1
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Kirsebom LA, Liu F, McClain WH. The discovery of a catalytic RNA within RNase P and its legacy. J Biol Chem 2024; 300:107318. [PMID: 38677513 PMCID: PMC11143913 DOI: 10.1016/j.jbc.2024.107318] [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] [Received: 09/18/2023] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Sidney Altman's discovery of the processing of one RNA by another RNA that acts like an enzyme was revolutionary in biology and the basis for his sharing the 1989 Nobel Prize in Chemistry with Thomas Cech. These breakthrough findings support the key role of RNA in molecular evolution, where replicating RNAs (and similar chemical derivatives) either with or without peptides functioned in protocells during the early stages of life on Earth, an era referred to as the RNA world. Here, we cover the historical background highlighting the work of Altman and his colleagues and the subsequent efforts of other researchers to understand the biological function of RNase P and its catalytic RNA subunit and to employ it as a tool to downregulate gene expression. We primarily discuss bacterial RNase P-related studies but acknowledge that many groups have significantly contributed to our understanding of archaeal and eukaryotic RNase P, as reviewed in this special issue and elsewhere.
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Affiliation(s)
- Leif A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, California, USA.
| | - William H McClain
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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2
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Gößringer M, Wäber NB, Wiegard JC, Hartmann RK. Characterization of RNA-based and protein-only RNases P from bacteria encoding both enzyme types. RNA (NEW YORK, N.Y.) 2023; 29:376-391. [PMID: 36604113 PMCID: PMC9945441 DOI: 10.1261/rna.079459.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
A small group of bacteria encode two types of RNase P, the classical ribonucleoprotein (RNP) RNase P as well as the protein-only RNase P HARP (homolog of Aquifex RNase P). We characterized the dual RNase P activities of five bacteria that belong to three different phyla. All five bacterial species encode functional RNA (gene rnpB) and protein (gene rnpA) subunits of RNP RNase P, but only the HARP of the thermophile Thermodesulfatator indicus (phylum Thermodesulfobacteria) was found to have robust tRNA 5'-end maturation activity in vitro and in vivo in an Escherichia coli RNase P depletion strain. These findings suggest that both types of RNase P are able to contribute to the essential tRNA 5'-end maturation activity in T. indicus, thus resembling the predicted evolutionary transition state in the progenitor of the Aquificaceae before the loss of rnpA and rnpB genes in this family of bacteria. Remarkably, T. indicus RNase P RNA is transcribed with a P12 expansion segment that is posttranscriptionally excised in vivo, such that the major fraction of the RNA is fragmented and thereby truncated by ∼70 nt in the native T. indicus host as well as in the E. coli complementation strain. Replacing the native P12 element of T. indicus RNase P RNA with the short P12 helix of Thermotoga maritima RNase P RNA abolished fragmentation, but simultaneously impaired complementation efficiency in E. coli cells, suggesting that intracellular fragmentation and truncation of T. indicus RNase P RNA may be beneficial to RNA folding and/or enzymatic activity.
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Affiliation(s)
- Markus Gößringer
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Nadine B Wäber
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Jana C Wiegard
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
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3
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Gopalan V, Nilsen T, Gopalan V, Altman AM, Stark BC, Feinstein SI, Koski R, Mickiewicz C, Stark B, Gegenheimer P, Kirsebom LA, Arnez JG, Forster AC, Kazakov SA, Yuan Y, Liu F, Jarrous N, Yang L, Jiang G, Jiang T, Rosenbaum JL, Miller G, DiMaio D, Carlson JR, McClain WH, Mathews MB, Kaempfer R, Deutscher MP, Chen LL, Li Y, Wang E, Patutina O, Zenkova M, Vlassov V, Lucks JB, Gopalan V. Tribute to Sidney Altman. RNA (NEW YORK, N.Y.) 2022; 28:1393-1429. [PMID: 36113877 PMCID: PMC9745839 DOI: 10.1261/rna.079397.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | - Ben Stark
- Department of Biology, Illinois Institute of Technology, Chicago, Illinois
| | | | | | | | | | | | | | | | | | - Li Yang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ge Jiang
- ShanghaiTech University, Shanghai, China
| | | | | | | | | | | | | | | | | | | | | | - Yong Li
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Enduo Wang
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences, Shanghai, China
| | | | | | | | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
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4
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Lönnberg H. Structural modifications as tools in mechanistic studies of the cleavage of RNA phosphodiester linkages. CHEM REC 2022; 22:e202200141. [PMID: 35832010 DOI: 10.1002/tcr.202200141] [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: 05/16/2022] [Revised: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH fundamentally differs from the spontaneous reactions of these bonds under the same conditions. While the predominant spontaneous reaction is isomerization of the 3',5'-phosphodiester linkages to their 2',5'-counterparts, this reaction has never been reported to compete with the enzymatic cleavage reaction, not even as a minor side reaction. Comparative kinetic measurements with structurally modified di-nucleoside monophosphates and oligomeric phosphodiesters have played an important role in clarification of mechanistic details of the buffer-independent and buffer-catalyzed reactions. More recently, heavy atom isotope effects and theoretical calculations have refined the picture. The primary aim of all these studies has been to form a solid basis for mechanistic analyses of the action of more complicated catalytic machineries. In other words, to contribute to conception of a plausible unified picture of RNA cleavage by biocatalysts, such as RNAse A, hammerhead ribozyme and DNAzymes. In addition, structurally modified trinucleoside monophosphates as transition state models for Group I and II introns have clarified some features of the action of large ribozymes.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
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5
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Rahman MS, Gulshan MA, Matsumura S, Ikawa Y. Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:715-729. [PMID: 32039645 DOI: 10.1080/15257770.2019.1687909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The modular structure of bacterial ribonuclease P (RNase P) ribozymes, which recognize tertiary structures of precursor tRNAs (pre-tRNAs) to cleave their 5' leader sequence, can be dissected physically into the two structured domain RNAs (S-domain and C-domain). Separately prepared S-domain RNA and C-domain RNA assemble to form bimolecular forms of RNase P ribozymes. We analyzed the effects of polyethylene glycols (PEGs) on pre-tRNA cleavage catalyzed by bimolecular RNase P ribozymes to examine the effects of molecular crowding on the reaction. PEG molecular crowders significantly enhanced the activities of bimolecular RNase P ribozymes, some of which were hardly active without PEGs.
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Affiliation(s)
- Md Sohanur Rahman
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Mst Ara Gulshan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
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6
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Wan F, Wang Q, Tan J, Tan M, Chen J, Shi S, Lan P, Wu J, Lei M. Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme. Nat Commun 2019; 10:2617. [PMID: 31197137 PMCID: PMC6565675 DOI: 10.1038/s41467-019-10496-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 05/09/2019] [Indexed: 12/18/2022] Open
Abstract
Ribonuclease P (RNase P) is an essential ribozyme responsible for tRNA 5′ maturation. Here we report the cryo-EM structures of Methanocaldococcus jannaschii (Mja) RNase P holoenzyme alone and in complex with a tRNA substrate at resolutions of 4.6 Å and 4.3 Å, respectively. The structures reveal that the subunits of MjaRNase P are strung together to organize the holoenzyme in a dimeric conformation required for efficient catalysis. The structures also show that archaeal RNase P is a functional chimera of bacterial and eukaryal RNase Ps that possesses bacterial-like two RNA-based anchors and a eukaryal-like protein-aided stabilization mechanism. The 3′-RCCA sequence of tRNA, which is a key recognition element for bacterial RNase P, is dispensable for tRNA recognition by MjaRNase P. The overall organization of MjaRNase P, particularly within the active site, is similar to those of bacterial and eukaryal RNase Ps, suggesting a universal catalytic mechanism for all RNase Ps. Ribonulease P is a conserved ribozyme present in all kingdoms of life that is involved in the 5′ maturation step of tRNAs. Here the authors determine the structure of an archaeal RNase P holoenzyme that reveals how archaeal RNase P recognizes its tRNA substrate and suggest a conserved catalytic mechanism amongst RNase Ps despite structural variability.
