1
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Hoffmann UA, Lichtenberg E, Rogh SN, Bilger R, Reimann V, Heyl F, Backofen R, Steglich C, Hess WR, Wilde A. The role of the 5' sensing function of ribonuclease E in cyanobacteria. RNA Biol 2024; 21:1-18. [PMID: 38469716 PMCID: PMC10939160 DOI: 10.1080/15476286.2024.2328438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y for 5'-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5' sensing, contrasting to the alternative 'direct entry' mode, which is independent of monophosphorylated 5' ends. Cyanobacteria, such as Synechocystis sp. PCC 6803 (Synechocystis), encode RNase E and RNase J homologues. Here, we constructed a Synechocystis strain lacking the 5' sensing function of RNase E and mapped on a transcriptome-wide level 283 5'-sensing-dependent cleavage sites. These included so far unknown targets such as mRNAs encoding proteins related to energy metabolism and carbon fixation. The 5' sensing function of cyanobacterial RNase E is important for the maturation of rRNA and several tRNAs, including tRNAGluUUC. This tRNA activates glutamate for tetrapyrrole biosynthesis in plant chloroplasts and in most prokaryotes. Furthermore, we found that increased RNase activities lead to a higher copy number of the major Synechocystis plasmids pSYSA and pSYSM. These results provide a first step towards understanding the importance of the different target mechanisms of RNase E outside Escherichia coli.
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Affiliation(s)
- Ute A. Hoffmann
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elisabeth Lichtenberg
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Said N. Rogh
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Raphael Bilger
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Viktoria Reimann
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Florian Heyl
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
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2
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Watanabe S, Stazic D, Georg J, Ohtake S, Sakamaki Y, Numakura M, Asayama M, Chibazakura T, Wilde A, Steglich C, Hess WR. Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp. PCC 6803. MLIFE 2023; 2:43-57. [PMID: 38818332 PMCID: PMC10989929 DOI: 10.1002/mlf2.12056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/07/2022] [Accepted: 12/15/2022] [Indexed: 06/01/2024]
Abstract
Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the posttranscriptional regulation of gene expression. A key endoribonuclease in Gram-negative bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria, such as Escherichia coli, feedback-regulate RNase E expression via the rne 5'-untranslated region (5' UTR) in cis. However, the mechanisms involved in the control of RNase E in other bacteria largely remain unknown. Cyanobacteria rely on solar light as an energy source for photosynthesis, despite the inherent ultraviolet (UV) irradiation. In this study, we first investigated globally the changes in gene expression in the cyanobacterium Synechocystis sp. PCC 6803 after a brief exposure to UV. Among the 407 responding genes 2 h after UV exposure was a prominent upregulation of rne mRNA level. Moreover, the enzymatic activity of RNase E rapidly increased as well, although the protein stability decreased. This unique response was underpinned by the increased accumulation of full-length rne mRNA caused by the stabilization of its 5' UTR and suppression of premature transcriptional termination, but not by an increased transcription rate. Mapping of RNA 3' ends and in vitro cleavage assays revealed that RNase E cleaves within a stretch of six consecutive uridine residues within the rne 5' UTR, indicating autoregulation. These observations suggest that RNase E in cyanobacteria contributes to reshaping the transcriptome during the UV stress response and that its required activity level is secured at the RNA level despite the enhanced turnover of the protein.
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Affiliation(s)
- Satoru Watanabe
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Damir Stazic
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
- Present address:
NexxiotPrime Tower (Hardstrasse 201)ZurichSwitzerland
| | - Jens Georg
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
| | - Shota Ohtake
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Yutaka Sakamaki
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Megumi Numakura
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Munehiko Asayama
- School of Agriculture, Molecular GeneticsIbaraki UniversityIbarakiJapan
| | - Taku Chibazakura
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Annegret Wilde
- Faculty of Biology, Molecular GeneticsUniversity of FreiburgFreiburgGermany
| | - Claudia Steglich
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
| | - Wolfgang R. Hess
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
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3
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Clarke JE, Sabharwal K, Kime L, McDowall KJ. The recognition of structured elements by a conserved groove distant from domains associated with catalysis is an essential determinant of RNase E. Nucleic Acids Res 2023; 51:365-379. [PMID: 36594161 PMCID: PMC9841416 DOI: 10.1093/nar/gkac1228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/11/2022] [Accepted: 12/08/2022] [Indexed: 01/04/2023] Open
Abstract
RNase E is an endoribonuclease found in many bacteria, including important human pathogens. Within Escherichia coli, it has been shown to have a major role in both the maturation of all classes of RNA involved in translation and the initiation of mRNA degradation. Thus, knowledge of the major determinants of RNase E cleavage is central to our understanding and manipulation of bacterial gene expression. We show here that the binding of RNase E to structured RNA elements is crucial for the processing of tRNA, can activate catalysis and may be important in mRNA degradation. The recognition of structured elements by RNase E is mediated by a recently discovered groove that is distant from the domains associated with catalysis. The functioning of this groove is shown here to be essential for E. coli cell viability and may represent a key point of evolutionary divergence from the paralogous RNase G family, which we show lack amino acid residues conserved within the RNA-binding groove of members of the RNase E family. Overall, this work provides new insights into the recognition and cleavage of RNA by RNase E and provides further understanding of the basis of RNase E essentiality in E. coli.
