Sigma E controls biogenesis of the antisense RNA MicA

Udekwu, Klas I.; Wagner, E. Gerhart H.

doi:10.1093/nar/gkl1154

Cited by 103 publications

(88 citation statements)

References 40 publications

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“…Transcription was shown to be important in the control of MicA RNA levels that are increased in stationary phase (Figueroa-Bossi et al 2006;Johansen et al 2006;Papenfort et al 2006;Udekwu and Wagner 2007). Here, we have shown for the first time that the growth phase regulation of MicA RNA is highly dependent on post-transcriptional control.…”

Section: Discussionmentioning

confidence: 61%

“…Moreover, MicA triggers the decay of ompA mRNA in an Hfq-dependent manner (Rasmussen et al 2005;Udekwu et al 2005;Johansen et al 2006). Recent studies have described their transcriptional regulation and established MicA and RybB RNAs as new members of the s E -regulon (Figueroa-Bossi et al 2006;Johansen et al 2006;Papenfort et al 2006;Udekwu and Wagner 2007).…”

Section: Introductionmentioning

confidence: 99%

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PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins

Andrade

Arraiano²

2008

RNA

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In this report, we demonstrate that exonucleolytic turnover is much more important in the regulation of sRNA levels than was previously recognized. For the first time, PNPase is introduced as a major regulatory feature controlling the levels of the small noncoding RNAs MicA and RybB, which are required for the accurate expression of outer membrane proteins (OMPs). In the absence of PNPase, the pattern of OMPs is changed. In stationary phase, MicA RNA levels are increased in the PNPase mutant, leading to a decrease in the levels of its target ompA mRNA and the respective protein. This growth phase regulation represents a novel pathway of control. We have evaluated other ribonucleases in the control of MicA RNA, and we showed that degradation by PNPase surpasses the effect of endonucleolytic cleavages by RNase E. RybB was also destabilized by PNPase. This work highlights a new role for PNPase in the degradation of small noncoding RNAs and opens the way to evaluate striking similarities between bacteria and eukaryotes.

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Section: Discussionmentioning

confidence: 61%

Section: Introductionmentioning

confidence: 99%

PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins

Andrade

Arraiano²

2008

RNA

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“…Our finding that vpsT is under the control of the unrelated VqmR sRNA in V. cholerae could indicate evolution of parallel regulatory pathways. Other examples like this exist: the V. cholerae VrrA sRNA and the E. coli MicA sRNA are not related to one another but both are controlled by the alternative sigma factor σ E and both base pair with the ompA mRNA (49,50). Likewise, in numerous bacterial species, sRNAs that are not related to one another are nonetheless required for responses to iron limitation, and all function by repressing mRNAs encoding iron-binding proteins (51).…”

Section: Discussionmentioning

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.

209

265

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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...

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“…Nearly one-third of the functional characterized sRNAs contribute to the control of the outer membrane protein (OMP) production. Some of these sRNAs are under the control of the σ factor RpoE (also known as σ E or σ 24 ) (Johansen et al 2006;Papenfort et al 2006;Udekwu and Wagner 2007;Johansen et al 2008), which regulates gene expression upon the accumulation of misfolded OMPs in the periplasmic space (Mecsas et al 1993;Missiakas et al 1996;Raivio and Silhavy 1999). However, only a few sRNAs have been reported to be transcribed by the σ factor RpoS (also known as σ S or σ 38 ) (Opdyke et al 2004;Padalon-Brauch et al 2008;Fröhlich et al 2012).…”

Section: Introductionmentioning

confidence: 99%

An RpoS-dependent sRNA regulates the expression of a chaperone involved in protein folding

Silva

Ortega

Viegas

et al. 2013

RNA

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Small noncoding RNAs (sRNAs) are usually expressed in the cell to face a variety of stresses. In this report we disclose the first target for SraL (also known as RyjA), a sRNA present in many bacteria, which is highly induced in stationary phase. We also demonstrate that this sRNA is directly transcribed by the major stress σ factor σ S (RpoS) in Salmonella enterica serovar Typhimurium. We show that SraL sRNA down-regulates the expression of the chaperone Trigger Factor (TF), encoded by the tig gene. TF is one of the three major chaperones that cooperate in the folding of the newly synthesized cytosolic proteins and is the only ribosome-associated chaperone known in bacteria. By use of bioinformatic tools and mutagenesis experiments, SraL was shown to directly interact with the 5 ′ UTR of the tig mRNA a few nucleotides upstream of the Shine-Dalgarno region. Namely, point mutations in the sRNA (SraL * ) abolished the repression of tig mRNA and could only down-regulate a tig transcript target with the respective compensatory mutations. We have also validated in vitro that SraL forms a stable duplex with the tig mRNA. This work constitutes the first report of a small RNA affecting protein folding. Taking into account that both SraL and TF are very well conserved in enterobacteria, this work will have important repercussions in the field.

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Sigma E controls biogenesis of the antisense RNA MicA

Cited by 103 publications

References 40 publications

PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins

PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins

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

An RpoS-dependent sRNA regulates the expression of a chaperone involved in protein folding

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