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Affiliation(s)
- Futang Wan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qianmin Wang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.,Shanghai Institute of Precision Medicine, Shanghai, 200125, China
| | - Jing Tan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ming Tan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Juan Chen
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.,Shanghai Institute of Precision Medicine, Shanghai, 200125, China
| | - Shaohua Shi
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.,Shanghai Institute of Precision Medicine, Shanghai, 200125, China
| | - Pengfei Lan
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China. .,Shanghai Institute of Precision Medicine, Shanghai, 200125, China.
| | - Jian Wu
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China. .,Shanghai Institute of Precision Medicine, Shanghai, 200125, China. .,Shanghai Key Laboratory of Translational Medicine on Ear and Nose diseases, Shanghai, 200125, China.
| | - Ming Lei
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China. .,Shanghai Institute of Precision Medicine, Shanghai, 200125, China. .,Key laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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7
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Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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8
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Lee TS, Radak BK, Harris ME, York DM. A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. ACS Catal 2016; 6:1853-1869. [PMID: 27774349 DOI: 10.1021/acscatal.5b02158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA enzymes serve as a potentially powerful platform from which to design catalysts and engineer new biotechnology. A fundamental understanding of these systems provides insight to guide design. The hepatitis delta virus ribozyme (HDVr) is a small, self-cleaving RNA motif widely distributed in nature, that has served as a paradigm for understanding basic principles of RNA catalysis. Nevertheless, questions remain regarding the precise roles of divalent metal ions and key nucleotides in catalysis. In an effort to establish a reaction mechanism model consistent with available experimental data, we utilize molecular dynamics simulations to explore different conformations and metal ion binding modes along the HDVr reaction path. Building upon recent crystallographic data, our results provide a dynamic model of the HDVr reaction mechanism involving a conformational switch between multiple non-canonical G25:U20 base pair conformations in the active site. These local nucleobase dynamics play an important role in catalysis by modulating the metal binding environments of two Mg2+ ions that support catalysis at different steps of the reaction pathway. The first ion plays a structural role by inducing a base pair flip necessary to obtain the catalytic fold in which C75 moves towards to the scissile phosphate in the active site. Ejection of this ion then permits a second ion to bind elsewhere in the active site and facilitate nucleophile activation. The simulations collectively describe a mechanistic scenario that is consistent with currently available experimental data from crystallography, phosphorothioate substitutions, and chemical probing studies. Avenues for further experimental verification are suggested.
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Affiliation(s)
- Tai-Sung Lee
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Brian K. Radak
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
- Argonne National Laboratory, Argonne, Illinois 60439, United State
| | - Michael E. Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Darrin M. York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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9
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Lönnberg T. Understanding Catalysis of Phosphate‐Transfer Reactions by the Large Ribozymes. Chemistry 2011; 17:7140-53. [DOI: 10.1002/chem.201100009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20140 Turku (Finland), Fax: (+358) 2‐333‐6700
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10
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Buzayan JM, Gerlach WL, Bruening G. Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing. Proc Natl Acad Sci U S A 2010; 83:8859-62. [PMID: 16593780 PMCID: PMC387032 DOI: 10.1073/pnas.83.23.8859] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The satellite RNA of tobacco ringspot virus depends upon tobacco ringspot virus for its replication and source of coat protein. The satellite RNA reduces virus accumulation and the severity of virus-induced symptoms. Repetitive sequence, dimeric, and higher forms of the satellite RNA are known to autolytically process to form biologically active monomeric RNA of 359 nucleotide residues [Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R. & Bruening, G. (1986) Science 231, 1577-1580], with a 5'-hydroxyl and a 2',3'-cyclic phosphodiester as the new terminal groups. We show here that transcripts of full-length and truncated DNA clones of the satellite RNA sequence also process in a nonenzymic reaction. One such transcript was an RNA that has about one-fourth of the satellite RNA sequence, representing the 3'-terminal and 5'-terminal portions of monomeric RNA joined in the junction that is cleaved in dimeric RNA. This RNA autolytically processed more efficiently than molecules with a larger proportion of the satellite RNA nucleotide sequence.
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Affiliation(s)
- J M Buzayan
- Department of Plant Pathology, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616
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11
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Lipfert J, Sim AYL, Herschlag D, Doniach S. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA (NEW YORK, N.Y.) 2010; 16:708-19. [PMID: 20194520 PMCID: PMC2844619 DOI: 10.1261/rna.1985110] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Riboswitches are gene-regulating RNAs that are usually found in the 5'-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg(2+), Ca(2+), and Mn(2+) facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.
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Affiliation(s)
- Jan Lipfert
- Department of Physics, Stanford University, Stanford, California 94305, USA
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12
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McClain WH, Lai LB, Gopalan V. Trials, travails and triumphs: an account of RNA catalysis in RNase P. J Mol Biol 2010; 397:627-46. [PMID: 20100492 DOI: 10.1016/j.jmb.2010.01.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 01/12/2010] [Accepted: 01/19/2010] [Indexed: 12/16/2022]
Abstract
Last December marked the 20th anniversary of the Nobel Prize in Chemistry to Sidney Altman and Thomas Cech for their discovery of RNA catalysts in bacterial ribonuclease P (an enzyme catalyzing 5' maturation of tRNAs) and a self-splicing rRNA of Tetrahymena, respectively. Coinciding with the publication of a treatise on RNase P, this review provides a historical narrative, a brief report on our current knowledge, and a discussion of some research prospects on RNase P.
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Affiliation(s)
- William H McClain
- Department of Bacteriology, College of Agriculture & Life Sciences, University of Wisconsin, Madison, WI 53706, USA.
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13
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Lai LB, Vioque A, Kirsebom LA, Gopalan V. Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Lett 2009; 584:287-96. [PMID: 19931535 DOI: 10.1016/j.febslet.2009.11.048] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 11/09/2009] [Accepted: 11/13/2009] [Indexed: 12/16/2022]
Abstract
For an enzyme functioning predominantly in a seemingly housekeeping role of 5' tRNA maturation, RNase P displays a remarkable diversity in subunit make-up across the three domains of life. Despite the protein complexity of this ribonucleoprotein enzyme increasing dramatically from bacteria to eukarya, the catalytic function rests with the RNA subunit during evolution. However, the recent demonstration of a protein-only human mitochondrial RNase P has added further intrigue to the compositional variability of this enzyme. In this review, we discuss some possible reasons underlying the structural diversity of the active sites, and use them as thematic bases for elaborating new directions to understand how functional variations might have contributed to the complex evolution of RNase P.
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Affiliation(s)
- Lien B Lai
- Department of Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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14
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15
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Marszalkowski M, Willkomm DK, Hartmann RK. 5'-end maturation of tRNA in aquifex aeolicus. Biol Chem 2008; 389:395-403. [PMID: 18208351 DOI: 10.1515/bc.2008.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
5'-End maturation of tRNA primary transcripts is thought to be ubiquitously catalyzed by ribonuclease P (RNase P), a ribonucleoprotein enzyme in the vast majority of organisms and organelles. In the hyperthermophilic bacterium Aquifex aeolicus, neither a gene for the RNA nor the protein component of bacterial RNase P has been identified in its sequenced genome. Here, we demonstrate the presence of an RNase P-like activity in cell lysates of A. aeolicus. Detection of activity was sensitive to the buffer conditions during cell lysis and partial purification, explaining why we failed to observe activity in the buffer system applied previously. RNase P-like activity of A. aeolicus depends on the presence of Mg2+ or Mn2+, persists at high temperatures, which inactivate RNase P enzymes from mesophilic bacteria, and is remarkably resistant to micrococcal nuclease treatment. While cellular RNA fractions from other Aquificales (A. pyrophilus, Hydrogenobacter thermophilus and Thermocrinis ruber) could be stimulated by bacterial RNase P proteins to catalyze tRNA 5'-end maturation, no such stimulation was observed with RNA from A. aeolicus. In conclusion, our results point to the possibility that RNase P-like activity in A. aeolicus is devoid of an RNA subunit or may include an RNA subunit with untypical features.
