1
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Taggart J, Dierksheide K, LeBlanc H, Lalanne JB, Durand S, Braun F, Condon C, Li GW. A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis. Nucleic Acids Res 2025; 53:gkaf030. [PMID: 39883015 PMCID: PMC11780869 DOI: 10.1093/nar/gkaf030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 01/03/2025] [Accepted: 01/17/2025] [Indexed: 01/31/2025] Open
Abstract
RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches-transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites-that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5'- and 3'-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.
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Affiliation(s)
- James C Taggart
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | - Hannah J LeBlanc
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sylvain Durand
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Frédérique Braun
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Ciarán Condon
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA
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2
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Banerjee T, Rothenberg E, Belasco JG. RNase E searches for cleavage sites in RNA by linear diffusion: direct evidence from single-molecule FRET. Nucleic Acids Res 2024; 52:6674-6686. [PMID: 38647084 PMCID: PMC11194081 DOI: 10.1093/nar/gkae279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 03/24/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024] Open
Abstract
The ability of obstacles in cellular transcripts to protect downstream but not upstream sites en masse from attack by RNase E has prompted the hypothesis that this mRNA-degrading endonuclease may scan 5'-monophosphorylated RNA linearly for cleavage sites, starting at the 5' end. However, despite its proposed regulatory importance, the migration of RNase E on RNA has never been directly observed. We have now used single-molecule FRET to monitor the dynamics of this homotetrameric enzyme on RNA. Our findings reveal that RNase E slides along unpaired regions of RNA without consuming a molecular source of energy such as ATP and that its forward progress can be impeded when it encounters a large structural discontinuity. This movement, which is bidirectional, occurs in discrete steps of variable length and requires an RNA ligand much longer than needed to occupy a single RNase E subunit. These results indicate that RNase E scans for cleavage sites by one-dimensional diffusion and suggest a possible molecular mechanism.
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Affiliation(s)
- Tithi Banerjee
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 450 E. 29th Street, New York, NY 10016, USA
| | - Joel G Belasco
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
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3
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Zhou Y, Sun H, Rapiejko AR, Vargas-Blanco DA, Martini MC, Chase MR, Joubran SR, Davis AB, Dainis JP, Kelly JM, Ioerger TR, Roberts LA, Fortune SM, Shell SS. Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs. J Biol Chem 2023; 299:105312. [PMID: 37802316 PMCID: PMC10641625 DOI: 10.1016/j.jbc.2023.105312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023] Open
Abstract
The mechanisms and regulation of RNA degradation in mycobacteria have been subject to increased interest following the identification of interplay between RNA metabolism and drug resistance. Mycobacteria encode multiple ribonucleases predicted to participate in mRNA degradation and/or processing of stable RNAs. RNase E is hypothesized to play a major role in mRNA degradation because of its essentiality in mycobacteria and its role in mRNA degradation in gram-negative bacteria. Here, we defined the impact of RNase E on mRNA degradation rates transcriptome-wide in the nonpathogenic model Mycolicibacterium smegmatis. RNase E played a rate-limiting role in degradation of the transcripts encoded by at least 89% of protein-coding genes, with leadered transcripts often being more affected by RNase E repression than leaderless transcripts. There was an apparent global slowing of transcription in response to knockdown of RNase E, suggesting that M. smegmatis regulates transcription in responses to changes in mRNA degradation. This compensation was incomplete, as the abundance of most transcripts increased upon RNase E knockdown. We assessed the sequence preferences for cleavage by RNase E transcriptome-wide in M. smegmatis and Mycobacterium tuberculosis and found a consistent bias for cleavage in C-rich regions. Purified RNase E had a clear preference for cleavage immediately upstream of cytidines, distinct from the sequence preferences of RNase E in gram-negative bacteria. We furthermore report a high-resolution map of mRNA cleavage sites in M. tuberculosis, which occur primarily within the RNase E-preferred sequence context, confirming that RNase E has a broad impact on the M. tuberculosis transcriptome.
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Affiliation(s)
- Ying Zhou
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Huaming Sun
- Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Abigail R Rapiejko
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Diego A Vargas-Blanco
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Maria Carla Martini
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Michael R Chase
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Samantha R Joubran
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Alexa B Davis
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Joseph P Dainis
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Jessica M Kelly
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Thomas R Ioerger
- Department of Computer Science & Engineering, Texas A&M University, College Station, Texas, USA
| | - Louis A Roberts
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA.
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4
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Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I. J Microbiol 2023; 61:211-220. [PMID: 36814003 DOI: 10.1007/s12275-023-00013-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 02/24/2023]
Abstract
RNase E is an essential enzyme in Escherichia coli. The cleavage site of this single-stranded specific endoribonuclease is well-characterized in many RNA substrates. Here, we report that the upregulation of RNase E cleavage activity by a mutation that affects either RNA binding (Q36R) or enzyme multimerization (E429G) was accompanied by relaxed cleavage specificity. Both mutations led to enhanced RNase E cleavage in RNA I, an antisense RNA of ColE1-type plasmid replication, at a major site and other cryptic sites. Expression of a truncated RNA I with a major RNase E cleavage site deletion at the 5'-end (RNA I-5) resulted in an approximately twofold increase in the steady-state levels of RNA I-5 and the copy number of ColE1-type plasmid in E. coli cells expressing wild-type or variant RNase E compared to those expressing RNA I. These results indicate that RNA I-5 does not efficiently function as an antisense RNA despite having a triphosphate group at the 5'-end, which protects the RNA from ribonuclease attack. Our study suggests that increased cleavage rates of RNase E lead to relaxed cleavage specificity on RNA I and the inability of the cleavage product of RNA I as an antisense regulator in vivo does not stem from its instability by having 5'-monophosphorylated end.
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5
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Richards J, Belasco JG. Graded impact of obstacle size on scanning by RNase E. Nucleic Acids Res 2023; 51:1364-1374. [PMID: 36620905 PMCID: PMC9943677 DOI: 10.1093/nar/gkac1242] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 01/10/2023] Open
Abstract
In countless bacterial species, the lifetimes of most mRNAs are controlled by the regulatory endonuclease RNase E, which preferentially degrades RNAs bearing a 5' monophosphate and locates cleavage sites within them by scanning linearly from the 5' terminus along single-stranded regions. Consequently, its rate of cleavage at distal sites is governed by any obstacles that it may encounter along the way, such as bound proteins or ribosomes or base pairing that is coaxial with the path traversed by this enzyme. Here, we report that the protection afforded by such obstacles is dependent on the size and persistence of the structural discontinuities they create, whereas the molecular composition of obstacles to scanning is of comparatively little consequence. Over a broad range of sizes, incrementally larger discontinuities are incrementally more protective, with corresponding effects on mRNA stability. The graded impact of such obstacles suggests possible explanations for why their effect on scanning is not an all-or-none phenomenon dependent simply on whether the size of the resulting discontinuity exceeds the step length of RNase E.
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Affiliation(s)
- Jamie Richards
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA,Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Joel G Belasco
- To whom correspondence should be addressed. Tel: +1 212 263 5409;
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6
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Zhang J, Hess WR, Zhang C. "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria. MLIFE 2022; 1:21-39. [PMID: 38818322 PMCID: PMC10989914 DOI: 10.1002/mlf2.12015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 06/01/2024]
Abstract
RNA turnover plays critical roles in the regulation of gene expression and allows cells to respond rapidly to environmental changes. In bacteria, the mechanisms of RNA turnover have been extensively studied in the models Escherichia coli and Bacillus subtilis, but not much is known in other bacteria. Cyanobacteria are a diverse group of photosynthetic organisms that have great potential for the sustainable production of valuable products using CO2 and solar energy. A better understanding of the regulation of RNA decay is important for both basic and applied studies of cyanobacteria. Genomic analysis shows that cyanobacteria have more than 10 ribonucleases and related proteins in common with E. coli and B. subtilis, and only a limited number of them have been experimentally investigated. In this review, we summarize the current knowledge about these RNA-turnover-related proteins in cyanobacteria. Although many of them are biochemically similar to their counterparts in E. coli and B. subtilis, they appear to have distinct cellular functions, suggesting a different mechanism of RNA turnover regulation in cyanobacteria. The identification of new players involved in the regulation of RNA turnover and the elucidation of their biological functions are among the future challenges in this field.
