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  • Hfq
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  • 11
    Language: English
    In: Genes & development, 01 November 2008, Vol.22(21), pp.2914-25
    Description: Noncoding RNA regulators have been implicated in almost all imaginable cellular processes. Here we review how regulatory small RNAs such as Spot42, SgrS, GlmY, and GlmZ and a cis-encoded ribozyme in glmS mRNA control sugar metabolism. Besides discussing the physiological implications, we show how the study of these molecules contributed to our understanding of the mechanisms and of general principles of RNA-based regulation. These include the post-transcriptional repression or activation of gene expression within polycistronic mRNAs; novel ribonucleoprotein complexes composed of small RNA, Hfq, and/or RNase E; and the hierarchical action of regulatory RNAs.
    Keywords: Carbohydrate Metabolism ; Bacterial Proteins -- Metabolism ; RNA, Bacterial -- Metabolism ; RNA, Untranslated -- Metabolism
    ISSN: 0890-9369
    E-ISSN: 15495477
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  • 12
    Language: English
    In: EMBO journal: European Molecular Biology Organization, 2016, Issue 9, pp.991-1011
    Description: The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3′‐located Rho‐independent terminators as a universal motif involved in Hfq–RNA interactions. Additionally, Hfq preferentially binds 5′ to sRNA‐target sites in mRNAs, and 3′ to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA–mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA‐target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP‐seq approach will bring new insights into post‐transcriptional gene regulation by RNA‐binding proteins in diverse bacterial species.
    Keywords: Clip ; Csra ; Hfq ; Non‐Coding Rna ; Peak Calling ; Post‐Transcriptional Control ; Small Rna ; Terminator ; Translation
    ISSN: 0261-4189
    Source: Fundación Dialnet
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  • 13
    In: EMBO Journal, 02 May 2016, Vol.35(9), pp.991-1011
    Description: The molecular roles of many ‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining crosslinking with deep sequencing (‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic ‐binding protein target sites. We have applied ‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3′‐located Rho‐independent terminators as a universal motif involved in Hfq– interactions. Additionally, Hfq preferentially binds 5′ to ‐target sites in s, and 3′ to seed sequences in s, reflecting a simple logic in how Hfq facilitates – interactions. Importantly, global knowledge of Hfq sites significantly improves ‐target predictions. CsrA binds sequences in apical loops and targets many virulence s. Overall, our generic ‐seq approach will bring new insights into post‐transcriptional gene regulation by ‐binding proteins in diverse bacterial species. A new pipeline for ‐seq in maps global –protein interactions and offers a tool for improved understanding of post‐transcriptional control in bacteria. Transcriptome‐wide mapping of Hfq and CsrA target sites by CLIP‐seq. Rho‐independent terminators comprise a general Hfq‐binding motif. Hfq binds 5′ to sRNA‐binding sites in mRNA targets and 3′ to seed sequences in cognate the sRNAs. CsrA preferentially recognizes AUGGA sequences present in loops of hairpin structures. CsrA binds and regulates many mRNAs encoding virulence factors. A new pipeline for CLIP‐seq in maps global RNA–protein interactions and offers a tool for improved understanding of post‐transcriptional control in bacteria.
    Keywords: Clip ; Csra ; Hfq ; Non‐Coding Rna ; Peak Calling ; Post‐Transcriptional Control ; Small Rna ; Terminator ; Translation
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 14
    Language: English
    In: RNA biology, 2014, Vol.11(5), pp.403-12
    Description: On June 4-8, 2013, the 3rd Conference on Regulation with RNA in Bacteria took place in Würzburg, Germany. Following two earlier meetings in Berlin and San Juan, this conference has established itself as the primary bi-annual meeting for everyone interested in RNA-based regulations in prokaryotes. The 2013 meeting was organized by Joel Belasco, Susan Gottesman, Franz Narberhaus, and Jörg Vogel. Close to 300 participants from more than 27 countries in Europe, North America, and Asia enjoyed four days of talks and posters on many experimental and biocomputational aspects of prokaryotic RNA biology.