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Affiliation(s)
- Michal Marszalkowski
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
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16
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Pulukkunat DK, Gopalan V. Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res 2008; 36:4172-80. [PMID: 18558617 PMCID: PMC2475606 DOI: 10.1093/nar/gkn360] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ribonuclease P (RNase P), a ribonucleoprotein (RNP) complex required for tRNA maturation, comprises one essential RNA (RPR) and protein subunits (RPPs) numbering one in bacteria, and at least four in archaea and nine in eukarya. While the bacterial RPR is catalytically active in vitro, only select euryarchaeal and eukaryal RPRs are weakly active despite secondary structure similarity and conservation of nucleotide identity in their putative catalytic core. Such a decreased archaeal/eukaryal RPR function might imply that their cognate RPPs provide the functional groups that make up the active site. However, substrate-binding defects might mask the ability of some of these RPRs, such as that from the archaeon Methanocaldococcus jannaschii (Mja), to catalyze precursor tRNA (ptRNA) processing. To test this hypothesis, we constructed a ptRNA-Mja RPR conjugate and found that indeed it self-cleaves efficiently (k(obs), 0.15 min(-1) at pH 5.5 and 55 degrees C). Moreover, one pair of Mja RPPs (POP5-RPP30) enhanced k(obs) for the RPR-catalyzed self-processing by approximately 100-fold while the other pair (RPP21-RPP29) had no effect; both binary RPP complexes significantly reduced the monovalent and divalent ionic requirement. Our results suggest a common RNA-mediated catalytic mechanism in all RNase P and help uncover parallels in RNase P catalysis hidden by plurality in its subunit make-up.
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Affiliation(s)
- Dileep K Pulukkunat
- Ohio State Biochemistry Program and Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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17
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Cuzic S, Heidemann KA, Wöhnert J, Hartmann RK. Escherichia coli RNase P RNA: substrate ribose modifications at G+1, but not nucleotide -1/+73 base pairing, affect the transition state for cleavage chemistry. J Mol Biol 2008; 379:1-8. [PMID: 18452950 DOI: 10.1016/j.jmb.2008.03.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 03/06/2008] [Accepted: 03/19/2008] [Indexed: 11/16/2022]
Abstract
The temperature dependence of processing of precursor tRNA(Gly) (ptRNA(Gly)) variants carrying a single 2'-OCH(3) or locked nucleic acid (LNA) modification at G+1 by Escherichia coli endoribonuclease P RNA was studied at rate-limiting chemistry. We show, for the first time, that these ribose modifications at nucleotide +1 increase the activation energy and alter the activation parameters for the transition state of hydrolysis at the canonical (c(0)) cleavage site (between nucleotides -1 and +1). The modified substrates, particularly the one with LNA at G+1, caused an increase in the activation enthalpy Delta H(double dagger), which was partly compensated for by a simultaneous increase in the activation entropy DeltaS(double dagger). NMR imino proton spectra of model acceptor stems derived from the same ptRNA variants unveiled that a riboT or U at -1 forms two hydrogen bonds with U+73, thus extending the acceptor stem by 1 bp. The non-canonical base pair is substantially stabilized by LNA substitution at nucleotides -1 or +1. To address if the activation energy increase owing to LNA at G+1 stems from dissociation of the U(-1)-U(+73) base pair as a prerequisite for interaction of U(+73) with U294 in endoribonuclease P RNA, we tested a ptRNA(Gly) variant that is capable of forming an extra C(-1)-G(+73) Watson-Crick base pair. However, compared with a control ptRNA (C at -1, U at +73), no significant change in activation parameters was observed for this ptRNA. Thus, our results argue against the possibility that breaking of an additional base pair at the end of the acceptor stem may present an energetic barrier for reaching the transition state of the chemical step for cleavage at the canonical (c(0)) phosphodiester.
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Affiliation(s)
- Simona Cuzic
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, D-35037 Marburg, Germany
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18
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Travers KJ, Boyd N, Herschlag D. Low specificity of metal ion binding in the metal ion core of a folded RNA. RNA (NEW YORK, N.Y.) 2007; 13:1205-13. [PMID: 17616553 PMCID: PMC1924890 DOI: 10.1261/rna.566007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The structure and activity of nucleic acids depend on their interactions with metal ions. Fundamental to these interactions is the degree of specificity observed between the metal ions and nucleic acids, and a complete description of nucleic acid folding requires that we understand the nature of the interactions with metal ions, including specificity. The prior demonstration that high concentrations of monovalent cations prevent nonspecific association of divalent ions with nucleic acids provides a novel and powerful means to examine site-specific metal ion binding isolated from complicating effects of the ion atmosphere. Using these high monovalent cation solution conditions we have monitored the affinity of a series of divalent metal ions for two site-specific metal ion binding sites in the P4-P6 domain of the Tetrahymena group I intron ribozyme. The metal ion core of this highly structured RNA binds two divalent metal ions under these conditions. Despite multiple metal ion-RNA interactions observed in the X-ray crystallographic structure of P4-P6 RNA at the metal ion binding sites, these sites exhibit low specificity among Mn(2+), Mg(2+), Ca(2+), Ni(2+), and Zn(2+). Nevertheless, the largest divalent metal ions tested, Sr(2+) and Ba(2+), were excluded from binding, exhibiting affinities at least two orders of magnitude weaker than observed for the other metal ions. Thus, a picture emerges of two metal ion binding sites, each with a high tolerance for metal ions with different properties but also with limits to accommodation. These limits presumably arise from steric or electrostatic features of the metal ion binding sites.
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Affiliation(s)
- Kevin J Travers
- Department of Biochemistry, Stanford University, Stanford, CA 94305-5307, USA
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19
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Serrano P, Gomez J, Martínez-Salas E. Characterization of a cyanobacterial RNase P ribozyme recognition motif in the IRES of foot-and-mouth disease virus reveals a unique structural element. RNA (NEW YORK, N.Y.) 2007; 13:849-59. [PMID: 17449727 PMCID: PMC1869033 DOI: 10.1261/rna.506607] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Translation initiation driven by internal ribosome entry site (IRES) elements is dependent on the structural organization of the IRES region. Picornavirus IRES are organized in structural domains, in which the terminal stem-loops participate in functional RNA-protein interactions. However, the mechanistic role performed by the central domain during internal initiation has not been elucidated yet. Here we show that the foot-and-mouth-disease virus IRES contains a structural motif that serves in vitro as substrate for the Synechocystis sp. RNase P ribozyme, a structure-dependent endonuclease that participates in tRNA precursor processing. Recognition of the IRES substrate was dose dependent, required high magnesium concentration, and resulted in the formation of cleavage products with 5' phosphate and 3' hydroxyl ends. Mapping of the core recognition motif indicated that it overlapped with the apical region of the central domain. Two IRES constructs containing nucleotide substitutions in the apical region of the central domain that reorganized RNA structure displayed an altered pattern of cleavage by the cyanobacterial ribozyme generating new cleavage events in nearby residues. From these data it is inferred that the central domain of the IRES region has evolved a tRNA structural mimicry that renders it a substrate for RNase P ribozyme reaction. Recognition of this motif was affected in defective IRES mutants with a local RNA structure reorganization, suggesting that its structural preservation is required for IRES activity.
