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  • Bacterial Proteins
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  • 1
    Article
    Article
    Stress sigma factor RpoS degradation and translation are sensitive to the state of central metabolism (2015)
    Details
    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
    DOI: 10.1073/pnas.1504639112
    URL: View this record in MEDLINE/PubMed
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  • 2
    Article
    Article
    Microbiology: Dicing defence in bacteria (2011)
    Details
    In: Nature, 2011, Vol.471(7340), p.588
    Keywords: RNA, Bacterial -- Genetics ; RNA, Guide -- Genetics ; Ribonuclease III -- Metabolism ; Streptococcus Pyogenes -- Genetics;
    ISSN: 0028-0836
    E-ISSN: 14764687
    DOI: 10.1038/471588a
    URL: View this record in Nature
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  • 3
    Article
    Article
    Dicing defence in bacteria (2011)
    Details
    Language: English
    In: Nature, 3/2011, Vol.471(7340), pp.588-589
    Description: [...] the use of a core RNase rather than a Cas-specific protein provides a clear example of crosstalk between the CRISPR system and bacterial metabolism. [...] Deltcheva et al. find that all of these elements (tracrRNA, Csn1 and RNase III) are necessary for immunity - that is, for S. pyogenes to destroy an invading plasmid containing sequences complementary to the CRISPR spacer.
    Keywords: Bacterial Proteins–Chemistry ; Bacterial Proteins–Genetics ; Bacterial Proteins–Immunology ; Bacterial Proteins–Metabolism ; Biological Evolution–Genetics ; DNA, Viral–Metabolism ; DNA, Viral–Genetics ; Models, Biological–Genetics ; Plasmids–Metabolism ; RNA Interference–Biosynthesis ; RNA Precursors–Genetics ; RNA Precursors–Immunology ; RNA Processing, Post-Transcriptional–Metabolism ; RNA, Bacterial–Genetics ; RNA, Bacterial–Metabolism ; RNA, Bacterial–Genetics ; RNA, Bacterial–Immunology ; RNA, Guide–Metabolism ; Ribonuclease III–Virology ; Streptococcus Pyogenes–Virology ; Streptococcus Pyogenes–Virology ; Streptococcus Pyogenes–Virology ; Streptococcus Pyogenes–Virology ; E Coli ; Bacteria ; Ribonucleic Acid–RNA ; Proteins ; Genomes ; Plasmids ; Organisms ; Bacterial Proteins ; DNA, Viral ; RNA Precursors ; RNA, Bacterial ; RNA, Guide ; Ribonuclease III;
    ISSN: 0028-0836
    E-ISSN: 1476-4687
    DOI: 10.1038/471588a
    Source: Nature Publishing Group (via CrossRef)
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  • 4
    Article
    Article
    Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA (2011)
    Details
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 3 May 2011, Vol.108(18), pp.7403-7407
    Description: Eukaryotic PIN (PilT N-terminal) domain proteins are ribonucleases involved in quality control, metabolism and maturation of mRNA and rRNA. The majority of prokaryotic PIN-domain proteins are encoded by the abundant vapBC toxin—antitoxin loci and inhibit translation by an unknown mechanism. Here we show that enteric VapCs are site-specific endonucleases that cleave tRNAfMet in the anticodon stem-loop between nucleotides +38 and +39 in vivo and in vitro. Consistently, VapC inhibited translation in vivo and in vitro. Translation-reactions could be reactivated by the addition of VapB and extra charged tRNA fMet . Similarly, ectopic production of tRNAfMet counteracted VapC in vivo. Thus, tRNAfMet is the only cellular target of VapC. Depletion of tRNAfMet by vapC induction was bacteriostatic and stimulated ectopic translation initiation at elongator codons. Moreover, addition of chloramphenicol to cells carrying vapBC induced VapC activity. Thus, by cleavage of tRNAfMet , VapC simultaneously may regulate global cellular translation and reprogram translation initiation.