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Affiliation(s)
- Ju‐Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Cheng‐Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
- Institut WUT‐AMUAix‐Marseille University and Wuhan University of TechnologyWuhanChina
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7
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Hui MP, Belasco JG. Multifaceted impact of a nucleoside monophosphate kinase on 5'-end-dependent mRNA degradation in bacteria. Nucleic Acids Res 2021; 49:11038-11049. [PMID: 34643703 PMCID: PMC8565310 DOI: 10.1093/nar/gkab884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/14/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Abstract
A key pathway for mRNA degradation in bacterial cells begins with conversion of the initial 5'-terminal triphosphate to a monophosphate, a modification that renders transcripts more vulnerable to attack by ribonucleases whose affinity for monophosphorylated 5' ends potentiates their catalytic efficacy. In Escherichia coli, the only proteins known to be important for controlling degradation via this pathway are the RNA pyrophosphohydrolase RppH, its heteromeric partner DapF, and the 5'-monophosphate-assisted endonucleases RNase E and RNase G. We have now identified the metabolic enzyme cytidylate kinase as another protein that affects rates of 5'-end-dependent mRNA degradation in E. coli. It does so by utilizing two distinct mechanisms to influence the 5'-terminal phosphorylation state of RNA, each dependent on the catalytic activity of cytidylate kinase and not its mere presence in cells. First, this enzyme acts in conjunction with DapF to stimulate the conversion of 5' triphosphates to monophosphates by RppH. In addition, it suppresses the direct synthesis of monophosphorylated transcripts that begin with cytidine by reducing the cellular concentration of cytidine monophosphate, thereby disfavoring the 5'-terminal incorporation of this nucleotide by RNA polymerase during transcription initiation. Together, these findings suggest dual signaling pathways by which nucleotide metabolism can impact mRNA degradation in bacteria.
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Affiliation(s)
- Monica P Hui
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.,Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Joel G Belasco
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.,Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
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8
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Substrate-dependent effects of quaternary structure on RNase E activity. Genes Dev 2021; 35:286-299. [PMID: 33446571 PMCID: PMC7849360 DOI: 10.1101/gad.335828.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/15/2020] [Indexed: 11/25/2022]
Abstract
RNase E is an essential, multifunctional ribonuclease encoded in E. coli by the rne gene. Structural analysis indicates that the ribonucleolytic activity of this enzyme is conferred by rne-encoded polypeptide chains that (1) dimerize to form a catalytic site at the protein-protein interface, and (2) multimerize further to generate a tetrameric quaternary structure consisting of two dimerized Rne-peptide chains. We identify here a mutation in the Rne protein's catalytic region (E429G), as well as a bacterial cell wall peptidoglycan hydrolase (Amidase C [AmiC]), that selectively affect the specific activity of the RNase E enzyme on long RNA substrates, but not on short synthetic oligonucleotides, by enhancing enzyme multimerization. Unlike the increase in specific activity that accompanies concentration-induced multimerization, enhanced multimerization associated with either the E429G mutation or interaction of the Rne protein with AmiC is independent of the substrate's 5' terminus phosphorylation state. Our findings reveal a previously unsuspected substrate length-dependent regulatory role for RNase E quaternary structure and identify cis-acting and trans-acting factors that mediate such regulation.
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Angel-Lerma LE, Merino E, Kwon O, Medina-Aparicio L, Hernández-Lucas I, Alvarez AF, Georgellis D. Protein dosage of the lldPRD operon is correlated with RNase E-dependent mRNA processing. J Bacteriol 2020; 203:JB.00555-20. [PMID: 33361194 PMCID: PMC8095457 DOI: 10.1128/jb.00555-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/16/2020] [Indexed: 11/20/2022] Open
Abstract
The ability of Escherichia coli to grow on L-lactate as a sole carbon source depends on the expression of the lldPRD operon. A striking feature of this operon is that the transcriptional regulator (LldR) encoding gene is located between the permease (LldP) and the dehydrogenase (LldD) encoding genes. In this study we report that dosage of the LldP, LldR, and LldD proteins is not modulated on the transcriptional level. Instead, modulation of protein dosage is primarily correlated with RNase E-dependent mRNA processing events that take place within the lldR mRNA, leading to the immediate inactivation of lldR, to differential segmental stabilities of the resulting cleavage products, and to differences in the translation efficiencies of the three cistrons. A model for the processing events controlling the molar quantities of the proteins in the lldPRD operon is presented and discussed.ImportanceAdjustment of gene expression is critical for proper cell function. For the case of polycistronic transcripts, posttranscriptional regulatory mechanisms can be used to fine-tune the expression of individual cistrons. Here, we elucidate how protein dosage of the Escherichia coli lldPRD operon, which presents the paradox of having the gene encoding a regulator protein located between genes that code for a permease and an enzyme, is regulated. Our results demonstrate that the key event in this regulatory mechanism involves the RNase E-dependent cleavage of the primary lldPRD transcript at internal site(s) located within the lldR cistron, resulting in a drastic decrease of intact lldR mRNA, to differential segmental stabilities of the resulting cleavage products, and to differences in the translation efficiencies of the three cistrons.
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Affiliation(s)
- Lidia E Angel-Lerma
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ohsuk Kwon
- Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, Republic of Korea; Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Liliana Medina-Aparicio
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ismael Hernández-Lucas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adrián F Alvarez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Dimitris Georgellis
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
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10
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Richards J, Belasco JG. Widespread Protection of RNA Cleavage Sites by a Riboswitch Aptamer that Folds as a Compact Obstacle to Scanning by RNase E. Mol Cell 2020; 81:127-138.e4. [PMID: 33212019 DOI: 10.1016/j.molcel.2020.10.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/26/2022]
Abstract
Riboswitches are thought generally to function by modulating transcription elongation or translation initiation. In rare instances, ligand binding to a riboswitch has been found to alter the rate of RNA degradation by directly stimulating or inhibiting nearby cleavage. Here, we show that guanidine-induced pseudoknot formation by the aptamer domain of a guanidine III riboswitch from Legionella pneumophila has a different effect, stabilizing mRNA by protecting distal cleavage sites en masse from ribonuclease attack. It does so by creating a coaxially base-paired obstacle that impedes scanning from a monophosphorylated 5' end to those sites by the regulatory endonuclease RNase E. Ligand binding by other riboswitch aptamers peripheral to the path traveled by RNase E does not inhibit distal cleavage. These findings reveal that a riboswitch aptamer can function independently of any overlapping expression platform to regulate gene expression by acting directly to prolong mRNA longevity in response to ligand binding.
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Affiliation(s)
- Jamie Richards
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Joel G Belasco
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA.
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11
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Yan H, Cheng Y, Wang L, Chen W. Function analysis of RNase E in the filamentous cyanobacterium Anabaena sp. PCC 7120. Res Microbiol 2020; 171:194-202. [PMID: 32590060 DOI: 10.1016/j.resmic.2020.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
RNase E is an endoribonuclease and plays a central role in RNA metabolism. Cyanobacteria, as ancient oxygen-producing photosynthetic bacteria, also contain RNase E homologues. Here, we introduced mutations into the S1 subdomain (F53A), the 5'-sensor subdomain (R160A), and the DNase I subdomain (D296A) according to the key activity sites of Escherichia coli RNase E. The results of degradation assays demonstrated that Asp296 is important to RNase E activity in Anabaena sp. PCC 7120 (hereafter PCC 7120). The docking model of RNase E in PCC 7120 (AnaRne) and RNA suggested a possible recognition mechanism of AnaRne to RNA. Moreover, overexpression of AnaRne and its N-terminal catalytic domain (AnaRneN) in vivo led to the abnormal cell division and inhibited the growth of PCC 7120. The quantitative analysis showed a significant decrease of ftsZ transcription in the case of overexpression of AnaRne or AnaRneN and ftsZ mRNA could be directly degraded by AnaRne through degradation assays in vitro, indicating that AnaRne was related to the expression of ftsZ and eventually affected cell division. In essence, our studies expand the understanding of the structural and functional evolutionary basis of RNase E and lay a foundation for further analysis of RNA metabolism in cyanobacteria.
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Affiliation(s)
- Huaduo Yan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yarui Cheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Li Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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12
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Both Enolase and the DEAD-Box RNA Helicase CrhB Can Form Complexes with RNase E in Anabaena sp. Strain PCC 7120. Appl Environ Microbiol 2020; 86:AEM.00425-20. [PMID: 32303553 DOI: 10.1128/aem.00425-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/14/2020] [Indexed: 11/20/2022] Open
Abstract
At present, little is known about the RNA metabolism driven by the RNA degradosome in cyanobacteria. RNA helicase and enolase are the common components of the RNA degradosome in many bacteria. Here, we provide evidence that both enolase and the DEAD-box RNA helicase CrhB can interact with RNase E in Anabaena (Nostoc) sp. strain PCC 7120 (referred to here as PCC 7120). Furthermore, we found that the C-terminal domains of CrhB and AnaEno (enolase of PCC 7120) are required for the interaction, respectively. Moreover, their recognition motifs for AnaRne (RNase E of PCC 7120) turned out to be located in the N-terminal catalytic domain, which is obviously different from those identified previously in Proteobacteria We also demonstrated in enzyme activity assays that CrhB can induce AnaRne to degrade double-stranded RNA with a 5' tail. Furthermore, we investigated the localization of CrhB and AnaRne by green fluorescent protein (GFP) translation fusion in situ and found that they both localized in the center of the PCC 7120 cytoplasm. This localization pattern is also different from the membrane binding of RNase E and RhlB in Escherichia coli Together with the previous identification of polynucleotide phosphorylase (PNPase) in PCC 7120, our results show that there is an RNA degradosome-like complex with a different assembly mechanism in cyanobacteria.IMPORTANCE In all domains of life, RNA turnover is important for gene regulation and quality control. The process of RNA metabolism is regulated by many RNA-processing enzymes and assistant proteins, where these proteins usually exist as complexes. However, there is little known about the RNA metabolism, as well as about the RNA degradation complex. In the present study, we described an RNA degradosome-like complex in cyanobacteria and revealed an assembly mechanism different from that of E. coli Moreover, CrhB could help RNase E in Anabaena sp. strain PCC 7120 degrade double-stranded RNA with a 5' tail. In addition, CrhB and AnaRne have similar cytoplasm localizations, in contrast to the membrane localization in E. coli.
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13
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Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
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Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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Richards J, Belasco JG. Obstacles to Scanning by RNase E Govern Bacterial mRNA Lifetimes by Hindering Access to Distal Cleavage Sites. Mol Cell 2019; 74:284-295.e5. [PMID: 30852060 DOI: 10.1016/j.molcel.2019.01.044] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/11/2018] [Accepted: 01/29/2019] [Indexed: 12/27/2022]
Abstract
The diversity of mRNA lifetimes in bacterial cells is difficult to reconcile with the relaxed cleavage site specificity of RNase E, the endonuclease most important for governing mRNA degradation. This enzyme has generally been thought to locate cleavage sites by searching freely in three dimensions. However, our results now show that its access to such sites in 5'-monophosphorylated RNA is hindered by obstacles-such as bound proteins or ribosomes or coaxial small RNA (sRNA) base pairing-that disrupt the path from the 5' end to those sites and prolong mRNA lifetimes. These findings suggest that RNase E searches for cleavage sites by scanning linearly from the 5'-terminal monophosphate along single-stranded regions of RNA and that its progress is impeded by structural discontinuities encountered along the way. This discovery has major implications for gene regulation in bacteria and suggests a general mechanism by which other prokaryotic and eukaryotic regulatory proteins can be controlled.
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Affiliation(s)
- Jamie Richards
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA.
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15
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Abstract
In this issue of Molecular Cell, Chao et al. (2017) investigate the important role of the low-specificity endonuclease RNase E in shaping the transcriptome of a bacterial pathogen by functioning as both a degradative enzyme and an RNA maturase.
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Affiliation(s)
- Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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16
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Luciano DJ, Vasilyev N, Richards J, Serganov A, Belasco JG. A Novel RNA Phosphorylation State Enables 5' End-Dependent Degradation in Escherichia coli. Mol Cell 2017; 67:44-54.e6. [PMID: 28673541 DOI: 10.1016/j.molcel.2017.05.035] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/10/2017] [Accepted: 05/26/2017] [Indexed: 01/08/2023]
Abstract
RNA modifications that once escaped detection are now thought to be pivotal for governing RNA lifetimes in both prokaryotes and eukaryotes. For example, converting the 5'-terminal triphosphate of bacterial transcripts to a monophosphate triggers 5' end-dependent degradation by RNase E. However, the existence of diphosphorylated RNA in bacteria has never been reported, and no biological role for such a modification has ever been proposed. By using a novel assay, we show here for representative Escherichia coli mRNAs that ~35%-50% of each transcript is diphosphorylated. The remainder is primarily monophosphorylated, with surprisingly little triphosphorylated RNA evident. Furthermore, diphosphorylated RNA is the preferred substrate of the RNA pyrophosphohydrolase RppH, whose biological function was previously assumed to be pyrophosphate removal from triphosphorylated transcripts. We conclude that triphosphate-to-monophosphate conversion to induce 5' end-dependent RNA degradation is a two-step process in E. coli involving γ-phosphate removal by an unidentified enzyme to enable subsequent β-phosphate removal by RppH.
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Affiliation(s)
- Daniel J Luciano
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Jamie Richards
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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17
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Abstract
This review provides a description of the known Escherichia coli ribonucleases (RNases), focusing on their structures, catalytic properties, genes, physiological roles, and possible regulation. Currently, eight E. coli exoribonucleases are known. These are RNases II, R, D, T, PH, BN, polynucleotide phosphorylase (PNPase), and oligoribonuclease (ORNase). Based on sequence analysis and catalytic properties, the eight exoribonucleases have been grouped into four families. These are the RNR family, including RNase II and RNase R; the DEDD family, including RNase D, RNase T, and ORNase; the RBN family, consisting of RNase BN; and the PDX family, including PNPase and RNase PH. Seven well-characterized endoribonucleases are known in E. coli. These are RNases I, III, P, E, G, HI, and HII. Homologues to most of these enzymes are also present in Salmonella. Most of the endoribonucleases cleave RNA in the presence of divalent cations, producing fragments with 3'-hydroxyl and 5'-phosphate termini. RNase H selectively hydrolyzes the RNA strand of RNA?DNA hybrids. Members of the RNase H family are widely distributed among prokaryotic and eukaryotic organisms in three distinct lineages, RNases HI, HII, and HIII. It is likely that E. coli contains additional endoribonucleases that have not yet been characterized. First of all, endonucleolytic activities are needed for certain known processes that cannot be attributed to any of the known enzymes. Second, homologues of known endoribonucleases are present in E. coli. Third, endonucleolytic activities have been observed in cell extracts that have different properties from known enzymes.
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18
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Kushwaha M, Salis HM. A portable expression resource for engineering cross-species genetic circuits and pathways. Nat Commun 2015; 6:7832. [PMID: 26184393 PMCID: PMC4518296 DOI: 10.1038/ncomms8832] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 06/16/2015] [Indexed: 12/24/2022] Open
Abstract
Genetic circuits and metabolic pathways can be reengineered to allow organisms to process signals and manufacture useful chemicals. However, their functions currently rely on organism-specific regulatory parts, fragmenting synthetic biology and metabolic engineering into host-specific domains. To unify efforts, here we have engineered a cross-species expression resource that enables circuits and pathways to reuse the same genetic parts, while functioning similarly across diverse organisms. Our engineered system combines mixed feedback control loops and cross-species translation signals to autonomously self-regulate expression of an orthogonal polymerase without host-specific promoters, achieving nontoxic and tuneable gene expression in diverse Gram-positive and Gram-negative bacteria. Combining 50 characterized system variants with mechanistic modelling, we show how the cross-species expression resource's dynamics, capacity and toxicity are controlled by the control loops' architecture and feedback strengths. We also demonstrate one application of the resource by reusing the same genetic parts to express a biosynthesis pathway in both model and non-model hosts. Organism-specific genetic parts are often used to express circuits and pathways, limiting their portability. Here the authors engineer a cross-species expression resource, without using host-specific parts, to control protein and pathway expression in non-model bacteria.
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Affiliation(s)
- Manish Kushwaha
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Howard M Salis
- 1] Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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19
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TheCorynebacterium glutamicumNCgl2281 Gene Encoding an RNase E/G Family Endoribonuclease Can Complement theEscherichia coli rng::catMutation but Not therne-1Mutation. Biosci Biotechnol Biochem 2014; 73:2281-6. [DOI: 10.1271/bbb.90371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Kim D, Song S, Lee M, Go H, Shin E, Yeom JH, Ha NC, Lee K, Kim YH. Modulation of RNase E activity by alternative RNA binding sites. PLoS One 2014; 9:e90610. [PMID: 24598695 PMCID: PMC3944109 DOI: 10.1371/journal.pone.0090610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/02/2014] [Indexed: 12/18/2022] Open
Abstract
Endoribonuclease E (RNase E) affects the composition and balance of the RNA population in Escherichia coli via degradation and processing of RNAs. In this study, we investigated the regulatory effects of an RNA binding site between amino acid residues 25 and 36 (24LYDLDIESPGHEQK37) of RNase E. Tandem mass spectrometry analysis of the N-terminal catalytic domain of RNase E (N-Rne) that was UV crosslinked with a 5′-32P-end-labeled, 13-nt oligoribonucleotide (p-BR13) containing the RNase E cleavage site of RNA I revealed that two amino acid residues, Y25 and Q36, were bound to the cytosine and adenine of BR13, respectively. Based on these results, the Y25A N-Rne mutant was constructed, and was found to be hypoactive in comparison to wild-type and hyperactive Q36R mutant proteins. Mass spectrometry analysis showed that Y25A and Q36R mutations abolished the RNA binding to the uncompetitive inhibition site of RNase E. The Y25A mutation increased the RNA binding to the multimer formation interface between amino acid residues 427 and 433 (427LIEEEALK433), whereas the Q36R mutation enhanced the RNA binding to the catalytic site of the enzyme (65HGFLPL*K71). Electrophoretic mobility shift assays showed that the stable RNA-protein complex formation was positively correlated with the extent of RNA binding to the catalytic site and ribonucleolytic activity of the N-Rne proteins. These mutations exerted similar effects on the ribonucleolytic activity of the full-length RNase E in vivo. Our findings indicate that RNase E has two alternative RNA binding sites for modulating RNA binding to the catalytic site and the formation of a functional catalytic unit.
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Affiliation(s)
- Daeyoung Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Saemee Song
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hayoung Go
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Eunkyoung Shin
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Nam-Chul Ha
- Department of Manufacturing Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
- * E-mail: (KL); (Y-HK)
| | - Yong-Hak Kim
- Department of Microbiology, Catholic University of Daegu School of Medicine, Daegu, Republic of Korea
- * E-mail: (KL); (Y-HK)
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21
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Initiation of mRNA decay in bacteria. Cell Mol Life Sci 2013; 71:1799-828. [PMID: 24064983 PMCID: PMC3997798 DOI: 10.1007/s00018-013-1472-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 09/01/2013] [Accepted: 09/03/2013] [Indexed: 12/24/2022]
Abstract
The instability of messenger RNA is fundamental to the control of gene expression. In bacteria, mRNA degradation generally follows an "all-or-none" pattern. This implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. Studies of E. coli and B. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. The early view that mRNA decay in these two model organisms is radically different has given way to new models that can be resumed by "different enzymes-similar strategies". The recent characterization of key ribonucleases sheds light on an impressive case of convergent evolution that illustrates that the surprisingly similar functions of these totally unrelated enzymes are of general importance to RNA metabolism in bacteria. We now know that the major mRNA decay pathways initiate with an endonucleolytic cleavage in E. coli and B. subtilis and probably in many of the currently known bacteria for which these organisms are considered representative. We will discuss here the different pathways of eubacterial mRNA decay, describe the major players and summarize the events that can precede and/or favor nucleolytic inactivation of a mRNA, notably the role of the 5' end and translation initiation. Finally, we will discuss the role of subcellular compartmentalization of transcription, translation, and the RNA degradation machinery.
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22
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An advanced monitoring platform for rational design of recombinant processes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012. [PMID: 23207722 DOI: 10.1007/10_2012_169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Bioprocess engineering is an application-oriented science in an interdisciplinary environment, and a meaningful combination of different scientific disciplines is the only way to meet the challenges of bioprocess complexity. Setting up a reasoned process monitoring platform is the first step in an iterative procedure aiming at process and systems understanding, being the key to rational and innovative bioprocess design. This chapter describes a comprehensive process monitoring platform and how the resulting knowledge is translated into new strategies in process and/or host cell design.
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23
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Maeda T, Wachi M. 3' Untranslated region-dependent degradation of the aceA mRNA, encoding the glyoxylate cycle enzyme isocitrate lyase, by RNase E/G in Corynebacterium glutamicum. Appl Environ Microbiol 2012; 78:8753-61. [PMID: 23042181 PMCID: PMC3502937 DOI: 10.1128/aem.02304-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 10/02/2012] [Indexed: 11/20/2022] Open
Abstract
We previously reported that the Corynebacterium glutamicum RNase E/G encoded by the rneG gene (NCgl2281) is required for the 5' maturation of 5S rRNA. In the search for the intracellular target RNAs of RNase E/G other than the 5S rRNA precursor, we detected that the amount of isocitrate lyase, an enzyme of the glyoxylate cycle, increased in rneG knockout mutant cells grown on sodium acetate as the sole carbon source. Rifampin chase experiments showed that the half-life of the aceA mRNA was about 4 times longer in the rneG knockout mutant than in the wild type. Quantitative real-time PCR analysis also confirmed that the level of aceA mRNA was approximately 3-fold higher in the rneG knockout mutant strain than in the wild type. Such differences were not observed in other mRNAs encoding enzymes involved in acetate metabolism. Analysis by 3' rapid amplification of cDNA ends suggested that RNase E/G cleaves the aceA mRNA at a single-stranded AU-rich region in the 3' untranslated region (3'-UTR). The lacZ fusion assay showed that the 3'-UTR rendered lacZ mRNA RNase E/G dependent. These findings indicate that RNase E/G is a novel regulator of the glyoxylate cycle in C. glutamicum.
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Affiliation(s)
- Tomoya Maeda
- Department of Bioengineering, Tokyo Institute of Technology, Yokohama, Japan
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24
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Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity. Proc Natl Acad Sci U S A 2012; 109:7019-24. [PMID: 22509045 DOI: 10.1073/pnas.1120181109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNase E plays an essential role in RNA processing and decay and tethers to the cytoplasmic membrane in Escherichia coli; however, the function of this membrane-protein interaction has remained unclear. Here, we establish a mechanistic role for the RNase E-membrane interaction. The reconstituted highly conserved N-terminal fragment of RNase E (NRne, residues 1-499) binds specifically to anionic phospholipids through electrostatic interactions. The membrane-binding specificity of NRne was confirmed using circular dichroism difference spectroscopy; the dissociation constant (K(d)) for NRne binding to anionic liposomes was 298 nM. E. coli RNase G and RNase E/G homologs from phylogenetically distant Aquifex aeolicus, Haemophilus influenzae Rd, and Synechocystis sp. were found to be membrane-binding proteins. Electrostatic potentials of NRne and its homologs were found to be conserved, highly positive, and spread over a large surface area encompassing four putative membrane-binding regions identified in the "large" domain (amino acids 1-400, consisting of the RNase H, S1, 5'-sensor, and DNase I subdomains) of E. coli NRne. In vitro cleavage assay using liposome-free and liposome-bound NRne and RNA substrates BR13 and GGG-RNAI showed that NRne membrane binding altered its enzymatic activity. Circular dichroism spectroscopy showed no obvious thermotropic structural changes in membrane-bound NRne between 10 and 60 °C, and membrane-bound NRne retained its normal cleavage activity after cooling. Thus, NRne membrane binding induced changes in secondary protein structure and enzymatic activation by stabilizing the protein-folding state and increasing its binding affinity for its substrate. Our results demonstrate that RNase E-membrane interaction enhances the rate of RNA processing and decay.
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25
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From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome. Q Rev Biophys 2011; 45:105-45. [DOI: 10.1017/s003358351100014x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AbstractThe RNA degradosome is a massive multi-enzyme assembly that occupies a nexus in RNA metabolism and post-transcriptional control of gene expression inEscherichia coliand many other bacteria. Powering RNA turnover and quality control, the degradosome serves also as a machine for processing structured RNA precursors during their maturation. The capacity to switch between destructive and processing modes involves cooperation between degradosome components and is analogous to the process of RNA surveillance in other domains of life. Recruitment of components and cellular compartmentalisation of the degradosome are mediated through small recognition domains that punctuate a natively unstructured segment within a scaffolding core. Dynamic in conformation, variable in composition and non-essential under certain laboratory conditions, the degradosome has nonetheless been maintained throughout the evolution of many bacterial species, due most likely to its diverse contributions in global cellular regulation. We describe the role of the degradosome and its components in RNA decay pathways inE. coli, and we broadly compare these pathways in other bacteria as well as archaea and eukaryotes. We discuss the modular architecture and molecular evolution of the degradosome, its roles in RNA degradation, processing and quality control surveillance, and how its activity is regulated by non-coding RNA. Parallels are drawn with analogous machinery in organisms from all life domains. Finally, we conjecture on roles of the degradosome as a regulatory hub for complex cellular processes.
