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  • 1
    Language: English
    In: Journal of Bacteriology, Feb, 2014, Vol.196(3-4), p.754(8)
    Description: The stationary phase/general stress response sigma factor RpoS (sigma 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: Escherichia Coli -- Research ; Escherichia Coli -- Physiological Aspects ; Post-translational Modifications -- Analysis ; Transfer Rna -- Research ; Translational Research
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 2
    In: Molecular Microbiology, October 2016, Vol.102(2), pp.244-259
    Description: RgsA is a phylogenetically conserved small regulatory RNA (sRNA) in species. This sRNA has been shown to be directly controlled by the major stationary phase and stress sigma factor (RpoS), and also indirectly regulated by the GacS/GacA two‐component system. However, the role and the regulatory targets of this sRNA remain unclear. Here, two direct regulatory targets of RgsA, the mRNAs coding for the global transcriptional regulator Fis and the acyl carrier protein AcpP, were identified in . RgsA downregulates the synthesis of Fis and AcpP by base‐pairing, and this regulation requires the RNA chaperone protein Hfq. Alignment of RgsA homologs in revealed a conserved core region, which is strictly required for RgsA target recognition. Specifically, RgsA inhibits expression via an 11 + 11 bp RNA duplex, whereas this interaction region is not sufficient for repression and the 35 nt downstream region is also required. Interestingly, two functional start codons initiate mRNA translation and both are repressed by RgsA. Furthermore, deletion of significantly increased swarming motility in . Together, this study suggests a novel regulatory role of sRNA in which the versatile transcriptional regulator Fis and the stress regulator RpoS are connected by RgsA. RgsA is a conserved sRNA in species. Two direct regulatory targets of RgsA, the mRNAs coding for the global transcriptional regulator Fis and the acyl carrier protein AcpP, were identified in . RgsA downregulates the synthesis of Fis and AcpP by base‐pairing, this regulation requires the RNA chaperone protein Hfq. Our study suggests a novel regulatory role of sRNA in which the versatile transcriptional regulator Fis and the stress regulator RpoS are connected by RgsA.
    Keywords: Phylogeny ; Stationary Phase ; Translation ; Motility ; Codons ; Swarming ; Stress ; Transcription ; Chaperones ; Sigma Factor ; Acyl Carrier Protein ; Pseudomonas Aeruginosa ; Cell Biology;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 3
    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
    E-ISSN: 1098-5530
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  • 4
    Language: English
    In: Journal of Bacteriology, June, 2007, Vol.189(11-12), p.4243(14)
    Description: RybB is a small, Hfq-binding noncoding RNA originally identified in a screen of conserved intergenic regions in Escherichia coli. Fusions of the rybB promoter to lacZ were used to screen plasmid genomic libraries and genomic transposon mutants for regulators of rybB expression. A number of plasmids, including some carrying rybB, negatively regulated the fusion. An insertion in the rep helicase and one upstream of dnaK decreased expression of the fusion. Multicopy suppressors of these insertions led to identification of two plasmids that stimulated the fusion. One contained the gene for the response regulator OmpR; the second contained mipA, encoding a murein hydrolase. The involvement of MipA and OmpR in cell surface synthesis suggested that the rybB promoter might be dependent on [[sigma].sup.E]. The sequence upstream of the + 1 of rybB contains a consensus [[sigma].sup.E] promoter. The activity of rybB-lacZ was increased in cells lacking the RseA anti-sigma factor and when [[sigma].sup.E] was overproduced from a heterologous promoter. The activity of rybB-lacZ and the detection of RybB were totally abolished in an rpoE-null strain. In vitro, [[sigma].sup.E] efficiently transcribes from this promoter. Both a rybB mutation and an hfq mutation significantly increased expression of both rybB-lacZ and rpoE-lacZ fusions, consistent with negative regulation of the [[sigma].sup.E] response by RybB and other small RNAs. Based on the plasmid screens, NsrR, a repressor sensitive to nitric oxide, was also found to negatively regulate [[sigma].sup.E]-dependent promoters in an RseA-independent fashion.
    Keywords: Escherichia Coli -- Genetic Aspects ; Escherichia Coli -- Research ; Genetic Regulation -- Research ; Plasmids -- Research ; Cell Surface Antigens -- Research
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 5
    In: FEMS Microbiology Letters, 2010, Vol. 305(2), pp.143-147
    Description: Staphylococcus aureus extracellular adherence protein (EAP) is secreted, but it can redock on the bacterial cell surface via neutral phosphatase (Nptase). EAP binds to certain blood proteins and to itself, and through these affinities, it contributes to adherence and aggregation. It has been demonstrated previously that EAP expression is iron regulated and it contributes to biofilm formation under iron-deplete conditions. In this study, we found that EAP and Nptase also play a role in biofilm formation under iron-replete conditions in the presence of human serum.
