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  • Article  (59)
  • 2017  (59)
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  • Article  (59)
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  • 2017  (59)
  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 27 June 2017, Vol.114(26), pp.6824-6829
    Description: The functions of many bacterial RNA-binding proteins remain obscure because of a lack of knowledge of their cellular ligands. Although well-studied cold-shock protein A (CspA) family members are induced and function at low temperature, others are highly expressed in infection-relevant conditions. Here, we have profiled transcripts bound in vivo by the CspA family members of serovar Typhimurium to link the constitutively expressed CspC and CspE proteins with virulence pathways. Phenotypic assays in vitro demonstrated a crucial role for these proteins in membrane stress, motility, and biofilm formation. Moreover, double deletion of and fully attenuates in systemic mouse infection. In other words, the RNA ligand-centric approach taken here overcomes a problematic molecular redundancy of CspC and CspE that likely explains why these proteins have evaded selection in previous virulence factor screens in animals. Our results highlight RNA-binding proteins as regulators of pathogenicity and potential targets of antimicrobial therapy. They also suggest that globally acting RNA-binding proteins are more common in bacteria than currently appreciated.
    Keywords: RNA-Binding Protein ; Salmonella ; Bacterial Pathogenesis ; Cold-Shock Protein ; Stress Response ; Bacterial Proteins ; Cold Shock Proteins and Peptides ; Heat-Shock Proteins ; RNA-Binding Proteins ; Salmonella Infections ; Salmonella Typhimurium ; Virulence Factors
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    In: EMBO Journal, 01 February 2017, Vol.36(3), pp.245-247
    Description: While bacteria were long thought to rely primarily on transcriptional control, it is now well established that they also use numerous small s to regulate translation and stability. There has recently been a surge in studies, including one by Waters ([Waters SA, 2017]) in this issue of , that have used clever variations of the ‐seq technique to comprehensively map small –target networks. Several recent studies have used clever variations of RNA‐seq techniques to comprehensively map small RNA–target networks involved in controlling bacterial gene expression.
    Keywords: Biology ; Chemistry;
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 3
    Language: English
    In: EMBO journal: European Molecular Biology Organization, 2017, Issue 3, pp.245-247
    ISSN: 0261-4189
    Source: Fundación Dialnet
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  • 4
    Language: English
    In: Nucleic acids research, 02 June 2017, Vol.45(10), pp.6147-6167
    Description: Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of -35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.
    Keywords: Gene Expression Regulation, Bacterial ; Transcriptome ; Bacterial Proteins -- Metabolism ; Host Factor 1 Protein -- Metabolism ; Micrornas -- Genetics ; Molecular Chaperones -- Metabolism ; Neisseria Meningitidis -- Genetics ; RNA, Bacterial -- Genetics ; RNA, Messenger -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 5
    Language: English
    In: Nucleic acids research, 20 June 2017, Vol.45(11), pp.e96
    Description: RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches. We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using position-specific scoring matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome of Escherichia coli. APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available at https://pypi.python.org/pypi/bio-apricot.
    Keywords: Sequence Analysis, Protein ; Software ; RNA-Binding Proteins -- Chemistry
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 6
    Language: English
    In: EMBO journal: European Molecular Biology Organization, 2017, Issue 8, pp.1029-1045
    Description: Research into post‐transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and Salmonella enterica has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ‐dependent sRNAs are largely unknown. Here, we report in Salmonella Typhimurium the mode‐of‐action of RaiZ, a ProQ‐dependent sRNA that is made from the 3′ end of the mRNA encoding ribosome‐inactivating protein RaiA. We show that RaiZ is a base‐pairing sRNA that represses in trans the mRNA of histone‐like protein HU‐α. RaiZ forms an RNA duplex with the ribosome‐binding site of hupA mRNA, facilitated by ProQ, to prevent 30S ribosome loading and protein synthesis of HU‐α. Similarities and differences between ProQ‐ and Hfq‐mediated regulation will be discussed.
