The primary transcriptome of the major human pathogen Helicobacter pylori

Genome sequencing of the Gram-negative Epsilonproteobacterium Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and small RNA (sRNA) output. H. pylori was even regarded as a bacterium without riboregulation as it lacks homologues of enterobacterial small RNAs as well as the RNA chaperone Hfq, a key player in sRNA-mediated regulation in many bacteria.

Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing the analysis of transcriptomes from both eukaryotes and prokaryotes. Recently, we have developed a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts that allowed us to present a global map of H. pylori transcriptional start sites (TSS) and its operon structure. We discovered hundreds of TSS within operons, and opposite to annotated genes, suggesting that the complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. Furthermore, we also discovered an unexpected number of ~60 sRNAs including potential regulators of cis- and trans-encoded target mRNAs indicating that riboregulation constitutes an important layer of gene regulation in Helicobacter. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species.

Based on the transcriptome dataset, we propose H. pylori as a new model organism for sRNA-mediated regulation in bacteria without the common RNA chaperone Hfq. This includes the functional characterization of abundant sRNAs and antisense RNAs especially with respect to their potential role in virulence as well as the identification of associated RNA-binding proteins and new regulatory mechanisms. For example, microarray-based analyses of whole-transcriptome changes or proteome analyses of sRNA deletion or overexpression mutants will help to identify target genes. Research in H. pylori will also help to shed light on sRNA-mediated regulation in other Epsilon-proteobacteria, including widespread and emerging pathogens such as Campylobacter.