US20140115726A1 - New tale-protein scaffolds and uses thereof - Google Patents

New tale-protein scaffolds and uses thereof Download PDF

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US20140115726A1
US20140115726A1 US14/009,509 US201214009509A US2014115726A1 US 20140115726 A1 US20140115726 A1 US 20140115726A1 US 201214009509 A US201214009509 A US 201214009509A US 2014115726 A1 US2014115726 A1 US 2014115726A1
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chimeric protein
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Philippe Duchateau
Alexandre Juillerat
Julien Valton
Claudia Bertonati
Jean-Charles Epinat
George H. Silva
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Cellectis SA
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Definitions

  • the present invention relates to new Transcription Activator-Like Effector proteins and more particularly new Transcription Activator-Like Effector Nucleases (TALENs) that can efficiently target and process nucleic acids.
  • the present invention also concerns methods to use these new Transcription Activator-Like Effector proteins.
  • the present invention also relates to vectors, compositions and kits in which Transcription Activator-Like Effector proteins of the present invention are used.
  • TAL effectors Transcription activator-like effectors
  • Natural TAL effectors are produced by phytopathogenic bacteria and function upon infection as transcription activators of plant genes [for review see (Bogdanove, Schornack et al. 2010; Christian, Cermak et al. 2010)]. Since the isolation of the first TAL effectors gene (Bonas, Stall et al. 1989), the presence of repetitive motifs nearly identical within the central domain has been questioned. Today this central domain has been shown to be responsible for DNA recognition through a new type of DNA-binding domain (Boch, Scholze et al. 2009; Moscou and Bogdanove 2009). Each repeat is made usually of 33 or 34 amino acids and mediates the recognition of 1 nucleotide of the DNA target through 2 critical amino acids located at positions 12 and 13 in each repeat.
  • RVD right-variable di-residue
  • TALEN TAL Nuclease
  • the targeted sequence must start by a T, then T and A should be disfavored at position 1 and 2 respectively. They found also a strong bias towards the RVD-NG at the last position of the repeat arrays. Finally, the target DNA should have a low G content (9 ⁇ 8%). The robustness of these rules is not yet established. So far, the most established limitations when one want to design a TALEN against a chosen sequence is the presence of a T at the beginning of each target DNA sequence. Actually this essential T is not imposed by a specific RVD as it interacts directly with the N-terminal domain of the protein, and thus is not governed by the so called RVD code.
  • ZFN are classically heterodimeric proteins that bind two DNA sequences separated by 6 bp.
  • the TALEN described so far were all designed following the same architecture i.e. TALEN acts as heterodimers proteins in which the nuclease catalytic domain such Fok1 is fused to the TALE C-terminal region.
  • TALEN acts as heterodimers proteins in which the nuclease catalytic domain such Fok1 is fused to the TALE C-terminal region.
  • the optimal length of the DNA sequence separating the two binding domains had to be determined.
  • ZFNs DNA targets contain almost exclusively 6 bp intervening sequences, TALEN appears to tolerate a much more wide range of DNA length and as expected, appears to be dependent on the TALE scaffold used.
  • a spacer length below 10 nucleotides did not allowed efficient cleavage in vitro as did the C-terminal truncation bearing the 95 first amino acids of the C-terminal domain.
  • TALEN bearing the 28 first residues of the C-terminal domain showed nuclease activity in vitro when tested on target comprising spacer from 10 to 24 bps, with a maximal activity for spacer of 12-13 bps. Sequences narrower than 8 bp did not allow significant cleavage activity. Even though some guidance's were described (Cermak, Doyle et al. 2011) to help designing active TALEN, too few data are available today to confirm their benefits.
  • the inventors have developed a new type of TAL effector proteins and particularly a new type of TALEN that can be engineered to specifically recognize and process target nucleic acid efficiently, overpassing the actual limitations.
  • the present invention relates to new Transcription Activator-Like Effector proteins and more particularly new Transcription Activator-Like Effector Nucleases (TALENs) that can efficiently target and process nucleic acids.
  • the present invention also concerns methods to use these new Transcription Activator-Like Effector proteins for various applications.
  • the present invention also concerns the creation of functional single-polypeptide fusion proteins, i.e chimeric proteins derived from a Transcription Activator-Like Effector for simple and efficient vectorization.
  • the present invention also relates to vectors, compositions and kits in which chimeric proteins of the present invention derived of Transcription Activator-Like Effector are used.
  • FIG. 1 General description of a chimeric protein according to the present invention.
  • FIG. 2 Activity of AvrBs3-derived TALEN in yeast (30° C.); AvrBs3-derived TALEN is represented by a black bar and negative control (empty vector) and positive control (I-SceI meganuclease) are represented by grey bars. Activities are normalized to the positive control.
  • FIG. 3 Activity of AVRBs3-derived TALEN in mammalian cells (Extrachromosomic assay in CHO-K1); AvrBs3-derived TALEN is represented by a black curve, negative control (empty vector) by a dark grey curve and positive control (I-SceI meganuclease) by a light grey curve
  • FIG. 4 Activity of N152 AvrBs3-derived TALEN in yeast (30° C.); truncated variants is represented by a grey bars and AvrBs3-derived TALEN (control wt) is represented by a black bar. Activities are normalized to the AvrBs3-derived TALEN (Control wt) (SEQ ID NO: 5) activity on its 15 bp target (Avr15) (SEQ ID NO: 6).
  • FIG. 5 Impact of truncations of the TALE C-terminal domain on AvrBs3-derived TALEN in yeast; truncated variants are represented by grey bars and AvrBs3-derived TALEN (control wt) is represented by a black bar; Activities are normalized to the AvrBs3-derived TALEN (Control wt) (SEQ ID NO: 5) activity on its 15 bp target (Avr15) (SEQ ID NO: 6).
  • FIG. 6 Activity in yeast of AvrBs3-derived TALENs comprising truncations of the C-terminal domain against targets of various spacer lengths. Effect of spacer length on: A, AVRBS3 TALEN having the C-terminal domain truncated after position E886 (C0) (SEQ ID NO: 19); C0 truncated variant is represented by grey bars and AvrBs3-derived TALEN is represented by black bars. Activities are normalized to the AvrBs3-derived TALEN (Control wt) activity on its 15 bp target (Avr15). * indicates no detectable activity.
  • C AVRBS3 TALEN having the C-terminal domain truncated after position G914 (C28) (SEQ ID NO: 21); C28 truncated variant is represented by grey bars and AvrBs3-derived TALEN is represented by black bars.
  • Activities are normalized to the AvrBs3-derived TALEN (Control wt) activity on its 15 bp target (Avr15). * indicates no activity over negative control.
  • D AVRBS3 TALEN having the C-terminal domain truncated after position L926 (C40) (SEQ ID NO: 22); C40 truncated variant is represented by grey bars and AvrBs3-derived TALEN is represented by black bars. Activities are normalized to the AvrBs3-derived TALEN (Control wt) activity on its 15 bp target (Avr15). * indicates no activity over negative control.
  • F AVRBS3 TALEN having the C-terminal domain truncated after position T1003 (C115) (SEQ ID NO: 24); C115 truncated variant is represented by grey bars and AvrBs3-derived TALEN is represented by black bars.
  • Activities are normalized to the AvrBs3-derived TALEN (Control wt) activity on its 15 bp target (Avr15). * indicates no activity over negative control.
  • G AVRBS3 TALEN having the C-terminal domain truncated after position E1057 (C172) (SEQ ID NO: 25); C172 truncated variant is represented by grey bars and AvrBs3-derived TALEN is represented by black bars. Activities are normalized to the AvrBs3-derived TALEN (Control wt) activity on its 15 bp target (Avr15). * indicates no activity over negative control.
  • FIG. 7 Impact of nucleotide identity at position n of the target on the AvrBs3-derived TALEN activity (in yeast); Control target Avr15 with a T at position n is represented by a black bar. Activities are normalized to the AvrBs3-derived TALEN (Control wt) (SEQ ID NO: 5) activity on its 15 bp target (Avr15) (SEQ ID NO: 6).
  • FIG. 8 Activity of engineered TALENs in mammalian cells (Extrachromosomic assay in CHO-K1); DMDT2.1 TALEN (SEQ ID NO: 180, SEQ ID NO: 186, SEQ ID NO: 189; example 6) is represented by a dark grey curve, ILRGT2.1 TALEN (SEQ ID NO: 181, SEQ ID NO: 187, SEQ ID NO: 190; example 6) is represented by a black curve, HBBT1.1 TALEN (SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 192; example 6) is represented by a dark grey curve, negative control (empty vector) by a light grey dashed curve and positive control (I-SceI meganuclease) by a black dashed curve.
  • ILRGT2.1 TALEN SEQ ID NO: 181, SEQ ID NO: 187, SEQ ID NO: 190; example 6
  • HBBT1.1 TALEN SEQ ID NO: 182, S
  • FIG. 9 Schematic of chimeric protein configurations according to the invention.
  • FIG. 10 Schematic of the method for optimizing the control of double-stranded break activity of a chimeric protein according to the invention.
  • FIG. 11 Schematic of the method for increasing the number of targets that can be reach by a chimeric protein according to the invention.
  • FIG. 12 Activity of TALE-AvrBs3::TevI in yeast (37° C.).
  • the negative control consists in a TALEN without any RVDs.
  • n.d. indicates no detectable activity
  • + indicates an activity over 0.3 in yeast assay
  • +++ indicates an activity over 0.7 in yeast assay (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • FIG. 13 Activity of TALE-AvrBs3::TevI in mammalian cells.
  • pCLS8993 SEQ ID NO: 457
  • pCLS8994 SEQ ID NO: 458
  • Negative control empty vector
  • I-SceI meganuclease I-SceI meganuclease
  • FIG. 14 Activity of TALE-AvrBs3::NucA in yeast (37° C.).
  • the negative control is a target lacking a recognition site (neg. ctrl.: SEQ ID NO: 472).
  • Compact is a target having only one recognition site (SEQ ID NO: 468).
  • n.d. indicates no detectable activity, + indicates an activity over 0.3 in yeast assay at 37° C.; ++ indicates an activity over 0.5 in yeast assay at 37° C. and +++ indicates an activity over 0.7 in yeast assay at 37° C.
  • International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • FIG. 15 Activity of TALE-AvrBs3::ColE7 in yeast (37° C.).
  • the negative control is a target lacking a recognition site (neg. ctrl.: SEQ ID NO: 472).
  • Compact is a target having only one recognition site (SEQ ID NO: 468).
  • n.d. indicates no detectable activity, + indicates an activity over 0.3 in yeast assay at 37° C.; ++ indicates an activity over 0.5 in yeast assay at 37° C. and +++ indicates an activity over 0.7 in yeast assay at 37° C.
  • International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • FIGS. 16 to 19 Activity of asymmetrical TALENs in yeast (37° C.). n.d. indicates no detectable activity at 37° C., +/ ⁇ indicated an activity above 0.3 in yeast assay at 37° C.; + indicated an activity over 0.3 in yeast assay at 37° C.; ++ indicated an activity over 0.5 in yeast assay at 37° C.; +++ indicated an activity over 0.75 in yeast assay at 37° C. (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • FIG. 20 Activity of TALE-AvrBs3::EndoT7 in yeast (37° C.). n.d. indicates no detectable activity at 37° C., + indicated an activity over 0.3 in yeast assay at 37° C.; ++ indicated an activity over 0.5 in yeast assay at 37° C.; +++ indicated an activity over 0.75 in yeast assay at 37° C. (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • FIG. 21 Activity of colE7 (SEQ ID NO: 340), EndoT7 (SEQ ID NO: 363) and I-TevI (SEQ ID NO: 349) catalytic heads containing TALEN with various polypeptide linker in yeast (37° C.).
  • Compact is a target having only one recognition site (SEQ ID NO: 224).
  • n.d. indicates no detectable activity at 37° C., + indicated an activity over 0.3 in yeast assay at 37° C.; ++ indicated an activity over 0.5 in yeast assay at 37° C.; +++ indicated an activity over 0.75 in yeast assay at 37° C.
  • International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • FIG. 22 Activity of TALEN having various polypeptide linkers (37° C.).
  • the negative control is a target lacking recognition sites.
  • n.d. indicates no detectable activity at 37° C., +/ ⁇ indicated an activity above 0.7 in yeast assay at 37° C.; +++ indicated an activity over 0.70 in yeast assay at 37° C.
  • FIG. 23 Tal repeats arrays assembly and subcloning into yeast expression plasmids.
  • A Legend of materials used for TAL repeat assembly.
  • B immobilization of the first biotinylated TAL repeat fragment on a streptavidin coated solid support and ligation to a second TAL repeat harboring SfaNI compatible overhangs (BbvI overhangs displayed in red).
  • C consecutive ligation/restriction of TAL repeats to generate the complete TAL repeats array.
  • D SfaNI digestion of the TAL repeats array.
  • E BbvI digestion and recovery of the TAL repeats array.
  • FIG. 24 Influence of TAL repeat number on TALEN activity. TALEN activities of 52 different TALENs (SEQ ID NO: 507-558) bearing from 9.5 to 15.5 TAL repeats were determined. The mean values of TALEN activities are displayed as a function of TAL repeat number; error bars represent the standard deviation of activities of TALENs bearing the same number of TAL repeats.
  • FIG. 25 Influence of different single protein/DNA mismatches at position N-1 or N-2 on TALEN activity as a function of TAL repeat number.
  • RAGT2.4 TALENs bearing 15.5 or 11.5 Tal repeats (SEQ ID NO: 617 or 622) along with their respective DNA targets (top and bottom respectively).
  • FIG. 26 Influence of C-terminal domain substitution by polypeptide linkers 8, 27 and 35 on AvrBs3 TALEN nuclease activity in yeast.
  • AvrBs3 TALENs bearing polypeptide linkers 8, 27 and 35 (SEQ ID: 141, 160 and 168) as C-terminal domain were assayed toward AvrBs3 homodimeric targets bearing from 5 to 30 bp DNA spacer.
  • Their yeast activities are displayed as a function of spacer length.
  • FIG. 27 Activities for novel variations of the TALE::FokI scaffold.
  • the negative control consists in a TALEN without any RVDs. n.d. indicates no detectable activity, + indicates an activity between 0.3 and 0.5 in our assay, ++ indicates an activity between 0.5 and 0.7 in our assay and +++ indicates an activity over 0.7 in our assay (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • FIG. 28 Activities of combination TALE::FokI and FokI::TALE in yeast.
  • the negative control consists in a TALEN without any RVDs. n.d. indicates no detectable activity, ++ indicates an activity between 0.5 and 0.7 in our assay and +++ indicates an activity over 0.7 in our assay (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • Table 3 List of AvrBs3 targets with various spacer lengths (SEQ ID NO: 220 to 255).
  • Table 4 List of AvrBs3 targets with all combination at position n (SEQ ID NO: 171 to 174).
  • Table 5 List of AvrBs3/RAGT2 (heterodimer) targets with various spacer lengths (SEQ ID NO: 256 to 291).
  • Table 6 Activities of 27 custom TALEN tested as homodimers, in four different scaffolds (full wt C-terminal domain, C0 truncated C-terminal domain, C11 truncated C-terminal domain and C40 truncated C-terminal domain); (n.a: non available; n.d: non detected) (SEQ ID NO: 26 to 133).
  • Table 7 Binding and target sequences of 27 custom TALEN (homodimers) (SEQ ID NO: 193 to 219).
  • Table 8 List of AvrBs3 targets with various spacer lengths (SEQ ID NO: 220 to 255) including a target with only one recognition site (compact, SEQ ID NO: 468) and a negative control target (neg. ctrl., SEQ ID NO: 472) consisting in a target without any recognition site.
  • Table 9 List of AvrBs3 targets containing two identical recognition sequences juxtaposed with the 5′ ends proximal and separated by “spacer” DNA ranging from 5 to 35 bps (SEQ ID NO: 629 to 659).
  • Table 10 List of RagT2-R/AvrBs3 hybrid targets contain two different recognition sequences juxtaposed with the 3′ end of the first (RagT2-R) proximal to the 5′ end of the second (AvrBs3) and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 666 to 701),
  • the present invention relates to new Transcription Activator-Like Effector proteins and more particularly new Transcription Activator-Like Effector Nucleases (TALENs) that can efficiently target and process nucleic acids.
  • TALENs Transcription Activator-Like Effector Nucleases
  • the present invention relates to a chimeric protein derived from a Transcription Activator-Like Effector (TALE) comprising:
  • said chimeric protein further comprises a peptidic linker to fuse said catalytic domain to said core scaffold.
  • a chimeric protein constituted by a core scaffold comprising a DNA binding domain and a protein domain to process a nucleic acid target sequence.
