by generating DNA-binding polypeptides containing zinc finger domains is known in the art (U.S. Pat. Nos. 7,285,416, 7,521,241, 7,361,635, 7,273,923, 7,262,054, 7,220,719, 7,070,934, 7,013,219, 6,979,539, 6,933,113, 6,824,978, each of which is hereby herein incorporated by reference in its entirety). For instance, these effectors of the AvrBs3-like family are modified in order to bind to specific target DNA sequences. Such polypeptides might for instance be transcription activators or repressor proteins of transcription which are modified by the method of the present invention to specifically bind to genetic control regions in a promoter of or other regulatory region for a gene of interest in order to activate, repress or otherwise modulate transcription of said gene.
  • In a still further embodiment of the invention, the target DNA sequences are modified in order to be specifically recognized by a naturally occurring repeat domain or by a modified repeat domain. As one example, the target DNA sequences for members of the AvrBs3-like family can be inserted into promoters to generate novel controllable promoters that can be induced by the corresponding AvrBs3 effector. Secondary inducible systems can be constructed using a trans-activator and a target gene, wherein the trans-activator is a polypeptide wherein said polypeptide comprises at least a repeat domain comprising repeat units of the present invention that bind to said target gene and induce expression. The trans-activator and the target gene can be introduced into one cell line but may also be present in different cell lines and later be introgressed. In a further embodiment, disease-resistant plants can be constructed by inserting the target DNA sequence of a repeat domain containing polypeptide of the present invention in front of a gene which after expression leads to a defence reaction of the plant by activating a resistance-mediating gene.
  • In a further embodiment, custom DNA-binding polypeptides can be constructed by rearranging repeat unit types thus allowing the generation of repeat domains with novel target DNA binding specificity. Individual repeat units are nearly identical at the DNA level which precludes classical cloning strategies. The present invention provides a quick and inexpensive strategy to assemble custom polypeptides with repeat domains of the present invention. To improve cloning versatility such polypeptides, a two-step assembly method was designed. This method was used to assemble polypeptides with novel repeat types to study their target DNA recognition and binding specificity.
  • Summarily, any DNA sequence can be modified to enable binding by a repeat domain containing polypeptide of the present invention by introducing base pairs into any DNA region or specific regions of a gene or a genetic control element to specifically target a polypeptide having a repeat domain comprised of repeat units that will bind said modified DNA sequence in order to facilitate specific recognition and binding to each other.
  • The inventors have demonstrated that a truly modular DNA recognizing and preferably binding polypeptide can be efficiently produced, wherein the binding motif of said polypeptide is a repeat domain comprised of repeat units which are selected on the basis of their recognition capability of a combination of particular base pairs. Accordingly, it should be well within the capability of one of normal skill in the art to design a polypeptide capable of binding to any desired target DNA sequence simply by considering the sequence of base pairs present in the target DNA and combining in the appropriate order repeat units as binding motifs having the necessary characteristics to bind thereto. The greater the length of known sequence of the target DNA, the greater the number of modular repeat units that can be included in the polypeptide. For example, if the known sequence is only 9 bases long, then nine repeat units as defined above can be included in the polypeptide. If the known sequence is 27 bases long, then up to 27 repeat units could be included in the polypeptide. The longer the target DNA sequence, the lower the probability of its occurrence in any other given portion of DNA elsewhere in the genome.
  • Moreover, those repeat units selected for inclusion in the polypeptide could be artificially modified in order to modify their binding characteristics. Alternatively (or additionally) the length and amino acid sequence of the repeat unit could be varied as long as its binding characteristic is not affected.
  • Generally, it will be preferred to select those repeat units having high affinity and high specificity for the target DNA sequence.
  • As described herein, effectors can be designed to recognize any suitable target site, for regulation of expression of any endogenous gene of choice. Examples of endogenous genes suitable for regulation include VEGF, CCR5, ER.alpha., Her2/Neu, Tat, Rev, HBV C, S, X, and P, LDL-R, PEPCK, CYP7, Fibrinogen, ApoB, Apo E, Apo(a), renin, NF-.kappa.B, I-.kappa.B, TNF-.alpha., FAS ligand, amyloid precursor protein, atrial naturetic factor, ob-leptin, ucp-1, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-12, G-CSF, GM-CSF, Epo, PDGF, PAF, p53, Rb, fetal hemoglobin, dystrophin, eutrophin, GDNF, NGF, IGF-1, VEGF receptors fit and flk, topoisomerase, telomerase, bcl-2, cyclins, angiostatin, IGF, ICAM-1, STATS, c-myc, c-myb, TH, PTI-1, polygalacturonase, EPSP synthase, FAD2-1, delta-12 desaturase, delta-9 desaturase, delta-15 desaturase, acetyl-CoA carboxylase, acyl-ACP-thioesterase, ADP-glucose pyrophosphorylase, starch synthase, cellulose synthase, sucrose synthase, senescence-associated genes, heavy metal chelators, fatty acid hydroperoxide lyase, viral genes, protozoal genes, fungal genes, and bacterial genes. In general, suitable genes to be regulated include cytokines, lymphokines, growth factors, mitogenic factors, chemotactic factors, onco-active factors, receptors, potassium channels, G-proteins, signal transduction molecules, disease resistance genes, and other disease-related genes.
  • In another aspect, a method of modulating expression of a target gene in a cell is provided. The cell may be preferably a plant cell, a human cell, animal cell, fungal cell or any other living cell. The cells contain a polypeptide wherein said polypeptide comprises at least a repeat domain comprising repeat units, and these repeat units contain a hypervariable region and each repeat unit is responsible for the recognition of 1 base pair in said target DNA sequence. Said polypeptide is introduced either as DNA encoding for the polypeptide or the polypeptide is introduced per se into the cell by methods known in the art. Regardless of how introduced, the polypeptide should include at least one repeat domain that specifically recognizes and preferably binds to a target DNA sequence of base pairs and modulates the expression of a target gene. In a preferred embodiment, all repeat units contain a hypervariable region which determines recognition of base pairs in a target DNA sequence.
  • Examples of peptide sequences which can be linked to an effector of the present invention, for facilitating uptake of effectors into cells, include, but are not limited to: an 11 animo acid peptide of the tat protein of HIV; a 20 residue peptide sequence which corresponds to amino acids 84 103 of the p16 protein (see Fahraeus et al. (1996) Current Biology 6:84); the third helix of the 60-amino acid long homeodomain of Antennapedia (Derossi et al. (1994) J. Biol. Chem. 269:10444); the h region of a signal peptide such as the Kaposi fibroblast growth factor (K-FGF) h region; or the VP22 translocation domain from HSV (Elliot & O'Hare (1997) Cell 88:223 233). Other suitable chemical moieties that provide enhanced cellular uptake may also be chemically linked to effectors.
  • Toxin molecules also have the ability to transport polypeptides across cell membranes. Often, such molecules are composed of at least two parts (called “binary toxins”): a translocation or binding domain or polypeptide and a separate toxin domain or polypeptide. Typically, the translocation domain or polypeptide binds to a cellular receptor, and then the toxin is transported into the cell. Several bacterial toxins, including Clostridium perfringens iota toxin, diphtheria toxin (DT), Pseudomonas exotoxin A (PE), pertussis toxin (PT), Bacillus anthracis toxin, and pertussis adenylate cyclase (CYA), have been used in attempts to deliver peptides to the cell cytosol as internal or amino-terminal fusions (Arora et al. (1993) J. Biol. Chem. 268:3334 3341; Perelle et al. (1993) Infect. Immun. 61:5147 5156 (1993); Stenmark et al. (1991) J. Cell Biol. 113:1025 1032 (1991); Donnelly et al. (1993) Proc. Natl. Acad. Sci. USA 90:3530 3534; Carbonetti et al. (1995) Abstr. Annu. Meet. Am. Soc. Microbiol. 95:295; Sebo et al. (1995) Infect. Immun. 63:3851 3857; Klimpel et al. (1992) Proc. Natl. Acad. Sci. USA 89:10277 10281; and Novak et al. (1992) J. Biol. Chem. 267:17186 17193).
  • Effectors can also be introduced into an animal cell, preferably a mammalian cell, via liposomes and liposome derivatives such as immunoliposomes. The term “liposome” refers to vesicles comprised of one or more concentrically ordered lipid bilayers, which encapsulate an aqueous phase. The aqueous phase typically contains the compound to be delivered to the cell, in this case an effector. The liposome fuses with the plasma membrane, thereby releasing the effector into the cytosol. Alternatively, the liposome is phagocytosed or taken up by the cell in a transport vesicle. Once in the endosome or phagosome, the liposome either degrades or fuses with the membrane of the transport vesicle and releases its contents.
  • The invention particularly relates to the field of plant and agricultural technology. In one aspect, the present invention is directed to a method to modulate the expression of a target gene in plant cells, which method comprises providing plant cells with a polypeptide modified according to the invention, said polypeptide being capable of specifically recognizing a target nucleotide sequence, or a complementary strand thereof, within a target gene, and allowing said polypeptide to recognize and particularly bind to said target nucleotide sequence, whereby the expression of said target gene in said plant cells is modulated.
  • The polypeptide can be provided to the plant cells via any suitable methods known in the art. For example, the protein can be exogenously added to the plant cells and the plant cells are maintained under conditions such that the polypeptide is introduced into the plant cell, binds to the target nucleotide sequence and regulates the expression of the target gene in the plant cells. Alternatively, a nucleotide sequence, e.g., DNA or RNA, encoding the polypeptide can be expressed in the plant cells and the plant cells are maintained under conditions such that the expressed polypeptide binds to the target nucleotide sequence and regulates the expression of the target gene in the plant cells.
  • A preferred method to modulate the expression of a target gene in plant cells comprises the following steps: a) providing plant cells with an expression system for a polypeptide modified according to the invention, said polypeptide being capable of specifically recognizing, and preferably binding, to a target nucleotide sequence, or a complementary strand thereof, within an expression control element of a target gene, preferably a promoter; and b) culturing said plant cells under conditions wherein said polypeptide is produced and binds to said target nucleotide sequence, whereby expression of said target gene in said plant cells is modulated.
  • Any target nucleotide sequence can be modulated by the present method. For example, the target nucleotide sequence can be endogenous or exogenous to the target gene. In an embodiment of the invention the target nucleotide sequence can be present in a living cell or present in vitro. In a specific embodiment, the target nucleotide sequence is endogenous to the plant. The target nucleotide sequence can be located in any suitable place in relation to the target gene. For example, the target nucleotide sequence can be upstream or downstream of the coding region of the target gene. Alternatively, the target nucleotide sequence is within the coding region of the target gene. Preferably, the target nucleotide sequence is a promoter of a gene.
  • Any target gene can be modulated by the present method. For example, the target gene can encode a product that affects biosynthesis, modification, cellular trafficking, metabolism and degradation of a peptide, a protein, an oligonucleotide, a nucleic acid, a vitamin, an oligosaccharide, a carbohydrate, a lipid, or a small molecule. Furthermore, effectors can be used to engineer plants for traits such as increased disease resistance, modification of structural and storage polysaccharides, flavors, proteins, and fatty acids, fruit ripening, yield, color, nutritional characteristics, improved storage capability, and the like.
  • Therefore, the invention provides a method of altering the expression of a gene of interest in a target cell, comprising: determining (if necessary) at least part of the DNA sequence of the structural region and/or a regulatory region of the gene of interest; designing a polypeptide including the repeat units modified in accordance with the invention to recognize specific base pairs on the DNA of known sequence, and causing said modified polypeptide to be present in the target cell, (preferably in the nucleus thereof). (It will be apparent that the DNA sequence need not be determined if it is already known.)
  • The regulatory region could be quite remote from the structural region of the gene of interest (e.g. a distant enhancer sequence or similar).
  • In addition, the polypeptide may advantageously comprise functional domains from other proteins (e.g. catalytic domains from restriction endonucleases, recombinases, replicases, integrases and the like) or even “synthetic” effector domains. The polypeptide may also comprise activation or processing signals, such as nuclear localisation signals. These are of particular usefulness in targeting the polypeptide to the nucleus of the cell in order to enhance the binding of the polypeptide to an intranuclear target (such as genomic DNA).
  • The modified polypeptide may be synthesised in situ in the cell as a result of delivery to the cell of DNA directing expression of the polypeptide. Methods of facilitating delivery of DNA are well-known to those skilled in the art and include, for example, recombinant viral vectors (e.g. retroviruses, adenoviruses), liposomes and the like. Alternatively, the modified polypeptide could be made outside the cell and then delivered thereto. Delivery could be facilitated by incorporating the polypeptide into liposomes etc. or by attaching the polypeptide to a targeting moiety (such as the binding portion of an antibody or hormone molecule, or a membrane transition domain, or the translocation domain of a fungal or oomycete effector, or the cell-binding B-domain of the classical A-B family of bacterial toxins). Indeed, one significant advantage of the modified proteins of the invention in controlling gene expression would be the vector-free delivery of protein to target cells.
  • To the best knowledge of the inventors, design of a polypeptide containing modified repeat units capable of specifically recognizing base pairs in a target DNA sequence and its successful use in modulation of gene expression (as described herein) has never previously been demonstrated. Thus, the breakthrough of the present invention as disclosed herein presents numerous possibilities that extend beyond uses in plants. In one embodiment of the invention, effector polypeptides are designed for therapeutic and/or prophylactic use in regulating the expression of disease-associated genes. For example, said polypeptides could be used to inhibit the expression of foreign genes (e.g., the genes of bacterial or viral pathogens) in humans, other animals, or plants, or to modify the expression of mutated host genes (such as oncogenes).
  • The invention therefore also provides an effector polypeptide capable of inhibiting the expression of a disease-associated gene. Typically the polypeptide will not be a naturally occurring polypeptide but will be specifically designed to inhibit the expression of the disease-associated gene. Conveniently the effector polypeptide will be designed by any of the methods of the invention.
  • The invention also relates to the field of genome engineering. An effector polypeptide can be generated according to the invention to target a specific DNA sequence in a genome. Said polypeptide can be modified to contain an activity that directs modification of the target DNA sequence (e.g. site specific recombination or integration of target sequences). This method enables targeted DNA modifications in complex genomes.
  • In a still further embodiment of the invention, a polypeptide is provided which is modified to include at least a repeat domain comprising repeat units, the repeat units having hypervariable region for determining selective recognition of a base pair in a DNA sequence.
  • In a preferred embodiment, the polypeptide comprises within said repeat unit a hypervariable region which is selected from the following group in order to determine recognition of one of the following base pairs:
      • HD for recognition of C/G
      • NI for recognition of A/T
      • NG for recognition of T/A
      • NS for recognition of C/G or A/T or T/A or G/C
      • NN for recognition of G/C or A/T
      • IG for recognition of T/A
      • N for recognition of C/G or T/A
      • HG for recognition of T/A
      • H for recognition of T/A
      • NK for recognition of G/C
      • NH for recognition of G/C
      • NP for recognition of A/T or C/G or T/A
      • NT for recognition of A/T or G/C
      • HN for recognition of A/T or G/C
      • SH for recognition of G/C
      • SN for recognition of G/C and
      • IS for recognition of A/T.
  • The polypeptides of the present invention can further comprise within a repeat unit a hypervariable region which is selected from the following group in order to determine recognition of one of the following base pairs: HA for recognition of C/G; ND for recognition of C/G; HI for recognition of C/G; FIN for recognition of G/C; and NA for recognition of G/C.
  • The invention also comprises DNA which encodes for any one of the polypeptides described before.
  • In a still further embodiment, DNA is provided which is modified to include a base pair located in a target DNA sequence so that said base pair can be specifically recognized by a polypeptide which includes at least a repeat domain comprising repeat units, the repeat units having a hypervariable region which determine recognition of said base pair in said DNA. In one optional embodiment, said base pair is located in a gene expression control sequence. Due to the modular assembly of the repeat domain, a sequence of base pairs can be specifically targeted by said repeat domain.
  • In an alternative embodiment of the invention, said DNA is modified by a base pair selected from the following group in order to receive a selective and determined recognition by one of the following hypervariable regions:
      • C/G for recognition by HD
      • A/T for recognition by NI
      • T/A for recognition by NG
      • CT or A/T or T/A or G/C for recognition by NS
      • G/C or A/T for recognition by NN
      • T/A for recognition by IG.
      • C/G or T/A for recognition by N
      • T/A for recognition by HG
      • T/A for recognition by H
      • G/C for recognition by NK
      • G/C for recognition of NH
      • A/T or C/G or T/A for recognition of NP
      • A/T or G/C for recognition of NT
      • A/T or G/C for recognition of HN
      • G/C for recognition of SH
      • G/C for recognition of SN and
      • A/T for recognition of IS.
  • The DNA of the present invention can be modified to modified by a base pair selected from the following group in order to receive a selective and determined recognition by one of the following hypervariable regions: HA for recognition of C/G; ND for recognition of C/G; HI for recognition of C/G; HN for recognition of G/C; and NA for recognition of G/C.
  • In yet another aspect the invention provides a method of modifying a nucleic acid sequence of interest present in a sample mixture by binding thereto a polypeptide according to the invention, comprising contacting the sample mixture with said polypeptide having affinity for at least a portion of the sequence of interest, so as to allow the polypeptide to recognize and preferably bind specifically to the sequence of interest.
  • The term “modifying” as used herein is intended to mean that the sequence is considered modified simply by the binding of the polypeptide. It is not intended to suggest that the sequence of nucleotides is changed, although such changes (and others) could ensue following binding of the polypeptide to the nucleic acid of interest. Conveniently the nucleic acid sequence is DNA.
  • Modification of the nucleic acid of interest (in the sense of binding thereto by a polypeptide modified to contain modular repeat units) could be detected in any of a number of methods (e.g. gel mobility shift assays, use of labelled polypeptides—labels could include radioactive, fluorescent, enzyme or biotin/streptavidin labels).
  • Modification of the nucleic acid sequence of interest (and detection thereof) may be all that is required (e.g. in diagnosis of disease). Desirably, however, further processing of the sample is performed. Conveniently the polypeptide (and nucleic acid sequences specifically bound thereto) is separated from the rest of the sample. Advantageously the polypeptide-DNA complex is bound to a solid phase support, to facilitate such separation. For example, the polypeptide may be present in an acrylamide or agarose gel matrix or, more preferably, is immobilised on the surface of a membrane or in the wells of a microtitre plate.
  • In one embodiment of the invention, said repeat domain comprising repeat units is inserted in a bacterial, viral, fungal, oomycete, human, animal or plant polypeptide to achieve a targeted recognition and preferably binding of one or more specified base pairs in a DNA sequence, and optionally wherein said repeat units are taken from the repeat domains of AvrBs3-like family of proteins which are further optionally modified in order to obtain a pre-selected specific binding activity to one or more base pairs in a DNA sequence.
  • The invention encompasses isolated or substantially purified polynucleotide or protein compositions. An “isolated” or “purified” polynucleotide or protein, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or protein as found in its naturally occurring environment. Thus, an isolated or purified polynucleotide or protein is substantially free of other cellular material or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. Optimally, an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived. For example, in various embodiments, the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived. A protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein. When the protein of the invention or biologically active portion thereof is recombinantly produced, optimally culture medium represents less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of chemical precursors or non-protein-of-interest chemicals.
  • Fragments and variants of the disclosed DNA sequences and proteins encoded thereby are also encompassed by the present invention. By “fragment” is intended a portion of the DNA sequence or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of a DNA sequence comprising coding sequences may encode protein fragments that retain biological activity of the native protein and hence DNA recognition or binding activity to a target DNA sequence as herein described. Alternatively, fragments of a DNA sequence that are useful as hybridization probes generally do not encode proteins that retain biological activity or do not retain promoter activity. Thus, fragments of a DNA sequence may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full-length polynucleotide of the invention.
  • “Variants” is intended to mean substantially similar sequences. For DNA sequences, a variant comprises a DNA sequence having deletions (i.e., truncations) at the 5′ and/or 3′ end; deletion and/or addition of one or more nucleotides at one or more internal sites in the native polynucleotide; and/or substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a “native” DNA sequence or polypeptide comprises a naturally occurring DNA sequence or amino acid sequence, respectively. For DNA sequences, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the polypeptides of the invention. Variant DNA sequences also include synthetically derived DNA sequences, such as those generated, for example, by using site-directed mutagenesis but which still encode a protein of the invention. Generally, variants of a particular DNA sequence of the invention will have at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters as described elsewhere herein.
  • Variants of a particular DNA sequence of the invention (i.e., the reference DNA sequence) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant DNA sequence and the polypeptide encoded by the reference DNA sequence. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides of the invention is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
  • “Variant” protein is intended to mean a protein derived from the native protein by deletion (so-called truncation) of one or more amino acids at the N-terminal and/or C-terminal end of the native protein; deletion and/or addition of one or more amino acids at one or more internal sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein as described herein. Such variants may result from, for example, genetic polymorphism or from human manipulation. Biologically active variants of a protein of the invention will have at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native protein as determined by sequence alignment programs and parameters described elsewhere herein. A biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
  • The proteins of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants and fragments of the proteins can be prepared by mutations in the DNA. Methods for mutagenesis and polynucleotide alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York) and the references cited therein. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the protein of interest may be found in the model of Dayhoff et al. (1978) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C.), herein incorporated by reference. Conservative substitutions, such as exchanging one amino acid with another having similar properties, may be optimal.
  • The deletions, insertions, and substitutions of the protein sequences encompassed herein are not expected to produce radical changes in the characteristics of the protein. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays as described elsewhere herein or known in the art.
  • Variant DNA sequences and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.
  • In a PCR approaches, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any organism of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like.
  • In hybridization techniques, all or part of a known polynucleotide is used as a probe that selectively hybridizes to other corresponding polynucleotides present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen organism. The hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32P, or any other detectable marker. Thus, for example, probes for hybridization can be made by labeling synthetic oligonucleotides based on the DNA sequences of the invention. Methods for preparation of probes for hybridization and for construction of cDNA and genomic libraries are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
  • Hybridization of such sequences may be carried out under stringent conditions. By “stringent conditions” or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length, optimally less than 500 nucleotides in length.
  • Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.
  • Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)-500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ≧90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is optimal to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
  • It is recognized that the DNA sequences and proteins of the invention encompass polynucleotide molecules and proteins comprising a nucleotide or an amino acid sequence that is sufficiently identical to the DNA sequences or to the amino acid sequence disclosed herein. The term “sufficiently identical” is used herein to refer to a first amino acid or nucleotide sequence that contains a sufficient or minimum number of identical or equivalent (e.g., with a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have a common structural domain and/or common functional activity. For example, amino acid or nucleotide sequences that contain a common structural domain having at least about 70% identity, preferably 75% identity, more preferably 85%, 90%, 95%, 96%, 97%, 98% or 99% identity are defined herein as sufficiently identical.
  • To determine the percent identity of two amino acid sequences or of two nucleic acids, the sequences are aligned for optimal comparison purposes. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., percent identity=number of identical positions/total number of positions (e.g., overlapping positions)×100). In one embodiment, the two sequences are the same length. The percent identity between two sequences can be determined using techniques similar to those described below, with or without allowing gaps. In calculating percent identity, typically exact matches are counted.
  • The determination of percent identity between two sequences can be accomplished using a mathematical algorithm. A preferred, nonlimiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (1990) J. Mol. Biol. 215:403. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12, to obtain nucleotide sequences homologous to the polynucleotide molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3, to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov. Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller (1988) CABIOS 4:11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0), which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. Alignment may also be performed manually by inspection.
  • Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using the full-length sequences of the invention and using multiple alignment by mean of the algorithm Clustal W (Nucleic Acid Research, 22(22):4673-4680, 1994) using the program AlignX included in the software package Vector NTI Suite Version 7 (InforMax, Inc., Bethesda, Md., USA) using the default parameters; or any equivalent program thereof. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by CLUSTALW (Version 1.83) using default parameters (available at the European Bioinformatics Institute website: http://www.ebi.ac.uk/Tools/clustalw/html).
  • The DNA sequences of the invention can be provided in expression cassettes for expression in any prokaryotic or eukaryotic cell and/or organism of interest including, but not limited to, bacteria, fungi, algae, plants, and animals. The cassette will include 5′ and 3′ regulatory sequences operably linked to a DNA sequence of the invention. “Operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a polynucleotide or gene of interest and a regulatory sequence (i.e., a promoter) is functional link that allows for expression of the polynucleotide of interest. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame. The cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the DNA sequence to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
  • The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a DNA sequence of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants or other organism or non-human host cell. The regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the DNA sequence of the invention may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or DNA sequence of the invention may be heterologous to the host cell or to each other. As used herein, “heterologous” in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.
