TAL effector

TAL (transcription activator-like) effectors (often referred to as TALEs but not to be confused with the three amino acid loop extension family of proteins) are proteins secreted by Xanthomonas bacteria via their type III secretion system when they infect various plant species. These proteins can bind promoter sequences in the host plant and activate the expression of plant genes that aid bacterial infection. They recognize plant DNA sequences through a central repeat domain consisting of a variable number of ~34 amino acid repeats. There appears to be a one-to-one correspondence between the identity of two critical amino acids in each repeat and each DNA base in the target sequence. These proteins are interesting to researchers both for their role in disease of important crop species and the relative ease of retargeting them to bind new DNA sequences. Similar proteins can be found in the pathogenic bacterium Ralstonia solanacearum[1][2] and Burkholderia rhizoxinica.[3]

Function in plant pathogenesis

Xanthomonas are Gram-negative bacteria that can infect a wide variety of plant species including pepper, rice, citrus, cotton, tomato, and soybeans.[4] Some types of Xanthomonas cause localized leaf spot or leaf streak while others spread systemically and cause black rot or leaf blight disease. They inject a number of effector proteins, including TAL effectors, into the plant via their type III secretion system. TAL effectors (short for Transcription Activator-like effectors) have several motifs normally associated with eukaryotes including multiple nuclear localization signals and an acidic activation domain. When injected into plants, these proteins can enter the nucleus of the plant cell, bind plant promoter sequences, and activate transcription of plant genes that aid in bacterial infection.[4] Plants have developed a defense mechanism against type III effectors that includes R (resistance) genes triggered by these effectors. Some of these R genes appear to have evolved to contain TAL-effector binding sites similar to site in the intended target gene. This competition between pathogenic bacteria and the host plant has been hypothesized to account for the apparently malleable nature of the TAL effector DNA binding domain.[5]

DNA recognition

The most distinctive characteristic of TAL effectors is a central repeat domain containing between 1.5 and 33.5 repeats that are usually 34 residues in length (the C-terminal repeat is generally shorter and referred to as a “half repeat”).[4] A typical repeat sequence is LTPEQVVAIASHDGGKQALETVQRLLPVLCQAHG, but the residues at the 12th and 13th positions are hypervariable (these two amino acids are also known as the repeat variable diresidue or RVD). Two separate groups have shown that there is a simple relationship between the identity of these two residues in sequential repeats and sequential DNA bases in the TAL effector’s target site.[6][7] The first group, headed by Adam Bogdanove, broke this code computationally by searching for patterns in protein sequence alignments and DNA sequences of target promoters. The second group deduced the code through molecular analysis of the TAL effector AvrBs3 and its target DNA sequence in the promoter of a pepper gene activated by AvrBs3.[5] The experimentally validated code between RVD sequence and target DNA base[7] can be expressed as NI = A, HD = C, NG = T, NN = R (G or A), and NS = N (A, C, G, or T). Further studies have shown that the RVD NK can target G,[8][9] although TAL effector nucleases (TALEN) that exclusively use NK instead of NN to target G can be less active.[10] The crystal structure of a TAL effector bound to DNA indicates that each repeat comprises two alpha helices and a short RVD-containing loop where the second residue of the RVD makes sequence-specific DNA contacts while the first residue of the RVD stabilizes the RVD-containing loop.[11][12] Target sites of TAL effectors also tend to include a thymine flanking the 5’ base targeted by the first repeat; this appears to be due to a contact between this T and a conserved tryptophan in the region N-terminal of the central repeat domain.[11] However, this "zero" position does not always contain a thymine, as some scaffolds are more permissive.[13]

Engineering TAL effectors

This simple correspondence between amino acids in TAL effectors and DNA bases in their target sites makes them useful for protein engineering applications. Numerous groups have designed artificial TAL effectors capable of recognizing new DNA sequences in a variety of experimental systems.[7][8][9][14][15][16] Such engineered TAL effectors have been used to create artificial transcription factors that can be used to target and activate or repress endogenous genes in tomato,[8] Arabidopsis thaliana,[8] and human cells.[9][15][17][18]

Genetic constructs to encode TAL effector-based proteins can be made using either conventional gene synthesis or modular assembly.[15][18][19][20][21][22][23] A plasmid kit for assembling custom TALEN® and other TAL effector constructs is available through the public, not-for-profit repository Addgene. Webpages providing access to public software, protocols, and other resources for TAL effector-DNA targeting applications include the TAL Effector-Nucleotide Targeter and taleffectors.com.