  • a chimeric protein derived from a Transcription Activator-Like Effector (TALE) comprising:
  • the chimeric protein of the present invention is derived from any naturally occurring TAL effectors, such as those described in Bogdanove et al. (Boch and Bonas 2010; Bogdanove, Schornack et al. 2010) and listed in Boch et al. (Boch and Bonas 2010).
  • the chimeric protein of the present invention is derived from any TAL effectors of plant pathogenic bacteria in the genus Xanthomonas as listed in Boch et al (Boch and Bonas 2010) as a non-limiting example.
  • only one part of the core scaffold is derived from a TAL effector; as an illustrative example, only said set of Repeat Variable Dipeptide regions is derived from a TAL effector.
  • each RVD of said core scaffold is made of 30 to 42 amino acids, more preferably 33 or 34 wherein two critical amino acids located at positions 12 and 13 mediates the recognition of one nucleotide of said nucleic acid target sequence; equivalent two critical amino acids can be located at positions other than 12 and 13 specially in RVDs taller than 33 or 34 amino acids long.
  • RVDs associated with recognition of the different nucleotides are HD for recognizing C, NG for recognizing T, NI for recognizing A, NN for recognizing G or A, NS for recognizing A, C, G or T, HG for recognizing T, IG for recognizing T, NK for recognizing G, HA for recognizing C, ND for recognizing C, HI for recognizing C, HN for recognizing G, NA for recognizing G, SN for recognizing G or A and YG for recognizing T, TL for recognizing A, VT for recognizing A or G and SW for recognizing A.
  • RVDs associated with recognition of the nucleotides C, T, A, G/A and G respectively are selected from the group consisting of NN or NK for recognizing G, HD for recognizing C, NG for recognizing T and NI for recognizing A, TL for recognizing A, VT for recognizing A or G and SW for recognizing A.
  • RVDS associated with recognition of the nucleotide C are selected from the group consisting of N*
  • RVDS associated with recognition of the nucleotide T are selected from the group consisting of N* and H*, where * denotes a gap in the repeat sequence that corresponds to a lack of amino acid residue at the second position of the RVD.
  • critical amino acids 12 and 13 can be mutated towards other amino acid residues in order to modulate their specificity towards nucleotides A, T, C and G and in particular to enhance this specificity.
  • other amino acid residues is intended any of the twenty natural amino acid residues or unnatural amino acids derivatives.
  • said core scaffold of the present invention comprises between 8 and 30 RVDs. More preferably, said core scaffold of the present invention comprises between 8 and 20 RVDs; again more preferably 15 RVDs.
  • said core scaffold comprises an additional single truncated RVD made of 20 amino acids located at the C-terminus of said set of RVDs, i.e. an additional C-terminal half-RVD.
  • said core scaffold of the present invention comprises between 8.5 and 30.5 RVDs, “0.5” referring to previously mentioned half-RVD (or terminal RVD, or half-repeat). More preferably, said core scaffold of the present invention comprises between 8.5 and 20.5 RVDs, again more preferably, 15.5 RVDs.
  • said half-RVD is in a core scaffold context which allows a lack of specificity of said half-RVD toward nucleotides A, C, G, T. In a more preferred embodiment, said half-RVD is absent.
  • said core scaffold of the present invention comprises RVDs of different origins.
  • said core scaffold comprises RVDs originating from different naturally occurring TAL effectors.
  • internal structure of some RVDs of the core scaffold of the present invention are constituted by structures or sequences originated from different naturally occurring TAL effectors.
  • said core scaffold of the present invention comprises RVDs-like domains.
  • RVDs-like domains have a sequence different from naturally occurring RVDs but have the same function and/or global structure within said core scaffold of the present invention.
  • said RVDs-like domains are protein domains selected from the group consisting of Puf RNA binding protein or Ankyrin super-family.
  • Non-limiting examples of such proteins from which RVDs-like domain can be derived are given by SEQ ID NO: 398 and SEQ ID NO: 399 respectively corresponding to proteins fem-3 and aRep.
  • said core scaffold of the chimeric protein of the present invention comprises a mix of naturally occurring RVDs structures and RVDs-like domains.
  • said core scaffold of the present invention is entirely composed by RVDs-like domains that are not originated from pathogenic organisms.
  • said core scaffold of the chimeric protein of the present invention is totally artificial, i.e. without any RVDs-like domains derived from naturally occurring TAL effectors.
  • Such mutations can also overcome nucleic acid modifications such as DNA alkylation (acetylation, methylation) as a non-limiting example; in this case, the core scaffold of the chimeric protein of the invention can have a higher selectivity for a methylated or unmethylated target sequence; in other words, said core scaffold can tolerate nucleic acid methylation or can be specific of a methylated target sequence.
  • VVAIA and LLPVL amino acids motifs in RVDs may be of structural importance for hydrophobic contact between helices of adjacent RVD and may represent good candidate motifs to mutate for modulating the intra RVD interactions or interdependency between adjacent RVDs in a set of repeated variable domains and thus the affinity and specificity of subsequent TALENs.
  • RVDs variants mutated at these residues to modify interactions between adjacent RVDs resulting in a core scaffold of the present invention with more rigidity.
  • More or less rigidity in core scaffolds of the present invention allows to enhance or decrease protein-protein interactions within the structure of the scaffold, particularly when adjacent RVDs in said core scaffold are from different origins; also, it allows to modify protein-nucleic acid interactions between said core scaffold of the chimeric protein of the present invention and its nucleic acid target. Modifications of protein-protein or protein-nucleic acid interactions can be quantified by measuring biochemical constants [affinity (Ka)/dissociation (Kd)/turn over (Kcat) constants] associated with such interactions/reactions.
  • said core scaffold of the present invention comprises one additional domain at the N-terminus of said set of Repeat Variable Dipeptide regions.
  • said additional N-terminus domain is derived from the N-terminus domain of a naturally occurring TAL effector.
  • said additional N-terminus domain is the full-length N-terminus domain of a naturally occurring TAL effector N-terminus domain.
  • said additional N-terminus domain is a variant of a naturally occurring Tal effector.
  • said additional domain is a truncated variant of a naturally occurring TAL effector N-terminus domain.
  • said additional domain is a truncated version of AvrBs3 TAL effector.
  • said truncated version lacks at its C-terminus extremity the peptidic sequence that confers specificity to position 0 of the recognized and bound sequence, i.e. the “RVD0” repeat, named for a postulated 0 th repeat that has only weak sequence similarity but a predicted structural similarity to the repeats in Bogdanove et al. (Bogdanove 2010 current opinion).
  • said truncated version lacks at least one amino acid residue selected from the group consisting of the 152 first N-terminal amino acids residues. In another embodiment, said truncated version lacks more than the first 152 amino acids residues.
  • said additional N-terminus domain is a non-TAL effector originating domain.
  • said additional N-terminus domain is derived from a protein having non-specific nucleic acid binding characteristics.
  • said additional N-terminus domain is derived from a protein having non-specific DNA binding characteristics.
  • said additional N-terminus domain is derived from a protein having non-specific RNA binding characteristics.
  • said additional N-terminus domain is derived from a protein having specific nucleic acid binding characteristics, such as non-limiting examples, meganucleases or zinc-finger proteins or derivatives of those such as variants with only DNA binding activity.
  • said additional N-terminus domain is a chimeric domain comprising a TAL effector originating subdomain and a non-TAL effector originating subdomain.
  • said additional N-terminus domain is a variant increasing the affinity of said core scaffold of the chimeric protein of the present invention toward its binding nucleic acid sequence.
  • said additional N-terminus domain is a variant which allows overcoming sequence constraints associated with said RVD0, i.e. the necessity to have a T as the first base on binding nucleic acid sequence.
  • said additional N-terminus domain is a variant which allows changing this sequence constraint to A, G or C respectively.
  • said additional N-terminus domain is a variant which allow suppressing the sequence constraints associated with RVD0.
  • said additional N-terminus domain of the core scaffold of the chimeric protein of the present invention comprises a localization sequence (or signal) which allows targeting said chimeric protein toward a given organelle within an organism, a tissue or a cell.
  • localization signals are nuclear localization signals, chloroplastic localization signals or mitochondrial localization signals.
  • said additional N-terminus domain can comprise a nuclear export signal having the opposite effect of a nuclear localization signal to help targeting organelles such as chloroplasts or mitochondria.
  • additional N-terminus domains with a combination of several localization signals can be as a non-limiting example a nuclear localization signal and a tissue-specific signal to help addressing said chimeric protein of the present invention in the nuclear of tissue specific cells.
  • said additional N-terminal domain can be fused with a protein domain, a protein module, an antibody (or part of it) or a tag of interest, well-known in the art, for a specific application.
  • said additional N-terminal domain can be linked with a chemical molecule such as a small compound of interest for a defined application.
  • said additional domain at the N-terminus of said set of Repeat Variable Dipeptide regions of said core scaffold of the present invention is selected from the group consisting of SEQ ID NO: 292, SEQ ID NO: 293 and SEQ ID NO: 401 or derivatives thereof.
  • said core scaffold of the present invention comprises one additional domain at the C-terminus of said set of Repeat Variable Dipeptide regions.
  • said additional C-terminus domain is derived from the C-terminus domain of a naturally occurring TAL effector.
  • said additional C-terminus domain is the full-length C-terminus domain of a naturally occurring TAL effector.
  • said additional C-terminus domain is a variant of a naturally occurring Tal effector C-terminus domain.
  • said additional domain is a truncated variant of a naturally occurring TAL effector C-terminus domain.
  • said truncated version is a C-terminus domain without Activation Domain (SEQ ID NO: 400 and 402).
  • said additional domain is a truncated version of AvrBs3 TAL effector. In another embodiment, said additional domain is truncated after position E886 (C0). In another embodiment, said additional domain is truncated after position P897 (C11; SEQ ID NO: 295). In another embodiment, said additional domain is truncated after position G914 (C28; SEQ ID NO: 296). In another embodiment, said additional domain is truncated after position L926 (C40; SEQ ID NO: 297). In another embodiment, said additional domain is truncated after position D950 (C64; SEQ ID NO: 298).
  • said additional domain is truncated after position R1000 (C115; SEQ ID NO: 299). In another embodiment, said additional domain is truncated after position D1059 (C172; SEQ ID NO: 300) (amino acid numbering refers to C-terminus domain of AvrBs3 TAL effector).
  • said additional C-terminus domain is a non-TAL effector originating domain.
  • said additional C-terminus domain is derived from a protein having non-specific nucleic acid binding characteristics.
  • said additional C-terminus domain is derived from a protein having non-specific DNA binding characteristics.
  • said additional C-terminus domain is derived from a protein having non-specific RNA binding characteristics.
  • said additional C-terminus domain is derived from a protein having specific nucleic acid binding characteristics, such as non-limiting examples, meganucleases or zinc-finger proteins or derivatives of those such as variants with only DNA binding activity.
  • said additional C-terminus domain is a chimeric domain comprising a TAL effector originating subdomain and a non-TAL effector originating subdomain.
  • said additional C-terminus domain is a variant increasing the affinity of said core scaffold of the chimeric protein of the present invention toward its binding nucleic acid sequence.
  • said additional C-terminus domain of the core scaffold of the chimeric protein of the present invention comprises a localization sequence (or signal) which allows targeting said chimeric protein toward a given organelle within an organism, a tissue or a cell.
  • localization signals are nuclear localization signals, chloroplastic localization signals or mitochondrial localization signals.
  • said additional C-terminus domain can comprise a nuclear export signal having the opposite effect of a nuclear localization signal to help targeting organelles such as chloroplasts or mitochondria.
  • additional C-terminus domains with a combination of several localization signals can be as a non-limiting example a nuclear localization signal and a tissue-specific signal to help addressing said chimeric protein of the present invention in the nuclear of tissue specific cells.
  • said additional C-terminal domain can be fused with a protein domain, a protein module, an antibody (or part of it) or a tag of interest, well-known in the art, for a specific application.
  • said additional C-terminal domain can be linked with a chemical molecule such as a small compound of interest for a defined application.
  • said additional domain at the C-terminus of said set of Repeat Variable Dipeptide regions of said core scaffold of the present invention is selected from the group consisting of SEQ ID NO: 295 to 300, SEQ ID NO: 400 and SEQ ID NO: 402 or derivatives thereof.
  • said core scaffold of the chimeric protein according to the present invention comprises two additional domains respectively at the N-terminus and at the C-terminus of said set of Repeat Variable Dipeptide regions, as previously described.
  • said chimeric protein according to the present invention comprises at least one peptidic linker to fuse a protein domain to said core scaffold previously described.
  • said peptidic linker is flexible.
  • said peptidic linker is structured.
  • said peptidic linker sequence is selected from the group consisting of NFS1, NFS2, CFS1, RM2, BQY, QGPSG, LGPDGRKA, 1a8h — 1, 1 dnpA — 1, 1 d8cA — 2, 1 ckqA — 3, 1sbp — 1, 1 ev7A — 1, 1 alo — 3, 1amf — 1, 1 adjA — 3, 1 fcdC — 1, 1 al3 — 2, 1 g3p — 1, 1acc — 3, 1 ahjB — 1, 1acc — 1, 1 af7 — 1, 1 heiA — 1, 1bia — 2, 1 igtB — 1, 1 nfkA — 1, 1 au7A — 1, 1 bpoB — 1, 1 b0 pA — 2, 1 c05A — 2, 1gcb — 1, 1 bt3A — 1, 1 b3oB — 2, 16
  • the peptidic linker that can link said core scaffold to said protein domain of the chimeric protein according to the present invention can be selected from the group consisting of TAL1 to TAL37 (SEQ ID NO: 134 to SEQ ID NO: 170).
  • TAL1 to TAL37 SEQ ID NO: 134 to SEQ ID NO: 170.
  • a peptidic linker is not needed to fuse said core scaffold with said protein domain in order to obtain a chimeric protein according to the present invention.
  • more than one linker is needed to fuse several protein domains with said core scaffold according to the present invention.
  • two, three or four linkers can be used in the same chimeric protein according to the present invention.
  • said peptidic linker contains one or several active domains which allow its deployment under stimulation.
  • said peptidic linker can contain a calmodulin domain that changes its conformation under calcium stimulation; other protein domains changing their conformation under a specific metabolite interaction can be used.
  • such peptidic linker according to the present invention can contain a light sensitive domain which allows a change in peptidic linker structure from a folded inactive state toward an unfolded active state under light stimulation for example, or reverse.
  • Said peptidic linker can for example contain a first light-sensitive protein switch comprising a phytochrome-chromophore complex and a Phytochrome Interaction Factor (PIF) i.e. a second protein able to reversibly interact with said phytochrome-chromophore complex depending on the light activation/desactivation state.
  • PAF Phytochrome Interaction Factor
  • Other examples of active linkers can use small molecules such as Chemical Inducers of Dimerization (CID).
  • said chimeric protein according to the present invention comprises at least one protein domain or catalytic domain to process said nucleic acid target sequence.
  • the catalytic domain that is capable of processing said nucleic acid target sequence, when fused to said core scaffold according to the present invention is fused to the N-terminus part of said core scaffold.
  • said catalytic domain is fused to the C-terminus part of said core scaffold.
  • two catalytic domains are fused to both N-terminus part of said core scaffold and C-terminus of said core scaffold.
  • one or several catalytic domains to said core scaffold wherein said core scaffold comprises or not an additional domain at its N-terminus and/or at its C-terminus.
  • one or several peptidic linkers can be added for said fusions between the different domains of the chimeric protein according to the present invention.
  • several catalytic domains and several peptidic linkers is intended two or three or four or five as non-limiting examples.
  • said catalytic domain has an activity selected from the group consisting of nuclease activity, polymerase activity, kinase activity, phosphatase activity, methylase activity, topoisomerase activity, integrase activity, transposase activity, ligase activity, helicase activity, recombinase activity.
  • the catalytic domain fused to the core scaffold of the present invention can be a transcription activator or repressor (i.e. a transcription regulator), or a protein that interacts with or modifies other proteins implicated in DNA processing.
  • a transcription activator or repressor i.e. a transcription regulator
  • Non-limiting examples of DNA processing activities of said chimeric protein of the present invention include, for example, creating or modifying epigenetic regulatory elements, making site-specific insertions, deletions, or repairs in DNA, controlling gene expression, and modifying chromatin structure.
  • said catalytic domain has an endonuclease activity.
  • said protein domain has an exonuclease activity.
  • said catalytic domain is selected from the group consisting of proteins MmeI, Colicin-E7 (CEA7_ECOLX), Colicin-E9, APFL, EndA, Endo I (END1_ECOLI), Human Endo G (NUCG_HUMAN), Bovine Endo G (NUCG_BOVIN), R.HinP1I, I-BasI, I-BmoI, I-HmuI, I-TevI, I-TevII, I-TevIII, I-TwoI, R.MspI, R.MvaI, NucA, NucM, Vvn, Vvn_CLS, Staphylococcal nuclease (NUC_STAAU), Staphylococcal nuclease (NUC_STAHY),
  • the chimeric protein according to the present invention comprises a catalytic domain that is a polypeptide comprising an amino acid sequence having at least 80%, preferably at least 90%, more preferably at least 95% identity with any of SEQ ID NO: 339 to 397 and SEQ ID NO: 598-599.
