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  • Article  (12)
  • Base Sequence  (12)
  • Salmonella
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  • Article  (12)
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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 25 August 2015, Vol.112(34), pp.E4772-81
    Description: Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ(S) and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ(S) and, together, RprA and σ(S) orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.
    Keywords: Hfq ; Rpra ; Feedforward Control ; Plasmid Conjugation ; Srna ; Chromosomes, Bacterial ; DNA, Bacterial -- Genetics ; RNA, Bacterial -- Genetics ; Salmonella -- Genetics
    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, 27 March 2012, Vol.109(13), pp.E757-64
    Description: SgrS RNA is a model for the large class of Hfq-associated small RNAs that act to posttranscriptionally regulate bacterial mRNAs. The function of SgrS is well-characterized in nonpathogenic Escherichia coli, where it was originally shown to counteract glucose-phosphate stress by acting as a repressor of the ptsG mRNA, which encodes the major glucose transporter. We have discovered additional SgrS targets in Salmonella Typhimurium, a pathogen related to E. coli that recently acquired one-quarter of all genes by horizontal gene transfer. We show that the conserved short seed region of SgrS that recognizes ptsG was recruited to target the Salmonella-specific sopD mRNA of a secreted virulence protein. The SgrS-sopD interaction is exceptionally selective; we find that sopD2 mRNA, whose gene arose from sopD duplication during Salmonella evolution, is deaf to SgrS because of a nonproductive G-U pair in the potential SgrS-sopD2 RNA duplex vs. G-C in SgrS-sopD. In other words, SgrS discriminates the two virulence factor mRNAs at the level of a single hydrogen bond. Our study suggests that bacterial pathogens use their large suites of conserved Hfq-associated regulators to integrate horizontally acquired genes into existing posttranscriptional networks, just as conserved transcription factors are recruited to tame foreign genes at the DNA level. The results graphically illustrate the importance of the seed regions of bacterial small RNAs to select new targets with high fidelity and suggest that target predictions must consider all or none decisions by individual seed nucleotides.
    Keywords: Phylogeny ; Base Pairing -- Genetics ; Gene Transfer, Horizontal -- Genetics ; RNA, Bacterial -- Genetics ; Salmonella -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 3
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 23 November 2010, Vol.107(47), pp.20435-40
    Description: The abundant class of bacterial Hfq-associated small regulatory RNAs (sRNAs) parallels animal microRNAs in their ability to control multiple genes at the posttranscriptional level by short and imperfect base pairing. In contrast to the universal length and seed pairing mechanism of microRNAs, the sRNAs are heterogeneous in size and structure, and how they regulate multiple targets is not well understood. This paper provides evidence that a 5' located sRNA domain is a critical element for the control of a large posttranscriptional regulon. We show that the conserved 5' end of RybB sRNA recognizes multiple mRNAs of Salmonella outer membrane proteins by ≥7-bp Watson-Crick pairing. When fused to an unrelated sRNA, the 5' domain is sufficient to guide target mRNA degradation and maintain σ(E)-dependent envelope homeostasis. RybB sites in mRNAs are often conserved and flanked by 3' adenosine. They are found in a wide sequence window ranging from the upstream untranslated region to the deep coding sequence, indicating that some targets might be repressed at the level of translation, whereas others are repressed primarily by mRNA destabilization. Autonomous 5' domains seem more common in sRNAs than appreciated and might improve the design of synthetic RNA regulators.
    Keywords: Bacterial Outer Membrane Proteins -- Metabolism ; Gene Expression Regulation, Bacterial -- Genetics ; RNA, Messenger -- Metabolism ; Regulatory Sequences, Ribonucleic Acid -- Genetics ; Regulon -- Genetics ; Salmonella -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 4
    In: Molecular Microbiology, May 2012, Vol.84(3), pp.428-445
    Description: MicF is a textbook example of a small regulatory RNA (sRNA) that acts on a ‐encoded target mRNA through imperfect base pairing. Discovery of MicF as a post‐transcriptional repressor of the major porin OmpF established the paradigm for a meanwhile common mechanism of translational inhibition, through antisense sequestration of a ribosome binding site. However, whether MicF regulates additional genes has remained unknown for almost three decades. Here, we have harnessed the new superfolder variant of GFP for reporter–gene fusions to validate newly predicted targets of MicF in . We show that the conserved 5′ end of MicF acts by seed pairing to repress the mRNAs of global transcriptional regulator Lrp, and periplasmic protein YahO, while a second targeting region is also required to regulate the mRNA of the lipid A‐modifying enzyme LpxR. Interestingly, MicF targets at both the ribosome binding site and deep within the coding sequence. MicF binding in the coding sequence of decreases mRNA stability through exacerbating the use of a native RNase E site proximal to the short MicF‐ duplex. Altogether, this study assigns the classic MicF sRNA to the growing class of Hfq‐associated regulators that use diverse mechanisms to impact multiple loci.
