1
|
Sridhara S. Multiple structural flavors of RNase P in precursor tRNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1835. [PMID: 38479802 DOI: 10.1002/wrna.1835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 06/06/2024]
Abstract
The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
Collapse
Affiliation(s)
- Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
2
|
Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. THE PLANT CELL 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
Collapse
Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
3
|
Bhatta A, Dienemann C, Cramer P, Hillen HS. Structural basis of RNA processing by human mitochondrial RNase P. Nat Struct Mol Biol 2021; 28:713-723. [PMID: 34489609 PMCID: PMC8437803 DOI: 10.1038/s41594-021-00637-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing. Subunits TRMT10C and SDR5C1 form a subcomplex that binds conserved mitochondrial tRNA elements, including the anticodon loop, and positions the tRNA for methylation. The endonuclease PRORP is recruited and activated through interactions with its PPR and nuclease domains to ensure precise pre-tRNA cleavage. The structure provides the molecular basis for the first step of RNA processing in human mitochondria.
Collapse
Affiliation(s)
- Arjun Bhatta
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
| |
Collapse
|
4
|
Altman S, Angele-Martinez C. Inactivating Gene Expression with Antisense Modified Oligonucleotides. Acta Naturae 2021; 13:101-105. [PMID: 34707901 PMCID: PMC8526185 DOI: 10.32607/actanaturae.11522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
Modified nucleotides, including phosphoramidates and mesyl nucleotides, are
very effective in inactivating gene expression in bacteria. Gyr A
is the target gene in several organisms, including Plasmodium
falciparum. Antisense reactions with bacteria infecting citrus plants
are promising but incomplete. Human tissue culture cells assayed with a
different target are also susceptible to the presence of mesyl oligonucleotides.
Collapse
Affiliation(s)
- Sidney Altman
- Yale University New Haven CT USA, Arizona State University, Tempe AZUSA
| | | |
Collapse
|
5
|
de la Peña M, García-Robles I, Cervera A. The Hammerhead Ribozyme: A Long History for a Short RNA. Molecules 2017; 22:molecules22010078. [PMID: 28054987 PMCID: PMC6155905 DOI: 10.3390/molecules22010078] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 01/22/2023] Open
Abstract
Small nucleolytic ribozymes are a family of naturally occurring RNA motifs that catalyse a self-transesterification reaction in a highly sequence-specific manner. The hammerhead ribozyme was the first reported and the most extensively studied member of this family. However, and despite intense biochemical and structural research for three decades since its discovery, the history of this model ribozyme seems to be far from finished. The hammerhead ribozyme has been regarded as a biological oddity typical of small circular RNA pathogens of plants. More recently, numerous and new variations of this ribozyme have been found to inhabit the genomes of organisms from all life kingdoms, although their precise biological functions are not yet well understood.
Collapse
Affiliation(s)
- Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) (CSIC-UPV), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, C/Dr. Moliner 50, Burjassot, 46100 Valencia, Spain.
| | - Amelia Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) (CSIC-UPV), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
| |
Collapse
|
6
|
Schelcher C, Sauter C, Giegé P. Mechanistic and Structural Studies of Protein-Only RNase P Compared to Ribonucleoproteins Reveal the Two Faces of the Same Enzymatic Activity. Biomolecules 2016; 6:biom6030030. [PMID: 27348014 PMCID: PMC5039416 DOI: 10.3390/biom6030030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 11/16/2022] Open
Abstract
RNase P, the essential activity that performs the 5′ maturation of tRNA precursors, can be achieved either by ribonucleoproteins containing a ribozyme present in the three domains of life or by protein-only enzymes called protein-only RNase P (PRORP) that occur in eukaryote nuclei and organelles. A fast growing list of studies has investigated three-dimensional structures and mode of action of PRORP proteins. Results suggest that similar to ribozymes, PRORP proteins have two main domains. A clear functional analogy can be drawn between the specificity domain of the RNase P ribozyme and PRORP pentatricopeptide repeat domain, and between the ribozyme catalytic domain and PRORP N4BP1, YacP-like Nuclease domain. Moreover, both types of enzymes appear to dock with the acceptor arm of tRNA precursors and make specific contacts with the corner of pre-tRNAs. While some clear differences can still be delineated between PRORP and ribonucleoprotein (RNP) RNase P, the two types of enzymes seem to use, fundamentally, the same catalytic mechanism involving two metal ions. The occurrence of PRORP and RNP RNase P represents a remarkable example of convergent evolution. It might be the unique witness of an ongoing replacement of catalytic RNAs by proteins for enzymatic activities.
Collapse
Affiliation(s)
- Cédric Schelcher
- UPR 2357, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 rue du général Zimmer, F-67084 Strasbourg, France.
| | - Claude Sauter
- UPR 9002, Centre National de la Recherche Scientifique, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, Strasbourg F-67084, France.
| | - Philippe Giegé
- UPR 2357, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 rue du général Zimmer, F-67084 Strasbourg, France.
| |
Collapse
|
7
|
Klemm BP, Wu N, Chen Y, Liu X, Kaitany KJ, Howard MJ, Fierke CA. The Diversity of Ribonuclease P: Protein and RNA Catalysts with Analogous Biological Functions. Biomolecules 2016; 6:biom6020027. [PMID: 27187488 PMCID: PMC4919922 DOI: 10.3390/biom6020027] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 12/30/2022] Open
Abstract
Ribonuclease P (RNase P) is an essential endonuclease responsible for catalyzing 5' end maturation in precursor transfer RNAs. Since its discovery in the 1970s, RNase P enzymes have been identified and studied throughout the three domains of life. Interestingly, RNase P is either RNA-based, with a catalytic RNA subunit, or a protein-only (PRORP) enzyme with differential evolutionary distribution. The available structural data, including the active site data, provides insight into catalysis and substrate recognition. The hydrolytic and kinetic mechanisms of the two forms of RNase P enzymes are similar, yet features unique to the RNA-based and PRORP enzymes are consistent with different evolutionary origins. The various RNase P enzymes, in addition to their primary role in tRNA 5' maturation, catalyze cleavage of a variety of alternative substrates, indicating a diversification of RNase P function in vivo. The review concludes with a discussion of recent advances and interesting research directions in the field.