  • said catalytic domain of the chimeric protein of the invention has an identity with I-TevI (SEQ ID NO: 349). In another embodiment, said catalytic domain has an identity with I-TevI (SEQ ID NO: 349) and is fused to the N-terminal domain of said core scaffold. In another embodiment, said catalytic domain has an identity with I-TevI (SEQ ID NO: 349) and is fused to the C-terminal domain of said core scaffold. In another embodiment, said chimeric protein according to the present invention acts as a monomer wherein two of said monomer respectively bind one nucleic acid sequence adjacent to a nucleic acid target sequence thereby together processing said nucleic target sequence.
  • said chimeric protein comprises a catalytic domain having identity with I-TevI (SEQ ID NO: 349) and fused to the C-terminal domain of said core scaffold and acts as a monomer wherein two of said monomer respectively bind one nucleic acid sequence adjacent to a nucleic acid target sequence thereby together processing said nucleic target sequence.
  • the first and the second monomers have the same amino acid sequence or not.
  • said chimeric protein comprises a catalytic domain having identity with I-TevI (SEQ ID NO: 349) and fused to the C-terminal domain of said core scaffold acting as a first monomer binding one nucleic acid sequence adjacent to a nucleic acid target sequence and wherein a second chimeric protein monomer comprising I-TevI (SEQ ID NO: 349) or derivatives thereof fused to the N-terminus of said core scaffold acts as a second monomer binding another nucleic acid sequence adjacent to said nucleic acid target sequence, thereby together processing said nucleic target sequence.
  • said catalytic domain of the chimeric protein of the invention has an identity with NucA (SEQ ID NO: 355). In another embodiment, said catalytic domain has an identity with NucA (SEQ ID NO: 355) and is fused to the N-terminal domain of said core scaffold. In another embodiment, said catalytic domain has an identity with NucA (SEQ ID NO: 355) and is fused to the C-terminal domain of said core scaffold. In another embodiment, said catalytic domain of the chimeric protein of the invention has an identity with ColE7 (SEQ ID NO: 340). In another embodiment, said catalytic domain has an identity with ColE7 (SEQ ID NO: 340) and is fused to the N-terminal domain of said core scaffold. In another embodiment, said catalytic domain has an identity with ColE7 (SEQ ID NO: 340) and is fused to the C-terminal domain of said core scaffold.
  • said catalytic domain of the chimeric protein of the invention has an identity with FokI (SEQ ID NO: 600) and is fused to the N-terminal domain of said core scaffold.
  • said additional catalytic domain at the N-terminus of said core scaffold comprises an amino acid sequence having at least 80%, preferably at least 90%, more preferably at least 95% identity with Fok-I (SEQ ID NO: 600).
  • any combinations of two catalytic domains selected from the group consisting of proteins MmeI, Colicin-E7 (CEA7_ECOLX), Colicin-E9, APFL, EndA, Endo I (END1_ECOLI), Human Endo G (NUCG_HUMAN), Bovine Endo G (NUCG_BOVIN), R.HinP1I, I-BasI, I-BmoI, I-HmuI, I-TevI, I-TevII, I-TevIII, I-TwoI, R.MspI, R.MvaI, NucA, NucM, Vvn, Vvn_CLS, Staphylococcal nuclease (NUC_STAAU), Staphylococcal nuclease (NUC_STAHY), Micrococcal nuclease (NUC_SHIFL), Endonuclease yncB, Endodeoxyribonuclea
  • I-HmuI protein domain can be fused to the N-terminus part of said core scaffold and ColE7 protein domain can be fused to the C-terminus part of said core scaffold.
  • I-TevI protein domain can be fused to the N-terminus part of said core scaffold and ColE7 protein domain can be fused to the C-terminus part of said core scaffold.
  • it can be envisioned to fuse one protein domain between two core scaffolds according to the invention, each one comprising at least one set of RVDs. In this last case, the number of RVDs for each engineered core TALE scaffold can be the same or not.
  • the chimeric protein according to the present invention comprises, catalytic domains respectively fused to the C-terminus and to the N-terminus of said core scaffold and selected from those having identity with:
  • the chimeric protein according to the present invention comprises, catalytic domains respectively fused to the C-terminus and to the N-terminus of said core scaffold and selected from those having identity with:
  • said catalytic domain of the chimeric protein of the invention has an identity with FokI (SEQ ID NO: 600) which is fused to the N-terminal domain of said core scaffold, wherein said chimeric protein acts as a monomer and wherein a second monomer binds another nucleic acid sequence adjacent to a nucleic acid target sequence thereby together processing said nucleic acid target sequence.
  • the first and the second monomers have the same amino acid sequence or not.
  • said catalytic domain of the chimeric protein of the invention has an identity with FokI (SEQ ID NO: 600) which is fused to the N-terminal domain of said core scaffold, wherein said chimeric protein acts as a monomer and wherein a second monomer, comprising a catalytic domain having an identity with FokI (SEQ ID NO: 600) which is fused to the C-terminal domain of said core scaffold, binds another nucleic acid sequence adjacent to a nucleic acid target sequence thereby together processing said nucleic acid target sequence.
  • FokI SEQ ID NO: 600
  • the chimeric protein according to the invention can comprise from its N-terminus toward its C-terminus: A first set of RVDs, a first linker, a protein domain, a second linker, a second set of RVDs.
  • the chimeric protein according to the invention can comprise a N-terminus domain as previously mentioned, a first set of RVDs, a first linker, a protein domain, a second linker, a second set of RVDs and a C-terminus domain as previously mentioned (as illustrated on FIG. 9B ).
  • linkers used in this case of chimeric protein according to the present invention can be active linkers comprising active domains which allow a change of their structure under appropriate stimulation.
  • the chimeric protein comprises a core scaffold with any combination between an additional C-terminus domain according to the invention and an additional N-terminus domain according to the invention.
  • said protein domain within the chimeric protein according to the present invention is a first protein subdomain interacting with a second protein subdomain to form said catalytic entity able to process said nucleic acid target sequence.
  • said first protein subdomain is selected from some of the group listed in Table 2 (SEQ ID NO: 339 to 397), such as MmeI (SEQ ID NO: 339), R.PleI (SEQ ID NO: 369), MlyI (SEQ ID NO: 370) as non-limiting examples, a functional mutant, a variant or derivatives of these protein subdomains thereof.
  • said second protein subdomain is selected from some of the group listed in Table 2 (SEQ ID NO: 339 to 397 and SEQ ID NO: 598-599), such as MmeI (SEQ ID NO: 339), R.PleI (SEQ ID NO: 369), MlyI (SEQ ID NO: 370) as non-limiting examples, a functional mutant, a variant or derivatives of these protein subdomains thereof.
  • said protein domain within the chimeric protein according to the present invention is a first protein subdomain interacting with a second protein subdomain to form a protein entity catalytically active.
  • Said first protein subdomain can be used to measure, quantify or provoke protein-protein interactions at said nucleic target sequence according to the present invention.
  • Said first protein subdomain can be a protein module or protein subdomain known to mediate protein-protein interaction in cell signaling.
  • Said first protein subdomain can be used for diagnosis, analytical or therapeutic applications.
  • Said protein entity can be a reporter protein such as a fluorescent protein, luciferase, ⁇ -galactosidase as non-limiting examples.
  • a first part of the reporter protein can be fused to said first protein subdomain according to the present invention and a second part of the reporter protein can be fused to said second protein subdomain, wherein said reporter protein is only active when said first and second protein subdomains according to the present invention interact.
  • said first protein subdomain or the protein entity resulting from the interaction between first and second subdomains can be used as intracellular sensor for calcium level, pH, redox environment as non-limiting examples.
  • said protein domain or subdomains are usable for applications such as Fluorescence Resonance Energy Transfer (FRET) as a non-limiting example.
  • said protein domain or subdomains are coupled to a dye.
  • said protein domain within the chimeric protein according to the present invention can be an inactive subdomain and can react with more than one protein domain or subdomain to form an active protein entity, i.e. said active entity can be comprising two, three, four or several subdomains and being an enzyme or a fluorescent protein as non-limiting example.
  • said active entity formed with the chimeric protein according to the present invention can interact or react with another protein or protein domain having a different activity.
  • said active entity formed with the chimeric protein according to the present invention can be associated within, or located 5′ or located 3′ regarding the nucleic acid target sequence location with another protein or protein domain having a different activity in order to process said nucleic acid target sequence; as a non-limiting example, said chimeric protein according to the present invention can comprise a protein domain with a cleavase activity for its nucleic acid target sequence and can be associated with an exonuclease activity to increase the mutagenesis rate at its nucleic acid target sequence location.
  • said second protein subdomain interacting with said first protein subdomain to form said catalytic entity able to process said nucleic acid target sequence according to the present invention is fused to a core scaffold comprising a set of Repeat Variable Dipeptide regions (RVDs) able to bind a second unique nucleic sequence adjacent to said nucleic acid target sequence wherein each RVD comprises a pair of amino acids responsible for recognizing one nucleotide selected from the group consisting of HD for recognizing C, NG for recognizing T, NI for recognizing A, NN for recognizing G or A, NS for recognizing A, C, G or T, HG for recognizing T, IG for recognizing T, NK for recognizing G, HA for recognizing C, ND for recognizing C, HI for recognizing C, HN for recognizing G, NA for recognizing G, SN for recognizing G or A and YG for recognizing T, TL for recognizing A, VT for recognizing A or G and SW for recognizing A.
  • RVDs associated with recognition of the nucleotides C, T, A, G/A and G respectively are selected from the group consisting of NN or NK for recognizing G, HD for recognizing C, NG for recognizing T and NI for recognizing A, TL for recognizing A, VT for recognizing A or G and SW for recognizing A.
  • RVDS associated with recognition of the nucleotide C are selected from the group consisting of N*
  • RVDS associated with recognition of the nucleotide T are selected from the group consisting of N* and H*, where * denotes a gap in the repeat sequence that corresponds to a lack of amino acid residue at the second position of the RVD.
  • critical amino acids 12 and 13 can be mutated towards other amino acid residues in order to modulate their specificity towards nucleotides A, T, C and G and in particular to enhance this specificity.
  • other amino acid residues is intended any of the twenty natural amino acid residues or unnatural amino acids derivatives.
  • said core scaffold fused to said second protein subdomain can have the same scope of characteristics that those previously listed to describe the chimeric protein according to the present invention, regarding the origin of said core scaffold, the number of RVDs comprised in said core scaffold, the nature of those RVDs (natural, artificial or RVDs-like domains), the existence of additional N-terminus or C-terminus or both domains on this core scaffold, the existence of one or several localization signals on this core scaffold, the existence of one or several peptidic linkers on this core scaffold to fuse one or several protein domains on this core scaffold.
  • said chimeric protein according to the present invention can function as a dimer wherein a first and a second monomer are derived from a Transcription Activator-Like Effector (TALE).
  • TALE Transcription Activator-Like Effector
  • said chimeric protein according to the present invention can function as a dimer wherein said first monomer comprises:
  • RVDs associated with recognition of the nucleotides C, T, A, G/A and G respectively are selected from the group consisting of NN or NK for recognizing G, HD for recognizing C, NG for recognizing T and NI for recognizing A, TL for recognizing A, VT for recognizing A or G and SW for recognizing A.
  • RVDS associated with recognition of the nucleotide C are selected from the group consisting of N*
  • RVDS associated with recognition of the nucleotide T are selected from the group consisting of N* and H*, where * denotes a gap in the repeat sequence that corresponds to a lack of amino acid residue at the second position of the RVD.
  • critical amino acids 12 and 13 in said first and second monomers can be mutated towards other amino acid residues in order to modulate their specificity towards nucleotides A, T, C and G and in particular to enhance this specificity.
  • other amino acid residues is intended any of the twenty natural amino acid residues or unnatural amino acids derivatives.
  • said core scaffolds of the first and second monomers can have the same scope of characteristics that those previously listed to describe the chimeric protein according to the present invention, regarding the origin of said core scaffolds, the number of RVDs comprised in said core scaffolds, the nature of those RVDs (natural, artificial or RVDs-like domains), the existence of additional N-terminus or C-terminus or both domains on these core scaffolds, the existence of one or several localization signals on these core scaffolds, the existence of one or several peptidic linkers on these core scaffolds to fuse one or several protein domains on these core scaffolds.
  • At least one monomer is selected from the group consisting of SEQ ID NO: 19 to 133, SEQ ID NO: 180-182, and SEQ ID NO: 186-188, a functional mutant, a variant or a derivative thereof.
  • said first and second monomers are selected from the group consisting of SEQ ID NO: 19 to 133, SEQ ID NO: 180-182, and SEQ ID NO: 186-188, functional mutants, variants or derivatives thereof.
  • said first and second monomers are fused by a peptidic linker forming a single polypeptide chain for simple and efficient vectorization.
  • said peptidic linker contains one or several active domains which allow its deployment under stimulation, as previously mentioned.
  • said first and second monomers have the same amino acid sequences and recognize the same nucleic acid sequence adjacent to said nucleic target sequence. In another embodiment, said first and second monomers have different amino acid sequences and recognize the same nucleic acid sequence adjacent to said nucleic target sequence, i.e first and second monomers are isoschizomers. In another embodiment, said first and second monomers have the same amino acid sequences and recognize different nucleic acid sequences adjacent to said nucleic target sequence because of TAL code degeneracy. In another embodiment, said first and second monomers have different amino acid sequences and recognize different nucleic acid sequences adjacent to said nucleic target sequence.
  • said chimeric protein according to the present invention binds a first and a second nucleic acid sequences which are on the same nucleic acid strand adjacent of said nucleic acid target sequence. In another embodiment, said chimeric protein according to the present invention binds a first and a second nucleic acid sequences which are adjacent to said nucleic acid target sequence but not on the same nucleic acid strand. In another embodiment, said chimeric protein according to the present invention binds a first and a second nucleic acid sequences which are located 5′ of said nucleic acid target sequence. In another embodiment, said chimeric protein according to the present invention binds a first and a second nucleic acid sequences which are located 3′ of said nucleic acid target sequence. In another embodiment, said chimeric protein according to the present invention binds a first nucleic sequence which is 5′ located of said nucleic acid sequence target and a second nucleic acid sequence which is 3′ located of said nucleic acid target sequence. In another embodiment, said
  • said chimeric protein according to the present invention binds a first and a second nucleic acid sequences which are adjacent to said nucleic acid target sequence and separated by a nucleic acid sequence (i.e. the spacer) of 5-40 base pairs (bp), i.e. the spacer length.
  • said chimeric protein according to the present invention binds a first and a second nucleic acid sequences which are adjacent to said nucleic acid target sequence and separated by a spacer of 8 bp length.
  • FIG. 9 Some structures of chimeric dimer proteins according to the invention are given on FIG. 9 .
  • said chimeric dimer protein according to the present invention can be associated with a third chimeric protein comprising:
  • Said third chimeric protein can have the same scope of characteristics that those previously listed regarding the origin of said core scaffold, the number of RVDs comprised in said core scaffold, the nature of those RVDs (natural, artificial or RVDs-like domains), the existence of additional N-terminus or C-terminus or both domains on this core scaffold, the existence of one or several localization signals on this core scaffold, the existence of one or several peptidic linkers on this core scaffold to fuse one or several protein domains on this core scaffold and the nature and characteristics of its protein(s) domain(s) or subdomain(s).
  • said third chimeric protein binds a nucleic acid sequence within the nucleic acid target sequence to process by said first and second monomers previously described.
  • said third chimeric protein can have a binding sequence within the spacer separating the first and a second nucleic acid sequences recognized and bound by the first and second monomers of the chimeric dimer protein according to the invention.
  • said third chimeric protein comprises a protein domain with a catalytic activity to process nucleic acid target sequence that is different from that of the catalytically active entity formed by the protein subdomains of respective first and second monomers of the chimeric dimer protein according to the present invention.
  • first and second monomer protein subdomains can form a catalytically active entity with a cleavase activity towards the nucleic acid target sequence and said third chimeric protein can comprise a protein domain with an exonuclease activity to increase the mutagenesis rate a the nucleic acid target sequence location.
  • said third chimeric protein binds a nucleic acid sequence located 5′ regarding the nucleic acid target sequence to process by said first and second monomers previously described.
  • said third chimeric protein binds a nucleic acid sequence located 3′ regarding the nucleic acid target sequence to process by said first and second monomers previously described.