Target genes

TAL effectors can induce susceptibility genes that are members of the NODULIN3 (N3) gene family. These genes are essential for the development of the disease. In rice two genes,Os-8N3 and Os-11N3, are induced by TAL effectors. Os-8N3 is induced by PthXo1 and Os-11N3 is induced by PthXo3 and AvrXa7. Two hypotheses exist about possible functions for N3 proteins:

Applications

Engineered TAL effectors can also be fused to the cleavage domain of FokI to create TAL effector nucleases (TALEN) or to meganucleases (nucleases with longer recognition sites) to create "megaTALs."[24] Such fusions share some properties with zinc finger nucleases and may be useful for genetic engineering and gene therapy applications.[25]

TALEN-based approaches are used in the emerging fields of gene editing and genome engineering. TALEN fusions show activity in a yeast-based assay,[14][26] at endogenous yeast genes,[19] in a plant reporter assay,[16] at an endogenous plant gene,[20] at endogenous zebrafish genes,[10][27] at an endogenous rat gene,[28] and at endogenous human genes.[9][20][29] The human HPRT1 gene has been targeted at detectable, but unquantified levels.[20] In addition, TALEN constructs containing the FokI cleavage domain fused to a smaller portion of the TAL effector still containing the DNA binding domain have been used to target the endogenous NTF3 and CCR5 genes in human cells with efficiencies of up to 25%.[9] TAL effector nucleases have also been used to engineer human embryonic stem cells and induced pluripotent stem cells (IPSCs)[29] and to knock out the endogenous ben-1 gene in C. elegans.[30]

