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  • Article  (12)
  • Vogel, J.  (12)
  • SwePub (National Library of Sweden)  (12)
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  • Article  (12)
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  • 1
    Language: English
    In: Nucleic acids research, 15 November 2003, Vol.31(22), pp.6435-43
    Description: Recent bioinformatics-aided searches have identified many new small RNAs (sRNAs) in the intergenic regions of the bacterium Escherichia coli. Here, a shot-gun cloning approach (RNomics) was used to generate cDNA libraries of small sized RNAs. Besides many of the known sRNAs, we found new species that were not predicted previously. The present work brings the number of sRNAs in E.coli to 62. Experimental transcription start site mapping showed that some sRNAs were encoded from independent genes, while others were processed from mRNA leaders or trailers, indicative of a parallel transcriptional output generating sRNAs co-expressed with mRNAs. Two of these RNAs (SroA and SroG) consist of known (THI and RFN) riboswitch elements. We also show that two recently identified sRNAs (RyeB and SraC/RyeA) interact, resulting in RNase III-dependent cleavage. To the best of our knowledge, this represents the first case of two non-coding RNAs interacting by a putative antisense mechanism. In addition, intracellular metabolic stabilities of sRNAs were determined, including ones from previous screens. The wide range of half-lives (32 min) indicates that sRNAs cannot generally be assumed to be metabolically stable. The experimental characterization of sRNAs analyzed here suggests that the definition of an sRNA is more complex than previously assumed.
    Keywords: Escherichia Coli -- Genetics ; RNA, Bacterial -- Genetics ; RNA, Untranslated -- Genetics ; Transcription, Genetic -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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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
    Language: English
    In: Nature Reviews Microbiology, 2018, Vol.16(10), pp.601-615
    Description: RNA-binding proteins (RBPs) are central to most if not all cellular processes, dictating the fate of virtually all RNA molecules in the cell. Starting with pioneering work on ribosomal proteins, studies of bacterial RBPs have paved the way for molecular studies of RNA-protein interactions. Work over...
    Keywords: Medical And Health Sciences ; Basic Medicine ; Microbiology In The Medical Area ; Medicin Och Hälsovetenskap ; Medicinska Och Farmaceutiska Grundvetenskaper ; Mikrobiologi Inom Det Medicinska Området
    ISSN: 1740-1526
    E-ISSN: 17401534
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  • 4
    Language: English
    In: Molecular Cell, 07 June 2018, Vol.70(5), pp.971-982.e6
    Description: The conserved RNA-binding protein ProQ has emerged as the centerpiece of a previously unknown third large network of post-transcriptional control in enterobacteria. Here, we have used UV crosslinking and RNA sequencing (CLIP-seq) to map hundreds of ProQ binding sites in and . Our analysis of these binding sites, many of which are conserved, suggests that ProQ recognizes its cellular targets through RNA structural motifs found in small RNAs (sRNAs) and at the 3′ end of mRNAs. Using the mRNA as a model for 3′ end targeting, we reveal a function for ProQ in protecting mRNA against exoribonucleolytic activity. Taken together, our results underpin the notion that ProQ governs a post-transcriptional network distinct from those of the well-characterized sRNA-binding proteins, CsrA and Hfq, and suggest a previously unrecognized, sRNA-independent role of ProQ in stabilizing mRNAs. Using CLIP-seq, Holmqvist et al. map transcriptome-wide interactions of the emerging global RNA-binding protein ProQ in and . Their data suggest ProQ to target sRNAs and mRNA 3′ UTRs primarily through a structural code and to stabilize some mRNAs by counteracting 3′ exoribonuclease activity.
    Keywords: Proq ; Clip-Seq ; RNA-Binding Protein ; 3′ Utr ; Post-Transcriptional Control ; Exoribonuclease ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 5
    Language: English
    In: Current Biology, 29 December 2004, Vol.14(24), pp.2271-2276
    Description: More than 60 small RNAs (sRNA) have been identified in E. coli. The functions of the majority of these sRNAs are still unclear. For the few sRNAs characterized, expression and functional studies indicate that they act under stress conditions. Here, we describe a novel E. coli chromosome locus that is part of the SOS response to DNA damage. This locus encodes two sRNAs, IstR-1 and IstR-2, and a toxic peptide, TisB, encoded by tisAB mRNA. Transcription of tisAB and istR-2 is SOS regulated, whereas IstR-1 is present throughout growth. IstR-1 inhibits toxicity by base-pairing to a short region in the tisAB mRNA. This antisense interaction entails RNase III-dependent cleavage, thereby inactivating the mRNA for translation. In the absence of the SOS response, IstR-1 is present in high excess over its target. However, SOS induction leads to depletion of the IstR-1 pool, concomitant with accumulation of tisAB mRNA. Under such conditions, TisB exerts its toxic effect, slowing down growth. We propose that the inhibitory sRNA prevents inadvertent TisB synthesis during normal growth and, possibly, also limits SOS-induced toxicity. Our study adds the SOS regulon to the growing list of global regulatory circuits controlled by sRNA genes.