    Keywords: Gene Expression Regulation, Bacterial ; Bacterial Proteins -- Genetics ; Green Fluorescent Proteins -- Metabolism ; Porins -- Genetics ; RNA, Bacterial -- Metabolism ; RNA, Small Untranslated -- Metabolism ; Salmonella Typhimurium -- Metabolism;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 5
    Language: English
    In: Nucleic acids research, April 2012, Vol.40(8), pp.3623-40
    Description: A remarkable feature of many small non-coding RNAs (sRNAs) of Escherichia coli and Salmonella is their accumulation in the stationary phase of bacterial growth. Several stress response regulators and sigma factors have been reported to direct the transcription of stationary phase-specific sRNAs, but a widely conserved sRNA gene that is controlled by the major stationary phase and stress sigma factor, σ(S) (RpoS), has remained elusive. We have studied in Salmonella the conserved SdsR sRNA, previously known as RyeB, one of the most abundant stationary phase-specific sRNAs in E. coli. Alignments of the sdsR promoter region and genetic analysis strongly suggest that this sRNA gene is selectively transcribed by σ(S). We show that SdsR down-regulates the synthesis of the major Salmonella porin OmpD by Hfq-dependent base pairing; SdsR thus represents the fourth sRNA to regulate this major outer membrane porin. Similar to the InvR, MicC and RybB sRNAs, SdsR recognizes the ompD mRNA in the coding sequence, suggesting that this mRNA may be primarily targeted downstream of the start codon. The SdsR-binding site in ompD was localized by 3'-RACE, an experimental approach that promises to be of use in predicting other sRNA-target interactions in bacteria.
    Keywords: Gene Expression Regulation, Bacterial ; Bacterial Proteins -- Metabolism ; Porins -- Biosynthesis ; RNA, Small Untranslated -- Metabolism ; Salmonella -- Genetics ; Sigma Factor -- Metabolism
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 6
    Language: English
    In: Nucleic acids research, 01 December 2016, Vol.44(21), pp.10406-10422
    Description: Model enteric bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some sRNAs are remarkably well conserved, indicating that they serve cellular functions that go beyond the necessities of a single species. One of these 'core sRNAs' of largely unknown function is the abundant ∼100-nucleotide SdsR sRNA which is transcribed by the general stress σ-factor, σ and accumulates in stationary phase. In Salmonella, SdsR was known to inhibit the synthesis of the species-specific porin, OmpD. However, sdsR genes are present in almost all enterobacterial genomes, suggesting that additional, conserved targets of this sRNA must exist. Here, we have combined SdsR pulse-expression with whole genome transcriptomics to discover 20 previously unknown candidate targets of SdsR which include mRNAs coding for physiologically important regulators such as the carbon utilization regulator, CRP, the nucleoid-associated chaperone, StpA and the antibiotic resistance transporter, TolC. Processing of SdsR by RNase E results in two cellular SdsR variants with distinct target spectra. While the overall physiological role of this orphan core sRNA remains to be fully understood, the new SdsR targets present valuable leads to determine sRNA functions in resting bacteria.
    Keywords: Gene Expression Regulation, Bacterial ; RNA Interference ; RNA, Bacterial -- Genetics ; RNA, Small Untranslated -- Genetics ; Salmonella -- Genetics
    E-ISSN: 1362-4962
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 7
    Language: English
    In: eLife, 31 December 2014, Vol.3
    Description: Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. The sRNA RydC of Salmonella sp. and Escherichia coli is an example of this class of riboregulators. Like many other sRNAs, RydC bears a 'seed' region that recognises specific transcripts through base-pairing, and its activities are facilitated by the RNA chaperone Hfq. The crystal structure of RydC in complex with E. coli Hfq at a 3.48 Å resolution illuminates how the protein interacts with and presents the sRNA for target recognition. Consolidating the protein-RNA complex is a host of distributed interactions mediated by the natively unstructured termini of Hfq. Based on the structure and other data, we propose a model for a dynamic effector complex comprising Hfq, small RNA, and the cognate mRNA target.