    Keywords: Hu‐Α ; Proq ; Raiz ; Small Rna ; Translation Inhibition
    ISSN: 0261-4189
    Source: Fundación Dialnet
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  • 7
    In: EMBO Journal, 13 April 2017, Vol.36(8), pp.1029-1045
    Description: Research into post‐transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria and has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ‐dependent sRNAs are largely unknown. Here, we report in Typhimurium the mode‐of‐action of RaiZ, a ProQ‐dependent sRNA that is made from the 3′ end of the mRNA encoding ribosome‐inactivating protein RaiA. We show that RaiZ is a base‐pairing sRNA that represses in the mRNA of histone‐like protein HU‐α. RaiZ forms an RNA duplex with the ribosome‐binding site of mRNA, facilitated by ProQ, to prevent 30S ribosome loading and protein synthesis of HU‐α. Similarities and differences between ProQ‐ and Hfq‐mediated regulation will be discussed. The enterobacterial sRNA RaiZ functions independent of the Hfq RNA chaperone via the recently identified general RNA‐binding protein ProQ. ProQ acts in a dual manner, stabilizing the sRNA and facilitating translational repression of the nucleid protein HU‐α. RaiZ is a small RNA produced by RNase E‐mediated cleavage of the raiA mRNA. RaiZ strongly binds RNA chaperone ProQ, leading to RaiZ stabilization. RaiZ represses translation of the hupA mRNA by base pairing with its ribosome‐binding site. ProQ and RaiZ jointly prevent initiating ribosomes from loading on hupA mRNA. The global RNA‐binding protein ProQ stabilizes bacterial small RNA RaiZ and facilitates translational repression of its target mRNA, thus exemplifying an Hfq‐independent RNA regulon.
    Keywords: Hu‐Α ; Proq ; Raiz ; Small Rna ; Translation Inhibition
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 8
    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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  • 9
    In: Nature Reviews Molecular Cell Biology, 2017
    Description: RNA is involved in the regulation of multiple cellular processes, often by forming sequence-specific base pairs with cellular RNA or DNA targets that must be identified among the large number of nucleic acids in a cell. Several RNA-based regulatory systems in eukaryotes, bacteria and archaea, including microRNAs (miRNAs), small interfering RNAs (siRNAs), CRISPR RNAs (crRNAs) and small RNAs (sRNAs) that are dependent on the RNA chaperone protein Hfq, achieve specificity using similar strategies. Central to their function is the presentation of short 'seed sequences' within a ribonucleoprotein complex to facilitate the search for and recognition of targets.
    Keywords: Micrornas -- Metabolism ; RNA, Small Interfering -- Metabolism;
    ISSN: 1471-0072
    E-ISSN: 1471-0080
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  • 10
    Language: English
    In: Sci Rep, 2017, Vol.7(1), pp.9328-9328
    Description: Many pathogenic bacteria utilize specialized secretion systems to deliver proteins called effectors into eukaryotic cells for manipulation of host pathways. The vast majority of known effector targets are host proteins, whereas a potential targeting of host nucleic acids remains little explored. There is only one family of effectors known to target DNA directly, and effectors binding host RNA are unknown. Here, we take a two-pronged approach to search for RNA-binding effectors, combining biocomputational prediction of RNA-binding domains (RBDs) in a newly assembled comprehensive dataset of bacterial secreted proteins, and experimental screening for RNA binding in mammalian cells. Only a small subset of effectors were predicted to carry an RBD, indicating that if RNA targeting was common, it would likely involve new types of RBDs. Our experimental evaluation of effectors with predicted RBDs further argues for a general paucity of RNA binding activities amongst bacterial effectors. We obtained evidence that PipB2 and Lpg2844, effector proteins of Salmonella and Legionella species, respectively, may harbor novel biochemical activities. Our study presenting the first systematic evaluation of the RNA-targeting potential of bacterial effectors offers a basis for discussion of whether or not host RNA is a prominent target of secreted bacterial proteins.
    Keywords: Biology;
    ISSN: 2045-2322
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