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  • 1
    Online Resource
    Online Resource
    Cross-Regulation between Bacteria and Phages at a Posttranscriptional Level
    American Society for Microbiology ; 2018
    In:  Microbiology Spectrum Vol. 6, No. 4 ( 2018-07-27)
    Details
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 6, No. 4 ( 2018-07-27)
    Abstract: The study of bacteriophages (phages) and prophages has provided key insights into almost every cellular process as well as led to the discovery of unexpected new mechanisms and the development of valuable tools. This is exemplified for RNA-based regulation. For instance, the characterization and exploitation of the antiphage CRISPR (clustered regularly interspaced short palindromic repeat) systems is revolutionizing molecular biology. Phage-encoded proteins such as the RNA-binding MS2 protein, which is broadly used to isolate tagged RNAs, also have been developed as valuable tools. Hfq, the RNA chaperone protein central to the function of many base-pairing small RNAs (sRNAs), was first characterized as a bacterial host factor required for Qβ phage replication. The ongoing studies of RNAs are continuing to reveal regulatory connections between infecting phages, prophages, and bacteria and to provide novel insights. There are bacterial and prophage sRNAs that regulate prophage genes, which impact bacterial virulence as well as bacterial cell killing. Conversely, phage- and prophage-encoded sRNAs modulate the expression of bacterial genes modifying metabolism. An interesting subcategory of the prophage-encoded sRNAs are sponge RNAs that inhibit the activities of bacterial-encoded sRNAs. Phages also affect posttranscriptional regulation in bacteria through proteins that inhibit or alter the activities of key bacterial proteins involved in posttranscriptional regulation. However, what is most exciting about phage and prophage research, given the millions of phage-encoded genes that have not yet been characterized, is the vast potential for discovering new RNA regulators and novel mechanisms and for gaining insight into the evolution of regulatory RNAs.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    URL: Article
    DOI: 10.1128/microbiolspec.RWR-0027-2018
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 2807133-5
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  • 2
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    Online Resource
    FlrA ‐independent production of flagellar proteins is required for proper flagellation in Shewanella putrefaciens
    Wiley ; 2022
    In:  Molecular Microbiology Vol. 118, No. 6 ( 2022-12), p. 670-682
    Details
    In: Molecular Microbiology, Wiley, Vol. 118, No. 6 ( 2022-12), p. 670-682
    Abstract: Flagella are multiprotein complexes whose assembly and positioning require complex spatiotemporal control. Flagellar assembly is thought to be controlled by several transcriptional tiers, which are mediated through various master regulators. Here, we revisited the regulation of flagellar genes in polarly flagellated gammaproteobacteria by the regulators FlrA, RpoN (σ 54 ) and FliA (σ 28 ) in Shewanella putrefaciens CN‐32 at the transcript and protein level. We found that a number of regulatory and structural proteins were present in the absence of the main regulators, suggesting that initiation of flagella assembly and motor activation relies on the abundance control of only a few structural key components that are required for the formation of the MS‐ and C‐ring and the flagellar type III secretion system. We identified FlrA‐independent promoters driving expression of the regulators of flagellar number and positioning, FlhF and FlhG. Reduction of the gene expression levels from these promoters resulted in the emergence of hyperflagellation. This finding indicates that basal expression is required to adjust the flagellar counter in Shewanella . This is adding a deeper layer to the regulation of flagellar synthesis and assembly.