Collapse
Affiliation(s)
- Bradley P Klemm
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Nancy Wu
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yu Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103, USA.
| | - Xin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103, USA.
| | - Kipchumba J Kaitany
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Michael J Howard
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Carol A Fierke
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103, USA.
| |
Collapse
|
8
|
Brillante N, Gößringer M, Lindenhofer D, Toth U, Rossmanith W, Hartmann RK. Substrate recognition and cleavage-site selection by a single-subunit protein-only RNase P. Nucleic Acids Res 2016; 44:2323-36. [PMID: 26896801 PMCID: PMC4797305 DOI: 10.1093/nar/gkw080] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 02/01/2016] [Indexed: 01/22/2023] Open
Abstract
RNase P is the enzyme that removes 5′ extensions from tRNA precursors. With its diversity of enzyme forms—either protein- or RNA-based, ranging from single polypeptides to multi-subunit ribonucleoproteins—the RNase P enzyme family represents a unique model system to compare the evolution of enzymatic mechanisms. Here we present a comprehensive study of substrate recognition and cleavage-site selection by the nuclear single-subunit proteinaceous RNase P PRORP3 from Arabidopsis thaliana. Compared to bacterial RNase P, the best-characterized RNA-based enzyme form, PRORP3 requires a larger part of intact tRNA structure, but little to no determinants at the cleavage site or interactions with the 5′ or 3′ extensions of the tRNA. The cleavage site depends on the combined dimensions of acceptor stem and T domain, but also requires the leader to be single-stranded. Overall, the single-subunit PRORP appears mechanistically more similar to the complex nuclear ribonucleoprotein enzymes than to the simpler bacterial RNase P. Mechanistic similarity or dissimilarity among different forms of RNase P thus apparently do not necessarily reflect molecular composition or evolutionary relationship.
Collapse
Affiliation(s)
- Nadia Brillante
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Markus Gößringer
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany
| | - Dominik Lindenhofer
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany
| |
Collapse
|
9
|
Howard MJ, Klemm BP, Fierke CA. Mechanistic Studies Reveal Similar Catalytic Strategies for Phosphodiester Bond Hydrolysis by Protein-only and RNA-dependent Ribonuclease P. J Biol Chem 2015; 290:13454-64. [PMID: 25817998 DOI: 10.1074/jbc.m115.644831] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Indexed: 11/06/2022] Open
Abstract
Ribonuclease P (RNase P) is an endonuclease that catalyzes the essential removal of the 5' end of tRNA precursors. Until recently, all identified RNase P enzymes were a ribonucleoprotein with a conserved catalytic RNA component. However, the discovery of protein-only RNase P (PRORP) shifted this paradigm, affording a unique opportunity to compare mechanistic strategies used by naturally evolved protein and RNA-based enzymes that catalyze the same reaction. Here we investigate the enzymatic mechanism of pre-tRNA hydrolysis catalyzed by the NYN (Nedd4-BP1, YacP nuclease) metallonuclease of Arabidopsis thaliana, PRORP1. Multiple and single turnover kinetic data support a mechanism where a step at or before chemistry is rate-limiting and provide a kinetic framework to interpret the results of metal alteration, mutations, and pH dependence. Catalytic activity has a cooperative dependence on the magnesium concentration (nH = 2) under kcat/Km conditions, suggesting that PRORP1 catalysis is optimal with at least two active site metal ions, consistent with the crystal structure. Metal rescue of Asp-to-Ala mutations identified two aspartates important for enhancing metal ion affinity. The single turnover pH dependence of pre-tRNA cleavage revealed a single ionization (pKa ∼ 8.7) important for catalysis, consistent with deprotonation of a metal-bound water nucleophile. The pH and metal dependence mirrors that observed for the RNA-based RNase P, suggesting similar catalytic mechanisms. Thus, despite different macromolecular composition, the RNA and protein-based RNase P act as dynamic scaffolds for the binding and positioning of magnesium ions to catalyze phosphodiester bond hydrolysis.
Collapse
Affiliation(s)
| | | | - Carol A Fierke
- From the Departments of Biological Chemistry and Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
10
|
Ward WL, Plakos K, DeRose VJ. Nucleic acid catalysis: metals, nucleobases, and other cofactors. Chem Rev 2014; 114:4318-42. [PMID: 24730975 PMCID: PMC4002065 DOI: 10.1021/cr400476k] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Indexed: 12/17/2022]
Affiliation(s)
- W. Luke Ward
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Kory Plakos
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Victoria J. DeRose
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| |
Collapse
|
11
|
Transfer RNA post-transcriptional processing, turnover, and subcellular dynamics in the yeast Saccharomyces cerevisiae. Genetics 2013; 194:43-67. [PMID: 23633143 DOI: 10.1534/genetics.112.147470] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Transfer RNAs (tRNAs) are essential for protein synthesis. In eukaryotes, tRNA biosynthesis employs a specialized RNA polymerase that generates initial transcripts that must be subsequently altered via a multitude of post-transcriptional steps before the tRNAs beome mature molecules that function in protein synthesis. Genetic, genomic, biochemical, and cell biological approaches possible in the powerful Saccharomyces cerevisiae system have led to exciting advances in our understandings of tRNA post-transcriptional processing as well as to novel insights into tRNA turnover and tRNA subcellular dynamics. tRNA processing steps include removal of transcribed leader and trailer sequences, addition of CCA to the 3' mature sequence and, for tRNA(His), addition of a 5' G. About 20% of yeast tRNAs are encoded by intron-containing genes. The three-step splicing process to remove the introns surprisingly occurs in the cytoplasm in yeast and each of the splicing enzymes appears to moonlight in functions in addition to tRNA splicing. There are 25 different nucleoside modifications that are added post-transcriptionally, creating tRNAs in which ∼15% of the residues are nucleosides other than A, G, U, or C. These modified nucleosides serve numerous important functions including tRNA discrimination, translation fidelity, and tRNA quality control. Mature tRNAs are very stable, but nevertheless yeast cells possess multiple pathways to degrade inappropriately processed or folded tRNAs. Mature tRNAs are also dynamic in cells, moving from the cytoplasm to the nucleus and back again to the cytoplasm; the mechanism and function of this retrograde process is poorly understood. Here, the state of knowledge for tRNA post-transcriptional processing, turnover, and subcellular dynamics is addressed, highlighting the questions that remain.
