title: Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene.
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.affiliation: 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.
authors.forename: Raul A
authors.initials: RA
authors.lastname: Cernadas
authors.affiliation: 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.
authors.forename: Erin L
authors.initials: EL
authors.lastname: Doyle
authors.affiliation: Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America.
authors.forename: David O
authors.initials: DO
authors.lastname: Niño-Liu
authors.affiliation: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Wilkins
authors.affiliation: Department of Statistics, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Timothy
authors.initials: T
authors.lastname: Bancroft
authors.affiliation: 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.
authors.forename: Li
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Clarice L
authors.initials: CL
authors.lastname: Schmidt
authors.affiliation: Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Rico
authors.initials: R
authors.lastname: Caldo
authors.affiliation: Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Bing
authors.initials: B
authors.lastname: Yang
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America.
authors.forename: Frank F
authors.initials: FF
authors.lastname: White
authors.affiliation: Department of Statistics, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Dan
authors.initials: D
authors.lastname: Nettleton
authors.affiliation: 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.
authors.forename: Roger P
authors.initials: RP
authors.lastname: Wise
authors.affiliation: 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.
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Bogdanove
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D004252:DNA Mutational Analysis; D060467:Disease Resistance; D018506:Gene Expression Regulation, Plant; D055786:Gene Knockout Techniques; D017343:Genes, Plant; D054884:Host-Pathogen Interactions / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000382:microbiology*; D010935:Plant Diseases / Q000235:genetics*; D018515:Plant Leaves / Q000382:microbiology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014974:Xanthomonas / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins