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  • 2010  (31)
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  • 2010  (31)
  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 23 November 2010, Vol.107(47), pp.20435-40
    Description: The abundant class of bacterial Hfq-associated small regulatory RNAs (sRNAs) parallels animal microRNAs in their ability to control multiple genes at the posttranscriptional level by short and imperfect base pairing. In contrast to the universal length and seed pairing mechanism of microRNAs, the sRNAs are heterogeneous in size and structure, and how they regulate multiple targets is not well understood. This paper provides evidence that a 5' located sRNA domain is a critical element for the control of a large posttranscriptional regulon. We show that the conserved 5' end of RybB sRNA recognizes multiple mRNAs of Salmonella outer membrane proteins by ≥7-bp Watson-Crick pairing. When fused to an unrelated sRNA, the 5' domain is sufficient to guide target mRNA degradation and maintain σ(E)-dependent envelope homeostasis. RybB sites in mRNAs are often conserved and flanked by 3' adenosine. They are found in a wide sequence window ranging from the upstream untranslated region to the deep coding sequence, indicating that some targets might be repressed at the level of translation, whereas others are repressed primarily by mRNA destabilization. Autonomous 5' domains seem more common in sRNAs than appreciated and might improve the design of synthetic RNA regulators.
    Keywords: Bacterial Outer Membrane Proteins -- Metabolism ; Gene Expression Regulation, Bacterial -- Genetics ; RNA, Messenger -- Metabolism ; Regulatory Sequences, Ribonucleic Acid -- Genetics ; Regulon -- Genetics ; Salmonella -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    In: Molecular Microbiology, December 2010, Vol.78(6), pp.1327-1331
    Description: Although most bacterial small RNAs act to repress target mRNAs, some also activate messengers. The predominant mode of activation has been seen in ‘anti‐antisense’ regulation whereby a small RNA prevents the formation of an inhibitory 5′ mRNA structure that otherwise impairs translational initiation and protein synthesis. The translational activation might also stabilize the target yet this was considered a secondary effect in the examples known thus far. Two recent papers in investigate post‐transcriptional activation of collagenase mRNA by VR‐RNA, and streptokinase mRNA by FasX RNA, to suggest that small RNAs exert positive regulation of virulence genes primarily at the level of mRNA stabilization.
    Keywords: Protein Synthesis ; Messenger Rna;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 3
    In: Nature, 2010, Vol.464(7286), p.250
    Description: Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of ~60 small RNAs including the [straight epsilon]-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species. [PUBLICATION ]
    Keywords: 5' Untranslated Regions–Genetics ; Amino Acid Sequence–Genetics ; Base Sequence–Microbiology ; Cells, Cultured–Genetics ; Gene Expression Profiling–Genetics ; Genome, Bacterial–Chemistry ; Helicobacter Infections–Genetics ; Helicobacter Pylori–Metabolism ; Humans–Genetics ; Molecular Sequence Data–Genetics ; Nucleic Acid Conformation–Genetics ; Operon–Genetics ; RNA, Bacterial–Genetics ; RNA, Bacterial–Genetics ; RNA, Bacterial–Genetics ; RNA, Messenger–Genetics ; Sequence Alignment–Genetics ; Transcription, Genetic–Genetics ; Bacteria ; Proteins ; Microbiology ; Gene Expression ; RNA Polymerase ; Cell Division ; E Coli ; 5' Untranslated Regions ; 6s RNA ; RNA, Bacterial ; RNA, Messenger;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 4
    Language: English
    In: Nucleic acids research, October 2010, Vol.38(19), pp.6637-51
    Description: Post-transcriptional regulatory mechanisms are widespread in bacteria. Interestingly, current published data hint that some of these mechanisms may be non-random with respect to their phylogenetic distribution. Although small, trans-acting regulatory RNAs commonly occur in bacterial genomes, they have been better characterized in Gram-negative bacteria, leaving the impression that they may be less important for Firmicutes. It has been presumed that Gram-positive bacteria, in particular the Firmicutes, are likely to utilize cis-acting regulatory RNAs located within the 5' mRNA leader region more often than trans-acting regulatory RNAs. In this analysis we catalog, by a deep sequencing-based approach, both classes of regulatory RNA candidates for Bacillus subtilis, the model microorganism for Firmicutes. We successfully recover most of the known small RNA regulators while also identifying a greater number of new candidate RNAs. We anticipate these data to be a broadly useful resource for analysis of post-transcriptional regulatory strategies in B. subtilis and other Firmicutes.