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Affiliation(s)
| | | | - Louise Kime
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Kenneth J McDowall
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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4
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Hoffmann UA, Heyl F, Rogh SN, Wallner T, Backofen R, Hess WR, Steglich C, Wilde A. Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition. Nucleic Acids Res 2021; 49:13075-13091. [PMID: 34871439 PMCID: PMC8682795 DOI: 10.1093/nar/gkab1161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/26/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
Ribonucleases are crucial enzymes in RNA metabolism and post-transcriptional regulatory processes in bacteria. Cyanobacteria encode the two essential ribonucleases RNase E and RNase J. Cyanobacterial RNase E is shorter than homologues in other groups of bacteria and lacks both the chloroplast-specific N-terminal extension as well as the C-terminal domain typical for RNase E of enterobacteria. In order to investigate the function of RNase E in the model cyanobacterium Synechocystis sp. PCC 6803, we engineered a temperature-sensitive RNase E mutant by introducing two site-specific mutations, I65F and the spontaneously occurred V94A. This enabled us to perform RNA-seq after the transient inactivation of RNase E by a temperature shift (TIER-seq) and to map 1472 RNase-E-dependent cleavage sites. We inferred a dominating cleavage signature consisting of an adenine at the -3 and a uridine at the +2 position within a single-stranded segment of the RNA. The data identified mRNAs likely regulated jointly by RNase E and an sRNA and potential 3' end-derived sRNAs. Our findings substantiate the pivotal role of RNase E in post-transcriptional regulation and suggest the redundant or concerted action of RNase E and RNase J in cyanobacteria.
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Affiliation(s)
- Ute A Hoffmann
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Florian Heyl
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Said N Rogh
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Wallner
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
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5
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Ali N, Gowrishankar J. Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E. Nucleic Acids Res 2020; 48:847-861. [PMID: 31802130 PMCID: PMC6954427 DOI: 10.1093/nar/gkz1152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
RNase E is a 472-kDa homo-tetrameric essential endoribonuclease involved in RNA processing and turnover in Escherichia coli. In its N-terminal half (NTH) is the catalytic active site, as also a substrate 5′-sensor pocket that renders enzyme activity maximal on 5′-monophosphorylated RNAs. The protein's non-catalytic C-terminal half (CTH) harbours RNA-binding motifs and serves as scaffold for a multiprotein degradosome complex, but is dispensable for viability. Here, we provide evidence that a full-length hetero-tetramer, composed of a mixture of wild-type and (recessive lethal) active-site mutant subunits, exhibits identical activity in vivo as the wild-type homo-tetramer itself (‘recessive resurrection’). When all of the cognate polypeptides lacked the CTH, the active-site mutant subunits were dominant negative. A pair of C-terminally truncated polypeptides, which were individually inactive because of additional mutations in their active site and 5′-sensor pocket respectively, exhibited catalytic function in combination, both in vivo and in vitro (i.e. intragenic or allelic complementation). Our results indicate that adjacent subunits within an oligomer are separately responsible for 5′-sensing and cleavage, and that RNA binding facilitates oligomerization. We propose also that the CTH mediates a rate-determining initial step for enzyme function, which is likely the binding and channelling of substrate for NTH’s endonucleolytic action.
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Affiliation(s)
- Nida Ali
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, India
| | - Jayaraman Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
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6
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Mardle CE, Shakespeare TJ, Butt LE, Goddard LR, Gowers DM, Atkins HS, Vincent HA, Callaghan AJ. A structural and biochemical comparison of Ribonuclease E homologues from pathogenic bacteria highlights species-specific properties. Sci Rep 2019; 9:7952. [PMID: 31138855 PMCID: PMC6538622 DOI: 10.1038/s41598-019-44385-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 05/13/2019] [Indexed: 12/15/2022] Open
Abstract
Regulation of gene expression through processing and turnover of RNA is a key mechanism that allows bacteria to rapidly adapt to changing environmental conditions. Consequently, RNA degrading enzymes (ribonucleases; RNases) such as the endoribonuclease RNase E, frequently play critical roles in pathogenic bacterial virulence and are potential antibacterial targets. RNase E consists of a highly conserved catalytic domain and a variable non-catalytic domain that functions as the structural scaffold for the multienzyme degradosome complex. Despite conservation of the catalytic domain, a recent study identified differences in the response of RNase E homologues from different species to the same inhibitory compound(s). While RNase E from Escherichia coli has been well-characterised, far less is known about RNase E homologues from other bacterial species. In this study, we structurally and biochemically characterise the RNase E catalytic domains from four pathogenic bacteria: Yersinia pestis, Francisella tularensis, Burkholderia pseudomallei and Acinetobacter baumannii, with a view to exploiting RNase E as an antibacterial target. Bioinformatics, small-angle x-ray scattering and biochemical RNA cleavage assays reveal globally similar structural and catalytic properties. Surprisingly, subtle species-specific differences in both structure and substrate specificity were also identified that may be important for the development of effective antibacterial drugs targeting RNase E.
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Affiliation(s)
- Charlotte E Mardle
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Thomas J Shakespeare
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Louise E Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Layla R Goddard
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Darren M Gowers
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Helen S Atkins
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom.,University of Exeter, Exeter, United Kingdom.,London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Helen A Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom.
| | - Anastasia J Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom.