  • The termination region may be native with the transcriptional initiation region, may be native with the operably linked DNA sequence of interest, may be native with the host, or may be derived from another source (i.e., foreign or heterologous) to the promoter, the DNA sequence of interest, the plant host, or any combination thereof. Convenient termination regions for use in plants are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res. 15:9627-9639.
  • Where appropriate, the polynucleotides may be optimized for increased expression in a transformed organism. That is, the polynucleotides can be synthesized using codons preferred by the host for improved expression. See, for example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for a discussion of host-preferred codon usage. Methods are available in the art for synthesizing host-preferred gene, particularly plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.
  • Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
  • The expression cassettes may additionally contain 5′ leader sequences. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include: picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein et al. (1989) Proc. Natl. Acad. Sci. USA 86:6126-6130); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Gallie et al. (1995) Gene 165(2):233-238), MDMV leader (Maize Dwarf Mosaic Virus) (Virology 154:9-20), and human immunoglobulin heavy-chain binding protein (BiP) (Macejak et al. (1991) Nature 353:90-94); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader (TMV) (Gallie et al. (1989) in Molecular Biology of RNA, ed. Cech (Liss, New York), pp. 237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel et al. (1991) Virology 81:382-385). See also, Della-Cioppa et al. (1987) Plant Physiol. 84:965-968.
  • In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved.
  • A number of promoters can be used in the practice of the invention. The promoters can be selected based on the host of interest and the desired outcome. The nucleic acids can be combined with constitutive, tissue-preferred, or other promoters for expression in plants. Such constitutive promoters include, for example, the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theon. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026), and the like. Other constitutive promoters include, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611.
  • Tissue-preferred promoters can be utilized to target enhanced expression within a particular host tissue. Such tissue-preferred promoters for use in plants include, but are not limited to, leaf-preferred promoters, root-preferred promoters, seed-preferred promoters, and stem-preferred promoters. Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen. Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-196; Orozco et al. (1993) Plant Mol. Biol. 23(6):1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al. (1993) Plant J. 4(3):495-505. Such promoters can be modified, if necessary, for weak expression.
  • Generally, it will be beneficial to express the gene from an inducible promoter, particularly from a pathogen-inducible promoter. Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-1,3-glucanase, chitinase, etc. See, for example, Redolfi et al. (1983) Neth. J. Plant Pathol. 89:245-254; Uknes et al. (1992) Plant Cell 4:645-656; and Van Loon (1985) Plant Mol. Virol. 4:111-116. See also WO 99/43819, herein incorporated by reference.
  • Of interest are promoters that are expressed locally at or near the site of pathogen infection. See, for example, Marineau et al. (1987) Plant Mol. Biol. 9:335-342; Matton et al. (1989) Molecular Plant-Microbe Interactions 2:325-331; Somsisch et al. (1986) Proc. Natl. Acad. Sci. USA 83:2427-2430; Somsisch et al. (1988) Mol. Gen. Genet. 2:93-98; and Yang (1996) Proc. Natl. Acad. Sci. USA 93:14972-14977. See also, Chen et al. (1996) Plant J. 10:955-966; Zhang et al. (1994) Proc. Natl. Acad. Sci. USA 91:2507-2511; Warner et al. (1993) Plant J. 3:191-201; Siebertz et al. (1989) Plant Cell 1:961-968; U.S. Pat. No. 5,750,386 (nematode-inducible); and the references cited therein. Of particular interest is the inducible promoter for the maize PRms gene, whose expression is induced by the pathogen Fusarium moniliforme (see, for example, Cordero et al. (1992) Physiol. Mol. Plant. Path. 41:189-200).
  • Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-1a promoter, which is activated by salicylic acid. Other chemical-regulated promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
  • The expression cassette can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D). Additional selectable markers include phenotypic markers such as β-galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al. (2004) Biotechnol Bioeng 85:610-9 and Fetter et al. (2004) Plant Cell 16:215-28), cyan florescent protein (CYP) (Bolte et al. (2004) J. Cell Science 117:943-54 and Kato et al. (2002) Plant Physiol 129:913-42), and yellow florescent protein (PhiYFP™ from Evrogen, see, Bolte et al. (2004) J. Cell Science 117:943-54). For additional selectable markers, see generally, Yarranton (1992) Curr. Opin. Biotech. 3:506-511; Christopherson et al. (1992) Proc. Natl. Acad. Sci. USA 89:6314-6318; Yao et al. (1992) Cell 71:63-72; Reznikoff (1992) Mol. Microbiol. 6:2419-2422; Barkley et al. (1980) in The Operon, pp. 177-220; Hu et al. (1987) Cell 48:555-566; Brown et al. (1987) Cell 49:603-612; Figge et al. (1988) Cell 52:713-722; Deuschle et al. (1989) Proc. Natl. Acad. Aci. USA 86:5400-5404; Fuerst et al. (1989) Proc. Natl. Acad. Sci. USA 86:2549-2553; Deuschle et al. (1990) Science 248:480-483; Gossen (1993) Ph.D. Thesis, University of Heidelberg; Reines et al. (1993) Proc. Natl. Acad. Sci. USA 90:1917-1921; Labow et al. (1990) Mol. Cell. Biol. 10:3343-3356; Zambretti et al. (1992) Proc. Natl. Acad. Sci. USA 89:3952-3956; Baim et al. (1991) Proc. Natl. Acad. Sci. USA 88:5072-5076; Wyborski et al. (1991) Nucleic Acids Res. 19:4647-4653; Hillenand-Wissman (1989) Topics Mol. Struc. Biol. 10:143-162; Degenkolb et al. (1991) Antimicrob. Agents Chemother. 35:1591-1595; Kleinschnidt et al. (1988) Biochemistry 27:1094-1104; Bonin (1993) Ph.D. Thesis, University of Heidelberg; Gossen et al. (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; Oliva et al. (1992) Antimicrob. Agents Chemother. 36:913-919; Hlavka et al. (1985) Handbook of Experimental Pharmacology, Vol. 78 (Springer-Verlag, Berlin); Gill et al. (1988) Nature 334:721-724. Such disclosures are herein incorporated by reference.
  • The above list of selectable marker genes is not meant to be limiting. Any selectable marker gene can be used in the present invention.
  • Numerous plant transformation vectors and methods for transforming plants are available. See, for example, An, G. et al. (1986) Plant Pysiol., 81:301-305; Fry, J., et al. (1987) Plant Cell Rep. 6:321-325; Block, M. (1988) Theon. Appl Genet. 76:767-774; Hinchee, et al. (1990) Stadler. Genet. Symp. 203212.203-212; Cousins, et al. (1991) Aust. J. Plant Physiol. 18:481-494; Chee, P. P. and Slightom, J. L. (1992) Gene. 118:255-260; Christou, et al. (1992) Trends. Biotechnol. 10:239-246; D'Halluin, et al. (1992) Bio/Technol. 10:309-314; Dhir, et al. (1992) Plant Physiol. 99:81-88; Casas et al. (1993) Proc. Nat. Acad. Sci. USA 90:11212-11216; Christou, P. (1993) In Vitro Cell. Dev. Biol.-Plant; 29P:119-124; Davies, et al. (1993) Plant Cell Rep. 12:180-183; Dong, J. A. and Mchughen, A. (1993) Plant Sci. 91:139-148; Franklin, C. I. and Trieu, T. N. (1993) Plant. Physiol. 102:167; Golovkin, et al. (1993) Plant Sci. 90:41-52; Guo Chin Sci. Bull. 38:2072-2078; Asano, et al. (1994) Plant Cell Rep. 13; Ayeres N. M. and Park, W. D. (1994) Crit. Rev. Plant. Sci. 13:219-239; Barcelo, et al. (1994) Plant. J. 5:583-592; Becker, et al. (1994) Plant. J. 5:299-307; Borkowska et al. (1994) Acta. Physiol Plant. 16:225-230; Christou, P. (1994) Agro. Food. Ind. Hi Tech. 5: 17-27; Eapen et al. (1994) Plant Cell Rep. 13:582-586; Hartman, et al. (1994) Bio-Technology 12: 919923; Ritala, et al. (1994) Plant. Mol. Biol. 24:317-325; and Wan, Y. C. and Lemaux, P. G. (1994) Plant Physiol. 104:3748.
  • The methods of the invention involve introducing a polynucleotide construct comprising a DNA sequence into a host cell. By “introducing” is intended presenting to the plant the polynucleotide construct in such a manner that the construct gains access to the interior of the host cell. The methods of the invention do not depend on a particular method for introducing a polynucleotide construct into a host cell, only that the polynucleotide construct gains access to the interior of one cell of the host. Methods for introducing polynucleotide constructs into bacteria, plants, fungi and animals are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.
  • By “stable transformation” is intended that the polynucleotide construct introduced into a plant integrates into the genome of the host and is capable of being inherited by progeny thereof. By “transient transformation” is intended that a polynucleotide construct introduced into the host does not integrate into the genome of the host.
  • For the transformation of plants and plant cells, the DNA sequences of the invention are inserted using standard techniques into any vector known in the art that is suitable for expression of the DNA sequences in a host cell or organism of interest. The selection of the vector depends on the preferred transformation technique and the target host species to be transformed.
  • Methodologies for constructing plant expression cassettes and introducing foreign nucleic acids into plants are generally known in the art and have been previously described. For example, foreign DNA can be introduced into plants, using tumor-inducing (Ti) plasmid vectors. Other methods utilized for foreign DNA delivery involve the use of PEG mediated protoplast transformation, electroporation, microinjection whiskers, and biolistics or microprojectile bombardment for direct DNA uptake. Such methods are known in the art. (U.S. Pat. No. 5,405,765 to Vasil et al.; Bilang et al. (1991) Gene 100: 247-250; Scheid et al., (1991) Mol. Gen. Genet., 228: 104-112; Guerche et al., (1987) Plant Science 52: 111-116; Neuhause et al., (1987) Theor. Appl Genet. 75: 30-36; Klein et al., (1987) Nature 327: 70-73; Howell et al., (1980) Science 208:1265; Horsch et al., (1985) Science 227: 1229-1231; DeBlock et al., (1989) Plant Physiology 91: 694-701; Methods for Plant Molecular Biology (Weissbach and Weissbach, eds.) Academic Press, Inc. (1988) and Methods in Plant Molecular Biology (Schuler and Zielinski, eds.) Academic Press, Inc. (1989). The method of transformation depends upon the plant cell to be transformed, stability of vectors used, expression level of gene products and other parameters.
  • The DNA sequences of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids. Generally, such methods involve incorporating a polynucleotide construct of the invention within a viral DNA or RNA molecule. It is recognized that the a protein of the invention may be initially synthesized as part of a viral polyprotein, which later may be processed by proteolysis in vivo or in vitro to produce the desired recombinant protein. Further, it is recognized that promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotide constructs into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367 and 5,316,931; herein incorporated by reference.
  • In specific embodiments, the DNA sequences of the invention can be provided to a plant using a variety of transient transformation methods. Such transient transformation methods include, but are not limited to, the introduction of the protein or variants and fragments thereof directly into the plant or the introduction of a transcript encoding the protein into the plant. Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986) Mol. Gen. Genet. 202:179-185; Nomura et al. (1986) Plant Sci. 44:53-58; Hepler et al. (1994) Proc. Natl. Acad. Sci. 91: 2176-2180 and Hush et al. (1994) The Journal of Cell Science 107:775-784, all of which are herein incorporated by reference. Alternatively, the polynucleotide can be transiently transformed into the plant using techniques known in the art. Such techniques include Agrobacterium tumefaciens-mediated transient expression as described below.
  • The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a polynucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • The present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Plants of particular interest include, but are not limited to, and grain plants that provide seeds of interest, oil-seed plants, leguminous plants, and Arabidopsis thaliana. Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc. Oil-seed plants include cotton, soybean, safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc. Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
  • As used herein, the term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruits, roots, root tips, anthers, and the like. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
  • The present invention further encompasses the introduction of the DNA sequences of the invention into non-plant host cells, including, but not limited to, bacterial cells, yeast cells other fungal cells, human cells, and other animal cells. In addition, the invention encompasses the introduction of the DNA sequences into animals and other organisms by both stable and transient transformation methods.
  • As discussed herein, a DNA sequence of the present invention can be expressed in these eukaryotic systems. Synthesis of heterologous polynucleotides in yeast is well known (Sherman et al. (1982) Methods in Yeast Genetics, Cold Spring Harbor Laboratory). Two widely utilized yeasts for production of eukaryotic proteins are Saccharomyces cerevisiae and Pichia pastoris. Vectors, strains, and protocols for expression in Saccharomyces and Pichia are known in the art and available from commercial suppliers (e.g., Invitrogen). Suitable vectors usually have expression control sequences, such as promoters, including 3-phosphoglycerate kinase or alcohol oxidase, and an origin of replication, termination sequences and the like as desired.
  • The sequences of the present invention can also be ligated to various expression vectors for use in transfecting cell cultures of mammalian or insect origin. Illustrative cell cultures useful for the production of the peptides are mammalian cells. A number of suitable host cell lines capable of expressing intact proteins have been developed in the art, and include the HEK293, BHK21, and CHO cell lines. Expression vectors for these cells can include expression control sequences, such as an origin of replication, a promoter (e.g. the CMV promoter, a HSV tk promoter or pgk (phosphoglycerate kinase) promoter), an enhancer (Queen et al. (1986) Immunol. Rev. 89:49), and necessary processing information sites, such as ribosome binding sites, RNA splice sites, polyadenylation sites (e.g., an SV40 large T Ag poly A addition site), and transcriptional terminator sequences. Other animal cells useful for production of proteins of the present invention are available, for instance, from the American Type Culture Collection.
  • Appropriate vectors for expressing proteins of the present invention in insect cells are usually derived from the SF9 baculovirus. Suitable insect cell lines include mosquito larvae, silkworm, armyworm, moth and Drosophila cell lines such as a Schneider cell line (See, Schneider (1987) J. Embyol. Exp. Morphol. 27:353-365).
  • As with yeast, when higher animal or plant host cells are employed, polyadenylation or transcription terminator sequences are typically incorporated into the vector. An example of a terminator sequence is the polyadenylation sequence from the bovine growth hormone gene. Sequences for accurate splicing of the transcript may also be included. An example of a splicing sequence is the VP 1 intron from SV40 (Sprague et al. (1983) J. Virol. 45:773-781). Additionally, gene sequences to control replication in the host cell may be incorporated into the vector such as those found in bovine papilloma virus type-vectors (Saveria-Campo (1985) DNA Cloning Vol. II a Practical Approach, D. M. Glover, Ed., IRL Press, Arlington, Va., pp. 213-238).
  • Animal and lower eukaryotic (e.g., yeast) host cells are competent or rendered competent for transfection by various means. There are several well-known methods of introducing DNA into animal cells. These include: calcium phosphate precipitation, fusion of the recipient cells with bacterial protoplasts containing the DNA, treatment of the recipient cells with liposomes containing the DNA, DEAE dextrin, electroporation, biolistics, and micro-injection of the DNA directly into the cells. The transfected cells are cultured by means well known in the art (Kuchler (1997) Biochemical Methods in Cell Culture and Virology, Dowden, Hutchinson and Ross, Inc.).
  • Prokaryotes most frequently are represented by various strains of E. coli; however, other microbial strains may also be used in the method of the invention. Commonly used prokaryotic control sequences which are defined herein to include promoters for transcription initiation, optionally with an operator, along with ribosome binding sequences, include such commonly used promoters as the beta lactamase (penicillinase) and lactose (lac) promoter systems (Chang et al. (1977) Nature 198:1056), the tryptophan (trp) promoter system (Goeddel et al. (1980) Nucleic Acids Res. 8:4057) and the lambda derived P L promoter and N-gene ribosome binding site (Shimatake et al. (1981) Nature 292:128). The inclusion of selection markers in DNA vectors transfected in E coli. is also useful. Examples of such markers include genes specifying resistance to ampicillin, tetracycline, or chloramphenicol.
  • The vector is selected to allow introduction into the appropriate host cell. Bacterial vectors are typically of plasmid or phage origin. Appropriate bacterial cells are infected with phage vector particles or transfected with naked phage vector DNA. If a plasmid vector is used, the bacterial cells are transfected with the plasmid vector DNA. Expression systems for expressing a protein of the present invention are available using Bacillus sp. and Salmonella (Palva et al. (1983) Gene 22:229-235); Mosbach et al. (1983) Nature 302:543-545).
  • With respect to fusion proteins, “operably linked” is intended to mean a functional linkage between two or more elements or domains. If it recognized that a linker of one or more amino acids may be inserted in between each of the two or more elements to maintain the desired function of the two or more elements.
  • In one embodiment of the invention, fusion proteins comprise a repeat domain of the invention operably linked to at least one protein or part or domain thereof. In certain embodiments of the invention, the protein or part or domain thereof comprises a protein or functional part or domain thereof, that is capable of modifying DNA or RNA. In other embodiments, protein or functional part or domain thereof is capable of functioning as a transcriptional activator or a transcriptional repressor. Preferred proteins include, but are not limited to, transcription activators, a transcription repressors, a resistance-mediating proteins, nucleases, topoisomerases, ligases, integrases, recombinases, resolvases, methylases, acetylases, demethylases, and deacetylases.
  • The following examples are offered by way of illustration and not by way of limitation.
    • EXAMPLES Example 1 Identification of the Basis for DNA Specificity of TAL Effectors
  • The fact that AvrBs3 directly binds the UPA-box, a promoter element in induced target genes (Kay et al. (2007) Science 318, 648-651; Römer et al. (2007) Science 318:645-648), prompted us to investigate the basis for DNA-sequence specificity. Each repeat region generally consists of 34 amino acid, and the repeat units are nearly identical; however, amino acids 12 and 13 are hypervariable (Schornack et al. (2006) J. Plant Physiol. 163:256-272; FIG. 1A). The most C-terminal repeat of AvrBs3 shows sequence similarity to other repeat units only in its first 20 amino acids and is therefore referred to as half repeat. The repeat units can be classified into different repeat types based on their hypervariable 12th and 13th amino acids (FIG. 1B). Because the size of the UPA-box (18 (20)/19 (21) bp) almost corresponds to the number of repeat units (17.5) in AvrBs3, we considered the possibility that one repeat unit of AvrBs3 contacts one specific DNA base pair. When the repeat types of AvrBs3 ( amino acid 12 and 13 of each repeat) are projected onto the UPA box, it becomes evident that certain repeat types correlate with specific base pairs in the target DNA. For example, HD and NI repeat units have a strong preference for C and A, respectively (FIG. 1B). For simplicity, we designate only bases in the upper (sense) DNA strand. Our model of recognition specificity is supported by the fact that the AvrBs3 repeat deletion derivative AvrBs3Δrep16 which lacks four repeat units (Δ11-14; FIG. 5A, B) recognizes a shorter and different target DNA sequence (FIGS. 5 to 8). Based on sequence comparisons of UPA-boxes of AvrBs3-induced pepper genes and mutational analysis, the target DNA box of AvrBs3 appears to be 1 bp longer than the number of repeat units in AvrBs3. In addition, a T is conserved at the 5′ end of the UPA box immediately preceding the predicted recognition specificity of the first repeat (FIG. 1). Intriguingly, secondary structure predictions of the protein region preceding the first repeat and the repeat region show similarities, despite lack of amino acid-sequence conservation. This suggests an additional repeat, termed repeat 0 (FIG. 1B).
  • To further substantiate and extend our model (FIG. 1B), we predicted the yet unknown target DNA sequences of Xanthomonas TAL effectors based on the sequence of their repeat units, and inspected the promoters of known TAL target genes and their alleles for the presence of putative binding sites. We identified sequences matching the predicted specificity in promoters of alleles that are induced in response to the corresponding TAL effector, but not in non-induced alleles
  • (FIGS. 5C-F). The presence of these boxes suggests that the induced genes are direct targets of the corresponding TAL effectors. Based on the DNA base frequency for different repeat types in the target DNA sequences using eight TAL effectors we deduced a code for the DNA target specificity of certain repeat types (FIG. 1C, D; FIG. 5).
  • To experimentally validate our model we predicted target DNA sequences for the TAL effectors Hax2 (21.5 repeat units), Hax3 (11.5 repeat units), and Hax4 (14.5 repeat units) from the Brassicaceae-pathogen X. campestris pv. armoraciae (22). First, we derived target DNA boxes for Hax3 and Hax4, because they exclusively contain repeat-types present in AvrBs3 (amino acid 12/13: NI, HD, NG, NS; FIG. 1A, FIG. 2A) for which DNA binding and gene activation have been shown experimentally. The Hax3 and Hax4 target boxes were placed in front of the minimal (−55 to +25) tomato Bs4 promoter, which has very weak basal activity (Schornack et al. (2005) Mol. Plant-Microbe Interact. 18:1215-1225; FIG. 2B; FIG. 9), driving a promoterless uidA (β-glucuronidase, GUS) reporter gene. For transient expression studies, we transfected the reporter constructs together with cauliflower mosaic virus 35S-promoter driven effector genes hax3 and hax4 into Nicotiana benthamiana leaves using Agrobacterium-mediated T-DNA delivery. Qualitative and quantitative GUS assays demonstrated that promoters containing the Hax3- or Hax4-box were strongly and specifically induced in the presence of the corresponding effector (FIG. 2C). Likewise, we addressed the importance of the first nucleotide (T) in the predicted target DNA sequence of Hax3 and generated four different Hax3-boxes with either A, C, G or T at the 5′ end (FIG. 10A, B). Coexpression of hax3 and the reporter constructs in N. benthamiana demonstrated that only a promoter containing a Hax3-box with a 5′ T was strongly induced in the presence of Hax3 whereas the others led to weaker activation (FIG. 10C). This indicates that position 0 contributes to promoter activation specificity of Hax3 and likely other TAL effectors. To address the possibility that some repeat types confer broader specificity, i.e., recognize more than one base, we permutated the Hax4-box (FIG. 3A, B). Transient GUS assays showed that NI-, HD-, and NG-repeat units in Hax4 strongly favour recognition of the bases A, C, and T, respectively, whereas NS-repeat units recognize all four bases (FIG. 3B; FIG. 11). As several TAL effectors contain NN-repeat units (FIG. 5 and FIG. 15, Table 1), we generated ArtX1, an artificial TAL effector with NN-repeat units and deduced a corresponding DNA recognition sequence using our code (FIG. 3C). Analysis of ArtX1-box derivatives demonstrated that NN-repeat units recognize both A and G, with preference for G (FIG. 3C). This result confirms our prediction of the natural AvrXa27-box in rice which contains either an A or a G at positions corresponding to NN-repeat units (FIG. 5C). In addition, we derived two possible AvrXa10-boxes with either A or G at positions corresponding to NN-repeat units in AvrXa10. Both reporter constructs were induced efficiently by AvrXa10 (FIG. 12). Together, these data strongly suggest that some repeat types recognize specific base pairs whereas others are more flexible.
  • An exceptional TAL effector is Hax2 because it contains 35 amino acids per repeat instead of the typical 34 amino acid-repeat units (Kay et al. (2005) Mol. Plant-Microbe Interact. 18:838-848). In addition, Hax2 contains a rare amino acid combination in its second repeat (amino acids 12/13: IG; FIG. 2A). We permutated the corresponding third base of the Hax2-box and analyzed reporter gene activation with the effector Hax2 using the transient assay. This showed that an IG repeat confers specificity for T (FIG. 13). The Hax2-box only leads to promoter activation by Hax2, but not by Hax3 or Hax4 (FIG. 2C). This demonstrates that 35 amino acid-repeat units function like 34 amino acid-repeat units. This is supported by the fact that the TAL effector AvrHah1 which contains 35 amino acid repeat units, induces Bs3-mediated resistance (Schornack et al. (2008) New Phytol. 179:546-556). The repeat types of AvrHah1 match to the UPA-box in the Bs3 promoter (FIG. 5A, B).
  • Interestingly, the expression of hax2 in Arabidopsis thaliana leads to purple coloured leaves, indicating an accumulation of anthocyanin (FIGS. 14A, B). To identify Hax2 target genes we analyzed promoter regions of the A. thaliana genome using pattern search (Patmatch, TAIR; www.arabidopsis.org) with degenerated Hax2-box sequences. One of the putative Hax2 target genes encodes the MYB transcription factor PAP1 (At1G56650) which controls anthocyanin biosynthesis (Borevitz et al. (2000) Plant Cell 12:2383-2394). Semiquantitative analysis of the PAP1 transcript level demonstrated that expression of PAP1 is strongly induced by Hax2 (FIG. 14C). Visual inspection of the PAP1 promoter region revealed the presence of a suboptimal Hax2-box (FIGS. 14D, E). Based on the code for TAL effector repeat types (FIG. 1D) and the data described above we predicted putative target DNA sequences for additional TAL effectors some of which are important virulence factors (FIG. 15, Table 1).
  • Because the repeat number in TAL effectors ranges from 1.5 to 28.5, a key question is whether effectors with few repeat units can activate gene expression. Therefore, we tested how the number of repeat units influences target gene expression. For this, we constructed artificial effectors containing the N- and C-terminal regions of Hax3 and a repeat domain with 0.5 to 15.5 HD-repeat units (specificity for C). For technical reasons, the first repeat in all cases was NI (specificity for A). The corresponding target DNA box consists of 17 C-residues preceded by TA (FIGS. 4A, B). Promoter activation by the artificial effectors was measured using the transient Bs4-promoter GUS-assay in N. benthamiana. While at least 6.5 repeat units were needed for gene induction, 10.5 or more repeat units led to strong reporter gene activation (FIG. 4C). These data demonstrate that a minimal number of repeat units is required to recognize the artificial target DNA-box and activate gene expression. The results also suggest that effectors with fewer repeat numbers are largely inactive. We have shown that the repeat region of TAL effectors has a sequential nature that corresponds to a consecutive target DNA sequence. Hence, it should be feasible to generate effectors with novel DNA-binding specificities. Three artificial effectors were generated (ArtX1, ArtX2, ArtX3), each with randomly assembled 12.5 repeat units (FIGS. 3C, D), and tested for induction of Bs4 promoter-reporter fusions containing predicted target DNA-sequences. All three artificial effectors strongly and specifically induced the GUS reporter only in presence of the corresponding target DNA-box (FIG. 3E; FIG. 11). Our model for recognition specificity of TAL effectors in which one repeat unit contacts one base pair in the DNA via amino acids 12 and 13 of each repeat enables to predict the binding specificity of TAL effectors and identification of plant target genes. As many TAL effectors are major virulence factors the knowledge of plant target genes will greatly enhance our understanding of plant disease development caused by xanthomonads. In addition, we successfully designed artificial effectors that act as transcription factors with specific DNA-binding domains. Previously, zinc finger transcription factors containing a tandem arrangement of zinc finger units have been engineered to bind specific target DNA sequences.
  • Similarly, TAL effectors have a linear DNA-binding specificity that can easily be rearranged. It has not escaped our notice that the postulated right-handed superhelical structure of the repeat regions in TAL effectors immediately suggests a possible mechanism for interaction with the right-handed helix of the genetic material. It will be important to determine the structure of the novel DNA-binding domain of TAL effectors complexed with target DNA.
  • The following paragraphs describe further embodiments of the invention:
    • 1) Prediction of DNA-Binding Specificities of Naturally Occurring Avrbs3-Homologous Proteins and Generation of Resistant Plants.
  • The repeat units of the repeat domain of naturally occurring effectors of the AvrBs3-family encode a corresponding DNA-binding specificity. These recognition sequences can be predicted with the recognition code.
  • The artificial insertion of the predicted recognition sequences in front of a gene in transgenic plants leads to expression of the gene if the corresponding AvrBs3-like effector is translocated into the plant cell (e.g. during a bacterial infection).
  • If the recognition sequence is inserted in front of a gene whose expression leads to a defence reaction (resistance-mediating gene) of the plant, such constructed transgenic plants are resistant against an infection of plant pathogenic bacteria which translocate the corresponding effector.
    • 2) The Identification of Plant Genes Whose Expression is Induced by a Specific Effector of the AvrBs3-Family
  • The prediction of DNA target sequences of a corresponding effector of the AvrBs3-family in the promoter region of plant genes is an indication for the inducible expression of these genes by the effector. Using the method according to the invention it is possible to predict inducible plant genes. Predictions are particularly straightforward in sequenced genomes.
    • 3) Use of Other Effectors as Transcriptional Activators in Expression Systems
  • Analogous to the use of Hax3 and Hax4, the predicted DNA binding sequences of other members of the AvrBs3-family can be inserted into promoters to generate new controllable promoters which can be induced by the corresponding effector.
    • 4) Construction of a Secondarily Inducible System
  • Two constructs are introduced into plants. First, a hax3 gene whose expression is under control of an inducible promoter. Secondly, a target gene that contains the Hax3-box in the promoter.