Collapse
|
12
|
Abstract
Ribonuclease P (RNase P) is one of the first ribozymes discovered and it is found in all phylogenetic groups. It is responsible for processing the 5' end of pre-tRNAs as well as other RNA molecules. RNase P is formed by an RNA molecule responsible for catalysis and one or more proteins. Structural studies of the proteins from different organisms, the bacterial RNA component, and a bacterial RNase P holoenzyme/tRNA complex provide insights into the mechanism of this universal ribozyme. Together with the existing wealth of biochemical information, these studies provide atomic-level information on the mechanism of RNase P and continue to expand our understanding of the structure and architecture of large RNA molecules and ribonucleoprotein complexes, the nature of catalysis by ribozymes, the structural basis of recognition of RNA by RNA molecules, and the evolution of enzymes from the prebiotic, RNA-based world to the modern world.
Collapse
Affiliation(s)
- Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA.
| |
Collapse
|
13
|
Pinker F, Bonnard G, Gobert A, Gutmann B, Hammani K, Sauter C, Gegenheimer PA, Giegé P. PPR proteins shed a new light on RNase P biology. RNA Biol 2013; 10:1457-68. [PMID: 23925311 PMCID: PMC3858429 DOI: 10.4161/rna.25273] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A fast growing number of studies identify pentatricopeptide repeat (PPR) proteins as major players in gene expression processes. Among them, a subset of PPR proteins called PRORP possesses RNase P activity in several eukaryotes, both in nuclei and organelles. RNase P is the endonucleolytic activity that removes 5′ leader sequences from tRNA precursors and is thus essential for translation. Before the characterization of PRORP, RNase P enzymes were thought to occur universally as ribonucleoproteins, although some evidence implied that some eukaryotes or cellular compartments did not use RNA for RNase P activity. The characterization of PRORP reveals a two-domain enzyme, with an N-terminal domain containing multiple PPR motifs and assumed to achieve target specificity and a C-terminal domain holding catalytic activity. The nature of PRORP interactions with tRNAs suggests that ribonucleoprotein and protein-only RNase P enzymes share a similar substrate binding process.
Collapse
Affiliation(s)
- Franziska Pinker
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France; Institut de Biologie Moléculaire et Cellulaire du CNRS; Architecture et Réactivité de l'ARN; Université de Strasbourg; Strasbourg, France
| | - Géraldine Bonnard
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Anthony Gobert
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Bernard Gutmann
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Kamel Hammani
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Claude Sauter
- Institut de Biologie Moléculaire et Cellulaire du CNRS; Architecture et Réactivité de l'ARN; Université de Strasbourg; Strasbourg, France
| | | | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| |
Collapse
|
14
|
Gobert A, Pinker F, Fuchsbauer O, Gutmann B, Boutin R, Roblin P, Sauter C, Giegé P. Structural insights into protein-only RNase P complexed with tRNA. Nat Commun 2013; 4:1353. [PMID: 23322041 PMCID: PMC3562450 DOI: 10.1038/ncomms2358] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 12/05/2012] [Indexed: 01/21/2023] Open
Abstract
RNase P is the essential activity removing 5'-leader sequences from transfer RNA precursors. RNase P was always associated with ribonucleoprotein complexes before the discovery of protein-only RNase P enzymes called PRORPs (PROteinaceous RNase P) in eukaryotes. Here we provide biophysical and functional data to understand the mode of action of PRORP enzymes. Activity assays and footprinting experiments show that the anticodon domain of transfer RNA is dispensable, whereas individual residues in D and TψC loops are essential for PRORP function. PRORP proteins are characterized in solution and a molecular envelope is derived from small-angle X-ray scattering. Conserved residues are shown to be involved in the binding of one zinc atom to PRORP. These results facilitate the elaboration of a model of the PRORP/transfer RNA interaction. The comparison with the ribonucleoprotein RNase P/transfer RNA complex suggests that transfer RNA recognition by PRORP proteins is similar to that by ribonucleoprotein RNase P.
Collapse
MESH Headings
- Arabidopsis/metabolism
- Arabidopsis Proteins/chemistry
- Arabidopsis Proteins/metabolism
- Models, Biological
- Models, Molecular
- Protein Binding
- RNA/chemistry
- RNA Precursors/chemistry
- RNA, Mitochondrial
- RNA, Plant/chemistry
- RNA, Plant/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Recombination, Genetic/genetics
- Regulatory Sequences, Ribonucleic Acid
- Ribonuclease P/chemistry
- Ribonuclease P/metabolism
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/metabolism
- Scattering, Small Angle
- Solutions
- Spectrophotometry, Atomic
- X-Ray Diffraction
- Zinc/metabolism
Collapse
Affiliation(s)
- Anthony Gobert
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
- These authors contributed equally to this work
| | - Franziska Pinker
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Architecture et Réactivité de l'ARN, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
- These authors contributed equally to this work
| | - Olivier Fuchsbauer
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Architecture et Réactivité de l'ARN, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Bernard Gutmann
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - René Boutin
- Laboratoire d’Hydrologie et de Géochimie du CNRS, 1, rue Blessig, 67084 Strasbourg, France
| | - Pierre Roblin
- Synchrotron SOLEIL, l'Orme des Merisiers Saint-Aubin, 91410 Gif-sur-Yvette, France
- URBIA-Nantes, INRA Centre de Nantes, 60 rue de la Géraudière, 44316 Nantes, France
| | - Claude Sauter
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Architecture et Réactivité de l'ARN, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| |
Collapse
|
15
|
Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing. Proc Natl Acad Sci U S A 2012; 109:16149-54. [PMID: 22991464 DOI: 10.1073/pnas.1209062109] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of tRNA precursors. Typically these enzymes are ribonucleoproteins with a conserved RNA component responsible for catalysis. However, protein-only RNase P (PRORP) enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. PRORP enzymes are nuclear encoded and conserved among many eukaryotes, having evolved recently as yeast mitochondrial genomes encode an RNase P RNA. Here we report the crystal structure of PRORP1 from A. thaliana at 1.75 Å resolution, revealing a prototypical metallonuclease domain tethered to a pentatricopeptide repeat (PPR) domain by a structural zinc-binding domain. The metallonuclease domain is a unique high-resolution structure of a Nedd4-BP1, YacP Nucleases (NYN) domain that is a member of the PIN domain-like fold superfamily, including the FLAP nuclease family. The structural similarity between PRORP1 and the FLAP nuclease family suggests that they evolved from a common ancestor. Biochemical data reveal that conserved aspartate residues in PRORP1 are important for catalytic activity and metal binding and that the PPR domain also enhances activity, likely through an interaction with pre-tRNA. These results provide a foundation for understanding tRNA maturation in organelles. Furthermore, these studies allow for a molecular-level comparison of the catalytic strategies used by the only known naturally evolved protein and RNA-based catalysts that perform the same biological function, pre-tRNA maturation, thereby providing insight into the differences between the prebiotic RNA world and the present protein-dominated world.
