Small RNA sX13: a multifaceted regulator of virulence in the plant pathogen Xanthomonas

PLoS Pathog. 2013 Sep;9(9):e1003626. doi: 10.1371/journal.ppat.1003626. Epub 2013 Sep 12.

Abstract

Small noncoding RNAs (sRNAs) are ubiquitous posttranscriptional regulators of gene expression. Using the model plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv), we investigated the highly expressed and conserved sRNA sX13 in detail. Deletion of sX13 impinged on Xcv virulence and the expression of genes encoding components and substrates of the Hrp type III secretion (T3S) system. qRT-PCR analyses revealed that sX13 promotes mRNA accumulation of HrpX, a key regulator of the T3S system, whereas the mRNA level of the master regulator HrpG was unaffected. Complementation studies suggest that sX13 acts upstream of HrpG. Microarray analyses identified 63 sX13-regulated genes, which are involved in signal transduction, motility, transcriptional and posttranscriptional regulation and virulence. Structure analyses of in vitro transcribed sX13 revealed a structure with three stable stems and three apical C-rich loops. A computational search for putative regulatory motifs revealed that sX13-repressed mRNAs predominantly harbor G-rich motifs in proximity of translation start sites. Mutation of sX13 loops differentially affected Xcv virulence and the mRNA abundance of putative targets. Using a GFP-based reporter system, we demonstrated that sX13-mediated repression of protein synthesis requires both the C-rich motifs in sX13 and G-rich motifs in potential target mRNAs. Although the RNA-binding protein Hfq was dispensable for sX13 activity, the hfq mRNA and Hfq::GFP abundance were negatively regulated by sX13. In addition, we found that G-rich motifs in sX13-repressed mRNAs can serve as translational enhancers and are located at the ribosome-binding site in 5% of all protein-coding Xcv genes. Our study revealed that sX13 represents a novel class of virulence regulators and provides insights into sRNA-mediated modulation of adaptive processes in the plant pathogen Xanthomonas.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Capsicum / microbiology
  • Chemotaxis
  • Gene Expression Regulation, Bacterial*
  • Mutation
  • Nucleic Acid Conformation
  • Nucleotide Motifs
  • Oligonucleotide Array Sequence Analysis
  • Plant Leaves / microbiology
  • Protein Biosynthesis
  • RNA Stability
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism*
  • RNA, Messenger / metabolism
  • RNA, Small Untranslated / chemistry
  • RNA, Small Untranslated / metabolism*
  • Signal Transduction
  • Virulence
  • Virulence Factors / chemistry
  • Virulence Factors / genetics
  • Virulence Factors / metabolism*
  • Xanthomonas / growth & development
  • Xanthomonas / metabolism*
  • Xanthomonas / pathogenicity

Substances

  • Bacterial Proteins
  • RNA, Bacterial
  • RNA, Messenger
  • RNA, Small Untranslated
  • Virulence Factors

Grants and funding

This work was supported by grants from the Deutsche Forschungsgemeinschaft to UB and AB. (SPP 1258; “Sensory and Regulatory RNAs in Prokaryotes”) and the “Graduiertenkolleg” (GRK 1591) to UB, and by the Bundesministerium für Bildung und Forschung (grant 0313105) to AB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.