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  • Pfeiffer, Verena  (10)
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  • 1
    Language: English
    In: Molecular cell, 2012, Vol.47(6), pp.943-953
    Description: Numerous small non-coding RNAs (sRNAs) in bacteria modulate rates of translation initiation and degradation of target mRNAs, which they recognize through base-pairing facilitated by the RNA chaperone Hfq. Recent evidence indicates that the ternary complex of Hfq, sRNA and mRNA guides endoribonuclease RNase E to initiate turnover of both the RNAs. We show that a sRNA not only guides RNase E to a defined site in a target RNA, but also allosterically activates the enzyme by presenting a monophosphate group at the 5′-end of the cognate-pairing “seed.” Moreover, in the absence of the target the 5′-monophosphate makes the sRNA seed region vulnerable to an attack by RNase E against which Hfq confers no protection. These results suggest that the chemical signature and pairing status of the sRNA seed region may help to both ‘proofread’ recognition and activate mRNA cleavage, as part of a dynamic process involving cooperation of RNA, Hfq and RNase E. ; p. 943-953.
    Keywords: Translation (Genetics) ; Messenger Rna ; Bacteria ; Non-Coding Rna ; Ribonucleases
    ISSN: 1097-2765
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  • 2
    Language: English
    In: Molecular Cell, 28 September 2012, Vol.47(6), pp.943-953
    Description: Numerous small non-coding RNAs (sRNAs) in bacteria modulate rates of translation initiation and degradation of target mRNAs, which they recognize through base-pairing facilitated by the RNA chaperone Hfq. Recent evidence indicates that the ternary complex of Hfq, sRNA and mRNA guides endoribonuclease RNase E to initiate turnover of both the RNAs. We show that a sRNA not only guides RNase E to a defined site in a target RNA, but also allosterically activates the enzyme by presenting a monophosphate group at the 5′-end of the cognate-pairing “seed.” Moreover, in the absence of the target the 5′-monophosphate makes the sRNA seed region vulnerable to an attack by RNase E against which Hfq confers no protection. These results suggest that the chemical signature and pairing status of the sRNA seed region may help to both ‘proofread’ recognition and activate mRNA cleavage, as part of a dynamic process involving cooperation of RNA, Hfq and RNase E. ► Small RNA-mRNA duplex can recruit single-strand specific endoribonuclease RNase E ► sRNA can guide and allosterically activate RNase E to initiate target mRNA degradation ► The allosteric signal is a monophosphate group on the 5' end of the sRNA ► The 5' monophosphate may contribute to proofreading of sRNA action
    Keywords: Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 3
    In: Molecular Microbiology, January 2007, Vol.63(1), pp.193-217
    Description: The RNA chaperone, Hfq, plays a diverse role in bacterial physiology beyond its original role as a host factor required for replication of Q RNA bacteriophage. In this study, we show that Hfq is involved in the expression and secretion of virulence factors in the facultative intracellular pathogen, . A deletion strain is highly attenuated in mice after both oral and intraperitoneal infection, and shows a severe defect in invasion of epithelial cells and a growth defect in both epithelial cells and macrophages . Surprisingly, we find that these phenotypes are largely independent of the previously reported requirement of Hfq for expression of the stationary phase sigma factor, RpoS. Our results implicate Hfq as a key regulator of multiple aspects of virulence including regulation of motility and outer membrane protein (OmpD) expression in addition to invasion and intracellular growth. These pleiotropic effects are suggested to involve a network of regulatory small non‐coding RNAs, placing Hfq at the centre of post‐transcriptional regulation of virulence gene expression in . In addition, the mutation appears to cause a chronic activation of the RpoE‐mediated envelope stress response which is likely due to a misregulation of membrane protein expression.
    Keywords: Ribonucleic Acid–RNA ; Gene Expression ; Salmonella ; Genotype & Phenotype ; Proteins ; Cell Growth ; Pathology;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 4
    In: Molecular Microbiology, May 2008, Vol.68(4), pp.890-906
    Description: Post‐transcriptional repression of porin synthesis has emerged as a major function of Hfq‐dependent, small non‐coding RNAs (sRNAs). Many enterobacteria express OmpX‐like porins, a family of outer membrane proteins whose physiological roles and structural properties have been studied intensively. While regulatory sRNAs have been identified for most major and many minor porins of and , a post‐transcriptional regulator of OmpX levels has never been found. Here, we have taken a ‘reverse target search’ approach by systematic inactivation of sRNA genes, and screening 35 sRNA deletion strains for effects on OmpX synthesis. We have identified the Hfq‐dependent CyaR (formerly RyeE) sRNA as an repressor. Global transcriptomic profiling following induction of CyaR expression suggests that mRNA is the primary target of this sRNA under standard growth conditions. The results of phylogenetic and mutational analyses suggest that a conserved RNA hairpin of CyaR, featuring a C‐rich apical loop, acts to sequester the Shine–Dalgarno sequence of mRNA and to inhibit translational initiation. We have also discovered that expression is tightly controlled by the cyclic AMP receptor protein, CRP. This represents a new link between porin repression and nutrient availability that is likely to be widely conserved among enterobacteria.