Collapse
|
16
|
Pavlova LV, Gössringer M, Weber C, Buzet A, Rossmanith W, Hartmann RK. tRNA processing by protein-only versus RNA-based RNase P: kinetic analysis reveals mechanistic differences. Chembiochem 2012; 13:2270-6. [PMID: 22976545 DOI: 10.1002/cbic.201200434] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Indexed: 11/07/2022]
Abstract
In Arabidopsis thaliana, RNase P function, that is, endonucleolytic tRNA 5'-end maturation, is carried out by three homologous polypeptides ("proteinaceous RNase P" (PRORP) 1, 2 and 3). Here we present the first kinetic analysis of these enzymes. For PRORP1, a specificity constant (k(react)/K(m(sto))) of 3×10(6) M(-1) min(-1) was determined under single-turnover conditions. We demonstrate a fundamentally different sensitivity of PRORP enzymes to an Rp-phosphorothioate modification at the canonical cleavage site in a 5'-precursor tRNA substrate; whereas processing by bacterial RNase P is inhibited by three orders of magnitude in the presence of this sulfur substitution and Mg(2+) as the metal-ion cofactor, the PRORP enzymes are affected by not more than a factor of five under the same conditions, without significantly increased miscleavage. These findings indicate that the catalytic mechanism utilized by proteinaceous RNase P is different from that of RNA-based bacterial RNase P, taking place without a direct metal-ion coordination to the (pro-)Rp substituent. As Rp-phosphorothioate and inosine modification at all 26 G residues of the tRNA body had only minor effects on processing by PRORP, we conclude that productive PRORP-substrate interaction is not critically dependent on any of the affected (pro-)Rp oxygens or guanosine 2-amino groups.
Collapse
Affiliation(s)
- Liudmila V Pavlova
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | | | | | | | | | | |
Collapse
|
17
|
Goldfarb KC, Borah S, Cech TR. RNase P branches out from RNP to protein: organelle-triggered diversification? Genes Dev 2012; 26:1005-9. [PMID: 22588715 DOI: 10.1101/gad.193581.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RNase P is the enzyme that removes 5' leader sequences from precursor tRNAs. Remarkably, in most organisms, RNase P is a ribonucleoprotein particle where the RNA component is responsible for catalysis. In this issue of Genes & Development, Gutmann and colleagues (pp. 1022-1027) report the first organism, Arabidopsis thaliana, to employ protein-only RNase P in both its nucleus and organelles. An intriguing possibility is that replacement of RNase P ribonucleoprotein particles (RNPs) by proteins may have been triggered by the acquisition of organelles.
Collapse
Affiliation(s)
- Katherine C Goldfarb
- Howard Hughes Medical Institute, University of Colorado Biofrontiers Institute, Boulder Colorado 80309, USA
| | | | | |
Collapse
|
18
|
Krehan M, Heubeck C, Menzel N, Seibel P, Schön A. RNase MRP RNA and RNase P activity in plants are associated with a Pop1p containing complex. Nucleic Acids Res 2012; 40:7956-66. [PMID: 22641852 PMCID: PMC3439889 DOI: 10.1093/nar/gks476] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
RNase P processes the 5'-end of tRNAs. An essential catalytic RNA has been demonstrated in Bacteria, Archaea and the nuclei of most eukaryotes; an organism-specific number of proteins complement the holoenzyme. Nuclear RNase P from yeast and humans is well understood and contains an RNA, similar to the sister enzyme RNase MRP. In contrast, no protein subunits have yet been identified in the plant enzymes, and the presence of a nucleic acid in RNase P is still enigmatic. We have thus set out to identify and characterize the subunits of these enzymes in two plant model systems. Expression of the two known Arabidopsis MRP RNA genes in vivo was verified. The first wheat MRP RNA sequences are presented, leading to improved structure models for plant MRP RNAs. A novel mRNA encoding the central RNase P/MRP protein Pop1p was identified in Arabidopsis, suggesting the expression of distinct protein variants from this gene in vivo. Pop1p-specific antibodies precipitate RNase P activity and MRP RNAs from wheat extracts. Our results provide evidence that in plants, Pop1p is associated with MRP RNAs and with the catalytic subunit of RNase P, either separately or in a single large complex.
