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  • 1
    Language: English
    Description: The bacterial endoribonuclease RNase E occupies a pivotal position in the control of gene expression, as its actions either commit transcripts to an irreversible fate of rapid destruction or unveil their hidden functions through specific processing. Moreover, the enzyme contributes to quality control of rRNAs. The activity of RNase E can be directed and modulated by signals provided through regulatory RNAs that guide the enzyme to specific transcripts that are to be silenced. Early in its evolutionary history, RNase E acquired a natively unfolded appendage that recruits accessory proteins and RNA. These accessory factors facilitate the activity of RNase E and include helicases that remodel RNA and RNA-protein complexes, and polynucleotide phosphorylase, a relative of the archaeal and eukaryotic exosomes. RNase E also associates with enzymes from central metabolism, such as enolase and aconitase. RNase E-based complexes are diverse in composition, but generally bear mechanistic parallels with eukaryotic machinery involved in RNA-induced gene regulation and transcript quality control. That these similar processes arose independently underscores the universality of RNA-based regulation in life. Here we provide a synopsis and perspective of the contributions made by RNase E to sustain robust gene regulation with speed and accuracy.
    Description: Wellcome Trust
    Keywords: Eukaryotic Cells ; Bacteria ; Archaea ; Endoribonucleases ; Aconitate Hydratase ; Phosphopyruvate Hydratase ; Polyribonucleotide Nucleotidyltransferase ; Rna Helicases ; Rna, Bacterial ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Rna Processing, Post-Transcriptional ; Exosomes
    Source: DSpace@Cambridge
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  • 2
    Language: English
    In: Biochimica et biophysica acta, 2013, Vol.1829(6-7), pp.514-22
    Description: Bacterial transcripts each have a characteristic half-life, suggesting that the processes of RNA degradation work in an active and selective manner. Moreover, the processes are well controlled, thereby ensuring that degradation is orderly and coordinated. Throughout much of the bacterial kingdom, RNA degradation processes originate through the actions of assemblies of key RNA enzymes, known as RNA degradosomes. Neither conserved in composition, nor unified by common evolutionary ancestry, RNA degradosomes nonetheless can be found in divergent bacterial lineages, implicating a common requirement for the co-localisation of RNA metabolic activities. We describe how the cooperation of components in the representative degradosome of Escherichia coli may enable controlled access to transcripts, so that they have defined and programmable lifetimes. We also discuss how this cooperation contributes to precursor processing and to the riboregulation of intricate post-transcriptional networks in the control of gene expression. The E. coli degradosome interacts with the cytoplasmic membrane, and we discuss how this interaction may spatially organise the assembly and contribute to subunit cooperation and substrate capture. This article is part of a Special Issue entitled: RNA Decay mechanisms.
    Keywords: Multienzyme Complexes ; Polyribonucleotide Nucleotidyltransferase ; RNA Helicases ; RNA Stability ; Endoribonucleases -- Genetics ; RNA, Bacterial -- Genetics
    ISSN: 0006-3002
    E-ISSN: 18782434
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 3
    Language: English
    In: Nucleic acids research, 09 January 2018, Vol.46(1), pp.387-402
    Description: The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane. We have structurally characterized a subassembly of the degradosome-comprising a 248-residue segment of the natively unstructured part of RNase E, the DEAD-box helicase RhlB and the glycolytic enzyme enolase, and provide evidence that it serves as a flexible recognition centre that can co-recruit small regulatory RNA and the RNA chaperone Hfq. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition centre, facilitates pairing to cognate transcripts and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing.
