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  • AGRIS (United Nations, Food and Agriculture Organization)  (18)
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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
    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
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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
    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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  • 5
    In: Molecular Microbiology, April 2010, Vol.76(2), pp.467-479
    Description: Numerous small RNAs regulators of gene expression exist in bacteria. A large class of them binds to the RNA chaperone Hfq and act by base pairing interactions with their target mRNA, thereby affecting their translation and/or stability. They often have multiple direct targets, some of which may be regulators themselves, and production of a single sRNA can therefore affect the expression of dozens of genes. We show in this study that the synthesis of the pleiotropic PhoPQ two‐component system is repressed by MicA, a σ‐dependent sRNA regulator of porin biogenesis. MicA directly pairs with mRNA in the translation initiation region of and presumably inhibits translation by competing with ribosome binding. Consequently, MicA downregulates several members of the PhoPQ regulon. By linking PhoPQ to σ, our findings suggest that major cellular processes such as Mg transport, virulence, LPS modification or resistance to antimicrobial peptides are modulated in response to envelope stress. In addition, we found that Hfq strongly affects the expression of independently of MicA, raising the possibility that even more sRNAs, which remain to be identified, could regulate PhoPQ synthesis.
    Keywords: Messenger Rna ; Peptides ; Gene Expression ; Biosynthesis;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 6
    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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  • 7
    Language: English
    In: Current Opinion in Microbiology, April 2013, Vol.16(2), pp.140-147
    Description: ► Regulated degradation by ATP-dependent proteases frequently depends upon delivery of the substrate by adaptors. ► Regulation of activity of adaptors by anti-adaptors allows environmental modulation of protein turnover. ► Structural studies are uncovering how adaptors bind and hand over the substrate to the protease. Elimination of non-functional or unwanted proteins is critical for cell growth and regulation. In bacteria, ATP-dependent proteases target cytoplasmic proteins for degradation, contributing to both protein quality control and regulation of specific proteins, thus playing roles parallel to that of the proteasome in eukaryotic cells. Adaptor proteins provide a way to modulate the substrate specificity of the proteases and allow regulated proteolysis. Advances over the past few years have provided new insight into how adaptor proteins interact with both substrates and proteases and how adaptor functions are regulated. An important advance has come with the recognition of the critical roles of anti-adaptor proteins in regulating adaptor availability.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 8
    Language: English
    In: Molecular Cell, 28 September 2012, Vol.47(6), pp.825-826
    Description: In this issue of , describe how a bacterial sRNA can lead to degradation of an mRNA by pairing within the coding region of the mRNA; the 5′ monophosphate end of the sRNA activates RNase E, leading to rapid cleavage of the paired mRNA.
    Keywords: Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 9
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 24 August 2010, Vol.107(34), pp.15223-15228
    Description: Siderophores are essential factors for iron (Fe) acquisition in bacteria during colonization and infection of eukaryotic hosts, which restrain iron access through iron-binding protein, such as lactoferrin and transferrin. The synthesis of siderophores by Escherichia coli is considered to be fully regulated at the transcriptional level by the Fe-responsive transcriptional repressor Fur. Here we characterized two different pathways that promote the production of the siderophore enterobactin via the action of the small RNA RyhB. First, RyhB is required for normal expression of an important enterobactin biosynthesis polycistron, entCEBAH. Second, RyhB directly represses the translation of cysE, which encodes a serine acetyltransferase that uses serine as a substrate for cysteine biosynthesis. Reduction of CysE activity by RyhB allows serine to be used as building blocks for enterobactin synthesis through the nonribosomal peptide synthesis pathway. Thus, RyhB plays an essential role in siderophore production and may modulate bacterial virulence through optimization of siderophore production.
    Keywords: Physical sciences -- Earth sciences -- Geology ; Physical sciences -- Chemistry -- Chemical compounds ; Biological sciences -- Biology -- Genetics ; Biological sciences -- Biology -- Microbiology ; Physical sciences -- Chemistry -- Chemical compounds ; Behavioral sciences -- Psychology -- Personality psychology ; Biological sciences -- Biochemistry -- Metabolism ; Biological sciences -- Biology -- Genetics ; Biological sciences -- Biology -- Microbiology ; Physical sciences -- Chemistry -- Chemical compounds
    ISSN: 00278424
    E-ISSN: 10916490
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  • 10
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 26 May 2009, Vol.106(21), pp.8477-8482
    Description: Orthogonal, parallel and independent systems are one key foundation for synthetic biology. The synthesis of orthogonal systems that are uncoupled from evolutionary constraints, and selectively abstracted from cellular regulation, is an emerging approach to making biology more amenable to engineering. Here, we combine orthogonal transcription by T7 RNA polymerase and translation by orthogonal ribosomes (O-ribosomes), creating an orthogonal gene expression pathway in Escherichia coli. We design and implement compact, orthogonal gene expression networks. In particular we focus on creating transcription-translation feed-forward loops (FFLs). The transcription-translation FFLs reported cannot be created by using the cells' gene expression machinery and introduce information-processing delays on the order of hours into gene expression. We ref actor the rRNA operon, uncoupling the synthesis of the orthogonal 16S rRNA for the O-ribosome from the synthesis and processing of the rest of the rRNA operon, thereby defining a minimal module that can be added to the cell for O-ribosome production. The minimal O-ribosome permits the rational alteration of the delay in an orthogonal gene expression FFL. Overall this work demonstrates that system-level dynamic properties are amenable to rational manipulation and design in orthogonal systems. In the future this system may be further evolved and tuned to provide a spectrum of tailored dynamics in gene expression and investigate the effects of delays in cellular decisionmaking processes.
    Keywords: Biological sciences -- Biology -- Genetics ; Biological sciences -- Biology -- Cytology ; Biological sciences -- Biology -- Genetics ; Physical sciences -- Chemistry -- Chemical compounds ; Physical sciences -- Physics -- Fundamental forces ; Physical sciences -- Chemistry -- Chemical compounds ; Physical sciences -- Physics -- Mechanics ; Biological sciences -- Bioengineering -- Synthetic biology ; Biological sciences -- Biology -- Genetics ; Physical sciences -- Chemistry -- Chemical compounds ; Biological sciences -- Biology -- Genetics ; Biological sciences -- Biology -- Cytology ; Biological sciences -- Biology -- Genetics ; Physical sciences -- Chemistry -- Chemical compounds ; Physical sciences -- Physics -- Fundamental forces ; Physical sciences -- Chemistry -- Chemical compounds ; Physical sciences -- Physics -- Mechanics ; Biological sciences -- Bioengineering -- Synthetic biology ; Biological sciences -- Biology -- Genetics ; Physical sciences -- Chemistry -- Chemical compounds
    ISSN: 00278424
    E-ISSN: 10916490
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