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Affiliation(s)
- Paula Serrano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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20
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Getz MM, Andrews AJ, Fierke CA, Al-Hashimi HM. Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation. RNA (NEW YORK, N.Y.) 2007; 13:251-66. [PMID: 17194721 PMCID: PMC1781369 DOI: 10.1261/rna.264207] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The P4 helix is an essential element of ribonuclease P (RNase P) that is believed to bind catalytically important metals. Here, we applied a combination of NMR residual dipolar couplings (RDCs) and a recently introduced domain-elongation strategy for measuring "motionally decoupled" relaxation data to characterize the structural dynamics of the P4 helix from Bacillus subtilis RNase P. In the absence of divalent ions, the two P4 helical domains undergo small amplitude (approximately 13 degrees) collective motions about an average interhelical angle of 10 degrees. The highly conserved U7 bulge and helical residue C8, which are proposed to be important for substrate recognition and metal binding, are locally mobile at pico- to nanosecond timescales and together form the pivot point for the collective domain motions. Chemical shift mapping reveals significant association of Mg2+ ions at the P4 major groove near the flexible pivot point at residues (A5, G22, G23) previously identified to bind catalytically important metals. The Mg2+ ions do not, however, significantly alter the structure or dynamics of P4. Analysis of results in the context of available X-ray structures of the RNA component of RNase P and structural models that include the pre-tRNA substrate suggest that the internal motions observed in P4 likely facilitate adaptive changes in conformation that take place during folding and substrate recognition, possibly aided by interactions with Mg2+ ions. Our results add to a growing view supporting the existence of functionally important internal motions in RNA occurring at nanosecond timescales.
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Affiliation(s)
- Melissa M Getz
- Department of Chemistry, University of Michigan, Ann Arbor 48109, USA
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21
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Altman S. Ribonuclease P: an enzyme with a catalytic RNA subunit. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 62:1-36. [PMID: 2471397 DOI: 10.1002/9780470123089.ch1] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- S Altman
- Department of Biology, Yale University, New Haven, Connecticut 06520
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22
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Seif E, Cadieux A, Lang BF. Hybrid E. coli--Mitochondrial ribonuclease P RNAs are catalytically active. RNA (NEW YORK, N.Y.) 2006; 12:1661-70. [PMID: 16894220 PMCID: PMC1557692 DOI: 10.1261/rna.52106] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNase P is a ribonucleoprotein that cleaves tRNA precursors at their 5'-end. Mitochondrion-encoded RNA subunits of mitochondrial RNase P (mtP-RNA) have been identified in jakobid flagellates such as Reclinomonas americana, in the prasinophyte alga Nephroselmis olivacea, and in several ascomycete and zygomycete fungi. While the structures of ascomycete mtP-RNAs are highly reduced, those of jakobids, prasinophytes, and zygomycetes retain most conserved features of their bacterial counterparts. Therefore, these mtP-RNAs might be active in vitro in the absence of a protein subunit, as are bacterial P-RNAs. Here we present a comparative structural analysis including seven newly characterized jakobid mtP-RNAs. We investigate ribozyme activities of mtP-RNAs and find that even the most bacteria-like molecules of jakobids are inactive in vitro. However, when certain domains of jakobid and N. olivacea mtP-RNAs are replaced with those from Escherichia coli, these hybrid RNAs show catalytic activity. In vitro mutagenesis of these hybrid mtP-RNAs shows that various structural elements play a critical role in ribozyme catalysis and provide further support for the presence of these elements in mtP-RNAs. These include GNRA tetraloops in helix P14 and P18 of Jakoba libera, and a remnant P3 pairing in Seculamonas ecuadoriensis. Finally, we will discuss reasons for the failure of mtP-RNAs to show catalytic activity in the absence of P-proteins based on our mutagenesis analysis.
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Affiliation(s)
- Elias Seif
- Canadian Institute for Advanced Research, Robert-Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
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23
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Warneckes JM, Green CJ, Hartmann RK. Role of Metal Ions In The Cleavage Mechanism by The E. Coli Rnase P Holoenzyme. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jens M. Warneckes
- a Medizinische Universität zu Lübeck , Institut für Biochemie , Ratzeburger Allee 160, D-23538, Lübeck , Germany
| | | | - Roland K. Hartmann
- a Medizinische Universität zu Lübeck , Institut für Biochemie , Ratzeburger Allee 160, D-23538, Lübeck , Germany
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24
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Isolation of New Self-Cleaving Ribozymes with in vitro Selection. B KOREAN CHEM SOC 2005. [DOI: 10.5012/bkcs.2005.26.12.2033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Kikovska E, Mikkelsen NE, Kirsebom LA. The naturally trans-acting ribozyme RNase P RNA has leadzyme properties. Nucleic Acids Res 2005; 33:6920-30. [PMID: 16332695 PMCID: PMC1310964 DOI: 10.1093/nar/gki993] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Divalent metal ions promote hydrolysis of RNA backbones generating 5′OH and 2′;3′P as cleavage products. In these reactions, the neighboring 2′OH act as the nucleophile. RNA catalyzed reactions also require divalent metal ions and a number of different metal ions function in RNA mediated cleavage of RNA. In one case, the LZV leadzyme, it was shown that this catalytic RNA requires lead for catalysis. So far, none of the naturally isolated ribozymes have been demonstrated to use lead to activate the nucleophile. Here we provide evidence that RNase P RNA, a naturally trans-acting ribozyme, has leadzyme properties. But, in contrast to LZV RNA, RNase P RNA mediated cleavage promoted by Pb2+ results in 5′ phosphate and 3′OH as cleavage products. Based on our findings, we infer that Pb2+ activates H2O to act as the nucleophile and we identified residues both in the substrate and RNase P RNA that most likely influenced the positioning of Pb2+ at the cleavage site. Our data suggest that Pb2+ can promote cleavage of RNA by activating either an inner sphere H2O or a neighboring 2′OH to act as nucleophile.
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Affiliation(s)
| | - Nils-Egil Mikkelsen
- Department of Molecular Biology, Swedish Agricultural UniversityBox 590, Biomedical Centre, SE-751 23 Uppsala, Sweden
| | - Leif A. Kirsebom
- To whom correspondence should be addressed. Tel: +46 18 471 4068; Fax: +46 18 53 03 96;
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26
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Cech TR. Self-splicing and enzymatic activity of an intervening sequence RNA from Tetrahymena. Biosci Rep 2005; 24:362-85. [PMID: 16134019 DOI: 10.1007/s10540-005-2738-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Thomas R Cech
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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27
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Abstract
The theory of the liquid-glass transition is extended to describe the polymerization of RNA in a nucleotide-condensed state. In the glassy state the ribose subunits are joined by a 2'-5' or 3'-5' phosphodiester linkage to form the ribose-phosphate backbone similar to oligosaccharides and polysaccharides. The occurrence of the glass transition requires two conditions: (1) a supercooled state in a nucleotide-condensed state should exist below the temperature at which the whole RNA hydrolyzes; (2) the Gibbs free energy due to the Kauzmann entropy, which obeys a Curie law with a negative sign, must be larger than the height of the potential barrier for nucleotides to overcome to form the binding.
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Affiliation(s)
- Toyoyuki Kitamura
- Ecole Normale Supérieure de Lyon, 46, Allée d'Italie, 69364 Lyon Cedex 07, France
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28
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Cuzic S, Hartmann RK. Studies on Escherichia coli RNase P RNA with Zn2+ as the catalytic cofactor. Nucleic Acids Res 2005; 33:2464-74. [PMID: 15867194 PMCID: PMC1088067 DOI: 10.1093/nar/gki540] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We demonstrate, for the first time, catalysis by Escherichia coli ribonuclease P (RNase P) RNA with Zn2+ as the sole divalent metal ion cofactor in the presence of ammonium, but not sodium or potassium salts. Hill analysis suggests a role for two or more Zn2+ ions in catalysis. Whereas Zn2+ destabilizes substrate ground state binding to an extent that precludes reliable Kd determination, Co(NH3)63+ and Sr2+ in particular, both unable to support catalysis by themselves, promote high-substrate affinity. Zn2+ and Co(NH3)63+ substantially reduce the fraction of precursor tRNA molecules capable of binding to RNase P RNA. Stimulating and inhibitory effects of Sr2+ on the ribozyme reaction with Zn2+ as cofactor could be rationalized by a model involving two Sr2+ ions (or two classes of Sr2+ ions). Both ions improve substrate affinity in a cooperative manner, but one of the two inhibits substrate conversion in a non-competitive mode with respect to the substrate and the Zn2+. A single 2′-fluoro modification at nt −1 of the substrate substantially weakened the inhibitory effect of Sr2+. Our results demonstrate that the studies on RNase P RNA with metal cofactors other than Mg2+ entail complex effects on structural equilibria of ribozyme and substrate RNAs as well as E·S formation apart from the catalytic performance.