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26
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Laalami S, Putzer H. mRNA degradation and maturation in prokaryotes: the global players. Biomol Concepts 2011; 2:491-506. [DOI: 10.1515/bmc.2011.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/26/2011] [Indexed: 11/15/2022] Open
Abstract
AbstractThe degradation of messenger RNA is of universal importance for controlling gene expression. It directly affects protein synthesis by modulating the amount of mRNA available for translation. Regulation of mRNA decay provides an efficient means to produce just the proteins needed and to rapidly alter patterns of protein synthesis. In bacteria, the half-lives of individual mRNAs can differ by as much as two orders of magnitude, ranging from seconds to an hour. Most of what we know today about the diverse mechanisms of mRNA decay and maturation in prokaryotes comes from studies of the two model organisms Escherichia coli and Bacillus subtilis. Their evolutionary distance provided a large picture of potential pathways and enzymes involved in mRNA turnover. Among them are three ribonucleases, two of which have been discovered only recently, which have a truly general role in the initiating events of mRNA degradation: RNase E, RNase J and RNase Y. Their enzymatic characteristics probably determine the strategies of mRNA metabolism in the organism in which they are present. These ribonucleases are coded, alone or in various combinations, in all prokaryotic genomes, thus reflecting how mRNA turnover has been adapted to different ecological niches throughout evolution.
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Affiliation(s)
- Soumaya Laalami
- CNRS UPR 9073, affiliated with Univ Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Harald Putzer
- CNRS UPR 9073, affiliated with Univ Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France
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27
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Maeda T, Wachi M. Corynebacterium glutamicum RNase E/G-type endoribonuclease encoded by NCgl2281 is involved in the 5′ maturation of 5S rRNA. Arch Microbiol 2011; 194:65-73. [DOI: 10.1007/s00203-011-0728-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/06/2011] [Accepted: 06/14/2011] [Indexed: 11/25/2022]
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28
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Lee M, Yeom JH, Jeon CO, Lee K. Studies on a Vibrio vulnificus functional ortholog of Escherichia coli RNase E imply a conserved function of RNase E-like enzymes in bacteria. Curr Microbiol 2010; 62:861-5. [PMID: 21046401 DOI: 10.1007/s00284-010-9771-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 09/14/2010] [Indexed: 10/18/2022]
Abstract
RNase E (Rne) plays a key role in the processing and degradation of RNA in Escherichia coli. In the genome of Vibrio vulnificus, one open reading frame potentially encodes a protein homologous to E. coli RNase E, designated RNase EV, which N-terminal (1-500 amino acids) has 86.4% amino acid identity to the N-terminal catalytic part of RNase E (N-Rne). Here, we report that both the full-length and the N-terminal part of RNase EV (N-RneV) functionally complement E. coli RNase E and their expression consequently supports normal growth of RNase E-depleted E. coli cells. E. coli cells expressing N-RneV showed copy numbers of ColE1-type plasmid similar to that of E. coli cells expressing N-Rne, indicating in vivo ribonucleolytic activity of N-RneV on RNA I, an antisense regulator of ColE1-type plasmid replication. In vitro cleavage assays further showed that N-RneV has cleavage activity and specificity of RNase E on RNase E-targeted sequence of RNA I (BR13). Our findings suggest that RNase E-like proteins have conserved enzymatic properties that determine substrate specificity across species.
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Affiliation(s)
- Minho Lee
- Department of Life Science, Chung-Ang University, 221 Hueksok-Dong, Dongjak-Gu, Seoul, 156-756, Republic of Korea
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29
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Kime L, Jourdan SS, Stead JA, Hidalgo-Sastre A, McDowall KJ. Rapid cleavage of RNA by RNase E in the absence of 5' monophosphate stimulation. Mol Microbiol 2010; 76:590-604. [PMID: 19889093 PMCID: PMC2948425 DOI: 10.1111/j.1365-2958.2009.06935.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2009] [Indexed: 11/28/2022]
Abstract
The best characterized pathway for the initiation of mRNA degradation in Escherichia coli involves the removal of the 5'-terminal pyrophosphate to generate a monophosphate group that stimulates endonucleolytic cleavage by RNase E. We show here however, using well-characterized oligonucleotide substrates and mRNA transcripts, that RNase E can cleave certain RNAs rapidly without requiring a 5'-monophosphorylated end. Moreover, the minimum substrate requirement for this mode of cleavage, which can be categorized as 'direct' or 'internal' entry, appears to be multiple single-stranded segments in a conformational context that allows their simultaneous interaction with RNase E. While previous work has alluded to the existence of a 5' end-independent mechanism of mRNA degradation, the relative simplicity of the requirements identified here for direct entry suggests that it could represent a major means by which mRNA degradation is initiated in E. coli and other organisms that contain homologues of RNase E. Our results have implications for the interplay of translation and mRNA degradation and models of gene regulation by small non-coding RNAs.
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Affiliation(s)
| | | | - Jonathan A Stead
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLS2 9JT, England, UK
| | - Ana Hidalgo-Sastre
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLS2 9JT, England, UK
| | - Kenneth J McDowall
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLS2 9JT, England, UK
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30
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Jourdan SS, Kime L, McDowall KJ. The sequence of sites recognised by a member of the RNase E/G family can control the maximal rate of cleavage, while a 5'-monophosphorylated end appears to function cooperatively in mediating RNA binding. Biochem Biophys Res Commun 2009; 391:879-83. [PMID: 19945430 DOI: 10.1016/j.bbrc.2009.11.156] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 11/21/2009] [Indexed: 11/16/2022]
Abstract
Members of the RNase E/G family are multimeric, 5'-end-sensing, single-strand-specific endoribonucleases that are found in chloroplasts as well as bacteria, and have central roles in RNA processing and degradation. A well-studied member of this family is Escherichia coli RNase G. Recently, we have shown that the interaction of this enzyme with a 5'-monophosphorylated end can enhance substrate binding in vitro and the decay of mRNA in vivo. We show here that a single-stranded site despite not being sufficient for rapid cleavage makes a substantial contribution to the binding of RNase G. Moreover, we find that the sequence of a site bound by RNase G can moderate the maximal rate by at least an order of magnitude. This supports a model for the RNase E/G family in which a single-stranded segment(s) can cooperate in the binding of enzyme that subsequently cleaves preferentially at another site. We also provide evidence that in order to promote cleavage a 5'-monophosphorylated end needs to be linked physically to a single-stranded site, indicating that it functions cooperatively. Our results are discussed in terms of recent X-ray crystal structures and models for the initiation of bacterial mRNA degradation.
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Affiliation(s)
- Stefanie Simone Jourdan
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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31
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Regulation of ribonuclease E activity by the L4 ribosomal protein of Escherichia coli. Proc Natl Acad Sci U S A 2009; 106:864-9. [PMID: 19144914 DOI: 10.1073/pnas.0810205106] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whereas ribosomal proteins (r-proteins) are known primarily as components of the translational machinery, certain of these r-proteins have been found to also have extraribosomal functions. Here we report the novel ability of an r-protein, L4, to regulate RNA degradation in Escherichia coli. We show by affinity purification, immunoprecipitation analysis, and E. coli two-hybrid screening that L4 interacts with a site outside of the catalytic domain of RNase E to regulate the endoribonucleolytic functions of the enzyme, thus inhibiting RNase E-specific cleavage in vitro, stabilizing mRNAs targeted by RNase E in vivo, and controlling plasmid DNA replication by stabilizing an antisense regulatory RNA normally attacked by RNase E. Broader effects of the L4-RNase E interaction on E. coli transcripts were shown by DNA microarray analysis, which revealed changes in the abundance of 65 mRNAs encoding the stress response proteins HslO, Lon, CstA, YjiY, and YaeL, as well as proteins involved in carbohydrate and amino acid metabolism and transport, transcription/translation, and DNA/RNA synthesis. Analysis of mRNA stability showed that the half lives of stress-responsive transcripts were increased by ectopic expression of L4, which normally increases along with other r-proteins in E. coli under stress conditions, and also by inactivation of RNase E. Our finding that L4 can inhibit RNase E-dependent decay may account at least in part for the elevated production of stress-induced proteins during bacterial adaptation to adverse environments.
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Carpousis AJ, Luisi BF, McDowall KJ. Endonucleolytic initiation of mRNA decay in Escherichia coli. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:91-135. [PMID: 19215771 DOI: 10.1016/s0079-6603(08)00803-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Instability is a fundamental property of mRNA that is necessary for the regulation of gene expression. In E. coli, the turnover of mRNA involves multiple, redundant pathways involving 3'-exoribonucleases, endoribonucleases, and a variety of other enzymes that modify RNA covalently or affect its conformation. Endoribonucleases are thought to initiate or accelerate the process of mRNA degradation. A major endoribonuclease in this process is RNase E, which is a key component of the degradative machinery amongst the Proteobacteria. RNase E is the central element in a multienzyme complex known as the RNA degradosome. Structural and functional data are converging on models for the mechanism of activation and regulation of RNase E and its paralog, RNase G. Here, we discuss current models for mRNA degradation in E. coli and we present current thinking on the structure and function of RNase E based on recent crystal structures of its catalytic core.
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Affiliation(s)
- Agamemnon J Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS et Université Paul Sabatier, 31062 Toulouse, France
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Uzan M. RNA processing and decay in bacteriophage T4. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:43-89. [PMID: 19215770 DOI: 10.1016/s0079-6603(08)00802-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteriophage T4 is the archetype of virulent phage. It has evolved very efficient strategies to subvert host functions to its benefit and to impose the expression of its genome. T4 utilizes a combination of host and phage-encoded RNases and factors to degrade its mRNAs in a stage-dependent manner. The host endonuclease RNase E is used throughout the phage development. The sequence-specific, T4-encoded RegB endoribonuclease functions in association with the ribosomal protein S1 to functionally inactivate early transcripts and expedite their degradation. T4 polynucleotide kinase plays a role in this process. Later, the viral factor Dmd protects middle and late mRNAs from degradation by the host RNase LS. T4 codes for a set of eight tRNAs and two small, stable RNA of unknown function that may contribute to phage virulence. Their maturation is assured by host enzymes, but one phage factor, Cef, is required for the biogenesis of some of them. The tRNA gene cluster also codes for a homing DNA endonuclease, SegB, responsible for spreading the tRNA genes to other T4-related phage.
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Affiliation(s)
- Marc Uzan
- Institut Jacques Monod, CNRS-Universites Paris, Paris, France
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34
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Identification of amino acid residues in the catalytic domain of RNase E essential for survival of Escherichia coli: functional analysis of DNase I subdomain. Genetics 2008; 179:1871-9. [PMID: 18660536 DOI: 10.1534/genetics.108.088492] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNase E is an essential Escherichia coli endoribonuclease that plays a major role in the decay and processing of a large fraction of RNAs in the cell. To better understand the molecular mechanisms of RNase E action, we performed a genetic screen for amino acid substitutions in the catalytic domain of the protein (N-Rne) that knock down the ability of RNase E to support survival of E. coli. Comparative phylogenetic analysis of RNase E homologs shows that wild-type residues at these mutated positions are nearly invariably conserved. Cells conditionally expressing these N-Rne mutants in the absence of wild-type RNase E show a decrease in copy number of plasmids regulated by the RNase E substrate RNA I, and accumulation of 5S ribosomal RNA, M1 RNA, and tRNA(Asn) precursors, as has been found in Rne-depleted cells, suggesting that the inability of these mutants to support cellular growth results from loss of ribonucleolytic activity. Purified mutant proteins containing an amino acid substitution in the DNase I subdomain, which is spatially distant from the catalytic site posited from crystallographic studies, showed defective binding to an RNase E substrate, p23 RNA, but still retained RNA cleavage activity-implicating a previously unidentified structural motif in the DNase I subdomain in the binding of RNase E to targeted RNA molecules, demonstrating the role of the DNase I domain in RNase E activity.
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35
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Horie Y, Ito Y, Ono M, Moriwaki N, Kato H, Hamakubo Y, Amano T, Wachi M, Shirai M, Asayama M. Dark-induced mRNA instability involves RNase E/G-type endoribonuclease cleavage at the AU-box and SD sequences in cyanobacteria. Mol Genet Genomics 2007; 278:331-46. [PMID: 17661085 DOI: 10.1007/s00438-007-0254-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 05/21/2007] [Indexed: 11/29/2022]
Abstract
Light-responsive gene expression is crucial to photosynthesizing organisms. Here, we studied functions of cis-elements (AU-box and SD sequences) and a trans-acting factor (ribonuclease, RNase) in light-responsive expression in cyanobacteria. The results indicated that AU-rich nucleotides with an AU-box, UAAAUAAA, just upstream from an SD confer instability on the mRNA under darkness. An RNase E/G homologue, Slr1129, of the cyanobacterium Synechocystis sp. strain PCC 6803 was purified and confirmed capable of endoribonucleolytic cleavage at the AU- (or AG)-rich sequences in vitro. The cleavage depends on the primary target sequence and secondary structure of the mRNA. Complementation tests using Escherichia coli rne/rng mutants showed that Slr1129 fulfilled the functions of both the RNase E and RNase G. An analysis of systematic mutations in the AU-box and SD sequences showed that the cis-elements also affect significantly mRNA stability in light-responsive genes. These results strongly suggested that dark-induced mRNA instability involves RNase E/G-type cleavage at the AU-box and SD sequences in cyanobacteria. The mechanical impact and a possible common mechanism with RNases for light-responsive gene expression are discussed.
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Affiliation(s)
- Yoshinao Horie
- Laboratory of Molecular Genetics, School of Agriculture, Ibaraki University, Ami, Inashiki, Ibaraki 300-0393, Japan
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36
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Zeller ME, Csanadi A, Miczak A, Rose T, Bizebard T, Kaberdin V. Quaternary structure and biochemical properties of mycobacterial RNase E/G. Biochem J 2007; 403:207-15. [PMID: 17201693 PMCID: PMC1828891 DOI: 10.1042/bj20061530] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The RNase E/G family of endoribonucleases plays the central role in numerous post-transcriptional mechanisms in Escherichia coli and, presumably, in other bacteria, including human pathogens. To learn more about specific properties of RNase E/G homologues from pathogenic Gram-positive bacteria, a polypeptide comprising the catalytic domain of Mycobacterium tuberculosis RNase E/G (MycRne) was purified and characterized in vitro. In the present study, we show that affinity-purified MycRne has a propensity to form dimers and tetramers in solution and possesses an endoribonucleolytic activity, which is dependent on the 5'-phosphorylation status of RNA. Our data also indicate that the cleavage specificities of the M. tuberculosis RNase E/G homologue and its E. coli counterpart are only moderately overlapping, and reveal a number of sequence determinants within MycRne cleavage sites that differentially affect the efficiency of cleavage. Finally, we demonstrate that, similar to E. coli RNase E, MycRne is able to cleave in an intercistronic region of the putative 9S precursor of 5S rRNA, thus suggesting a common function for RNase E/G homologues in rRNA processing.
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Affiliation(s)
- Mirijam-Elisabeth Zeller
- *Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr. Bohrgasse 9/4, A-1030 Vienna, Austria
| | - Agnes Csanadi
- *Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr. Bohrgasse 9/4, A-1030 Vienna, Austria
- †Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary
| | - Andras Miczak
- †Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary
| | - Thierry Rose
- ‡Unité d'Immunogénétique Cellulaire, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Thierry Bizebard
- §Institut de Biologie Physico-chimique, UPR CNRS 9073, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Vladimir R. Kaberdin
- *Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr. Bohrgasse 9/4, A-1030 Vienna, Austria
- To whom correspondence should be addressed (email )
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Sakai T, Nakamura N, Umitsuki G, Nagai K, Wachi M. Increased production of pyruvic acid by Escherichia coli RNase G mutants in combination with cra mutations. Appl Microbiol Biotechnol 2007; 76:183-92. [PMID: 17483940 DOI: 10.1007/s00253-007-1006-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 04/13/2007] [Accepted: 04/15/2007] [Indexed: 12/01/2022]
Abstract
The Escherichia coli RNase G is known as an endoribonuclease responsible for the 5'-end maturation of 16S rRNA and degradation of several specific mRNAs such as adhE and eno mRNAs. In this study, we found that an RNase G mutant derived from the MC1061 strain did not grow on a glucose minimal medium. Genetic analysis revealed that simultaneous defects of cra and ilvIH, encoding a transcriptional regulator of glycolysis/gluconeogenesis and one of isozymes of acetohydroxy acid synthase, respectively, were required for this phenomenon to occur. The results of additional experiments presented here indicate that the RNase G mutation, in combination with cra mutation, caused the increased production of pyruvic acid from glucose, which was then preferentially converted to valine due to the ilvIH mutation, resulting in depletion of isoleucine. In fact, the rng cra double mutant produced increased amount of pyruvate in the medium. These results suggest that the RNase G mutation could be applied in the breeding of producer strains of pyruvate and its derivatives such as valine.
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Affiliation(s)
- Taro Sakai
- Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
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38
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Abstract
This chapter discusses several topics relating to the mechanisms of mRNA decay. These topics include the following: important physical properties of mRNA molecules that can alter their stability; methods for determining mRNA half-lives; the genetics and biochemistry of proteins and enzymes involved in mRNA decay; posttranscriptional modification of mRNAs; the cellular location of the mRNA decay apparatus; regulation of mRNA decay; the relationships among mRNA decay, tRNA maturation, and ribosomal RNA processing; and biochemical models for mRNA decay. Escherichia coli has multiple pathways for ensuring the effective decay of mRNAs and mRNA decay is closely linked to the cell's overall RNA metabolism. Finally, the chapter highlights important unanswered questions regarding both the mechanism and importance of mRNA decay.
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39
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Abstract
Studies in pro- and eukaryotes have revealed that translation can determine the stability of a given messenger RNA. In bacteria, intrinsic mRNA signals can confer efficient ribosome binding, whereas translational feedback inhibition or environmental cues can interfere with this process. Such regulatory mechanisms are often controlled by RNA-binding proteins, small noncoding RNAs and structural rearrangements within the 5' untranslated region. Here, we review molecular events occurring in the 5' untranslated region of primarily Escherichia coli mRNAs with regard to their effects on mRNA stability.
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Affiliation(s)
- Vladimir R Kaberdin
- Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at Vienna Biocenter, Vienna, Austria.
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40
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Truncaite L, Zajanckauskaite A, Arlauskas A, Nivinskas R. Transcription and RNA processing during expression of genes preceding DNA ligase gene 30 in T4-related bacteriophages. Virology 2006; 344:378-90. [PMID: 16225899 DOI: 10.1016/j.virol.2005.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/01/2005] [Accepted: 09/02/2005] [Indexed: 10/25/2022]
Abstract
Early gene expression in bacteriophage T4 is controlled primarily by the unique early promoters, while T4-encoded RegB endoribonuclease promotes degradation of many early messages contributing to the rapid shift of gene expression from the early to middle stages. The regulatory region for the genes clustered upstream of DNA ligase gene 30 of T4 was known to carry two strong early promoters and two putative RegB sites. Here, we present the comparative analysis of the regulatory events in this region of 16 T4-type bacteriophages. The regulatory elements for control of this gene cluster, such as rho-independent terminator, at least one early promoter, the sequence for stem-loop structure, and the RegB cleavage sites have been found to be conserved in the phages studied. Also, we present experimental evidence that the initial cleavage by RegB of phages TuIa and RB69 enables degradation of early phage mRNAs by the major Escherichia coli endoribonuclease, RNase E.
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Affiliation(s)
- Lidija Truncaite
- Department of Gene Engineering, Institute of Biochemistry, Mokslininku 12, 08662 Vilnius, Lithuania
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41
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De Gregorio E, Silvestro G, Petrillo M, Carlomagno MS, Di Nocera PP. Enterobacterial repetitive intergenic consensus sequence repeats in yersiniae: genomic organization and functional properties. J Bacteriol 2005; 187:7945-54. [PMID: 16291667 PMCID: PMC1291288 DOI: 10.1128/jb.187.23.7945-7954.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome-wide analyses carried out in silico revealed that the DNA repeats called enterobacterial repetitive intergenic consensus sequences (ERICs), which are present in several Enterobacteriaceae, are overrepresented in yersiniae. From the alignment of DNA regions from the wholly sequenced Yersinia enterocolitica 8081 and Yersinia pestis CO92 strains, we could establish that ERICs are miniature mobile elements whose insertion leads to duplication of the dinucleotide TA. ERICs feature long terminal inverted repeats (TIRs) and can fold as RNA into hairpin structures. The proximity to coding regions suggests that most Y. enterocolitica ERICs are cotranscribed with flanking genes. Elements which either overlap or are located next to stop codons are preferentially inserted in the same (or B) orientation. In contrast, ERICs located far apart from open reading frames are inserted in the opposite (or A) orientation. The expression of genes cotranscribed with A- and B-oriented ERICs has been monitored in vivo. In mRNAs spanning B-oriented ERICs, upstream gene transcripts accumulated at lower levels than downstream gene transcripts. This difference was abolished by treating cells with chloramphenicol. We hypothesize that folding of B-oriented elements is impeded by translating ribosomes. Consequently, upstream RNA degradation is triggered by the unmasking of a site for the RNase E located in the right-hand TIR of ERIC. A-oriented ERICs may act in contrast as upstream RNA stabilizers or may have other functions. The hypothesis that ERICs act as regulatory RNA elements is supported by analyses carried out in Yersinia strains which either lack ERIC sequences or carry alternatively oriented ERICs at specific loci.
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Affiliation(s)
- Eliana De Gregorio
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Facoltà di Medicina, Università Federico II, Napoli, Italy
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42
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Briegel KJ, Baker A, Jain C. Identification and analysis of Escherichia coli ribonuclease E dominant-negative mutants. Genetics 2005; 172:7-15. [PMID: 16204212 PMCID: PMC1456196 DOI: 10.1534/genetics.105.048553] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Escherichia coli (E. coli) ribonuclease E protein (RNase E) is implicated in the degradation and processing of a large fraction of RNAs in the cell. To understand RNase E function in greater detail, we developed an efficient selection method for identifying nonfunctional RNase E mutants. A subset of the mutants was found to display a dominant-negative phenotype, interfering with wild-type RNase E function. Unexpectedly, each of these mutants contained a large truncation within the carboxy terminus of RNase E. In contrast, no point mutants that conferred a dominant-negative phenotype were found. We show that a representative dominant-negative mutant can form mixed multimers with RNase E and propose a model to explain how these mutants can block wild-type RNase E function in vivo.
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Affiliation(s)
- Karoline J Briegel
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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43
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Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 2005; 437:1187-91. [PMID: 16237448 DOI: 10.1038/nature04084] [Citation(s) in RCA: 234] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Accepted: 07/26/2005] [Indexed: 11/08/2022]
Abstract
The coordinated regulation of gene expression is required for homeostasis, growth and development in all organisms. Such coordination may be partly achieved at the level of messenger RNA stability, in which the targeted destruction of subsets of transcripts generates the potential for cross-regulating metabolic pathways. In Escherichia coli, the balance and composition of the transcript population is affected by RNase E, an essential endoribonuclease that not only turns over RNA but also processes certain key RNA precursors. RNase E cleaves RNA internally, but its catalytic power is determined by the 5' terminus of the substrate, even if this lies at a distance from the cutting site. Here we report crystal structures of the catalytic domain of RNase E as trapped allosteric intermediates with RNA substrates. Four subunits of RNase E catalytic domain associate into an interwoven quaternary structure, explaining why the subunit organization is required for catalytic activity. The subdomain encompassing the active site is structurally congruent to a deoxyribonuclease, making an unexpected link in the evolutionary history of RNA and DNA nucleases. The structure explains how the recognition of the 5' terminus of the substrate may trigger catalysis and also sheds light on the question of how RNase E might selectively process, rather than destroy, specific RNA precursors.