    Keywords: Biology
    ISSN: 0960-9822
    E-ISSN: 1879-0445
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  • 6
    Language: English
    In: Environmental Technology, 02 September 2017, Vol.38(17), pp.2130-2142
    Description: Raw municipal wastewater from a full-scale wastewater treatment plant was physicochemically pretreated in a large pilot-scale system comprising coagulation, flocculation, microsieve and microfiltration operated in various configurations. The produced microsieve filtrates and microfiltration...
    Keywords: Forward Osmosis ; Non-Biological Treatment ; Microfiltration ; Microsieve ; Physicochemical Pretreatment ; Wastewater Treatment ; Engineering
    ISSN: 0959-3330
    E-ISSN: 1479-487X
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  • 7
    Language: English
    In: Environmental Technology, 01 February 2018, Vol.39(3), pp.264-276
    Description: Municipal wastewater treatment commonly involves mechanical, biological and chemical treatment steps to protect humans and the environment from adverse effects. Membrane technology has gained increasing attention as an alternative to conventional...
    Keywords: Biogas Production ; Forward Osmosis ; Membrane Filtration ; Seawater ; Wastewater Treatment ; Engineering
    ISSN: 0959-3330
    E-ISSN: 1479-487X
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  • 8
    Language: English
    In: Environmental Technology, 17 September 2017, Vol.38(18), pp.2295-2304
    Description: Municipal wastewater treatment involves mechanical, biological and chemical treatment steps for protecting the environment from adverse effects. The biological treatment step consumes the most energy and can create greenhouse gases. This study investigates municipal wastewater treatment without...
    Keywords: Biomimetic Membrane ; Forward Osmosis ; Membrane Fouling ; Microfiltration ; Microsieving ; Wastewater Treatment ; Engineering
    ISSN: 0959-3330
    E-ISSN: 1479-487X
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  • 9
    In: Molecular Microbiology, October 2008, Vol.70(1), pp.100-111
    Description: We discovered a new small non‐coding RNA (sRNA) gene, of O1 strain A1552. A mutant overproduces OmpA porin, and we demonstrate that the 140 nt VrrA RNA represses translation by base‐pairing with the 5′ region of the mRNA. The RNA chaperone Hfq is not stringently required for VrrA action, but expression of the gene requires the membrane stress sigma factor, σ, suggesting that VrrA acts on in response to periplasmic protein folding stress. We also observed that OmpA levels inversely correlated with the number of outer membrane vesicles (OMVs), and that VrrA increased OMV production comparable to loss of OmpA. VrrA is the first sRNA known to control OMV formation. Moreover, a mutant showed a fivefold increased ability to colonize the intestines of infant mice as compared with the wild type. There was increased expression of the main colonization factor of , the toxin co‐regulated pili, in the mutant as monitored by immunoblot detection of the TcpA protein. VrrA overproduction caused a distinct reduction in the TcpA protein level. Our findings suggest that VrrA contributes to bacterial fitness in certain stressful environments, and modulates infection of the host intestinal tract.
    Keywords: Cholera ; Ribonucleic Acid–RNA ; Bacteria ; Membranes ; Mutation ; Gene Expression ; Proteins ; Microbiology;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 10
    Language: English
    In: Current Opinion in Microbiology, 2007, Vol.10(3), pp.262-270
    Description: Small noncoding RNAs have been discovered at a staggering rate in and many other bacteria. Most of the sRNAs of known function regulate gene expression by binding to specific mRNAs or proteins. Given the scores of sRNAs of unknown function, the identification of their cellular targets has become urgent. Here, we review the diverse strategies that have been used to identify and validate bacterial sRNA targets. These include the pulse-expression of sRNAs followed by global transcriptome analysis (microarrays), new biocomputational prediction algorithms, and novel reporter gene fusions to validate candidate target gene regulation.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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