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  • Escherichia Coli Proteins
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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
    In: Molecular Microbiology, December 2011, Vol.82(6), pp.1545-1562
    Description: A major class of small bacterial RNAs (sRNAs) regulate translation and mRNA stability by pairing with target mRNAs, dependent upon the RNA chaperone Hfq. Hfq, related to the Lsm/Sm families of splicing proteins, binds the sRNAs and stabilizes them and stimulates pairing with mRNAs . Although Hfq is abundant, the sRNAs, when induced, are similarly abundant. Therefore, Hfq may be limiting for sRNA function. We find that, when overexpressed, a number of sRNAs competed with endogenous sRNAs for binding to Hfq. This correlated with lower accumulation of the sRNAs (presumably a reflection of the loss of Hfq binding), and lower activity of the sRNAs in regulating gene expression. Hfq was limiting for both positive and negative regulation by the sRNAs. In addition, deletion of the gene for an expressed and particularly effective competitor sRNA improved the regulation of genes by other sRNAs, suggesting that Hfq is limiting during normal growth conditions. These results support the existence of a hierarchy of sRNA competition for Hfq, modulating the function of some sRNAs.
    Keywords: Messenger Rna ; Protein Binding ; Gene Expression ; Genes ; Escherichia Coli ; Proteins;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 3
    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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  • 4
    Language: English
    In: Journal of bacteriology, 25 January 2016, Vol.198(7), pp.1101-13
    Description: Bacteria use multidrug efflux pumps to export drugs and toxic compounds out of the cell. One of the most important efflux pumps in Escherichia coli is the AcrAB-TolC system. Small regulatory RNAs (sRNAs) are known to be major posttranscriptional regulators that can enhance or repress translation by binding to the 5' untranslated region (UTR) of mRNA targets with the help of a chaperone protein, Hfq. In this study, we investigated the expression of acrA, acrB, and tolC translational fusions using 27 Hfq-dependent sRNAs overexpressed from plasmids. No significant sRNA regulation of acrA or acrB was detected. SdsR (also known as RyeB), an abundant and well-conserved stationary-phase sRNA, was found to repress the expression of tolC, the gene encoding the outer membrane protein of many multidrug resistance efflux pumps. This repression was shown to be by direct base pairing occurring upstream from the ribosomal binding site. SdsR overexpression and its regulation of tolC were found to reduce resistance to novobiocin and crystal violet. Our results suggest that additional targets for SdsR exist that contribute to increased antibiotic sensitivity and reduced biofilm formation. In an effort to identify phenotypes associated with single-copy SdsR and its regulation of tolC, the effect of a deletion of sdsR or mutations in tolC that should block SdsR pairing were investigated using a Biolog phenotypic microarray. However, no significant phenotypes were identified. Therefore, SdsR appears to modulate rather than act as a major regulator of its targets. AcrAB-TolC is a major efflux pump present in E. coli and Gram-negative bacteria used to export toxic compounds; the pump confers resistance to many antibiotics of unrelated classes. In this study, we found that SdsR, a small RNA expressed in stationary phase, repressed the expression of tolC, resulting in increased sensitivity to some antibiotics. This extends the findings of previous studies showing that sRNAs contribute to the regulation of many outer membrane proteins; manipulating or enhancing their action might help in sensitizing bacteria to antibiotics.
