Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape ofBordetella pertussis

Abstract

Bordetella pertussis is the causative agent of whooping cough, a respiratory disease still considered as a major public health threat and for which recent re-emergence has been observed. Constant reshuffling of Bordetella pertussis genome organization was observed during evolution. These rearrangements are essentially mediated by Insertion Sequences (IS), a mobile genetic elements present in more than 230 copies in the genome, which are supposed to be one of the driving forces enabling the pathogen to escape from vaccine-induced immunity.Here we use high-throughput sequencing approaches (RNA-seq and differential RNA-seq), to decipher Bordetella pertussis transcriptome characteristics and to evaluate the impact of IS elements on transcriptome architecture. Transcriptional organization was determined by identification of transcription start sites and revealed also a large variety of non-coding RNAs including sRNAs, leaderless mRNAs or long 3′ and 5′UTR including seven riboswitches. Unusual topological organizations, such as overlapping 5′- or 3′-extremities between oppositely orientated mRNA were also unveiled. The pivotal role of IS elements in the transcriptome architecture and their effect on the transcription of neighboring genes was examined. This effect is mediated by the introduction of IS harbored promoters or by emergence of hybrid promoters. This study revealed that in addition to their impact on genome rearrangements, most of the IS also impact on the expression of their flanking genes. Furthermore, the transcripts produced by IS are strain-specific due to the strain to strain variation in IS copy number and genomic context.

Identification of RNA 3’ ends and termination sites in Haloferax volcanii

“…Of the 1,543 TTS detected, 14.4% (222 TTS) of them were located in a gene on the opposite strand, thus resulting in antisense RNAs. Up to 75% of all genes were found to be associated with antisense RNAs in bacteria (39)(40)(41). Studies with archaea painted a similar picture (21,42).…”

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing

“…Therefore, for sites with a relative antisense signal less than four times the global deduced antisense shadow, the signal from the less productive strand was ignored. To deduce the global antisense shadow, we applied the same strategy as described in Amman et al (2018) for each chromosome and merged the single values by forming the average weighted by the chromosome length. The observed antisense shadows range between 0.34% and 1.74%.…”

Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis

“…Recently, we applied high-throughput sequencing approaches (RNA-seq and differential RNA-seq) to decipher the transcriptional landscape of B. pertussis (Amman et al 2018). One of the sRNAs discovered by dRNA-seq analysis was identified as an unknown transcript located within the intergenic region between BP2736 and BP2735 genes and originating from the negative strand ( Fig.…”

“…The extensive impact of the hfq gene deletion on transcriptomic profiles in B. pertussis motivated us to search for regulatory RNAs on a genome-wide scale. A recently determined primary transcriptome of B. pertussis (Amman et al 2018) revealed a large variety of noncoding RNAs, including sRNAs. In this study, we characterize one of the identified sRNAs, which, based on its possible function, was designated RgtA (repressor of glutamate transport).…”