title: Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.
abstract: The Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) is an important model to elucidate the mechanisms involved in the interaction with the host. To gain insight into the transcriptome of the Xcv strain 85-10, we took a differential RNA sequencing (dRNA-seq) approach. Using a novel method to automatically generate comprehensive transcription start site (TSS) maps we report 1421 putative TSSs in the Xcv genome. Genes in Xcv exhibit a poorly conserved -10 promoter element and no consensus Shine-Dalgarno sequence. Moreover, 14% of all mRNAs are leaderless and 13% of them have unusually long 5'-UTRs. Northern blot analyses confirmed 16 intergenic small RNAs and seven cis-encoded antisense RNAs in Xcv. Expression of eight intergenic transcripts was controlled by HrpG and HrpX, key regulators of the Xcv type III secretion system. More detailed characterization identified sX12 as a small RNA that controls virulence of Xcv by affecting the interaction of the pathogen and its host plants. The transcriptional landscape of Xcv is unexpectedly complex, featuring abundant antisense transcripts, alternative TSSs and clade-specific small RNAs.
authors.affiliation: Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, Institute for Biology, D-06099 Halle, Germany. cornelius.schubert@genetik.uni-halle.de
authors.forename: Cornelius
authors.initials: C
authors.lastname: Schmidtke
authors.forename: Sven
authors.initials: S
authors.lastname: Findeiss
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.forename: Juliane
authors.initials: J
authors.lastname: Kuhfuss
authors.forename: Steve
authors.initials: S
authors.lastname: Hoffmann
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Ulla
authors.initials: U
authors.lastname: Bonas
mesh_terms: D020121:5' Untranslated Regions; D001426:Bacterial Proteins / Q000235:genetics; D016680:Genome, Bacterial; D015233:Models, Statistical; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D012323:RNA Processing, Post-Transcriptional; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D059467:Transcriptome; D037521:Virulence Factors / Q000235:genetics* / Q000378:metabolism; D016959:Xanthomonas campestris / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D020121:5' Untranslated Regions; D001426:Bacterial Proteins; D058727:RNA, Small Untranslated; D037521:Virulence Factors
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