    Keywords: Genetic Research -- Genetic Aspects ; Genetic Research -- Physiological Aspects ; Bacterial Genetics -- Genetic Aspects ; Bacterial Genetics -- Physiological Aspects ; Cyclic Adenosine Monophosphate -- Genetic Aspects ; Cyclic Adenosine Monophosphate -- Physiological Aspects ; Salmonella -- Genetic Aspects ; Salmonella -- Physiological Aspects ; Rna -- Genetic Aspects ; Rna -- Physiological Aspects ; Porins -- Genetic Aspects ; Porins -- Physiological Aspects;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 5
    Language: English
    In: Nucleic acids research, 2007, Vol.35(22), pp.7651-64
    Description: In pathogenic bacteria, a large number of sRNAs coordinate adaptation to stress and expression of virulence genes. To better understand the turnover of regulatory sRNAs in the model pathogen, Salmonella typhimurium, we have constructed mutants for several ribonucleases (RNase E, RNase G, RNase III, PNPase) and Poly(A) Polymerase I. The expression profiles of four sRNAs conserved among many enterobacteria, CsrB, CsrC, MicA and SraL, were analysed and the processing and stability of these sRNAs was studied in the constructed strains. The degradosome was a common feature involved in the turnover of these four sRNAs. PAPI-mediated polyadenylation was the major factor governing SraL degradation. RNase III was revealed to strongly affect MicA decay. PNPase was shown to be important in the decay of these four sRNAs. The stability of CsrB and CsrC seemed to be independent of the RNA chaperone, Hfq, whereas the decay of SraL and MicA was Hfq-dependent. Taken together, the results of this study provide initial insight into the mechanisms of sRNA decay in Salmonella, and indicate specific contributions of the RNA decay machinery components to the turnover of individual sRNAs.
    Keywords: RNA, Bacterial -- Metabolism ; RNA, Untranslated -- Metabolism ; Ribonucleases -- Physiology ; Salmonella Typhimurium -- Enzymology
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 6
    In: Molecular Microbiology, December 2007, Vol.66(5), pp.1174-1191
    Description: The pathogenicity island (SPI‐1) encodes ∼35 proteins involved in assembly of a type III secretion system (T3SS) which endows with the ability to invade eukaryotic cells. We have discovered a novel SPI‐1 gene, , which expresses an abundant small non‐coding RNA (sRNA). The gene, which we identified in a global search for new RNA genes, is activated by the major SPI‐1 transcription factor, HilD, under conditions that favour host cell invasion. The RNA chaperone, Hfq, is essential for the stability of the ∼80 nt InvR RNA. Hfq binds InvR with high affinity , and InvR co‐immunoprecipitates with FLAG epitope‐tagged Hfq in extracts. Surprisingly, deletion/overexpression of revealed no phenotype in SPI‐1 regulation. In contrast, we find that InvR represses the synthesis of the abundant OmpD porin encoded by the core genome. As is conserved in the early branching , we speculate that porin repression by InvR may have aided successful establishment of the SPI‐1 T3SS after horizontal acquisition in the lineage. This study identifies the first regulatory RNA of an enterobacterial pathogenicity island, and new roles for Hfq and HilD in SPI‐1 gene expression.
    Keywords: Ribonucleic Acid–RNA ; Salmonella ; Bacteria ; Bacteriology ; Protein Synthesis ; Genomics;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 7
    In: Molecular Microbiology, December 2006, Vol.62(6), pp.1674-1688
    Description: The bacterial envelope stress response (ESR) is triggered by the accumulation of misfolded outer membrane proteins (OMPs) upon envelope damage or excessive OMP synthesis, and is mediated by the alternative sigma factor, σ. Activation of the σ pathway causes a rapid downregulation of major mRNAs, which prevents further build‐up of unassembled OMPs and liberates the translocation and folding apparatus under conditions that require envelope remodelling. The factors that facilitate the rapid removal of the unusually stable mRNAs in the ESR were previously unknown. We report that in the ESR relies upon two highly conserved, σ‐controlled small non‐coding RNAs, RybB and MicA. By using a transcriptomic approach and kinetic analyses of target mRNA decay , RybB was identified as the factor that selectively accelerates the decay of multiple major mRNAs upon induction of the ESR, while MicA is proposed to facilitate rapid decay of the single mRNA. In unstressed bacterial cells, the two σ‐dependent small RNAs function within a surveillance loop to maintain envelope homeostasis and to achieve autoregulation of σ.
