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  • Article  (27)
  • Vogel, Jorg  (27)
  • Escherichia Coli
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  • Article  (27)
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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 27 June 2017, Vol.114(26), pp.6824-6829
    Description: The functions of many bacterial RNA-binding proteins remain obscure because of a lack of knowledge of their cellular ligands. Although well-studied cold-shock protein A (CspA) family members are induced and function at low temperature, others are highly expressed in infection-relevant conditions. Here, we have profiled transcripts bound in vivo by the CspA family members of serovar Typhimurium to link the constitutively expressed CspC and CspE proteins with virulence pathways. Phenotypic assays in vitro demonstrated a crucial role for these proteins in membrane stress, motility, and biofilm formation. Moreover, double deletion of and fully attenuates in systemic mouse infection. In other words, the RNA ligand-centric approach taken here overcomes a problematic molecular redundancy of CspC and CspE that likely explains why these proteins have evaded selection in previous virulence factor screens in animals. Our results highlight RNA-binding proteins as regulators of pathogenicity and potential targets of antimicrobial therapy. They also suggest that globally acting RNA-binding proteins are more common in bacteria than currently appreciated.
    Keywords: RNA-Binding Protein ; Salmonella ; Bacterial Pathogenesis ; Cold-Shock Protein ; Stress Response ; Bacterial Proteins ; Cold Shock Proteins and Peptides ; Heat-Shock Proteins ; RNA-Binding Proteins ; Salmonella Infections ; Salmonella Typhimurium ; Virulence Factors
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    In: Nature, 2011, Vol.471(7340), p.602
    Description: CRISPR/Cas systems constitute a widespread class of immunity systems that protect bacteria and archaea against phages and plasmids, and commonly use repeat/spacer-derived short crRNAs to silence foreign nucleic acids in a sequence-specific manner. Although the maturation of crRNAs represents a key event in CRISPR activation, the responsible endoribonucleases (CasE, Cas6, Csy4) are missing in many CRISPR/Cas subtypes. Here, differential RNA sequencing of the human pathogen Streptococcus pyogenes uncovered tracrRNA, a trans -encoded small RNA with 24 nucleotide complementarity to the repeat regions of crRNA precursor transcripts. We show that tracrRNA directs the maturation of crRNAs by the activities of the widely conserved endogenous RNase III and the CRISPR-associated Csn1 protein; all these components are essential to protect S. pyogenes against prophage-derived DNA. Our study reveals a novel pathway of small guide RNA maturation and the first example of a host factor (RNase III) required for bacterial RNA-mediated immunity against invaders.
    Keywords: Article;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 3
    In: Molecular Microbiology, April 2012, Vol.84(1), pp.1-5
    Description: The transcription factor CsgD governing the production of curli fimbriae and cellulose is a key player in the complex regulatory circuit that decides whether form biofilms. The gene itself is tightly controlled at the level of transcription by a large array of DNA‐binding proteins, but what happens after transcription is less understood. In this issue of , Jørgensen (2012), Mika (2012) and Thomason (2012) report on small RNAs (McaS, RprA and GcvB) that together with the RNA‐chaperone Hfq regulate the mRNAs of and other biofilm genes, and illustrate the burgeoning concept that the 5′ region of bacterial mRNA serves as a hub for sRNA‐mediated signal integration at the post‐transcriptional level.
    Keywords: Transcription (Genetics) ; Proteins ; Messenger Rna ; Genes ; Cellulose;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 4
    Language: English
    In: PLoS ONE, 2011, Vol.6(3), p.e17296
    Description: P-bodies are dynamic aggregates of RNA and proteins involved in several post-transcriptional regulation processes. P-bodies have been shown to play important roles in regulating viral infection, whereas their interplay with bacterial pathogens, specifically intracellular bacteria that extensively manipulate host cell pathways, remains unknown. Here, we report that Salmonella infection induces P-body disassembly in a cell type-specific manner, and independently of previously characterized pathways such as inhibition of host cell RNA synthesis or microRNA-mediated gene silencing. We show that the Salmonella -induced P-body disassembly depends on the activation of the SPI-2 encoded type 3 secretion system, and that the secreted effector protein SpvB plays a major role in this process. P-body disruption is also induced by the related pathogen, Shigella flexneri , arguing that this might be a new mechanism by which intracellular bacterial pathogens subvert host cell function.
    Keywords: Research Article ; Biology ; Medicine ; Infectious Diseases ; Microbiology ; Molecular Biology ; Cell Biology
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 10 September 2013, Vol.110(37), pp.E3487-96
    Description: Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene expression regulators. Much like eukaryotic microRNAs, these sRNAs typically target multiple mRNAs through short seed pairing, thereby acting as global posttranscriptional regulators. In some bacteria, evidence for hundreds to possibly more than 1,000 different sRNAs has been obtained by transcriptome sequencing. However, the experimental identification of possible targets and, therefore, their confirmation as functional regulators of gene expression has remained laborious. Here, we present a strategy that integrates phylogenetic information to predict sRNA targets at the genomic scale and reconstructs regulatory networks upon functional enrichment and network analysis (CopraRNA, for Comparative Prediction Algorithm for sRNA Targets). Furthermore, CopraRNA precisely predicts the sRNA domains for target recognition and interaction. When applied to several model sRNAs, CopraRNA revealed additional targets and functions for the sRNAs CyaR, FnrS, RybB, RyhB, SgrS, and Spot42. Moreover, the mRNAs gdhA, lrp, marA, nagZ, ptsI, sdhA, and yobF-cspC were suggested as regulatory hubs targeted by up to seven different sRNAs. The verification of many previously undetected targets by CopraRNA, even for extensively investigated sRNAs, demonstrates its advantages and shows that CopraRNA-based analyses can compete with experimental target prediction approaches. A Web interface allows high-confidence target prediction and efficient classification of bacterial sRNAs.