  • Induction of the expression of hax3 leads to production of the Hax3 protein that then induces the expression of the target gene. The described two-component construction leads to a twofold expression switch which allows a variable expression of the target gene. The trans-activator and the target gene can also be present first in different plant lines and can be introgressed at will. Analogous to this, Hax4 and the corresponding Hax4-box can be used. This system can also be used with other members of the AvrBs3-family or artificial derivatives and predicted DNA-target sequences. The functionality of the system could already be verified. Transgenic Arabidopsis thaliana plants were constructed, which contain an inducible avrBs3 gene as well as a Bs3 gene under control of its native promoter, whose expression can be induced by AvrBs3. The induction of expression of avrBs3 leads to expression of Bs3 and therefore to cell death. See, WO 2009/042753, herein incorporated by reference.
    • 5) Construction of Disease-Resistant Plants
  • If the DNA target sequence of an AvrBs3-similar effector is inserted in front of a gene whose expression leads to a defence reaction (resistance-mediating gene) of the plant, correspondingly constructed transgenic plants will be resistant against infection of plant pathogenic organisms, which make this effector available. Such a resistance-mediating gene can for example lead to a local cell death which prevents spreading of the organisms/pathogens, or induce the basal or systemic resistance of the plant cell.
    • 6) Generation of Repeat Domains for the Detection of a Specific DNA Sequence and Induction of Transcription of Following Genes
  • The modular architecture of the central repeat domain enables the targeted construction of definite DNA binding specificities and with this the induction of transcription of selected plant genes. The DNA binding specificities can either be artificially inserted in front of target genes so that novel effector-DNA-box variants are generated for the inducible expression of target genes. Moreover, repeat domains can be constructed that recognize a naturally occurring DNA sequence in organisms. The advantage of this approach is that the expression of any gene in non-transgenic organisms can be induced if a corresponding effector of the invention is present in the cells of this organism.
  • Introduction of the effector can be done in different ways:
  • (1) transfer via bacteria with a protein transport system (e.g. type-III secretion system);
    (2) cell-bombardment with an artificial AvrBs3-protein;
    (3) transfer of a DNA-segment that leads to production of the effector, via introgression, Agrobacterium, viral vectors or cell-bombardment; or
    (4) other methods that result in uptake of the effector protein by the target cell
  • The central repeat domain of effectors of the AvrBs3-family is a new type of DNA binding domain (Kay et al., 2007). The decryption of the specificity of the single repeat units now allows the targeted adaptation of the DNA-binding specificity of this region. The DNA binding region can be translationally fused to other functional domains to generate sequence-specific effects. Below, four examples of such protein fusions are given.
    • 7) Construction of Transcriptional Activators for the Inducible Expression of Genes in Cells of Living Organisms
  • The effectors of the AvrBs3-like family induce the expression of genes in plant cells. For this, the C-terminus of the protein is essential, which contains a transcriptional activation domain and nuclear localization sequences that mediate the import of the protein into the plant nucleus. The C-terminus of the AvrBs3-homologous protein can be modified in such a way that it mediates the expression of genes in fungal, animal, or human systems. Thereby, effectors can constructed that function as transcriptional activators in humans, other animals, or fungi. Thus, the methods according to the invention can be applied not only to plants, but also to other living organisms.
    • 8) Use of Effectors as Transcriptional Repressors
  • The DNA binding specificity of the repeat domain can be used together with other domains in protein fusions to construct effectors that act as specific repressors. These effectors exhibit a DNA binding specificity that has been generated in such a way that they bind to promoters of target genes. In contrast to the TAL effectors which are transcription activators, these effectors are constructed to block the expression of target genes. Like classical repressors, these effectors are expected to cover promoter sequences by their recognition of, or binding to, a target DNA sequence and make them inaccessible for factors that otherwise control the expression of the target genes. Alternatively, or in addition, the repeat domains can be fused to a transcription-repressing domain, such as an EAR motif (Ohta et al. Plant Cell 13:1959-1968 (2001)).
    • 9) Use of Repeat Domains for Labelling and Isolation of Specific Sequences
  • The capability of a repeat domain to recognize a specific target DNA sequence an be used together with other domains to label specific DNA sequences. C-terminally a GFP (“green-fluorescent-protein”) can for example be fused to an artificial repeat domain that detects a desired DNA sequence. This fusion protein binds in vivo and in vitro to a corresponding DNA sequence. The position of this sequence on the chromosome can be localized using the fused GFP-protein. In an analogous way, other protein domains that enable a cellular localization of the protein (e.g. by FISH) can be fused to a specific artificial repeat domain which targets the protein to a corresponding DNA sequence in the genome of the cell. In addition, the DNA recognition specificity of repeat domains of the invention can be used to isolate specific DNA sequences. For this, the AvrBs3-like protein can be immobilized to a matrix and interacts with corresponding DNA molecules that contain a matching sequence. Therefore, specific DNA sequences can be isolated from a mixture of DNA molecules.
    • 10) Use of Repeat Domains for the Endonucleolytic Cleavage of DNA
  • The DNA recognition specificity of the repeat domain can be fused to a suitable restriction endonuclease to specifically cleave DNA. Therefore, the sequence-specific binding of the repeat domain leads to localization of the fusion protein to few specific sequences, so that the endonuclease specifically cleaves the DNA at the desired location. By means of the recognition of target DNA sequences, unspecific nucleases such as FokI can be changed into specific endonucleases analogous to work done with zinc finger nucleases. For example, the optimal distance between the two effector DNA target sites would be determined to that would be required to support dimerization of two FokI domains. This would be accomplished by analysis of a collection of constructs in which the two DNA binding sites are separated by differently sized spacer sequences. Using this approach enables one to determine the distances that allow nuclease-mediated DNA cleavage to occur and the functional analysis of additional effector nucleases that target different DNA sequences. In an alternative approach, a newly developed single-chain FokI dimer (Mino et al. (2009) J Biotechnol 140:156-161) is employed. In this approach two FokI catalytic domains are transcriptionally fused to a single repeat domain of the invention. Thus, functionality of a corresponding nuclease no longer relies on intermolecular dimerization of two FokI domains that are located on two different proteins. This type of construct has been used successfully in the context of zinc finger-based DNA binding motifs. Moreover, these methods enable very specific cuts at only a few positions in complex DNA-molecules. These methods can amongst other things be used to introduce double-strand breaks in vivo and selectively incorporate donor DNA at these positions. These methods can also be used to specifically insert transgenes.
  • 11) Construction of Repeat Domains with Custom-Designed Repeat Order
  • Due to the high similarity between the individual repeat units of a repeat domain, construction of a custom DNA-binding polypeptide as described above might not be feasible through methods involving traditional cloning methods. As detailed in this example, a repeat domain with a repeat unit order that matches a desired DNA-sequence in a promoter of interest, such as the Bs4 promoter (FIGS. 17B, C), is determined based on the recognition code of the present invention. Generation of a specific 11.5 repeat unit order was accomplished using “Golden gate” cloning (Engler et al. (2008) PLoS ONE 3:e3647). As building blocks, we subcloned the N- and C-terminus of Hax3 as well as the 12 individual repeat units resembling the 11.5 repeat units. Each building block contained individual flanking BsaI sites (FIG. 18) that allowed an ordered assembly of the fragments into a custom effector polypeptide. The effector (ARTBs4) was correctly assembled from the total of 14 fragments into a BsaI-compatible binary vector that allows Agrobacterium-mediated expression of the custom effector polypeptide as an N-terminally tagged GFP fusion in plant cells (FIG. 18).
    • 12) Use of Effectors as Viral Repressors
  • The nucleotide binding specificity of the repeat domain can be used to design effectors that disrupt viral replication in cells. These effectors will exhibit a nucleotide binding specificity targeted to nucleotide sequence in viral origins of replication and other sequences critical to viral function. No additional protein domains need to be fused to these repeat domain proteins in order to block viral function. They act like classical repressors by covering origins of replication or other key sequences, including promoters, enhancers, long terminal repeat units, and internal ribosome entry sites, by binding and making them inaccessible for host or viral factors, including viral encoded RNA-dependent RNA polymerase, nucleocapsid proteins and integrases, which participate in viral replication and function. This type of strategy has been used successfully with zinc-finger proteins (Sera (2005) J. Vir. 79:2614-2619; Takenaka et al. (2007) Nucl Acids Symposium Series 51:429-430).
  • Summarizing, the present invention additionally covers isolated nucleic acid molecules to be used in any of the methods of the present invention, transformed plants comprising a heterologous polynucleotide stably incorporated in their genome and comprising the nucleotide molecule described above, preferably operably linked to a promoter element and/or operably linked to a gene of interest. The transformed plant is preferably a monocot or a dicot. The invention covers also seeds of the transformed plants. The invention covers human and non-human host cells transformed with any of the polynucleotides of the invention or the polypeptides of the invention. The promoters used in combination with any of the nucleotides and polypeptides of the invention are preferably tissue specific promoters, chemical-inducible promoters and promoters inducible by pathogens.
  • While the present invention can be used in animal and plant systems, one preferred optional embodiment refers to the use in plant systems. The term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seed, leaves, flowers, branches, fruits, roots, root tips, anthers and the like. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
    • Materials and Methods
  • Bacterial strains and growth conditions. Escherichia coli were cultivated at 37° C. in lysogeny broth (LB) and Agrobacterium tumefaciens GV3101 at 30° C. in yeast extract broth (YEB) supplemented with appropriate antibiotics.
  • Plant material and inoculations. Nicotiana benthamiana plants were grown in the greenhouse (day and night temperatures of 23° C. and 19° C., respectively) with 16 h light and 40 to 60% humidity. Mature leaves of five- to seven-week-old plants were inoculated with Agrobacterium using a needleless syringe as described previously (S1). Inoculated plants were transferred to a Percival growth chamber (Percival Scientific) with 16 h light, 22° C. and 18° C. night temperature.
  • Construction of artificial effectors. The construction of effectors with modified repeat region was based on ligation of Esp3I (Fermentas) restriction fragments. Esp3I cuts outside of its recognition sequence and typically once per repeat. To construct a GATEWAY (Invitrogen)-compatible ENTRY-vector for generation of effectors of the invention, the N- and C-termini of hax3 were amplified by PCR using a proof reading polymerase (HotStar HiFidelity Polymerase Kit; Qiagen), combined by SOE (splicing by overlap extension)-PCR and inserted into pCR8/GW/TOPO resulting in a hax3-derivative with 1.5 repeat units (pC3SE26; first repeat=NI; last half repeat=NG). A 1 bp frame-shift preceding the start codon was inserted by site-directed mutagenesis to allow in frame N-terminal fusions using GATEWAY recombination (Invitrogen) resulting in pC3SEIF. Single repeat units were amplified from TAL effectors using a forward primer binding to most repeat units and repeat-specific reverse primers. Both primers included the naturally present Esp3I sites. To avoid amplification of more than one repeat, template DNA was digested with Esp3I prior to the PCR reaction. PCR-products were digested with Esp3I and cloned into Esp3I-digested pC3SE26 yielding Hax3-derivatives with 2.5 repeat units where a single repeat can be excised with Esp3I (HD-repeat=repeat 5 of Hax3; NI-repeat=repeat 11 of Hax3; NG-repeat=repeat 4 of Hax4; NN-repeat=G13N mutant of repeat 4 of Hax4). The ArtHD effector backbone construct consists of the N- and C-terminus of Hax3 with the last half repeat mutated into a HD-repeat. The resulting construct was restricted by Esp3I and dephosphorylated. DNA fragments encoding repeat units were excised with Esp3I from pC3SE26-derivatives containing a single HD-repeat and purified via agarose gels. Ligation was performed using a molar excess of insert to vector to facilitate concatemer ligation and transformed into E. coli. The number of repeat units was determined in recombinant plasmids using StuI and HincII. ArtX1-3 effectors with a random combination of repeat types were generated by isolating DNA fragments encoding repeat units as described above from cloned single NI-, HD-, NN-, and NG-repeat units (specificities for A, C, G/A, and T, respectively). The fragments were added in equal molar amounts each to the concatemer ligation reaction with vector pC3SEIF. Plasmids containing effectors of the invention with 12.5 repeat units were chosen for subsequent analysis. Effectors were cloned by GATEWAY-recombination (Invitrogen) into pGWB6 (S2) for expression of N-terminal GFP-effector fusions. Oligonucleotide sequences are available upon request. All constructs were sequenced.
  • GUS reporter constructs. The minimal Bs4 promoter was amplified by PCR and inserted into pENTR/D-TOPO (Invitrogen) with target DNA boxes at the 5′ end (S3; FIG. S5). Promoter derivatives were cloned into pGWB3 (S2) containing a promoterless uidA gene.
  • Construction of hax2-transgenic A. thaliana. hax2 was cloned under control of the inducible alcA promoter from Aspergillus nidulans into a GATEWAY-compatible derivative of the binary T-DNA vector binSRNACatN (Zeneca Agrochemicals) containing the 35S-driven alcR ethanol-dependent regulator gene and a nptII selection marker. AlcR drives ethanol-dependent induction of the alcA promoter (S4). T-DNA containing these genes was transformed into A. thaliana Col-0 via A. tumefaciens using floral dip inoculation (S5). Transformants were selected as kanamycin-resistant plants on sterile medium.
  • Construction of ARTBs4, an artificial effector. “Golden gate” cloning (Engler et al. (2008) PLoS ONE 3:e3647) was used to assemble effectors with 11.5 specifically ordered repeat units. The N- and C-terminus of Hax3 and 12 individual repeat units resembling the 11.5 repeat units were subcloned. Each building block contained individual flanking BsaI sites that allowed an ordered assembly of the fragments into an artificial effector. For the targeted assembly of effectors with any desired repeat composition, the building block repertoire of repeat units was expanded. To allow for target specificity to any of the four natural bases (A, C, G, and T) in DNA, four different repeat types were chosen, based on the amino acids 12 and 13 per repeat unit. The four repeat types and their specificities are: NI=A; HD=C; NG=T, NN=G or A. To generate a universally applicable assembly kit, four units corresponding to each of the four repeat unit types were cloned with flanking BsaI sites for each of the 12 repeat positions. The sum of 48 building blocks resembles a library that can be used to assemble effectors with 11.5 repeat units with any composition of the four repeat unit types.
  • β-Glucuronidase (GUS) assays. For transient GUS assays Agrobacterium strains delivering effector constructs and GUS reporter constructs were mixed 1:1, and inoculated into Nicotiana benthamiana leaves with an OD600 of 0.8. Two leaf discs (0.9 cm diameter) were sampled two days post infiltration (dpi) and quantitative GUS activity was determined using 4-methyl-umbelliferyl-β-D-glucuronide (MUG), as described previously (Si). Proteins were quantified using Bradford assays (BioRad). Data correspond to triplicate samples from different plants. For qualitative GUS assays, leaf discs were sampled 2 dpi, incubated in X-Gluc (5-bromo-4-chloro-3-indolyl-β-D-glucuronide) staining solution (S3), destained in ethanol, and dried. Experiments were performed at least twice with similar results.
  • Expression of hax2, hax3, and hax4. hax2, hax3, and hax4 were expressed in planta under control of the constitutive cauliflower mosaic virus 35S promoter using pAGH2, pAGH3, and pAGH4 (S6).
  • DNaseI footprinting. DNaseI footprinting was performed as described (S7) with the following modifications: Fluorescently labeled PCR products of Bs3 and Bs3-E promoter DNA were generated using plasmids pCRBluntII-TOPO::FPBs3 (Bs3 promoter fragment from −211 to +108) and pCRBluntII-TOPO::FPBs3-E (Bs3-E promoter fragment from −224 to +108), respectively, as template and Phusion DNA polymerase (Finnzymes). Fluorescently labeled PCR product of UPA20-ubm-r16 promoter DNA was generated using plasmid pCRBluntII-TOPO::FPU20-ubm-r16 (UPA20 promoter fragment from −213 to +86 containing the ubm-r16 mutation (S7) as template and Phusion DNA polymerase (Finnzymes). Plasmids pCRBluntII-TOPO::FPBs3, pCRBluntII-TOPO::FPBs3-E and pCRBluntII-TOPO::FPU20-ubm-r16 were sequenced, using the Thermo Sequenase Dye Primer Manual Cycle Sequencing Kit (USB) according to the manufacturer's instructions. An internal Gene Scan-500 LIZ Size Standard (Applied Biosystems) was used to determine the DNA fragment size.
    • Example 2 Identification of a TAL Repeat Unit That Binds to G Nucleotides
  • The DNA binding domain of TAL effectors is composed of tandem-arranged 34-amino acid repeat units. The amino acid sequences of the repeat units are mostly conserved, except for two adjacent highly variable residues (HVRs) at positions 12 and 13 that define DNA target specificity (Boch et al. (2009) Science 326:1509-1512; Moscou & Bogdanove (2009) Science 326:1501). Functional analysis identified HVR motifs that bind preferentially to A (NI), C(HD), T (NG, IG) or equally well to G and A (NN) (Boch et al. (2009) Science 326:1509-1512). Bioinformatic analysis revealed HVRs that in the given promoter-TAL effector interactions match specifically to G (Moscou & Bogdanove (2009) Science 326:1501). However this, analysis was based on a single (HN & NA) or two (NK) interaction sites. In our view the number of interaction sites is too low to make reliable conclusions on the HVR specificity. Yet, these HVRs can be considered as suitable candidates that may mediate specific binding to G.
  • In order to clarify the target specificity of HVRs with unknown specificity we made use of the well-characterized interaction between AvrBs3 and the UPA box in the Bs3 promoter. Using site directed mutagenesis we replaced the HVR NI in the 5th and the 6th repeat unit by NK resulting in AvrBs3-NK5/6. In the wildtype Bs3 promoter the NI residues of the 5th and the 6th repeat both match to A nucleotides. Using site-directed mutagenesis we replaced the two A nucleotides in the Bs3 promoter by two C, G and T nucleotides. The wildtype Bs3 promoter and the three promoter mutants were fused to an uidA reporter gene and tested via Agrobacterium tumefaciens transient expression in combination with either wildtype AvrBs3 or AvrBs3-NK5/6 in Nicotiana benthamiana leaves. GUS assays revealed that AvrBs3-NK5/6 activated the GUS reporter only in combination with the “GG” Bs3 promoter mutant while AvrBs3 activated only the Bs3 wildtype promoter construct.
  • Our analysis suggests that NK pairs specifically to G and thus provides an option to generate more specific repeat arrays and also to specifically target G-rich target sequences.
    • Example 3 Method for Generation of Designer Effectors via Golden Gate Cloning
  • The DNA binding domain of TAL effectors is composed of tandem-arranged 34-amino acid repeat units. The amino acid sequences of the repeat units are mostly conserved, except for two adjacent highly variable residues (HVRs) at positions 12 and 13 that define DNA target specificity (Boch et al. (2009) Science 326:1509-1512; Moscou & Bogdanove (2009) Science 326:1501). Different HVR motifs bind with different levels of specificity to individual A, C, G or T nucleotides. Importantly, statistical analysis suggests that tandem arranged repeat units do not to interfere with the specificity of adjacent units (Moscou & Bogdanove (2009) Science 326:1501). Thus modular assembly of repeat units with pre-characterized specificities is likely to provide an efficient way for generation of DNA-recognition modules with desired DNA specificity.
  • However, the generation of DNA constructs that encode desired repeat domains is challenging due to the fact that the repeat units are almost identical. In the past we have used chemical synthesis to generate effectors genes that encode 17.5 repeat units with the desired HVR composition. To maximize the differences between repeat units at the DNA level we exploited the degeneracy of the genetic code. The codon-optimized sequence of the 17.5 repeat unit encoding DNA sequence was, in contrast to the corresponding TAL effector wildtype gene, PCR-amplifiable and amenable to PCR-based mutagenesis. Our findings also demonstrate that chemical synthesis of effector repeat domains is generally feasible. However, chemical synthesis does not allow rapid and cost-efficient generation of multiple effectors with desired HVR composition. Furthermore this approach will most likely not allow generation of repeat domains with 20 or more repeat units.
  • The recently developed “Golden-Gate cloning” provides an alternative approach for generation of repeat unit arrays of desired composition. The strategy is based on the use of type IIS restriction enzymes, which cut outside of their recognition sequence. We will work with the type IIS enzyme BsaI, which creates a 4-bp sticky end. Due to the fact, that recognition and cleavage site are separated in type IIS enzymes we can generate by BsaI restriction in principle 256 (44) different sticky ends which provides the basis for multi fragment ligations. With proper design of the cleavage sites, two or more fragments cut by type IIS restriction enzymes can be ligated into a product lacking the original restriction site (Engler et al. (2008) PLoS ONE 3:e3647; Engler et al. (2009) PLoS ONE 4:e5553).
  • However in practice there are two limitations to this method. Due to exonuclease activity in some reactions, single stranded overhanging DNA sticky ends are reduced from four to three bases, effectively making the number of compatible sticky ends only 16 (24). Secondly, the efficiency of the ligation reactions decreases precipitously with large numbers of inserts, such as would be needed to create an effector with 17.5 repeat units as typically found in naturally occurring functional TAL effectors. To circumvent these limitations, we have designed a two-stage ligation process that allows the effective production of effectors of 20, 30, 40 or more repeat units.
  • The basis for our “repeat-array building kit” is a set of “insert plasmids” that contain individual repeat units (one repeat unit per plasmid), “intermediate vectors” that contain repeat domains consisting of sets of 10 repeat units, and one “acceptor vector” that contains the N- and C-terminal non-repeat region of a TAL effector. All repeat units are designed in such a way that the BsaI recognition sites flank the insert in the insert plasmids.
  • To simplify the explanation of the multi-fragment ligation we define herein the different ends of the repeat unit genes with upper case letters (instead of the sequence overhang of the sticky end) and indicate their orientation (N- or C-terminus of the repeat unit) with N or C in square brackets (e.g. A[C]). The insert plasmid containing the 1st repeat unit gene is designed in such a way that BsaI treatment creates A[N] and B[C] termini. The 2nd repeatunit gene has B[N] and C[C] termini upon BsaI cleavage, while BsaI cleavage of the insert plasmid with the 3rd repeat unit gene results in C[N] and D[C] termini, and so on. Since only compatible ends can be fused, the B[C] terminus of the 1st repeat unit gene will fuse specifically to the B[N] terminus of the 2nd repeat unit gene. Similarly the C[C] terminus of the 2nd repeat unit gene will ligate specifically to the C[N] terminus of the 3rd repeat unit gene and so on.
  • BsaI digestion releases the repeat units with 4-bp sticky overhangs that are compatible only with the designed adjacent repeat units. The BsaI recognition site itself remains in the cleaved insert plasmid vector and the released insert has no BsaI recognition site. The repeat units are joined together in the order specified by the overhanging ends in a cut-ligation reaction (cleavage and ligation running simultaneously). Due to the simultaneous action of BsaI and ligase the religation of repeat units into the insert donor vector is avoided since this restores the BsaI recognition site. By contrast the desired ligation products lack the BsaI recognition sites. This experimental design makes this cloning procedure highly efficient.
  • To generate effectors that are designed to recognize specific base sequences, four variants are made for each repeat unit position. These variants are individual repeat units with specific nucleotide recognition specificity, (e.g. HD residues at position 12 and 13 for recognition of a C base, NI for A, and so on). The variant for each position is made with the appropriate sticky ends for each repeat unit, for example A[N] and B[C] termini for repeat unit 1, such that there are four possible insert plasmids for repeat unit one, chosen based on the desired DNA recognition. There are four variants for repeat unit 2, with different nucleotide recognition specificity and B[N] and C[C] termini, and so on for each repeat position
  • Ligations are carried out in two stages. In the first stage, 10 repeat units are combined into an intermediate vector. Different sets of 10 repeat units can be combined in intermediate vectors. Intermediate vector 1 contains repeat units 1-10, intermediate vector 2 contains repeat units 11-20 and so on. In the second stage, separately assembled 10 repeat units are combined into acceptor vectors. The acceptor vector also contains the N- and C-terminal non-repeat areas of the effector, such that a complete effector comprised of 10, 20, 30 40 or other multiples of 10 repeat units is assembled in the final construct. The intermediate vector has BsaI sites in the insert for introducing the 10 repeat unit fragments and also has flanking BpiI sites in the flanking vector sequence. BpiI is another type IIS enzyme with a recognition site distinct from BsaI. Using BsaI, the 10 repeat units are first assembled into the “intermediate vector” and using BpiI the assembled 10 mers are released as one fragment. This fragment is ligated in a BpiI cut-ligase reaction with the acceptor vector, which contains BpiI sites between the N- and C-terminal non-repeat areas of the TAL effector. In this case only 2-4 inserts are ligated into the acceptor vector. This allows to make each ligation highly specific and to assemble easily 40 and more repeat units.
  • The acceptor vector in which the repeat unit array is finally cloned, represents a GATEWAY Entry clone and thus allows recombination-based transfer of the effector into any desired expression construct. Currently the acceptor vector is designed to generate a TAL-type transcription factor. However, with few modifications the acceptor vector allows also fusions of the repeat array to the FokI endonuclease or other desired functional domains.
  • A schematic of this method is provided in FIG. 19A-D.
    • Example 4 Production and Testing of Target DNA-Specific Nucleases
  • Fusion proteins comprising a repeat domain of the invention that recognizes a target DNA sequence and a FokI nuclease (“TAL-type-nucleases”) are produced as described by any of the method disclosed herein or known in the art. The fusion proteins are tested for nuclease activity by incubation with corresponding target DNA. The repeat domain DNA target site is cloned into the multiple cloning site of a plasmid vector (e.g., bluescript). As negative controls, either an “empty vector” that contains no TAL-nuclease target site or cloned target sites with mutations are used. Before treatment of the DNA substrate with the TAL-type nuclease, the vector is linearized by treatment with a suitable standard endonuclease that cleaves in the vector backbone. This linearized vector is incubated with in vitro generated repeat domain-FokI nuclease fusion proteins and the products analyzed by agarose gel electrophoresis. The detection of two DNA fragments in gel electrophoresis is indicative for specific nuclease mediated cleavage. By contrast, the negative controls that do not contain a target site that is recognized by repeat domain are unaffected by treatment with the repeat domain-FokI nuclease fusion protein. DNA-driven, cell-free systems for in vitro gene expression and protein synthesis are used to generate repeat domain-FokI nuclease fusion proteins (e.g. T7 High-Yield Protein Expression System; Promega). To use such systems, repeat domain-FokI nuclease fusion protein nucleotide sequences are cloned in front of a T7 RNA polymerase. Such fusion proteins that are produced via in vitro transcription and translation are used in DNA cleavage assays without further purification.
    • Example 5 Determination of Additional Recognition Specificites
  • Further experiments were conducted essentially as described hereinabove to determine the recognition specificities of additional amino acid pairs in the hypervariable region. DNA binding domains were constructed using Golden Gate Cloning as described in Example 3. The experiments conducted and the experimental results obtained are provided in FIGS. 20-27 and their respective figure legends.
  • From these experiments, the recognition specificity for the amino acids found at positions 12 and 13 in a repeat unit and the base pair in the target DNA sequence were determined for the following amino acid pairs:
      • NH for recognition of G/C
      • NP for recognition of A/T or C/G or T/A
      • NT for recognition of A/T or G/C
      • HN for recognition of A/T or G/C
      • SH for recognition of G/C
      • SN for recognition of G/C and
      • IS for recognition of A/T.
  • It is recognized that the recognition specificities set forth in this Example can be used in the methods of the present invention. It is further recognized that the recognition specificities set forth in this Example can be used to produce compositions of the present invention, such as, for example, polypeptides and DNA. Preferably, the recognition specificities set forth in this Example are used in such methods or to produce such compositions in combination with any of the other recognition specificities disclosed herein.
  • The article “a” and “an” are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one or more element.
  • Throughout the specification the word “comprising,” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.
  • All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. Additionally, each of the following patent applications is hereby herein incorporated referenced in its entirety: DE 10 2009 004 659.3 filed Jan. 12, 2009, EP 09165328 filed Jul. 13, 2009, and U.S. 61/225,043 filed Jul. 13, 2009.
  • Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.