    Keywords: Chemistry ; Anatomy & Physiology;
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 4
    Language: English
    In: BBA - Gene Regulatory Mechanisms, June 2013, Vol.1829(6-7), pp.514-522
    Description: Bacterial transcripts each have a characteristic half-life, suggesting that the processes of RNA degradation work in an active and selective manner. Moreover, the processes are well controlled, thereby ensuring that degradation is orderly and coordinated. Throughout much of the bacterial kingdom, RNA degradation processes originate through the actions of assemblies of key RNA enzymes, known as RNA degradosomes. Neither conserved in composition, nor unified by common evolutionary ancestry, RNA degradosomes nonetheless can be found in divergent bacterial lineages, implicating a common requirement for the co-localisation of RNA metabolic activities. We describe how the cooperation of components in the representative degradosome of may enable controlled access to transcripts, so that they have defined and programmable lifetimes. We also discuss how this cooperation contributes to precursor processing and to the riboregulation of intricate post-transcriptional networks in the control of gene expression. The degradosome interacts with the cytoplasmic membrane, and we discuss how this interaction may spatially organise the assembly and contribute to subunit cooperation and substrate capture. This article is part of a Special Issue entitled: RNA Decay mechanisms.
    Keywords: RNA Decay ; RNA Processing ; Ribonuclease ; Rnase E ; RNA Degradosome ; Srna ; Biology ; Chemistry
    ISSN: 1874-9399
    E-ISSN: 18764320
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  • 5
    Description: The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. The extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane. We have structurally characterised a subassembly of the degradosome - comprising a 248-residue segment of the natively unstructured part of RNase E, the DEAD-box helicase RhlB, and the glycolytic enzyme enolase – and provide evidence that it serves as a flexible recognition centre that can co-recruit small regulatory RNA (sRNA) and the RNA chaperone Hfq. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition centre, facilitates pairing to cognate transcripts, and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing....
    ISSN: 0305-1048
    Source: DataCite
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  • 6
    Language: English
    In: Molecular cell, 2012, Vol.47(6), pp.943-953
    Description: Numerous small non-coding RNAs (sRNAs) in bacteria modulate rates of translation initiation and degradation of target mRNAs, which they recognize through base-pairing facilitated by the RNA chaperone Hfq. Recent evidence indicates that the ternary complex of Hfq, sRNA and mRNA guides endoribonuclease RNase E to initiate turnover of both the RNAs. We show that a sRNA not only guides RNase E to a defined site in a target RNA, but also allosterically activates the enzyme by presenting a monophosphate group at the 5′-end of the cognate-pairing “seed.” Moreover, in the absence of the target the 5′-monophosphate makes the sRNA seed region vulnerable to an attack by RNase E against which Hfq confers no protection. These results suggest that the chemical signature and pairing status of the sRNA seed region may help to both ‘proofread’ recognition and activate mRNA cleavage, as part of a dynamic process involving cooperation of RNA, Hfq and RNase E. ; p. 943-953.
    Keywords: Translation (Genetics) ; Messenger Rna ; Bacteria ; Non-Coding Rna ; Ribonucleases
    ISSN: 1097-2765
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  • 7
    Language: English
    In: Molecular Cell, 18 October 2018, Vol.72(2), pp.275-285.e4
    Description: The endoribonuclease RNase E is a principal factor in RNA turnover and processing that helps to exercise fine control of gene expression in bacteria. While its catalytic activity can be strongly influenced by the chemical identity of the 5′ end of RNA substrates, the enzyme can also cleave numerous substrates irrespective of the chemistry of their 5′ ends through a mechanism that has remained largely unexplained. We report structural and functional data illuminating details of both operational modes. Our crystal structure of RNase E in complex with the sRNA RprA reveals a duplex recognition site that saddles an inter-protomer surface to help present substrates for cleavage. Our data also reveal an autoinhibitory pocket that modulates the overall activity of the ribonuclease. Taking these findings together, we propose how RNase E uses versatile modes of RNA recognition to achieve optimal activity and specificity. RNase E is a central ribonuclease of RNA metabolism and post-transcriptional control of gene expression. Through structural and functional analyses, Bandyra et al. reveal how the enzyme activity can be favored by recognition of the 5′ end and RNA secondary structure. The data also reveal a conserved autoinhibitory motif that suppresses RNase E intrinsic activity.
