Revisiting the TALE repeat

Abstract

Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33–35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

Keywords

TAL effectors / DNA / recognition / plasticity

References

[1] Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr58: 1948-1954

[2] Bai J, Choi SH, Ponciano G, Leung H, Leach JE (2000) Xanthomonas oryzae pv. oryzae avirulence genes contribute differently and specifically to pathogen aggressiveness. Mol Plant Microbe Interact13: 1322-1329

[3] Beumer KJ, Trautman JK, Christian M, Dahlem TJ, Lake CM, Hawley RS, Grunwald DJ, Voytas DF, Carroll D (2013) Comparing ZFNs and TALENs for gene targeting in Drosophila. G3 (Bethesda)3(10): 1717-1725

[4] Boch J, Bonas U (2010) Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol48: 419-436

[5] Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science326: 1509-1512

[6] Bogdanove AJ, Voytas DF (2011) TAL effectors: customizable proteins for DNA targeting. Science333: 1843-1846

[7] Bonas U, Conrads-Strauch J, Balbo I (1993) Resistance in tomato to Xanthomonas campestris pv vesicatoria is determined by alleles of the pepper-specific avirulence gene avrBs3. Mol Gen Genet238: 261-269

[8] Carlson DF, Tan W, Lillico SG, Stverakova D, Proudfoot C, Christian M, Voytas DF, Long CR, Whitelaw CBA, Fahrenkrug SC (2012) Efficient TALEN-mediated gene knockout in livestock. Proc Natl Acad Sci USA109(43): 17382-17387

[9] Christian M, Qi Y, Zhang Y, Voytas DF (2013) Targeted mutagenesis of Arabidopsis thaliana using engineered TAL effector nucleases (TALENs). G3( Bethesda)3(10): 1697-1705

[10] Das AK, Cohen PW, Barford D (1998) The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPRmediated protein-protein interactions. EMBO J17: 1192-1199

[11] Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu JK, Shi Y, Yan N (2012a) Structural basis for sequence-specific recognition of DNA by TAL effectors. Science335: 720-723

[12] Deng D, Yin P, Yan C, Pan X, Gong X, Qi S, Xie T, Mahfouz M, Zhu JK, Yan N (2012b) Recognition of methylated DNA by TAL effectors. Cell Res22: 1502-1504

[13] Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ (2013) TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol23(8): 390-398

[14] Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr60: 2126-2132

[15] Gao H, Wu X, Chai J, Han Z (2012) Crystal structure of a TALE protein reveals an extended N-terminal DNA binding region. Cell Res22: 1716-1720

[16] Gu K, Yang B, Tian D, Wu L, Wang D, Sreekala C, Yang F, Chu Z, Wang GL, White FF (2005) R gene expression induced by a type-III effector triggers disease resistance in rice. Nature435: 1122-1125

[17] Heigwer F, Kerr G, Walther N, Glaeser K, Pelz O, Breinig M, Boutros M (2013) E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Res41(20): e190

[18] Huang P, Xiao A, Zhou M, Zhu Z, Lin S, Zhang B (2011) Heritable gene targeting in zebrafish using customized TALENs. Nat Biotechnol29: 699-700

[19] Kim Y, Kweon J, Kim A, Chon JK, Yoo JY, Kim HJ, Kim S, Lee C, Jeong E, Chung E (2013) A library of TAL effector nucleases spanning the human genome. Nat Biotechnol31: 251-258

[20] Mahfouz MM, Li L, Shamimuzzaman M, Wibowo A, Fang X, Zhu JK (2011) De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proc Natl Acad Sci USA108: 2623-2628

[21] Mak AN, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL (2012) The crystal structure of TAL effector PthXo1 bound to its DNA target. Science335: 716-719

[22] McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr40: 658-674

[23] McMahon MA, Rahdar M, Porteus M (2012) Gene editing: not just for translation anymore. Nat Methods9: 28-31

[24] Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science326: 1501

[25] Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol276: 307-326

[26] Panda SK, Wefers B, Ortiz O, Floss T, Schmid B, Haass C, Wurst W, Kuhn R (2013) Highly efficient targeted mutagenesis in mice using TALENs. Genetics195(3): 703-713

[27] Pavletich NP, Pabo CO (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science252: 809-817

[28] Schrodinger LLC (2010) The PyMOL molecular graphics system, Version 1.3r1

[29] Streubel J, Blucher C, Landgraf A, Boch J (2012) TAL effector RVD specificities and efficiencies. Nat Biotechnol30: 593-595

[30] Swarup S, Yang Y, Kingsley MT, Gabriel DW (1992) An Xanthomonas citri pathogenicity gene, pthA, pleiotropically encodes gratuitous avirulence on nonhosts. Mol Plant Microbe Interact5: 204-213

[31] White FF, Yang B (2009) Host and pathogen factors controlling the rice–Xanthomonas oryzae interaction. Plant Physiol150: 1677-1686

[32] Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr67: 235-242

[33] Yang J, Zhang Y, Yuan P, Zhou Y, Cai C, Ren Q, Wen D, Chu C, Qi H, Wei W (2014) Complete decoding of TAL effectors for DNA recognition. Cell Res.

[34] Yin P, Deng D, Yan C, Pan X, Xi JJ, Yan N, Shi Y (2012) Specific DNA-RNA hybrid recognition by TAL effectors. Cell Rep2: 707-713

[35] Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, Wang Z, Long J, He J, Wang H-W, Wang J, Zhu J-K, Shi Y, Yan N (2013) Structural basis for the modular recognition of single stranded RNA by PPR proteins. Nature504: 168-171

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2014 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.