    Keywords: Cascade ; Hfq ; RNA Stability ; RNA-Seq Crispr ; Bioinformatics ; Ribonucleoprotein Complex ; Small RNA ; Gene Expression Regulation, Bacterial ; Bacteria -- Genetics ; RNA, Bacterial -- Genetics
    E-ISSN: 1555-8584
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 15
    Language: English
    In: RNA Biology, 01 May 2014, Vol.11(5), pp.403-412
    Description: On June 4-8, 2013, the 3rd Conference on Regulation with RNA in Bacteria took place in Würzburg, Germany. Following two earlier meetings in Berlin and San Juan, this conference has established itself as the primary bi-annual meeting for everyone...
    Keywords: Cascade ; Hfq ; RNA Stability ; RNA-Seq Crispr ; Bioinformatics ; Ribonucleoprotein Complex ; Small RNA ; Anatomy & Physiology
    ISSN: 1547-6286
    E-ISSN: 1555-8584
    Source: Taylor & Francis (Taylor & Francis Group)
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  • 16
    Language: English
    In: RNA Biology, 01 April 2012, Vol.9(4), pp.520-531
    Description: Helicobacter pylori, one of the most prevalent human pathogens, used to be thought to lack small regulatory RNAs (sRNAs) which are otherwise considered abundant in all bacteria. However, our recent analysis of the primary transcriptome of H. pylori discovered an unexpectedly large number of...
    Keywords: RNA-Seq ; Small RNA ; Hfq ; Helicobacter Pylori ; RNA Binding Proteins ; Affinity Chromatography ; Post-Transcriptional Control ; Co-Immunoprecipitation ; Anatomy & Physiology
    ISSN: 1547-6286
    E-ISSN: 1555-8584
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  • 17
    Language: English
    In: Methods in molecular biology (Clifton, N.J.), 2012, Vol.905, pp.177-200
    Description: Small regulatory RNAs (sRNAs) are short, generally noncoding RNAs that act posttranscriptionally to control target gene expression. Over the past 10 years there has been a rapid expansion in the discovery and characterization of sRNAs in a diverse range of bacteria. Paradigm shifts in our understanding of the breadth of posttranscriptional control by sRNAs were achieved in a number of pioneering studies that involved immunoprecipitation of a known RNA chaperone, the near-ubiquitous Hfq, followed by sequencing to identify novel putative regulators and targets. To perform the converse experiment, we previously developed a method which uses an aptamer-tagged sRNA to allow purification of in vivo assembled RNA-protein complexes and subsequent identification of bound proteins. We successfully implemented this protocol using the Hfq-associated sRNA, InvR, tagged with a tandem repeat of the commonly used MS2-aptamer. Incorporation of the aptamer had no effect on sRNA stability or activity. InvR-MS2 could be effectively purified along with associated proteins, such as Hfq, using maltose binding protein fused to the MS2 coat protein (MBP-MS2) immobilized on an amylose column. Mass-spectroscopy was also used to identify previously uncharacterized protein partners. These results have been described previously (Said et al., Nucleic Acids Res 37:e133, 2009) and thus the figures presented here are intended solely as an illustrative guide to complement this detailed step-by-step protocol.
    Keywords: Aptamers, Nucleotide -- Metabolism ; RNA, Small Untranslated -- Metabolism ; RNA-Binding Proteins -- Metabolism
    ISBN: 9781617799488
    ISSN: 10643745
    E-ISSN: 1940-6029
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 18
    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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  • 19
    Language: English
    In: Molecular Cell, 05 January 2017, Vol.65(1), pp.39-51
    Description: Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in . A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small RNAs whereby RNase E acts together with the RNA chaperone Hfq to liberate stable 3′ fragments from various precursor RNAs. Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post-transcriptional regulators. Chao et al. discover that the essential bacterial RNase E cleaves numerous transcripts at preferred sites by sensing uridine as a 2-nt ruler. RNase E processing of various precursor RNAs produces many small regulatory RNAs, constituting a major small-RNA biogenesis pathway in bacteria.
    Keywords: Rnase E ; RNA Degradome ; Non-Coding RNA ; Hfq ; 3′ Utr ; Arcz ; Rpra ; Srna Maturation ; Uridine Ruler ; Tier-Seq ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 20
    Language: English
    In: RNA Biology, 01 July 2007, Vol.4(3), pp.160-164
    Keywords: Anatomy & Physiology
    ISSN: 1547-6286
    E-ISSN: 1555-8584
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