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7
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Nouaille S, Mondeil S, Finoux AL, Moulis C, Girbal L, Cocaign-Bousquet M. The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression. Nucleic Acids Res 2017; 45:11711-11724. [PMID: 28977619 PMCID: PMC5714132 DOI: 10.1093/nar/gkx781] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/28/2017] [Indexed: 01/19/2023] Open
Abstract
Changing mRNA stability is a major post-transcriptional way of controlling gene expression, particularly in newly encountered conditions. As the concentration of mRNA is the result of an equilibrium between transcription and degradation, it is generally assumed that at constant transcription, any change in mRNA concentration is the consequence of mRNA stabilization or destabilization. However, the literature reports many cases of opposite variations in mRNA concentration and stability in bacteria. Here, we analyzed the causal link between the concentration and stability of mRNA in two phylogenetically distant bacteria Escherichia coli and Lactococcus lactis. Using reporter mRNAs, we showed that modifying the stability of an mRNA had unpredictable effects, either higher or lower, on its concentration, whereas increasing its concentration systematically reduced stability. This inverse relationship between the concentration and stability of mRNA was generalized to native genes at the genome scale in both bacteria. Higher mRNA turnover in the case of higher concentrations appears to be a simple physical mechanism to regulate gene expression in the bacterial kingdom. The consequences for bacterial adaptation of this control of the stability of an mRNA by its concentration are discussed.
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Affiliation(s)
- Sébastien Nouaille
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Sophie Mondeil
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Anne-Laure Finoux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Claire Moulis
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Laurence Girbal
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
| | - Muriel Cocaign-Bousquet
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France. 135 av de Rangueil. 31077 Toulouse Cedex 4, France
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8
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Ikeda Y, Okada Y, Sato A, Kanai T, Tomita M, Atomi H, Kanai A. An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. Sci Rep 2017; 7:12674. [PMID: 28978920 PMCID: PMC5627344 DOI: 10.1038/s41598-017-13062-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/12/2017] [Indexed: 12/28/2022] Open
Abstract
Ribosome biogenesis and turnover are processes necessary for cell viability and proliferation, and many kinds of proteins are known to regulate these processes. However, many questions still remain, especially in the Archaea. Generally, several ribonucleases are required to process precursor rRNAs to their mature forms, and to degrade rRNAs for quality control. Here, we found that FAU-1, which is known to be an RNA binding protein, possesses an RNase activity against precursor 5S rRNA derived from P. furiosus and T. kodakarensis in the order Thermococcales in vitro. An in vitro analysis revealed that UA sequences in the upstream of 5S rRNA were preferentially degraded by addition of FAU-1. Moreover, a fau-1 gene deletion mutant of T. kodakarensis showed a delay of exponential phase, reduction of maximum cell number and significant changes in the nucleotide sequence lengths of its 5S, 16S, and 23S rRNAs in early exponential phase. Our results suggest that FAU-1 is a potential RNase involved in rRNA stability through maturation and/or degradation processes.
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Affiliation(s)
- Yoshiki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.
| | - Yasuhiro Okada
- Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
| | - Tamotsu Kanai
- Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
| | - Haruyuki Atomi
- Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
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9
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Richards J, Belasco JG. Distinct Requirements for 5'-Monophosphate-assisted RNA Cleavage by Escherichia coli RNase E and RNase G. J Biol Chem 2015; 291:5038-48. [PMID: 26694614 DOI: 10.1074/jbc.m115.702555] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 11/06/2022] Open
Abstract
RNase E and RNase G are homologous endonucleases that play important roles in RNA processing and decay in Escherichia coli and related bacterial species. Rapid mRNA degradation is facilitated by the preference of both enzymes for decay intermediates whose 5' end is monophosphorylated. In this report we identify key characteristics of RNA that influence the rate of 5'-monophosphate-assisted cleavage by these two ribonucleases. In vitro, both require at least two and prefer three or more unpaired 5'-terminal nucleotides for such cleavage; however, RNase G is impeded more than RNase E when fewer than four unpaired nucleotides are present at the 5' end. Each can tolerate any unpaired nucleotide (A, G, C, or U) at either of the first two positions, with only modest biases. The optimal spacing between the 5' end and the scissile phosphate appears to be eight nucleotides for RNase E but only six for RNase G. 5'-Monophosphate-assisted cleavage also occurs, albeit more slowly, when that spacing is greater or at most one nucleotide shorter than the optimum, but there is no simple inverse relationship between increased spacing and the rate of cleavage. These properties are also manifested during 5'-end-dependent mRNA degradation in E. coli.