    Keywords: E. Coli ; Hfq ; RNA–Protein Interactions ; Rydc ; Biophysics ; Gene Regulation ; Natively Unstructured Protein ; Srna ; Structural Biology ; Host Factor 1 Protein -- Metabolism ; RNA, Bacterial -- Metabolism
    E-ISSN: 2050-084X
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  • 8
    In: Molecular Microbiology, October 2009, Vol.74(1), pp.139-158
    Description: The small RNA, ArcZ (previously RyhA/SraH), was discovered in several genome‐wide screens in and . Its high degree of genomic conservation, its frequent recovery by shotgun sequencing, and its association with the RNA chaperone, Hfq, identified ArcZ as an abundant enterobacterial ‘core’ small RNA, yet its function remained unknown. Here, we report that ArcZ acts as a post‐transcriptional regulator in , repressing the mRNAs of the widely distributed (serine uptake) and (oxidative stress) genes, and of STM3216, a horizontally acquired methyl‐accepting chemotaxis protein (MCP). Both and STM3216 are regulated by sequestration of the ribosome binding site. In contrast, the mRNA is targeted in the coding sequence (CDS), arguing that CDS targeting is more common than appreciated. Transcriptomic analysis of an deletion strain further argued for the existence of a distinct set of loci specifically regulated by ArcZ. In contrast, increased expression of the sRNA altered the steady‐state levels of 〉 16% (〉 750) of all mRNAs, and rendered the bacteria non‐motile. Deep sequencing detected a dramatically changed profile of Hfq‐bound sRNAs and mRNAs, suggesting that the unprecedented pleiotropic effects by a single sRNA might in part be caused by altered post‐transcriptional regulation.
    Keywords: Ribonucleic Acid–RNA ; E Coli ; Microbiology ; Genomics ; Binding Sites ; Bacterial Proteins ; Gene Expression;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 9
    In: Molecular Microbiology, May 2008, Vol.68(4), pp.890-906
    Description: Post‐transcriptional repression of porin synthesis has emerged as a major function of Hfq‐dependent, small non‐coding RNAs (sRNAs). Many enterobacteria express OmpX‐like porins, a family of outer membrane proteins whose physiological roles and structural properties have been studied intensively. While regulatory sRNAs have been identified for most major and many minor porins of and , a post‐transcriptional regulator of OmpX levels has never been found. Here, we have taken a ‘reverse target search’ approach by systematic inactivation of sRNA genes, and screening 35 sRNA deletion strains for effects on OmpX synthesis. We have identified the Hfq‐dependent CyaR (formerly RyeE) sRNA as an repressor. Global transcriptomic profiling following induction of CyaR expression suggests that mRNA is the primary target of this sRNA under standard growth conditions. The results of phylogenetic and mutational analyses suggest that a conserved RNA hairpin of CyaR, featuring a C‐rich apical loop, acts to sequester the Shine–Dalgarno sequence of mRNA and to inhibit translational initiation. We have also discovered that expression is tightly controlled by the cyclic AMP receptor protein, CRP. This represents a new link between porin repression and nutrient availability that is likely to be widely conserved among enterobacteria.
    Keywords: Genetic Research -- Genetic Aspects ; Genetic Research -- Physiological Aspects ; Bacterial Genetics -- Genetic Aspects ; Bacterial Genetics -- Physiological Aspects ; Cyclic Adenosine Monophosphate -- Genetic Aspects ; Cyclic Adenosine Monophosphate -- Physiological Aspects ; Salmonella -- Genetic Aspects ; Salmonella -- Physiological Aspects ; Rna -- Genetic Aspects ; Rna -- Physiological Aspects ; Porins -- Genetic Aspects ; Porins -- Physiological Aspects;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 10
    Language: English
    In: Molecular Cell, 2008, Vol.32(6), pp.827-837
    Description: Small noncoding RNAs (sRNAs) have predominantly been shown to repress bacterial mRNAs by masking the Shine-Dalgarno (SD) or AUG start codon sequence, thereby preventing 30S ribosome entry and, consequently, translation initiation. However, many recently identified sRNAs lack obvious SD and AUG complementarity, indicating that sRNA-mediated translational control could also take place at other mRNA sites. We report that RybB sRNA represses mRNA translation by pairing with the 5′ coding region. Results of systematic antisense interference with 30S binding to and unrelated mRNAs suggest that sRNAs can act as translational repressors by sequestering sequences within the mRNA down to the fifth codon, even without SD and AUG start codon pairing. This “five codon window” for translational control in the 5′ coding region of mRNA not only has implications for sRNA target predictions but might also apply to -regulatory systems such as RNA thermosensors and riboswitches.
    Keywords: RNA ; Microbio ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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