    Keywords: Physical sciences -- Chemistry -- Chemical compounds -- Antitoxins ; Physical sciences -- Chemistry -- Chemical compounds -- Antitoxins ; Biological sciences -- Biology -- Genetics -- Antitoxins ; Biological sciences -- Biochemistry -- Biomolecules -- Antitoxins ; Physical sciences -- Chemistry -- Chemical compounds -- Antitoxins ; Biological sciences -- Biology -- Genetics -- Antitoxins ; Biological sciences -- Biology -- Genetics -- Antitoxins ; Biological sciences -- Biology -- Cytology -- Antitoxins ; Health sciences -- Medical sciences -- Immunology -- Antitoxins ; Biological sciences -- Biology -- Genetics -- Antitoxins
    ISSN: 00278424
    E-ISSN: 10916490
    DOI: 10.1073/pnas.1019587108
    URL: View this record in JSTOR
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  • 5
    Article
    Article
    Stress Reduction, Bacterial Style (2017)
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    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
    DOI: 10.1128/JB.00433-17
    URL: View this record in MEDLINE/PubMed
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  • 6
    Article
    Article
    Positive regulation by small RNAs and the role of Hfq (2010)
    Details
    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
    DOI: 10.1073/pnas.1004435107
    URL: View this record in MEDLINE/PubMed
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  • 7
    Article
    Article
    Control of bacterial iron homeostasis by manganese (2010)
    Details
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 8 June 2010, Vol.107(23), pp.10691-10695
    Description: Perception and response to nutritional iron availability by bacteria are essential to control cellular iron homeostasis. The Irr protein from Bradyrhizobium japonicum senses iron through the status of heme biosynthesis to globally regulate iron-dependent gene expression. Heme binds directly to Irr to trigger its degradation. Here, we show that severe manganese limitation created by growth of a Mn²⁺ transport mutant in manganese-limited media resulted in a cellular iron deficiency. In wild-type cells, Irr levels were attenuated under manganese limitation, resulting in reduced promoter occupancy of target genes and altered iron-dependent gene expression. Irr levels were high regardless of manganese availability in a heme-deficient mutant, indicating that manganese normally affects heme-dependent degradation of Irr. Manganese altered the secondary structure of Irr in vitro and inhibited binding of heme to the protein. We propose that manganese limitation destabilizes Irr under low-iron conditions by lowering the threshold of heme that can trigger Irr degradation. The findings implicate a mechanism for the control of iron homeostasis by manganese in a bacterium.
    Keywords: Physical sciences -- Chemistry -- Chemical elements ; Physical sciences -- Chemistry -- Chemical elements ; Biological sciences -- Biology -- Genetics ; Physical sciences -- Chemistry -- Chemical compounds ; Biological sciences -- Biology -- Genetics ; Biological sciences -- Biology -- Microbiology ; Biological sciences -- Biology -- Cytology ; Biological sciences -- Biology -- Physiology ; Biological sciences -- Biochemistry -- Metabolism ; Biological sciences -- Biology -- Physiology
    ISSN: 00278424
    E-ISSN: 10916490
    DOI: 10.1073/pnas.1002342107
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  • 8
    Article
    Article
    Complex transcriptional and post‐transcriptional regulation of an enzyme for lipopolysaccharide modification (2013)
    Details
    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
    DOI: 10.1111/mmi.12257
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  • 9
    Article
    Article
    Legionella pneumophila 6S RNA optimizes intracellular multiplication (2010)
    Details
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 20 April 2010, Vol.107(16), pp.7533-7538
    Description: Legionella pneumophila is a Gram-negative opportunistic human pathogen that infects and multiplies in a broad range of phagocytic protozoan and mammalian phagocytes. Based on the observation that small regulatory RNAs (sRNAs) play an important role in controlling virulence-related genes in several pathogenic bacteria, we attempted to identify sRNAs expressed by L. pneumophila. We used computational prediction followed by experimental verification to identify and characterize sRNAs encoded in the L. pneumophila genome. A 50-mer probe microarray was constructed to test the expression of predicted sRNAs in bacteria grown under a variety of conditions. This strategy successfully identified 22 expressed RNAs, out of which 6 were confirmed by northern blot and RACE. One of the identified sRNAs is highly expressed in postexponential phase, and computational prediction of its secondary structure reveals a striking similarity to the structure of 6S RNA, a widely distributed prokaryotic sRNA, known to regulate the activity of σ⁷⁰-containing RNA polymerase. A 70-mer probe microarray was used to identify genes affected by L. pneumophila 6S RNA in stationary phase. The 6S RNA positively regulates expression of genes encoding type IVB secretion system effectors, stress response genes such as groES and recA, as well as many genes involved in acquisition of nutrients and genes with unknown or hypothetical functions. Deletion of 6S RNA significantly reduced L. pneumophila intracellular multiplication in both protist and mammalian host cells, but had no detectable effect on growth in rich media.
    Keywords: Physical sciences -- Chemistry -- Chemical compounds -- Legionella pneumophila ; Biological sciences -- Biology -- Microbiology -- Legionella pneumophila ; Biological sciences -- Biology -- Genetics -- Legionella pneumophila ; Biological sciences -- Biology -- Genetics -- Legionella pneumophila ; Biological sciences -- Biology -- Cytology -- Legionella pneumophila ; Biological sciences -- Biology -- Microbiology -- Legionella pneumophila ; Biological sciences -- Biology -- Microbiology -- Legionella pneumophila ; Biological sciences -- Biology -- Genetics -- Legionella pneumophila ; Biological sciences -- Biology -- Genetics -- Legionella pneumophila ; Biological sciences -- Biology -- Physiology -- Legionella pneumophila
    ISSN: 00278424
    E-ISSN: 10916490
    DOI: 10.1073/pnas.0911764107
    URL: View this record in JSTOR
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  • 10
    Article
    Article
    Mechanism of Positive Regulation by DsrA and RprA Small Noncoding RNAs: Pairing Increases Translation and Protects rpoS mRNA from Degradation (2010)
    Details
    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
    DOI: 10.1128/JB.00464-10
    URL: View this record in ASM
    URL: View full text in ASM (subscribers only)
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