Down-regulation of Outer Membrane Proteins by Noncoding RNAs: Unraveling the cAMP–CRP- and σE-Dependent CyaR–ompX Regulatory Case

Johansen, Jesper; Eriksen, Maiken; Kallipolitis, Birgitte H.; Valentin‐Hansen, Poul

doi:10.1016/j.jmb.2008.06.058

Cited by 108 publications

(91 citation statements)

References 41 publications

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“…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: 95%

Role of polynucleotide phosphorylase in sRNA function in Escherichia coli

Lay¹,

Gottesman²

2011

RNA

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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.

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“…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: 95%

Role of polynucleotide phosphorylase in sRNA function in Escherichia coli

Lay¹,

Gottesman²

2011

RNA

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“…These 5' tails were shown to bind to the 5' part of the coding sequence of target mRNAs that include or not the initiation codon and the SD sequence. 26,[39][40][41][42][43][44] Of interest, only relatively short regions of complementarity, including stretches of 3 to 6 base pairs rich in GC, are sufficient for repression in vivo. 39,41,45 It remains to be shown whether these nucleotides represent the initial contacts that may be the rate-limiting step of the RNA-mRNA binding reaction.…”

Section: Perspectivesmentioning

confidence: 99%

The role of mRNA structure in translational control in bacteria

Geissmann¹,

Marzi²,

Romby³

2009

RNA Biology

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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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Down-regulation of Outer Membrane Proteins by Noncoding RNAs: Unraveling the cAMP–CRP- and σE-Dependent CyaR–ompX Regulatory Case

Cited by 108 publications

References 41 publications

Role of polynucleotide phosphorylase in sRNA function in Escherichia coli

Role of polynucleotide phosphorylase in sRNA function in Escherichia coli

The role of mRNA structure in translational control in bacteria

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

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