Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene

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dc.contributor.author Cernadas, Raul A.
dc.contributor.author Doyle, Erin L.
dc.contributor.author Niño-Liu, David O.
dc.contributor.author Wilkins, Katherine E.
dc.contributor.author Bancroft, Timothy
dc.contributor.author Wang, Li
dc.contributor.author Schmidt, Clarice L.
dc.contributor.author Caldo, Rico
dc.contributor.author Yang, Bing
dc.contributor.author White, Frank F.
dc.contributor.author Nettleton, Dan
dc.contributor.author Wise, Roger P.
dc.contributor.author Bogdanove, Adam J.
dc.date.accessioned 2014-05-09T13:48:50Z
dc.date.available 2014-05-09T13:48:50Z
dc.date.issued 2014-05-09
dc.identifier.uri http://hdl.handle.net/2097/17722
dc.description.abstract Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo), which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. A TAL effector finds its target(s) via a partially degenerate code whereby the modular effector amino acid sequence identifies nucleotide sequences to which the protein binds. Virulence contributions of some Xoo TAL effectors have been shown, and their relevant targets, susceptibility (S) genes, identified, but the role of TAL effectors in leaf streak is uncharacterized. We used host transcript profiling to compare leaf streak to blight and to probe functions of Xoc TAL effectors. We found that Xoc and Xoo induce almost completely different host transcriptional changes. Roughly one in three genes upregulated by the pathogens is preceded by a candidate TAL effector binding element. Experimental analysis of the 44 such genes predicted to be Xoc TAL effector targets verified nearly half, and identified most others as false predictions. None of the Xoc targets is a known bacterial blight S gene. Mutational analysis revealed that Tal2g, which activates two genes, contributes to lesion expansion and bacterial exudation. Use of designer TAL effectors discriminated a sulfate transporter gene as the S gene. Across all targets, basal expression tended to be higher than genome-average, and induction moderate. Finally, machine learning applied to real vs. falsely predicted targets yielded a classifier that recalled 92% of the real targets with 88% precision, providing a tool for better target prediction in the future. Our study expands the number of known TAL effector targets, identifies a new class of S gene, and improves our ability to predict functional targeting. en_US
dc.language.iso en_US en_US
dc.relation.uri http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003972 en_US
dc.subject Bacterial leaf streak of rice en_US
dc.subject Xanthomonas oryzae pv. oryzicola (Xoc) en_US
dc.subject TAL effectors en_US
dc.title Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene en_US
dc.type Article (publisher version) en_US
dc.date.published 2014 en_US
dc.citation.doi doi:10.1371/journal.ppat.1003972 en_US
dc.citation.issue 2 en_US
dc.citation.jtitle PLoS Pathogens en_US
dc.citation.spage e1003972 en_US
dc.citation.volume 10 en_US
dc.contributor.authoreid fwhite en_US


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