Antisense transcription in Pseudomonas aeruginosa.

Denitsa Eckweiler,Susanne Häussler

doi:10.1099/mic.0.000664

Abstract

A large number of antisense transcripts have been detected in diverse microbial genomes and considerable effort has been devoted to elucidating the functional role of antisense transcription. In this study, we reanalysed extensive RNA sequencing data from the opportunistic pathogen Pseudomonas aeruginosa and found that the majority of genes have a propensity for antisense transcription. Although antisense transcripts were found in more than 80 % of the genes of the P. aeruginosa genome, the majority of sequencing reads were mapping sense and only a minority (<2 %) were mapping antisense to genes. Similarly to the sense expression levels, the antisense expression levels varied under different environmental conditions, with the sense and antisense expression levels often being inversely regulated and modulated by the activity of alternative sigma factors. Environment-modulated antisense transcription showed a bias towards being antisense to genes within regions of genomic plasticity and to those encoding small regulatory RNAs. In the future, the validation and functional characterization of antisense transcripts, and novel transcripts that are antisense to small regulatory RNAs in particular, have the potential to contribute to our understanding of the various levels of transcriptional regulation and its dynamics in the bacterial pathogen P. aeruginosa.

Highlights

With the emergence of high-throughput RNA sequencing approaches, an unexpected number of antisense (AS) RNA transcripts have been detected in diverse microbial genomes [1,2,3,4,5]
We previously recorded strand-specific single-nucleotideresolution mRNA sequence data for the P. aeruginosa type strain PA14 grown under 14 different environmental conditions
The distribution of normalized gene expression for all transcribed PA14 genes indicated that almost the entire genome of P. aeruginosa PA14 is transcriptionally active above the calculated sensitivity limit under at least one environmental condition [26]

Summary

Introduction

With the emergence of high-throughput RNA sequencing approaches, an unexpected number (several hundred) of antisense (AS) RNA transcripts have been detected in diverse microbial genomes [1,2,3,4,5]. Increasing information on the abundance, size and genomic localization of asRNA is currently being acquired [5,6,7,8,9,10,11]. It is still a matter of debate as to whether highly abundant asRNAs are functionally relevant [12,13,14,15]. There are increasing reports of cis-encoded regulatory asRNAs that overlap and are perfectly complementary to their target genes encoded on the opposite strand of the same genomic locus [25]

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