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Affiliation(s)
- Jamie Richards
- From the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Joel G Belasco
- From the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016
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10
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Aït-Bara S, Carpousis AJ. RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs. Mol Microbiol 2015; 97:1021-135. [PMID: 26096689 DOI: 10.1111/mmi.13095] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/29/2022]
Abstract
Ribonuclease E (RNase E) of Escherichia coli, which is the founding member of a widespread family of proteins in bacteria and chloroplasts, is a fascinating enzyme that still has not revealed all its secrets. RNase E is an essential single-strand specific endoribonuclease that is involved in the processing and degradation of nearly every transcript in E. coli. A striking enzymatic property is a preference for substrates with a 5' monophosphate end although recent work explains how RNase E can overcome the protection afforded by the 5' triphosphate end of a primary transcript. Other features of E. coli RNase E include its interaction with enzymes involved in RNA degradation to form the multienzyme RNA degradosome and its localization to the inner cytoplasmic membrane. The N-terminal catalytic core of the RNase E protomer associates to form a tetrameric holoenzyme. Each RNase E protomer has a large C-terminal intrinsically disordered (ID) noncatalytic region that contains sites for interactions with protein components of the RNA degradosome as well as RNA and phospholipid bilayers. In this review, RNase E homologs have been classified into five types based on their primary structure. A recent analysis has shown that type I RNase E in the γ-proteobacteria forms an orthologous group of proteins that has been inherited vertically. The RNase E catalytic core and a large ID noncatalytic region containing an RNA binding motif and a membrane targeting sequence are universally conserved features of these orthologs. Although the ID noncatalytic region has low composition and sequence complexity, it is possible to map microdomains, which are short linear motifs that are sites of interaction with protein and other ligands. Throughout bacteria, the composition of the multienzyme RNA degradosome varies with species, but interactions with exoribonucleases (PNPase, RNase R), glycolytic enzymes (enolase, aconitase) and RNA helicases (DEAD-box proteins, Rho) are common. Plasticity in RNA degradosome composition is due to rapid evolution of RNase E microdomains. Characterization of the RNase E-PNPase interaction in α-proteobacteria, γ-proteobacteria and cyanobacteria suggests that it arose independently several times during evolution, thus conferring an advantage in control and coordination of RNA processing and degradation.
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Affiliation(s)
- Soraya Aït-Bara
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte, Institut, National de la Santé et de la Recherche Médicale & Université d'Auvergne, Clermont-Ferrand, 63001, France
| | - Agamemnon J Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100, Centre National de la Recherche Scientifique et Université de Toulouse 3, Toulouse, 31062, France
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11
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Kime L, Vincent HA, Gendoo DMA, Jourdan SS, Fishwick CWG, Callaghan AJ, McDowall KJ. The first small-molecule inhibitors of members of the ribonuclease E family. Sci Rep 2015; 5:8028. [PMID: 25619596 PMCID: PMC4306137 DOI: 10.1038/srep08028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/16/2014] [Indexed: 11/08/2022] Open
Abstract
The Escherichia coli endoribonuclease RNase E is central to the processing and degradation of all types of RNA and as such is a pleotropic regulator of gene expression. It is essential for growth and was one of the first examples of an endonuclease that can recognise the 5'-monophosphorylated ends of RNA thereby increasing the efficiency of many cleavages. Homologues of RNase E can be found in many bacterial families including important pathogens, but no homologues have been identified in humans or animals. RNase E represents a potential target for the development of new antibiotics to combat the growing number of bacteria that are resistant to antibiotics in use currently. Potent small molecule inhibitors that bind the active site of essential enzymes are proving to be a source of potential drug leads and tools to dissect function through chemical genetics. Here we report the use of virtual high-throughput screening to obtain small molecules predicted to bind at sites in the N-terminal catalytic half of RNase E. We show that these compounds are able to bind with specificity and inhibit catalysis of Escherichia coli and Mycobacterium tuberculosis RNase E and also inhibit the activity of RNase G, a paralogue of RNase E.
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Affiliation(s)
- Louise Kime
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Helen A. Vincent
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Deena M. A. Gendoo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Stefanie S. Jourdan
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Colin W. G. Fishwick
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Anastasia J. Callaghan
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Kenneth J. McDowall
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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12
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Abstract
RNase E is a major intracellular endoribonuclease in many bacteria and participates in most aspects of RNA processing and degradation. RNase E requires a divalent metal ion for its activity. We show that only Mg(2+) and Mn(2+) will support significant rates of activity in vitro against natural RNAs, with Mn(2+) being preferred. Both Mg(2+) and Mn(2+) also support cleavage of an oligonucleotide substrate with similar kinetic parameters for both ions. Salts of Ni(2+) and Zn(2+) permitted low levels of activity, while Ca(2+), Co(3+), Cu(2+), and Fe(2+) did not. A mutation to one of the residues known to chelate Mg(2+), D346C, led to almost complete loss of activity dependent on Mg(2+); however, the activity of the mutant enzyme was fully restored by the presence of Mn(2+) with kinetic parameters fully equivalent to those of wild-type enzyme. A similar mutation to the other chelating residue, D303C, resulted in nearly full loss of activity regardless of metal ion. The properties of RNase E D346C enabled a test of the ionic requirements of RNase E in vivo. Plasmid shuffling experiments showed that both rneD303C (i.e., the rne gene encoding a D-to-C change at position 303) and rneD346C were inviable whether or not the selection medium was supplied with MnSO4, implying that RNase E relies on Mg(2+) exclusively in vivo.
