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  • 1
    Language: English
    In: Current Opinion in Microbiology, April 2013, Vol.16(2), pp.109-111
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 2
    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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  • 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: Current Opinion in Microbiology, April 2016, Vol.30, pp.50-57
    Description: RNA modifications are known to abound in stable tRNA and rRNA, where they cluster around functionally important regions. However, RNA-seq based techniques profiling entire transcriptomes are now uncovering an abundance of modified ribonucleotides in mRNAs and noncoding RNAs, too. While most of the recent progress in understanding the regulatory influence of these new RNA modifications stems from eukaryotes, there is growing evidence in bacteria for modified nucleotides beyond the stable RNA species, including modifications of small regulatory RNAs. Given their small genome size, good genetic tractability, and ample knowledge of modification enzymes, bacteria offer excellent model systems to decipher cellular functions of RNA modifications in many diverse physiological contexts. This review highlights how new global approaches combining classic analysis with new sequencing techniques may usher in an era of bacterial epitranscriptomics.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 5
    Language: English
    In: Current Opinion in Microbiology, April 2015, Vol.24, pp.132-139
    Description: Most studies of small regulatory RNAs in bacteria have focussed on conserved transcripts in intergenic regions. However, several recent developments including single-nucleotide resolution transcriptome profiling by RNA-seq and increased knowledge of the cellular targets of the RNA chaperone Hfq suggest that the bacterial world of functional small RNAs is more diverse. One emerging class are small RNAs that are identical to the 3′ regions of known mRNAs, but are produced either by transcription from internal promoters or by mRNA processing. Using several recently discovered examples of such sRNAs, we discuss their biogenesis and modes of action, and illustrate how they can facilitate mRNA crosstalk in various physiological processes.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 6
    Language: English
    In: Current Opinion in Microbiology, June 2014, Vol.19, pp.97-105
    Description: RNA-sequencing has revolutionized the quantitative and qualitative analysis of transcriptomes in both prokaryotes and eukaryotes. It provides a generic approach for gene expression profiling, annotation of transcript boundaries and operons, as well as identifying novel transcripts including small noncoding RNA molecules and antisense RNAs. We recently developed a differential RNA-seq (dRNA-seq) method which in addition to the above, yields information as to whether a given RNA is a primary or processed transcript. Originally applied to describe the primary transcriptome of the gastric pathogen , dRNA-seq has since provided global maps of transcriptional start sites in diverse species, informed new biology in the CRISPR-Cas9 system, advanced to a tool for comparative transcriptomics, and inspired simultaneous RNA-seq of pathogen and host.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 7
    Language: English
    In: Current Opinion in Microbiology, October 2017, Vol.39, pp.152-160
    Description: The identification of new RNA functions and the functional annotation of transcripts in genomes represent exciting yet challenging endeavours of modern biology. Crucial insights into the biological roles of RNA molecules can be gained from the identification of the proteins with which they form specific complexes. Modern interactome techniques permit to profile RNA–protein interactions in a genome-wide manner and identify new RNA classes associated with globally acting RNA-binding proteins. Applied to a variety of organisms, these methods are already revolutionising our understanding of RNA-mediated biological processes. Here, we focus on one such approach — Gradient sequencing or Grad-seq — which has recently guided the discovery of protein ProQ and its associated small RNAs as a new domain of post-transcriptional control in bacteria.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 8
    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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  • 9
    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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  • 10
    Language: English
    In: Current Opinion in Microbiology, 2009, Vol.12(6), pp.674-682
    Description: Small regulatory RNAs (sRNAs) commonly act to downregulate gene expression. In bacteria, however, sRNAs have also been shown to activate genes by a variety of direct or indirect mechanisms. Several sRNAs (DsrA, GlmZ, RNAIII, RprA, RyhB, and Qrr) act as direct translational activators by an ‘anti-antisense mechanism’ in the 5′ mRNA region to liberate a sequestered ribosome binding site, while pairing of GadY sRNA to the 3′-end alters processing and increases stability of its target mRNA. Indirect activation includes cases of RNA mimicry in which degradation of the activating GlmZ sRNA is suppressed by the highly similar GlmY sRNA, or where a pseudo-target mRNA traps MicM sRNA to derepress porin synthesis.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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