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  • 1
    Language: English
    In: Nature Reviews Microbiology, 2018, Vol.16(10), pp.601-615
    Description: RNA-binding proteins (RBPs) are central to most if not all cellular processes, dictating the fate of virtually all RNA molecules in the cell. Starting with pioneering work on ribosomal proteins, studies of bacterial RBPs have paved the way for molecular studies of RNA-protein interactions. Work over the years has identified major RBPs that act on cellular transcripts at the various stages of bacterial gene expression and that enable their integration into post-transcriptional networks that also comprise small non-coding RNAs. Bacterial RBP research has now entered a new era in which RNA sequencing-based methods permit mapping of RBP activity in a truly global manner in vivo. Moreover, the soaring interest in understudied members of host-associated microbiota and environmental communities is likely to unveil new RBPs and to greatly expand our knowledge of RNA-protein interactions in bacteria.
    Keywords: Medical And Health Sciences ; Basic Medicine ; Microbiology In The Medical Area ; Medicin Och Hälsovetenskap ; Medicinska Och Farmaceutiska Grundvetenskaper ; Mikrobiologi Inom Det Medicinska Området
    ISSN: 1740-1526
    E-ISSN: 17401534
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  • 2
    Language: English
    In: Molecular Cell, 07 June 2018, Vol.70(5), pp.785-799
    Description: Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms. Collectively, this creates a need for global RNA biology approaches that can rapidly and comprehensively analyze the RNA composition of a bacterium of interest. We review such approaches with a focus on RNA-seq as a versatile tool to investigate the different layers of gene expression in which RNA is made, processed, regulated, modified, translated, and turned over. RNA-seq-based approaches are revolutionizing how bacterial RNA biology can be studied. Hör, Gorski, and Vogel review the available global methods that can be used to chart the increasingly diverse number of RNA species and functions in any microbe of interest.
    Keywords: RNA-Seq ; Non-Coding RNA ; Small RNA ; Transcription ; RNA-Binding Protein ; Post-Transcriptional Control ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 3
    Language: English
    In: Molecular Cell, 07 June 2018, Vol.70(5), pp.971-982.e6
    Description: The conserved RNA-binding protein ProQ has emerged as the centerpiece of a previously unknown third large network of post-transcriptional control in enterobacteria. Here, we have used UV crosslinking and RNA sequencing (CLIP-seq) to map hundreds of ProQ binding sites in and . Our analysis of these binding sites, many of which are conserved, suggests that ProQ recognizes its cellular targets through RNA structural motifs found in small RNAs (sRNAs) and at the 3′ end of mRNAs. Using the mRNA as a model for 3′ end targeting, we reveal a function for ProQ in protecting mRNA against exoribonucleolytic activity. Taken together, our results underpin the notion that ProQ governs a post-transcriptional network distinct from those of the well-characterized sRNA-binding proteins, CsrA and Hfq, and suggest a previously unrecognized, sRNA-independent role of ProQ in stabilizing mRNAs. Using CLIP-seq, Holmqvist et al. map transcriptome-wide interactions of the emerging global RNA-binding protein ProQ in and . Their data suggest ProQ to target sRNAs and mRNA 3′ UTRs primarily through a structural code and to stabilize some mRNAs by counteracting 3′ exoribonuclease activity.
    Keywords: Proq ; Clip-Seq ; RNA-Binding Protein ; 3′ Utr ; Post-Transcriptional Control ; Exoribonuclease ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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