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  • Sigma Factor
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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 21 April 2015, Vol.112(16), pp.5159-64
    Description: RpoS, the stationary phase/stress sigma factor of Escherichia coli, regulates a large cohort of genes important for the cell to deal with suboptimal conditions. Its level increases quickly in the cell in response to many stresses and returns to low levels when growth resumes. Increased RpoS results from increased translation and decreased RpoS degradation. Translation is positively regulated by small RNAs (sRNAs). Protein stability is positively regulated by anti-adaptors, which prevent the RssB adaptor-mediated degradation of RpoS by the ClpXP protease. Inactivation of aceE, a subunit of pyruvate dehydrogenase (PDH), was found to increase levels of RpoS by affecting both translation and protein degradation. The stabilization of RpoS in aceE mutants is dependent on increased transcription and translation of IraP and IraD, two known anti-adaptors. The aceE mutation also leads to a significant increase in rpoS translation. The sRNAs known to positively regulate RpoS are not responsible for the increased translation; sequences around the start codon are sufficient for the induction of translation. PDH synthesizes acetyl-CoA; acetate supplementation allows the cell to synthesize acetyl-CoA by an alternative, less favored pathway, in part dependent upon RpoS. Acetate addition suppressed the effects of the aceE mutant on induction of the anti-adaptors, RpoS stabilization, and rpoS translation. Thus, the bacterial cell responds to lowered levels of acetyl-CoA by inducing RpoS, allowing reprogramming of E. coli metabolism.
    Keywords: Clpxp ; Rpos ; Rssb ; Acetyl Coa ; Pyruvate Dehydrogenase ; Protein Biosynthesis ; Proteolysis ; Stress, Physiological ; Bacterial Proteins -- Metabolism ; Escherichia Coli -- Metabolism ; Sigma Factor -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Article
    Article
    Language: English
    In: Journal of bacteriology, 15 October 2017, Vol.199(20)
    Description: Bacteria have robust responses to a variety of stresses. In particular, bacteria like have multiple cell envelope stress responses, and generally we evaluate what these responses are doing by the repair systems they induce. However, probably at least as important in interpreting what is being sensed as stress are the genes that these stress systems downregulate, directly or indirectly. This is discussed here for the Cpx and sigma E systems of .
    Keywords: Cpx ; Hfq ; Escherichia Coli -- Genetics ; Escherichia Coli Proteins -- Genetics
    E-ISSN: 1098-5530
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  • 3
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 25 May 2010, Vol.107(21), pp.9602-7
    Description: Bacterial small noncoding RNAs carry out both positive and negative regulation of gene expression by pairing with mRNAs; in Escherichia coli, this regulation often requires the RNA chaperone Hfq. Three small regulatory RNAs (sRNAs), DsrA, RprA, and ArcZ, positively regulate translation of the sigma factor RpoS, each pairing with the 5' leader to open up an inhibitory hairpin. In vitro, rpoS interaction with sRNAs depends upon an (AAN)(4) Hfq-binding site upstream of the pairing region. Here we show that both Hfq and this Hfq binding site are required for RprA or ArcZ to act in vivo and to form a stable complex with rpoS mRNA in vitro; both were partially dispensable for DsrA at 37 degrees C. ArcZ sRNA is processed from 121 nt to a stable 56 nt species that contains the pairing region; only the 56 nt ArcZ makes a strong Hfq-dependent complex with rpoS. For each of these sRNAs, the stability of the sRNA*mRNA complexes, rather than their rate of formation, best predicted in vivo activity. These studies demonstrate that binding of Hfq to the rpoS mRNA is critical for sRNA regulation under normal conditions, but if the stability of the sRNA*mRNA complex is sufficiently high, the requirement for Hfq can be bypassed.