Claims (53)

1. A method for producing a polypeptide that selectively recognizes at least one base pair in a target DNA sequence, the method comprising synthesizing a polypeptide comprising a repeat domain, wherein the repeat domain comprises at least one repeat unit derived from a transcription activator-like (TAL) effector, wherein the repeat unit comprises a hypervariable region which determines recognition of a base pair in the target DNA sequence, wherein the repeat unit is responsible for the recognition of one base pair in the DNA sequence, and wherein the hypervariable region comprises a member selected from the group consisting of:
(a) HD for recognition of C/G;
(b) NI for recognition of A/T;
(c) NG for recognition of T/A;
(d) NS for recognition of C/G or A/T or T/A or G/C;
(e) NN for recognition of G/C or A/T;
(f) IG for recognition of T/A;
(g) N for recognition of C/G or T/A;
(h) HG for recognition of C/G or T/A;
(i) H for recognition of T/A;
(j) NK for recognition of G/C;
(k) NH for recognition of G/C;
(l) NP for recognition of A/T or C/G or T/A;
(m) NT for recognition of A/T or G/C;
(n) HN for recognition of A/T or G/C;
(o) SH for recognition of G/C;
(p) SN for recognition of G/C; and
(q) IS for recognition of A/T;
wherein the repeat domain comprises at least one repeat unit which comprises a hypervariable region comprising (k), (l), (m), (n), (o), (p), or (q).
2. (canceled)
3. The method of claim 1, wherein the hypervariable region corresponds to amino acids 12 and 13 in the repeat unit.
4. The method of claim 1, wherein the repeat domain comprises 1.5 to 40.5 repeat units.
5. The method of claim 1, wherein the repeat domain comprises 11.5 to 33.5 repeat units.
6. The method of claim 1, wherein the polypeptide further comprises at least one additional domain that is operably linked to the repeat domain.
7. The method of claim 6, wherein the additional domain comprises a bacterial, viral, fungal, oomycete, human, animal, plant, or artificial protein, or part thereof.
8. The method of claim 6, wherein the additional domain comprises a protein or functional part or domain thereof, that is capable of modifying DNA or RNA.
9. The method of claim 6, wherein the additional domain comprises a protein or functional part or domain thereof selected from the group consisting of: a transcription activator, a transcription repressor, a resistance-mediating protein, a nuclease, a topoisomerase, a ligase, an integrase, a recombinase, a resolvase, a methylase, an acetylase, a demethylase, and a deacetylase.
10. The method of claim 1, wherein the repeat domain of the polypeptide is synthesized by expressing a DNA sequence encoding the polypeptide and where the DNA sequence encoding the polypeptide is assembled by preassembling the repeat units in one or more target vectors that can subsequently be assembled into a final vector comprising the DNA sequence encoding the polypeptide.
11. The method of claim 1, wherein the repeat unit comprises 30 to 40 amino acids.
12. The method of claim 11, wherein the repeat unit comprises 33, 34, 35 or 39 amino acids.
13. The method of claim 1, wherein the polypeptide recognizes at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 base pairs in the target DNA sequence.
14. The method of claim 13, wherein the polypeptide recognizes all of the base pairs in the target DNA sequence.
15. The method of claim 13, wherein the polypeptide is capable of binding to the target DNA sequence.
16. A polypeptide produced by the method of claim 1.
17. The polypeptide of claim 16, wherein the polypeptide is not naturally occurring.
18. A polynucleotide molecule comprising a coding sequence for the polypeptide produced by the method of claim 1.
19. The polynucleotide molecule of claim 18, wherein the polynucleotide molecule is not naturally occurring.
20. An expression cassette comprising a promoter operably linked to the polynucleotide molecule of claim 18.
21. A non-human host cell comprising the expression cassette of claim 20.
22. The host cell of claim 21, wherein the host cell is a bacterial cell, a fungal cell, an animal cell, or a plant cell.
23. A transformed, non-human organism comprising the expression cassette of claim 20.
24. The transformed organism of claim 23, wherein the organism is a fungus, an animal, or a plant.
25. A method for selectively recognizing a base pair in a DNA sequence by a polypeptide, the method comprising constructing a polypeptide comprising a repeat domain, wherein the repeat domain comprises at least one repeat unit derived from a TAL effector, wherein the repeat unit comprises a hypervariable region which determines recognition of a base pair in the DNA sequence, wherein the repeat unit is responsible for the recognition of one base pair in the DNA sequence, and wherein the hypervariable region comprises a member selected from the group consisting of:
(a) HD for recognition of C/G;
(b) NI for recognition of A/T;
(c) NG for recognition of T/A;
(d) NS for recognition of C/G or A/T or T/A or G/C;
(e) NN for recognition of G/C or A/T;
(f) IG for recognition of T/A;
(g) N for recognition of C/G or T/A;
(h) HG for recognition of C/G or T/A;
(i) H for recognition of T/A;
(j) NK for recognition of G/C;
(k) NH for recognition of G/C;
(l) NP for recognition of A/T or C/G or T/A;
(m) NT for recognition of A/T or G/C;
(n) HN for recognition of A/T or G/C;
(o) SH for recognition of G/C;
(p) SN for recognition of G/C; and
(q) IS for recognition of A/T;
wherein the repeat domain comprises at least one repeat unit which comprises a hypervariable region comprising (k), (l), (m), (n), (o), (p), or (q).
26. (canceled)
27. The method of claim 25, wherein the hypervariable region corresponds to amino acids 12 and 13 in the repeat unit.
28. The method of claim 25, wherein the repeat domain comprises 1.5 to 40.5 repeat units.
29. The method of claim 25, wherein the repeat domain comprises 11.5 to 33.5 repeat units.
30. The method of claim 25, wherein the polypeptide further comprises at one additional domain that is operably linked to the repeat domain.
31. The method of claim 25, wherein the repeat unit comprises 30 to 40 amino acids.
32. The method of claim 31, wherein the repeat unit comprises 33, 34, 35 or 39 amino acids.
33. The method of claim 25, wherein the repeat domain comprising repeat units is inserted in a bacterial, viral, fungal, oomycete, human, animal or plant polypeptide to achieve a targeted recognition and preferably binding of one or more specified base pairs in a DNA sequence, and optionally wherein the repeat unit is derived from the repeat domains of AvrBs3-like effectors which are further optionally modified in order to obtain a pre-selected specific activity to one or more base pairs in a DNA sequence.
34. The method of claim 25, wherein the repeat domain comprising the repeat unit is contained in a polypeptide controlling the transcription of a gene, optionally in transcription activator or repressor proteins, optionally in AvrBs3-like proteins, e.g. in AvrBs3 or Hax effector proteins.
35. The method of claim 25, wherein the N-terminal region of a repeat domain confers a recognition specificity for a T/A 5′ of the recognition specificity of the repeat unit.
36. The method of claim 25, wherein the base pair in the DNA sequence is inserted into an expression control element combined with a gene, the expression control element being targeted by a transcription control protein comprising the hypervariable region in the repeat unit recognizing the base pair located in the expression control element to specifically control the expression of the gene, wherein the expression control element is preferably a promoter.
37. The method of claim 36, wherein the gene is a resistance mediating gene in order to obtain a disease resistant organism, the expression control element being optionally the target sequence for an AvrBs3-like effector protein.
38. A method of modulating expression of a target gene in a cell, wherein cells are provided which contain a polypeptide wherein the polypeptide comprises a repeat domain, wherein the repeat domain comprises at least one repeat unit derived from a TAL effector, wherein the repeat unit comprises a hypervariable region which determines recognition of a base pair in a DNA sequence, wherein the repeat unit is responsible for the recognition of one base pair in the DNA sequence, and wherein the hypervariable region comprises a member selected from the group consisting of:
(a) HD for recognition of C/G;
(b) NI for recognition of A/T;
(c) NG for recognition of T/A;
(d) NS for recognition of C/G or A/T or T/A or G/C;
(e) NN for recognition of G/C or A/T;
(f) IG for recognition of T/A;
(g) N for recognition of C/G or T/A;
(h) HG for recognition of C/G or T/A;
(i) H for recognition of T/A;
(j) NK for recognition of G/C;
(k) NH for recognition of G/C;
(l) NP for recognition of A/T or C/G or T/A;
(m) NT for recognition of A/T or G/C;
(n) HN for recognition of A/T or G/C;
(o) SH for recognition of G/C;
(p) SN for recognition of G/C; and
(q) IS for recognition of A/T;
wherein the repeat domain comprises at least one repeat unit which comprises a hypervariable region comprising (k), (l), (m), (n), (o), (p), or (q).
39. (canceled)
40. A polypeptide comprising a repeat domain, wherein the repeat domain comprises at least one repeat unit derived from a TAL effector, wherein the repeat unit comprises a hypervariable region which determines recognition of a base pair in a DNA sequence, wherein the repeat unit is responsible for the recognition of one base pair in the DNA sequence, and wherein the hypervariable region comprises a member selected from the group consisting of:
(a) HD for recognition of C/G;
(b) NI for recognition of A/T;
(c) NG for recognition of T/A;
(d) NS for recognition of C/G or A/T or T/A or G/C;
(e) NN for recognition of G/C or A/T;
(f) IG for recognition of T/A;
(g) N for recognition of C/G or T/A;
(h) HG for recognition of C/G or T/A;
(i) H for recognition of T/A;
(j) NK for recognition of G/C;
(k) NH for recognition of G/C;
(l) NP for recognition of A/T or C/G or T/A;
(m) NT for recognition of A/T or G/C;
(n) HN for recognition of A/T or G/C;
(o) SH for recognition of G/C;
(p) SN for recognition of G/C; and
(q) IS for recognition of A/T;
wherein the repeat domain comprises at least one repeat unit which comprises a hypervariable region comprising (k), (l), (m), (n), (o), (p), or (q).
41. (canceled)
42. A polynucleotide molecule comprising a coding sequence for the polypeptide of claim 40.
43. A DNA which is modified to include a at least one base pair located in a target DNA sequence so that the base pair can be specifically recognized by a polypeptide comprising a repeat domain, wherein the repeat domain comprises at least one repeat unit derived from a TAL effector, wherein the repeat unit comprises a hypervariable region which determines recognition of a base pair in the DNA sequence, wherein the repeat unit is responsible for the recognition of one base pair in the DNA sequence, and wherein the base pair is selected from the group consisting of:
(a) G/C for recognition of NH;
(b) A/T or C/G or T/A for recognition of NP;
(c) A/T or G/C for recognition of NT;
(d) A/T or G/C for recognition of HN;
(e) G/C for recognition of SH;
(f) G/C for recognition of SN; and
(g) A/T for recognition of IS.
44. The DNA of claim 43, wherein at least one additional base pair is selected from the group consisting of:
(h) C/G for recognition by HD;
(i) A/T for recognition by NI;
(j) T/A for recognition by NG;
(k) CT or A/T or T/A or G/C for recognition by NS;
(l) G/C or A/T for recognition by NN;
(m) T/A for recognition by IG;
(n) C/G or T/A for recognition by N;
(o) T/A for recognition by HG;
(p) T/A for recognition by H; and
(q) G/C for recognition by NK.
45. The DNA of claim 43, wherein the base pair is located in a promoter or other gene regulatory sequence.
46. The DNA of claim 43, wherein the DNA is not naturally occurring.
47. A vector comprising the DNA of claim 43.
48. A non-human host cell comprising the DNA of claim 43.
49. The host cell of claim 43, wherein the host cell is a bacterial cell, a fungal cell, an animal cell, or a plant cell.
50. A transformed, non-human organism comprising the DNA of claim 43.
51. The transformed organism of claim 50, wherein the organism is a fungus, an animal, or a plant.
52. A method for producing a DNA comprising a target DNA sequence that is selectively recognized by a polypeptide comprising a repeat domain, wherein the repeat domain comprises at least one repeat unit derived from a TAL effector, wherein the repeat unit comprises a hypervariable region which determines recognition of a base pair in the target DNA sequence, wherein the repeat unit is responsible for the recognition of one base pair in the target DNA sequence, the method comprising synthesizing a DNA comprising a base pair that is capable of being recognized by the repeat unit, and wherein the base pair is selected from the group consisting of:
(a) C/G for recognition by HD;
(b) A/T for recognition by NI;
(c) T/A for recognition by NG;
(d) CT or A/T or T/A or G/C for recognition by NS;
(e) G/C or A/T for recognition by NN;
(f) T/A for recognition by IG;
(g) C/G or T/A for recognition by N;
(h) T/A for recognition by HG;
(i) T/A for recognition by H;
(j) G/C for recognition by NK;
(k) G/C for recognition of NH;
(l) A/T or C/G or T/A for recognition of NP;
(m) A/T or G/C for recognition of NT;
(n) A/T or G/C for recognition of HN;
(o) G/C for recognition of SH;
(p) G/C for recognition of SN; and
(q) A/T for recognition of IS and
wherein the repeat domain comprises at least one repeat unit which comprises a hypervariable region comprising at least one member selected from the group consisting of
(i) NH for recognition of G/C;
(ii) NP for recognition of A/T or C/G or T/A;
(iii) NT for recognition of A/T or G/C;
(iv) HN for recognition of A/T or G/C;
(v) SH for recognition of G/C;
(vi) SN for recognition of G/C; and
(vii) IS for recognition of A/T.
53. (canceled)
US13/019,526 2009-01-12 2011-02-02 Modular dna-binding domains and methods of use Abandoned US20110239315A1 (en)

