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  • Article  (18)
  • Vogel, Jorg  (18)
  • RNA, Untranslated  (18)
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  • Article  (18)
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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 11 October 2016, Vol.113(41), pp.11591-11596
    Description: The functional annotation of transcriptomes and identification of noncoding RNA (ncRNA) classes has been greatly facilitated by the advent of next-generation RNA sequencing which, by reading the nucleotide order of transcripts, theoretically allows the rapid profiling of all transcripts in a cell. However, primary sequence per se is a poor predictor of function, as ncRNAs dramatically vary in length and structure and often lack identifiable motifs. Therefore, to visualize an informative RNA landscape of organisms with potentially new RNA biology that are emerging from microbiome and environmental studies requires the use of more functionally relevant criteria. One such criterion is the association of RNAs with functionally important cognate RNA-binding proteins. Here we analyze the full ensemble of cellular RNAs using gradient profiling by sequencing (Grad-seq) in the bacterial pathogen Salmonella enterica, partitioning its coding and noncoding transcripts based on their network of RNA-protein interactions. In addition to capturing established RNA classes based on their biochemical profiles, the Grad-seq approach enabled the discovery of an overlooked large collective of structured small RNAs that form stable complexes with the conserved protein ProQ. We show that ProQ is an abundant RNA-binding protein with a wide range of ligands and a global influence on Salmonella gene expression. Given its generic ability to chart a functional RNA landscape irrespective of transcript length and sequence diversity, Grad-seq promises to define functional RNA classes and major RNA-binding proteins in both model species and genetically intractable organisms.
    Keywords: Hfq ; Proq ; RNA–Protein Interaction ; Noncoding RNA ; Small RNA ; Bacterial Proteins -- Metabolism ; High-Throughput Nucleotide Sequencing -- Methods ; RNA, Bacterial -- Metabolism ; RNA-Binding Proteins -- Metabolism ; Salmonella Enterica -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    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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  • 3
    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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  • 4
    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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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 31 May 2016, Vol.113(22), pp.E3101-10
    Description: Staphylococcus aureus is a major bacterial pathogen, which causes severe blood and tissue infections that frequently emerge by autoinfection with asymptomatically carried nose and skin populations. However, recent studies report that bloodstream isolates differ systematically from those found in the nose and skin, exhibiting reduced toxicity toward leukocytes. In two patients, an attenuated toxicity bloodstream infection evolved from an asymptomatically carried high-toxicity nasal strain by loss-of-function mutations in the gene encoding the transcription factor repressor of surface proteins (rsp). Here, we report that rsp knockout mutants lead to global transcriptional and proteomic reprofiling, and they exhibit the greatest signal in a genome-wide screen for genes influencing S. aureus survival in human cells. This effect is likely to be mediated in part via SSR42, a long-noncoding RNA. We show that rsp controls SSR42 expression, is induced by hydrogen peroxide, and is required for normal cytotoxicity and hemolytic activity. Rsp inactivation in laboratory- and bacteremia-derived mutants attenuates toxin production, but up-regulates other immune subversion proteins and reduces lethality during experimental infection. Crucially, inactivation of rsp preserves bacterial dissemination, because it affects neither formation of deep abscesses in mice nor survival in human blood. Thus, we have identified a spontaneously evolving, attenuated-cytotoxicity, nonhemolytic S. aureus phenotype, controlled by a pleiotropic transcriptional regulator/noncoding RNA virulence regulatory system, capable of causing S. aureus bloodstream infections. Such a phenotype could promote deep infection with limited early clinical manifestations, raising concerns that bacterial evolution within the human body may contribute to severe infection.
    Keywords: Ssr42 ; Staphylococcus Aureus ; Bloodstream Infection ; Rsp ; Toxicity Regulator ; Apoptosis ; Abscess -- Etiology ; Bacteremia -- Etiology ; Bacterial Proteins -- Genetics ; Mutation -- Genetics ; RNA, Untranslated -- Genetics ; Staphylococcal Infections -- Complications ; Virulence Factors -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 6
    Language: English
    In: Genome biology, 11 October 2011, Vol.12(10), pp.R98
    Description: Gene function analysis of the obligate intracellular bacterium Chlamydia pneumoniae is hampered by the facts that this organism is inaccessible to genetic manipulations and not cultivable outside the host. The genomes of several strains have been sequenced; however, very little information is available on the gene structure and transcriptome of C. pneumoniae. Using a differential RNA-sequencing approach with specific enrichment of primary transcripts, we defined the transcriptome of purified elementary bodies and reticulate bodies of C. pneumoniae strain CWL-029; 565 transcriptional start sites of annotated genes and novel transcripts were mapped. Analysis of adjacent genes for co-transcription revealed 246 polycistronic transcripts. In total, a distinct transcription start site or an affiliation to an operon could be assigned to 862 out of 1,074 annotated protein coding genes. Semi-quantitative analysis of mapped cDNA reads revealed significant differences for 288 genes in the RNA levels of genes isolated from elementary bodies and reticulate bodies. We have identified and in part confirmed 75 novel putative non-coding RNAs. The detailed map of transcription start sites at single nucleotide resolution allowed for the first time a comprehensive and saturating analysis of promoter consensus sequences in Chlamydia. The precise transcriptional landscape as a complement to the genome sequence will provide new insights into the organization, control and function of genes. Novel non-coding RNAs and identified common promoter motifs will help to understand gene regulation of this important human pathogen.
    Keywords: Genome, Bacterial ; Transcriptome ; Chlamydophila Pneumoniae -- Genetics ; Gene Expression Profiling -- Methods ; RNA, Bacterial -- Genetics
    ISSN: 14656906
    E-ISSN: 1474-760X
    E-ISSN: 14656914
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  • 7
    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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  • 8
    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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  • 9
    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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  • 10
    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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