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Affiliation(s)
- Anastasia J Callaghan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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44
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Niemitalo O, Neubauer A, Liebal U, Myllyharju J, Juffer AH, Neubauer P. Modelling of translation of human protein disulfide isomerase in Escherichia coli—A case study of gene optimisation. J Biotechnol 2005; 120:11-24. [PMID: 16111781 DOI: 10.1016/j.jbiotec.2005.05.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 04/21/2005] [Accepted: 05/04/2005] [Indexed: 11/30/2022]
Abstract
Recombinant human protein disulfide isomerase (PDI) was expressed in vivo in Escherichia coli using a non-optimised gene sequence and an optimised sequence with four 5' codons substituted by synonymous codons that take less time to translate. The optimisation resulted in a 2-fold increase of total PDI concentration and by successive optimisation with expression at low temperature in a 10-fold increase of the amount of soluble PDI in comparison with the original wild-type construct. The improvement can be due to a faster clearing of the ribosome binding site on the mRNA, elevating the translation initiation rate and resulting in higher ribosome loading and better ribosome protection of the PDI mRNA against endonucleolytic cleavage by RNase. This hypothesis was supported by a novel computer simulation model of E. coli translational ribosome traffic based upon the stochastic Gillespie algorithm. The study indicates the applicability of such models in optimisation of recombinant protein sequences.
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Affiliation(s)
- Olli Niemitalo
- Bioprocess Engineering Laboratory, Department of Process and Environmental Engineering, University of Oulu, Oulu, Finland
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45
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Komarova AV, Tchufistova LS, Dreyfus M, Boni IV. AU-rich sequences within 5' untranslated leaders enhance translation and stabilize mRNA in Escherichia coli. J Bacteriol 2005; 187:1344-9. [PMID: 15687198 PMCID: PMC545611 DOI: 10.1128/jb.187.4.1344-1349.2005] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Accepted: 11/05/2004] [Indexed: 11/20/2022] Open
Abstract
We have shown previously that when the Escherichia coli chromosomal lacZ gene is put under the control of an extended Shine-Dalgarno (SD) sequence (10 or 6 nucleotides in length), the translation efficiency can be highly variable, depending on the presence of AU-rich targets for ribosomal protein S1 in the mRNA leader. Here, the same strains have been used to examine the question of how strong ribosome binding to extended SD sequences affects the stability of lacZ mRNAs translated with different efficiencies. The steady-state concentration of the lacZ transcripts has been found to vary over a broad range, directly correlating with translation efficiency but not with the SD duplex stability. The observed strain-to-strain variations in lacZ mRNA level became far less marked in the presence of the rne-1 mutation, which partially inactivates RNase E. Together, the results show that (i) an SD sequence, even one that is very long, cannot stabilize the lacZ mRNA in E. coli if translation is inefficient; (ii) inefficiently translated lacZ transcripts are sensitive to RNase E; and (iii) AU-rich elements inserted upstream of a long SD sequence enhance translation and stabilize mRNA, despite the fact that they constitute potential RNase E sites. These data strongly support the idea that the lacZ mRNA in E. coli can be stabilized only by translating, and not by stalling, ribosomes.
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Affiliation(s)
- Anastassia V Komarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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46
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Wang Z, Yuan Z, Hengge UR. Processing of plasmid DNA with ColE1-like replication origin. Plasmid 2004; 51:149-61. [PMID: 15109822 DOI: 10.1016/j.plasmid.2003.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Revised: 11/06/2003] [Indexed: 12/22/2022]
Abstract
With the increasing utilization of plasmid DNA as a biopharmaceutical drug, there is a rapidly growing need for high quality plasmid DNA for drug applications. Although there are several different kinds of replication origins, ColE1-like replication origin is the most extensively used origin in biotechnology. This review addresses problems in upstream and downstream processing of plasmid DNA with ColE1-like origin as drug applications. In upstream processing of plasmid DNA, regulation of replication of ColE1-like origin was discussed. In downstream processing of plasmid DNA, we analyzed simple, robust, and scalable methods, which can be used in the efficient production of pharmaceutical-grade plasmid DNA.
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Affiliation(s)
- Zhijun Wang
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032 Shanghai, People's Republic of China.
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47
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Redko Y, Tock MR, Adams CJ, Kaberdin VR, Grasby JA, McDowall KJ. Determination of the catalytic parameters of the N-terminal half of Escherichia coli ribonuclease E and the identification of critical functional groups in RNA substrates. J Biol Chem 2003; 278:44001-8. [PMID: 12947103 DOI: 10.1074/jbc.m306760200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribonuclease E is required for the rapid decay and correct processing of RNA in Escherichia coli. A detailed understanding of the hydrolysis of RNA by this and related enzymes will require the integration of structural and molecular data with quantitative measurements of RNA hydrolysis. Therefore, an assay for RNaseE that can be set up to have relatively high throughput while being sensitive and quantitative will be advantageous. Here we describe such an assay, which is based on the automated high pressure liquid chromatography analysis of fluorescently labeled RNA samples. We have used this assay to optimize reaction conditions, to determine for the first time the catalytic parameters for a polypeptide of RNaseE, and to investigate the RNaseE-catalyzed reaction through the modification of functional groups within an RNA substrate. We find that catalysis is dependent on both protonated and unprotonated functional groups and that the recognition of a guanosine sequence determinant that is upstream of the scissile bond appears to consist of interactions with the exocyclic 2-amino group, the 7N of the nucleobase and the imino proton or 6-keto group. Additionally, we find that a ribose-like sugar conformation is preferred in the 5'-nucleotide of the scissile phosphodiester bond and that a 2'-hydroxyl group proton is not essential. Steric bulk at the 2' position in the 5'-nucleotide appears to be inhibitory to the reaction. Combined, these observations establish a foundation for the functional interpretation of a three-dimensional structure of the catalytic domain of RNaseE when solved.
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Affiliation(s)
- Yulia Redko
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Manton Building, LS2 9JT Leeds, United Kingdom
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48
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Callaghan AJ, Grossmann JG, Redko YU, Ilag LL, Moncrieffe MC, Symmons MF, Robinson CV, McDowall KJ, Luisi BF. Quaternary Structure and Catalytic Activity of the Escherichia coli Ribonuclease E Amino-Terminal Catalytic Domain. Biochemistry 2003; 42:13848-55. [PMID: 14636052 DOI: 10.1021/bi0351099] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNase E is an essential endoribonuclease that plays a central role in the processing and degradation of RNA in Escherichia coli and other bacteria. Most endoribonucleases have been shown to act distributively; however, Feng et al. [(2002) Proc. Natl. Acad. Sci. U.S.A. 99, 14746-14751] have recently found that RNase E acts via a scanning mechanism. A structural explanation for the processivity of RNase E is provided here, with our finding that the conserved catalytic domain of E. coli RNase E forms a homotetramer. Nondissociating nanoflow-electrospray mass spectrometry suggests that the tetramer binds up to four molecules of a specific substrate RNA analogue. The tetrameric assembly of the N-terminal domain of RNase E is consistent with crystallographic analyses, which indicate that the tetramer possesses approximate D(2) dihedral symmetry. Using X-ray solution scattering data and symmetry restraints, a solution shape is calculated for the tetramer. This shape, together with limited proteolysis data, suggests that the S1-RNA binding domains of RNase E lie on the periphery of the tetramer. These observations have implications for the structure and function of the RNase E/RNase G ribonuclease family and for the assembly of the E. coli RNA degradosome, in which RNase E is the central component.
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Affiliation(s)
- Anastasia J Callaghan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Abstract
This review focuses on the enzymes and pathways of RNA processing and degradation in Bacillus subtilis, and compares them to those of its gram-negative counterpart, Escherichia coli. A comparison of the genomes from the two organisms reveals that B. subtilis has a very different selection of RNases available for RNA maturation. Of 17 characterized ribonuclease activities thus far identified in E. coli and B. subtilis, only 6 are shared, 3 exoribonucleases and 3 endoribonucleases. Some enzymes essential for cell viability in E. coli, such as RNase E and oligoribonuclease, do not have homologs in B. subtilis, and of those enzymes in common, some combinations are essential in one organism but not in the other. The degradation pathways and transcript half-lives have been examined to various degrees for a dozen or so B. subtilis mRNAs. The determinants of mRNA stability have been characterized for a number of these and point to a fundamentally different process in the initiation of mRNA decay. While RNase E binds to the 5' end and catalyzes the rate-limiting cleavage of the majority of E. coli RNAs by looping to internal sites, the equivalent nuclease in B. subtilis, although not yet identified, is predicted to scan or track from the 5' end. RNase E can also access cleavage sites directly, albeit less efficiently, while the enzyme responsible for initiating the decay of B. subtilis mRNAs appears incapable of direct entry. Thus, unlike E. coli, RNAs possessing stable secondary structures or sites for protein or ribosome binding near the 5' end can have very long half-lives even if the RNA is not protected by translation.
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Affiliation(s)
- Ciarán Condon
- UPR 9073, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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