    Type of Medium: Online Resource
    ISSN: 0950-382X , 1365-2958
    URL: Issue
    URL: Article
    DOI: 10.1111/mmi.v118.6
    DOI: 10.1111/mmi.14993
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 1501537-3
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  • 3
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    Online Resource
    Quorum sensing signal–response systems in Gram-negative bacteria
    Springer Science and Business Media LLC ; 2016
    In:  Nature Reviews Microbiology Vol. 14, No. 9 ( 2016-9), p. 576-588
    Details
    In: Nature Reviews Microbiology, Springer Science and Business Media LLC, Vol. 14, No. 9 ( 2016-9), p. 576-588
    Type of Medium: Online Resource
    ISSN: 1740-1526 , 1740-1534
    URL: Article
    DOI: 10.1038/nrmicro.2016.89
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 2121463-3
    SSG: 12
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  • 4
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    Online Resource
    Small Proteins; Big Questions
    American Society for Microbiology ; 2022
    In:  Journal of Bacteriology Vol. 204, No. 1 ( 2022-01-18)
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 204, No. 1 ( 2022-01-18)
    Abstract: In recent years, there has been increased appreciation that a whole category of proteins, small proteins of around 50 amino acids or fewer in length, has been missed by annotation as well as by genetic and biochemical assays. With the increased recognition that small proteins are stable within cells and have regulatory functions, there has been intensified study of these proteins. As a result, important questions about small proteins in bacteria and archaea are coming to the fore. Here, we give an overview of these questions, the initial answers, and the approaches needed to address these questions more fully. More detailed discussions of how small proteins can be identified by ribosome profiling and mass spectrometry approaches are provided by two accompanying reviews (N. Vazquez-Laslop, C. M. Sharma, A. S. Mankin, and A. R. Buskirk, J Bacteriol 204:e00294-21, 2022, https://doi.org/10.1128/JB.00294-21 ; C. H. Ahrens, J. T. Wade, M. M. Champion, and J. D. Langer, J Bacteriol 204:e00353-21, 2022, https://doi.org/10.1128/JB.00353-21 ). We are excited by the prospects of new insights and possible therapeutic approaches coming from this emerging field.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.00341-21
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs : Hfq-dependent small RNAs from 3′ UTRs
    Wiley ; 2012
    In:  The EMBO Journal Vol. 31, No. 20 ( 2012-10-17), p. 4005-4019
    Details
    In: The EMBO Journal, Wiley, Vol. 31, No. 20 ( 2012-10-17), p. 4005-4019
    Type of Medium: Online Resource
    ISSN: 0261-4189
    URL: Article
    DOI: 10.1038/emboj.2012.229
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2012
    detail.hit.zdb_id: 1467419-1
    detail.hit.zdb_id: 586044-1
    SSG: 12
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  • 6
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    Online Resource
    6S RNA, a Global Regulator of Transcription
    American Society for Microbiology ; 2018
    In:  Microbiology Spectrum Vol. 6, No. 3 ( 2018-06)
    Details
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 6, No. 3 ( 2018-06)
    Abstract: 6S RNA is a small RNA regulator of RNA polymerase (RNAP) that is present broadly throughout the bacterial kingdom. Initial functional studies in Escherichia coli revealed that 6S RNA forms a complex with RNAP resulting in regulation of transcription, and cells lacking 6S RNA have altered survival phenotypes. The last decade has focused on deepening the understanding of several aspects of 6S RNA activity, including (i) addressing questions of how broadly conserved 6S RNAs are in diverse organisms through continued identification and initial characterization of divergent 6S RNAs; (ii) the nature of the 6S RNA-RNAP interaction through examination of variant proteins and mutant RNAs, cross-linking approaches, and ultimately a cryo-electron microscopic structure; (iii) the physiological consequences of 6S RNA function through identification of the 6S RNA regulon and promoter features that determine 6S RNA sensitivity; and (iv) the mechanism and cellular impact of 6S RNA-directed synthesis of product RNAs (i.e., pRNA synthesis). Much has been learned about this unusual RNA, its mechanism of action, and how it is regulated; yet much still remains to be investigated, especially regarding potential differences in behavior of 6S RNAs in diverse bacteria.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    URL: Article
    DOI: 10.1128/microbiolspec.RWR-0019-2018
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 2807133-5
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  • 7
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    Online Resource
    Small Regulatory RNAs in the Enterobacterial Response to Envelope Damage and Oxidative Stress
    American Society for Microbiology ; 2018
    In:  Microbiology Spectrum Vol. 6, No. 4 ( 2018-07-27)
    Details
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 6, No. 4 ( 2018-07-27)
    Abstract: The ability of bacteria to thrive in diverse habitats and to adapt to ever-changing environmental conditions relies on the rapid and stringent modulation of gene expression. It has become evident in the past decade that small regulatory RNAs (sRNAs) are central components of networks controlling the bacterial responses to stress. Functioning at the posttranscriptional level, sRNAs base-pair with cognate mRNAs to alter translation, stability, or both to either repress or activate the targeted transcripts; the RNA chaperone Hfq participates in stabilizing sRNAs and in promoting pairing between target and sRNA. In particular, sRNAs act at the heart of crucial stress responses, including those dedicated to overcoming membrane damage and oxidative stress, discussed here. The bacterial cell envelope is the outermost protective barrier against the environment and thus is constantly monitored and remodeled. Here, we review the integration of sRNAs into the complex networks of several major envelope stress responses of Gram-negative bacteria, including the RpoE (σ E ), Cpx, and Rcs regulons. Oxidative stress, caused by bacterial respiratory activity or induced by toxic molecules, can lead to significant damage of cellular components. In Escherichia coli and related bacteria, sRNAs also contribute significantly to the function of the RpoS (σ S )-dependent general stress response as well as the specific OxyR- and SoxR/S-mediated responses to oxidative damage. Their activities in gene regulation and crosstalk to other stress-induced regulons are highlighted.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    URL: Article