Priority Applications (9)

Application Number Priority Date Filing Date Title
US13/019,526 US20110239315A1 (en) 2009-01-12 2011-02-02 Modular dna-binding domains and methods of use
US13/218,050 US8470973B2 (en) 2009-01-12 2011-08-25 Modular DNA-binding domains and methods of use
PCT/IB2012/000373 WO2012104729A1 (en) 2011-02-02 2012-02-02 Modular dna-binding domains and methods of use
US13/755,826 US20130217119A1 (en) 2009-01-12 2013-01-31 Modular dna-binding domains and methods of use
US14/153,241 US9017967B2 (en) 2009-01-12 2014-01-13 Modular DNA-binding domains and methods of use
US14/625,698 US9453054B2 (en) 2009-01-12 2015-02-19 Modular DNA-binding domains and methods of use
US15/222,498 US9809628B2 (en) 2009-01-12 2016-07-28 Modular DNA-binding domains and methods of use
US15/724,420 US10590175B2 (en) 2009-01-12 2017-10-04 Modular DNA-binding domains and methods of use
US16/781,646 US11827676B2 (en) 2009-01-12 2020-02-04 Modular DNA-binding domains and methods of use

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
DE102009004659 2009-01-12
DE102009004659.3 2009-01-12
US22504309P 2009-07-13 2009-07-13
EP09165328 2009-07-13
EP09165328A EP2206723A1 (en) 2009-01-12 2009-07-13 Modular DNA-binding domains
PCT/IB2010/000154 WO2010079430A1 (en) 2009-01-12 2010-01-12 Modular dna-binding domains and methods of use
US13/016,297 US9353378B2 (en) 2009-01-12 2011-01-28 Modular DNA-binding domains and methods of use
US13/019,526 US20110239315A1 (en) 2009-01-12 2011-02-02 Modular dna-binding domains and methods of use

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
US13/016,297 Continuation-In-Part US9353378B2 (en) 2009-01-12 2011-01-28 Modular DNA-binding domains and methods of use

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US13/218,050 Continuation US8470973B2 (en) 2009-01-12 2011-08-25 Modular DNA-binding domains and methods of use
US13/755,826 Continuation US20130217119A1 (en) 2009-01-12 2013-01-31 Modular dna-binding domains and methods of use

Publications (1)

Publication Number Publication Date
US20110239315A1 true US20110239315A1 (en) 2011-09-29

Family

ID=45894600

Family Applications (8)

Application Number Title Priority Date Filing Date
US13/019,526 Abandoned US20110239315A1 (en) 2009-01-12 2011-02-02 Modular dna-binding domains and methods of use
US13/218,050 Active US8470973B2 (en) 2009-01-12 2011-08-25 Modular DNA-binding domains and methods of use
US13/755,826 Abandoned US20130217119A1 (en) 2009-01-12 2013-01-31 Modular dna-binding domains and methods of use
US14/153,241 Active US9017967B2 (en) 2009-01-12 2014-01-13 Modular DNA-binding domains and methods of use
US14/625,698 Active US9453054B2 (en) 2009-01-12 2015-02-19 Modular DNA-binding domains and methods of use
US15/222,498 Active US9809628B2 (en) 2009-01-12 2016-07-28 Modular DNA-binding domains and methods of use
US15/724,420 Active US10590175B2 (en) 2009-01-12 2017-10-04 Modular DNA-binding domains and methods of use
US16/781,646 Active 2032-02-17 US11827676B2 (en) 2009-01-12 2020-02-04 Modular DNA-binding domains and methods of use

Family Applications After (7)

Application Number Title Priority Date Filing Date
US13/218,050 Active US8470973B2 (en) 2009-01-12 2011-08-25 Modular DNA-binding domains and methods of use
US13/755,826 Abandoned US20130217119A1 (en) 2009-01-12 2013-01-31 Modular dna-binding domains and methods of use
US14/153,241 Active US9017967B2 (en) 2009-01-12 2014-01-13 Modular DNA-binding domains and methods of use
US14/625,698 Active US9453054B2 (en) 2009-01-12 2015-02-19 Modular DNA-binding domains and methods of use
US15/222,498 Active US9809628B2 (en) 2009-01-12 2016-07-28 Modular DNA-binding domains and methods of use
US15/724,420 Active US10590175B2 (en) 2009-01-12 2017-10-04 Modular DNA-binding domains and methods of use
US16/781,646 Active 2032-02-17 US11827676B2 (en) 2009-01-12 2020-02-04 Modular DNA-binding domains and methods of use

Country Status (2)

Country Link
US (8) US20110239315A1 (en)
WO (1) WO2012104729A1 (en)

Cited By (115)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20110145940A1 (en) * 2009-12-10 2011-06-16 Voytas Daniel F Tal effector-mediated dna modification
US8450107B1 (en) 2011-11-30 2013-05-28 The Broad Institute Inc. Nucleotide-specific recognition sequences for designer TAL effectors
WO2013113911A3 (en) * 2012-02-02 2013-10-03 Ludwig-Maximilians-Universität München Nucleotide sequences involved in plant pest resistance
WO2013163394A1 (en) 2012-04-25 2013-10-31 Regeneron Pharmaceuticals, Inc. Nuclease-mediated targeting with large targeting vectors
WO2013166315A1 (en) 2012-05-02 2013-11-07 Dow Agrosciences Llc Targeted modification of malate dehydrogenase
WO2013169802A1 (en) 2012-05-07 2013-11-14 Sangamo Biosciences, Inc. Methods and compositions for nuclease-mediated targeted integration of transgenes
WO2013136175A3 (en) * 2012-03-15 2013-11-21 Cellectis Repeat variable diresidues for targeting nucleotides
WO2014039702A2 (en) 2012-09-07 2014-03-13 Dow Agrosciences Llc Fad2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
WO2014071219A1 (en) 2012-11-01 2014-05-08 Factor Bioscience Inc. Methods and products for expressing proteins in cells
WO2014165612A2 (en) 2013-04-05 2014-10-09 Dow Agrosciences Llc Methods and compositions for integration of an exogenous sequence within the genome of plants
US20150037809A1 (en) * 2012-03-23 2015-02-05 Cellectis, S.A. Method to overcome dna chemical modifications sensitivity of engineered tale dna binding domains
WO2015052335A1 (en) * 2013-10-11 2015-04-16 Cellectis Methods and kits for detecting nucleic acid sequences of interest using dna-binding protein domain
WO2015066638A2 (en) 2013-11-04 2015-05-07 Dow Agrosciences Llc Optimal maize loci
WO2015066636A2 (en) 2013-11-04 2015-05-07 Dow Agrosciences Llc Optimal maize loci
WO2015066643A1 (en) 2013-11-04 2015-05-07 Dow Agrosciences Llc Optimal soybean loci
WO2015088643A1 (en) 2013-12-11 2015-06-18 Regeneron Pharmaceuticals, Inc. Methods and compositions for the targeted modification of a genome
US20150167010A1 (en) * 2013-03-15 2015-06-18 Monsanto Technology, Llc Methods for targeted transgene-integration using custom site-specific dna recombinases
WO2015089375A1 (en) 2013-12-13 2015-06-18 The General Hospital Corporation Soluble high molecular weight (hmw) tau species and applications thereof
WO2015130931A1 (en) 2014-02-28 2015-09-03 Dow Agrosciences Llc Root specific expression conferred by chimeric gene regulatory elements
WO2015188109A1 (en) 2014-06-06 2015-12-10 Regeneron Pharmaceuticals, Inc. Methods and compositions for modifying a targeted locus
WO2015200805A2 (en) 2014-06-26 2015-12-30 Regeneron Pharmaceuticals, Inc. Methods and compositions for targeted genetic modifications and methods of use
WO2016005449A1 (en) 2014-07-08 2016-01-14 Vib Vzw Means and methods to increase plant yield
US9279816B2 (en) 2012-11-15 2016-03-08 Board Of Trustees Of The University Of Arkansas Methods and kits for isolation and analysis of a chromatin region
WO2016061374A1 (en) 2014-10-15 2016-04-21 Regeneron Pharmaceuticals, Inc. Methods and compositions for generating or maintaining pluripotent cells
US20160186151A1 (en) * 2013-08-09 2016-06-30 Hiroshima University Polypeptide Containing DNA-Binding Domain
US9422577B2 (en) 2011-12-05 2016-08-23 Factor Bioscience Inc. Methods and products for transfecting cells
WO2016168229A1 (en) 2015-04-15 2016-10-20 Dow Agrosciences Llc Plant promoter for transgene expression
WO2016168230A2 (en) 2015-04-15 2016-10-20 Dow Agrosciences Llc Plant promoter for transgene expression
US9506915B2 (en) 2012-11-15 2016-11-29 Board Of Trustees Of The University Of Arkansas Methods and kits for isolation and analysis of a chromatin region
WO2017053164A1 (en) 2015-09-22 2017-03-30 Dow Agrosciences Llc Plant promoter and 3' utr for transgene expression
WO2017070298A1 (en) 2015-10-22 2017-04-27 Dow Agrosciences Llc Plant promoter for transgene expression
WO2017078935A1 (en) 2015-11-04 2017-05-11 Dow Agrosciences Llc Plant promoter for transgene expression
US9708589B2 (en) 2012-12-18 2017-07-18 Monsanto Technology Llc Compositions and methods for custom site-specific DNA recombinases
US9770489B2 (en) 2014-01-31 2017-09-26 Factor Bioscience Inc. Methods and products for nucleic acid production and delivery
WO2017180180A2 (en) 2015-09-22 2017-10-19 Dow Agrosciences Llc Plant promoter and 3' utr for transgene expression
US9822372B2 (en) 2012-12-12 2017-11-21 The Broad Institute Inc. CRISPR-Cas component systems, methods and compositions for sequence manipulation
WO2018023014A1 (en) 2016-07-29 2018-02-01 Regeneron Pharmaceuticals, Inc. Mice comprising mutations resulting in expression of c-truncated fibrillin-1
WO2018029034A1 (en) 2016-08-09 2018-02-15 Vib Vzw Cellulose synthase inhibitors and mutant plants
WO2018035377A1 (en) 2016-08-17 2018-02-22 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
US9914930B2 (en) 2012-09-07 2018-03-13 Dow Agrosciences Llc FAD3 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US9937207B2 (en) 2013-03-21 2018-04-10 Sangamo Therapeutics, Inc. Targeted disruption of T cell receptor genes using talens
WO2018067265A1 (en) 2016-10-03 2018-04-12 Dow Agrosciences Llc Plant promoter for transgene expression
WO2018067264A1 (en) 2016-10-03 2018-04-12 Dow Agrosciences Llc Plant promoter for transgene expression
US10006011B2 (en) 2013-08-09 2018-06-26 Hiroshima University Polypeptide containing DNA-binding domain
WO2018136758A1 (en) 2017-01-23 2018-07-26 Regeneron Pharmaceuticals, Inc. Hsd17b13 variants and uses thereof
EP3354732A1 (en) 2014-06-23 2018-08-01 Regeneron Pharmaceuticals, Inc. Nuclease-mediated dna assembly
US10113162B2 (en) 2013-03-15 2018-10-30 Cellectis Modifying soybean oil composition through targeted knockout of the FAD2-1A/1B genes
WO2018226560A1 (en) 2017-06-05 2018-12-13 Regeneron Pharmaceuticals, Inc. B4galt1 variants and uses thereof
GB201820109D0 (en) 2018-12-11 2019-01-23 Vib Vzw Plants with a lignin trait and udp-glycosyltransferase mutation
WO2019043082A1 (en) 2017-08-29 2019-03-07 Kws Saat Se Improved blue aleurone and other segregation systems
US10233465B2 (en) 2013-11-04 2019-03-19 Dow Agrosciences Llc Optimal soybean loci
EP3456831A1 (en) 2013-04-16 2019-03-20 Regeneron Pharmaceuticals, Inc. Targeted modification of rat genome
EP3460063A1 (en) 2013-12-11 2019-03-27 Regeneron Pharmaceuticals, Inc. Methods and compositions for the targeted modification of a genome
WO2019067875A1 (en) 2017-09-29 2019-04-04 Regeneron Pharmaceuticals, Inc. Non-human animals comprising a humanized ttr locus and methods of use
US10301637B2 (en) 2014-06-20 2019-05-28 Cellectis Potatoes with reduced granule-bound starch synthase
US10377998B2 (en) 2013-12-12 2019-08-13 The Broad Institute, Inc. CRISPR-CAS systems and methods for altering expression of gene products, structural information and inducible modular CAS enzymes
EP3543339A1 (en) 2015-02-13 2019-09-25 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
EP3561050A1 (en) 2013-02-20 2019-10-30 Regeneron Pharmaceuticals, Inc. Genetic modification of rats
US10494621B2 (en) 2015-06-18 2019-12-03 The Broad Institute, Inc. Crispr enzyme mutations reducing off-target effects
US10501404B1 (en) 2019-07-30 2019-12-10 Factor Bioscience Inc. Cationic lipids and transfection methods
WO2019236943A2 (en) 2018-06-07 2019-12-12 The Brigham And Women's Hospital, Inc. Methods for generating hematopoietic stem cells
WO2019234141A1 (en) 2018-06-06 2019-12-12 Vib Vzw NOVEL MUTANT PLANT CINNAMOYL-CoA REDUCTASE PROTEINS
US10513698B2 (en) 2012-12-21 2019-12-24 Cellectis Potatoes with reduced cold-induced sweetening
US10550372B2 (en) 2013-12-12 2020-02-04 The Broad Institute, Inc. Systems, methods and compositions for sequence manipulation with optimized functional CRISPR-Cas systems
US10550402B2 (en) 2016-02-02 2020-02-04 Cellectis Modifying soybean oil composition through targeted knockout of the FAD3A/B/C genes
US10577630B2 (en) 2013-06-17 2020-03-03 The Broad Institute, Inc. Delivery and use of the CRISPR-Cas systems, vectors and compositions for hepatic targeting and therapy
EP3653048A1 (en) 2014-12-19 2020-05-20 Regeneron Pharmaceuticals, Inc. Methods and compositions for targeted genetic modification through single-step multiple targeting
WO2020123377A1 (en) 2018-12-10 2020-06-18 Neoimmunetech, Inc. Nrf-2 deficient cells and uses thereof
WO2020131632A1 (en) 2018-12-20 2020-06-25 Regeneron Pharmaceuticals, Inc. Nuclease-mediated repeat expansion
US10696986B2 (en) 2014-12-12 2020-06-30 The Board Institute, Inc. Protected guide RNAS (PGRNAS)
US10711285B2 (en) 2013-06-17 2020-07-14 The Broad Institute, Inc. Optimized CRISPR-Cas double nickase systems, methods and compositions for sequence manipulation
US10774338B2 (en) 2014-01-16 2020-09-15 The Regents Of The University Of California Generation of heritable chimeric plant traits
US10781444B2 (en) 2013-06-17 2020-09-22 The Broad Institute, Inc. Functional genomics using CRISPR-Cas systems, compositions, methods, screens and applications thereof
WO2020206134A1 (en) 2019-04-04 2020-10-08 Regeneron Pharmaceuticals, Inc. Methods for scarless introduction of targeted modifications into targeting vectors
WO2020206139A1 (en) 2019-04-04 2020-10-08 Regeneron Pharmaceuticals, Inc. Non-human animals comprising a humanized coagulation factor 12 locus
WO2020206162A1 (en) 2019-04-03 2020-10-08 Regeneron Pharmaceuticals, Inc. Methods and compositions for insertion of antibody coding sequences into a safe harbor locus
US10801017B2 (en) 2011-11-30 2020-10-13 The Broad Institute, Inc. Nucleotide-specific recognition sequences for designer TAL effectors
US10837024B2 (en) 2015-09-17 2020-11-17 Cellectis Modifying messenger RNA stability in plant transformations
US10851357B2 (en) 2013-12-12 2020-12-01 The Broad Institute, Inc. Compositions and methods of use of CRISPR-Cas systems in nucleotide repeat disorders
WO2020247452A1 (en) 2019-06-04 2020-12-10 Regeneron Pharmaceuticals, Inc. Non-human animals comprising a humanized ttr locus with a beta-slip mutation and methods of use
WO2020247812A1 (en) 2019-06-07 2020-12-10 Regeneron Pharmaceuticals, Inc. Non-human animals comprising a humanized albumin locus
WO2020252340A1 (en) 2019-06-14 2020-12-17 Regeneron Pharmaceuticals, Inc. Models of tauopathy
US10930367B2 (en) 2012-12-12 2021-02-23 The Broad Institute, Inc. Methods, models, systems, and apparatus for identifying target sequences for Cas enzymes or CRISPR-Cas systems for target sequences and conveying results thereof
US10946108B2 (en) 2013-06-17 2021-03-16 The Broad Institute, Inc. Delivery, use and therapeutic applications of the CRISPR-Cas systems and compositions for targeting disorders and diseases using viral components
WO2021092513A1 (en) 2019-11-08 2021-05-14 Regeneron Pharmaceuticals, Inc. Crispr and aav strategies for x-linked juvenile retinoschisis therapy
US11008588B2 (en) 2013-06-17 2021-05-18 The Broad Institute, Inc. Delivery, engineering and optimization of tandem guide systems, methods and compositions for sequence manipulation
WO2021108363A1 (en) 2019-11-25 2021-06-03 Regeneron Pharmaceuticals, Inc. Crispr/cas-mediated upregulation of humanized ttr allele
US11041173B2 (en) 2012-12-12 2021-06-22 The Broad Institute, Inc. Delivery, engineering and optimization of systems, methods and compositions for sequence manipulation and therapeutic applications
US11039586B2 (en) 2013-03-15 2021-06-22 Monsanto Technology Llc Creation and transmission of megaloci
WO2021178556A1 (en) 2020-03-04 2021-09-10 Regeneron Pharmaceuticals, Inc. Methods and compositions for sensitization of tumor cells to immune therapy
US11149267B2 (en) 2013-10-28 2021-10-19 The Broad Institute, Inc. Functional genomics using CRISPR-Cas systems, compositions, methods, screens and applications thereof
US11155795B2 (en) 2013-12-12 2021-10-26 The Broad Institute, Inc. CRISPR-Cas systems, crystal structure and uses thereof
US11312972B2 (en) 2016-11-16 2022-04-26 Cellectis Methods for altering amino acid content in plants through frameshift mutations
US11322225B2 (en) * 2018-08-08 2022-05-03 Deep Genomics Incorporated Systems and methods for determining effects of therapies and genetic variation on polyadenylation site selection
US11384360B2 (en) 2012-06-19 2022-07-12 Regents Of The University Of Minnesota Gene targeting in plants using DNA viruses
US11407985B2 (en) 2013-12-12 2022-08-09 The Broad Institute, Inc. Delivery, use and therapeutic applications of the CRISPR-Cas systems and compositions for genome editing
US11466306B2 (en) 2013-02-14 2022-10-11 Osaka University Method for isolating specific genomic regions with use of molecule capable of specifically binding to endogenous DNA sequence
US11479782B2 (en) 2017-04-25 2022-10-25 Cellectis Alfalfa with reduced lignin composition
WO2022240846A1 (en) 2021-05-10 2022-11-17 Sqz Biotechnologies Company Methods for delivering genome editing molecules to the nucleus or cytosol of a cell and uses thereof
WO2022251644A1 (en) 2021-05-28 2022-12-01 Lyell Immunopharma, Inc. Nr4a3-deficient immune cells and uses thereof
WO2022256437A1 (en) 2021-06-02 2022-12-08 Lyell Immunopharma, Inc. Nr4a3-deficient immune cells and uses thereof
US11555198B2 (en) 2012-11-01 2023-01-17 Cellectis Sa Method for making nicotiana plants with mutations in XylT and FucT alleles using rare-cutting endonucleases
US11578312B2 (en) 2015-06-18 2023-02-14 The Broad Institute Inc. Engineering and optimization of systems, methods, enzymes and guide scaffolds of CAS9 orthologs and variants for sequence manipulation
WO2023064924A1 (en) 2021-10-14 2023-04-20 Codiak Biosciences, Inc. Modified producer cells for extracellular vesicle production
WO2023081923A1 (en) 2021-11-08 2023-05-11 Frequency Therapeutics, Inc. Platelet-derived growth factor receptor (pdgfr) alpha inhibitors and uses thereof
WO2023129974A1 (en) 2021-12-29 2023-07-06 Bristol-Myers Squibb Company Generation of landing pad cell lines
WO2023131637A1 (en) 2022-01-06 2023-07-13 Vib Vzw Improved silage grasses
WO2023131616A1 (en) 2022-01-05 2023-07-13 Vib Vzw Means and methods to increase abiotic stress tolerance in plants
WO2023144199A1 (en) 2022-01-26 2023-08-03 Vib Vzw Plants having reduced levels of bitter taste metabolites
WO2023220603A1 (en) 2022-05-09 2023-11-16 Regeneron Pharmaceuticals, Inc. Vectors and methods for in vivo antibody production
WO2023225665A1 (en) 2022-05-19 2023-11-23 Lyell Immunopharma, Inc. Polynucleotides targeting nr4a3 and uses thereof
WO2024026474A1 (en) 2022-07-29 2024-02-01 Regeneron Pharmaceuticals, Inc. Compositions and methods for transferrin receptor (tfr)-mediated delivery to the brain and muscle
WO2024031053A1 (en) 2022-08-05 2024-02-08 Regeneron Pharmaceuticals, Inc. Aggregation-resistant variants of tdp-43
WO2024064958A1 (en) 2022-09-23 2024-03-28 Lyell Immunopharma, Inc. Methods for culturing nr4a-deficient cells
WO2024064952A1 (en) 2022-09-23 2024-03-28 Lyell Immunopharma, Inc. Methods for culturing nr4a-deficient cells overexpressing c-jun

