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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 Pathog. 2014 Feb; 10(2):e1003972.PP

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.

Authors+Show Affiliations

Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America ; Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America ; Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa, United States of America.Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America.Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.Department of Statistics, Iowa State University, Ames, Iowa, United States of America.Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America ; Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America.Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America.Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America.Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America.Department of Statistics, Iowa State University, Ames, Iowa, United States of America.Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America ; Corn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, Iowa, United States of America.Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America ; Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

24586171

Citation

Cernadas, Raul A., 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, no. 2, 2014, pp. e1003972.
Cernadas RA, Doyle EL, Niño-Liu DO, 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 Pathog. 2014;10(2):e1003972.
Cernadas, R. A., Doyle, E. L., Niño-Liu, D. O., Wilkins, K. E., Bancroft, T., Wang, L., Schmidt, C. L., Caldo, R., Yang, B., White, F. F., Nettleton, D., Wise, R. P., & Bogdanove, A. J. (2014). 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, 10(2), e1003972. https://doi.org/10.1371/journal.ppat.1003972
Cernadas RA, 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 Pathog. 2014;10(2):e1003972. PubMed PMID: 24586171.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. AU - Cernadas,Raul A, AU - Doyle,Erin L, AU - Niño-Liu,David O, AU - Wilkins,Katherine E, AU - Bancroft,Timothy, AU - Wang,Li, AU - Schmidt,Clarice L, AU - Caldo,Rico, AU - Yang,Bing, AU - White,Frank F, AU - Nettleton,Dan, AU - Wise,Roger P, AU - Bogdanove,Adam J, Y1 - 2014/02/27/ PY - 2013/09/28/received PY - 2014/01/17/accepted PY - 2014/3/4/entrez PY - 2014/3/4/pubmed PY - 2014/10/4/medline SP - e1003972 EP - e1003972 JF - PLoS pathogens JO - PLoS Pathog VL - 10 IS - 2 N2 - 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. SN - 1553-7374 UR - https://www.unboundmedicine.com/medline/citation/24586171/Code_assisted_discovery_of_TAL_effector_targets_in_bacterial_leaf_streak_of_rice_reveals_contrast_with_bacterial_blight_and_a_novel_susceptibility_gene_ L2 - https://dx.plos.org/10.1371/journal.ppat.1003972 DB - PRIME DP - Unbound Medicine ER -