    Keywords: Mrna Turnover ; Envelopes ; Outer Membrane Proteins ; Kinetics ; Non-Coding RNA ; Stress ; Homeostasis ; Sigma Factor ; Translocation ; Salmonella ; RNA ; Genetics & Taxonomy;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 8
    In: Nature Structural & Molecular Biology, 2009, Vol.16(8), p.840
    Description: Bacterial small noncoding RNAs (sRNAs) generally recognize target mRNAs in the 5' region to prevent 30S ribosomes from initiating translation. It was thought that the mRNA coding sequence (CDS) was refractory to sRNA-mediated repression, because elongating 70S ribosomes have an efficient RNA helicase activity that prevents stable target pairing. We report that the Hfq-associated MicC sRNA silences Salmonella typhimurium ompD mRNA via a [less than or equal to] 12-bp RNA duplex within the CDS (codons 23-26) that is essential and sufficient for repression. MicC does not inhibit translational initiation at this downstream position but instead acts by accelerating RNase E-dependent ompD mRNA decay. We propose an alternative gene-silencing pathway within bacterial CDS wherein sRNAs repress targets by endonucleolytic mRNA destabilization rather than by the prototypical inhibition of translational initiation. The discovery of CDS targeting markedly expands the sequence space for sRNA target predictions in bacteria.
    Keywords: Bacterial Genetics -- Research ; Gene Silencing -- Health Aspects ; Gene Silencing -- Research ; Messenger Rna -- Physiological Aspects ; Messenger Rna -- Research ; Ribosomes -- Physiological Aspects ; Ribosomes -- Research;
    ISSN: 1545-9993
    E-ISSN: 15459985
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  • 9
    Language: English
    In: Molecular microbiology, December 2007, Vol.66(5), pp.1174-91
    Description: The Salmonella pathogenicity island (SPI-1) encodes approximately 35 proteins involved in assembly of a type III secretion system (T3SS) which endows Salmonella with the ability to invade eukaryotic cells. We have discovered a novel SPI-1 gene, invR, which expresses an abundant small non-coding RNA (sRNA). The invR gene, which we identified in a global search for new Salmonella sRNA genes, is activated by the major SPI-1 transcription factor, HilD, under conditions that favour host cell invasion. The RNA chaperone, Hfq, is essential for the in vivo stability of the approximately 80 nt InvR RNA. Hfq binds InvR with high affinity in vitro, and InvR co-immunoprecipitates with FLAG epitope-tagged Hfq in Salmonella extracts. Surprisingly, deletion/overexpression of invR revealed no phenotype in SPI-1 regulation. In contrast, we find that InvR represses the synthesis of the abundant OmpD porin encoded by the Salmonella core genome. As invR is conserved in the early branching Salmonella bongori, we speculate that porin repression by InvR may have aided successful establishment of the SPI-1 T3SS after horizontal acquisition in the Salmonella lineage. This study identifies the first regulatory RNA of an enterobacterial pathogenicity island, and new roles for Hfq and HilD in SPI-1 gene expression.
    Keywords: Gene Expression Regulation, Bacterial ; Porins -- Biosynthesis ; RNA, Untranslated -- Metabolism ; Salmonella -- Genetics
    ISSN: 0950-382X
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  • 10
    Language: English
    In: Molecular microbiology, December 2006, Vol.62(6), pp.1674-88
    Description: The bacterial envelope stress response (ESR) is triggered by the accumulation of misfolded outer membrane proteins (OMPs) upon envelope damage or excessive OMP synthesis, and is mediated by the alternative sigma factor, sigmaE. Activation of the GE pathway causes a rapid downregulation of major omp mRNAs, which prevents further build-up of unassembled OMPs and liberates the translocation and folding apparatus under conditions that require envelope remodelling. The factors that facilitate the rapid removal of the unusually stable omp mRNAs in the ESR were previously unknown. We report that in Salmonella the ESR relies upon two highly conserved, sigmaE-controlled small non-coding RNAs, RybB and MicA. By using a transcriptomic approach and kinetic analyses of target mRNA decay in vivo, RybB was identified as the factor that selectively accelerates the decay of multiple major omp mRNAs upon induction of the ESR, while MicA is proposed to facilitate rapid decay of the single ompA mRNA. In unstressed bacterial cells, the two oE-dependent small RNAs function within a surveillance loop to maintain envelope homeostasis and to achieve autoregulation of oE.
    Keywords: Bacterial Outer Membrane Proteins -- Metabolism ; RNA, Messenger -- Metabolism ; RNA, Untranslated -- Metabolism ; Salmonella -- Metabolism ; Sigma Factor -- Metabolism
    ISSN: 0950-382X
    E-ISSN: 13652958
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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