An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains
Transcription Activators-Like Effectors (TALEs) belong to a family of virulence proteins from the Xanthomonas genus of bacterial plant pathogens that are translocated into the plant cell. In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for T...
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| creator | Pérez-Quintero, Alvaro L Rodriguez-R, Luis M Dereeper, Alexis López, Camilo Koebnik, Ralf Szurek, Boris Cunnac, Sebastien |
| description | Transcription Activators-Like Effectors (TALEs) belong to a family of virulence proteins from the Xanthomonas genus of bacterial plant pathogens that are translocated into the plant cell. In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures of TALE-DNA complexes were recently reported. Accurate prediction of TAL Effector Binding Elements (EBEs) is essential to elucidate the biological functions of the many sequenced TALEs as well as for robust design of artificial TALE DNA-binding domains in biotechnological applications. In this work a program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions. To gain a systems perspective on the large TALE repertoires from X. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs. |
| doi_str_mv | 10.1371/journal.pone.0068464 |
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In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures of TALE-DNA complexes were recently reported. Accurate prediction of TAL Effector Binding Elements (EBEs) is essential to elucidate the biological functions of the many sequenced TALEs as well as for robust design of artificial TALE DNA-binding domains in biotechnological applications. In this work a program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions. To gain a systems perspective on the large TALE repertoires from X. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0068464</identifier><identifier>PMID: 23869221</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino acids ; Analysis ; Arabidopsis - genetics ; Bacteria ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - physiology ; Binding Sites ; Bioinformatics ; Biological effects ; Biology ; Convergence ; Deoxyribonucleic acid ; Disease ; Disease susceptibility ; DNA ; DNA binding proteins ; Effectors ; Gene expression ; Gene Regulatory Networks ; Genes ; Genetic aspects ; Genomes ; Genomics ; Life Sciences ; Methods ; Nuclei ; Nuclei (cytology) ; Oryza ; Oryza - genetics ; Plant resistance ; Proteins ; Robust design ; Software ; Strains (organisms) ; Transcription (Genetics) ; Transcription factors ; Transcription Factors - chemistry ; Transcription Factors - genetics ; Transcription Factors - physiology ; Virulence ; Xanthomonas - genetics ; Xanthomonas oryzae</subject><ispartof>PloS one, 2013-07, Vol.8 (7), p.e68464-e68464</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Pérez-Quintero et al. 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Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23869221</pmid><doi>10.1371/journal.pone.0068464</doi><tpages>e68464</tpages><orcidid>https://orcid.org/0000-0003-3530-8251</orcidid><orcidid>https://orcid.org/0000-0002-1808-7082</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2013-07, Vol.8 (7), p.e68464-e68464 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1400164470 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Amino acids Analysis Arabidopsis - genetics Bacteria Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - physiology Binding Sites Bioinformatics Biological effects Biology Convergence Deoxyribonucleic acid Disease Disease susceptibility DNA DNA binding proteins Effectors Gene expression Gene Regulatory Networks Genes Genetic aspects Genomes Genomics Life Sciences Methods Nuclei Nuclei (cytology) Oryza Oryza - genetics Plant resistance Proteins Robust design Software Strains (organisms) Transcription (Genetics) Transcription factors Transcription Factors - chemistry Transcription Factors - genetics Transcription Factors - physiology Virulence Xanthomonas - genetics Xanthomonas oryzae |
| title | An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-20T10%3A44%3A18IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=An%20improved%20method%20for%20TAL%20effectors%20DNA-binding%20sites%20prediction%20reveals%20functional%20convergence%20in%20TAL%20repertoires%20of%20Xanthomonas%20oryzae%20strains&rft.jtitle=PloS%20one&rft.au=P%C3%A9rez-Quintero,%20Alvaro%20L&rft.date=2013-07-15&rft.volume=8&rft.issue=7&rft.spage=e68464&rft.epage=e68464&rft.pages=e68464-e68464&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0068464&rft_dat=%3Cgale_plos_%3EA478270096%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1400164470&rft_id=info:pmid/23869221&rft_galeid=A478270096&rft_doaj_id=oai_doaj_org_article_a45e7f669dc845b4b1d4dd806637b925&rfr_iscdi=true |