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  • Article  (13)
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  • 1
    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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  • 2
    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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  • 3
    Language: English
    In: Current Opinion in Microbiology, February 2017, Vol.35, pp.78-87
    Description: Understanding how bacteria cause disease requires knowledge of which genes are expressed and how they are regulated during infection. While RNA-seq is now a routine method for gene expression analysis in bacterial pathogens, the past years have also witnessed a surge of novel RNA-seq based approaches going beyond standard mRNA profiling. These include variations of the technique to capture post-transcriptional networks controlled by small RNAs and to discover associated RNA-binding proteins in the pathogen itself. Dual RNA-seq analyzing pathogen and host simultaneously has revealed roles of noncoding RNAs during infection and enabled the correlation of bacterial gene activity with specific host responses. Single-cell RNA-seq studies have addressed how heterogeneity among individual host cells may determine infection outcomes.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 4
    Language: English
    In: The Plant cell, January 2012, Vol.24(1), pp.123-36
    Description: Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here, we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identification of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons, indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions and opposite to annotated genes, demonstrating the existence of numerous noncoding RNA candidates.
    Keywords: Chloroplasts -- Genetics ; DNA-Directed RNA Polymerases -- Metabolism ; Hordeum -- Enzymology ; Plastids -- Enzymology ; RNA, Untranslated -- Genetics
    ISSN: 10404651
    E-ISSN: 1532-298X
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  • 5
    Language: English
    In: Research in Microbiology, 2009, Vol.160(4), pp.278-287
    Description: Small noncoding RNAs (sRNAs), often in conjunction with Hfq protein, have increasingly been shown to regulate multiple rather than individual mRNAs, thereby reprogramming gene expression at the post-transcriptional level. This review summarizes how and when several such regulators (CyaR, DsrA, GcvB, OmrAB, RNAIII, RybB, RyhB) act upon multiple targets.
    Keywords: Noncoding Rnas ; RNA Chaperone Hfq ; Dsra ; Ryhb ; Rnaiii ; ABC Transport Systems ; Iron Homeostasis ; Outer Membrane Proteins ; Virulence Factors ; Salmonella ; Stapylococcus Aureus ; Biology
    ISSN: 0923-2508
    E-ISSN: 1769-7123
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  • 6
    Language: English
    In: Journal of Molecular Biology, 26 October 2007, Vol.373(3), pp.521-528
    Description: Many bacterial genes of related function are organized in operons and transcribed as polycistronic mRNAs to ensure the coordinate expression of the individual cistrons. Post-transcriptional modulation of such mRNAs can alter the expression of downstream cistrons, resulting in discoordinate protein synthesis from an operon mRNA. Several factors, including small non-coding RNAs (sRNAs), have been described that act collectively as repressors within polycistronic mRNAs. We describe the first case of discoordinated operon expression in which a downstream cistron is activated at the post-transcriptional level. We report that GlmY sRNA activates GlmS synthesis from the mRNA without altering GlmU expression. The sRNA is shown to be structurally and functionally conserved in diverse enterobacteria; its transcription may be controlled by the alternative sigma factor, σ . Our data suggest that Gram-negative bacteria evolved a mechanism of riboregulation that is distinct from the riboswitch mechanism of Gram-positive bacteria.