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13
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Clarke JE, Kime L, Romero A D, McDowall KJ. Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli. Nucleic Acids Res 2014; 42:11733-51. [PMID: 25237058 PMCID: PMC4191395 DOI: 10.1093/nar/gku808] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli endoribonuclease E has a major influence on gene expression. It is essential for the maturation of ribosomal and transfer RNA as well as the rapid degradation of messenger RNA. The latter ensures that translation closely follows programming at the level of transcription. Recently, one of the hallmarks of RNase E, i.e. its ability to bind via a 5'-monophosphorylated end, was shown to be unnecessary for the initial cleavage of some polycistronic tRNA precursors. Here we show using RNA-seq analyses of ribonuclease-deficient strains in vivo and a 5'-sensor mutant of RNase E in vitro that, contrary to current models, 5'-monophosphate-independent, 'direct entry' cleavage is a major pathway for degrading and processing RNA. Moreover, we present further evidence that direct entry is facilitated by RNase E binding simultaneously to multiple unpaired regions. These simple requirements may maximize the rate of degradation and processing by permitting multiple sites to be surveyed directly without being constrained by 5'-end tethering. Cleavage was detected at a multitude of sites previously undescribed for RNase E, including ones that regulate the activity and specificity of ribosomes. A potentially broad role for RNase G, an RNase E paralogue, in the trimming of 5'-monophosphorylated ends was also revealed.
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Affiliation(s)
- Justin E Clarke
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Louise Kime
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Romero A
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Kenneth J McDowall
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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14
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Kime L, Clarke JE, Romero A. D, Grasby JA, McDowall KJ. Adjacent single-stranded regions mediate processing of tRNA precursors by RNase E direct entry. Nucleic Acids Res 2014; 42:4577-89. [PMID: 24452799 PMCID: PMC3985628 DOI: 10.1093/nar/gkt1403] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/09/2013] [Accepted: 12/22/2013] [Indexed: 01/06/2023] Open
Abstract
The RNase E family is renowned for being central to the processing and decay of all types of RNA in many species of bacteria, as well as providing the first examples of endonucleases that can recognize 5'-monophosphorylated ends thereby increasing the efficiency of cleavage. However, there is increasing evidence that some transcripts can be cleaved efficiently by Escherichia coli RNase E via direct entry, i.e. in the absence of the recognition of a 5'-monophosphorylated end. Here, we provide biochemical evidence that direct entry is central to the processing of transfer RNA (tRNA) in E. coli, one of the core functions of RNase E, and show that it is mediated by specific unpaired regions that are adjacent, but not contiguous to segments cleaved by RNase E. In addition, we find that direct entry at a site on the 5' side of a tRNA precursor triggers a series of 5'-monophosphate-dependent cleavages. Consistent with a major role for direct entry in tRNA processing, we provide additional evidence that a 5'-monophosphate is not required to activate the catalysis step in cleavage. Other examples of tRNA precursors processed via direct entry are also provided. Thus, it appears increasingly that direct entry by RNase E has a major role in bacterial RNA metabolism.
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Affiliation(s)
- Louise Kime
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK and Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| | - Justin E. Clarke
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK and Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| | - David Romero A.
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK and Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| | - Jane A. Grasby
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK and Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| | - Kenneth J. McDowall
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK and Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
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15
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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: 94] [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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16
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Abstract
Though lacking a well-defined three-dimensional structure, intrinsically unstructured proteins are ubiquitous in nature. These molecules play crucial roles in many cellular processes, especially signaling and regulation. Surprisingly, even enzyme catalysis can tolerate substantial disorder. This observation contravenes conventional wisdom but is relevant to an understanding of how protein dynamics modulates enzyme function. This chapter reviews properties and characteristics of disordered proteins, emphasizing examples of enzymes that lack defined structures, and considers implications of structural disorder for catalytic efficiency and evolution.
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17
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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: 1.2] [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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18
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Karzbrun E, Shin J, Bar-Ziv RH, Noireaux V. Coarse-grained dynamics of protein synthesis in a cell-free system. PHYSICAL REVIEW LETTERS 2011; 106:048104. [PMID: 21405367 DOI: 10.1103/physrevlett.106.048104] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Indexed: 05/30/2023]
Abstract
A complete gene expression reaction is reconstituted in a cell-free system comprising the entire endogenous transcription, translation, as well as mRNA and protein degradation machinery of E. coli. In dissecting the major reaction steps, we derive a coarse-grained enzymatic description of biosynthesis and degradation, from which ten relevant rate constants and concentrations are determined. Governed by zeroth-order degradation, protein expression follows a sharp transition from undetectable levels to constant-rate accumulation, without reaching steady state.
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Affiliation(s)
- Eyal Karzbrun
- Department of Materials and Interfaces, the Weizmann Institute of Science, Rehovot, Israel
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19
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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: 62] [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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20
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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: 0.7] [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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21
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Hurley JM, Woychik NA. Bacterial toxin HigB associates with ribosomes and mediates translation-dependent mRNA cleavage at A-rich sites. J Biol Chem 2009; 284:18605-13. [PMID: 19423702 DOI: 10.1074/jbc.m109.008763] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most pathogenic Proteus species are primarily associated with urinary tract infections, especially in persons with indwelling catheters or functional/anatomic abnormalities of the urinary tract. Urinary tract infections caused by Proteus vulgaris typically form biofilms and are resistant to commonly used antibiotics. The Rts1 conjugative plasmid from a clinical isolate of P. vulgaris carries over 300 predicted open reading frames, including antibiotic resistance genes. The maintenance of the Rts1 plasmid is ensured in part by the HigBA toxin-antitoxin system. We determined the precise mechanism of action of the HigB toxin in vivo, which is distinct from other known toxins. We demonstrate that HigB is an endoribonuclease whose enzymatic activity is dependent on association with ribosomes through the 50 S subunit. Using primer extension analysis of several test mRNAs, we showed that HigB cleaved extensively across the entire length of coding regions only at specific recognition sequences. HigB mediated cleavage of 100% of both in-frame and out-of-frame AAA sequences. In addition, HigB cleaved approximately 20% of AA sequences in coding regions and occasionally cut single As. Remarkably, the cleavage specificity of HigB coincided with one of the most frequently used codons in the AT-rich Proteus spp., AAA (lysine). Therefore, the HigB-mediated plasmid maintenance system for the Rts1 plasmid highlights the intimate relationship between host cells and extrachromosomal DNA that enables the dynamic acquisition of genes that impart a spectrum of survival advantages, including those encoding multidrug resistance and virulence factors.