Families Citing this family (71)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10920242B2 (en) 2011-02-25 2021-02-16 Recombinetics, Inc. Non-meiotic allele introgression
US9458205B2 (en) 2011-11-16 2016-10-04 Sangamo Biosciences, Inc. Modified DNA-binding proteins and uses thereof
WO2013160230A1 (en) 2012-04-23 2013-10-31 Bayer Cropscience Nv Targeted genome engineering in plants
SI24177A (en) 2012-09-20 2014-03-31 Kemijski inštitut Bistable switching genetically switch with a pair of cross-žing repressors and a positive feedback loop on the basis of DNA-binding proteins
US9957515B2 (en) 2013-03-15 2018-05-01 Cibus Us Llc Methods and compositions for targeted gene modification
AU2014247151A1 (en) 2013-04-02 2015-10-08 Bayer Cropscience Nv Targeted genome engineering in eukaryotes
CA2942407C (en) 2014-03-14 2023-09-26 Cibus Us Llc Methods and compositions for increasing efficiency of targeted gene modification using oligonucleotide-mediated gene repair
US9522936B2 (en) 2014-04-24 2016-12-20 Sangamo Biosciences, Inc. Engineered transcription activator like effector (TALE) proteins
CN113337533A (en) 2014-12-23 2021-09-03 先正达参股股份有限公司 Methods and compositions for identifying and enriching cells comprising site-specific genomic modifications
PL3064587T3 (en) 2015-03-06 2020-03-31 Leibniz-Institut Für Pflanzenbiochemie (Ipb) Library of synthetic promoters for coordinated gene expression in eukaryotic cells or organisms
MX2018008106A (en) 2015-12-30 2019-03-14 Novartis Ag Immune effector cell therapies with enhanced efficacy.
EA201891629A1 (en) 2016-02-09 2019-03-29 Сибас Юс Ллс METHODS AND COMPOSITIONS FOR IMPROVING THE EFFICIENCY OF TARGETED MODIFICATION OF GENES WITH THE APPLICATION OF MEDIATED OLIGONUCLEOTIDE REPAIR GENES
BR112018074101A2 (en) 2016-05-26 2019-03-06 Nunhems Bv seedless fruit plants
US20190309274A1 (en) 2016-08-16 2019-10-10 Bluebird Bio, Inc. Il-10 receptor alpha homing endonuclease variants, compositions, and methods of use
MA46059A (en) 2016-08-23 2019-07-03 Bluebird Bio Inc HOMING TIM3 ENDONUCLEASE VARIANTS, COMPOSITIONS AND METHODS FOR USE
EP4248979A3 (en) 2016-09-08 2023-12-20 2seventy bio, Inc. Pd-1 homing endonuclease variants, compositions, and methods of use
WO2018064387A1 (en) 2016-09-28 2018-04-05 Novartis Ag Porous membrane-based macromolecule delivery system
WO2018071565A1 (en) 2016-10-11 2018-04-19 Bluebird Bio, Inc. TCRa HOMING ENDONUCLEASE VARIANTS
GB201617559D0 (en) 2016-10-17 2016-11-30 University Court Of The University Of Edinburgh The Swine comprising modified cd163 and associated methods
CA3040157A1 (en) 2016-10-17 2018-04-26 Bluebird Bio, Inc. Tgf.beta.r2 endonuclease variants, compositions, and methods of use
WO2018083606A1 (en) 2016-11-01 2018-05-11 Novartis Ag Methods and compositions for enhancing gene editing
JP6948718B2 (en) 2016-11-28 2021-10-13 国立大学法人大阪大学 Genome editing method
US11278570B2 (en) 2016-12-16 2022-03-22 B-Mogen Biotechnologies, Inc. Enhanced hAT family transposon-mediated gene transfer and associated compositions, systems, and methods
CN110730821B (en) 2016-12-16 2023-12-08 比莫根生物科技公司 Enhanced hAT family transposon mediated gene transfer and related compositions, systems and methods
DK3583203T3 (en) 2017-02-15 2024-01-02 2Seventy Bio Inc DONOR REPAIR TEMPLATES MULTIPLEX GENOMEDIATION
US20200048359A1 (en) 2017-02-28 2020-02-13 Novartis Ag Shp inhibitor compositions and uses for chimeric antigen receptor therapy
BR112019018124A2 (en) 2017-03-22 2020-04-07 Intellia Therapeutics Inc compositions and methods for immunooncology
EP3615055A1 (en) 2017-04-28 2020-03-04 Novartis AG Cells expressing a bcma-targeting chimeric antigen receptor, and combination therapy with a gamma secretase inhibitor
US20200179511A1 (en) 2017-04-28 2020-06-11 Novartis Ag Bcma-targeting agent, and combination therapy with a gamma secretase inhibitor
US20210147818A1 (en) 2017-05-25 2021-05-20 Bluebird Bio, Inc. Cblb endonuclease variants, compositions, and methods of use
US20200362355A1 (en) 2017-06-15 2020-11-19 The Regents Of The University Of California Targeted non-viral dna insertions
EP3645721A1 (en) 2017-06-30 2020-05-06 Novartis AG Methods for the treatment of disease with gene editing systems
WO2019070974A1 (en) 2017-10-04 2019-04-11 Bluebird Bio, Inc. Pcsk9 endonuclease variants, compositions, and methods of use
EA202091056A1 (en) 2017-10-27 2020-09-17 Те Риджентс Оф Те Юниверсити Оф Калифорния TARGETED REPLACEMENT OF ENDOGENIC T-CELL RECEPTORS
EP3501268B1 (en) 2017-12-22 2021-09-15 KWS SAAT SE & Co. KGaA Regeneration of plants in the presence of histone deacetylase inhibitors
EP3508581A1 (en) 2018-01-03 2019-07-10 Kws Saat Se Regeneration of genetically modified plants
CN111566121A (en) 2018-01-12 2020-08-21 巴斯夫欧洲公司 Gene for determining number of spikelets per ear QTL on wheat 7a chromosome
EP3545756A1 (en) 2018-03-28 2019-10-02 KWS SAAT SE & Co. KGaA Regeneration of plants in the presence of inhibitors of the histone methyltransferase ezh2
CA3097648A1 (en) * 2018-04-18 2019-10-24 Altius Institute For Biomedical Sciences Animal pathogen-derived polypeptides and uses thereof for genetic engineering
US20210047405A1 (en) 2018-04-27 2021-02-18 Novartis Ag Car t cell therapies with enhanced efficacy
EP3567111A1 (en) 2018-05-09 2019-11-13 KWS SAAT SE & Co. KGaA Gene for resistance to a pathogen of the genus heterodera
EP3802825A1 (en) 2018-06-08 2021-04-14 Intellia Therapeutics, Inc. Compositions and methods for immunooncology
WO2019238908A1 (en) 2018-06-15 2019-12-19 KWS SAAT SE & Co. KGaA Methods for enhancing genome engineering efficiency
US20220025388A1 (en) 2018-06-15 2022-01-27 KWS SAAT SE & Co. KGaA Methods for improving genome engineering and regeneration in plant
EP3806619A1 (en) 2018-06-15 2021-04-21 Nunhems B.V. Seedless watermelon plants comprising modifications in an abc transporter gene
WO2019238911A1 (en) 2018-06-15 2019-12-19 KWS SAAT SE & Co. KGaA Methods for improving genome engineering and regeneration in plant ii
WO2019246486A2 (en) 2018-06-21 2019-12-26 B-Mogen Biotechnologies, Inc. ENHANCED hAT FAMILY TRANSPOSON-MEDIATED GENE TRANSFER AND ASSOCIATED COMPOSITIONS, SYSTEMS, AND METHODS
EP3814493A4 (en) * 2018-06-27 2022-03-30 Altius Institute For Biomedical Sciences Nucleic acid binding domains and methods of use thereof
EP3623379A1 (en) 2018-09-11 2020-03-18 KWS SAAT SE & Co. KGaA Beet necrotic yellow vein virus (bnyvv)-resistance modifying gene
JP7288915B2 (en) 2018-10-04 2023-06-08 株式会社カネカ DNA constructs used for plant genome editing
WO2020072059A1 (en) 2018-10-04 2020-04-09 Bluebird Bio, Inc. Cblb endonuclease variants, compositions, and methods of use
EP3918080A1 (en) 2019-01-29 2021-12-08 The University Of Warwick Methods for enhancing genome engineering efficiency
EP3708651A1 (en) 2019-03-12 2020-09-16 KWS SAAT SE & Co. KGaA Improving plant regeneration
CN113646429A (en) 2019-04-05 2021-11-12 国立大学法人大阪大学 Method for producing knock-in cell
EP3757219A1 (en) 2019-06-28 2020-12-30 KWS SAAT SE & Co. KGaA Enhanced plant regeneration and transformation by using grf1 booster gene
EP4010004A4 (en) * 2019-08-07 2023-09-13 Altius Institute For Biomedical Sciences Compositions and methods for modulation of gene expression
CN115335528A (en) 2019-11-12 2022-11-11 科沃施种子欧洲股份两合公司 Cyst nematode pathogen resistance genes
JPWO2021095847A1 (en) 2019-11-14 2021-05-20
JP7448120B2 (en) 2019-11-14 2024-03-12 国立研究開発法人農業・食品産業技術総合研究機構 Method for introducing genome editing enzymes into plant cells using plasma
KR20220093189A (en) * 2019-12-03 2022-07-05 노오쓰웨스턴유니버시티 Modular cell-free protein expression vectors to accelerate biological design in cells
IL293517A (en) 2019-12-24 2022-08-01 Selexis Sa Targeted integration in mammalian sequences enhancing gene expression
JPWO2021193865A1 (en) 2020-03-26 2021-09-30
CA3173889A1 (en) 2020-05-04 2021-11-11 Saliogen Therapeutics, Inc. Transposition-based therapies
US20230332104A1 (en) 2020-06-11 2023-10-19 Novartis Ag Zbtb32 inhibitors and uses thereof
WO2022097663A1 (en) 2020-11-06 2022-05-12 エディットフォース株式会社 Foki nuclease domain variant
EP4019638A1 (en) 2020-12-22 2022-06-29 KWS SAAT SE & Co. KGaA Promoting regeneration and transformation in beta vulgaris
EP4019639A1 (en) 2020-12-22 2022-06-29 KWS SAAT SE & Co. KGaA Promoting regeneration and transformation in beta vulgaris
WO2023042104A1 (en) 2021-09-16 2023-03-23 Novartis Ag Novel transcription factors
WO2023095034A1 (en) 2021-11-24 2023-06-01 Novartis Ag Modulators of adeno-associated virus transduction and uses thereof
GB202118058D0 (en) 2021-12-14 2022-01-26 Univ Warwick Methods to increase yields in crops
GB2621813A (en) 2022-06-30 2024-02-28 Univ Newcastle Preventing disease recurrence in Mitochondrial replacement therapy

Citations (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5436150A (en) * 1992-04-03 1995-07-25 The Johns Hopkins University Functional domains in flavobacterium okeanokoities (foki) restriction endonuclease
US5487994A (en) * 1992-04-03 1996-01-30 The Johns Hopkins University Insertion and deletion mutants of FokI restriction endonuclease
US5792640A (en) * 1992-04-03 1998-08-11 The Johns Hopkins University General method to clone hybrid restriction endonucleases using lig gene
US6326166B1 (en) * 1995-12-29 2001-12-04 Massachusetts Institute Of Technology Chimeric DNA-binding proteins
US6368227B1 (en) * 2000-11-17 2002-04-09 Steven Olson Method of swinging on a swing
US20110129898A1 (en) * 2009-05-18 2011-06-02 Yannick Doyon Methods and compositions for increasing nuclease activity
US20110136895A1 (en) * 2007-09-27 2011-06-09 Sangamo Biosciences, Inc. Methods and compositions for modulating PD1
US20110145940A1 (en) * 2009-12-10 2011-06-16 Voytas Daniel F Tal effector-mediated dna modification
US20110158957A1 (en) * 2009-11-10 2011-06-30 Sangamo Biosciences, Inc. Targeted disruption of T cell receptor genes using engineered zinc finger protein nucleases
US20110167521A1 (en) * 2009-10-22 2011-07-07 Dow Agrosciences Llc Engineered zinc finger proteins targeting plant genes involved in fatty acid biosynthesis
US20110203012A1 (en) * 2010-01-21 2011-08-18 Dotson Stanton B Methods and compositions for use of directed recombination in plant breeding
US20110201118A1 (en) * 2010-06-14 2011-08-18 Iowa State University Research Foundation, Inc. Nuclease activity of tal effector and foki fusion protein
US20110201055A1 (en) * 2010-02-08 2011-08-18 Yannick Doyon Engineered cleavage half-domains