  • said chimeric dimer protein according to the present invention can be associated with a core scaffold comprising a set of Repeat Variable Dipeptide regions (RVDs) able to bind a nucleic acid sequence adjacent to a nucleic acid target sequence to process wherein each RVD comprises a pair of amino acids responsible for recognizing one nucleotide selected from the group consisting of HD for recognizing C, NG for recognizing T, NI for recognizing A, NN for recognizing G or A, NS for recognizing A, C, G or T, HG for recognizing T, IG for recognizing T, NK for recognizing G, HA for recognizing C, ND for recognizing C, HI for recognizing C, HN for recognizing G, NA for recognizing G, SN for recognizing G or A, YG for recognizing T, TL for recognizing A, VT for recognizing A or G, SW for recognizing A, N* for recognizing C or T and H* for recognizing T (where * denotes a gap
  • said core scaffold associated with said chimeric dimer protein according to the present invention can have a binding sequence within the spacer separating the first and a second nucleic acid sequences recognized and bound by the first and second monomers of the chimeric dimer protein according to the invention.
  • said core scaffold associated with said chimeric dimer protein according to the present invention allows to control the processing activity of said chimeric dimer protein according to the present invention on its nucleic acid target sequence.
  • said core scaffold associated with said chimeric dimer protein according to the present invention allows to block the access of said chimeric dimer protein according to the present invention on its nucleic acid target sequence.
  • the expression of said core scaffold to control the processing activity of said chimeric dimer protein can be a cell-cycle or tissue dependent expression, allowing a cell-cycle or tissue dependent control of said chimeric dimer protein activity towards its nucleic acid target sequence.
  • a blocking core scaffold can also be used in combination with a chimeric protein according to the invention wherein said core scaffold binds the nucleic acid target sequence of said chimeric protein according to the invention to allow a control, a cell-cycle or time dependent control of said chimeric protein activity towards its nucleic acid sequence.
  • said chimeric protein according to the present invention can function as a trimer wherein a third monomer is derived from a Transcription Activator-Like Effector (TALE) and comprises:
  • TALE Transcription Activator-Like Effector
  • Said third monomer core can have the same scope of characteristics that those previously listed to describe a chimeric protein according to the present invention, regarding the origin of said core scaffold, the number of RVDs comprised in said core scaffold, the nature of those RVDs (natural, artificial or RVDs-like domains), the existence of additional N-terminus or C-terminus or both domains on this core scaffold, the existence of one or several localization signals on this core scaffold, the existence of one or several peptidic linkers on this core scaffold to fuse one or several protein domains on this core scaffold and the nature and characteristics of its protein(s) domain(s) or subdomain(s).
  • said third monomer binds a nucleic acid sequence within the nucleic acid target sequence to process by said first and second monomers previously described.
  • said third monomer can have a binding sequence within the spacer separating the first and a second nucleic acid sequences recognized and bound by the first and second monomers of the chimeric trimer protein according to the invention.
  • said third monomer binds a nucleic acid sequence located 5′ regarding the nucleic acid target sequence to process by said first and second monomers previously described.
  • said third monomer binds a nucleic acid sequence located 3′ regarding the nucleic acid target sequence to process by said first and second monomers previously described.
  • said third protein subdomain can be used to measure, quantify or provoke protein-protein interactions at said nucleic target sequence according to the present invention.
  • Said third protein subdomain can be a protein module or protein subdomain known to mediate protein-protein interaction in cell signaling.
  • Said third protein subdomain can be used for diagnosis, analytical or therapeutic applications.
  • Said third protein subdomain can be usable for applications such as Fluorescence Resonance Energy Transfer (FRET) as non-limiting example.
  • FRET Fluorescence Resonance Energy Transfer
  • said third protein subdomain is usable in FRET as a donor molecule, subdomains of first and second monomers being successive and compatible acceptor molecules.
  • said third protein subdomain is usable in FRET as an acceptor molecule, one of the subdomains of first and second monomers being respectively successive and compatible donor and acceptor molecules.
  • Said third protein subdomain can be coupled to a dye.
  • first, second and third subdomains of respective monomers constituting the chimeric trimer protein according to the invention can be a successive and compatible trio of “dyes” usable in FRET applications, more specific than the usual FRET applications using two successive and compatible dyes.
  • a recombinant polynucleotide encoding a chimeric protein or a monomer of a chimeric dimer protein as previously described according to the present invention.
  • Is also encompassed a vector comprising a recombinant polynucleotide encoding a chimeric protein or a monomer of a chimeric dimer protein as previously described according to the present invention.
  • Is also encompassed a host cell which comprises a vector and/or a recombinant polynucleotide encoding a chimeric protein or a monomer of a chimeric dimer protein as previously described according to the present invention.
  • non-human transgenic animal comprising a vector and/or a recombinant polynucleotide encoding a chimeric protein or a monomer of a chimeric dimer protein as previously described according to the present invention.
  • transgenic plant comprising a vector and/or a recombinant polynucleotide encoding a chimeric protein or a monomer of a chimeric dimer protein as previously described according to the present invention.
  • the present invention also relates to a kit comprising a chimeric protein or a monomer of a chimeric dimer protein according to the present invention or a vector and/or a recombinant polynucleotide encoding a chimeric protein or a monomer of a chimeric dimer protein as previously described according to the present invention and instructions for use said kit.
  • the present invention also relates to a composition comprising a chimeric protein or a monomer of a chimeric dimer protein according to the present invention or a vector and/or a recombinant polynucleotide encoding a chimeric protein or a monomer of a chimeric dimer protein as previously described according to the present invention and a carrier. More preferably, is a pharmaceutical composition comprising a chimeric protein or a monomer of a chimeric dimer protein according to the present invention or a vector and for a recombinant polynucleotide encoding a chimeric protein or a monomer of a chimeric dimer protein as previously described according to the present invention and a pharmaceutically active carrier.
  • the chimeric protein or a monomer of a chimeric dimer protein according to the present invention and a pharmaceutically acceptable excipient are administered in a therapeutically effective amount.
  • Such a combination is said to be administered in a “therapeutically effective amount” if the amount administered is physiologically significant.
  • An agent is physiologically significant if its presence results in a detectable change in the physiology of the recipient.
  • an agent is physiologically significant if its presence results in a decrease in the severity of one or more symptoms of the targeted disease and in a genome correction of the lesion or abnormality.
  • Vectors comprising targeting DNA and/or nucleic acid encoding chimeric protein or a monomer of a chimeric dimer protein according to the present invention can be introduced into a cell by a variety of methods (e.g., injection, direct uptake, projectile bombardment, liposomes, electroporation). Chimeric proteins or monomers of chimeric dimer proteins according to the present invention can be stably or transiently expressed into cells using expression vectors. Techniques of expression in eukaryotic cells are well known to those in the art. (See Current Protocols in Human Genetics: Chapter 12 “Vectors For Gene Therapy” & Chapter 13 “Delivery Systems for Gene Therapy”).
  • the chimeric protein or a monomer of a chimeric dimer protein according to the present invention is substantially non-immunogenic, i.e., engender little or no adverse immunological response.
  • a variety of methods for ameliorating or eliminating deleterious immunological reactions of this sort can be used in accordance with the invention.
  • the chimeric protein or a monomer of a chimeric dimer protein according to the present invention is substantially free of N-formyl methionine.
  • Another way to avoid unwanted immunological reactions is to conjugate the chimeric protein or a monomer of a chimeric dimer protein according to the present invention to polyethylene glycol (“PEG”) or polypropylene glycol (“PPG”) (preferably of 500 to 20,000 daltons average molecular weight (MW)).
  • PEG polyethylene glycol
  • PPG polypropylene glycol
  • Conjugation with PEG or PPG can provide non-immunogenic, physiologically active, water soluble chimeric proteins or monomers of chimeric dimer proteins conjugates with anti-viral activity. Similar methods also using a polyethylene-polypropylene glycol copolymer are described in Saifer et al. (U.S. Pat. No. 5,006,333).
  • the present invention also relates to methods for use of said chimeric protein or a monomer of a chimeric dimer protein according to the invention for various applications ranging from targeted DNA cleavage to targeted gene regulation.
  • catalytical activities such as nuclease activity (endonuclease and exonuclease), polymerase activity, kinase activity, phosphatase activity, methylase activity, topoisomerase activity, integrase activity, transposase activity, ligase activity, helicase activity, recombinase activity]
  • nuclease activity encoded DNA clease activity
  • phosphatase activity phosphatase activity
  • methylase activity topoisomerase activity
  • integrase activity transposase activity
  • ligase activity helicase activity
  • recombinase activity the number and the combinations of several protein domains fused to said core scaffold, chimeric protein or a
  • the present invention relates to a method for increasing targeted HR (and mutagenesis via NHEJ) when Double-Strand break activity is promoted in a chimeric protein or a monomer of a chimeric dimer protein according to the present invention targeting a DNA target sequence according to the invention.
  • the addition of at least two catalytically active cleavase domains according to the invention allows to increase Double-strand break-induced mutagenesis by leading to a loss of genetic information and preventing any scarless re-ligation of targeted genomic locus of interest by NHEJ.
  • the present invention relates to a method for increasing targeted HR in a more conservative fashion (with less mutagenesis via NHEJ) when Single-Strand Break activity is promoted in a chimeric protein or a monomer of a chimeric dimer protein according to the present invention targeting a DNA target sequence according to the invention.
  • the present invention relates to a method for increasing excision of a single-strand of DNA spanning the binding region of a chimeric protein or a monomer of a chimeric dimer protein according to the present invention when both one cleavase enhancer domain and one nickase enhancer domain, respectively, are fused to both N-terminus and C-terminus of at least one of the core scaffold of a chimeric protein or a monomer of a chimeric dimer protein according to the present invention.
  • the present invention relates to a method for treatment of a genetic disease caused by a mutation in a specific single double-stranded DNA target sequence in a gene, comprising administering to a subject in need thereof an effective amount of a chimeric protein or a monomer of a chimeric dimer protein, according to the present invention, a functional mutant, a variant or a derivative thereof.
  • said chimeric protein, a functional mutant, a variant or a derivative thereof for treatment of a genetic disease is independent of single-nucleotide polymorphisms (SNPs) that occur in the respective genomes of subjects in need thereof, due to TALE code degeneracy.
  • SNPs single-nucleotide polymorphisms
  • the present invention relates to a method for treatment of a genetic disease caused by a mutation in a nucleic acid target sequence, comprising administering to a subject in need thereof, in order to cure said genetic disease, an effective amount of a chimeric protein or a monomer of a chimeric dimer protein, according to the present invention, a functional mutant, a variant or a derivative thereof wherein said chimeric protein overcomes the genomic variations of subjects due to SNPs.
  • Said method of the present invention allows the treatment of said genetic disease by constructing and administering one unique chimeric protein according to the invention to every subjects in need thereof, whatever SNPs profiles around said mutation responsible for genetic disease in these subjects.
  • said method of the present invention avoids the need to construct and administer one personalized chimeric protein for each subject in need thereof that takes into account each SNP profile around the mutation to cure.
  • said unique chimeric protein to cure said genetic disease according to the present invention can comprise degenerated RVDs in its core scaffold such as NN for recognizing G or A, NS for recognizing A, C, G or T or SN for recognizing G or A.
  • said method of the present invention allows to treat this genetic disease by constructing and administering a unique chimeric protein according to the present invention wherein said core scaffold of said chimeric protein comprises a SN-type RVD for recognizing either G, either A, present in the genome of every subjects at SNPs location, in order to bind said genomic sequence around said SNP and treat said genetic disease.
  • said method can be used to overcome interspecies sequence variations.
  • the present invention relates to a method for inserting a transgene into a specific single double-stranded DNA target sequence of a genomic locus of a cell, tissue or non-human animal, or a plant wherein at least one chimeric protein or a monomer of a chimeric dimer protein of the present invention is transitory or not introduced into said cell, tissue, non-human animal or plant.
  • the present invention relates to a method for optimizing the control of nucleic acid processing activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence.
  • the present invention relates to a method for optimizing the control of nucleic acid processing activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating an optimum core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of nucleic acid processing activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating an optimum C-terminal truncation of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of nucleic acid processing activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating an optimum N-terminal truncation of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of nucleic acid processing activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating two optimum C-terminal truncations of the core scaffold structure to an optimum spacer length as illustrated on FIGS. 10 and 11 .
  • the present invention relates to a method for optimizing the control of nucleic acid processing activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating two optimum N-terminal truncations of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence.
  • the present invention relates to a method for optimizing the control of double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating an optimum core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating an optimum C-terminal truncation of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating two optimum C-terminal truncations of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating two different optimum C-terminal truncations of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating an optimum N-terminal truncation of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating two optimum N-terminal truncations of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating two different optimum N-terminal truncations of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the sequence of said locus of a given genome an optimal C-terminal truncation of the core scaffold of said chimeric protein as illustrated on FIG. 11 .
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the sequence of said locus of a given genome an optimal C-terminal truncation of the core scaffold of said chimeric protein, wherein said spacer length can be comprised between 5 and 40 bp.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the sequence of said locus of a given genome an optimal C-terminal truncation of the core scaffold of said chimeric protein, wherein said spacer length can be comprised between 8 and 40 bp.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the binding site within said locus an optimal C-terminal truncation of the core scaffold of said chimeric protein.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the binding site within said locus, wherein said sequence of said locus is poor in T, an optimal C-terminal truncation of the core scaffold of said chimeric protein.
  • the present invention relates to a method for optimizing the control of double-stranded break location of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating two optimum C-terminal truncations of the core scaffold structure to an optimum spacer length wherein said association allows placing the cleavage site at a more desired location within said spacer as illustrated on FIG. 10 .
  • said association between two optimum C-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at a more desired location that is not in the center of said spacer as illustrated on FIGS. 10 B and C.
  • said association between two optimum C-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at a more desired location that is in the left part (i.e 5′ located regarding the center of the spacer) of said spacer as illustrated on FIG. 10 C.
  • said association between two optimum C-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at a more desired location that is in the right part (i.e 3′ located regarding the center of the spacer) of said spacer as illustrated on FIG. 10 B.
  • said association between two optimum C-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at the center of said spacer as illustrated on FIG. 10 A.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the sequence of said locus of a given genome an optimal N-terminal truncation of the core scaffold of said chimeric protein.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the sequence of said locus of a given genome an optimal N-terminal truncation of the core scaffold of said chimeric protein, wherein said spacer length can be comprised between 5 and 40 bp.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the sequence of said locus of a given genome an optimal N-terminal truncation of the core scaffold of said chimeric protein, wherein said spacer length can be comprised between 8 and 40 bp.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the binding site within said locus an optimal N-terminal truncation of the core scaffold of said chimeric protein.
  • the present invention relates to a method for increasing the number of targets that can be reach by a chimeric protein of the present invention, in a locus of a given genome, by associating to a spacer length imposed by the binding site within said locus, wherein said sequence of said locus is poor in T, an optimal N-terminal truncation of the core scaffold of said chimeric protein.
  • the present invention relates to a method for optimizing the control of double-stranded break location of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by associating two optimum N-terminal truncations of the core scaffold structure to an optimum spacer length wherein said association allows placing the cleavage site at a more desired location within said spacer.
  • said association between two optimum N-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at a more desired location that is not in the center of said spacer.
  • said association between two optimum N-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at a more desired location that is in the left part (i.e 5′ located regarding the center of the spacer) of said spacer.
  • said association between two optimum N-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at a more desired location that is in the right part (i.e 3′ located regarding the center of the spacer) of said spacer.
  • said association between two optimum N-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at the center of said spacer.
  • the present invention relates to a method for optimizing the control of nucleic acid processing activity, the double-stranded break activity of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence, by respectively associating two optimum N-terminal and C-terminal truncations of the core scaffold structure to an optimum spacer length.
  • the present invention relates to a method for optimizing the control of double-stranded break location of a chimeric protein (or a monomer of a chimeric dimer protein according to the present invention) within its nucleic acid target sequence by respectively associating two optimum N-terminal and C-terminal truncations of the core scaffold structure to an optimum spacer length wherein said association allows placing the cleavage site at a more desired location within said spacer
  • Amino acid residues in a polypeptide sequence are designated herein according to the one-letter code, in which, for example, Q means Gln or Glutamine residue, R means Arg or Arginine residue and D means Asp or Aspartic acid residue.
  • Amino acid substitution means the replacement of one amino acid residue with another, for instance the replacement of an Arginine residue with a Glutamine residue in a peptide sequence is an amino acid substitution.
  • DNA or nucleic acid processing activity refers to a particular/given enzymatic activity of a protein domain comprised in a chimeric protein according to the invention such as in the expression “a protein domain to process said nucleic acid target sequence”.
  • Said DNA or nucleic acid processing activity can refer to a cleavage activity, either a cleavase activity either a nickase activity, more broadly a nuclease activity but also a polymerase activity, a kinase activity, a phosphatase activity, a methylase activity, a topoisomerase activity, an integrase activity, a transposase activity, a ligase, a helicase or recombinase activity as non-limiting examples.