Collapse
Affiliation(s)
- Mario Krehan
- Molekulare Zelltherapie, Biotechnologisch-Biomedizinisches Zentrum, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | | | | | | | | |
Collapse
|
19
|
Stoppel R, Meurer J. The cutting crew - ribonucleases are key players in the control of plastid gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1663-73. [PMID: 22140236 DOI: 10.1093/jxb/err401] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chloroplast biogenesis requires constant adjustment of RNA homeostasis under conditions of on-going developmental and environmental change and its regulation is achieved mainly by post-transcriptional control mechanisms mediated by various nucleus-encoded ribonucleases. More than 180 ribonucleases are annotated in Arabidopsis, but only 17 are predicted to localize to the chloroplast. Although different ribonucleases act at different RNA target sites in vivo, most nucleases that attack RNA are thought to lack intrinsic cleavage specificity and show non-specific activity in vitro. In vivo, specificity is thought to be imposed by auxiliary RNA-binding proteins, including members of the huge pentatricopeptide repeat family, which protect RNAs from non-specific nucleolytic attack by masking otherwise vulnerable sites. RNA stability is also influenced by secondary structure, polyadenylation, and ribosome binding. Ribonucleases may cleave at internal sites (endonucleases) or digest successively from the 5' or 3' end of the polynucleotide chain (exonucleases). In bacteria, RNases act in the maturation of rRNA and tRNA precursors, as well as in initiating the degradation of mRNAs and small non-coding RNAs. Many ribonucleases in the chloroplasts of higher plants possess homologies to their bacterial counterparts, but their precise functions have rarely been described. However, many ribonucleases present in the chloroplast process polycistronic rRNAs, tRNAs, and mRNAs. The resulting production of monocistronic, translationally competent mRNAs may represent an adaptation to the eukaryotic cellular environment. This review provides a basic overview of the current knowledge of RNases in plastids and highlights gaps to stimulate future studies.
Collapse
Affiliation(s)
- Rhea Stoppel
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology/Botany, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | | |
Collapse
|
20
|
Abstract
Nuclear ribonuclease (RNase) P is a ubiquitous essential ribonucleoprotein complex, one of only two known RNA-based enzymes found in all three domains of life. The RNA component is the catalytic moiety of RNases P across all phylogenetic domains; it contains a well-conserved core, whereas peripheral structural elements are diverse. RNA components of eukaryotic RNases P tend to be less complex than their bacterial counterparts, a simplification that is accompanied by a dramatic reduction of their catalytic ability in the absence of protein. The size and complexity of the protein moieties increase dramatically from bacterial to archaeal to eukaryotic enzymes, apparently reflecting the delegation of some structural functions from RNA to proteins and, perhaps, in response to the increased complexity of the cellular environment in the more evolutionarily advanced organisms; the reasons for the increased dependence on proteins are not clear. We review current information on RNase P and the closely related universal eukaryotic enzyme RNase MRP, focusing on their functions and structural organization.
Collapse
Affiliation(s)
- Olga Esakova
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | |
Collapse
|
21
|
Gobert A, Gutmann B, Taschner A, Gössringer M, Holzmann J, Hartmann RK, Rossmanith W, Giegé P. A single Arabidopsis organellar protein has RNase P activity. Nat Struct Mol Biol 2010; 17:740-4. [PMID: 20473316 DOI: 10.1038/nsmb.1812] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 03/19/2010] [Indexed: 12/18/2022]
Abstract
The ubiquitous endonuclease RNase P is responsible for the 5' maturation of tRNA precursors. Until the discovery of human mitochondrial RNase P, these enzymes had typically been found to be ribonucleoproteins, the catalytic activity of which is associated with the RNA component. Here we show that, in Arabidopsis thaliana mitochondria and plastids, a single protein called 'proteinaceous RNase P' (PRORP1) can perform the endonucleolytic maturation of tRNA precursors that defines RNase P activity. In addition, PRORP1 is able to cleave tRNA-like structures involved in the maturation of plant mitochondrial mRNAs. Finally, we show that Arabidopsis PRORP1 can replace the bacterial ribonucleoprotein RNase P in Escherichia coli cells. PRORP2 and PRORP3, two paralogs of PRORP1, are both localized in the nucleus.
Collapse
Affiliation(s)
- Anthony Gobert
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Strasbourg, France
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
The ability to interfere with gene expression is of crucial importance to unravel the function of genes and is also a promising therapeutic strategy. Here we discuss methodologies for inhibition of target RNAs based on the cleavage activity of the essential enzyme, Ribonuclease P (RNase P). RNase P-mediated cleavage of target RNAs can be directed by external guide sequences (EGSs) or by the use of the catalytic M1 RNA from E. coli linked to a guide sequence (M1GSs). These are not only basic tools for functional genetic studies in prokaryotic and eukaryotic cells but also promising antibacterial, anticancer and antiviral agents.
Collapse
Affiliation(s)
- Eirik Wasmuth Lundblad
- Reference Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway.
| | | |
Collapse
|
23
|
Abstract
The chloroplast genome encodes proteins required for photosynthesis, gene expression, and other essential organellar functions. Derived from a cyanobacterial ancestor, the chloroplast combines prokaryotic and eukaryotic features of gene expression and is regulated by many nucleus-encoded proteins. This review covers four major chloroplast posttranscriptional processes: RNA processing, editing, splicing, and turnover. RNA processing includes the generation of transcript 5' and 3' termini, as well as the cleavage of polycistronic transcripts. Editing converts specific C residues to U and often changes the amino acid that is specified by the edited codon. Chloroplasts feature introns of groups I and II, which undergo protein-facilitated cis- or trans-splicing in vivo. Each of these RNA-based processes involves proteins of the pentatricopeptide motif-containing family, which does not occur in prokaryotes. Plant-specific RNA-binding proteins may underpin the adaptation of the chloroplast to the eukaryotic context.
Collapse
Affiliation(s)
- David B Stern
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA.
| | | | | |
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Lien B Lai
- Department of Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | | | | | | |
Collapse
|
25
|
Abstract
The "RNA World" hypothesis suggests that life developed from RNA enzymes termed ribozymes, which carry out reactions without assistance from proteins. Ribonuclease (RNase) P is one ribozyme that appears to have adapted these origins to modern cellular life by adding protein to the RNA core in order to broaden the potential functions. This RNA-protein complex plays diverse roles in processing RNA, but its best-understood reaction is pre-tRNA maturation, resulting in mature 5' ends of tRNAs. The core catalytic activity resides in the RNA subunit of almost all RNase P enzymes but broader substrate tolerance is required for recognizing not only the diverse sequences of tRNAs, but also additional cellular RNA substrates. This broader substrate tolerance is provided by the addition of protein to the RNA core and allows RNase P to selectively recognize different RNAs, and possibly ribonucleoprotein (RNP) substrates. Thus, increased protein content correlated with evolution from bacteria to eukaryotes has further enhanced substrate potential enabling the enzyme to function in a complex cellular environment.
