title: Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny.
abstract: Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls expression of the genes encoding the structural and functional components of the type III secretion system (T3SS) and the type three secreted effector proteins (T3E) that are collectively essential for virulence. HrpL also regulates expression of an under-explored suite of non-type III effector genes (non-T3E), including toxin production systems and operons not previously associated with virulence. We implemented and refined genome-wide transcriptional analysis methods using cDNA-derived high-throughput sequencing (RNA-seq) data to characterize the HrpL regulon from six isolates of P. syringae spanning the diversity of the species. Our transcriptomes, mapped onto both complete and draft genomes, significantly extend earlier studies. We confirmed HrpL-regulation for a majority of previously defined T3E genes in these six strains. We identified two new T3E families from P. syringae pv. oryzae 1_6, a strain within the relatively underexplored phylogenetic Multi-Locus Sequence Typing (MLST) group IV. The HrpL regulons varied among strains in gene number and content across both their T3E and non-T3E gene suites. Strains within MLST group II consistently express the lowest number of HrpL-regulated genes. We identified events leading to recruitment into, and loss from, the HrpL regulon. These included gene gain and loss, and loss of HrpL regulation caused by group-specific cis element mutations in otherwise conserved genes. Novel non-T3E HrpL-regulated genes include an operon that we show is required for full virulence of P. syringae pv. phaseolicola 1448A on French bean. We highlight the power of integrating genomic, transcriptomic, and phylogenetic information to drive concise functional experimentation and to derive better insight into the evolution of virulence across an evolutionarily diverse pathogen species.
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Tatiana S
authors.initials: TS
authors.lastname: Mucyn
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Scott
authors.initials: S
authors.lastname: Yourstone
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Abigail L
authors.initials: AL
authors.lastname: Lind
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Surojit
authors.initials: S
authors.lastname: Biswas
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Marc T
authors.initials: MT
authors.lastname: Nishimura
authors.affiliation: School of Plant Sciences, The University of Arizona, Tucson, Arizona, United States of America.
authors.forename: David A
authors.initials: DA
authors.lastname: Baltrus
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America ; Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Jason S
authors.initials: JS
authors.lastname: Cumbie
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America ; Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America ; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Jeff H
authors.initials: JH
authors.lastname: Chang
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Corbin D
authors.initials: CD
authors.lastname: Jones
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Jeffery L
authors.initials: JL
authors.lastname: Dangl
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America ; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Grant
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D058947:Bacterial Secretion Systems / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D009876:Operon / Q000502:physiology; D010802:Phylogeny; D044224:Pseudomonas syringae / Q000235:genetics* / Q000472:pathogenicity; D012808:Sigma Factor / Q000235:genetics* / Q000378:metabolism; D037521:Virulence Factors / Q000096:biosynthesis / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems; D004268:DNA-Binding Proteins; C085855:HrpL protein, Pseudomonas syringae; D012808:Sigma Factor; D037521:Virulence Factors