  • Nucleotides are designated as follows: one-letter code is used for designating the base of a nucleoside: a is adenine, t is thymine, c is cytosine, and g is guanine.
  • r represents g or a (purine nucleotides)
  • k represents g or t
  • s represents g or c
  • w represents a or t
  • m represents a or c
  • y represents t or c (pyrimidine nucleotides)
  • d represents g, a or t
  • v represents g, a or c
  • b represents g, t or c
  • h represents a, t or c
  • n represents g, a, t or c.
  • variant by “variant”, “chimeric protein variant” or “TALEN variant”, it is intended a chimeric protein, a chimeric protein derived from a Transcription Activator-like Effector (TALE) or a TALEN obtained by replacement of at least one residue in the amino acid sequence of the parent chimeric protein, parent chimeric protein derived from a Transcription Activator-like Effector (TALE) or parent TALEN with at least a different amino acid.
  • TALE Transcription Activator-like Effector
  • TALE Transcription Activator-like Effector
  • peptide linker or “peptidic linker” it is intended to mean a peptide sequence which allows the connection of different monomers or different parts comprised in a fusion protein such as between a core scaffold and a protein domain in a chimeric protein according to the present invention and which allows the adoption of a correct conformation for said fusion protein activity and/or specificity.
  • Peptide linkers can be of various sizes, from 3 amino acids to 50 amino acids as a non limiting indicative range. Peptide linkers can also be qualified as structured or unstructured. Peptide linkers can be qualified as active linkers when they comprise active domains that are able to change their structural conformation under appropriate stimulation.
  • one cell type related to the chosen cell type or organism is intended a cell type or an organism sharing characteristics with said chosen cell type or said chosen organism; this cell type or organism related to the chosen cell type or organism, can be derived from said chosen cell type or organism or not.
  • subdomain it is intended a protein subdomain or a protein part that interacts with another protein subdomain or protein part to form an active entity and/or a catalytic active entity possibly bearing nucleic acid or DNA processing activity of said chimeric protein according to the invention.
  • targeting DNA construct/minimal repair matrix/repair matrix it is intended to mean a DNA construct comprising a first and second portion that are homologous to regions 5′ and 3′ of the DNA target in situ.
  • the DNA construct also comprises a third portion positioned between the first and second portion which comprise some homology with the corresponding DNA sequence in situ or alternatively comprise no homology with the regions 5′ and 3′ of the DNA target in situ.
  • a homologous recombination event is stimulated between the genome containing the targeted gene comprised in the locus of interest and the repair matrix, wherein the genomic sequence containing the DNA target is replaced by the third portion of the repair matrix and a variable part of the first and second portions of the repair matrix.
  • mutant is intended a catalytically active mutant of a protein or a protein domain; such mutant can have the same activity compared to its parent protein or protein domain or additional properties.
  • This definition applies to chimeric proteins or protein domains that constitute chimeric proteins according to the present invention.
  • derivatives of these proteins or protein domains that comprise the entirety or part of these proteins or protein domains fused to other proteic or chemical parts such as tags, antibodies, polyethylene glycol as non-limiting examples.
  • single polypeptide chain is used to qualify a chimeric protein according to the invention which functions as a dimer wherein one first monomer and one second monomer are fused by a peptidic linker.
  • DNA target is intended a polynucleotide sequence that can be processed by a chimeric protein according to the present invention.
  • DNA target refers to a specific DNA location, preferably a genomic location in a cell, but also a portion of genetic material that can exist independently to the main body of genetic material such as plasmids, episomes, virus, transposons or in organelles such as mitochondria or chloroplasts as non-limiting examples.
  • the nucleic acid target sequence is defined by the 5′ to 3′ sequence of one strand of said target, as indicate above for Avr15 (SEQ ID NO: 6) as a non-limiting example.
  • Adjacent is used to distinguish between 1) the nucleic acid sequence recognized and bound by a set of specific RVDs comprised in the core scaffold of said chimeric protein according to the invention and 2) the nucleic acid target sequence to be processed by said chimeric protein according to the invention, said nucleic sequences 1) and 2) being adjacent.
  • said chimeric protein according to the invention functions as a dimer comprising respectively two monomers
  • the term adjacent is equally used to qualify the nucleic acid target sequence regarding the first nucleic acid sequence recognized and bound by the first monomer and to qualify the nucleic acid target sequence regarding the second nucleic acid sequence recognized and bound by the second monomer.
  • the nucleic acid sequence adjacent to the nucleic acid target sequence is meant the recognition/binding site of said chimeric protein according to the invention.
  • delivery vector or “delivery vectors” is intended any delivery vector which can be used in the present invention to put into cell contact (i.e “contacting”) or deliver inside cells or subcellular compartments agents/chemicals and molecules (proteins or nucleic acids) needed in the present invention. It includes, but is not limited to liposomal delivery vectors, viral delivery vectors, drug delivery vectors, chemical carriers, polymeric carriers, lipoplexes, polyplexes, dendrimers, microbubbles (ultrasound contrast agents), nanoparticles, emulsions or other appropriate transfer vectors. These delivery vectors allow delivery of molecules, chemicals, macromolecules (genes, proteins), or other vectors such as plasmids, peptides developed by Diatos. In these cases, delivery vectors are molecule carriers. By “delivery vector” or “delivery vectors” is also intended delivery methods to perform transfection.
  • vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • a “vector” in the present invention includes, but is not limited to, a viral vector, a plasmid, a RNA vector or a linear or circular DNA or RNA molecule which may consists of a chromosomal, non chromosomal, semi-synthetic or synthetic nucleic acids.
  • Preferred vectors are those capable of autonomous replication (episomal vector) and/or expression of nucleic acids to which they are linked (expression vectors). Large numbers of suitable vectors are known to those of skill in the art and commercially available.
  • Viral vectors include retrovirus, adenovirus, parvovirus (e.g. adenoassociated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g.
  • RNA viruses such as picornavirus and alphavirus
  • double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomega-lovirus), and poxvirus (e.g., vaccinia, fowlpox and canarypox).
  • herpesvirus e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomega-lovirus
  • poxvirus e.g., vaccinia, fowlpox and canarypox
  • Other viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example.
  • retroviruses examples include: avian leukosis-sarcoma, mammalian C-type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
  • lentiviral vector HIV-Based lentiviral vectors that are very promising for gene delivery because of their relatively large packaging capacity, reduced immunogenicity and their ability to stably transduce with high efficiency a large range of different cell types.
  • Lentiviral vectors are usually generated following transient transfection of three (packaging, envelope and transfer) or more plasmids into producer cells.
  • lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface.
  • the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex.
  • the product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration in the DNA of infected cells.
  • integrated lentiviral vectors or LV
  • integrated lentiviral vectors or LV
  • non integrative lentiviral vectors or NILV is meant efficient gene delivery vectors that do not integrate the genome of a target cell through the action of the virus integrase.
  • One type of preferred vector is an episome, i.e., a nucleic acid capable of extra-chromosomal replication.
  • Preferred vectors are those capable of autonomous replication and/or expression of nucleic acids to which they are linked.
  • Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as “expression vectors.
  • a vector according to the present invention comprises, but is not limited to, a YAC (yeast artificial chromosome), a BAC (bacterial artificial), a baculovirus vector, a phage, a phagemid, a cosmid, a viral vector, a plasmid, a RNA vector or a linear or circular DNA or RNA molecule which may consist of chromosomal, non chromosomal, semi-synthetic or synthetic DNA.
  • expression vectors of utility in recombinant DNA techniques are often in the form of “plasmids” which refer generally to circular double stranded DNA loops which, in their vector form are not bound to the chromosome.
  • Vectors can comprise selectable markers, for example: neomycin phosphotransferase, histidinol dehydrogenase, dihydrofolate reductase, hygromycin phosphotransferase, herpes simplex virus thymidine kinase, adenosine deaminase, glutamine synthetase, and hypoxanthine-guanine phosphoribosyl transferase for eukaryotic cell culture; TRP1 for S. cerevisiae ; tetracyclin, rifampicin or ampicillin resistance in E. coli .
  • selectable markers for example: neomycin phosphotransferase, histidinol dehydrogenase, dihydrofolate reductase, hygromycin phosphotransferase, herpes simplex virus thymidine kinase, adenosine deaminase
  • said vectors are expression vectors, wherein a sequence encoding a polypeptide of interest is placed under control of appropriate transcriptional and translational control elements to permit production or synthesis of said polypeptide. Therefore, said polynucleotide is comprised in an expression cassette. More particularly, the vector comprises a replication origin, a promoter operatively linked to said encoding polynucleotide, a ribosome binding site, a RNA-splicing site (when genomic DNA is used), a polyadenylation site and a transcription termination site. It also can comprise an enhancer or silencer elements. Selection of the promoter will depend upon the cell in which the polypeptide is expressed. Suitable promoters include tissue specific and/or inducible promoters.
  • inducible promoters are: eukaryotic metallothionine promoter which is induced by increased levels of heavy metals, prokaryotic lacZ promoter which is induced in response to isopropyl- ⁇ -D-thiogalacto-pyranoside (IPTG) and eukaryotic heat shock promoter which is induced by increased temperature.
  • tissue specific promoters are skeletal muscle creatine kinase, prostate-specific antigen (PSA), ⁇ -antitrypsin protease, human surfactant (SP) A and B proteins, ⁇ -casein and acidic whey protein genes.
  • Inducible promoters may be induced by pathogens or stress, more preferably by stress like cold, heat, UV light, or high ionic concentrations (reviewed in Potenza C et al. 2004, In vitro Cell Dev Biol 40:1-22). Inducible promoter may be induced by chemicals (reviewed in (Moore, Samalova et al. 2006); (Padidam 2003); (Wang, Zhou et al. 2003); (Zuo and Chua 2000).
  • Delivery vectors and vectors can be associated or combined with any cellular permeabilization techniques such as sonoporation or electroporation or derivatives of these techniques.
  • cell or cells any prokaryotic or eukaryotic living cells, cell lines derived from these organisms for in vitro cultures, primary cells from animal or plant origin.
  • primary cell or “primary cells” are intended cells taken directly from living tissue (i.e. biopsy material) and established for growth in vitro, that have undergone very few population doublings and are therefore more representative of the main functional components and characteristics of tissues from which they are derived from, in comparison to continuous tumorigenic or artificially immortalized cell lines. These cells thus represent a more valuable model to the in vivo state they refer to.
  • eukaryotic cells refer to a fungal, plant or animal cell or a cell line derived from the organisms listed below and established for in vitro culture. More preferably, the fungus is of the genus Aspergillus, Penicillium, Acremonium, Trichoderma, Chrysoporium, Mortierella, Kluyveromyces or Pichia ; More preferably, the fungus is of the species Aspergillus niger, Aspergillus nidulans, Aspergillus oryzae, Aspergillus terreus, Penicillium chrysogenum, Penicillium citrinum, Acremonium Chrysogenum, Trichoderma reesei, Mortierella alpine, Chrysosporium lucknowense, Kluyveromyces lactis, Pichia pastoris or Pichia ciferrii.
  • the plant is of the genus Arabidospis, Nicotiana, Solanum, lactuca, Brassica, Oryza, Asparagus, Pisum, Medicago, Zea, Hordeum, Secale, Triticum, Capsicum, Cucumis, Cucurbita, Citrullis, Citrus, Sorghum ; More preferably, the plant is of the species Arabidospis thaliana, Nicotiana tabaccum, Solanum lycopersicum, Solanum tuberosum, Solanum melongena, Solanum esculentum, Lactuca saliva, Brassica napus, Brassica oleracea, Brassica rapa, Oryza glaberrima, Oryza sativa, Asparagus officinalis, Pisum sativum, Medicago sativa, zea mays, Hordeum vulgare, Secale cereal, Triticum aestivum, Triticum durum, Capsicum sativus,
  • the animal cell is of the genus Homo, Rattus, Mus, Sus, Bos, Danio, Canis, Felis, Equus, Salmo, Oncorhynchus, Gallus, Meleagris, Drosophila, Caenorhabditis ; more preferably, the animal cell is of the species Homo sapiens, Rattus norvegicus, Mus musculus, Sus scrofa, Bos taurus, Danio rerio, Canis lupus, Felis catus, Equus caballus, Salmo salar, Oncorhynchus mykiss, Gallus gallus, Meleagris gallopavo, Drosophila melanogaster, Caenorhabditis elegans.
  • the cell can be a plant cell, a mammalian cell, a fish cell, an insect cell or cell lines derived from these organisms for in vitro cultures or primary cells taken directly from living tissue and established for in vitro culture.
  • cell lines can be selected from the group consisting of CHO-K1 cells; HEK293 cells; Caco2 cells; U2-OS cells; NIH 3T3 cells; NSO cells; SP2 cells; CHO-S cells; DG44 cells; K-562 cells, U-937 cells; MRC5 cells; IMR90 cells; Jurkat cells; HepG2 cells; HeLa cells; HT-1080 cells; HCT-116 cells; Hu-h7 cells; Huvec cells; Molt 4 cells.
  • All these cell lines can be modified by the method of the present invention to provide cell line models to produce, express, quantify, detect, study a gene or a protein of interest; these models can also be used to screen biologically active molecules of interest in research and production and various fields such as chemical, biofuels, therapeutics and agronomy as non-limiting examples.
  • homologous is intended a sequence with enough identity to another one to lead to homologous recombination between sequences, more particularly having at least 95% identity, preferably 97% identity and more preferably 99%.
  • identity refers to sequence identity between two nucleic acid molecules or polypeptides. Identity can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base, then the molecules are identical at that position. A degree of similarity or identity between nucleic acid or amino acid sequences is a function of the number of identical or matching nucleotides at positions shared by the nucleic acid sequences. Various alignment algorithms and/or programs may be used to calculate the identity between two sequences, including FASTA, or BLAST which are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with, e.g., default setting.
  • mutation is intended the substitution, deletion, insertion of one or more nucleotides/amino acids in a polynucleotide (cDNA, gene) or a polypeptide sequence. Said mutation can affect the coding sequence of a gene or its regulatory sequence. It may also affect the structure of the genomic sequence or the structure/stability of the encoded mRNA.
  • double-strand break-induced mutagenesis refers to a mutagenesis event consecutive to an NHEJ event following an endonuclease-induced DSB, leading to insertion/deletion at the cleavage site of an endonuclease.
  • gene is meant the basic unit of heredity, consisting of a segment of DNA arranged in a linear manner along a chromosome, which codes for a specific protein or segment of protein.
  • a gene typically includes a promoter, a 5′ untranslated region, one or more coding sequences (exons), optionally introns, a 3′ untranslated region.
  • the gene may further comprise a terminator, enhancers and/or silencers.
  • transgene refers to a sequence encoding a polypeptide.
  • the polypeptide encoded by the transgene is either not expressed, or expressed but not biologically active, in the cell, tissue or individual in which the transgene is inserted.
  • the transgene encodes a therapeutic polypeptide useful for the treatment of an individual.
  • gene of interest refers to any nucleotide sequence encoding a known or putative gene product.
  • locus is the specific physical location of a DNA sequence (e.g. of a gene) on a chromosome.
  • locus usually refers to the specific physical location of a chimeric protein's nucleic target sequence on a chromosome.
  • locus which comprises a target sequence that is recognized and cleaved by a chimeric protein according to the invention, is referred to as “locus according to the invention”.
  • the expression “genomic locus of interest” is used to qualify a nucleic acid sequence in a genome that can be a putative target for a double-strand break according to the invention.
  • genomic locus of interest of the present invention can not only qualify a nucleic acid sequence that exists in the main body of genetic material (i.e. in a chromosome) of a cell but also a portion of genetic material that can exist independently to said main body of genetic material such as plasmids, episomes, virus, transposons or in organelles such as mitochondria or chloroplasts as non-limiting examples.
  • loss of genetic information is understood the elimination or addition of at least one given DNA fragment (at least one nucleotide) or sequence within the intervening sequence between at least two processing sites of the chimeric protein of the present invention or between two chimeric proteins according to the present invention.
  • This loss of genetic information can be, as a non-limiting example, the elimination of an intervening sequence between two processing sites of two chimeric proteins according to the present invention.
  • this loss of genetic information can also be an excision of a single-strand of DNA spanning the binding region of a chimeric protein according to the present invention
  • scarless re-ligation or “scarless religation” is intended the perfect re-ligation event, without loss of genetic information (no insertion/deletion events) of the DNA broken ends through NHEJ process after the creation of a double-strand break event.
  • Imprecise NHEJ is intended the re-ligation of nucleic acid ends generated by a DSB, with insertions or deletions of nucleotides. Imprecise NHEJ is an outcome and not a repair pathway and can result from different NHEJ pathways (Ku dependent or Ku independent as non-limiting examples).
  • fusion protein is intended the result of a well-known process in the art consisting in the joining of two or more genes which originally encode for separate proteins or part of them, the translation of said “fusion gene” resulting in a single polypeptide with functional properties derived from each of the original proteins.
  • chimeric protein any fusion protein comprising a core scaffold comprising a set of RVDs to bind a nucleic acid sequence and one protein domain to process a nucleic acid target sequence adjacent to said bound nucleic acid sequence.
  • Said chimeric protein according to the present invention can function as a dimer wherein each monomer (a monomer of a chimeric dimer protein in this case) constituting said chimeric dimer protein comprises a set of RVDs to bind a nucleic acid sequence and one protein domain to process a nucleic acid target sequence adjacent to said bound nucleic acid sequence.
  • protein domain or “catalytic domain” is meant the nucleic acid target sequence processing part of said chimeric protein according to the present invention.
  • Said protein domain or catalytic domain can provide any catalytical activity as classified and named according to the reaction they catalyze [Enzyme Commission number (EC number) at http://www.chem.qmul.ac.uk/iubmb/enzyme/)].
  • Said protein domain or catalytic domain can be a catalytically active entity by itself.
  • Said protein domain or catalytic domain can be a protein subdomain that needs to interact with another protein subdomain to form a dimeric protein domain active entity.
  • said protein domain or catalytic domain can be a first protein subdomain interacting with a second protein subdomain of another chimeric monomer protein according to the invention to form the catalytically active protein entity able to process the nucleic acid target sequence.
  • TALEN TALE-nuclease
  • TALEN Transcription Activator Like Effector
  • Said TALEN is a subclass of chimeric protein according to the present invention.
  • spacer is meant the nucleic acid area that separates the two nucleic acid sequences recognized and bound by each monomer constituting a chimeric dimer protein according to the invention.
  • spacer length is meant the nucleic acid distance that separates the two nucleic acid sequences recognized and bound by each monomer constituting a chimeric dimer protein according to the invention.
  • said nucleic acid target sequence of the chimeric protein according to the present invention can be encompassed in said spacer.
  • Said nucleic acid target sequence of the chimeric protein according to the present invention can be identical to said spacer.
  • Said nucleic acid target sequence of the chimeric protein according to the present invention can be different of said spacer.
  • phrases “selected from the group consisting of,” “chosen from,” and the like include mixtures of the specified materials.
  • the amino acid sequences of the N-terminal, C-terminal domains and RVDS were based on the AvrBs3 TAL (ref: GenBank: X16130.1, SEQ ID NO: 1).
  • Nter wt or WT Nter (SEQ ID NO: 292), i.e. corresponding to the N terminal domain of natural AvrBs3 (SEQ ID NO: 1) except an Ala residue in position 2]
  • Cter wt or WT Cter (SEQ ID NO: 400) lacking the activation domain of the C-terminal domain of natural AvrBs3 (SEQ ID NO: 1)
  • nuclease catalytic head were synthesized (TopGene Technologies) and subcloned into the pCLS0542 (SEQ ID NO: 2) yeast expression plasmid, using NcoI and EagI restriction enzymes, leading to the backbone plasmid pCLS7183 (referred as backbone wt, SEQ ID NO: 3).
  • the C-terminal and the N-terminal domains are separated by two BsmBI restriction sites.
  • the AvrBs3-derived set of repeat domains (RVDs) (SEQ ID NO: 4) was subcloned in the pCLS7183 using type IIs restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence, leading to pCLS7184 and subsequent AvrBs3-derived TALEN (referred as control wt, SEQ ID NO: 5). All the yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al.
  • the AvrBs3-derived TALEN was tested at 30° C. in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) as homodimer (two identical recognition sequences are placed facing each other on both DNA strands) on the target Avr15 (SEQ ID NO: 6, Table 3). TALEN cleavage activity levels on its respective target in yeast are shown on FIG. 2 .
  • the DNA encoding a HA tag, the N-terminal domain (referred as Nter wt), the C-terminal domain (referred as Cter wt) and the nuclease catalytic head were synthesized and subcloned into the pCLS1853 (SEQ ID NO: 7) mammalian expression plasmid, using AscI and XhoI restriction enzymes, leading to the backbone plasmid pCLS7111 (SEQ ID NO: 8).
  • the C-terminal and the N-terminal domains are separated by two BsmBI restriction sites.
  • the AvrBs3-derived set of repeat domains (SEQ ID NO: 4) was subcloned in the pCLS7111 using type IIs restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence, leading to pCLS7509 and subsequent TALEN (SEQ ID NO: 9).
  • All the mammalian target reporter plasmids containing the TALEN DNA target sequences were constructed using standard gateway Gateway protocol (INVITROGEN) into a CHO reporter vector (Grizot, Epinat et al.; Arnould, Chames et al. 2006).
  • Activity of AvrBs3-derived TALEN was tested in our extrachromosomal assay in mammalian cells (CHO K1) as homodimer (two identical recognition sequences are placed facing each other on both DNA strands) on the target Avr15 (SEQ ID NO: 6, Table 3).
  • CHO K1 cells were transfected in a 96-well plate format with 75 or 200 ng of target vector and an increasing quantity of each variant DNA from 0.7 to 25 ng, in the presence of PolyFect reagent (1 ⁇ L per well). The total amount of transfected DNA was completed to 125 or 250 ng (target DNA, variant DNA, carrier DNA) using an empty vector. 72 hours after transfection, culture medium was removed and 150 ⁇ l of lysis/revelation buffer for ⁇ -galactosidase liquid assay was added. After incubation at 37° C., OD was measured at 420 nm. The entire process is performed on an automated Velocity11 BioCel platform (Grizot, Epinat et al.).
  • TALEN cleavage activity levels on their respective targets in mammalian cells are shown on FIG. 3 .
  • Truncations of the first 153 (numbering based on SEQ ID NO:1)_amino acids residues of the N-terminal domain of the AvrBs3-derived TALEN (pCLS7184, SEQ ID NO: 5) were realized.
  • DNA sequence corresponding to amino acids D154 to N228 was amplified by PCR, using the backbone plasmid pCLS7183 (referred as backbone wt, SEQ ID NO: 3) as template, to add a NcoI restriction site in 5′ and a XmnI restriction site in 3′.
  • the PCR construct was subcloned in the TALEN yeast expression backbone (pCLS7183, SEQ ID NO: 3) to replace the sequence of the N-terminal domain (referred as Nter wt) comprised between the NcoI and XmnI restriction sites, leading to pCLS7724 (SEQ ID NO: 10). All DNA sequences were validated by sequencing.
  • the AvrBs3-derived set of repeat domains (SEQ ID NO: 4) was subcloned in the pCLS7724 using type IIs restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence, leading to pCLS7725 and subsequent TALEN (SEQ ID NO: 11).
  • This truncated variant was screened in our yeast SSA assay (see Example 1) as homodimer (two identical recognition sequences are placed facing each other on both DNA strands) on the target Avr15 (SEQ ID NO: 6, Table 3). Activity level of the truncated variant is shown on FIG. 4 .
  • Incremental truncation of the DNA coding for the N-terminal domain of the AvrBs3-derived TALEN (pCLS7184, SEQ ID NO: 5), starting from the 5′ of the coding strand, allows the identification of minimal N-terminal domains that could still lead active TALEN.
  • the complete sequence of the N-terminal domain of AvrBs3 is amplified by PCR. Restriction site BsmBI, XmnI and SacI or AatII are introduced, in this specific order at the 3′ of the coding strand. After digestion with SacI or AatII, incremental truncation of the 5′ is performed using a 3′ ⁇ 5′ exonuclease III.
  • RVDs The AvrBs3-derived set of repeat domains (RVDs) (SEQ ID NO: 4) or any other previously synthesized RVD sequence is subcloned in the previously constructed plasmids using type IIs restriction enzymes BsmBI for the receiving plasmid. All created constructions are screened in our yeast SSA assay (see Example 1) for activity and specificity toward the AvrBs3 target or any other targets.
  • a particular truncated variant is judged useful if it provides, a minimal 5% retention in activity of the starting AvrBs3-derived TALEN (SEQ ID NO: 5) on its Avr15 target (SEQ ID NO: 6), more preferably a minimal 10% retention, more preferably 20%, more preferably 30%, more preferably 40%, more preferably 50%, again more preferably a retention in activity greater than 50%.
  • a particular variant is judged useful if it provides, on any targets having a C, G or A at position 0, a minimal 5% retention in activity of the starting AvrBs3-derived TALEN (SEQ ID NO: 5) on its Avr15 target (SEQ ID NO: 6), more preferably a minimal 10% retention, more preferably 20%, more preferably 30%, more preferably 40%, more preferably 50%, again more preferably a retention in activity greater than 50%.
  • a particular variant is judged useful if it provides, on any or all targets, a minimal 5% retention in activity of the starting AvrBs3-derived TALEN (SEQ ID NO: 5) on its Avr15 target (SEQ ID NO: 6), more preferably a minimal 10% retention, more preferably 20%, more preferably 30%, more preferably 40%, more preferably 50%, again more preferably a retention in activity greater than 50%.
  • DNA sequences corresponding to truncations (numbering based on SEQ ID NO:1) after positions E886 (C0), P897 (C11), G914 (C28), L926 (C40), D950 (C64), R1000 (C115) and D1059 (C172) were amplified by PCR, using the backbone plasmid pCLS7183 (referred as backbone wt, SEQ ID NO: 3) as template, to add a XmnI restriction site in 5′ and a BamHI restriction site in 3′ (Protein sequences of truncated C-terminal domains C11 to C172 are respectively given in SEQ ID NO: 295 to 300).
  • PCR constructs were subcloned in the TALEN yeast expression backbone (pCLS7183, SEQ ID NO: 3) to replace the sequence of the full C-terminal domain, leading to pCLS7820, pCLS7802, pCLS7806, pCLS7808, pCLS7810, pCLS7812, pCLS7816 (SEQ ID NO: 12 to 18). All DNA sequences were validated by sequencing.
  • the AvrBs3-derived set of repeat domains (SEQ ID NO: 4) was subcloned in pCLS7820, pCLS7802, pCLS7806, pCLS7808, pCLS7810, pCLS7812, pCLS7816 (SEQ ID NO: 12 to 18) and using type IIs restriction enzymes (BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence) leading to pCLS7821, pCLS7803, pCLS7807, pCLS7809, pCLS7811, pCLS7813, pCLS7817 and subsequent TALENs (SEQ ID NO: 19 to 25).
  • type IIs restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence
  • TAL effectors possess a characteristic truncated RVD (the so-called half repeat) at the end (C-terminus) of the repeat region.
  • This half repeat is supposed to target specifically the last base of the target sequenced.
  • an Avrbs3-derived TALEN (pCLS7184, SEQ ID NO: 5) was screened, in our yeast assay, for activity on four identical targets except for the last base (A, T, G or C, in the n position, SEQ ID NO: 171 to 174, Table 4). No significant differences in activity were observed on the four targets as shown on FIG. 7 indicating the lack of specificity of the last half RVD in this TALEN context.
  • linker library is then subcloned in pCLS7183 (SEQ ID NO: 3) via the XmaI and BamHI restriction sites to replace the C-terminal domain of the AvrBs3-derived TALEN (pCLS7184, SEQ ID NO: 5).
  • RVDs The AvrBs3-derived set of repeat domains (RVDs) or any other RVD sequences having or lacking the terminal half RVD is cloned in this backbone library plasmid as described in Example 3A and resulting clones are screened in our yeast SSA assay (see Example 1).
  • a particular polypeptide linker domain is judged useful if it provides a minimal 5% retention in activity of the starting AvrBs3-derived TALEN (SEQ ID NO: 5) on its Avr15 target (SEQ ID NO: 6), more preferably a minimal 10% retention, more preferably 20%, more preferably 30%, more preferably 40%, more preferably 50%, again more preferably a retention in activity greater than 50%.
  • polypeptide linker The DNA (so called “polypeptide linker”) coding for, seven different polypeptides (SEQ ID NO: 479 to 485) were prepared by PCR using standard molecular biology procedures. These linkers contain, at the DNA level, a XmaI and a BamHI restriction sites in their 5′ and 3′ ends respectively. These seven linkers were then subcloned individually into a XmaI and BamHI pre-digested backbone pCLS9943 (SEQ ID NO: 486) via the XmaI and BamHI restriction sites to create a new C-terminal domain linker scaffold (pCLS12233 to 12238 and pCLS12270, SEQ ID NO: 487 to 493).
  • This backbone, pCLS9943 contains an additional N-terminal NLS sequence followed by an HA tag and a C11 truncated C-terminal domain compared to the original pCLS7183.
  • the RVD arrays coding for RAGT2.3 (SEQ ID NO: 494) were subcloned individually in the pCLS12233 to pCLS12237 and pCLS12270 using type IIs restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence, leading to the seven constructs, pCLS12945 to pCLS12951 (SEQ ID NO: 495 to 501).
  • Linkers #8, #27 and #35 (SEQ ID NO: 141, 160 and 168 respectively) showed significant activity toward AvrBs3 target in our yeast assay ( FIG. 26 ).
  • Activity is detected for targets with a spacer ranging from 15 to 30 bp for the TALEN having the full C-terminal domain, activity is detected for targets with a spacer ranging from 8 to 30 bp for the TALEN having the truncation C0 or C11, activity is detected for targets with a spacer ranging from 9 bp to 30 bp for the TALEN having the truncation C28, activity is detected for targets with a spacer ranging from 11 to 30 bp for the TALEN having the truncation C40, activity is detected for targets with a spacer ranging from 12 bp to 30 bp for the TALEN having the truncation C64 and C115 and activity is detected for targets with a spacer ranging from 13 to 30 bp for the TALEN having the truncation C172.
  • heterodimeric TALEN requires such large pseudo palindromic binding sites, such sequences are unlikely to be naturally present in genomic target. Relationship between spacer length and C-terminal truncations has been studied. In such a case of heterodimeric targets, C-terminal truncations on both TALENs do not require being identical and asymmetrical truncations have been tested.
  • Results show that different truncations can be associated in the same TALEN, modulating the activity over the spacer length space.
  • Such kinds of architectures (asymmetrical) direct more precisely the cleavage on the target spacer, either on the left part or on the right part or on center part.
  • results allow optimizing the control of double-stranded break localization of a TALEN within its nucleic acid target sequence by associating two optimum C-terminal truncations of the core scaffold structure to an optimum spacer length wherein said association allows placing the cleavage site at a more desired location within said spacer.
  • Said association between two optimum C-terminal truncations of the core scaffold structure and an optimum spacer length allows placing the cleavage site at a more desired location that is in the center of said spacer or not i.e either in the left part (5′ located regarding the center of the spacer) of said spacer, either in the right part (3′ located regarding the center of the spacer) of said spacer.
  • TALEN couples are combinations of AvrBs3-derived (SEQ ID NO: 5) and RAGT2R (SEQ ID NO: 127) parent TALEN containing respectively C0, C11, C40, C117 and Cter WT C-terminal domains for AvrBs3-derived constructs and C0, C11, C40 and Cter WT C-terminal domains for RAGT2R constructs.
  • the DNA encoding a nuclear localization sequence NLS, either a HA tag or a S tag, the N-terminal domain, the C11 truncated C-terminal domain and a nuclease catalytic head was synthesized (TopGene Technologies) and subcloned into the pCLS1853 (SEQ ID NO: 7) mammalian expression plasmid, using AscI and XhoI restriction enzymes, leading to the backbone plasmids pCLS8425 (HA tag) and pCLS8429 (S tag) (SEQ ID NO: 175 and 176).
  • the C-terminal and the N-terminal domains are separated by two BsmBI restriction sites.
  • the set of repeat domains (RVDs) binding the left part of the DNA target sequence DMDT2.1, ILRGT2.1, and HBBT1.1 (SEQ ID NO: 189, SEQ ID NO: 190 and SEQ ID NO: 192) were subcloned in the pCLS8425 using type IIs restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence, leading to pCLS8453 (DMDT2.1 left; SEQ ID NO: 180), pCLS8445 (ILRGT2.1 left; SEQ ID NO: 181), and pCLS8461 (HBBT1.1 left; SEQ ID NO: 182) and subsequent left monomer TALENs (SEQ ID NO: 180 to 182).
  • RVDs The set of repeat domains (RVDs) binding the right part of the DNA target sequence DMDT2.1, ILRGT2.1, and HBBT1.1 (SEQ ID NO: 183 to 185) were subcloned in the pCLS8429 using type IIs restriction enzymes BsmBI for the receiving plasmids and BbvI and SfaNI for the inserted RVD sequences, leading to pCLS8457 (DMDT2.1 right; SEQ ID NO: 186), pCLS8449 (ILRGT2.1 left; SEQ ID NO: 187), and pCLS8465 (HBBT1.1 left; SEQ ID NO: 188) and subsequent TALEN (SEQ ID NO: 186 to 188).