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Affiliation(s)
- Jennifer M Hurley
- Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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22
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Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA. Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage. Mol Microbiol 2009; 71:1071-87. [DOI: 10.1111/j.1365-2958.2008.06572.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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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: 8.1] [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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24
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Beloglazova N, Brown G, Zimmerman MD, Proudfoot M, Makarova KS, Kudritska M, Kochinyan S, Wang S, Chruszcz M, Minor W, Koonin EV, Edwards AM, Savchenko A, Yakunin AF. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem 2008; 283:20361-71. [PMID: 18482976 DOI: 10.1074/jbc.m803225200] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process. Here we show that the CAS2 proteins represent a novel family of endoribonucleases. Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions. A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The crystal structure of SSO1404 was solved at 1.6A resolution revealing the first ribonuclease with a ferredoxin-like fold. Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue. Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs.
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Affiliation(s)
- Natalia Beloglazova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
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25
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Tadmor AD, Tlusty T. A coarse-grained biophysical model of E. coli and its application to perturbation of the rRNA operon copy number. PLoS Comput Biol 2008; 4:e1000038. [PMID: 18437222 PMCID: PMC2320978 DOI: 10.1371/journal.pcbi.1000038] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 02/19/2008] [Indexed: 11/23/2022] Open
Abstract
We propose a biophysical model of Escherichia coli that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential steady-state growth, growing in a temporally and spatially constant environment, rich in resources. We apply this model to a series of past measurements, where the growth rate and rRNA-to-protein ratio have been measured for seven E. coli strains with an rRNA operon copy number ranging from one to seven (the wild-type copy number). These experiments show that growth rate markedly decreases for strains with fewer than six copies. Using the model, we were able to reproduce these measurements. We show that the model that best fits these data suggests that the volume fraction of macromolecules inside E. coli is not fixed when the rRNA operon copy number is varied. Moreover, the model predicts that increasing the copy number beyond seven results in a cytoplasm densely packed with ribosomes and proteins. Assuming that under such overcrowded conditions prolonged diffusion times tend to weaken binding affinities, the model predicts that growth rate will not increase substantially beyond the wild-type growth rate, as indicated by other experiments. Our model therefore suggests that changing the rRNA operon copy number of wild-type E. coli cells growing in a constant rich environment does not substantially increase their growth rate. Other observations regarding strains with an altered rRNA operon copy number, such as nucleoid compaction and the rRNA operon feedback response, appear to be qualitatively consistent with this model. In addition, we discuss possible design principles suggested by the model and propose further experiments to test its validity. A bacterium like E. coli can be thought of as a self-replicating factory, where inventory synthesis, degradation, and management is concerted according to a well-defined set of rules encoded in the organism's genome. Since the organism's survival depends on this set of rules, these rules were most likely optimized by evolution. Therefore, by writing down these rules, what could one learn about Escherichia coli? We examined E. coli growing in the simplest imaginable environment, one constant in space and time and rich in resources, and attempted to identify the rules that relate the genome to the cell composition and self-replication time. With more than 4,400 genes, a full-scale model would be prohibitively complicated, and therefore we “coarse-grained” E. coli by lumping together genes and proteins of similar function. We used this model to examine measurements of strains with reduced copy number of ribosomal-RNA genes, and also to show that increasing this copy number overcrowds the cell with ribosomes and proteins. As a result, there appears to be an optimum copy number with respect to the wild-type genome, in agreement with observation. We hope that this model will improve and further challenge our understanding of bacterial physiology, also in more complicated environments.
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Affiliation(s)
- Arbel D. Tadmor
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Tsvi Tlusty
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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26
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Complementing structural information of modular proteins with small angle neutron scattering and contrast variation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:603-11. [DOI: 10.1007/s00249-008-0278-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2007] [Revised: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 11/25/2022]
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27
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Kime L, Jourdan SS, McDowall KJ. Identifying and characterizing substrates of the RNase E/G family of enzymes. Methods Enzymol 2008; 447:215-41. [PMID: 19161846 DOI: 10.1016/s0076-6879(08)02212-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of RNA decay and processing in Escherichia coli has revealed a central role for RNase E, an endonuclease that is essential for cell viability. This enzyme is required for the normal rapid decay of many transcripts and is involved in the processing of precursors of 16S and 5S ribosomal RNA, transfer RNA, the transfer-messenger RNA, and the RNA component of RNase P. Although there is reasonable knowledge of the repertoire of transcripts cleaved by RNase E in E. coli, a detailed understanding of the molecular recognition events that control the cleavage of RNA by this key enzyme is only starting to emerge. Here we describe methods for identifying sites of endonucleolytic cleavage and determining whether they depend on functional RNase E. This is illustrated with the pyrG eno bicistronic transcript, which is cleaved in the intergenic region primarily by an RNase E-dependent activity and not as previously thought by RNase III. We also describe the use of oligoribonucleotide and in vitro-transcribed substrates to investigate cis-acting factors such as 5'-monophosphorylation, which can significantly enhance the rate of cleavage but is insufficient to ensure processivity. Most of the approaches that we describe can be applied to the study of homologs of E. coli RNase E, which have been found in approximately half of the eubacteria that have been sequenced.
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Affiliation(s)
- Louise Kime
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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28
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Ko JH, Han K, Kim Y, Sim S, Kim KS, Lee SJ, Cho B, Lee K, Lee Y. Dual Function of RNase E for Control of M1 RNA Biosynthesis in Escherichia coli. Biochemistry 2007; 47:762-70. [DOI: 10.1021/bi701528j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jae-hyeong Ko
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
| | - Kook Han
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
| | - Yool Kim
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
| | - Soyeong Sim
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
| | - Kwang-sun Kim
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
| | - Sang-Joon Lee
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
| | - Bongrae Cho
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
| | - Kangryul Lee
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
| | - Younghoon Lee
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea, Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea, and Department of Chemistry, Catholic University of Korea, Bucheon 420-743, Korea
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29
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Jourdan SS, McDowall KJ. Sensing of 5′ monophosphate by Escherichia coli RNase G can significantly enhance association with RNA and stimulate the decay of functional mRNA transcripts in vivo. Mol Microbiol 2007; 67:102-15. [DOI: 10.1111/j.1365-2958.2007.06028.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Condon C. Maturation and degradation of RNA in bacteria. Curr Opin Microbiol 2007; 10:271-8. [PMID: 17560162 DOI: 10.1016/j.mib.2007.05.008] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 05/21/2007] [Indexed: 11/20/2022]
Abstract
RNA decay plays an important role, not only in recycling nucleotides but also in determining the rapidity with which cells can react to changing growth conditions. The degradation process can be regulated, thus providing an often-underestimated means of controlling gene expression. Recent developments in the field of RNA maturation and decay in two key model organisms, Escherichia coli and Bacillus subtilis, include the resolution of the structures of many of the participants in these processes in E. coli and the identification of an enzyme in B. subtilis that appears to fit the bill as a major player in RNA decay in this organism.
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Affiliation(s)
- Ciarán Condon
- CNRS UPR 9073 (affiliated with Université de Paris 7 - Denis Diderot), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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31
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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: 1.9] [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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32
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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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33
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Bardey V, Vallet C, Robas N, Charpentier B, Thouvenot B, Mougin A, Hajnsdorf E, Régnier P, Springer M, Branlant C. Characterization of the molecular mechanisms involved in the differential production of erythrose-4-phosphate dehydrogenase, 3-phosphoglycerate kinase and class II fructose-1,6-bisphosphate aldolase in Escherichia coli. Mol Microbiol 2005; 57:1265-87. [PMID: 16102000 DOI: 10.1111/j.1365-2958.2005.04762.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A gapA-pgk gene tandem coding the glyceraldehyde 3-phosphate dehydrogenase and 3-phosphoglycerate kinase, is most frequently found in bacteria. However, in Enterobacteriaceae, gapA is replaced by an epd open reading frame (ORF) coding an erythrose-4-phosphate dehydrogenase and an fbaA ORF coding the class II fructose-1,6-bisphosphate aldolase follows pgk. Although epd expression is very low in Escherichia coli, we show that, in the presence of glucose, the 3 epd, pgk and fbaA ORFs are efficiently cotranscribed from promoter epd P0. Conservation of promoter epd P0 is likely due to its important role in modulation of the metabolic flux during glycolysis and gluconeogenesis. As a consequence, we found that the epd translation initiation region and ORF have been adapted in order to limit epd translation and to create an efficient RNase E entry site. We also show that fbaA is cotranscribed with pgk, from promoter epd P0 or an internal pgk P1 promoter of the extended -10 class. The differential expression of pgk and fbaA also depends upon an RNase E segmentation process, leading to individual mRNAs with different stabilities. The secondary structures of the RNA regions containing the RNase E sites were experimentally determined which brings important information on the structural features of RNase E ectopic sites.
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Affiliation(s)
- Vincent Bardey
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy I, Faculté des Sciences et Techniques, BP 239, 54506 Vandoeuvre-lès-Nancy, Cedex, France
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34
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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: 222] [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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35
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Thayer JR, Barreto V, Rao S, Pohl C. Control of oligonucleotide retention on a pH-stabilized strong anion exchange column. Anal Biochem 2005; 338:39-47. [PMID: 15707934 DOI: 10.1016/j.ab.2004.11.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Indexed: 11/23/2022]
Abstract
Strong anion exchange columns are preferred for oligonucleotide analyses due to their ability to effectively control secondary structure and poly(G) interactions. Methacrylate-based anion exchange phases minimize hydrophobic interactions with oligonucleotides, but they also tend to hydrolyze under alkaline conditions. In this article, we report the use of an anion exchange column prepared from a new class of methacrylate monomers designed to improve hydrolytic stability. This column is used to show predictable adjustment of oligonucleotide retention by eluent pH and composition. Features of the new column include (i) large, predictable, pH-dependent retention shifts (varying with specific changes in 5' or 3' terminal bases with NaCl-based eluents); (ii) reduced retention when solvent is added to NaCl-based eluents; and (iii) suppression of much of the column's hydrophobic interactions when CH3CN is used with NaClO4-based eluents at a neutral pH (i.e., this eluent system separates oligonucleotides primarily in order of their length). These observations will aid the development of elution conditions for both size-dependent and base sequence-dependent (or base composition-dependent) separations.