    DOI: 10.1128/microbiolspec.RWR-0022-2018
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 2807133-5
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  • 8
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    Online Resource
    Sponges and Predators in the Small RNA World
    American Society for Microbiology ; 2018
    In:  Microbiology Spectrum Vol. 6, No. 4 ( 2018-07-27)
    Details
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 6, No. 4 ( 2018-07-27)
    Abstract: Most noncoding small RNAs (sRNAs) that regulate gene expression do so by base-pairing with mRNAs, affecting their translation and/or stability. Regulators as evolutionarily distant as the trans -encoded sRNAs of bacteria and the microRNAs (miRNAs) of higher eukaryotes share the property of targeting short sequence segments that occur in multiple copies in bacterial and eukaryotic transcriptomes. This target promiscuity has major implications for sRNA function. On the one hand, it allows the sRNA to coordinately control several different targets and thus be at the center of regulatory networks. On the other hand, it allows the existence of target mimics or decoys that divert the sRNA/miRNA away from bona fide targets and thus serve as mechanisms to regulate the regulator. In addition, by competing for pairing with the same sRNA, bona fide targets establish a cross talk that can impact on each other’s expression levels. Here we review evidence that target mimicry and competition are important components of the regulatory architecture of bacterial sRNA networks.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    URL: Article
    DOI: 10.1128/microbiolspec.RWR-0021-2018
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 2807133-5
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  • 9
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    Online Resource
    Type I Toxin-Antitoxin Systems: Regulating Toxin Expression via Shine-Dalgarno Sequence Sequestration and Small RNA Binding
    American Society for Microbiology ; 2018
    In:  Microbiology Spectrum Vol. 6, No. 4 ( 2018-07-27)
    Details
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 6, No. 4 ( 2018-07-27)
    Abstract: Toxin-antitoxin (TA) systems are small genetic loci composed of two adjacent genes: a toxin and an antitoxin that prevents toxin action. Despite their wide distribution in bacterial genomes, the reasons for TA systems being on chromosomes remain enigmatic. In this review, we focus on type I TA systems, composed of a small antisense RNA that plays the role of an antitoxin to control the expression of its toxin counterpart. It does so by direct base-pairing to the toxin-encoding mRNA, thereby inhibiting its translation and/or promoting its degradation. However, in many cases, antitoxin binding is not sufficient to avoid toxicity. Several cis -encoded mRNA elements are also required for repression, acting to uncouple transcription and translation via the sequestration of the ribosome binding site. Therefore, both antisense RNA binding and compact mRNA folding are necessary to tightly control toxin synthesis and allow the presence of these toxin-encoding systems on bacterial chromosomes.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    URL: Article
    DOI: 10.1128/microbiolspec.RWR-0030-2018
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 2807133-5
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  • 10
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    Online Resource
    RNA Localization in Bacteria
    American Society for Microbiology ; 2018
    In:  Microbiology Spectrum Vol. 6, No. 5 ( 2018-09-07)
    Details
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 6, No. 5 ( 2018-09-07)
    Abstract: Diverse mechanisms and functions of posttranscriptional regulation by small regulatory RNAs and RNA-binding proteins have been described in bacteria. In contrast, little is known about the spatial organization of RNAs in bacterial cells. In eukaryotes, subcellular localization and transport of RNAs play important roles in diverse physiological processes, such as embryonic patterning, asymmetric cell division, epithelial polarity, and neuronal plasticity. It is now clear that bacterial RNAs also can accumulate at distinct sites in the cell. However, due to the small size of bacterial cells, RNA localization and localization-associated functions are more challenging to study in bacterial cells, and the underlying molecular mechanisms of transcript localization are less understood. Here, we review the emerging examples of RNAs localized to specific subcellular locations in bacteria, with indications that subcellular localization of transcripts might be important for gene expression and regulatory processes. Diverse mechanisms for bacterial RNA localization have been suggested, including close association to their genomic site of transcription, or to the localizations of their protein products in translation-dependent or -independent processes. We also provide an overview of the state of the art of technologies to visualize and track bacterial RNAs, ranging from hybridization-based approaches in fixed cells to in vivo imaging approaches using fluorescent protein reporters and/or RNA aptamers in single living bacterial cells. We conclude with a discussion of open questions in the field and ongoing technological developments regarding RNA imaging in eukaryotic systems that might likewise provide novel insights into RNA localization in bacteria.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    URL: Article
    DOI: 10.1128/microbiolspec.RWR-0024-2018
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 2807133-5
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