  • the plasmids pair pCLS8453 and pCLS8457 were co-transformed, with its DMDT2.1 target into CHO-K1 cells in order to express the heterodimeric TALEN.
  • Activity of the TALEN was screened in our mammalian SSA assay (see example 1).
  • the plasmids pair pCLS8445 and pCLS8549 were co-transformed, with its ILRGT2.1 target, into CHO-K1 cells in order to express the heterodimeric TALEN.
  • Activity of the TALEN was screened in our mammalian SSA assay (see example 1).
  • the plasmids pair pCLS8461 and pCLS8465 were co-transformed, with its HBBT1.1 target, into CHO-K1 cells in order to express the heterodimeric TALEN.
  • Activity of the TALEN was screened in our mammalian SSA assay (see example 1).
  • TALENs activity levels in this assay indicate that they cleave their target sequence in the CHO mammalian cells ( FIG. 8 ).
  • the catalytic domain of I-TevI (SEQ ID NO: 349), a member of the GIY-YIG endonuclease family, was fused to a TAL backbone, composed of a N-terminal domain, a central core composed of RVDs and a C-terminal domain, to create a new class of TALEN (TALE::TevI). To distinguish the orientation (N-terminal vs.
  • construct names are written as either CD::TALE-RVD (catalytic domain is fused N-terminal to the TALE domain) or TALE-RVD::CD (catalytic domain is fused C-terminal to the TALE domain), where “-RVD” optionally designates the sequence recognized by the TALE domain and “CD” is the catalytic domain type.
  • TALE-AvrBs3::TevI novel TALE::TevI constructions that target AvrBs3 sequence for example, thus named TALE-AvrBs3::TevI.
  • a core TALE scaffold ST2 (SEQ ID NO: 464) onto which (a) different sets of RVD domains could be inserted to change DNA binding specificity, and; (b) a selection of I-TevI-derived catalytic domains could be attached, N- or C-terminal, to effect DNA cleavage (or nicking) was generated.
  • the sT2 truncated scaffold was generated by the PCR from a full-length core TALEN scaffold template (pCLS7183, SEQ ID NO: 3) using primers CMP_G061 (SEQ ID NO: 440) and CMP_G065 (SEQ ID NO: 441) and was cloned into vector pCLS7865 (SEQ ID NO: 442) to generate pCLS7865-cTAL11_CFS1 (pCLS9009, SEQ ID NO: 443) where CFS1 designates the amino acid sequence -GSSG- (with underlying restriction site BamHI and Kpn21 in the coding DNA to facilitate cloning).
  • the DNA sequence coding for the RVDs to target the AvrBs3 site was subcloned into both plasmids pCLS9010 (SEQ ID NO: 451) and pCLS9011 (SEQ ID NO: 452) using Type IIS restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence to create the subsequent TALE-AvrBs3::TevI constructs cT11Avr_TevD01 (pCLS9012, SEQ ID NO: 453) and cT11Avr_TevD02 (pCLS9013, SEQ ID NO: 454), respectively.
  • TALE-AvrBs3::TevI constructs were sequenced and the insert transferred to additional vectors as needed (see below and Example 7b).
  • TALE-AvrBs3::TevI yeast expression plasmids pCLS8523 (SEQ ID NO: 455) and pCLS8524 (SEQ ID NO: 456), were prepared by yeast in vivo cloning using plasmids pCLS9012 and pCLS9013 (SEQ ID NO: 453 and 454), respectively.
  • plasmid pCLS9012; SEQ ID NO: 453 or pCLS9013, SEQ ID NO: 454 linearized by digestion with BssHII and 1 ng of the pCLS0542 (SEQ ID NO: 2) plasmid DNA linearized by digestion with NcoI and EagI were used to transform the yeast S. cerevisiae strain FYC2-6A (MAT ⁇ , trp1 ⁇ 63, leu2 ⁇ 1, his3 ⁇ 200) using a high efficiency LiAc transformation protocol (Arnould et al. 2007).
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • TALE-AvrBs3::TevI constructs were tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on pseudo palindromic targets in order to compare activity with a standard TALE-AvrBs3::FokI TALEN, which requires two binding sites for activity.
  • AvrBS3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 220 to 255, Table 3).
  • TALE-AvrBs3::TevI activity levels on their respective targets in yeast cells are shown on FIG. 12 .
  • Data summarized in FIG. 12 show that TALE-AvrBs3::TevI is active against several targets in Yeast.
  • DNA encoding the TALE-AvrBs3::TevI construct from either pCLS9012 (SEQ ID NO: 453) or pCLS9013 (SEQ ID NO: 454) was subcloned into the pCLS1853 (SEQ ID NO: 7) mammalian expression plasmid using AscI and XhoI restriction enzymes for the receiving plasmid and BssHII and XhoI restriction enzymes for the TALE-AvrBs3::TevI insert, leading to the mammalian expression plasmids pCLS8993 and pCLS8994 (SEQ ID NO: 457 and 458), respectively.
  • All mammalian target reporter plasmids containing the TALEN DNA target sequences were constructed using the standard Gateway protocol (INVITROGEN) into a CHO reporter vector (Arnould, Chames et al. 2006, Grizot, Epinat et al. 2010).
  • the TALE-AvrBs3::TevI constructs were tested in an extrachromosomal assay in mammalian cells (CHO K1) on pseudo palindromic targets in order to compare activity with a standard TALE-AvrBs3::FokI TALEN, which requires two binding sites for activity.
  • AvrBS3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 220 to 255, Table 3).
  • CHO K1 cells were transfected in a 96-well plate format with 75 ng of target vector and an increasing quantity of each variant DNA from 0.7 to 25 ng, in the presence of PolyFect reagent (1 ⁇ L per well). The total amount of transfected DNA was completed to 125 ng (target DNA, variant DNA, carrier DNA) using an empty vector. Seventy-two hours after transfection, culture medium was removed and 150 ⁇ l of lysis/revelation buffer for ⁇ -galactosidase liquid assay was added. After incubation at 37° C., optical density was measured at 420 nm. The entire process is performed on an automated Velocity11 BioCel platform (Grizot, Epinat et al. 2009).
  • TALE-AvrBs3::TevI constructs (12.5 ng DNA transfected) on the Avr15 target (SEQ ID NO: 230) are shown on FIG. 13 .
  • TALE-AvrBs3::TevI appears to be efficient to cleave the target sequence.
  • Variants differing by truncations of the C-terminal domain of the AvrBs3-derived TALEN are chosen as starting scaffolds.
  • a subset of these variants includes truncation after positions E886 (C0), P897 (C11), G914 (C28), L926 (C40), D950 (C64), R1000 (C115), D1059 (C172) (the protein domains of truncated C-terminal domains C11 to C172 are respectively given in SEQ ID NO: 295 to 300) and P1117 [also referred as Cter wt or WT Cter (SEQ ID NO: 400) lacking the activation domain of the C-terminal domain of natural AvrBs3 (SEQ ID NO: 1)].
  • the plasmids coding for the variant scaffolds containing the AvrBs3-derived N-terminal domain, the AvrBs3-derived set of repeat domains and the truncated AvrBs3-derived C-terminal domain [pCLS7821, pCLS7803, pCLS7807, pCLS7809, pCLS7811, pCLS7813, pCLS7817 (SEQ ID NO: 19 to 25) which are based on the pCLS7184 (SEQ ID NO: 5)] allow cloning of any catalytic domain in fusion to the C-terminal domain, using the restriction sites BamHI and EagI.
  • Variants of the catalytic domain of I-TevI are designed from the N-terminal region of I-TevI.
  • a subset of these variants includes truncations of the catalytic domain, the deletion-intolerant region of its linker, the deletion-tolerant region of its linker and its zinc finger (SEQ ID: 459 to 462) (Liu, dansereau et al. 2008).
  • the DNA corresponding to these variants of I-TevI is amplified by the PCR to introduce, at the DNA level, a BamHI (at the 5′ of the coding strand) and a EagI (at the 3′ of the coding strand) restriction site and, at the protein level, a linker (for example -SGGSGS- stretch, SEQ ID NO: 463) between the C terminal domain of the TAL and the variant of the catalytic domain of I-TevI.
  • the final TALE::TevI constructs are generated by insertion of the variant of I-TevI catalytic domains into the scaffold variants using BamHI and EagI and standard molecular biology procedures.
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • the TALE-AvrBs3::TevI constructs were tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al.
  • AvrBS3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 220 to 255, Table 3).
  • NucA (SEQ ID NO: 355), a nonspecific endonuclease from Anabaena sp., was fused to a TALE-derived scaffold (composed of a N-terminal domain, a central core composed of RVDs and a C-terminal domain) to create a new class of cTALEN (TALE::NucA). To distinguish the orientation (N-terminal vs.
  • construct names are written as either CD::TALE-RVD (catalytic domain is fused N-terminal to the TALE domain) or TALE-RVD::CD (catalytic domain is fused C-terminal to the TALE domain), where “-RVD” optionally designates the sequence recognized by the TALE domain and “CD” is the catalytic domain type.
  • TALE-AvrBs3::NucA novel TALE::NucA constructions that target for example the AvrBs3 sequence, and are thus named TALE-AvrBs3::NucA.
  • the wild-type NucA endonuclease can be inhibited by complex formation with the NuiA protein (SEQ ID NO: 473).
  • the NuiA protein can function as a protein domain to modulate the activity of NucA or TALE::NucA constructs.
  • a core TALE scaffold, sT2 (SEQ ID NO: 464) was selected onto which (a) different sets of RVD domains could be inserted to change DNA binding specificity, and; (b) a selection of NucA-derived catalytic domains could be attached, N- or C-terminal, to effect DNA cleavage (or nicking).
  • the sT2 truncated scaffold was generated by the PCR from a full-length core TALEN scaffold template (pCLS7183, SEQ ID NO: 3) using primers CMP_G061 (SEQ ID NO: 440) and CMP_G065 (SEQ ID NO: 441) and was cloned into vector pCLS7865 (SEQ ID NO: 442) to generate pCLS7865-cTAL11_CFS1 (pCLS9009, SEQ ID NO: 443), where CFS1 designates the amino acid sequence -GSSG- (with underlying restriction sites BamHI and Kpn2I in the coding DNA to facilitate cloning).
  • the NucA (SEQ ID NO: 355) catalytic domain corresponding to amino acid residues 25 to 274, was subcloned into the pCLS9009 backbone (SEQ ID NO: 443) by restriction and ligation using BamHI and EagI restriction sites, yielding pCLS7865-cT11_NucA (pCLS9937, SEQ ID NO: 465).
  • the fusion contains the dipeptide -GS- linking the TALE-derived DNA binding domain and NucA-derived catalytic domain.
  • the cloning step also brings at the amino acid level an AAD sequence at the Cter of the NucA catalytic domain.
  • the DNA sequence coding for the RVDs to target the AvrBs3 site was subcloned into plasmid pCLS9937 (SEQ ID NO: 465) using Type IIS restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence to create the subsequent TALE-AvrBs3::NucA construct cT11Avr_NucA (pCLS9938, SEQ ID NO: 466).
  • the TALE-AvrBs3::NucA construct was sequenced and the insert transferred to additional vectors as needed (see below).
  • the final TALE-AvrBs3::NucA yeast expression plasmid, pCLS9924 (SEQ ID NO: 467), was prepared by yeast in vivo cloning using plasmid pCLS9938 (SEQ ID NO: 466).
  • plasmid pCLS9938 approximately 40 ng of plasmid (pCLS9938) linearized by digestion with BssHII and 1 ng of the pCLS0542 (SEQ ID NO: 2) plasmid DNA linearized by digestion with NcoI and EagI were used to transform the yeast S. cerevisiae strain FYC2-6A (MAT ⁇ , trp1 ⁇ 63, leu2 ⁇ 1, his3 ⁇ 200) using a high efficiency LiAc transformation protocol (Arnould et al. 2007).
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • the TALE-AvrBs3::NucA construct was tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on pseudo palindromic targets in order to compare activity with a standard TALE-AvrBs3::FokI TALEN, which requires two binding sites for activity.
  • AvrBS3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 220 to 255, Table 8).
  • constructs were tested on a target having only a single AvrBs3 recognition site (SEQ ID NO: 468; Table 8).
  • Variants differing by truncations of the C-terminal domain of the AvrBs3-derived TALEN are chosen as starting scaffolds.
  • a subset of these variants includes truncation after positions E886 (C0), P897 (C11), G914 (C28), L926 (C40), D950 (C64), R1000 (C115), D1059 (C172) (the protein domains of truncated C-terminal domains C11 to C172 are respectively given in SEQ ID NO: 295 to 300) and P1117 [also referred as Cter wt or WT Cter (SEQ ID NO: 400) lacking the activation domain of the C-terminal domain of natural AvrBs3 (SEQ ID NO: 1)].
  • the plasmids coding for the variant scaffolds containing the AvrBs3-derived N-terminal domain, the AvrBs3-derived set of repeat domains and the truncated AvrBs3-derived C-terminal domain [pCLS7821, pCLS7803, pCLS7807, pCLS7809, pCLS7811, pCLS7813, pCLS7817 (SEQ ID NO: 19 to 25) which are based on the pCLS7184 (SEQ ID NO: 5)] allow cloning of any catalytic domain in fusion to the C-terminal domain, using the restriction sites BamHI and EagI.
  • the DNA corresponding to amino acid residues 25 to 274 of NucA is amplified by the PCR to introduce, at the DNA level, a BamHI (at the 5′ of the coding strand) and a EagI (at the 3′ of the coding strand) restriction site and, at the protein level, a linker (for example -SGGSGS- stretch, SEQ ID NO: 463) between the C terminal domain of the TALE and the NucA catalytic domain.
  • the final TALE::NucA constructs are generated by insertion of the NucA catalytic domain into the scaffold variants using BamHI and EagI and standard molecular biology procedures.
  • the cloning step also brings at the amino acid level an AAD sequence at the Cter of the NucA catalytic domain.
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • TALE-AvrBs3::NucA constructs were tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on pseudo palindromic targets in order to compare activity with a standard TALE-AvrBs3::FokI TALEN, which requires two binding sites for activity.
  • AvrBs3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 220 to 255, Table 8).
  • TALE-AvrBs3::NucA constructs were tested on a target having only a single AvrBs3 recognition site (SEQ ID NO: 468).
  • Data summarized in FIG. 14 show that TALE-AvrBs3::NucA constructs are active on all targets having at least one AvrBs3 recognition site, according to the chimeric protein of the present invention.
  • the catalytic domain of ColE7 (SEQ ID NO: 478 of ColE7 protein SEQ ID NO: 340), a nonspecific endonuclease from E. coli , was fused to a TALE-derived scaffold (composed of a N-terminal domain, a central core composed of RVDs and a C-terminal domain) to create a new class of cTALEN (TALE::ColE7).
  • TALE derived scaffold
  • construct names are written as either CD::TALE-RVD (catalytic domain is fused N-terminal to the TALE domain) or TALE-RVD::CD (catalytic domain is fused C-terminal to the TALE domain), where “-RVD” optionally designates the sequence recognized by the TALE domain and “CD” is the catalytic domain type.
  • TALE-AvrBs3::ColE7 novel TALE::ColE7 constructions that target for example the AvrBs3 sequence, and are thus named TALE-AvrBs3::ColE7.
  • the wild-type ColE7 endonuclease can be inhibited by complex formation with the Im7 immunity protein (SEQ ID NO: 474).
  • the Im7 protein can function as auxiliary protein domain to modulate the nuclease activity of ColE7 or TALE::ColE7 constructs.
  • a core TALE scaffold, sT2 (SEQ ID NO: 464) was selected onto which (a) different sets of RVD domains could be inserted to change DNA binding specificity, and; (b) a selection of ColE7-derived catalytic domains could be attached, N- or C-terminal, to effect DNA cleavage (or nicking).
  • the sT2 truncated scaffold was generated by the PCR from a full-length core TALEN scaffold template (pCLS7183, SEQ ID NO: 3) using primers CMP_G061 (SEQ ID NO: 440) and CMP_G065 (SEQ ID NO: 441) and was cloned into vector pCLS7865 (SEQ ID NO: 442) to generate pCLS7865-cTAL11_CFS1 (pCLS9009, SEQ ID NO: 443), where CFS1 designates the amino acid sequence -GSSG- (with underlying restriction sites BamHI and Kpn2I in the coding DNA to facilitate cloning).
  • the ColE7 (SEQ ID NO: 478) catalytic domain was subcloned into the pCLS9009 backbone by restriction and ligation using Kpn2I and EagI restriction sites, yielding pCLS7865-cT11_ColE7 (pCLS9939, SEQ ID NO: 475).