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Affiliation(s)
- J R Thayer
- Dionex Corporation, Sunnyvale, CA 94085, USA.
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36
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Kaberdin VR, Bizebard T. Characterization of Aquifex aeolicus RNase E/G. Biochem Biophys Res Commun 2005; 327:382-92. [PMID: 15629127 DOI: 10.1016/j.bbrc.2004.12.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Indexed: 11/26/2022]
Abstract
The RNase E/G homologue from the thermophilic eubacterium Aquifex aeolicus has been overexpressed in Escherichia coli, purified, and characterized in vitro. We show that A. aeolicus RNase E/G has a temperature-dependent, endoribonucleolytic activity. The enzyme site-specifically cleaves oligonucleotides and structured RNAs at locations that are partly overlapping or completely different when compared to the positions of E. coli RNase E and RNase G cleavage sites. The efficiency of cleavage by A. aeolicus RNase E/G is dependent on the 5'-phosphorylation status of RNA suggesting differential susceptibility of primary transcripts and their degradative intermediates to the nuclease activity of this enzyme in vivo. Similar to E. coli RNase E, A. aeolicus RNase E/G is able to selectively cleave internucleotide bonds in the 3'-5' direction, and to cut in intercistronic regions of putative tRNA precursors, thus suggesting a common function for RNase E/G homologues in eubacteria.
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Affiliation(s)
- Vladimir R Kaberdin
- Max F. Perutz Laboratories, Department of Microbiology and Genetics, University Departments at the Vienna Biocenter, Dr. Bohrgasse 9/4, A-1030 Vienna, Austria.
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37
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Callaghan AJ, Redko Y, Murphy LM, Grossmann JG, Yates D, Garman E, Ilag LL, Robinson CV, Symmons MF, McDowall KJ, Luisi BF. “Zn-Link”: A Metal-Sharing Interface that Organizes the Quaternary Structure and Catalytic Site of the Endoribonuclease, RNase E†. Biochemistry 2005; 44:4667-75. [PMID: 15779893 DOI: 10.1021/bi0478244] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribonuclease E is an essential hydrolytic endonuclease in Escherichia coli, and it plays a central role in maintaining the balance and composition of the messenger RNA population. The enzyme is also required for rRNA and tRNA processing. We have shown earlier that the highly conserved catalytic domain of E. coli RNase E is a homotetramer [Callaghan, A. J. et al. (2003) Biochemistry 42, 13848-13855]. Here, we report that this quaternary organization requires zinc. Two protomers share a single zinc ion, and quantitative analysis indicates that each protein contributes two cysteine thiols toward the coordination of the metal. The candidate cysteines are part of a motif that is conserved in the RNase E protein family, and mutation of these residues causes the partial loss of zinc, the complete disruption of the tetramer into dimers, and effective catalytic inactivation. However, these mutations do not affect RNA binding. The tetramer can be artificially maintained by disulfide bond formation, which fully displaces the zinc but largely preserves the catalytic activity. Thus, catalytic activity does not require zinc directly but does require the quaternary structure, for which the metal is essential. We propose that the RNase E tetramer has two nonequivalent subunit interfaces, one of which is mediated by a single, tetrathiol-zinc complex, which we refer to as a "Zn-link" motif. One or both interfaces organize the active site, which is distinct from the primary site of RNA binding.
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Affiliation(s)
- Anastasia J Callaghan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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38
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Jiang X, Belasco JG. Catalytic activation of multimeric RNase E and RNase G by 5'-monophosphorylated RNA. Proc Natl Acad Sci U S A 2004; 101:9211-6. [PMID: 15197283 PMCID: PMC438955 DOI: 10.1073/pnas.0401382101] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNase E is an endonuclease that plays a central role in RNA processing and degradation in Escherichia coli. Like its E. coli homolog RNase G, RNase E shows a marked preference for cleaving RNAs that bear a monophosphate, rather than a triphosphate or hydroxyl, at the 5' end. To investigate the mechanism by which 5'-terminal phosphorylation can influence distant cleavage events, we have developed fluorogenic RNA substrates that allow the activity of RNase E and RNase G to be quantified much more accurately and easily than before. Kinetic analysis of the cleavage of these substrates by RNase E and RNase G has revealed that 5' monophosphorylation accelerates the reaction not by improving substrate binding, but rather by enhancing the catalytic potency of these ribonucleases. Furthermore, the presence of a 5' monophosphate can increase the specificity of cleavage site selection within an RNA. Although monomeric forms of RNase E and RNase G can cut RNA, the ability of these enzymes to discriminate between RNA substrates on the basis of their 5' phosphorylation state requires the formation of protein multimers. Among the molecular mechanisms that could account for these properties are those in which 5'-end binding by one enzyme subunit induces a protein structural change that accelerates RNA cleavage by another subunit.
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Affiliation(s)
- Xunqing Jiang
- Skirball Institute of Biomolecular Medicine and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
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