    Keywords: Bacterial Outer Membrane Proteins -- Metabolism ; Carrier Proteins -- Metabolism ; Escherichia Coli -- Metabolism ; Escherichia Coli Proteins -- Metabolism ; Gene Expression Regulation, Bacterial -- Physiology ; Membrane Transport Proteins -- Metabolism ; RNA, Bacterial -- Metabolism
    ISSN: 00219193
    E-ISSN: 1098-5530
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  • 5
    Language: English
    In: Nucleic acids research, 19 August 2016, Vol.44(14), pp.6907-23
    Description: Post-transcriptional regulation of transcription factors contributes to regulatory circuits. We created translational reporter fusions for multiple central regulators in Escherichia coli and examined the effect of Hfq-dependent non-coding RNAs on these fusions. This approach yields an 'RNA landscape,' identifying Hfq-dependent sRNAs that regulate a given fusion. No significant sRNA regulation of crp or fnr was detected. hns was regulated only by DsrA, as previously reported. Lrp and SoxS were both found to be regulated post-transcriptionally. Lrp, ' L: eucine-responsive R: egulatory P: rotein,' regulates genes involved in amino acid biosynthesis and catabolism and other cellular functions. sRNAs DsrA, MicF and GcvB each independently downregulate the lrp translational fusion, confirming previous reports for MicF and GcvB. MicF and DsrA interact with an overlapping site early in the lrp ORF, while GcvB acts upstream at two independent sites in the long lrp leader. Surprisingly, GcvB was found to be responsible for significant downregulation of lrp after oxidative stress; MicF also contributed. SoxS, an activator of genes used to combat oxidative stress, is negatively regulated by sRNA MgrR. This study demonstrates that while not all global regulators are subject to sRNA regulation, post-transcriptional control by sRNAs allows multiple environmental signals to affect synthesis of the transcriptional regulator.
    Keywords: Gene Expression Regulation, Bacterial ; Transcription, Genetic ; Escherichia Coli -- Genetics ; Escherichia Coli Proteins -- Genetics ; Leucine-Responsive Regulatory Protein -- Genetics ; RNA, Bacterial -- Metabolism ; Trans-Activators -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 6
    In: Molecular Microbiology, November 2012, Vol.86(3), pp.524-538
    Description: Small ‐dependent non‐coding regulatory s (s) that alter stability and expression by pairing with target s have increasingly been shown to be important in influencing the behaviour of bacteria. In , and , which encode the master regulator of flagellar synthesis, are co‐transcribed from a promoter that is regulated by multiple transcription factors that respond to different environmental cues. Here, we show that the 5′ untranslated region (5′ ) of the also serves as a hub to integrate additional environmental cues into the decision to make flagella. Four s, , , and , negatively regulated and one , , positively regulated motility and expression by base‐pairing with the 5′ of this . Another , , positively regulated motility independent of regulation of . Furthermore, we demonstrate that the regulation of motility by the / two component system is in part due to its regulation of . is the first that has been shown to be both positively and negatively regulated by direct pairing to s. Moreover, both positive regulation by and negative regulation by require the same binding site in the .
    Keywords: Biology;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 7
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 17 March 1998, Vol.95(6), pp.2731-2732
    Description: In the unending wars of organism vs. organism, the growth of bacteriophage and the defenses raised by bacteria were among the first recognized and continue to provide new variations and insights on ways to defend oneself. A paper in this issue of the Proceedings demonstrates that prokaryotes, like eukaryotes, have chosen proteolytic self-destruction as a route to protection from attack, albeit a protection for the community rather than for the cell under attack (1).
