Antisense RNA that affects Rhodopseudomonas palustris quorum-sensing signal receptor expression

Abstract

Quorum sensing in the bacterium Rhodopseudomonas palustris involves the RpaI signal synthase, which produces p -coumaroyl-homoserine lactone ( p C-HSL) and RpaR, which is a p C-HSL–dependent transcriptional activator. There is also an antisense rpaR transcript (as rpaR ) of unknown function. Recent RNAseq studies have revealed that bacterial antisense RNAs are abundant, but little is known about the function of these molecules. Because as rpaR expression is quorum sensing dependent, we sought to characterize its production and function. We show that as rpaR is approximately 300–600 bases and is produced in response to p C-HSL and RpaR. There is an RpaR-binding site centered 51.5 bp from the mapped as rpaR transcript start site. We show that as rpaR overexpression reduces RpaR levels, rpaI expression, and p C-HSL production. We also generated an as rpaR mutant, which shows elevated RpaR levels, and elevated rpaI expression. Thus, as rpaR inhibits rpaR translation, and this inhibition results in suppression of RpaR-dependent rpaI expression and, thus, p C-HSL production. The R. palustris as rpaR represents an antisense RNA for which an activity can be measured and for which a distinct regulatory circuit related to a function is elucidated. It also represents yet another subtle regulatory layer for acyl-homoserine lactone quorum-sensing signal-responsive transcription factors.

Identification of a p -Coumarate Degradation Regulon in Rhodopseudomonas palustris by Xpression, an Integrated Tool for Prokaryotic RNA-Seq Data Processing

“…This allowed us to capture "sense" reads that reflect the expression levels of genes and also "antisense" reads that may reflect the expression levels of antisense RNAs. We found no evidence for antisense RNAs in the example shown here, but in other recent work, Xpression revealed the presence of an antisense RNA that modulates quorum sensing in R. palustris (7,8). Intergenic data can be useful for visualizing the transcription start site of a gene, and this can be seen in the igtop reads mapped to the genome in Fig.…”

Colonization strategies of Pseudomonas fluorescens Pf0-1: activation of soil-specific genes important for diverse and specific environments

“…Most of these antisense RNA (asRNA) molecules are of unknown function, and are thought-provoking because they support the concept that bacterial genomes have ‘dark matter’, functional regions not easily detectable with standard gene-finding algorithms [47]. Recent functional studies have begun to assign roles to asRNA molecules [for example [13,40,44,48], and those uncovered in this study provide a rich resource for future experiments which will further expand our understanding of the genetics of soil survival and persistence.…”

Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N -Acyl-Homoserine Lactone Autoinducers

“…3C and 4). Differences in expression levels of nwiI and nwiR suggest that, like many LuxI/R QS systems, the transcriptional regulation of these genes is complex (10,(61)(62)(63). Precisely timed expression of nwiR during and after a transition to slow growth is likely critical for QS-controlled gene expression, but further studies are needed to identify QSregulated genes.…”