    Keywords: Bacillus Subtilis -- Genetics ; RNA, Small Untranslated -- Analysis
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 5
    Language: English
    In: Nucleic acids research, January 2010, Vol.38(3), pp.868-77
    Description: Chlamydia trachomatis is an obligate intracellular pathogenic bacterium that has been refractory to genetic manipulations. Although the genomes of several strains have been sequenced, very little information is available on the gene structure of these bacteria. We used deep sequencing to define the transcriptome of purified elementary bodies (EB) and reticulate bodies (RB) of C. trachomatis L2b, respectively. Using an RNA-seq approach, we have mapped 363 transcriptional start sites (TSS) of annotated genes. Semi-quantitative analysis of mapped cDNA reads revealed differences in the RNA levels of 84 genes isolated from EB and RB, respectively. We have identified and in part confirmed 42 genome- and 1 plasmid-derived novel non-coding RNAs. The genome encoded non-coding RNA, ctrR0332 was one of the most abundantly and differentially expressed RNA in EB and RB, implying an important role in the developmental cycle of C. trachomatis. The detailed map of TSS in a thus far unprecedented resolution as a complement to the genome sequence will help to understand the organization, control and function of genes of this important pathogen.
    Keywords: Chlamydia Trachomatis -- Genetics ; RNA, Bacterial -- Genetics ; RNA, Untranslated -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 6
    Language: English
    In: Biophysical Journal, 01/2010, Vol.98(3), S1, pp.488a-489a
    ISSN: 00063495
    Source: Elsevier (via CrossRef)
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  • 7
    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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  • 8
    Language: English
    In: Cell Host & Microbe, 2010, Vol.8(1), pp.116-127
    Description: Bacteria constitute a large and diverse class of infectious agents, causing devastating diseases in humans, animals, and plants. Our understanding of gene expression control, which forms the basis for successful prevention and treatment strategies, has until recently neglected the many roles that regulatory RNAs might have in bacteria. In recent years, several such regulators have been found to facilitate host-microbe interactions and act as key switches between saprophytic and pathogenic lifestyles. This review covers the versatile regulatory RNA mechanisms employed by bacterial pathogens and highlights the dynamic interplay between riboregulation and virulence factor expression.
    Keywords: Biology
    ISSN: 1931-3128
    E-ISSN: 1934-6069
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  • 9
    Language: English
    In: Nucleic acids research, October 2010, Vol.38(19), pp.6620-36
    Description: Using an experimental approach, we investigated the RNome of the pathogen Staphylococcus aureus to identify 30 small RNAs (sRNAs) including 14 that are newly confirmed. Among the latter, 10 are encoded in intergenic regions, three are generated by premature transcription termination associated with riboswitch activities, and one is expressed from the complementary strand of a transposase gene. The expression of four sRNAs increases during the transition from exponential to stationary phase. We focused our study on RsaE, an sRNA that is highly conserved in the bacillales order and is deleterious when over-expressed. We show that RsaE interacts in vitro with the 5' region of opp3A mRNA, encoding an ABC transporter component, to prevent formation of the ribosomal initiation complex. A previous report showed that RsaE targets opp3B which is co-transcribed with opp3A. Thus, our results identify an unusual case of riboregulation where the same sRNA controls an operon mRNA by targeting two of its cistrons. A combination of biocomputational and transcriptional analyses revealed a remarkably coordinated RsaE-dependent downregulation of numerous metabolic enzymes involved in the citrate cycle and the folate-dependent one-carbon metabolism. As we observed that RsaE accumulates transiently in late exponential growth, we propose that RsaE functions to ensure a coordinate downregulation of the central metabolism when carbon sources become scarce.
    Keywords: RNA, Small Untranslated -- Metabolism ; Staphylococcus Aureus -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 10
    Language: English
    In: RNA Biology, 01 September 2010, Vol.7(5), pp.621-627
    Description: The main mediator of the lipopolysaccharide (LPS) response in macrophages is activation of Toll-like receptor 4 (TLR4). This generates interferon-beta (INF-beta) production that stimulates increased expression of the RNA editing enzyme ADAR1. To determine if there is an increase in RNA editing in mature miRNA in response to TLR4 activation upon Salmonella infection of macrophages we analyzed small RNA deep sequencing data. Interestingly, we found that direct infection of macrophage cell lines with Salmonella does not result in an increase of edited mature miRNA. Thus, despite elevated levels of ADAR1 during TLR4 activation of macrophages mediated by Salmonella infection, ADAR1 does not result in redirection of miRNA. The most common consequence of ADAR activity on miRNA is a reduction in the mature miRNA level due to interference with miRNA processing of pri-miRNA. However, we found very few miRNAs with reductions in level, and no significant difference between miRNAs previously reported to be edited and those reported to be not edited. In particular, we did not see significant decrease in mir-22 and mir-142, nor editing of pri-mir-22 or pri-mir-142 in infected RAW macrophages. Thus, ADAR1 has very little, if any, effect on the miRNA machinery following TL4 activation by Salmonella infection.
    Keywords: Anatomy & Physiology
    ISSN: 1547-6286
    E-ISSN: 1555-8584
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