    Keywords: Small Non-Coding RNA ; Glms ; Discoordinate Operon Expression ; Sigma 54 ; Biology ; Chemistry
    ISSN: 0022-2836
    E-ISSN: 1089-8638
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  • 7
    Language: English
    In: Current Opinion in Microbiology, 2009, Vol.12(5), pp.536-546
    Description: Following the pioneering screens for small regulatory RNAs (sRNAs) in in 2001, sRNAs are now being identified in almost every branch of the eubacterial kingdom. Experimental strategies have become increasingly important for sRNA discovery, thanks to increased availability of tiling arrays and fast progress in the development of high-throughput cDNA sequencing (RNA-Seq). The new technologies also facilitate genome-wide discovery of potential target mRNAs by sRNA pulse-expression coupled to transcriptomics, and immunoprecipitation with RNA-binding proteins such as Hfq. Moreover, the staggering rate of new sRNAs demands mechanistic analysis of target regulation. We will also review the available toolbox for wet lab-based research, including and reporter systems, genetic methods and biochemical co-purification of sRNA interaction partners.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 8
    Language: English
    In: PLoS Biology, 2008, Vol.6(3), p.e64
    Description: Small noncoding RNAs (sRNA) can function as posttranscriptional activators of gene expression to regulate stress responses and metabolism. We here describe the mechanisms by which two sRNAs, GlmY and GlmZ, activate the Escherichia coli glmS mRNA, coding for an essential enzyme in amino-sugar metabolism. The two sRNAs, although being highly similar in sequence and structure, act in a hierarchical manner. GlmZ, together with the RNA chaperone, Hfq, directly activates glmS mRNA translation by an anti-antisense mechanism. In contrast, GlmY acts upstream of GlmZ and positively regulates glmS by antagonizing GlmZ RNA inactivation. We also report the first example, to our knowledge, of mRNA expression being controlled by the poly(A) status of a chromosomally encoded sRNA. We show that in wild-type cells, GlmY RNA is unstable due to 3′ end polyadenylation; whereas in an E. coli pcnB mutant defective in RNA polyadenylation, GlmY is stabilized and accumulates, which in turn stabilizes GlmZ and causes GlmS overproduction. Our study reveals hierarchical action of two well-conserved sRNAs in a complex regulatory cascade that controls the glmS mRNA. Similar cascades of noncoding RNA regulators may operate in other organisms. ; Hierarchical action of regulators is a fundamental principle in gene expression control, and is well understood in protein-based signaling pathways. We have discovered that small noncoding RNAs (sRNAs), a new class of gene expression regulators, can also act hierarchically and form a regulatory cascade. Two highly similar sRNAs function after transcription to activate the mRNA, which codes for an essential function in amino-sugar metabolism. It is somewhat unusual for two sRNAs to act upon the same target mRNA, and despite their seeming homology, these two sRNAs (GlmY and GlmZ) employ different molecular mechanisms and function hierarchically to activate expression: GlmZ directly activates translation via disruption of an mRNA structure that inhibits translation, whereas GlmY controls the processing of GlmZ to prevent the inactivation of this direct activator. We also found that GlmY is itself controlled by an RNA processing event (3′ end polyadenylation), which typically destabilizes bacterial RNA. Our data unequivocally demonstrate that is exceptionally dependent on RNA-based mechanisms for its genetic control. Given the large number of noncoding RNAs of unknown function, we believe that similar regulatory RNA cascades may operate in other organisms. ; A regulatory RNA cascade that posttranscriptionally activates the mRNA is identified, with two highly similar small noncoding RNAs acting hierarchically in a manner thus far known only in protein-based regulatory circuits.
    Keywords: Research Article ; Biochemistry ; Genetics And Genomics ; Molecular Biology
    ISSN: 1544-9173
    E-ISSN: 1545-7885
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  • 9
    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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  • 10
    Language: English
    In: Current Opinion in Microbiology, 2006, Vol.9(6), pp.605-611
    Description: Recent systematic genome searches revealed that bacteria encode a tremendous number of small non-coding RNAs (sRNAs). Whereas most of these molecules remain of unknown function, it has become increasingly clear that many of them will act to modulate gene expression at the post-transcriptional level. Where studied in more detail, sRNAs have often been found to control the expression of outer membrane proteins (OMPs). Enterobacteria such as and are now known to encode at least eight OMP-regulating sRNAs (InvR, MicA, MicC, MicF, OmrAB, RseX and RybB). These sRNAs exert their functions under a variety of growth and stress conditions, including the σ -mediated envelope stress response. An sRNA–OMP network is emerging in which some sRNAs act specifically on a single mRNA, whereas others control multiple mRNA targets.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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