    Keywords: 〈Kwd〉〈Italic〉Staphylococcus〈/Italic〉〈/Kwd〉 ; Eap ; Biofilm
    ISSN: 0378-1097
    E-ISSN: 1574-6968
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  • 6
    Language: English
    In: RNA (New York, N.Y.), May 2016, Vol.22(5), pp.729-42
    Description: The translation of rpoS(σ(S)), the general stress/stationary phase sigma factor, is tightly regulated at the post-transcriptional level by several factors via mechanisms that are not clearly defined. One of these factors is MiaA, the enzyme necessary for the first step in theN(6)-isopentyl-2-thiomethyl adenosinemethyl adenosine 37 (ms(2)i(6)A37) tRNA modification. We tested the hypothesis that an elevated UUX-Leucine/total leucine codon ratio can be used to identify transcripts whose translation would be sensitive to loss of the MiaA-dependent modification. We identified iraPas another candidate MiaA-sensitive gene, based on the UUX-Leucine/total leucine codon ratio. AniraP-lacZ fusion was significantly decreased in the abse nce of MiaA, consistent with our predictive model. To determine the role of MiaA in UUX-Leucine decoding in rpoS and iraP, we measured β-galactosidase-specific activity of miaA(-)rpo Sandira P translational fusions upon overexpression of leucine tRNAs. We observed suppression of the MiaA effect on rpoS, and notira P, via overexpression of tRNA(LeuX)but not tRNA(LeuZ) We also tested the hypothesis that the MiaA requirement for rpoS and iraP translation is due to decoding of UUX-Leucine codons within the rpoS and iraP transcripts, respectively. We observed a partial suppression of the MiaA requirement for rpoS and iraP translational fusions containing one or both UUX-Leucine codons removed. Taken together, this suggests that MiaA is necessary for rpoS and iraP translation through proper decoding of UUX-Leucine codons and that rpoS and iraP mRNAs are both modification tunable transcripts (MoTTs) via the presence of the modification.
    Keywords: Miaa ; Rpos ; Leu Codon ; Trna Modification ; Translation ; Codon ; Protein Biosynthesis ; Bacterial Proteins -- Genetics ; Escherichia Coli Proteins -- Genetics ; Leucine -- Genetics ; RNA, Transfer -- Genetics ; Sigma Factor -- Genetics
    ISSN: 13558382
    E-ISSN: 1469-9001
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  • 7
    Language: English
    In: Frontiers in Cellular and Infection Microbiology, 01 March 2016, Vol.6
    Description: Hallmarks of Yersinia pathogenesis include the ability to form biofilms on surfaces, the ability to establish close contact with eukaryotic target cells and the ability to hijack eukaryotic cell signaling and take over control of strategic cellular processes. Many of these virulence traits...
    Keywords: Metabolism ; Acidity ; Temperature ; Camp ; Rova Regulator ; Transition Metals ; Biology
    E-ISSN: 2235-2988
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  • 8
    Language: English
    In: Biomolecules, 01 May 2017, Vol.7(2), p.39
    Description: Previous work demonstrated that efficient RNA Polymerase sigma S-subunit (RpoS) translation requires the N6-isopentenyladenosine i6A37 transfer RNA (tRNA) modification for UUX-Leu decoding. Here we investigate the effect of two additional tRNA modification systems on RpoS translation; the analysis...
    Keywords: S2u34 Trna Modification ; C/U34m Trna Modification ; I6a37 Trna Modification ; Rpos ; Hfq ; Miaa ; Trml ; Tusa ; Leucine ; Codon Bias ; Anatomy & Physiology
    E-ISSN: 2218-273X
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  • 9
    In: The Journal of Bacteriology, 2007, Vol. 189(11), p.4243
    Description: RybB is a small, Hfq-binding noncoding RNA originally identified in a screen of conserved intergenic regions in Escherichia coli. Fusions of the rybB promoter to lacZ were used to screen plasmid genomic libraries and genomic transposon mutants for regulators of rybB expression. A number of plasmids, including some carrying rybB, negatively regulated the fusion. An insertion in the rep helicase and one upstream of dnaK decreased expression of the fusion. Multicopy suppressors of these insertions led to identification of two plasmids that stimulated the fusion. One contained the gene for the response regulator OmpR; the second contained mipA, encoding a murein hydrolase. The involvement of MipA and OmpR in cell surface synthesis suggested that the rybB promoter might be dependent on sigma(E). The sequence upstream of the +1 of rybB contains a consensus sigma(E) promoter. The activity of rybB-lacZ was increased in cells lacking the RseA anti-sigma factor and when sigma(E) was overproduced from a heterologous promoter. The activity of rybB-lacZ and the detection of RybB were totally abolished in an rpoE-null strain. In vitro, sigma(E) efficiently transcribes from this promoter. Both a rybB mutation and an hfq mutation significantly increased expression of both rybB-lacZ and rpoE-lacZ fusions, consistent with negative regulation of the sigma(E) response by RybB and other small RNAs. Based on the plasmid screens, NsrR, a repressor sensitive to nitric oxide, was also found to negatively regulate sigma(E)-dependent promoters in an RseA-independent fashion.
    Keywords: Gene Expression Regulation, Bacterial ; Escherichia Coli -- Genetics ; Escherichia Coli Proteins -- Genetics ; RNA, Bacterial -- Genetics ; Sigma Factor -- Genetics;
    ISSN: 0021-9193
    ISSN: 00219193
    E-ISSN: 10985530
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  • 10
    Language: English
    In: BMC Microbiology, 01 December 2018, Vol.18(1), pp.1-10
    Description: Abstract Background Appreciable evidence suggest that dysbiosis in microbiota, reflected in gut microbial imbalance plays a key role in the pathogenesis of neuropsychiatric disorders including depression and inflammatory diseases. Recently,...
    Keywords: Nmda Receptor ; Lactobacillus ; Turicibacter ; Ruminococcus ; Sarcina ; Mucispirillum ; Biology
    E-ISSN: 1471-2180
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