Collapse
Affiliation(s)
- Michael C. Marvin
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, Michigan 48109-0606
| | - David R. Engelke
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, Michigan 48109-0606
| |
Collapse
|
26
|
tRNA recognition, processing, and disease: hypotheses around an unorthodox type of RNase P in human mitochondria. Mitochondrion 2009; 9:284-8. [PMID: 19376274 DOI: 10.1016/j.mito.2009.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 03/24/2009] [Indexed: 11/24/2022]
Abstract
RNase P is the endonuclease responsible for the maturation of the 5' ends of tRNAs. A catalytic RNA component was long considered the premier attribute of the enzyme family. Ignoring this heritage, human mitochondria make their RNase P of three proteins only. While one of them appears to be the metallonuclease actually responsible for phosphodiester hydrolysis, the other two have been recruited from unrelated biochemical pathways and may be critical for substrate recognition. One of them is moreover identical to a previously identified amyloid-beta-binding protein, whereby it could link tRNA processing to mitochondrial dysfunction in Alzheimer's disease.
Collapse
|
27
|
Schuster G, Stern D. RNA polyadenylation and decay in mitochondria and chloroplasts. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:393-422. [PMID: 19215778 DOI: 10.1016/s0079-6603(08)00810-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mitochondria and chloroplasts were originally acquired by eukaryotic cells through endosymbiotic events and retain their own gene expression machinery. One hallmark of gene regulation in these two organelles is the predominance of posttranscriptional control, which is exerted both at the gene-specific and global levels. This review focuses on their mechanisms of RNA degradation, and therefore mainly on the polyadenylation-stimulated degradation pathway. Overall, mitochondria and chloroplasts have retained the prokaryotic RNA decay system, despite evolution in the number and character of the enzymes involved. However, several significant differences exist, of which the presence of stable poly(A) tails, and the location of PNPase in the intermembrane space in animal mitochondria, are perhaps the most remarkable. The known and predicted proteins taking part in polyadenylation-stimulated degradation pathways are described, both in chloroplasts and four mitochondrial types: plant, yeast, trypanosome, and animal.
Collapse
Affiliation(s)
- Gadi Schuster
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | | |
Collapse
|
28
|
Abstract
Ribonuclease P (RNase P) is an essential enzyme that catalyzes the 5' endonucleolytic cleavage of precursor transfer RNAs (pretRNAs). It is found in all phylogenetic domains: bacteria, archaea and eukaryotes. The bacterial enzyme consists of a single, catalytic RNA subunit and one small protein, while the archaeal and eukaryotic enzymes have 4-10 proteins in addition to a similar RNA subunit. The bacterial RNA acts as a ribozyme at high salt in vitro; however the added protein optimizes kinetics and makes specific contacts with the pre-tRNA substrate. The bacterial protein subunit also appears to be required for the processing of non-tRNA substrates by broadening recognition tolerance. In addition, the immense increase in protein content in the eukaryotic enzymes suggests substantially enlarged capacity for recognition of additional substrates. Recently intron-encoded box C/D snoRNAs were shown to be likely substrates for RNase P, with several lines of evidence suggesting that the nuclear holoenzyme binds tightly to, and can cleave single-stranded RNA in a sequence dependent fashion. The possible involvement of RNase P in additional RNA processing or turnover pathways would be consistent with previous findings that RNase MRP, a variant of RNase P that has evolved to participate in ribosomal RNA processing, is also involved in turnover of specific messenger RNAs. Here, involvement of RNase P in multiple RNA processing pathways is discussed.
Collapse
Affiliation(s)
- Michael C. Marvin
- Department of Biological Chemistry; University of Michigan School of Medicine; Ann Arbor, Michigan USA
| | - David R. Engelke
- Department of Biological Chemistry; University of Michigan School of Medicine; Ann Arbor, Michigan USA
| |
Collapse
|
29
|
Hartmann RK, Gössringer M, Späth B, Fischer S, Marchfelder A. The making of tRNAs and more - RNase P and tRNase Z. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:319-68. [PMID: 19215776 DOI: 10.1016/s0079-6603(08)00808-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transfer-RNA (tRNA) molecules are essential players in protein biosynthesis. They are transcribed as precursors, which have to be extensively processed at both ends to become functional adaptors in protein synthesis. Two endonucleases that directly interact with the tRNA moiety, RNase P and tRNase Z, remove extraneous nucleotides on the molecule's 5'- and 3'-side, respectively. The ribonucleoprotein enzyme RNase P was identified almost 40 years ago and is considered a vestige from the "RNA world". Here, we present the state of affairs on prokaryotic RNase P, with a focus on recent findings on its role in RNA metabolism. tRNase Z was only identified 6 years ago, and we do not yet have a comprehensive understanding of its function. The current knowledge on prokaryotic tRNase Z in tRNA 3'-processing is reviewed here. A second, tRNase Z-independent pathway of tRNA 3'-end maturation involving 3'-exonucleases will also be discussed.
Collapse
Affiliation(s)
- Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany
| | | | | | | | | |
Collapse
|
30
|
Abstract
Major progress in the study of RNase P has resulted from crystallography of bacterial catalytic subunits and the discovery of catalytic activity in eukaryotes. Several new substrates have also been identified, primarily in bacteria but also in yeast. Our current world should be called the "RNA-protein world" rather than the "protein world".
Collapse
Affiliation(s)
- Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, CT 06511, USA.
| |
Collapse
|
31
|
Willkomm DK, Hartmann RK. An important piece of the RNase P jigsaw solved. Trends Biochem Sci 2007; 32:247-50. [PMID: 17485211 DOI: 10.1016/j.tibs.2007.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 04/30/2007] [Indexed: 11/21/2022]
Abstract
RNase P is the ribonucleoprotein enzyme that generates the mature 5' ends of tRNAs throughout all three kingdoms of life. Long known to function as a ribozyme in bacteria and several archaea, it has remained unclear if eukaryal RNase P has entirely lost this RNA-alone catalytic capacity (i.e. the ability to perform catalysis even if the protein part of the enzyme is removed). This controversial debate has now ended after the recent demonstration that eukaryal RNase P also exhibits ribozyme activity.