Family Cites Families (81)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US697953A (en) 1901-09-04 1902-04-15 Robert w scott Knitting-machine.
US4179337A (en) 1973-07-20 1979-12-18 Davis Frank F Non-immunogenic polypeptides
US4535060A (en) 1983-01-05 1985-08-13 Calgene, Inc. Inhibition resistant 5-enolpyruvyl-3-phosphoshikimate synthetase, production and use
US5380831A (en) 1986-04-04 1995-01-10 Mycogen Plant Science, Inc. Synthetic insecticidal crystal protein gene
US4761373A (en) 1984-03-06 1988-08-02 Molecular Genetics, Inc. Herbicide resistance in plants
US4683195A (en) 1986-01-30 1987-07-28 Cetus Corporation Process for amplifying, detecting, and/or-cloning nucleic acid sequences
US5569597A (en) 1985-05-13 1996-10-29 Ciba Geigy Corp. Methods of inserting viral DNA into plant material
US4940835A (en) 1985-10-29 1990-07-10 Monsanto Company Glyphosate-resistant plants
CA1293460C (en) 1985-10-07 1991-12-24 Brian Lee Sauer Site-specific recombination of dna in yeast
US4810648A (en) 1986-01-08 1989-03-07 Rhone Poulenc Agrochimie Haloarylnitrile degrading gene, its use, and cells containing the gene
EP0242236B2 (en) 1986-03-11 1996-08-21 Plant Genetic Systems N.V. Plant cells resistant to glutamine synthetase inhibitors, made by genetic engineering
US4975374A (en) 1986-03-18 1990-12-04 The General Hospital Corporation Expression of wild type and mutant glutamine synthetase in foreign hosts
US5273894A (en) 1986-08-23 1993-12-28 Hoechst Aktiengesellschaft Phosphinothricin-resistance gene, and its use
US5276268A (en) 1986-08-23 1994-01-04 Hoechst Aktiengesellschaft Phosphinothricin-resistance gene, and its use
US5013659A (en) 1987-07-27 1991-05-07 E. I. Du Pont De Nemours And Company Nucleic acid fragment encoding herbicide resistant plant acetolactate synthase
US5268463A (en) 1986-11-11 1993-12-07 Jefferson Richard A Plant promoter α-glucuronidase gene construct
US5608142A (en) 1986-12-03 1997-03-04 Agracetus, Inc. Insecticidal cotton plants
US4873192A (en) 1987-02-17 1989-10-10 The United States Of America As Represented By The Department Of Health And Human Services Process for site specific mutagenesis without phenotypic selection
US5006333A (en) 1987-08-03 1991-04-09 Ddi Pharmaceuticals, Inc. Conjugates of superoxide dismutase coupled to high molecular weight polyalkylene glycols
US5316931A (en) 1988-02-26 1994-05-31 Biosource Genetics Corp. Plant viral vectors having heterologous subgenomic promoters for systemic expression of foreign genes
US5162602A (en) 1988-11-10 1992-11-10 Regents Of The University Of Minnesota Corn plants tolerant to sethoxydim and haloxyfop herbicides
US5501967A (en) 1989-07-26 1996-03-26 Mogen International, N.V./Rijksuniversiteit Te Leiden Process for the site-directed integration of DNA into the genome of plants
US5484956A (en) 1990-01-22 1996-01-16 Dekalb Genetics Corporation Fertile transgenic Zea mays plant comprising heterologous DNA encoding Bacillus thuringiensis endotoxin
DE69133128T2 (en) 1990-04-12 2003-06-18 Syngenta Participations Ag Tissue-specific promoters
US5204253A (en) 1990-05-29 1993-04-20 E. I. Du Pont De Nemours And Company Method and apparatus for introducing biological substances into living cells
US5498830A (en) 1990-06-18 1996-03-12 Monsanto Company Decreased oil content in plant seeds
US5767366A (en) 1991-02-19 1998-06-16 Louisiana State University Board Of Supervisors, A Governing Body Of Louisiana State University Agricultural And Mechanical College Mutant acetolactate synthase gene from Ararbidopsis thaliana for conferring imidazolinone resistance to crop plants
US5399680A (en) 1991-05-22 1995-03-21 The Salk Institute For Biological Studies Rice chitinase promoter
AU2515592A (en) 1991-08-23 1993-03-16 University Of Florida A novel method for the production of transgenic plants
ES2140416T3 (en) 1991-08-27 2000-03-01 Novartis Ag PROTEINS WITH INSECTICIDED PROPERTIES AGAINST HOMOPTERIC INSECTS AND THEIR USE IN PLANT PROTECTION.
CA2112999C (en) 1991-10-04 2007-04-24 Mark A. Conkling Pathogen-resistant transgenic plants
TW261517B (en) 1991-11-29 1995-11-01 Mitsubishi Shozi Kk
US5356802A (en) 1992-04-03 1994-10-18 The Johns Hopkins University Functional domains in flavobacterium okeanokoites (FokI) restriction endonuclease
US5591616A (en) 1992-07-07 1997-01-07 Japan Tobacco, Inc. Method for transforming monocotyledons
IL108241A (en) 1992-12-30 2000-08-13 Biosource Genetics Corp Plant expression system comprising a defective tobamovirus replicon integrated into the plant chromosome and a helper virus
ATE513037T1 (en) 1993-02-12 2011-07-15 Univ Johns Hopkins FUNCTIONAL DOMAIN OF THE RESTRICTION ENDONUCLEASES FROM FLAVOBACTERIUM OKEANOKOITES (FOKI)
US5789156A (en) 1993-06-14 1998-08-04 Basf Ag Tetracycline-regulated transcriptional inhibitors
US5814618A (en) 1993-06-14 1998-09-29 Basf Aktiengesellschaft Methods for regulating gene expression
US5837458A (en) 1994-02-17 1998-11-17 Maxygen, Inc. Methods and compositions for cellular and metabolic engineering
US5605793A (en) 1994-02-17 1997-02-25 Affymax Technologies N.V. Methods for in vitro recombination
US6808904B2 (en) 1994-06-16 2004-10-26 Syngenta Participations Ag Herbicide-tolerant protox genes produced by DNA shuffling
US5608144A (en) 1994-08-12 1997-03-04 Dna Plant Technology Corp. Plant group 2 promoters and uses thereof
US7285416B2 (en) 2000-01-24 2007-10-23 Gendaq Limited Regulated gene expression in plants
US5659026A (en) 1995-03-24 1997-08-19 Pioneer Hi-Bred International ALS3 promoter
US5853973A (en) 1995-04-20 1998-12-29 American Cyanamid Company Structure based designed herbicide resistant products
US6084155A (en) 1995-06-06 2000-07-04 Novartis Ag Herbicide-tolerant protoporphyrinogen oxidase ("protox") genes
JPH10117776A (en) 1996-10-22 1998-05-12 Japan Tobacco Inc Transformation of indica rice
CA2315549A1 (en) 1998-02-26 1999-09-02 Pioneer Hi-Bred International, Inc. Family of maize pr-1 genes and promoters
ATE342985T1 (en) 1998-02-26 2006-11-15 Pioneer Hi Bred Int CORN ALPHA-TUBULIN 3-18 PROMOTER
GB9819693D0 (en) 1998-09-10 1998-11-04 Zeneca Ltd Glyphosate formulation
US7013219B2 (en) 1999-01-12 2006-03-14 Sangamo Biosciences, Inc. Regulation of endogenous gene expression in cells using zinc finger proteins
US7070934B2 (en) 1999-01-12 2006-07-04 Sangamo Biosciences, Inc. Ligand-controlled regulation of endogenous gene expression
US6534261B1 (en) 1999-01-12 2003-03-18 Sangamo Biosciences, Inc. Regulation of endogenous gene expression in cells using zinc finger proteins
EP1147209A2 (en) 1999-02-03 2001-10-24 The Children's Medical Center Corporation Gene repair involving the induction of double-stranded dna cleavage at a chromosomal target site
US6451732B1 (en) 1999-06-04 2002-09-17 Syngenta, Limited Herbicidal compositions of glyphosate trimesium
CA2407460C (en) 2000-04-28 2013-06-25 Sangamo Biosciences, Inc. Targeted modification of chromatin structure
US9234187B2 (en) 2001-01-22 2016-01-12 Sangamo Biosciences, Inc. Modified zinc finger binding proteins
US7262054B2 (en) 2002-01-22 2007-08-28 Sangamo Biosciences, Inc. Zinc finger proteins for DNA binding and gene regulation in plants
WO2009095742A1 (en) 2008-01-31 2009-08-06 Cellectis New i-crei derived single-chain meganuclease and uses thereof
ATE531796T1 (en) 2002-03-21 2011-11-15 Sangamo Biosciences Inc METHODS AND COMPOSITIONS FOR USING ZINC FINGER ENDONUCLEASES TO IMPROVE HOMOLOGOUS RECOMBINATION
US7361635B2 (en) 2002-08-29 2008-04-22 Sangamo Biosciences, Inc. Simultaneous modulation of multiple genes
EP1590453B1 (en) 2003-01-28 2013-11-27 Cellectis Custom-made meganuclease and use thereof
US7888121B2 (en) 2003-08-08 2011-02-15 Sangamo Biosciences, Inc. Methods and compositions for targeted cleavage and recombination
US7189691B2 (en) 2004-04-01 2007-03-13 The Administrators Of The Tulane Educational Fund Methods and compositions for treating leukemia
WO2007060495A1 (en) 2005-10-25 2007-05-31 Cellectis I-crei homing endonuclease variants having novel cleavage specificity and use thereof
WO2008010009A1 (en) 2006-07-18 2008-01-24 Cellectis Meganuclease variants cleaving a dna target sequence from a rag gene and uses thereof
EP2235050A1 (en) 2007-09-28 2010-10-06 Two Blades Foundation Bs3 resistance gene and methods of use
AU2009313275B2 (en) 2008-11-10 2015-08-20 Two Blades Foundation Pathogen-inducible promoters and their use in enhancing the disease resistance of plants
US9206404B2 (en) 2008-12-04 2015-12-08 Sangamo Biosciences, Inc. Method of deleting an IgM gene in an isolated rat cell
EP2206723A1 (en) 2009-01-12 2010-07-14 Bonas, Ulla Modular DNA-binding domains
WO2011002503A1 (en) 2009-06-30 2011-01-06 Sangamo Biosciences, Inc. Rapid screening of biologically active nucleases and isolation of nuclease-modified cells
US20120178647A1 (en) 2009-08-03 2012-07-12 The General Hospital Corporation Engineering of zinc finger arrays by context-dependent assembly
US8586526B2 (en) 2010-05-17 2013-11-19 Sangamo Biosciences, Inc. DNA-binding proteins and uses thereof
JP5940977B2 (en) 2009-08-11 2016-06-29 サンガモ バイオサイエンシーズ， インコーポレイテッド Homozygous organisms by targeted modification
JP2013511979A (en) 2009-11-27 2013-04-11 ビーエーエスエフ プラント サイエンス カンパニー ゲーエムベーハー Chimeric endonuclease and use thereof
CA2781693C (en) 2009-11-27 2018-12-18 Basf Plant Science Company Gmbh Chimeric endonucleases and uses thereof
BR112012012588B1 (en) 2009-11-27 2019-03-26 Basf Plant Science Company Gmbh ENDONUCLEASE, METHOD FOR HOMOLOGICAL RECOMBINATION OF POLINUCLEOTIDES AND METHOD FOR DIRECTED POLINUCLEOTIDE MUTATION
AU2011215557B2 (en) 2010-02-09 2016-03-10 Sangamo Therapeutics, Inc. Targeted genomic modification with partially single-stranded donor molecules
CA2796600C (en) 2010-04-26 2019-08-13 Sangamo Biosciences, Inc. Genome editing of a rosa locus using zinc-finger nucleases
EP2392208B1 (en) 2010-06-07 2016-05-04 Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Fusion proteins comprising a DNA-binding domain of a Tal effector protein and a non-specific cleavage domain of a restriction nuclease and their use
US9401201B1 (en) 2015-05-22 2016-07-26 Qualcomm Incorporated Write driver for memory

Patent Citations (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5436150A (en) * 1992-04-03 1995-07-25 The Johns Hopkins University Functional domains in flavobacterium okeanokoities (foki) restriction endonuclease
US5487994A (en) * 1992-04-03 1996-01-30 The Johns Hopkins University Insertion and deletion mutants of FokI restriction endonuclease
US5792640A (en) * 1992-04-03 1998-08-11 The Johns Hopkins University General method to clone hybrid restriction endonucleases using lig gene
US6326166B1 (en) * 1995-12-29 2001-12-04 Massachusetts Institute Of Technology Chimeric DNA-binding proteins
US6368227B1 (en) * 2000-11-17 2002-04-09 Steven Olson Method of swinging on a swing
US20110136895A1 (en) * 2007-09-27 2011-06-09 Sangamo Biosciences, Inc. Methods and compositions for modulating PD1
US20110129898A1 (en) * 2009-05-18 2011-06-02 Yannick Doyon Methods and compositions for increasing nuclease activity
US20110167521A1 (en) * 2009-10-22 2011-07-07 Dow Agrosciences Llc Engineered zinc finger proteins targeting plant genes involved in fatty acid biosynthesis
US20110158957A1 (en) * 2009-11-10 2011-06-30 Sangamo Biosciences, Inc. Targeted disruption of T cell receptor genes using engineered zinc finger protein nucleases
US20110145940A1 (en) * 2009-12-10 2011-06-16 Voytas Daniel F Tal effector-mediated dna modification
US20110203012A1 (en) * 2010-01-21 2011-08-18 Dotson Stanton B Methods and compositions for use of directed recombination in plant breeding
US20110201055A1 (en) * 2010-02-08 2011-08-18 Yannick Doyon Engineered cleavage half-domains
US20110201118A1 (en) * 2010-06-14 2011-08-18 Iowa State University Research Foundation, Inc. Nuclease activity of tal effector and foki fusion protein

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
Bonas et al., Resistance in tomato to Xanthomonas campestris pv vesicatoria is determined by alleles of the pepper-specific avirulence gene avrBs3; Mol Gen Genet, vol. 328, pp. 261-269, 1993 *
Kay et al., Detailed analysis of the DNA recognition motifs of the Xanthomonas type III effectors AvrBs3 and AvrBs3deltarep16; The Plant Journal, vol. 59, pp. 859-871, 2009 *
Zhu et al., AvrXa10 Contains an Acidic Transcriptional Activation Domain in the Functionally Conserved C Terminus; Molecular Plant-Microbe Interactions, vol. 11, no. 8, pp. 824-832, 1998 *