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Affiliation(s)
| | - Roland K. Hartmann
- To whom correspondence should be addressed. Tel: +49 6421 28 25827; Fax: +49 6421 28 25854;
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29
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Zahler NH, Sun L, Christian EL, Harris ME. The pre-tRNA nucleotide base and 2'-hydroxyl at N(-1) contribute to fidelity in tRNA processing by RNase P. J Mol Biol 2004; 345:969-85. [PMID: 15644198 DOI: 10.1016/j.jmb.2004.10.080] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Revised: 10/20/2004] [Accepted: 10/27/2004] [Indexed: 10/26/2022]
Abstract
Fidelity in tRNA processing by the RNase P RNA from Escherichia coli depends, in part, on interactions with the nucleobase and 2' hydroxyl group of N(-1), the nucleotide immediately upstream of the site of RNA strand cleavage. Here, we report a series of biochemical and structure-function studies designed to address how these interactions contribute to cleavage site selection. We find that simultaneous disruption of cleavage site nucleobase and 2' hydroxyl interactions results in parallel reactions leading to correct cleavage and mis-cleavage one nucleotide upstream (5') of the correct site. Changes in Mg(2+) concentration and pH can influence the fraction of product that is incorrectly processed, with pH effects attributable to differences in the rate-limiting steps for the correct and mis-cleavage reaction pathways. Additionally, we provide evidence that interactions with the 2' hydroxyl group adjacent to the reactive phosphate group also contribute to catalysis at the mis-cleavage site. Finally, disruption of the adjacent 2'-hydroxyl contact has a greater effect on catalysis when pairing between the ribozyme and N(-1) is also disrupted, and the effects of simultaneously disrupting these contacts on binding are also non-additive. One implication of these results is that mis-cleavage will result from any combination of active site modifications that decrease the rate of correct cleavage beyond a certain threshold. Indeed, we find that inhibition of correct cleavage and corresponding mis-cleavage also results from disruption of any combination of active site contacts including metal ion interactions and conserved pairing interactions with the 3' RCCA sequence. Such redundancy in interactions needed for maintaining fidelity may reflect the necessity for multiple substrate recognition in vivo. These studies provide a framework for interpreting effects of substrate modifications on RNase P cleavage fidelity and provide evidence for interactions with the nucleobase and 2' hydroxyl group adjacent to the reactive phosphate group in the transition state.
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Affiliation(s)
- Nathan H Zahler
- Department of Biochemistry, Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106-4973, USA
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30
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Schmitz M. Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy. Nucleic Acids Res 2004; 32:6358-66. [PMID: 15576680 PMCID: PMC535670 DOI: 10.1093/nar/gkh961] [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: 11/13/2022] Open
Abstract
The solution structures of two 27 nt RNA hairpins and their complexes with cobalt(III)-hexammine [Co(NH(3))(6)(3+)] were determined by NMR spectroscopy. The RNA hairpins are variants of the P4 region from Escherichia coli RNase P RNA: a U-to-A mutant changing the identity of the bulged nucleotide, and a U-to-C, C-to-U double mutant changing only the bulge position. Structures calculated from NMR constraints show that the RNA hairpins adopt different conformations. In the U-to-C, C-to-U double mutant, the conserved bulged uridine in the P4 wild-type stem is found to be shifted in the 3'-direction by one nucleotide when compared with the wild-type structure. Co(NH(3))(6)(3+) is used as a spectroscopic probe for Mg(H(2)O)(6)(2+) binding sites because both complexes have octahedral symmetry and have similar radii. Intermolecular NOE crosspeaks between Co(NH(3))(6)(3+) and RNA protons were used to locate the site of Co(NH(3))(6)(3+) binding to both RNA hairpins. The metal ion binds in the major groove near a bulge loop in both mutants, but is shifted 3' by about one base pair in the double mutant. The change of the metal ion binding site is compared with results obtained on corresponding mutant RNase P RNA molecules as reported by Harris and co-workers (RNA, 1, 210-218).
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Affiliation(s)
- Michael Schmitz
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany.
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31
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Brännvall M, Kikovska E, Kirsebom LA. Cross talk between the +73/294 interaction and the cleavage site in RNase P RNA mediated cleavage. Nucleic Acids Res 2004; 32:5418-29. [PMID: 15477392 PMCID: PMC524293 DOI: 10.1093/nar/gkh883] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To monitor functionally important metal ions and possible cross talk in RNase P RNA mediated cleavage we studied cleavage of substrates, where the 2'OH at the RNase P cleavage site (at -1) and/or at position +73 had been replaced with a 2' amino group (or 2'H). Our data showed that the presence of 2' modifications at these positions affected cleavage site recognition, ground state binding of substrate and/or rate of cleavage. Cleavage of 2' amino substituted substrates at different pH showed that substitution of Mg2+ by Mn2+ (or Ca2+), identity of residues at and near the cleavage site, and addition of C5 protein influenced the frequency of miscleavage at -1 (cleavage at the correct site is referred to as +1). From this we infer that these findings point at effects mediated by protonation/deprotonation of the 2' amino group, i.e. an altered charge distribution, at the site of cleavage. Moreover, our data suggested that the structural architecture of the interaction between the 3' end of the substrate and RNase P RNA influence the charge distribution at the cleavage site as well as the rate of cleavage under conditions where the chemistry is suggested to be rate limiting. Thus, these data provide evidence for cross talk between the +73/294 interaction and the cleavage site in RNase P RNA mediated cleavage. We discuss the role metal ions might play in this cross talk and the likelihood that at least one functionally important metal ion is positioned in the vicinity of, and use the 2'OH at the cleavage site as an inner or outer sphere ligand.
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Affiliation(s)
- Mathias Brännvall
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24 Uppsala, Sweden
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32
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33
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Persson T, Cuzic S, Hartmann RK. Catalysis by RNase P RNA: unique features and unprecedented active site plasticity. J Biol Chem 2003; 278:43394-401. [PMID: 12904300 DOI: 10.1074/jbc.m305939200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metal ions are essential cofactors for precursor tRNA (ptRNA) processing by bacterial RNase P. The ribose 2'-OH at nucleotide (nt) -1 of ptRNAs is known to contribute to positioning of catalytic Me2+. To investigate the catalytic process, we used ptRNAs with single 2'-deoxy (2'-H), 2'-amino (2'-N), or 2'-fluoro (2'-F) modifications at the cleavage site (nt -1). 2' modifications had small (2.4-7.7-fold) effects on ptRNA binding to E. coli RNase P RNA in the ground state, decreasing substrate affinity in the order 2'-OH > 2'-F > 2'-N > 2'-H. Effects on the rate of the chemical step (about 10-fold for 2'-F, almost 150-fold for 2'-H and 2'-N) were much stronger, and, except for the 2'-N modification, resembled strikingly those observed in the Tetrahymena ribozyme-catalyzed reaction at corresponding position. Mn2+ rescued cleavage of the 2'-N but also the 2'-H-modified ptRNA, arguing against a direct metal ion coordination at this location. Miscleavage between nt -1 and -2 was observed for the 2'-N-ptRNA at low pH (further influenced by the base identities at nt -1 and +73), suggesting repulsion of a catalytic metal ion due to protonation of the amino group. Effects caused by the 2'-N modification at nt -1 of the substrate allowed us to substantiate a mechanistic difference in phosphodiester hydrolysis catalyzed by Escherichia coli RNase P RNA and the Tetrahymena ribozyme: a metal ion binds next to the 2' substituent at nt -1 in the reaction catalyzed by RNase P RNA, but not at the corresponding location in the Tetrahymena ribozyme reaction.