Collapse
Affiliation(s)
- Dagmar K Willkomm
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, D-35037 Marburg, Germany
| | | |
Collapse
|
32
|
Abstract
Ribonuclease P (RNase P) is a ubiquitous endonuclease that catalyses the maturation of the 5' end of transfer RNA (tRNA). Although it carries out a biochemically simple reaction, RNase P is a complex ribonucleoprotein particle composed of a single large RNA and at least one protein component. In bacteria and some archaea, the RNA component of RNase P can catalyse tRNA maturation in vitro in the absence of proteins. The discovery of the catalytic activity of the bacterial RNase P RNA triggered numerous mechanistic and biochemical studies of the reactions catalysed by the RNA alone and by the holoenzyme and, in recent years, structures of individual components of the RNase P holoenzyme have been determined. The goal of the present review is to summarize what is known about the bacterial RNase P, and to bring together the recent structural results with extensive earlier biochemical and phylogenetic findings.
Collapse
Affiliation(s)
- Alexei V Kazantsev
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA
| | | |
Collapse
|
33
|
Evans D, Marquez SM, Pace NR. RNase P: interface of the RNA and protein worlds. Trends Biochem Sci 2006; 31:333-41. [PMID: 16679018 DOI: 10.1016/j.tibs.2006.04.007] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/07/2006] [Accepted: 04/24/2006] [Indexed: 01/27/2023]
Abstract
Ribonuclease P (RNase P) is an endonuclease involved in processing tRNA. It contains both RNA and protein subunits and occurs in all three domains of life: namely, Archaea, Bacteria and Eukarya. The RNase P RNA subunits from bacteria and some archaea are catalytically active in vitro, whereas those from eukaryotes and most archaea require protein subunits for activity. RNase P has been characterized biochemically and genetically in several systems, and detailed structural information is emerging for both RNA and protein subunits from phylogenetically diverse organisms. In vitro reconstitution of activity is providing insight into the role of proteins in the RNase P holoenzyme. Together, these findings are beginning to impart an understanding of the coevolution of the RNA and protein worlds.
Collapse
Affiliation(s)
- Donald Evans
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Campus Box 347, Boulder, CO 80309-0347, USA
| | | | | |
Collapse
|
34
|
Hall TA, Brown JW. Interactions between RNase P protein subunits in archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2005; 1:247-54. [PMID: 15810434 PMCID: PMC2685574 DOI: 10.1155/2004/743956] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A yeast two-hybrid system was used to identify protein-protein interactions between the ribonuclease P (RNase P) protein subunits Mth11p, Mth687p, Mth688p and Mth1618p from the archaeon Methanothermobacter thermoautotrophicus. Clear interactions between Mth688p and Mth687p, and between Mth1618p and Mth11p, were confirmed by HIS3 and LacZ reporter expression. Weaker interactions of Mth687p and Mth688p with Mth 11p, and Mth11p with itself, are also suggested. These interactions resemble, and confirm, those previously seen among the homologs of these proteins in the more complex yeast RNase P holoenzyme.
Collapse
Affiliation(s)
- Thomas A. Hall
- Ibis Therapeutics, 2292 Faraday Ave., Carlsbad, CA 92008, USA
| | - James W. Brown
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA
- Corresponding author ()
| |
Collapse
|
35
|
Abstract
The 5'-end maturation of tRNAs is catalyzed by the ribonucleoprotein enzyme ribonuclease P (RNase P) in all organisms. Here we provide, for the first time, a comprehensive overview on the representation of individual RNase P protein homologs within the Eukarya and Archaea. Most eukaryotes have homologs for all four protein subunits (Pop4, Rpp1, Pop5 and Rpr2) present in the majority of Archaea. Pop4 is the only RNase P protein subunit identifiable in all Eukarya and Archaea with available genome sequences. Remarkably, there is no structural homology between bacterial and archaeal-eukaryotic RNase P proteins. The simplest interpretation is that RNase P has an 'RNA-alone' origin and progenitors of Bacteria and Archaea diverged very early in evolution and then pursued completely different strategies in the recruitment of protein subunits during the transition from the 'RNA-alone' to the 'RNA-protein' state of the enzyme.
Collapse
Affiliation(s)
- Enno Hartmann
- Institut für Biologie, Universität zu Lübeck, Ratzeburger Allee 160, D-23538, Lübeck, Germany.
| | | |
Collapse
|
36
|
Seif ER, Forget L, Martin NC, Lang BF. Mitochondrial RNase P RNAs in ascomycete fungi: lineage-specific variations in RNA secondary structure. RNA (NEW YORK, N.Y.) 2003; 9:1073-83. [PMID: 12923256 PMCID: PMC1370472 DOI: 10.1261/rna.5880403] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Accepted: 06/18/2003] [Indexed: 05/19/2023]
Abstract
The RNA subunit of mitochondrial RNase P (mtP-RNA) is encoded by a mitochondrial gene (rnpB) in several ascomycete fungi and in the protists Reclinomonas americana and Nephroselmis olivacea. By searching for universally conserved structural elements, we have identified previously unknown rnpB genes in the mitochondrial DNAs (mtDNAs) of two fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces octosporus; in the budding yeast Pichia canadensis; and in the archiascomycete Taphrina deformans. The expression of mtP-RNAs of the predicted size was experimentally confirmed in the two fission yeasts, and their precise 5' and 3' ends were determined by sequencing of cDNAs generated from circularized mtP-RNAs. Comparative RNA secondary structure modeling shows that in contrast to mtP-RNAs of the two protists R. americana and N. olivacea, those of ascomycete fungi all have highly reduced secondary structures. In certain budding yeasts, such as Saccharomycopsis fibuligera, we find only the two most conserved pairings, P1 and P4. A P18 pairing is conserved in Saccharomyces cerevisiae and its close relatives, whereas nearly half of the minimum bacterial consensus structure is retained in the RNAs of fission yeasts, Aspergillus nidulans and Taphrina deformans. The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed.