    Keywords: RNA-Mediated Regulation ; Protein-RNA Interactions ; Small Regulatory RNA ; Rnase E ; RNA Structure ; RNA Processing ; RNA Degradation ; Protein-RNA Structure ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 8
    Language: English
    In: Microbiology spectrum, April 2018, Vol.6(2)
    Description: The bacterial endoribonuclease RNase E occupies a pivotal position in the control of gene expression, as its actions either commit transcripts to an irreversible fate of rapid destruction or unveil their hidden functions through specific processing. Moreover, the enzyme contributes to quality control of rRNAs. The activity of RNase E can be directed and modulated by signals provided through regulatory RNAs that guide the enzyme to specific transcripts that are to be silenced. Early in its evolutionary history, RNase E acquired a natively unfolded appendage that recruits accessory proteins and RNA. These accessory factors facilitate the activity of RNase E and include helicases that remodel RNA and RNA-protein complexes, and polynucleotide phosphorylase, a relative of the archaeal and eukaryotic exosomes. RNase E also associates with enzymes from central metabolism, such as enolase and aconitase. RNase E-based complexes are diverse in composition, but generally bear mechanistic parallels with eukaryotic machinery involved in RNA-induced gene regulation and transcript quality control. That these similar processes arose independently underscores the universality of RNA-based regulation in life. Here we provide a synopsis and perspective of the contributions made by RNase E to sustain robust gene regulation with speed and accuracy.
    Keywords: Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Bacteria -- Enzymology ; Endoribonucleases -- Metabolism ; RNA, Bacterial -- Metabolism
    E-ISSN: 2165-0497
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 9
    Language: English
    In: Molecular Cell, 28 September 2012, Vol.47(6), pp.943-953
    Description: Numerous small non-coding RNAs (sRNAs) in bacteria modulate rates of translation initiation and degradation of target mRNAs, which they recognize through base-pairing facilitated by the RNA chaperone Hfq. Recent evidence indicates that the ternary complex of Hfq, sRNA and mRNA guides endoribonuclease RNase E to initiate turnover of both the RNAs. We show that a sRNA not only guides RNase E to a defined site in a target RNA, but also allosterically activates the enzyme by presenting a monophosphate group at the 5′-end of the cognate-pairing “seed.” Moreover, in the absence of the target the 5′-monophosphate makes the sRNA seed region vulnerable to an attack by RNase E against which Hfq confers no protection. These results suggest that the chemical signature and pairing status of the sRNA seed region may help to both ‘proofread’ recognition and activate mRNA cleavage, as part of a dynamic process involving cooperation of RNA, Hfq and RNase E. ► Small RNA-mRNA duplex can recruit single-strand specific endoribonuclease RNase E ► sRNA can guide and allosterically activate RNase E to initiate target mRNA degradation ► The allosteric signal is a monophosphate group on the 5' end of the sRNA ► The 5' monophosphate may contribute to proofreading of sRNA action
    Keywords: Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 10
    Article
    Article
    Apollo - University of Cambridge Repository
    Description: The bacterial endoribonuclease RNase E occupies a pivotal position in the control of gene expression, as its actions either commit transcripts to an irreversible fate of rapid destruction or unveil their hidden functions through specific processing. Moreover, the enzyme contributes to quality control of rRNAs. The activity of RNase E can be directed and modulated by signals provided through regulatory RNAs that guide the enzyme to specific transcripts that are to be silenced. Early in its evolutionary history, RNase E acquired a natively unfolded appendage that recruits accessory proteins and RNA. These accessory factors facilitate the activity of RNase E and include helicases that remodel RNA and RNA-protein complexes, and polynucleotide phosphorylase, a relative of the archaeal and eukaryotic exosomes. RNase E also associates with enzymes from central metabolism, such as enolase and aconitase. RNase E-based complexes are diverse in composition, but generally bear mechanistic parallels with eukaryotic machinery involved in RNA-induced gene regulation and transcript quality control. That these similar processes arose independently underscores the universality of RNA-based regulation in life. Here we provide a synopsis and perspective of the contributions made by RNase E to sustain robust gene regulation with speed and accuracy....
    Keywords: Eukaryotic Cells ; Bacteria ; Archaea ; Endoribonucleases ; Aconitate Hydratase ; Phosphopyruvate Hydratase ; Polyribonucleotide Nucleotidyltransferase ; Rna Helicases ; Rna, Bacterial ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Rna Processing, Post-Transcriptional ; Exosomes
    ISSN: 2165-0497
    Source: DataCite
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