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  • 1
    Language: English
    In: Current Opinion in Microbiology, 2010, Vol.13(1), pp.24-33
    Description: The ubiquitous RNA-binding protein, Hfq, has been shown to be required for the fitness and virulence of an increasing number of bacterial pathogens. Mutants lacking Hfq are often sensitive to host defense mechanisms and highly attenuated in animal models, albeit there is considerable variation in both severity and extent of phenotypes. RNomics and deep sequencing (RNA-seq) approaches discovered the small RNA and mRNA targets of Hfq, and indicated that this protein might impact on the expression of up to 20% of all genes in some organisms, including genes of type 3 secretion systems Hfq also facilitates post-transcriptional cross-talk between the core and variable genome regions of bacterial pathogens, and might help integrate horizontally acquired virulence genes into existing regulatory networks.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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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. [PUBLICATION ]
    Keywords: Bacterial Proteins–Chemistry ; Bacterial Proteins–Genetics ; Bacterial Proteins–Immunology ; Bacterial Proteins–Metabolism ; Conserved Sequence–Genetics ; DNA, Viral–Metabolism ; DNA, Viral–Genetics ; Escherichia Coli–Genetics ; Models, Biological–Metabolism ; Prophages–Biosynthesis ; RNA Precursors–Genetics ; RNA Precursors–Immunology ; RNA Processing, Post-Transcriptional–Metabolism ; RNA, Bacterial–Genetics ; RNA, Bacterial–Metabolism ; RNA, Bacterial–Genetics ; RNA, Bacterial–Immunology ; RNA, Guide–Metabolism ; Ribonuclease III–Virology ; Streptococcus Pyogenes–Virology ; Streptococcus Pyogenes–Virology ; Streptococcus Pyogenes–Virology ; Streptococcus Pyogenes–Virology ; E Coli ; Bacteria ; Bacteriology ; Plasmids ; Proteins ; Bacterial Proteins ; DNA, Viral ; RNA Precursors ; RNA, Bacterial ; RNA, Guide ; Ribonuclease III;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 3
    Language: English
    In: Nature, 28 January 2016, Vol.529(7587), pp.496-501
    Description: Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK-STAT signalling, and we identify infection-specific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes.
    Keywords: Gene Expression Regulation -- Genetics ; Host-Pathogen Interactions -- Genetics ; RNA, Bacterial -- Genetics ; RNA, Untranslated -- Genetics ; Salmonella Typhimurium -- Genetics
    ISSN: 00280836
    E-ISSN: 1476-4687
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  • 4
    In: EMBO Journal, 03 June 2015, Vol.34(11), pp.1478-1492
    Description: There is an expanding list of examples by which one can posttranscriptionally influence the expression of others. This can involve sponges that sequester regulatory s of s in the same regulon, but the underlying molecular mechanism of such cross talk remains little understood. Here, we report sponge‐mediated cross talk in the posttranscriptional network of GcvB, a conserved Hfq‐dependent small with one of the largest regulons known in bacteria. We show that decay from the locus encoding an amino acid transporter generates a stable fragment (SroC) that base‐pairs with GcvB. This interaction triggers the degradation of GcvB by ase E, alleviating the GcvB‐mediated repression of other amino acid‐related transport and metabolic genes. Intriguingly, since the itself is a target of GcvB, the SroC sponge seems to enable both an internal feed‐forward loop to activate its parental in and activation of many ‐encoded s in the same pathway. Disabling this cross talk affects bacterial growth when peptides are the sole carbon and nitrogen sources. Decay of the bacterial GcvB , which keeps it from regulating its targets, is triggered by a 3′‐‐derived fragment from a target . This ability of s to compete for regulatory interaction presents a new mode of cross talk in bacteria. . Decay of the bacterial GcvB s, which keeps it from regulating its m targets, is triggered by a 3′‐‐derived fragment from a target m. This ability of ms to compete for regulatory interaction presents a new mode of cross talk in bacteria.
    Keywords: G Cv B ; H Fq ; Noncoding Rna ; Rn Ase E ; S Ro C
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 5
    Language: English
    In: EMBO journal: European Molecular Biology Organization, 2015, Issue 11, pp.1478-1492
    Description: There is an expanding list of examples by which one mRNA can posttranscriptionally influence the expression of others. This can involve RNA sponges that sequester regulatory RNAs of mRNAs in the same regulon, but the underlying molecular mechanism of such mRNA cross talk remains little understood. Here, we report sponge-mediated mRNA cross talk in the posttranscriptional network of GcvB, a conserved Hfq-dependent small RNA with one of the largest regulons known in bacteria. We show that mRNA decay from the gltIJKL locus encoding an amino acid ABC transporter generates a stable fragment (SroC) that base-pairs with GcvB. This interaction triggers the degradation of GcvB by RNase E, alleviating the GcvB-mediated mRNA repression of other amino acid-related transport and metabolic genes. Intriguingly, since the gltIJKL mRNA itself is a target of GcvB, the SroC sponge seems to enable both an internal feed-forward loop to activate its parental mRNA in cis and activation of many trans-encoded mRNAs in the same pathway. Disabling this mRNA cross talk affects bacterial growth when peptides are the sole carbon and nitrogen sources.