    Keywords: Biological sciences -- Biology -- Microbiology -- Ribonucleoproteins ; Biological sciences -- Biochemistry -- Biomolecules -- Ribonucleoproteins ; Physical sciences -- Chemistry -- Chemical compounds -- Ribonucleoproteins ; Biological sciences -- Biology -- Cytology -- Ribonucleoproteins ; Biological sciences -- Biology -- Genetics -- Ribonucleoproteins ; Biological sciences -- Biology -- Genetics -- Ribonucleoproteins ; Biological sciences -- Biology -- Cytology -- Ribonucleoproteins ; Biological sciences -- Biology -- Biological taxonomies -- Ribonucleoproteins ; Health sciences -- Medical conditions -- Infections -- Ribonucleoproteins ; Health sciences -- Medical sciences -- Pharmaceutics -- Ribonucleoproteins
    ISSN: 00278424
    E-ISSN: 10916490
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  • 8
    Language: English
    In: Journal of Molecular Biology, 09 October 2013, Vol.425(19), pp.3678-3697
    Description: The RNA chaperone protein Hfq is required for the function of all small RNAs (sRNAs) that regulate mRNA stability or translation by limited base pairing in . While there have been numerous studies to characterize Hfq activity and the importance of specific residues, there has been only limited characterization of Hfq mutants . Here, we use a set of reporters as well as co-immunoprecipitation to examine 14 Hfq mutants expressed from the chromosome. The majority of the proximal face residues, as expected, were important for the function of sRNAs. The failure of sRNAs to regulate target mRNAs in these mutants can be explained by reduced sRNA accumulation. Two of the proximal mutants, D9A and F39A, acted differently from the others in that they had mixed effects on different sRNA/mRNA pairs and, in the case of F39A, showed differential sRNA accumulation. Mutations of charged residues at the rim of Hfq interfered with positive regulation and gave mixed effects for negative regulation. Some, but not all, sRNAs accumulated to lower levels in rim mutants, suggesting qualitative differences in how individual sRNAs are affected by Hfq. The distal face mutants were expected to disrupt binding of ARN motifs found in mRNAs. They were more defective for positive regulation than negative regulation at low mRNA expression, but the defects could be suppressed by higher levels of mRNA expression. We discuss the implications of these observations for Hfq binding to RNA and mechanisms of action. ► analysis of 14 chromosomally expressed mutants reveals differential consequences of specific amino acid substitutions. ► Phenotypes confirm a critical role for the proximal face of Hfq in sRNA binding. ► The rim of the Hfq hexamer is important for positive regulation by sRNAs. ► Individual sRNA:mRNA pairs show different sensitivities to mutants. ► The results suggest unexpected complexity in how Hfq promotes sRNA-based regulation.
    Keywords: Dsra ; Arcz ; Mcas ; Ryhb ; Chix ; Biology ; Chemistry
    ISSN: 0022-2836
    E-ISSN: 1089-8638
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  • 9
    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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  • 10
    In: EMBO Journal, 14 October 2015, Vol.34(20), pp.2557-2573
    Description: Many bacteria use small s (s) and the chaperone Hfq to regulate stability and translation. Hfq, a ring‐shaped homohexamer, has multiple faces that can bind both s and their targets. We find that Hfq has at least two distinct ways in which it interacts with s; these different binding properties have strong effects on the stability of the and the sequence requirements of regulated s. Class I s depend on proximal and rim Hfq sites for stability and turn over rapidly. Class s are more stable and depend on the proximal and distal Hfq sites for stabilization. Using deletions and chimeras, we find that while Class I s regulate targets with previously defined repeats, Class s regulate s carrying ‐rich rim‐binding sites. We discuss how these different binding modes may correlate with different roles in the cell, with Class I s acting as emergency responders and Class s acting as silencers. The RNA chaperone Hfq is required for most sRNA‐mediated regulation in bacteria. This study finds that sRNAs and mRNAs utilize distinct binding surfaces on Hfq, resulting in a combinatorial interaction that determines both sRNA stability and regulatory strength. Hfq‐binding sRNAs and their target mRNAs fall into two classes, reflecting different modes of binding to Hfq. Class I sRNAs bind the proximal and rim surfaces of Hfq, while their mRNA targets bind the distal surface. Class II sRNAs bind the proximal and distal surfaces of Hfq, while their mRNA targets bind the rim. Class II sRNAs are generally more stable and may exclude class I mRNAs from binding Hfq. The RNA chaperone Hfq is required for most sRNA‐mediated regulation in bacteria. This study finds that sRNAs and mRNAs utilize distinct binding surfaces on Hfq, resulting in a combinatorial interaction that determines both sRNA stability and regulatory strength.
    Keywords: Chix ; Hfq ; Mgrr ; Ryhb
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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