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Affiliation(s)
- Tina Persson
- Universität zu Lübeck, Institut für Biochemie, Ratzeburger Allee 160, D-23538 Lübeck, Germany
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34
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Kaye NM, Zahler NH, Christian EL, Harris ME. Conservation of helical structure contributes to functional metal ion interactions in the catalytic domain of ribonuclease P RNA. J Mol Biol 2002; 324:429-42. [PMID: 12445779 DOI: 10.1016/s0022-2836(02)01094-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Like protein enzymes, catalytic RNAs contain conserved structure motifs important for function. A universal feature of the catalytic domain of ribonuclease P RNA is a bulged-helix motif within the P1-P4 helix junction. Here, we show that changes in bulged nucleotide identity and position within helix P4 affect both catalysis and substrate binding, while a subset of the mutations resulted only in catalytic defects. We find that the proximity of the bulge to sites of metal ion coordination in P4 is important for catalysis; moving the bulge distal to these sites and deleting it had similarly large effects, while moving it proximal to these sites had only a moderate effect on catalysis. To test whether the effects of the mutations are linked to metal ion interactions, we used terbium-dependent cleavage of the phosphate backbone to probe metal ion-binding sites in the wild-type and mutant ribozymes. We detect cleavages at specific sites within the catalytic domain, including helix P4 and J3/4, which have previously been shown to participate directly in metal ion interactions. Mutations introduced into P4 cause local changes in the terbium cleavage pattern due to alternate metal ion-binding configurations with the helix. In addition, a bulge deletion mutation results in a 100-fold decrease in the single turnover cleavage rate constant at saturating magnesium levels, and a reduced affinity for magnesium ions important for catalysis. In light of the alternate terbium cleavage pattern in P4 caused by bulge deletion, this decreased ability to utilize magnesium ions for catalysis appears to be due to localized structural changes in the ribozyme's catalytic core that weaken metal ion interactions in P4 and J3/4. The information reported here, therefore, provides evidence that the universal conservation of the P4 structure is based in part on optimization of metal ion interactions important for catalysis.
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Affiliation(s)
- Nicholas M Kaye
- Center for RNA Molecular Biology, and Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH 44106, USA
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35
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Heubeck C, Schön A. Cyanelle ribonuclease P: isolation and structure-function studies of an organellar ribonucleoprotein enzyme. Methods Enzymol 2002; 342:118-34. [PMID: 11586887 DOI: 10.1016/s0076-6879(01)42540-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- C Heubeck
- Institut für Biochemie, Universität Würzburg, Biozentrum D-97074 Würzburg, Germany
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36
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Affiliation(s)
- L A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
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37
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Abstract
Combinations of chemical and genetic approaches were used to study the function of divalent metal ions in cleavage of RNA by the ribozyme RNase P RNA. We show that different divalent metal ions have differential effects on cleavage site recognition and rescue of cleavage activity by mixing divalent metal ions that do not promote cleavage by themselves. We conclude that efficient and correct cleavage is the result of cooperativity between divalent metal ions bound at different sites in the RNase P RNA-substrate complex. Complementation of a mutant RNase P RNA phenotype as a result of divalent metal ion replacement is demonstrated also. This finding together with other data indicate that one of the metal ions involved in this cooperativity is positioned near the cleavage site. The possibility that the Mg(2+)/Ca(2+) ratio might regulate the activity of biocatalysts that depend on RNA for activity is discussed.
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Affiliation(s)
- M Brännvall
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala University, SE-751 24 Uppsala, Sweden
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38
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McCourt M, Shibata M, McIver JW, Rein R. A molecular orbital study of a model of the Mg2+ coordination complex of the self splicing reaction of ribosomal RNA. J Mol Struct 2001; 179:145-52. [PMID: 11542141 DOI: 10.1016/0166-1280(88)80119-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.
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Affiliation(s)
- M McCourt
- Chemistry Department, State University of New York at Buffalo 14214, USA
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39
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Wagner M, Fingerhut C, Gross HJ, Schön A. The first phytoplasma RNase P RNA provides new insights into the sequence requirements of this ribozyme. Nucleic Acids Res 2001; 29:2661-5. [PMID: 11410676 PMCID: PMC55747 DOI: 10.1093/nar/29.12.2661] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A high variability of RNase P RNA structures is seen among members of the Mycoplasma group. To gain further insight into the structure-function relations of this ribozyme, we have searched for the RNase P RNA gene from more distant relatives, the phytoplasmas. These mycoplasma-like organisms are the aetiological agents of many severe plant diseases. We report the sequence and catalytic properties of RNase P RNA from the phytoplasma causing apple proliferation disease. The primary and postulated secondary structure of this 443 nt long RNA are most similar to those of Acholeplasma, supporting the phylogenetic position of this pathogen. Remarkably, the extremely AT-rich (73.6%) phytoplasma RNA differs from the known bacterial consensus sequence by a single base pair, which is positioned close to the substrate cleavage site in current three-dimensional models. Phytoplasma RNase P RNA functions as an efficient ribozyme in vitro. Conversion of its sequence to the full consensus and kinetic analysis of the resulting mutant RNAs suggests that neither the sequence alone, nor the type of pairing at this position is crucial for substrate binding or catalysis by the RNase P ribozyme. These results refine the bacterial consensus structure close to the catalytic core and thus improve our understanding of RNase P RNA function.
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MESH Headings
- Acholeplasmataceae/enzymology
- Acholeplasmataceae/genetics
- Base Pairing
- Base Sequence
- Binding Sites
- Catalysis
- Consensus Sequence/genetics
- Endoribonucleases/chemistry
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli Proteins
- Kinetics
- Magnesium/pharmacology
- Molecular Sequence Data
- Mutation/genetics
- Nucleic Acid Conformation
- Phylogeny
- Plant Diseases/microbiology
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Stability/genetics
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/genetics
- RNA, Transfer, Tyr/metabolism
- Ribonuclease P
- Structure-Activity Relationship
- Thermodynamics
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Affiliation(s)
- M Wagner
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Biozentrum, Am Hubland, D-97074 Würzburg, Germany
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40
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Takagi Y, Warashina M, Stec WJ, Yoshinari K, Taira K. Recent advances in the elucidation of the mechanisms of action of ribozymes. Nucleic Acids Res 2001; 29:1815-34. [PMID: 11328865 PMCID: PMC37246 DOI: 10.1093/nar/29.9.1815] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The cleavage of RNA can be accelerated by a number of factors. These factors include an acidic group (Lewis acid) or a basic group that aids in the deprotonation of the attacking nucleophile, in effect enhancing the nucleophilicity of the nucleophile; an acidic group that can neutralize and stabilize the leaving group; and any environment that can stabilize the pentavalent species that is either a transition state or a short-lived intermediate. The catalytic properties of ribozymes are due to factors that are derived from the complicated and specific structure of the ribozyme-substrate complex. It was postulated initially that nature had adopted a rather narrowly defined mechanism for the cleavage of RNA. However, recent findings have clearly demonstrated the diversity of the mechanisms of ribozyme-catalyzed reactions. Such mechanisms include the metal-independent cleavage that occurs in reactions catalyzed by hairpin ribozymes and the general double-metal-ion mechanism of catalysis in reactions catalyzed by the Tetrahymena group I ribozyme. Furthermore, the architecture of the complex between the substrate and the hepatitis delta virus ribozyme allows perturbation of the pK(a) of ring nitrogens of cytosine and adenine. The resultant perturbed ring nitrogens appear to be directly involved in acid/base catalysis. Moreover, while high concentrations of monovalent metal ions or polyamines can facilitate cleavage by hammerhead ribozymes, divalent metal ions are the most effective acid/base catalysts under physiological conditions.