    Keywords: Gcvb ; Hfq ; Noncoding Rna ; Rnase E ; Sroc
    ISSN: 0261-4189
    Source: Fundación Dialnet
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  • 6
    Language: English
    In: Molecular Cell, 04 February 2016, Vol.61(3), pp.352-363
    Description: Small RNAs (sRNAs) from conserved noncoding genes are crucial regulators in bacterial signaling pathways but have remained elusive in the Cpx response to inner membrane stress. Here we report that an alternative biogenesis pathway releasing the conserved mRNA 3′ UTR of stress chaperone CpxP as an ∼60-nt sRNA provides the noncoding arm of the Cpx response. This so-called CpxQ sRNA, generated by general mRNA decay through RNase E, acts as an Hfq-dependent repressor of multiple mRNAs encoding extracytoplasmic proteins. Both CpxQ and the Cpx pathway are required for cell survival under conditions of dissipation of membrane potential. Our discovery of CpxQ illustrates how the conversion of a transcribed 3′ UTR into an sRNA doubles the output of a single mRNA to produce two factors with spatially segregated functions during inner membrane stress: a chaperone that targets problematic proteins in the periplasm and a regulatory RNA that dampens their synthesis in the cytosol. Chao and Vogel discover that a small RNA cleaved off the 3′ end of an mRNA provides the elusive regulatory noncoding arm of the bacterial Cpx response to inner membrane stress.
    Keywords: Cpx Pathway ; Cpxp ; Cpxq ; 3′ Utr ; Hfq ; Rnase E ; Noncoding RNA ; Nhab ; Envelope Stress ; Membrane Potential ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 7
    In: EMBO Journal, 17 October 2012, Vol.31(20), pp.4005-4019
    Description: The small RNAs associated with the protein Hfq constitute one of the largest classes of post‐transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free‐standing genes. Here, deep sequencing of Hfq‐bound transcripts from multiple stages of growth of revealed a plethora of new small RNA species from within mRNA loci, including DapZ, which overlaps with the 3′ region of the biosynthetic gene, . Synthesis of the DapZ small RNA is independent of DapB protein synthesis, and is controlled by HilD, the master regulator of invasion genes. DapZ carries a short G/U‐rich domain similar to that of the globally acting GcvB small RNA, and uses GcvB‐like seed pairing to repress translation of the major ABC transporters, DppA and OppA. This exemplifies double functional output from an mRNA locus by the production of both a protein and an Hfq‐dependent ‐acting RNA. Our atlas of Hfq targets suggests that the 3′ regions of mRNA genes constitute a rich reservoir that provides the Hfq network with new regulatory small RNAs. Deep sequencing of Hfq‐binding RNAs isolated from at different growth stages reveals that the 3′ UTR of bacterial mRNAs are a rich source of regulatory small RNAs which modulate gene expression in trans.
    Keywords: Abc Transporter ; Dapz ; Gcvb ; Hfq ; 3′ Utr
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 8
    Language: English
    In: Journal of Bacteriology, 2016, Vol.198(3-4), p.427(9)
    Description: Recent breakthroughs in next-generation sequencing technologies have led to the identification of small noncoding RNAs (sRNAs) as a new important class of regulatory molecules. In prokaryotes, sRNAs are often bound to the chaperone protein Hfq, which allows them to interact with their partner mRNA(s). We screened the genome of the zoonotic and human pathogen Brucella suis 1330 for the presence of this class of RNAs. We designed a coimmunoprecipitation strategy that relies on the use of Hfq as a bait to enrich the sample with sRNAs and eventually their target mRNAs. By deep sequencing analysis of the Hfq-bound transcripts, we identified a number of mRNAs and 33 sRNA candidates associated with Hfq. The expression of 10 sRNAs in the early stationary growth phase was experimentally confirmed by Northern blotting and/or reverse transcriptase PCR. IMPORTANCE Brucella organisms are facultative intracellular pathogens that use stealth strategies to avoid host defenses. Adaptation to the host environment requires tight control of gene expression. Recently, small noncoding RNAs (sRNAs) and the sRNA chaperone Hfq have been shown to play a role in the fine-tuning of gene expression. Here we have used RNA sequencing to identify RNAs associated with the B. suis Hfq protein. We have identified a novel list of 33 sRNAs and 62 Hfq-associated mRNAs for future studies aiming to understand the intracellular lifestyle of this pathogen.
    Keywords: Brucella – Research ; Brucella – Genetic Aspects ; DNA Sequencing – Usage ; Transcription (Genetics) – Research
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 9
    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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  • 10
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 15 May 2012, Vol.109(20), pp.E1277-86
    Description: More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with σ(70) (including phoP, slyA, and invF) from which we identified the -10 and -35 motifs of σ(70)-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and 〈20% were found throughout the Enterobacteriaceae. This description of the transcriptional map of SL1344 advances our understanding of S. Typhimurium, arguably the most important bacterial infection model.
    Keywords: Gene Expression Regulation, Bacterial -- Genetics ; RNA, Small Untranslated -- Genetics ; Regulatory Sequences, Ribonucleic Acid -- Genetics ; Salmonella Typhimurium -- Genetics ; Transcription, Genetic -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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