See also

References

  1. ↑ Heuer, H.; Yin, Y. -N.; Xue, Q. -Y.; Smalla, K.; Guo, J. -H. (2007). "Repeat Domain Diversity of avrBs3-Like Genes in Ralstonia solanacearum Strains and Association with Host Preferences in the Field". Applied and Environmental Microbiology 73 (13): 4379–4384. doi:10.1128/AEM.00367-07. PMC 1932761. PMID 17468277.
  2. ↑ Lixin Li, Ahmed Atef, Agnieszka Piatek, Zahir Ali, Marek Piatek, Mustapha Aouida, Altanbadralt Sharakuu, Ali Mahjoub, Guangchao Wang, Suhail Khan, Nina V Fedoroff, Jian-Kang Zhu, Magdy M Mahfouz (July 2013). "Characterization and DNA-binding specificities of Ralstonia TAL-like effectors". Molecular plant 6 (4): 1318–1330. doi:10.1093/mp/sst006. PMC 3716395. PMID 23300258.
  3. ↑ de Lange, Orlando; Christina Wolf; Jörn Dietze; Janett Elsaesser; Robert Morbitzer; Thomas Lahaye (2014). "Programmable DNA-binding proteins from Burkholderia provide a fresh perspective on the TALE-like repeat domain". Nucleic Acids Research 42 (11): 7436–49. doi:10.1093/nar/gku329. PMC 4066763. PMID 24792163.
  4. 1 2 3 Boch J, Bonas U (September 2010). "XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function". Annual Review of Phytopathology 48: 419–36. doi:10.1146/annurev-phyto-080508-081936. PMID 19400638.
  5. 1 2 Voytas DF, Joung JK (December 2009). "Plant science. DNA binding made easy". Science 326 (5959): 1491–2. Bibcode:2009Sci...326.1491V. doi:10.1126/science.1183604. PMID 20007890.
  6. ↑ Moscou MJ, Bogdanove AJ (December 2009). "A simple cipher governs DNA recognition by TAL effectors". Science 326 (5959): 1501. Bibcode:2009Sci...326.1501M. doi:10.1126/science.1178817. PMID 19933106.
  7. 1 2 3 Boch J, Scholze H, Schornack S, et al. (December 2009). "Breaking the code of DNA binding specificity of TAL-type III effectors". Science 326 (5959): 1509–12. Bibcode:2009Sci...326.1509B. doi:10.1126/science.1178811. PMID 19933107.
  8. 1 2 3 4 Morbitzer, R.; Romer, P.; Boch, J.; Lahaye, T. (2010). "Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors". Proceedings of the National Academy of Sciences 107 (50): 21617–21622. Bibcode:2010PNAS..10721617M. doi:10.1073/pnas.1013133107. PMC 3003021. PMID 21106758.
  9. 1 2 3 4 5 Miller, J. C.; Tan, S.; Qiao, G.; Barlow, K. A.; Wang, J.; Xia, D. F.; Meng, X.; Paschon, D. E.; Leung, E.; Hinkley, S. J.; Dulay, G. P.; Hua, K. L.; Ankoudinova, I.; Cost, G. J.; Urnov, F. D.; Zhang, H. S.; Holmes, M. C.; Zhang, L.; Gregory, P. D.; Rebar, E. J. (2010). "A TALE nuclease architecture for efficient genome editing". Nature Biotechnology 29 (2): 143–148. doi:10.1038/nbt.1755. PMID 21179091.
  10. 1 2 Huang, P.; Xiao, A.; Zhou, M.; Zhu, Z.; Lin, S.; Zhang, B. (2011). "Heritable gene targeting in zebrafish using customized TALENs". Nature Biotechnology 29 (8): 699–700. doi:10.1038/nbt.1939.
  11. 1 2 Mak, A. N. -S.; Bradley, P.; Cernadas, R. A.; Bogdanove, A. J.; Stoddard, B. L. (2012). "The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target". Science 335: 716–719. doi:10.1126/science.1216211.
  12. ↑ Deng, D.; Yan, C.; Pan, X.; Mahfouz, M.; Wang, J.; Zhu, J. -K.; Shi, Y.; Yan, N. (2012). "Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors". Science 335: 720–3. doi:10.1126/science.1215670. PMC 3586824. PMID 22223738.
  13. ↑ Stella, Stefano; Molina, Rafael; Yefimenko, Igor; Prieto, Jesús; Silva, George; Bertonati, Claudia; Juillerat, Alexandre; Duchateau, Phillippe; Montoya, Guillermo (2013-09-01). "Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism". Acta Crystallographica. Section D, Biological Crystallography 69 (Pt 9): 1707–1716. doi:10.1107/S0907444913016429. ISSN 1399-0047. PMC 3760130. PMID 23999294.
  14. 1 2 Christian M, Cermak T, Doyle EL, et al. (July 2010). "TAL Effector Nucleases Create Targeted DNA Double-strand Breaks". Genetics 186 (2): 757–61. doi:10.1534/genetics.110.120717. PMC 2942870. PMID 20660643.
  15. 1 2 3 Zhang, F.; Cong, L.; Lodato, S.; Kosuri, S.; Church, G. M.; Arlotta, P. (2011). "Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription". Nature Biotechnology 29 (2): 149–53. doi:10.1038/nbt.1775. PMC 3084533. PMID 21248753.