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Affiliation(s)
- Y Takagi
- Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Science City 305-8562, Japan
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41
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Brännvall M, Mikkelsen NE, Kirsebom LA. Monitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions. Nucleic Acids Res 2001; 29:1426-32. [PMID: 11266542 PMCID: PMC31289 DOI: 10.1093/nar/29.7.1426] [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: 11/14/2022] Open
Abstract
Lead(II)-induced cleavage can be used as a tool to probe conformational changes in RNA. In this report, we have investigated the conformation of M1 RNA, the catalytic subunit of Escherichia coli RNase P, by studying the lead(II)-induced cleavage pattern in the presence of various divalent metal ions. Our data suggest that the overall conformation of M1 RNA is very similar in the presence of Mg(2+), Mn(2+), Ca(2+), Sr(2+) and Ba(2+), while it is changed compared to the Mg(2+)-induced conformation in the presence of other divalent metal ions, Cd(2+) for example. We also observed that correct folding of some M1 RNA domains is promoted by Pb(2+), while folding of other domain(s) requires the additional presence of other divalent metal ions, cobalt(III) hexamine or spermidine. Based on the suppression of Pb(2+) cleavage at increasing concentrations of various divalent metal ions, our findings suggest that different divalent metal ions bind with different affinities to M1 RNA as well as to an RNase P hairpin-loop substrate and yeast tRNA(Phe). We suggest that this approach can be used to obtain information about the relative binding strength for different divalent metal ions to RNA in general, as well as to specific RNA divalent metal ion binding sites. Of those studied in this report, Mn(2+) is generally among the strongest RNA binders.
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Affiliation(s)
- M Brännvall
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24 Uppsala, Sweden
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42
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Stathopoulos C, Tekos A, Zarkadis IK, Drainas D. Extensive deproteinization of Dictyostelium discoideum RNase P reveals a new catalytic activity. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:2134-40. [PMID: 11277937 DOI: 10.1046/j.1432-1327.2001.02092.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nuclear Dictyostelium discoideum RNase P was subjected to vigorous deproteinization procedures. After treatment with proteinase K followed by phenol extraction of samples containing D. discoideum RNase P activity, a new enzymatic activity was recovered. The proteinase K/phenol/SDS treated enzyme cleaves Schizossacharomyces pombe tRNAser (supS1), D. discoideum tRNASer and tRNALeu precursors several nucleotides upstream of the cleavage site of RNase P, liberating products with 5'-hydroxyl ends. This activity seems to be associated with one or two RNA molecules copurifying with D. discoideum RNase P activity as judged by its inhibition in the presence of micrococcal nuclease, which is in contrast to its resistance to proteinase K/phenol/SDS treatment.
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Affiliation(s)
- C Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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43
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Tekos A, Tsagla A, Stathopoulos C, Drainas D. Inhibition of eukaryotic ribonuclease P activity by aminoglycosides: kinetic studies. FEBS Lett 2000; 485:71-5. [PMID: 11086168 DOI: 10.1016/s0014-5793(00)02190-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of several aminoglycoside antibiotics on ribonuclease P (RNase P) was investigated using an in vitro experimental system from Dictyostelium discoideum. Detailed kinetic analysis showed that all aminoglycosides tested (tobramycin, gentamicin, kanamycin, paromomycin, neomycin) behave as classical non-competitive inhibitors, with neomycin being the strongest inhibitor. The inhibition effect is attributed to the electrostatic competition of the cationic aminoglycosides with magnesium ions required for catalysis. Increasing Mg(2+) ion concentrations reduced the effect of aminoglycosides on RNase P activity. Detailed kinetic analysis showed that aminoglycosides compete with Mg(2+) for common binding sites on RNase P holoenzyme.
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Affiliation(s)
- A Tekos
- Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
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44
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Park IK, Sung JS. K(+) and Mg(2+) ions promote the self-splicing of the td intron RNA inhibited by spectinomycin. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1492:94-9. [PMID: 10858535 DOI: 10.1016/s0167-4781(00)00088-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of Mg(2+) and K(+) ions on the self-splicing inhibition of the td (thymidylate synthase gene) intron RNA by spectinomycin were investigated. The maximum splicing activity occurred at 20 mM KCl. The K(m) and V(max) values for GTP in the presence of 5 mM Mg(2+) are 2.25 microM and 0.55 min(-1), whereas those for GTP both in the presence of 5 mM Mg(2+) and 5 mM K(+) are 1.23 microM and 0. 46 min(-1), respectively. Spectinomycin at 10 mM concentration inhibited the splicing by about 10%, but at 20 mM concentration, the splicing rate was inhibited by about 63%. The splicing inhibition by the low concentration of spectinomycin was overcome markedly as the concentration of Mg(2+) ion was raised. At 30 mM spectinomycin, however, the splicing inhibition was not significantly affected by increasing the concentration of Mg(2+). A similar activation of the splicing rate was observed as the concentration of K(+) ion was increased. The concentration of K(+) ion required for the normal recovery of the splicing was much higher than that of Mg(2+) ion. Unlike Mg(2+) ion, 30 mM K(+) ion effectively alleviated the splicing inhibition by spectinomycin at its high concentration. The results indicate that K(+) and Mg(2+) ions may show mechanistically different interactions with spectinomycin in the self-splicing reaction of the td intron RNA.
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Affiliation(s)
- I K Park
- Department of Biology, Dongguk University, Seoul, 100-715, South
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45
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Kilani AF, Trang P, Jo S, Hsu A, Kim J, Nepomuceno E, Liou K, Liu F. RNase P ribozymes selected in vitro to cleave a viral mRNA effectively inhibit its expression in cell culture. J Biol Chem 2000; 275:10611-22. [PMID: 10744757 DOI: 10.1074/jbc.275.14.10611] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An in vitro selection procedure was used to select RNase P ribozyme variants that efficiently cleaved the sequence of the mRNA encoding thymidine kinase of herpes simplex virus 1. Of the 45 selected variants sequenced, 25 ribozymes carried a common mutation at nucleotides 224 and 225 of RNase P catalytic RNA from Escherichia coli (G(224)G(225) --> AA). These selected ribozymes exhibited at least 10 times higher cleavage efficiency (k(cat)/K(m)) than that derived from the wild type ribozyme. Our results suggest that the mutated A(224)A(225) are in close proximity to the substrate and enhance substrate binding of the ribozyme. When these ribozyme variants were expressed in herpes simplex virus 1-infected cells, the levels of thymidine kinase mRNA and protein were reduced by 95-99%. Our study provides the first direct evidence that RNase P ribozyme variants isolated by the selection procedure can be used for the construction of gene-targeting ribozymes that are highly effective in tissue culture. These results demonstrate the potential for using RNase P ribozymes as gene-targeting agents against any mRNA sequences, and using the selection procedure as a general approach for the engineering of RNase P ribozymes.
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MESH Headings
- Animals
- Base Sequence
- Clone Cells
- Endoribonucleases/chemistry
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- Escherichia coli Proteins
- Genetic Engineering
- Genetic Variation
- Herpesvirus 1, Human/enzymology
- Herpesvirus 1, Human/genetics
- Kinetics
- Molecular Sequence Data
- Mutagenesis
- Nucleic Acid Conformation
- Oligodeoxyribonucleotides
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Proteins/metabolism
- Ribonuclease P
- Sequence Alignment
- Thymidine Kinase/genetics
- Transcription, Genetic
- Transfection
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Affiliation(s)
- A F Kilani
- Program of Infectious Diseases and Immunity, Program of Comparative Biochemistry, School of Public Health, University of California, Berkeley, California 94720, USA
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46
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Park BH, Lee JH, Kim M, Lee Y. Effects of C5 protein on Escherichia coli RNase P catalysis with a precursor tRNA(Phe) bearing a single mismatch in the acceptor stem. Biochem Biophys Res Commun 2000; 268:136-40. [PMID: 10652227 DOI: 10.1006/bbrc.2000.2095] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Escherichia coli RNase P, an RNA-processing enzyme that cleaves precursor tRNAs to generate the mature 5'-end, is composed of a catalytic component (M1 RNA) and a protein cofactor (C5 protein). In this study, effects of C5 protein on the RNase P catalysis with a precursor E. coli tRNA(Phe) having a single mismatch in the acceptor stem were examined. This mutant precursor unexpectedly generated upstream cleavage products at the -8 position as well as normal cleavage products at the +1 position. The cleavage at the -8 position was essentially effective only in the presence of C5 protein. Possible secondary structures for cleavage at the -8 position deviate significantly from the structures of the known RNase P substrates, implying that C5 protein can allow the enzyme to broaden the substrate specificity more than previously appreciated.