Cited By (234)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10619153B2 (en) 2009-12-10 2020-04-14 Regents Of The University Of Minnesota TAL effector-mediated DNA modification
US8586363B2 (en) 2009-12-10 2013-11-19 Regents Of The University Of Minnesota TAL effector-mediated DNA modification
US10400225B2 (en) 2009-12-10 2019-09-03 Regents Of The University Of Minnesota TAL effector-mediated DNA modification
US8697853B2 (en) 2009-12-10 2014-04-15 Regents Of The University Of Minnesota TAL effector-mediated DNA modification
US8450471B2 (en) 2009-12-10 2013-05-28 Regents Of The University Of Minnesota TAL effector-mediated DNA modification
US20110145940A1 (en) * 2009-12-10 2011-06-16 Voytas Daniel F Tal effector-mediated dna modification
US9758775B2 (en) 2009-12-10 2017-09-12 Regents Of The University Of Minnesota TAL effector-mediated DNA modification
US11274294B2 (en) 2009-12-10 2022-03-15 Regents Of The University Of Minnesota TAL effector-mediated DNA modification
US8440431B2 (en) 2009-12-10 2013-05-14 Regents Of The University Of Minnesota TAL effector-mediated DNA modification
US8440432B2 (en) 2009-12-10 2013-05-14 Regents Of The University Of Minnesota Tal effector-mediated DNA modification
WO2013082519A3 (en) * 2011-11-30 2014-09-04 The Broad Institute Inc. Nucleotide-specific recognition sequences for designer tal effectors
EP2821505A3 (en) * 2011-11-30 2015-07-08 The Broad Institute, Inc. Nucleotide-specific recognition sequences for designer tal effectors
US8507272B2 (en) 2011-11-30 2013-08-13 The Broad Institute Inc. Nucleotide-specific recognition sequences for designer TAL effectors
US8614092B2 (en) 2011-11-30 2013-12-24 The Broad Institute Inc. Nucleotide-specific recognition sequences for designer TAL effectors
US10801017B2 (en) 2011-11-30 2020-10-13 The Broad Institute, Inc. Nucleotide-specific recognition sequences for designer TAL effectors
US8481309B2 (en) 2011-11-30 2013-07-09 The Broad Institute Inc. Nucleotide-specific recognition sequences for designer TAL effectors
US8450107B1 (en) 2011-11-30 2013-05-28 The Broad Institute Inc. Nucleotide-specific recognition sequences for designer TAL effectors
EP2821413A1 (en) * 2011-11-30 2015-01-07 The Broad Institute, Inc. Nucleotide-specific recognition sequences for designer tal effectors
US11312937B2 (en) 2011-11-30 2022-04-26 The Broad Institute, Inc. Nucleotide-specific recognition sequences for designer TAL effectors
US10662410B1 (en) 2011-12-05 2020-05-26 Factor Bioscience Inc. Methods and products for transfecting cells
US9422577B2 (en) 2011-12-05 2016-08-23 Factor Bioscience Inc. Methods and products for transfecting cells
US11708586B2 (en) 2011-12-05 2023-07-25 Factor Bioscience Inc. Methods and products for transfecting cells
US11466293B2 (en) 2011-12-05 2022-10-11 Factor Bioscience Inc. Methods and products for transfecting cells
US10982229B2 (en) 2011-12-05 2021-04-20 Factor Bioscience Inc. Methods and products for transfecting cells
US10472611B2 (en) 2011-12-05 2019-11-12 Factor Bioscience Inc. Methods and products for transfecting cells
US9605277B2 (en) 2011-12-05 2017-03-28 Factor Bioscience, Inc. Methods and products for transfecting cells
US10829738B2 (en) 2011-12-05 2020-11-10 Factor Bioscience Inc. Methods and products for transfecting cells
US11692203B2 (en) 2011-12-05 2023-07-04 Factor Bioscience Inc. Methods and products for transfecting cells
US9605278B2 (en) 2011-12-05 2017-03-28 Factor Bioscience Inc. Methods and products for transfecting cells
WO2013113911A3 (en) * 2012-02-02 2013-10-03 Ludwig-Maximilians-Universität München Nucleotide sequences involved in plant pest resistance
WO2013136175A3 (en) * 2012-03-15 2013-11-21 Cellectis Repeat variable diresidues for targeting nucleotides
US11778993B2 (en) 2012-03-15 2023-10-10 Cellectis, S.A. Repeat variable diresidues for targeting nucleotides
EP3799878A3 (en) * 2012-03-15 2021-07-14 Cellectis Repeat variable diresidues for targeting nucleotides
EP3141259A3 (en) * 2012-03-15 2017-04-19 Cellectis Repeat variable diresidues for targeting nucleotides
EP3415158A3 (en) * 2012-03-15 2019-01-16 Cellectis Repeat variable diresidues for targeting nucleotides
US20150037809A1 (en) * 2012-03-23 2015-02-05 Cellectis, S.A. Method to overcome dna chemical modifications sensitivity of engineered tale dna binding domains
US20190338273A1 (en) * 2012-03-23 2019-11-07 Cellectis Method to overcome dna chemical modifications sensitivity of engineered tale dna binding domains
US10301614B2 (en) * 2012-03-23 2019-05-28 Cellectis Method to overcome DNA chemical modifications sensitivity of engineered tale DNA binding domains
US11220683B2 (en) * 2012-03-23 2022-01-11 Cellectis Method to overcome DNA chemical modifications sensitivity of engineered TALE DNA binding domains
US9834786B2 (en) 2012-04-25 2017-12-05 Regeneron Pharmaceuticals, Inc. Nuclease-mediated targeting with large targeting vectors
WO2013163394A1 (en) 2012-04-25 2013-10-31 Regeneron Pharmaceuticals, Inc. Nuclease-mediated targeting with large targeting vectors
US10301646B2 (en) 2012-04-25 2019-05-28 Regeneron Pharmaceuticals, Inc. Nuclease-mediated targeting with large targeting vectors
US11085092B2 (en) 2012-05-02 2021-08-10 Corteva Agriscience Llc Targeted modification of malate dehydrogenase
US10358684B2 (en) 2012-05-02 2019-07-23 Dow Agrosciences Llc Targeted modification of malate dehydrogenase
US9523098B2 (en) 2012-05-02 2016-12-20 Dow Agrosciences Llc Targeted modification of malate dehydrogenase
WO2013166315A1 (en) 2012-05-02 2013-11-07 Dow Agrosciences Llc Targeted modification of malate dehydrogenase
WO2013169802A1 (en) 2012-05-07 2013-11-14 Sangamo Biosciences, Inc. Methods and compositions for nuclease-mediated targeted integration of transgenes
US10174331B2 (en) 2012-05-07 2019-01-08 Sangamo Therapeutics, Inc. Methods and compositions for nuclease-mediated targeted integration of transgenes
US11384360B2 (en) 2012-06-19 2022-07-12 Regents Of The University Of Minnesota Gene targeting in plants using DNA viruses
US9914930B2 (en) 2012-09-07 2018-03-13 Dow Agrosciences Llc FAD3 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US10844389B2 (en) 2012-09-07 2020-11-24 Dow Agrosciences Llc FAD2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
WO2014039702A2 (en) 2012-09-07 2014-03-13 Dow Agrosciences Llc Fad2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US9493779B2 (en) 2012-09-07 2016-11-15 Dow Agrosciences Llc FAD2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US10961540B2 (en) 2012-09-07 2021-03-30 Dow Agrosciences Llc FAD3 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
EP3431600A1 (en) 2012-09-07 2019-01-23 Dow AgroSciences LLC Fad2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
WO2014039692A2 (en) 2012-09-07 2014-03-13 Dow Agrosciences Llc Fad2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
EP3406715A1 (en) 2012-09-07 2018-11-28 Dow AgroSciences LLC Fad3 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
EP3404099A1 (en) 2012-09-07 2018-11-21 Dow AgroSciences LLC Fad2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US10287595B2 (en) 2012-09-07 2019-05-14 Dow Agrosciences Llc Fad2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US10577616B2 (en) 2012-09-07 2020-03-03 Dow Agrosciences Llc FAD2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US9963711B2 (en) 2012-09-07 2018-05-08 Sangamo Therapeutics, Inc. FAD2 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US10526610B2 (en) 2012-09-07 2020-01-07 Dow Agrosciences Llc FAD3 performance loci and corresponding target site specific binding proteins capable of inducing targeted breaks
US9447395B2 (en) 2012-11-01 2016-09-20 Factor Bioscience Inc. Methods and products for expressing proteins in cells
WO2014071219A1 (en) 2012-11-01 2014-05-08 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US9376669B2 (en) 2012-11-01 2016-06-28 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US10752919B2 (en) 2012-11-01 2020-08-25 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US9657282B2 (en) 2012-11-01 2017-05-23 Factor Bioscience, Inc. Methods and products for expressing proteins in cells
US9487768B2 (en) 2012-11-01 2016-11-08 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US9758797B2 (en) 2012-11-01 2017-09-12 Factor Bioscience, Inc. Methods and products for expressing proteins in cells
US11339409B2 (en) 2012-11-01 2022-05-24 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US11339410B2 (en) 2012-11-01 2022-05-24 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US11555198B2 (en) 2012-11-01 2023-01-17 Cellectis Sa Method for making nicotiana plants with mutations in XylT and FucT alleles using rare-cutting endonucleases
US10752918B2 (en) 2012-11-01 2020-08-25 Factor Bioscience Inc. Methods and products for expressing proteins in cells
EP3786298A1 (en) 2012-11-01 2021-03-03 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US11332759B2 (en) 2012-11-01 2022-05-17 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US11332758B2 (en) 2012-11-01 2022-05-17 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US10590437B2 (en) 2012-11-01 2020-03-17 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US10415060B2 (en) 2012-11-01 2019-09-17 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US9464285B2 (en) 2012-11-01 2016-10-11 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US10752917B2 (en) 2012-11-01 2020-08-25 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US10724053B2 (en) 2012-11-01 2020-07-28 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US10767195B2 (en) 2012-11-01 2020-09-08 Factor Bioscience Inc. Methods and products for expressing proteins in cells
US11576317B2 (en) 2012-11-01 2023-02-14 Cellectis Sa Mutant Nicotiana benthamiana plant or cell with reduced XylT and FucT
US9863957B2 (en) 2012-11-15 2018-01-09 Bioventures, Llc Methods and kits for isolation and analysis of a chromatin region
US9279816B2 (en) 2012-11-15 2016-03-08 Board Of Trustees Of The University Of Arkansas Methods and kits for isolation and analysis of a chromatin region
US10209247B2 (en) 2012-11-15 2019-02-19 Bioventures, Llc Methods and kits for isolation and analysis of a chromatin region
US9506915B2 (en) 2012-11-15 2016-11-29 Board Of Trustees Of The University Of Arkansas Methods and kits for isolation and analysis of a chromatin region
US9822372B2 (en) 2012-12-12 2017-11-21 The Broad Institute Inc. CRISPR-Cas component systems, methods and compositions for sequence manipulation
US11041173B2 (en) 2012-12-12 2021-06-22 The Broad Institute, Inc. Delivery, engineering and optimization of systems, methods and compositions for sequence manipulation and therapeutic applications
US9840713B2 (en) 2012-12-12 2017-12-12 The Broad Institute Inc. CRISPR-Cas component systems, methods and compositions for sequence manipulation
US10930367B2 (en) 2012-12-12 2021-02-23 The Broad Institute, Inc. Methods, models, systems, and apparatus for identifying target sequences for Cas enzymes or CRISPR-Cas systems for target sequences and conveying results thereof
US10752886B2 (en) 2012-12-18 2020-08-25 Monsanto Technology Llc Compositions and methods for custom site-specific DNA recombinases
US9708589B2 (en) 2012-12-18 2017-07-18 Monsanto Technology Llc Compositions and methods for custom site-specific DNA recombinases
US10513698B2 (en) 2012-12-21 2019-12-24 Cellectis Potatoes with reduced cold-induced sweetening
US11466306B2 (en) 2013-02-14 2022-10-11 Osaka University Method for isolating specific genomic regions with use of molecule capable of specifically binding to endogenous DNA sequence
EP3561050A1 (en) 2013-02-20 2019-10-30 Regeneron Pharmaceuticals, Inc. Genetic modification of rats
US11039586B2 (en) 2013-03-15 2021-06-22 Monsanto Technology Llc Creation and transmission of megaloci
US10113162B2 (en) 2013-03-15 2018-10-30 Cellectis Modifying soybean oil composition through targeted knockout of the FAD2-1A/1B genes
US20150167010A1 (en) * 2013-03-15 2015-06-18 Monsanto Technology, Llc Methods for targeted transgene-integration using custom site-specific dna recombinases
US10793867B2 (en) * 2013-03-15 2020-10-06 Monsanto Technology, Llc Methods for targeted transgene-integration using custom site-specific DNA recombinases
US9937207B2 (en) 2013-03-21 2018-04-10 Sangamo Therapeutics, Inc. Targeted disruption of T cell receptor genes using talens
US10918668B2 (en) 2013-03-21 2021-02-16 Sangamo Therapeutics, Inc. Targeted disruption of T cell receptor genes using engineered zinc finger protein nucleases
US10501748B2 (en) 2013-04-05 2019-12-10 Dow Agrosciences Llc Methods and compositions for integration of an exogenous sequence within the genome of plants
EP3679785A2 (en) 2013-04-05 2020-07-15 Dow AgroSciences LLC Methods and compositions for integration of an exogenous sequence within the genome of plants
US11198883B2 (en) 2013-04-05 2021-12-14 Dow Agrosciences Llc Methods and compositions for integration of an exogenous sequence within the genome of plants
WO2014165612A2 (en) 2013-04-05 2014-10-09 Dow Agrosciences Llc Methods and compositions for integration of an exogenous sequence within the genome of plants
EP3456831A1 (en) 2013-04-16 2019-03-20 Regeneron Pharmaceuticals, Inc. Targeted modification of rat genome
US11597949B2 (en) 2013-06-17 2023-03-07 The Broad Institute, Inc. Optimized CRISPR-Cas double nickase systems, methods and compositions for sequence manipulation
US11008588B2 (en) 2013-06-17 2021-05-18 The Broad Institute, Inc. Delivery, engineering and optimization of tandem guide systems, methods and compositions for sequence manipulation
US10781444B2 (en) 2013-06-17 2020-09-22 The Broad Institute, Inc. Functional genomics using CRISPR-Cas systems, compositions, methods, screens and applications thereof
US10711285B2 (en) 2013-06-17 2020-07-14 The Broad Institute, Inc. Optimized CRISPR-Cas double nickase systems, methods and compositions for sequence manipulation
US10946108B2 (en) 2013-06-17 2021-03-16 The Broad Institute, Inc. Delivery, use and therapeutic applications of the CRISPR-Cas systems and compositions for targeting disorders and diseases using viral components
US10577630B2 (en) 2013-06-17 2020-03-03 The Broad Institute, Inc. Delivery and use of the CRISPR-Cas systems, vectors and compositions for hepatic targeting and therapy
US11359186B2 (en) 2013-08-09 2022-06-14 Hiroshima University Polypeptide containing DNA-binding domain
US20220389396A1 (en) * 2013-08-09 2022-12-08 Hiroshima University Polypeptide Containing DNA-Binding Domain
US20160186151A1 (en) * 2013-08-09 2016-06-30 Hiroshima University Polypeptide Containing DNA-Binding Domain
US10006011B2 (en) 2013-08-09 2018-06-26 Hiroshima University Polypeptide containing DNA-binding domain
US10030235B2 (en) * 2013-08-09 2018-07-24 Hiroshima University Polypeptide containing DNA-binding domain
WO2015052335A1 (en) * 2013-10-11 2015-04-16 Cellectis Methods and kits for detecting nucleic acid sequences of interest using dna-binding protein domain
AU2014333776B2 (en) * 2013-10-11 2021-01-28 Cellectis Methods and kits for detecting nucleic acid sequences of interest using DNA-binding protein domain
US11149267B2 (en) 2013-10-28 2021-10-19 The Broad Institute, Inc. Functional genomics using CRISPR-Cas systems, compositions, methods, screens and applications thereof
WO2015066636A2 (en) 2013-11-04 2015-05-07 Dow Agrosciences Llc Optimal maize loci
US9909131B2 (en) 2013-11-04 2018-03-06 Dow Agrosciences Llc Optimal soybean loci
US10106804B2 (en) 2013-11-04 2018-10-23 Dow Agrosciences Llc Optimal soybean loci
US11098317B2 (en) 2013-11-04 2021-08-24 Corteva Agriscience Llc Optimal maize loci
US10093940B2 (en) 2013-11-04 2018-10-09 Dow Agrosciences Llc Optimal maize loci
US10233465B2 (en) 2013-11-04 2019-03-19 Dow Agrosciences Llc Optimal soybean loci
US10273493B2 (en) 2013-11-04 2019-04-30 Dow Agrosciences Llc Optimal maize loci
US11198882B2 (en) 2013-11-04 2021-12-14 Corteva Agriscience Llc Optimal maize loci
WO2015066638A2 (en) 2013-11-04 2015-05-07 Dow Agrosciences Llc Optimal maize loci
WO2015066643A1 (en) 2013-11-04 2015-05-07 Dow Agrosciences Llc Optimal soybean loci
EP3862434A1 (en) 2013-11-04 2021-08-11 Dow AgroSciences LLC Optimal soybean loci
US11149287B2 (en) 2013-11-04 2021-10-19 Corteva Agriscience Llc Optimal soybean loci
US11098316B2 (en) 2013-11-04 2021-08-24 Corteva Agriscience Llc Optimal soybean loci
WO2015088643A1 (en) 2013-12-11 2015-06-18 Regeneron Pharmaceuticals, Inc. Methods and compositions for the targeted modification of a genome
EP3460063A1 (en) 2013-12-11 2019-03-27 Regeneron Pharmaceuticals, Inc. Methods and compositions for the targeted modification of a genome
US11155795B2 (en) 2013-12-12 2021-10-26 The Broad Institute, Inc. CRISPR-Cas systems, crystal structure and uses thereof
US11591581B2 (en) 2013-12-12 2023-02-28 The Broad Institute, Inc. Compositions and methods of use of CRISPR-Cas systems in nucleotide repeat disorders
US11597919B2 (en) 2013-12-12 2023-03-07 The Broad Institute Inc. Systems, methods and compositions for sequence manipulation with optimized functional CRISPR-Cas systems
US10851357B2 (en) 2013-12-12 2020-12-01 The Broad Institute, Inc. Compositions and methods of use of CRISPR-Cas systems in nucleotide repeat disorders
US11407985B2 (en) 2013-12-12 2022-08-09 The Broad Institute, Inc. Delivery, use and therapeutic applications of the CRISPR-Cas systems and compositions for genome editing
US10550372B2 (en) 2013-12-12 2020-02-04 The Broad Institute, Inc. Systems, methods and compositions for sequence manipulation with optimized functional CRISPR-Cas systems
US11149259B2 (en) 2013-12-12 2021-10-19 The Broad Institute, Inc. CRISPR-Cas systems and methods for altering expression of gene products, structural information and inducible modular Cas enzymes
US10377998B2 (en) 2013-12-12 2019-08-13 The Broad Institute, Inc. CRISPR-CAS systems and methods for altering expression of gene products, structural information and inducible modular CAS enzymes
WO2015089375A1 (en) 2013-12-13 2015-06-18 The General Hospital Corporation Soluble high molecular weight (hmw) tau species and applications thereof
US10774338B2 (en) 2014-01-16 2020-09-15 The Regents Of The University Of California Generation of heritable chimeric plant traits
US9770489B2 (en) 2014-01-31 2017-09-26 Factor Bioscience Inc. Methods and products for nucleic acid production and delivery
EP4249036A2 (en) 2014-01-31 2023-09-27 Factor Bioscience Inc. Methods and products for nucleic acid production and delivery
US10124042B2 (en) 2014-01-31 2018-11-13 Factor Bioscience Inc. Methods and products for nucleic acid production and delivery
EP3690056A1 (en) 2014-01-31 2020-08-05 Factor Bioscience Inc. Methods and products for nucleic acid production and delivery
WO2015130931A1 (en) 2014-02-28 2015-09-03 Dow Agrosciences Llc Root specific expression conferred by chimeric gene regulatory elements
EP3708671A1 (en) 2014-06-06 2020-09-16 Regeneron Pharmaceuticals, Inc. Methods and compositions for modifying a targeted locus
WO2015188109A1 (en) 2014-06-06 2015-12-10 Regeneron Pharmaceuticals, Inc. Methods and compositions for modifying a targeted locus
US10301637B2 (en) 2014-06-20 2019-05-28 Cellectis Potatoes with reduced granule-bound starch synthase
EP3708663A1 (en) 2014-06-23 2020-09-16 Regeneron Pharmaceuticals, Inc. Nuclease-mediated dna assembly
EP3354732A1 (en) 2014-06-23 2018-08-01 Regeneron Pharmaceuticals, Inc. Nuclease-mediated dna assembly
EP3461885A1 (en) 2014-06-26 2019-04-03 Regeneron Pharmaceuticals, Inc. Methods and compositions for targeted genetic modifications and methods of use
WO2015200805A2 (en) 2014-06-26 2015-12-30 Regeneron Pharmaceuticals, Inc. Methods and compositions for targeted genetic modifications and methods of use
WO2016005449A1 (en) 2014-07-08 2016-01-14 Vib Vzw Means and methods to increase plant yield
WO2016061374A1 (en) 2014-10-15 2016-04-21 Regeneron Pharmaceuticals, Inc. Methods and compositions for generating or maintaining pluripotent cells
EP3561052A1 (en) 2014-10-15 2019-10-30 Regeneron Pharmaceuticals, Inc. Methods and compositions for generating or maintaining pluripotent cells
US10696986B2 (en) 2014-12-12 2020-06-30 The Board Institute, Inc. Protected guide RNAS (PGRNAS)
US11624078B2 (en) 2014-12-12 2023-04-11 The Broad Institute, Inc. Protected guide RNAS (pgRNAS)
EP3653048A1 (en) 2014-12-19 2020-05-20 Regeneron Pharmaceuticals, Inc. Methods and compositions for targeted genetic modification through single-step multiple targeting
US11241505B2 (en) 2015-02-13 2022-02-08 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
EP3543339A1 (en) 2015-02-13 2019-09-25 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
WO2016168230A2 (en) 2015-04-15 2016-10-20 Dow Agrosciences Llc Plant promoter for transgene expression
WO2016168229A1 (en) 2015-04-15 2016-10-20 Dow Agrosciences Llc Plant promoter for transgene expression
US10494621B2 (en) 2015-06-18 2019-12-03 The Broad Institute, Inc. Crispr enzyme mutations reducing off-target effects
US10876100B2 (en) 2015-06-18 2020-12-29 The Broad Institute, Inc. Crispr enzyme mutations reducing off-target effects
US11578312B2 (en) 2015-06-18 2023-02-14 The Broad Institute Inc. Engineering and optimization of systems, methods, enzymes and guide scaffolds of CAS9 orthologs and variants for sequence manipulation
US10837024B2 (en) 2015-09-17 2020-11-17 Cellectis Modifying messenger RNA stability in plant transformations
WO2017180180A2 (en) 2015-09-22 2017-10-19 Dow Agrosciences Llc Plant promoter and 3' utr for transgene expression
WO2017053164A1 (en) 2015-09-22 2017-03-30 Dow Agrosciences Llc Plant promoter and 3' utr for transgene expression
WO2017070298A1 (en) 2015-10-22 2017-04-27 Dow Agrosciences Llc Plant promoter for transgene expression
WO2017078935A1 (en) 2015-11-04 2017-05-11 Dow Agrosciences Llc Plant promoter for transgene expression
US10550402B2 (en) 2016-02-02 2020-02-04 Cellectis Modifying soybean oil composition through targeted knockout of the FAD3A/B/C genes
WO2018023014A1 (en) 2016-07-29 2018-02-01 Regeneron Pharmaceuticals, Inc. Mice comprising mutations resulting in expression of c-truncated fibrillin-1
WO2018029034A1 (en) 2016-08-09 2018-02-15 Vib Vzw Cellulose synthase inhibitors and mutant plants
US10137206B2 (en) 2016-08-17 2018-11-27 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
US10888627B2 (en) 2016-08-17 2021-01-12 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
US11904023B2 (en) 2016-08-17 2024-02-20 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
US10894092B2 (en) 2016-08-17 2021-01-19 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
US10363321B2 (en) 2016-08-17 2019-07-30 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
US10350304B2 (en) 2016-08-17 2019-07-16 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
US10576167B2 (en) 2016-08-17 2020-03-03 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
WO2018035377A1 (en) 2016-08-17 2018-02-22 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
US10369233B2 (en) 2016-08-17 2019-08-06 Factor Bioscience Inc. Nucleic acid products and methods of administration thereof
WO2018067265A1 (en) 2016-10-03 2018-04-12 Dow Agrosciences Llc Plant promoter for transgene expression
WO2018067264A1 (en) 2016-10-03 2018-04-12 Dow Agrosciences Llc Plant promoter for transgene expression
US11312972B2 (en) 2016-11-16 2022-04-26 Cellectis Methods for altering amino acid content in plants through frameshift mutations
WO2018136758A1 (en) 2017-01-23 2018-07-26 Regeneron Pharmaceuticals, Inc. Hsd17b13 variants and uses thereof
US11479782B2 (en) 2017-04-25 2022-10-25 Cellectis Alfalfa with reduced lignin composition
WO2018226560A1 (en) 2017-06-05 2018-12-13 Regeneron Pharmaceuticals, Inc. B4galt1 variants and uses thereof
WO2019043082A1 (en) 2017-08-29 2019-03-07 Kws Saat Se Improved blue aleurone and other segregation systems
US11697822B2 (en) 2017-08-29 2023-07-11 KWS SAAT SE & Co. KGaA Blue aleurone and other segregation systems
EP4276185A2 (en) 2017-09-29 2023-11-15 Regeneron Pharmaceuticals, Inc. Rodents comprising a humanized ttr locus and methods of use
WO2019067875A1 (en) 2017-09-29 2019-04-04 Regeneron Pharmaceuticals, Inc. Non-human animals comprising a humanized ttr locus and methods of use
WO2019234141A1 (en) 2018-06-06 2019-12-12 Vib Vzw NOVEL MUTANT PLANT CINNAMOYL-CoA REDUCTASE PROTEINS
WO2019236943A2 (en) 2018-06-07 2019-12-12 The Brigham And Women's Hospital, Inc. Methods for generating hematopoietic stem cells
US11322225B2 (en) * 2018-08-08 2022-05-03 Deep Genomics Incorporated Systems and methods for determining effects of therapies and genetic variation on polyadenylation site selection
WO2020123377A1 (en) 2018-12-10 2020-06-18 Neoimmunetech, Inc. Nrf-2 deficient cells and uses thereof
GB201820109D0 (en) 2018-12-11 2019-01-23 Vib Vzw Plants with a lignin trait and udp-glycosyltransferase mutation
WO2020131632A1 (en) 2018-12-20 2020-06-25 Regeneron Pharmaceuticals, Inc. Nuclease-mediated repeat expansion
WO2020206162A1 (en) 2019-04-03 2020-10-08 Regeneron Pharmaceuticals, Inc. Methods and compositions for insertion of antibody coding sequences into a safe harbor locus
WO2020206139A1 (en) 2019-04-04 2020-10-08 Regeneron Pharmaceuticals, Inc. Non-human animals comprising a humanized coagulation factor 12 locus
WO2020206134A1 (en) 2019-04-04 2020-10-08 Regeneron Pharmaceuticals, Inc. Methods for scarless introduction of targeted modifications into targeting vectors
WO2020247452A1 (en) 2019-06-04 2020-12-10 Regeneron Pharmaceuticals, Inc. Non-human animals comprising a humanized ttr locus with a beta-slip mutation and methods of use
WO2020247812A1 (en) 2019-06-07 2020-12-10 Regeneron Pharmaceuticals, Inc. Non-human animals comprising a humanized albumin locus
WO2020252340A1 (en) 2019-06-14 2020-12-17 Regeneron Pharmaceuticals, Inc. Models of tauopathy
US10611722B1 (en) 2019-07-30 2020-04-07 Factor Bioscience Inc. Cationic lipids and transfection methods
US11242311B2 (en) 2019-07-30 2022-02-08 Factor Bioscience Inc. Cationic lipids and transfection methods
US11814333B2 (en) 2019-07-30 2023-11-14 Factor Bioscience Inc. Cationic lipids and transfection methods
US10501404B1 (en) 2019-07-30 2019-12-10 Factor Bioscience Inc. Cationic lipids and transfection methods
US10556855B1 (en) 2019-07-30 2020-02-11 Factor Bioscience Inc. Cationic lipids and transfection methods
US10752576B1 (en) 2019-07-30 2020-08-25 Factor Bioscience Inc. Cationic lipids and transfection methods
WO2021092513A1 (en) 2019-11-08 2021-05-14 Regeneron Pharmaceuticals, Inc. Crispr and aav strategies for x-linked juvenile retinoschisis therapy
WO2021108363A1 (en) 2019-11-25 2021-06-03 Regeneron Pharmaceuticals, Inc. Crispr/cas-mediated upregulation of humanized ttr allele
WO2021178556A1 (en) 2020-03-04 2021-09-10 Regeneron Pharmaceuticals, Inc. Methods and compositions for sensitization of tumor cells to immune therapy
WO2022240846A1 (en) 2021-05-10 2022-11-17 Sqz Biotechnologies Company Methods for delivering genome editing molecules to the nucleus or cytosol of a cell and uses thereof
WO2022251644A1 (en) 2021-05-28 2022-12-01 Lyell Immunopharma, Inc. Nr4a3-deficient immune cells and uses thereof
WO2022256437A1 (en) 2021-06-02 2022-12-08 Lyell Immunopharma, Inc. Nr4a3-deficient immune cells and uses thereof
WO2023064924A1 (en) 2021-10-14 2023-04-20 Codiak Biosciences, Inc. Modified producer cells for extracellular vesicle production
WO2023081923A1 (en) 2021-11-08 2023-05-11 Frequency Therapeutics, Inc. Platelet-derived growth factor receptor (pdgfr) alpha inhibitors and uses thereof
WO2023129974A1 (en) 2021-12-29 2023-07-06 Bristol-Myers Squibb Company Generation of landing pad cell lines
WO2023131616A1 (en) 2022-01-05 2023-07-13 Vib Vzw Means and methods to increase abiotic stress tolerance in plants
WO2023131637A1 (en) 2022-01-06 2023-07-13 Vib Vzw Improved silage grasses
WO2023144199A1 (en) 2022-01-26 2023-08-03 Vib Vzw Plants having reduced levels of bitter taste metabolites
WO2023220603A1 (en) 2022-05-09 2023-11-16 Regeneron Pharmaceuticals, Inc. Vectors and methods for in vivo antibody production
WO2023225665A1 (en) 2022-05-19 2023-11-23 Lyell Immunopharma, Inc. Polynucleotides targeting nr4a3 and uses thereof
WO2024026474A1 (en) 2022-07-29 2024-02-01 Regeneron Pharmaceuticals, Inc. Compositions and methods for transferrin receptor (tfr)-mediated delivery to the brain and muscle
WO2024031053A1 (en) 2022-08-05 2024-02-08 Regeneron Pharmaceuticals, Inc. Aggregation-resistant variants of tdp-43
WO2024064958A1 (en) 2022-09-23 2024-03-28 Lyell Immunopharma, Inc. Methods for culturing nr4a-deficient cells
WO2024064952A1 (en) 2022-09-23 2024-03-28 Lyell Immunopharma, Inc. Methods for culturing nr4a-deficient cells overexpressing c-jun

Also Published As

Publication number Publication date
US20130217119A1 (en) 2013-08-22
US10590175B2 (en) 2020-03-17
US20200270312A1 (en) 2020-08-27
US20170051020A1 (en) 2017-02-23
US20120110685A1 (en) 2012-05-03
US9809628B2 (en) 2017-11-07
US20180141979A1 (en) 2018-05-24
US11827676B2 (en) 2023-11-28
US20150079602A1 (en) 2015-03-19
US20160194361A1 (en) 2016-07-07
US20210261628A9 (en) 2021-08-26
US9017967B2 (en) 2015-04-28
US9453054B2 (en) 2016-09-27
US8470973B2 (en) 2013-06-25
WO2012104729A1 (en) 2012-08-09

Similar Documents

Publication Publication Date Title
US11827676B2 (en) Modular DNA-binding domains and methods of use
US9353378B2 (en) Modular DNA-binding domains and methods of use
JP7303847B2 (en) Modular DNA binding domains and methods of use
AU2013204150A1 (en) Modular DNA-binding domains and methods of use

Legal Events

Date Code Title Description
STCB Information on status: application discontinuation

Free format text: ABANDONED -- FAILURE TO RESPOND TO AN OFFICE ACTION