    Keywords: E. Coli ; RNA–RNA Interaction ; Regulatory RNA ; RNA, Bacterial -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 6
    Language: English
    In: Cell, 11 April 2013, Vol.153(2), pp.426-437
    Description: Glucose homeostasis is strictly controlled in all domains of life. Bacteria that are unable to balance intracellular sugar levels and deal with potentially toxic phosphosugars cease growth and risk being outcompeted. Here, we identify the conserved haloacid dehalogenase (HAD)-like enzyme YigL as the previously hypothesized phosphatase for detoxification of phosphosugars and reveal that its synthesis is activated by an Hfq-dependent small RNA in . We show that the glucose-6-P-responsive small RNA SgrS activates YigL synthesis in a translation-independent fashion by the selective stabilization of a decay intermediate of the dicistronic messenger RNA (mRNA). Intriguingly, the major endoribonuclease RNase E, previously known to function together with small RNAs to degrade mRNA targets, is also essential for this process of mRNA activation. The exploitation of and targeted interference with regular RNA turnover described here may constitute a general route for small RNAs to rapidly activate both coding and noncoding genes. ► The bacterial small RNA SgrS posttranscriptionally activates the synthesis of YigL ► YigL is the previously hypothesized phosphatase that prevents phosphosugar toxicity ► SgrS activates yigL by a translation-independent mRNA-stabilization mechanism ► SgrS stabilizes an intermediate in the yigL mRNA decay pathway YigL, a long-sought bacterial phosphatase, regulates glucose-6-phosphate levels. A small regulatory RNA upregulates YigL synthesis by base pairing with the coding sequence of the preceding gene to interfere with endonucleolytic yigL mRNA decay.
    Keywords: Biology
    ISSN: 0092-8674
    E-ISSN: 1097-4172
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  • 7
    In: PLoS ONE, 2015, Vol.10(11)
    Description: Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizosphere-mimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis- encoded antisense RNAs, as well as trans- encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus . Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.
    Keywords: Research Article
    E-ISSN: 1932-6203
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  • 8
    In: Molecular Microbiology, September 2009, Vol.73(5), pp.737-741
    Description: Small regulatory RNAs (sRNAs) are well known to command bacterial protein synthesis by modulating the translation and decay of target mRNAs. Most sRNAs are specifically regulated by a cognate transcription factor under certain growth or stress conditions. Investigations of the conserved Hfq‐dependent MicM sRNA in (article by Poul Valentin‐Hansen and colleagues in this issue of ) and in have unravelled a novel type of gene regulation in which the chitobiose operon mRNA acts as an RNA trap to degrade the constitutively expressed MicM sRNA, thereby alleviating MicM‐mediated repression of the synthesis of the YbfM porin that is required for chitosugar uptake. The results suggest that ‘target’ mRNAs might be both prey and also predators of sRNAs.
    Keywords: Protein Synthesis ; Messenger Rna;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 9
    In: Molecular Microbiology, January 2009, Vol.71(1), pp.1-11
    Description: species are enterobacterial pathogens that have been exceptionally well investigated with respect to virulence mechanisms, microbial pathogenesis, genome evolution and many fundamental pathways of gene expression and metabolism. While these studies have traditionally focused on protein functions, has also become a model organism for RNA‐mediated regulation. The present review is dedicated to the non‐coding RNA world of : it covers small RNAs (sRNAs) that act as post‐transcriptional regulators of gene expression, novel Salmonella ‐regulatory RNA elements that sense metabolite and metal ion concentrations (or temperature), and globally acting RNA‐binding proteins such as CsrA or Hfq (inactivation of which cause drastic phenotypes and virulence defects). Owing to mosaic genome structure, some of the sRNAs are widely conserved in bacteria whereas others are very specific to species. Intriguingly, sRNAs of either type (CsrB/C, InvR, SgrS) facilitate cross‐talk between the core genome and its laterally acquired virulence regions. Work in also identified physiological functions (and mechanisms thereof) of RNA that had remained unknown in , and pioneered the use of high‐throughput sequencing technology to identify the sRNA and mRNA targets of bacterial RNA‐binding proteins.
    Keywords: Metabolites ; Proteins ; Messenger Rna ; Salmonella ; Gene Expression;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 10
    Language: English
    In: Genes & development, 15 May 2013, Vol.27(10), pp.1073-8
    Description: The abundant RNA-binding proteins CsrA and Hfq each impact bacterial physiology by working in conjunction with small RNAs to control large post-transcriptional regulons. The small RNAs involved were considered mechanistically distinct, regulating mRNAs either directly through Hfq-mediated base-pairing or indirectly by sequestering the global translational repressor CsrA. In this issue of Genes & Development, Jørgensen and colleagues (pp. 1132-1145) blur these distinctions with a dual-mechanism small RNA that acts through both Hfq and CsrA to regulate the formation of bacterial biofilms.
    Keywords: Csra ; Csrb ; Hfq ; Pga ; C-Di-Gmp ; Gene Expression Regulation, Bacterial ; Biofilms -- Growth & Development ; Escherichia Coli -- Genetics ; RNA, Bacterial -- Genetics
    ISSN: 08909369
    E-ISSN: 1549-5477
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