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Affiliation(s)
- B H Park
- Department of Chemistry, Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Taejon, 305-701, Korea
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47
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Warnecke JM, Sontheimer EJ, Piccirilli JA, Hartmann RK. Active site constraints in the hydrolysis reaction catalyzed by bacterial RNase P: analysis of precursor tRNAs with a single 3'-S-phosphorothiolate internucleotide linkage. Nucleic Acids Res 2000; 28:720-7. [PMID: 10637323 PMCID: PMC102553 DOI: 10.1093/nar/28.3.720] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Endonucleolytic processing of precursor tRNAs (ptRNAs) by RNase P yields 3'-OH and 5'-phosphate termini, and at least two metal ions are thought to be essential for catalysis. To determine if the hydrolysis reaction catalyzed by bacterial RNase P (RNAs) involves stabilization of the 3'-oxyanion leaving group by direct coordination to one of the catalytic metal ions, ptRNA substrates with single 3'- S -phosphorothiolate linkages at the RNase P cleavage site were synthesized. With a 3'- S -phosphorothiolate-modified ptRNA carrying a 7 nt 5'-flank, a complete shift of the cleavage site to the next unmodified phosphodiester in the 5'-direction was observed. Cleavage at the modified linkage was not restored in the presence of thiophilic metal ions, such as Mn(2+)or Cd(2+). To suppress aberrant cleavage, we also constructed a 3'- S -phosphorothiolate-modified ptRNA with a 1 nt 5'-flank. No detectable cleavage of this substrate was seen in reactions catalyzed by RNase P RNAs from Escherichia coli and Bacillus subtilis, independent of the presence of thiophilic metal ions. Ground state binding of modified ptRNAs was not impaired, suggesting that the 3'- S -phosphorothiolate modification specifically prevents formation of the transition state, possibly by excluding catalytic metal ions from the active site.
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MESH Headings
- Bacillus subtilis/enzymology
- Bacillus subtilis/genetics
- Base Sequence
- Binding Sites
- Cations, Divalent/metabolism
- Cytosine/chemistry
- Cytosine/metabolism
- Endoribonucleases/chemistry
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Escherichia coli Proteins
- Hydrolysis
- Kinetics
- Models, Chemical
- Molecular Weight
- Nucleic Acid Conformation
- Nucleotides/chemical synthesis
- Nucleotides/chemistry
- Nucleotides/genetics
- Nucleotides/metabolism
- Oligoribonucleotides/chemical synthesis
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/genetics
- Oligoribonucleotides/metabolism
- Organothiophosphorus Compounds/chemical synthesis
- Organothiophosphorus Compounds/chemistry
- Organothiophosphorus Compounds/metabolism
- RNA Precursors/chemical synthesis
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Transfer/chemical synthesis
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribonuclease P
- Substrate Specificity
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Affiliation(s)
- J M Warnecke
- Medizinische Universität zu Lübeck, Institut für Biochemie, Ratzeburger Allee 160, D-23538 Lübeck, Germany
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48
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Cole KB, Dorit RL. Acquisition of novel catalytic activity by the M1 RNA ribozyme: the cost of molecular adaptation. J Mol Biol 1999; 292:931-44. [PMID: 10525416 DOI: 10.1006/jmbi.1999.3098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ribonucleoprotein RNase P is a critical component of metabolism in all known organisms. In Escherichia coli, RNase P processes a vast array of substrates, including precursor-tRNAs and precursor 4. 5S RNA. In order to understand how such catalytic versatility is achieved and how novel catalytic activity can be acquired, we evolve the M1 RNA ribozyme (the catalytic component of E. coli RNase P) in vitro for cleavage of a DNA substrate. In so doing, we probe the consequences of enhancing catalytic activity on a novel substrate and investigate the cost this versatile enzyme pays for molecular adaptation. A total of 25 generations of in vitro evolution yield a population showing more than a 1000-fold increase in DNA substrate cleavage efficiency (kcat/KM) relative to wild-type M1 RNA. This enhancement is accompanied by a significant reduction in the ability of evolved ribozymes to process the ptRNA class of substrates but also a contrasting increase in activity on the p4.5S RNA class of substrates. This change in the catalytic versatility of the evolved ribozymes suggests that the acquired activity comes at the cost of substrate versatility, and indicates that E. coli RNase P catalytic flexibility is maintained in vivo by selection for the processing of multiple substrates. M1 RNA derivatives enhance cleavage of the DNA substrate by accelerating the catalytic step (kcat) of DNA cleavage, although overall processing efficiency is offset by reduced substrate binding. The enhanced ability to cleave a DNA substrate cannot be readily traced to any of the predominant mutations found in the evolved population, and must instead be due to multiple sequence changes dispersed throughout the molecule. This conclusion underscores the difficulty of correlating observed mutations with changes in catalytic behavior, even in simple biological catalysts for which three-dimensional models are available.
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Affiliation(s)
- K B Cole
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St, New Haven, CT, 06511, USA
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49
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Pomeranz Krummel DA, Altman S. Verification of phylogenetic predictions in vivo and the importance of the tetraloop motif in a catalytic RNA. Proc Natl Acad Sci U S A 1999; 96:11200-5. [PMID: 10500154 PMCID: PMC18011 DOI: 10.1073/pnas.96.20.11200] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
M1 RNA, the catalytic subunit of Escherichia coli RNase P, forms a secondary structure that includes five sequence variants of the tetraloop motif. Site-directed mutagenesis of the five tetraloops of M1 RNA, and subsequent steady-state kinetic analysis in vitro, with different substrates in the presence and absence of the protein cofactor, reveal that (i) certain mutants exhibit defects that vary in a substrate-dependent manner, and that (ii) the protein cofactor can correct the mutant phenotypes in vitro, a phenomenon that is also substrate dependent. Thermal denaturation curves of tetraloop mutants that exhibit kinetic defects differ from those of wild-type M1 RNA. Although the data collected in vitro underscore the importance of the tetraloop motif to M1 RNA function and structure, three of the five tetraloops we examined in vivo are essential for the function of E. coli RNase P. The kinetic data in vitro are not in total agreement with previous phylogenetic predictions but the data in vivo are, as only mutants in those tetraloops proposed to be involved in tertiary interactions fail to complement in vivo. Therefore, the tetraloop motif is critical for the stabilization of the structure of M1 RNA and essential to RNase P function in the cell.
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Affiliation(s)
- D A Pomeranz Krummel
- Department of Molecular, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA
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50
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Brännvall M, Kirsebom LA. Manganese ions induce miscleavage in the Escherichia coli RNase P RNA-catalyzed reaction. J Mol Biol 1999; 292:53-63. [PMID: 10493856 DOI: 10.1006/jmbi.1999.3048] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cleavage by the endoribonuclease RNase P requires the presence of divalent metal ions, of which Mg2+ promotes most efficient cleavage. Here we have studied the importance of there being Mg2+ in RNase P RNA catalysis. It is demonstrated that addition of Mn2+ resulted in a shift of the cleavage site and that this shift was associated with a change in the kinetic constants, in particular kcat. Our data further suggest that the influence of Mn2+ on cleavage site recognition depends on the -1/+73 base-pair in the substrate and the +73/294 base-pair in the RNase P RNA-substrate (RS)-complex. Based on our data we suggest that cleavage in the presence of Mg2+ as the only divalent metal ion proceeds through an intermediate which involves the establishment of the +73/294 base-pair in the RS-complex. By contrast, addition of Mn2+ favours an alternative pathway which results in a shift of the cleavage site. We also studied the influence of Mn2+ on cleavage site recognition and the kinetics of cleavage using various RNase P RNA derivatives carrying substitutions in the region of RNase P RNA that base-pair with the 3' terminal end of the substrate. From these results we conclude that a change in the structure of this RNase P RNA domain influences the involvement of a divalent metal ion(s) in the chemistry of cleavage.
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Affiliation(s)
- M Brännvall
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, SE-751 24, Sweden
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