    Keywords: Escherichia Coli -- Metabolism ; Host Factor 1 Protein -- Metabolism ; RNA, Bacterial -- Metabolism ; RNA, Untranslated -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 4
    In: EMBO Journal, 15 September 2010, Vol.29(18), pp.3094-3107
    Description: The alternative sigma factor RpoS responds to multiple stresses and activates a large number of genes that allow bacteria to adapt to changing environments. The accumulation of RpoS is regulated at multiple levels, including the regulation of its translation by small regulatory RNAs (sRNAs). A library of plasmids expressing each of 26 sRNAs that bind Hfq was created to globally and rapidly analyse regulation of an translational fusion. The approach can be easily applied to any gene of interest. When overexpressed, four sRNAs, including OxyS, previously shown to repress , were observed to repress the expression of the fusion. Along with DsrA and RprA, two previously defined activators of translation, a third new sRNA activator, ArcZ, was identified. The expression of is repressed by the aerobic/anaerobic‐sensing ArcA–ArcB two‐component system under anaerobic conditions and adds translational regulation to the ArcA–ArcB regulon. ArcZ directly represses, and is repressed by, transcription, providing a negative feedback loop that may affect functioning of the ArcA–ArcB regulon. The alternative bacterial sigma factor RpoS is upregulated in response to various cellular stresses and instigates large‐scale changes in gene expression required for adaptation. In this study, Gottesman and colleagues identify the ArcZ small RNA, which is regulated by the ArcA–ArcB two‐component system, as a positive regulator of translation.
    Keywords: Arca ; Arcz ; Hfq ; Rpos
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 5
    In: Molecular Microbiology, July 2013, Vol.89(1), pp.52-64
    Description: The / two‐component system activates many genes for lipopolysaccharide () modification when cells are grown at low concentrations. An additional target of and is , an Hfq‐dependent small that negatively regulates expression of , also encoding a protein that carries out modification. Examination of confirmed that effectively silences ; the phosphoethanolamine modification associated with is found in Δ::kan but not cells. igma has been reported to positively regulate , although the promoter does not have the expected igma recognition motifs. The effects of igma and deletion of on levels of were independent, and the same 5′ end was found in both cases. transcription and the behaviour of transcriptional and translational fusions demonstrate that igma acts directly at the level of transcription initiation for , from the same start point as igma 70. The results suggest that when igma is active, synthesis of transcript outstrips ‐dependent degradation; presumably the modification of is important under these conditions. Adding to the complexity of regulation is a second , , which also directly and negatively regulates .
    Keywords: Transcription (Genetics) -- Genetic Aspects ; Enzymes -- Genetic Aspects ; Rna -- Genetic Aspects ; Mitogens;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 6
    Language: English
    In: The Journal of Bacteriology, 2010, Vol. 192(21), p.5559
    Description: Small noncoding RNAs (sRNAs) regulate gene expression in Escherichia coli by base pairing with mRNAs and modulating translation and mRNA stability. The sRNAs DsrA and RprA stimulate the translation of the stress response transcription factor RpoS by base pairing with the 5' untranslated region of the rpoS mRNA. In the present study, we found that the rpoS mRNA was unstable in the absence of DsrA and RprA and that expression of these sRNAs increased both the accumulation and the half-life of the rpoS mRNA. Mutations in dsrA, rprA, or rpoS that disrupt the predicted pairing sequences and reduce translation of RpoS also destabilize the rpoS mRNA. We found that the rpoS mRNA accumulates in an RNase E mutant strain in the absence of sRNA expression and, therefore, is degraded by an RNase E-mediated mechanism. DsrA expression is required, however, for maximal translation even when rpoS mRNA is abundant. This suggests that DsrA protects rpoS mRNA from degradation by RNase E and that DsrA has a further activity in stimulating RpoS protein synthesis, rpoS mRNA is subject to degradation by an additional pathway, mediated by RNase III, which, in contrast to the RNase E-mediated pathway, occurs in the presence and absence of DsrA or RprA. rpoS mRNA and RpoS protein levels are increased in an RNase III mutant strain with or without the sRNAs, suggesting that the role of RNase III in this context is to reduce the translation of RpoS even when the sRNAs are acting to stimulate translation. doi: 10.1128/JB.00464-10
    Keywords: Messenger Rna -- Properties ; Protein Synthesis -- Research ; Bacterial Genetics -- Research ; Translation (Genetics) -- Research ; Escherichia Coli -- Genetic Aspects;
    ISSN: 0021-9193
    ISSN: 00219193
    E-ISSN: 10985530
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  • 7
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 31 July 2007, Vol.104(31), pp.12896-901
    Description: IraP is a small protein that interferes with the delivery of sigma(S) (RpoS) to the ClpXP protease by blocking the action of RssB, an adaptor protein for sigma(S) degradation. IraP was previously shown to mediate stabilization of sigma(S) during phosphate starvation. Here, we show that iraP is transcribed in response to phosphate starvation; this response is mediated by ppGpp. The iraP promoter is positively regulated by ppGpp, dependent on the discriminator region of the iraP promoter. Sensing of phosphate starvation requires SpoT but not RelA. The results demonstrate a target for positive regulation by ppGpp and suggest that the cell use of ppGpp to mediate a variety of starvation responses operates in part by modulating sigma(S) levels.
