High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

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.

Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation

“…Approximately 47% of the TSSs were antisense transcripts (Fig. 1B), which is a considerably higher fraction than reported for bacterial species such as Salmonella enterica (∼13%) (20) but is in good agreement with RNA-seq data from Helicobacter pylori (41%) (10), Campylobacter jejuni (44-47%) (21), and Escherichia coli (37%) (22).…”

Role of the Streptococcus mutans CRISPR-Cas Systems in Immunity and Cell Physiology

“…In Staphylococcus epidermidis and Streptococcus pyogenes the CRISPR-Cas systems were shown to prevent the acquisition of plasmids or prophages by blocking entry in a manner akin to that performed against phage DNA (30,31). Similar observations have been made in Enterococcus faecalis, Enterococcus faecium, and Campylobacter jejuni (32,33). However, recently in Streptococcus pneumoniae and Neisseria meningitidis, CRISPR-Cas systems were shown to prevent natural transformation (34,35).…”

The RNase R from Campylobacter jejuni Has Unique Features and Is Involved in the First Steps of Infection

“…This endoribonuclease may have an important role under a Mn 2ϩ -rich environment, considering that Mn 2ϩ is its preferred cofactor (11). Similarly to what was observed in other organisms, RNase III from C. jejuni is involved in the processing of 30 S rRNA (11,12) and participates in the maturation of CRISPR RNAs, which are key elements in the CRISPR (clustered regularly interspaced short palindromic repeats) system of bacterial adaptive immunity (12).…”