High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates

PLoS Genet. 2013 May;9(5):e1003495. doi: 10.1371/journal.pgen.1003495. Epub 2013 May 16.

Abstract

Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA-seq (dRNA-seq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNA-seq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNA-seq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNA-seq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into strain-specific transcriptome organization and sRNAs, and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Campylobacter jejuni / genetics*
  • Campylobacter jejuni / pathogenicity
  • Chromosome Mapping
  • Gastroenteritis / genetics*
  • Gastroenteritis / microbiology
  • Gene Expression Regulation, Bacterial
  • Genetic Variation*
  • Genome, Bacterial
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic
  • Transcription Initiation Site
  • Transcriptome*

Grant support

GD is supported by the Graduate School for Life Sciences (GSLS), Würzburg, and AH by the DFG Priority Program 1335 “Scalable Visual Analytics.” CMS supported by the ZINF Young Investigator program at the Research Center for Infectious Diseases (ZINF) in Würzburg, Germany, the Bavarian Research Network for Molecular Biosystems (BioSysNet), and the Daimler and Benz Foundation. This publication was funded by the German Research Foundation (DFG) and the University of Würzburg in the funding programme “Open Access Publishing.” The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.