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  • Article  (4)
  • Mika, Franziska  (4)
  • Salmonella
  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 23 November 2010, Vol.107(47), pp.20435-40
    Description: The abundant class of bacterial Hfq-associated small regulatory RNAs (sRNAs) parallels animal microRNAs in their ability to control multiple genes at the posttranscriptional level by short and imperfect base pairing. In contrast to the universal length and seed pairing mechanism of microRNAs, the sRNAs are heterogeneous in size and structure, and how they regulate multiple targets is not well understood. This paper provides evidence that a 5' located sRNA domain is a critical element for the control of a large posttranscriptional regulon. We show that the conserved 5' end of RybB sRNA recognizes multiple mRNAs of Salmonella outer membrane proteins by ≥7-bp Watson-Crick pairing. When fused to an unrelated sRNA, the 5' domain is sufficient to guide target mRNA degradation and maintain σ(E)-dependent envelope homeostasis. RybB sites in mRNAs are often conserved and flanked by 3' adenosine. They are found in a wide sequence window ranging from the upstream untranslated region to the deep coding sequence, indicating that some targets might be repressed at the level of translation, whereas others are repressed primarily by mRNA destabilization. Autonomous 5' domains seem more common in sRNAs than appreciated and might improve the design of synthetic RNA regulators.
    Keywords: Bacterial Outer Membrane Proteins -- Metabolism ; Gene Expression Regulation, Bacterial -- Genetics ; RNA, Messenger -- Metabolism ; Regulatory Sequences, Ribonucleic Acid -- Genetics ; Regulon -- Genetics ; Salmonella -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    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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  • 3
    Language: English
    In: Molecular Cell, 2008, Vol.32(6), pp.827-837
    Description: Small noncoding RNAs (sRNAs) have predominantly been shown to repress bacterial mRNAs by masking the Shine-Dalgarno (SD) or AUG start codon sequence, thereby preventing 30S ribosome entry and, consequently, translation initiation. However, many recently identified sRNAs lack obvious SD and AUG complementarity, indicating that sRNA-mediated translational control could also take place at other mRNA sites. We report that RybB sRNA represses mRNA translation by pairing with the 5′ coding region. Results of systematic antisense interference with 30S binding to and unrelated mRNAs suggest that sRNAs can act as translational repressors by sequestering sequences within the mRNA down to the fifth codon, even without SD and AUG start codon pairing. This “five codon window” for translational control in the 5′ coding region of mRNA not only has implications for sRNA target predictions but might also apply to -regulatory systems such as RNA thermosensors and riboswitches.
    Keywords: RNA ; Microbio ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 4
    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
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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