Small RNAs controlling outer membrane porins

Valentin‐Hansen, Poul; Johansen, Jesper; Rasmussen, Anders Aamann

doi:10.1016/j.mib.2007.03.001

Cited by 96 publications

(88 citation statements)

References 38 publications

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“…A significant portion of sRNA regulatory activity in E. coli and Salmonella is devoted to modulating the protein composition of the outer membrane, the compartment most directly involved in exchanges with the environment Vogel and Papenfort 2006;Valentin-Hansen et al 2007). All of the major porins and several outer membrane proteins (OMPs) are targets for regulation by one or more sRNAs.…”

mentioning

confidence: 99%

Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

Figueroa‐Bossi¹,

Valentini²,

Malleret³

et al. 2009

Genes Dev.

208

254

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A relevant, yet little recognized feature of antisense regulation is the possibility of switching roles between regulatory and regulated RNAs. Here we show that induction of a Salmonella gene relies on the conversion of a small RNA from effector to regulatory target. The chiP gene (formerly ybfM), identified and characterized in the present study, encodes a conserved enterobacterial chitoporin required for uptake of chitin-derived oligosaccharides. In the absence of inducer, chiP is kept silent by the action of a constitutively made small RNA, ChiX (formerly SroB, RybC), which pairs with a sequence at the 59 end of chiP mRNA. Silencing is relieved in the presence of chitooligosaccharides due to the accumulation of an RNA that pairs with ChiX and promotes its degradation. Anti-ChiX RNA originates from an intercistronic region of the chb operon, which comprises genes for chitooligosaccharide metabolism and whose transcription is activated in the presence of these sugars. We present evidence suggesting that the chb RNA destabilizes ChiX sRNA by invading the stem of its transcription terminator hairpin. Overall, our findings blur the distinction between effector and target in sRNA regulation, raising the possibility that some of the currently defined targets could actually be inhibitors of sRNA function.[Keywords: Antisense regulation; chitoporin; chitobiose; Hfq; small RNA] Supplemental material is available at http://www.genesdev.org.

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mentioning

confidence: 99%

Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

Figueroa‐Bossi¹,

Valentini²,

Malleret³

et al. 2009

Genes Dev.

208

254

View full text Add to dashboard Cite

show abstract

“…This leads to an MDR phenotype partly as a result of modified porin expression and reflects a rapid adaptive response to antibiotic stress. The control of bacterial membrane permeability is a complex process that is tightly regulated by an intricate network of systems that sense and respond to osmotic shock, pH, temperature, antibiotics and chemical stress 33,[80][81][82] .…”

Section: Discussionmentioning

confidence: 99%

The porin and the permeating antibiotic: a selective diffusion barrier in Gram-negative bacteria

2008

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“…First, the sRNA genes are generally highly regulated at the transcriptional level and are frequently expressed as components of global regulatory systems. Well studied regulatory cases include OxyR regulation of OxyS RNA (oxidative stress) (4), Fur regulation of RyhB RNA (iron limitation) (5), cAMP-CRP regulation of CyaR and Spot 42 RNA (glucose limitation) (6 -9), OmpR regulation of MicF, OmrA, and OmrB RNAs (osmotic shock) (10, 11), E -mediated transcription of MicA and RybB RNAs (envelope stress) (2,12), PhoPQ regulation of MgrR (Mg 2ϩ /Ca 2ϩ transport and virulence) (13), and LuxO control of Qrr1-4 (quorum sensing in Vibrio) (14). Furthermore, small RNA expression may be under control of a dedicated transcription factor, as exemplified by SgrR/SgrS RNA (glucose-phosphate stress) (15).…”

mentioning

confidence: 99%

Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli

Boysen

Møller‐Jensen

Kallipolitis

et al. 2010

Journal of Biological Chemistry

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103

101

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Small non-coding RNAs (sRNA) have emerged as important elements of gene regulatory circuits. In enterobacteria such as Escherichia coli and Salmonella many of these sRNAs interact with the Hfq protein, an RNA chaperone similar to mammalian Sm-like proteins and act in the post-transcriptional regulation of many genes. A number of these highly conserved ribo-regulators are stringently regulated at the level of transcription and are part of major regulons that deal with the immediate response to various stress conditions, indicating that every major transcription factor may control the expression of at least one sRNA regulator. Here, we extend this view by the identification and characterization of a highly conserved, anaerobically induced small sRNA in E. coli, whose expression is strictly dependent on the anaerobic transcriptional fumarate and nitrate reductase regulator (FNR). The sRNA, named FnrS, possesses signatures of base-pairing RNAs, and we show by employing global proteomic and transcriptomic profiling that the expression of multiple genes is negatively regulated by the sRNA. Intriguingly, many of these genes encode enzymes with "aerobic" functions or enzymes linked to oxidative stress. Furthermore, in previous work most of the potential target genes have been shown to be repressed by FNR through an undetermined mechanism. Collectively, our results provide insight into the mechanism by which FNR negatively regulates genes such as sodA, sodB, cydDC, and metE, thereby demonstrating that adaptation to anaerobic growth involves the action of a small regulatory RNA.In recent years non-coding RNAs have emerged as important components of regulatory circuits both in bacteria and eukaryotes (1-3). In enteric bacteria such as Escherichia coli and Salmonella more than a hundred different sRNAs 2 have been identified, and a major class consists of trans-encoded gene regulatory RNAs that act by an antisense mechanism to activate or, more frequently, to repress translation of target mRNAs. Many of these sRNAs are conserved in related species, are made in response to changes in environmental conditions, and are required for adaptation to stress or specific growth conditions. Several common features have been uncovered. First, the sRNA genes are generally highly regulated at the transcriptional level and are frequently expressed as components of global regulatory systems. Well studied regulatory cases include OxyR regulation of OxyS RNA (oxidative stress) (4), Fur regulation of RyhB RNA (iron limitation) (5), cAMP-CRP regulation of CyaR and Spot 42 RNA (glucose limitation) (6 -9), OmpR regulation of MicF, OmrA, and OmrB RNAs (osmotic shock) (10, 11), E -mediated transcription of MicA and RybB RNAs (envelope stress) (2, 12), PhoPQ regulation of MgrR (Mg 2ϩ /Ca 2ϩ transport and virulence) (13), and LuxO control of Qrr1-4 (quorum sensing in Vibrio) (14). Furthermore, small RNA expression may be under control of a dedicated transcription factor, as exemplified by SgrR/SgrS RNA (glucose-phosphate stress) (15). Second, pairin...

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Small RNAs controlling outer membrane porins

Cited by 96 publications

References 38 publications

Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

The porin and the permeating antibiotic: a selective diffusion barrier in Gram-negative bacteria

Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli

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