    Keywords: Bacterial Proteins -- Genetics ; Escherichia Coli Proteins -- Metabolism ; Sigma Factor -- Genetics
    ISSN: 0027-8424
    E-ISSN: 10916490
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  • 8
    Language: English
    In: Cell, 22 September 2016, Vol.167(1), pp.111-121.e13
    Description: Bacterial small RNAs (sRNAs) have been implicated in various aspects of post-transcriptional gene regulation. Here, we demonstrate that sRNAs also act at the level of transcription termination. We use the gene, which encodes a general stress sigma factor σ , as a model system, and show that sRNAs DsrA, ArcZ, and RprA bind the 5′UTR to suppress premature Rho-dependent transcription termination, both in vitro and in vivo. sRNA-mediated antitermination markedly stimulates transcription of  during the transition to the stationary phase of growth, thereby facilitating a rapid adjustment of bacteria to global metabolic changes. Next generation RNA sequencing and bioinformatic analysis indicate that Rho functions as a global “attenuator” of transcription, acting at the 5′UTR of hundreds of bacterial genes, and that its suppression by sRNAs is a widespread mode of bacterial gene regulation. Bacterial small RNAs balance the Rho-dependent termination pathway to prevent premature transcription termination, extending the role of these RNA regulators beyond post-transcriptional control.
    Keywords: Transcription Termination ; Antitermination ; Rho ; Srna ; Sigma Factor ; Stress Response ; Biology
    ISSN: 0092-8674
    E-ISSN: 1097-4172
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  • 9
    In: The Journal of Bacteriology, 2007, Vol. 189(13), p.4872
    Description: Escherichia coli cell viability during starvation is strongly dependent on the expression of the rpoS gene, encoding the RpoS sigma subunit of RNA polymerase. RpoS abundance has been reported to be regulated at many levels, including transcription initiation, translation, and protein stability. The regulatory RNA SsrA (or tmRNA) has both tRNA and mRNA activities, relieving ribosome stalling and cotranslationally tagging proteins. We report here that SsrA is needed for the correct high-level translation of RpoS. The ATP-dependent protease Lon was also found to negatively affect RpoS translation, but only at low temperature. We suggest that SsrA may indirectly improve RpoS translation by limiting ribosome stalling and depletion of some component of the translation machinery. [PUBLICATION ]
    Keywords: E Coli ; Bacteriology ; Genes ; Ribonucleic Acid–RNA ; RNA Polymerase;
    ISSN: 0021-9193
    ISSN: 00219193
    E-ISSN: 10985530
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  • 10
    Language: English
    In: Journal of bacteriology, February 2014, Vol.196(4), pp.754-61
    Description: The stationary phase/general stress response sigma factor RpoS (σ(S)) is necessary for adaptation and restoration of homeostasis in stationary phase. As a physiological consequence, its levels are tightly regulated at least at two levels. Multiple small regulatory RNA molecules modulate its translation, in a manner that is dependent on the RNA chaperone Hfq and the rpoS 5' untranslated region. ClpXP and the RssB adaptor protein degrade RpoS, unless it is protected by an anti-adaptor. We here find that, in addition to these posttranscriptional levels of regulation, tRNA modification also affects the steady-state levels of RpoS. We screened mutants of several RNA modification enzymes for an effect on RpoS expression and identified the miaA gene, encoding a tRNA isopentenyltransferase, as necessary for full expression of both an rpoS750-lacZ translational fusion and the RpoS protein. This effect is independent of rpoS, the regulatory RNAs, and RpoS degradation. RpoD steady-state levels were not significantly different in the absence of MiaA, suggesting that this is an RpoS-specific effect. The rpoS coding sequence is significantly enriched for leu codons that use MiaA-modified tRNAs, compared to rpoD and many other genes. Dependence on MiaA may therefore provide yet another way for RpoS levels to respond to growth conditions.
    Keywords: Gene Expression Regulation, Bacterial ; Alkyl and Aryl Transferases -- Metabolism ; Bacterial Proteins -- Biosynthesis ; Escherichia Coli -- Enzymology ; RNA, Transfer -- Metabolism ; Sigma Factor -- Biosynthesis
    ISSN: 00219193
    E-ISSN: 1098-5530
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