  • the fusion contains the dipeptide -GSSG- linking the TALE-derived DNA binding domain and ColE7-derived catalytic domain.
  • the DNA sequence coding for the RVDs to target the AvrBs3 site was subcloned into plasmid pCLS9939 (SEQ ID NO: 475) using Type IIS restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence to create the subsequent TALE-AvrBs3::ColE7 construct cT11Avr_ColE7 (pCLS9940, SEQ ID NO: 476).
  • the TALE-AvrBs3::ColE7 construct was sequenced and the insert transferred to additional vectors as needed (see below).
  • the final TALE-AvrBs3::ColE7 yeast expression plasmid, pCLS8589 was prepared by yeast in vivo cloning using plasmid pCLS9940 (SEQ ID NO: 476).
  • plasmid pCLS9940 approximately 40 ng of plasmid linearized by digestion with BssHII and 1 ng of the pCLS0542 (SEQ ID NO: 2) plasmid DNA linearized by digestion with NcoI and EagI were used to transform the yeast S. cerevisiae strain FYC2-6A (MAT ⁇ , trp1 ⁇ 63, leu2 ⁇ 1, his3 ⁇ 200) using a high efficiency LiAc transformation protocol (Arnould et al. 2007).
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • the TALE-AvrBs3::ColE7 construct was tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on pseudo palindromic targets in order to compare activity with a standard TALE-AvrBs3::FokI TALEN, which requires two binding sites for activity.
  • AvrBS3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 220 to 255, Table 8).
  • constructs were tested on a target having only a single AvrBs3 recognition site (SEQ ID NO: 468, Table 8).
  • TALE-AvrBs3::ColE7 activity levels on the respective targets in yeast cells are shown on FIG. 15 .
  • Variants differing by truncations of the C-terminal domain of the AvrBs3-derived TALEN are chosen as starting scaffolds.
  • a subset of these variants includes truncation after positions E886 (C0), P897 (C11), G914 (C28), L926 (C40), D950 (C64), R1000 (C115), D1059 (C172) (the protein domains of truncated C-terminal domains C11 to C172 are respectively given in SEQ ID NO: 295 to 300) and P1117 [also referred as Cter wt or WT Cter (SEQ ID NO: 400) lacking the activation domain of the C-terminal domain of natural AvrBs3 (SEQ ID NO: 1)].
  • the plasmids coding for the variant scaffolds containing the AvrBs3-derived N-terminal domain, the AvrBs3-derived set of repeat domains and the truncated AvrBs3-derived C-terminal domain [pCLS7821, pCLS7803, pCLS7807, pCLS7809, pCLS7811, pCLS7813, pCLS7817 (SEQ ID NO: 19 to 25) which are based on the pCLS7184 (SEQ ID NO: 5)] allow cloning of any catalytic domain in fusion to the C-terminal domain, using the restriction sites BamHI and EagI.
  • the DNA corresponding to the catalytic domain of ColE7 is amplified by the PCR to introduce, at the DNA level, a BamHI (at the 5′ of the coding strand) and a EagI (at the 3′ of the coding strand) restriction site and, at the protein level, a linker (for example -SGGSGS- stretch, SEQ ID NO: 463) between the C terminal domain of the TALE and the ColE7 catalytic domain.
  • a linker for example -SGGSGS- stretch, SEQ ID NO: 463
  • variants of the ColE7 endonuclease domain that modulate catalytic activity can be generated having changes (individually or combined) at the following positions: D493, R496, K497, H545, N560 and H573 [positions refer to the amino acid sequence of the entire ColE7 protein (SEQ ID NO: 340)].
  • the final TALE::ColE7 constructs are generated by insertion of the ColE7 catalytic domain into the scaffold variants using BamHI and EagI and standard molecular biology procedures.
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • the TALE-AvrBs3::ColE7 constructs are tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on pseudo palindromic targets in order to compare activity with a standard TALE-AvrBs3::FokI TALEN, which requires two binding sites for activity.
  • AvrBS3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 220 to 255, Table 8).
  • constructs were tested on a target having only a single AvrBs3 recognition site (SEQ ID NO: 468, Table 8).
  • Variants differing by truncations of the C-terminal domain of the AvrBs3-derived TALEN are chosen as starting scaffolds.
  • a subset of these variants includes truncation after positions E886 (C0), P897 (C11), G914 (C28), L926 (C40) and D950 (C64) (the protein domains of truncated C-terminal domains C11 to C64 are respectively given in SEQ ID NO: 295 to 298).
  • the plasmids coding for the variant scaffolds containing the AvrBs3-derived N-terminal domain, the AvrBs3-derived set of repeat domains and the truncated AvrBs3-derived C-terminal domain [pCLS7821, pCLS7803, pCLS7807, pCLS7809, pCLS7811, (SEQ ID NO: 19 to 23) which are based on the pCLS7184 (SEQ ID NO: 5)] allow cloning of any catalytic domain in fusion to the C-terminal domain, using the restriction sites BamHI and EagI.
  • the DNA corresponding to amino acid residues 2-149 of EndoT7 (SEQ ID NO: 363) is amplified by the PCR to introduce, at the DNA level, a BamHI (at the 5′ of the coding strand) and a EagI (at the 3′ of the coding strand) restriction site and, at the protein level, a linker (for example -SGGSGS- stretch, SEQ ID NO: 463) between the C terminal domain of the TALE and the EndoT7 catalytic domain.
  • the final TALE::EndoT7 constructs are generated by insertion of the EndoT7 catalytic domain into the scaffold variants using BamHI and EagI and standard molecular biology procedures.
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • the TALE-AvrBs3::EndoT7 constructs were tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on pseudo palindromic targets in order to compare activity with a standard TALE-AvrBs3::FokI TALEN, which requires two binding sites for activity.
  • AvrBs3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 220 to 255, Table 8).
  • Data summarized in FIG. 20 show that TALE-AvrBs3::EndoT7 constructs are active on targets having two AvrBs3 recognition site, according to the chimeric protein of the present invention.
  • linker library is then subcloned in pCLS7183 (SEQ ID NO: 3) via the XmaI and BamHI restriction sites to replace the C-terminal domain of the AvrBs3-derived TALEN (pCLS7184, SEQ ID NO: 5).
  • the AvrBs3-derived set of repeat domains (RVDs) or any other RVD sequences having or lacking the terminal half RVD is cloned in this backbone library plasmid as described in Example 3A.
  • DNA from the library is obtained, after scrapping of the colonies from the Petri dishes, using standard miniprep techniques.
  • the FokI catalytic head is removed using BamHI and EagI restriction enzymes, the remaining backbone being purified using standard gel extraction techniques.
  • DNA coding for 3 catalytic heads presented in table 2 (SEQ ID NO: 340, 349 and 363) were amplified by the PCR to introduce, at the DNA level, a BamHI (at the 5′ of the coding strand) and a EagI (at the 3′ of the coding strand) restriction site and, at the protein level, a linker (for example -SGGSGS -stretch, SEQ ID NO: 463) between the C-terminal domain library and the catalytic head. After BamHI and EagI digestion and purification, the DNA coding for the different catalytic heads were individually subcloned into the library scaffold previously prepared.
  • DNA from the final library is obtained, after scrapping of the colonies from Petri dishes, using standard miniprep techniques and the resulting libraries are screened in our yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on pseudo palindromic targets in order to compare activity with a standard TALE-AvrBs3::FokI TALEN, which requires two binding sites for activity.
  • AvrBs3 targets contain two identical recognition sequences juxtaposed with the 3′ ends proximal and separated by “spacer” DNA containing 15, 18, 21 and 24 bps (SEQ ID NO: 230, 233, 236 and 239, Table 8).
  • constructs were tested on a target having only a single AvrBs3 recognition site (SEQ ID NO: 468). Data summarized in FIG.
  • linkers of SEQ ID NO: 147, 150, 156 and 162 for colE7 linkers of SEQ ID NO: 134, 153, 154, 157, 162 and 166 for I-TevI and linkers of SEQ ID NO: 134, 152, 153, 159 and 166 for EndoT7 being active on targets having one or two AvrBs3 recognition sites ( FIG. 21 ) according to the chimeric protein of the present invention.
  • the 52 different TAL repeats arrays containing from 9.5 to 15.5 Tal repeats were synthesized using a solid support method consisting in a sequential assembly of TAL repeats through consecutive restriction/ligation/washing steps as shown in FIG. 23 .
  • the first TAL repeat (SEQ ID NO: 584 encoding SEQ ID NO: 585) was immobilized on a solid support through biotin/streptavidin interaction, digested by SfaNI type IIS restriction endonuclease and then ligated to a second TAL repeat (SEQ ID NO: 586 encoding SEQ ID NO: 587) harboring SfaNI compatible overhangs at its 5′ end ( FIG.
  • the resulting TAL repeats array (i.e containing TAL repeats 1 and 2) was then used as template for subsequent additions of the appropriate TAL repeats (SEQ ID NO: 588-591, encoding SEQ ID NO: 592-595 for HD, NI, respectively targeting nucleotides C, A and NN, NG respectively targeting nucleotides G and T) to generate the complete TAL repeats arrays RAGT2.3 ( FIG. 23C ).
  • the complete TAL repeats array was finally digested by SfaNI to generate SfaNI overhangs at its 3′ end ( FIG. 23D ) and then striped of the solid support using BbvI type IIS restriction endonuclease ( FIG. 23E ).
  • the digested TAL repeats array was recovered and subcloned into yeast or mammalian expression plasmids harboring the Nterminal domain of AvrBs3 TAL effector and the forty first amino acids of its Cterminal domain fused to FokI type IIS restriction endonuclease (pCLS 7808, i.e. SEQ ID NO: 596 encoding SEQ ID NO: 597, FIG. 23F ).
  • pCLS7808 was derived from pCLS0542 (SEQ ID NO: 2) using NcoI and XhoI restriction sites.
  • TAL effector DNA binding domains are known to be highly specific with respect to their cognate target (refs: 3, 25). This has been demonstrated for different TAL DNA binding domains by independent studies. However, the influence of TAL repeat number on such specificity is unclear. To address this question in a systematic manner, RAGT2.3 and RAGT2.4 TALENs were chosen as models, then the number of their TAL repeats (15.5, 13.5, 11.5 9.5 TAL repeats were iteratively reduced, according to the assembly method described in example 12 and their TALEN activity were characterized toward their respective homodimeric target degenerated in positions N and N-1 ( FIG. 25 , SEQ ID NO: 602-615). For the sake of clarity, FIG.
  • FIG. 25A displays the different components of a TALEN including the N and C-terminal domains, the TAL DNA binding domain bearing the terminal half repeat and FokI catalytic domain.
  • the FIG. 25B displays the organization of the homodimeric RAGT2.4 TALEN targets (SEQ ID NO: 601) used for our experiments including the location of thymine T0 and the positions N and N-1 degenerated in this study.
  • the FIG. 25C displays two examples of TALEN bearing 15.5 or 11.5 Tal repeats along with their respective DNA targets (top and bottom respectively, SEQ ID NO: 601).
  • the catalytic domain of FokI (SEQ ID NO: 600), starting at residue P381, was fused to a TALE-derived scaffold (composed of a N-terminal domain, a central core composed of RVDs and a C-terminal domain) to create a half-TALEN.
  • a TALE-derived scaffold composed of a N-terminal domain, a central core composed of RVDs and a C-terminal domain
  • construct names are written as either CD::TALE-RVD (catalytic domain is fused N-terminal to the TALE domain) or TALE-RVD::CD (catalytic domain is fused C-terminal to the TALE domain), where “-RVD” optionally designates the sequence recognized by the TALE domain and “CD” is the catalytic domain type.
  • FokI::TALE constructions that either work together with other FokI::TALE constructions in a conventional “head-to-head” configuration or can be paired with TALE::FokI constructions in a novel “tail-to-head” configuration, allowing for targeting a single DNA strand (when considering the requisite T 0 as 5′ for target readout).
  • a core TALE scaffold, sT2 (SEQ ID NO: 464) was selected onto which (a) different sets of RVD domains could be inserted to change DNA binding specificity, and; (b) a selection of FokI-derived catalytic domains could be attached, N- or C-terminal, to effect DNA cleavage (or nicking).
  • pCLS7865-cTAL11_NFS1 (pCLS9008, SEQ ID NO: 624), where NFS1 designates the amino acid sequence -GSSG- (with underlying restriction sites BamHI and Kpn2I in the coding DNA to facilitate cloning)
  • pCLS7865-cTAL11_CFS1 (pCLS9009, SEQ ID NO: 660), where CFS1 designates the amino acid sequence -GSSG- (with underlying restriction sites BamHI and Kpn2I in the coding DNA to facilitate cloning).
  • the catalytic domain of FokI (SEQ ID NO: 600) was subcloned by restriction and ligation into pCLS9008 (SEQ ID NO: 624) using NcoI and BamHI restriction sites, yielding the construct FokI_cT11 (SEQ ID NO: 625).
  • the fusion contains the peptide -GSSG- linking the TALE-derived DNA binding domain and FokI derived catalytic domain.
  • the DNA sequence coding for the RVDs to target the AvrBS3 site was subcloned into the FokI_cT11 (SEQ ID NO: 625) scaffold using Type IIS restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence to create the subsequent FokI::TALE-AvrBs3 construct FokI_cT11Avr (SEQ ID NO: 627). This construct was sequenced and the insert transferred to additional vectors as needed.
  • the final FokI::TALE-AvrBS3 yeast expression plasmid, pCLS8674 (SEQ ID NO: 628), was prepared by restriction and ligation of the FokI_cT11Avr (SEQ ID NO: 627) insert into pCLS0542 (SEQ ID NO: 2) using NcoI and EagI restriction enzymes.
  • Plasmid pCLS8674 (SEQ ID NO: 628) was used to transform the yeast S. cerevisiae strain FYC2-6A (MAT ⁇ , trp1 ⁇ 63, leu2 ⁇ 1, his3 ⁇ 200) using a high efficiency LiAc transformation protocol (Arnould et al. 2007).
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • the FokI::TALE-AvrBs3 construct was tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on pseudo palindromic targets, since the construct requires two binding sites for activity.
  • AvrBs3 targets contain two identical recognition sequences juxtaposed with the 5′ ends proximal ( FIG. 9 D) and separated by “spacer” DNA ranging from 5 to 35 bps (SEQ ID NO: 629 to 659, Table 9).
  • FokI::TALE-AvrBs3 activity levels on the respective targets in yeast cells are shown in FIG. 27 .
  • the catalytic domain of FokI (SEQ ID NO: 600) was subcloned by restriction and ligation into pCLS9009 (SEQ ID NO: 660) using Kpn2I and EagI restriction sites, yielding the construct cT11_FokI (SEQ ID NO: G661).
  • the fusion contains the peptide -GSSG- linking the TALE-derived DNA binding domain and FokI derived catalytic domain.
  • the DNA sequence coding for the RVDs to target the RagT2-R site was subcloned into the cT11_FokI (SEQ ID NO: 661) scaffold using Type IIS restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence to create the subsequent TALE-RagT2-R::FokI construct cT11RagT2-R_FokI (SEQ ID NO: 663). This construct was sequenced and the insert transferred to additional vectors as needed.
  • the final TALE-RagT2-R::FokI yeast expression plasmid, pCLS9827 (SEQ ID NO: 664), was prepared by restriction and ligation of the cT11RagT2-R_FokI (SEQ ID NO: 663) insert into pCLS7763 (SEQ ID NO: 665) using NcoI and EagI restriction enzymes.
  • the plasmid pair pCLS9827 (SEQ ID NO: 664) and pCLS8674 (SEQ ID NO: 628) was then used in co-transformation experiments in the standard yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • yeast target reporter plasmids containing the TALEN DNA target sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006).
  • the TALE-RagT2-R::FokI/FokI::TALE-AvrBs3 construct pairs were tested in a yeast SSA assay as previously described (International PCT Applications WO 2004/067736 and in Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) on asymmetric RagT2-R/AvrBs3 hybrid targets and compared with a parent standard TALEN (e.g. pCLS8674 (SEQ ID NO: 628) on appropriate pseudo palindromic targets (e.g. (SEQ ID NO: 629 to 659, Table 9).
  • TALEN e.g. pCLS8674 (SEQ ID NO: 628)
  • appropriate pseudo palindromic targets e.g. (SEQ ID NO: 629 to 659, Table 9).
  • RagT2-R/AvrBs3 hybrid targets contain two different recognition sequences juxtaposed with the 3′ end of the first (RagT2-R) proximal to the 5′ end of the second (AvrBs3) and separated by “spacer” DNA ranging from 5 to 40 bps (SEQ ID NO: 666 to 701, Table 10).
  • TALE-RagT2-R::FokI/FokI::TALE-AvrBs3 activity levels on the respective targets in yeast cells are shown in FIG. 28 .

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