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Code-Assisted Discovery of TAL Effector Targets in Bacterial Leaf Streak of Rice Reveals Contrast with Bacterial Blight and a Novel Susceptibility Gene
PLoS Pathogens
  • Raul A. Cernadas, Iowa State University
  • Erin L. Doyle, Iowa State University
  • David O. Niño-Liu, Iowa State University
  • Katherine E. Wilkins, Cornell University
  • Timothy J. Bancroft, Iowa State University
  • Li Wang, Iowa State University
  • Clarice L. Schmidt, Iowa State University
  • Rico Caldo, Iowa State University
  • Bing Yang, Iowa State University
  • Frank F. White, Kansas State University
  • Dan Nettleton, Iowa State University
  • Roger P. Wise, United States Department of Agriculture
  • Adam J. Bogdanove, Iowa State University
Document Type
Article
Publication Version
Published Version
Publication Date
2-27-2014
DOI
10.1371/journal.ppat.1004126
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.

Comments

This article is from PLoS Pathog 10(2): e1003972. doi:10.1371/journal.ppat.1003972. Posted with permission.

Rights
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Language
en
File Format
application/pdf
Citation Information
Raul A. Cernadas, Erin L. Doyle, David O. Niño-Liu, Katherine E. Wilkins, et al.. "Code-Assisted Discovery of TAL Effector Targets in Bacterial Leaf Streak of Rice Reveals Contrast with Bacterial Blight and a Novel Susceptibility Gene" PLoS Pathogens Vol. 10 Iss. 4 (2014) p. e1004126
Available at: http://works.bepress.com/dan-nettleton/71/