  16. 1 2 Mahfouz, M. M.; Li, L.; Shamimuzzaman, M.; Wibowo, A.; Fang, X.; Zhu, J. -K. (2011). "De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks". Proceedings of the National Academy of Sciences 108 (6): 2623–8. doi:10.1073/pnas.1019533108. PMC 3038751. PMID 21262818.
  17. ↑ Cong, Le; Ruhong Zhou; Yu-chi Kuo; Margaret Cunniff; Feng Zhang (24 July 2012). "Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains". Nature Communications. 968 3 (7): 968. Bibcode:2012NatCo...3E.968C. doi:10.1038/ncomms1962. PMID 22828628.
  18. 1 2 Geiβler, R.; Scholze, H.; Hahn, S.; Streubel, J.; Bonas, U.; Behrens, S. E.; Boch, J. (2011). Shiu, Shin-Han, ed. "Transcriptional Activators of Human Genes with Programmable DNA-Specificity". PLoS ONE 6 (5): e19509. doi:10.1371/journal.pone.0019509. PMC 3098229. PMID 21625585.
  19. 1 2 Li, T.; Huang, S.; Zhao, X.; Wright, D. A.; Carpenter, S.; Spalding, M. H.; Weeks, D. P.; Yang, B. (2011). "Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes". Nucleic Acids Research 39: 6315–6325. doi:10.1093/nar/gkr188.
  20. 1 2 3 4 Cermak, T.; Doyle, E. L.; Christian, M.; Wang, L.; Zhang, Y.; Schmidt, C.; Baller, J. A.; Somia, N. V.; Bogdanove, A. J.; Voytas, D. F. (2011). "Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting". Nucleic Acids Research 39 (12): e82. doi:10.1093/nar/gkr218. PMC 3130291. PMID 21493687.
  21. ↑ Morbitzer, R.; Elsaesser, J.; Hausner, J.; Lahaye, T. (2011). "Assembly of custom TALE-type DNA binding domains by modular cloning". Nucleic Acids Research 39: 5790–5799. doi:10.1093/nar/gkr151.
  22. ↑ Weber, E.; Gruetzner, R.; Werner, S.; Engler, C.; Marillonnet, S. (2011). Bendahmane, Mohammed, ed. "Assembly of Designer TAL Effectors by Golden Gate Cloning". PLoS ONE 6 (5): e19722. doi:10.1371/journal.pone.0019722.
  23. ↑ Sanjana, N. E.; Cong, L.; Zhou, Y.; Cunniff, M. M.; Feng, G.; Zhang, F. (2012). "A transcription activator-like effector toolbox for genome engineering". Nature Protocols 7 (1): 171–192. doi:10.1038/nprot.2011.431. PMID 22222791.
  24. ↑ Boissel, Sandrine; Jarjour, Jordan; Astrakhan, Alexander; Adey, Andrew; Gouble, Agnès; Duchateau, Philippe; Shendure, Jay; Stoddard, Barry L.; Certo, Michael T. (2014-02-01). "megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering". Nucleic Acids Research 42 (4): 2591–2601. doi:10.1093/nar/gkt1224. ISSN 1362-4962. PMC 3936731. PMID 24285304.
  25. ↑ Laura DeFrancesco (2011). "Move over ZFNs". Nature Biotechnology 29 (8): 681–684. doi:10.1038/nbt.1935.
  26. ↑ Li T, Huang S, Jiang WZ, et al. (August 2010). "TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain". Nucleic Acids Res 39 (1): 359–72. doi:10.1093/nar/gkq704. PMC 3017587. PMID 20699274.
  27. ↑ Sander, J. D.; Cade, L.; Khayter, C.; Reyon, D.; Peterson, R. T.; Joung, J. K.; Yeh, J. R. J. (2011). "Targeted gene disruption in somatic zebrafish cells using engineered TALENs". Nature Biotechnology 29 (8): 697–698. doi:10.1038/nbt.1934.
  28. ↑ Tesson, L.; Usal, C.; Ménoret, S. V.; Leung, E.; Niles, B. J.; Remy, S. V.; Santiago, Y.; Vincent, A. I.; Meng, X.; Zhang, L.; Gregory, P. D.; Anegon, I.; Cost, G. J. (2011). "Knockout rats generated by embryo microinjection of TALENs". Nature Biotechnology 29 (8): 695–696. doi:10.1038/nbt.1940. PMID 21822240.
  29. 1 2 Hockemeyer, D.; Wang, H.; Kiani, S.; Lai, C. S.; Gao, Q.; Cassady, J. P.; Cost, G. J.; Zhang, L.; Santiago, Y.; Miller, J. C.; Zeitler, B.; Cherone, J. M.; Meng, X.; Hinkley, S. J.; Rebar, E. J.; Gregory, P. D.; Urnov, F. D.; Jaenisch, R. (2011). "Genetic engineering of human pluripotent cells using TALE nucleases". Nature Biotechnology 29 (8): 731–734. doi:10.1038/nbt.1927. PMC 3152587. PMID 21738127.
  30. ↑ Wood, A. J.; Lo, T. -W.; Zeitler, B.; Pickle, C. S.; Ralston, E. J.; Lee, A. H.; Amora, R.; Miller, J. C.; Leung, E.; Meng, X.; Zhang, L.; Rebar, E. J.; Gregory, P. D.; Urnov, F. D.; Meyer, B. J. (2011). "Targeted Genome Editing Across Species Using ZFNs and TALENs". Science 333 (6040): 307. doi:10.1126/science.1207773. PMC 3489282. PMID 21700836.

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