Systematic deletion of <i>Salmonella</i> small RNA genes identifies CyaR, a conserved CRP‐dependent riboregulator of OmpX synthesis

Papenfort, Kai; Pfeiffer, Verena; Lucchini, Sacha; Sonawane, Avinash; Hinton, Jay C. D.; Vogel, Jörg

doi:10.1111/j.1365-2958.2008.06189.x

Cited by 148 publications

(141 citation statements)

References 93 publications

(182 reference statements)

Supporting

Mentioning

134

Contrasting

Unclassified

Order By: Relevance

“…Region R2 represents the major single-stranded sequence of VqmR and extends into stemloop 4. This result suggests that the single-stranded regions R1 and R2 participate in base pairing with target mRNAs (33). To test this hypothesis, we cloned eight of the repressed target mRNAs into a posttranscriptional reporter system (34).…”

Section: C H O Le R a E V H A R V E Y I V A N G U Il La R U Mmentioning

confidence: 99%

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

Papenfort¹,

Förstner

Cong³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

196

253

View full text Add to dashboard Cite

Quorum sensing (QS) is a process of cell-to-cell communication that enables bacteria to transition between individual and collective lifestyles. QS controls virulence and biofilm formation in Vibrio cholerae, the causative agent of cholera disease. Differential RNA sequencing (RNA-seq) of wild-type V. cholerae and a locked low-cell-density QS-mutant strain identified 7,240 transcriptional start sites with ∼47% initiated in the antisense direction. A total of 107 of the transcripts do not appear to encode proteins, suggesting they specify regulatory RNAs. We focused on one such transcript that we name VqmR. vqmR is located upstream of the vqmA gene encoding a DNA-binding transcription factor. Mutagenesis and microarray analyses demonstrate that VqmA activates vqmR transcription, that vqmR encodes a regulatory RNA, and VqmR directly controls at least eight mRNA targets including the rtx (repeats in toxin) toxin genes and the vpsT transcriptional regulator of biofilm production. We show that VqmR inhibits biofilm formation through repression of vpsT. Together, these data provide to our knowledege the first global annotation of the transcriptional start sites in V. cholerae and highlight the importance of posttranscriptional regulation for collective behaviors in this human pathogen.Q uorum sensing (QS) is a process of bacterial cell-to-cell communication that relies on the production, release, accumulation, and population-wide detection of extracellular signal molecules called autoinducers. Processes controlled by QS are unproductive when undertaken by an individual bacterium but become effective when performed in unison by the group. In the major human pathogen, Vibrio cholerae, QS orchestrates processes including biofilm formation and virulence factor production (1). In the V. cholerae QS circuit, at low cell density (LCD), LuxO∼P activates transcription of genes encoding four small regulatory RNAs (sRNAs), Qrr1-4, which promote translation of the low cell density master QS regulator, AphA, and repress translation of HapR, the high cell density (HCD) master QS regulator (2, 3). AphA directs the gene expression program for V. cholerae cells to act as individuals. At high cell density, in the presence of autoinducers, LuxO is dephosphorylated and inactivated (4). The Qrr sRNAs are not transcribed, AphA is not produced, and by contrast, the hapR mRNA is translated into HapR protein. HapR controls the gene expression program underpinning collective behaviors (5, 6). Thus, the absence or presence of the Qrr sRNAs directs whether or not V. cholerae engages in QS. The Qrr sRNAs belong to the family of Hfq-binding sRNAs that regulate gene expression through base pairing with target mRNAs (7).An explosion in the discovery of noncoding transcripts, including sRNAs, has occurred due to recently developed transcriptomic technologies such as high-throughput sequencing of cDNAs, e.g., RNA sequencing (RNA-seq). (8). Major advantages of RNA-seq over conventional methods include high sensitivity for low abundance transcripts, ind...

show abstract

Section: C H O Le R a E V H A R V E Y I V A N G U Il La R U Mmentioning

confidence: 99%

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

Papenfort¹,

Förstner

Cong³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

196

253

View full text Add to dashboard Cite

show abstract

“…mRNA instability (Johansen et al 2008;Papenfort et al 2008;De Lay and Gottesman 2009), mutations such as rne-131 block mRNA degradation (Fig. 7A,B).…”

Section: Suppression Of Pnp Mutant Phenotypes By Deletion Of the C Tementioning

confidence: 99%

Role of polynucleotide phosphorylase in sRNA function in Escherichia coli

Lay¹,

Gottesman²

2011

RNA

View full text Add to dashboard Cite

In Escherichia coli, many small noncoding regulatory RNAs (sRNAs) post-transcriptionally regulate gene expression by basepairing to mRNAs in a process that is mediated by the RNA chaperone Hfq. Binding of the sRNA to the mRNA can lead to increased or decreased mRNA stability and/or translation. It is not known if proteins other than Hfq are necessary for this process. In order to identify additional genes required for the post-transcriptional regulation of gene expression by Hfqdependent sRNAs, we developed a novel combined genetic selection and screen for mutants defective in sRNA regulation. In our combined genetic selection and screen, we isolated hfq mutants and mutants in pnp, encoding polynucleotide phosphorylase (PNPase). We show that loss-of-function mutations in pnp result in a decreased stability of several sRNAs including RyhB, SgrS, and CyaR and also decrease both the negative and positive regulation by sRNAs. The defect in stability of CyaR and in negative and positive regulation are suppressed by deletion mutations in RNase E. Altogether, our results suggest that the lack of sRNA-mediated regulation in the absence of an active form of PNPase is due to the rapid turnover of sRNA resulting from an increase in RNase E activity and/or an increase in access of other ribonucleases to sRNAs.

show abstract

“…34 The C-rich hairpin loop motif of S. typhimurium CyaR RNA also binds to the SD sequence of ompX mRNA to repress translation. 35 Therefore it is tempting to propose that C-rich motifs in non-coding RNAs of low GC content bacteria might be a signature for regulatory RNAs that repress translation initiation. This rule seems to apply to several novel ncRNAs from S. aureus (Geissmann T, et al unpublished data) and from B. subtilis.…”

Section: Perspectivesmentioning

confidence: 99%