Collapse
Affiliation(s)
- Elias R Seif
- Program in Evolutionary Biology, Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | | | | | | |
Collapse
|
37
|
Evolution of the Fungi and their Mitochondrial Genomes. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1874-5334(03)80010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
38
|
Abstract
Several tRNAs in the hyperthermophilic bacterium Aquifex aeolicus are encoded in clusters and as part of ribosomal RNA operons, implying the requirement for tRNA processing by ribonuclease P (RNase P). Intriguingly, neither a gene for the RNA nor the protein component of this ubiquitous ribonucleoprotein enzyme has been hitherto identified in the sequenced genome of A. aeolicus, despite extensive data mining. As a result of the present study, primer extension analysis revealed that tRNAs in A. aeolicus possess canonical mature 5' ends; yet we were unable to demonstrate RNase P holoenzyme or RNase P RNA alone activity in A. aeolicus extracts under a variety of reaction conditions utilizing mono- and dimeric ptRNA substrates. Processing of dimeric ptRNA transcripts in extracts of A. aeolicus disclosed at least one endoribonuclease which cleaves in the A/U-rich spacer of the tandem ptRNA, reminiscent of bacterial RNase E-like enzymes.
Collapse
MESH Headings
- Bacteria/cytology
- Bacteria/genetics
- Bacteria/metabolism
- Base Sequence
- DNA Primers/genetics
- DNA-Directed RNA Polymerases/genetics
- DNA-Directed RNA Polymerases/metabolism
- Electrophoresis, Polyacrylamide Gel/methods
- Molecular Sequence Data
- Nucleic Acid Conformation
- Open Reading Frames
- Operon
- Peptide Elongation Factor Tu/genetics
- Phosphorus Isotopes
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Templates, Genetic
- Transcription, Genetic/genetics
Collapse
Affiliation(s)
- Dagmar K Willkomm
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | | | | |
Collapse
|
39
|
Affiliation(s)
- T A Hall
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | |
Collapse
|
40
|
Affiliation(s)
- Venkat Gopalan
- Department of Biochemistry, Ohio State University, Columbus, Ohio 43210-1292, USA
| | | | | |
Collapse
|
41
|
Abstract
Ribonuclease P (RNase P) is an essential endonuclease that acts early in the tRNA biogenesis pathway. This enzyme catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs. RNase P activities have been identified in Bacteria, Archaea, and Eucarya, as well as organelles. Most forms of RNase P are ribonucleoproteins, i.e., they consist of an essential RNA subunit and protein subunits, although the composition of the enzyme in mitochondria and chloroplasts is still under debate. The recent purification of the eukaryotic nuclear RNase P has demonstrated a significantly larger protein content compared to the bacterial enzyme. Moreover, emerging evidence suggests that the eukaryotic RNase P has evolved into at least two related nuclear enzymes with distinct functions, RNase P and RNase MRP. Here we review current information on RNase P, with emphasis on the composition, structure, and functions of the eukaryotic nuclear holoenzyme, and its relationship with RNase MRP.
Collapse
Affiliation(s)
- Shaohua Xiao
- Department of Biological Chemistry, 3200 MSRB III, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - Felicia Scott
- Department of Biological Chemistry, 3200 MSRB III, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - David R. Engelke
- Department of Biological Chemistry, 3200 MSRB III, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, Michigan 48109-0606
| |
Collapse
|
42
|
Salavati R, Panigrahi AK, Stuart KD. Mitochondrial ribonuclease P activity of Trypanosoma brucei. Mol Biochem Parasitol 2001; 115:109-17. [PMID: 11377745 DOI: 10.1016/s0166-6851(01)00273-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ribonuclease P (RNase P) is an essential enzyme that cleaves the 5' leader sequences of precursor tRNAs (pre-tRNAs) to generate mature tRNAs. The RNase P-like activity from Trypanosoma brucei mitochondria (mtRNase P) was purified over 10000-fold by sequential column chromatography. This is the first demonstration of such activity from mitochondria of parasitic protozoa. Its apparent molecular weight is approximately 70 kDa, considerably less than bacterial RNase P. Preliminary characterizations revealed no RNA component that is essential for this activity. Like other RNase P activities, the cleavage generates mature tRNAs with a terminal 5'-phosphate at the cleavage site and the 5' leader sequence with a 3'-hydroxyl. Disruption of the pre-tRNA tertiary structure inhibits the cleavage of the substrates. These data suggest that although all mitochondrial tRNAs are encoded in nuclear DNA in T. brucei, these cells contain an RNase P in the mitochondrion that cleaves the 5' terminal leader sequences of pre-tRNAs to generate mature tRNAs. Cleavage by mtRNase P of a pre-tRNA substrate that was divided into two fragments was demonstrated. This shows the feasibility of artificial regulation of gene expression that can be achieved by creating a complex made of target mRNA and a complementary small oligonucleotide that resembles natural substrates for RNase P.
Collapse
Affiliation(s)
- R Salavati
- Department of Pathobiology, Seattle Biomedical Research Institute, University of Washington, 4, Nickerson Street, 98109, Seattle, WA, USA
| | | | | |
Collapse
|
43
|
Stribinskis V, Gao GJ, Sulo P, Ellis SR, Martin NC. Rpm2p: separate domains promote tRNA and Rpm1r maturation in Saccharomyces cerevisiae mitochondria. Nucleic Acids Res 2001; 29:3631-7. [PMID: 11522833 PMCID: PMC55890 DOI: 10.1093/nar/29.17.3631] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rpm2p is a protein subunit of yeast mitochondrial RNase P and is also required for the maturation of Rpm1r, the mitochondrially-encoded RNA subunit of the enzyme. Previous work demonstrated that an insertional disruption of RPM2, which produces the C-terminally truncated protein Rpm2-DeltaCp, supports growth on glucose but cells lose some or all of their mitochondrial genome and become petite. These petites, even if they retain the RPM1 locus, lose their ability to process the 5'-ends of mitochondrial tRNA. We report here that if strains containing the truncated RPM2 allele are created and maintained on respiratory carbon sources they have wild-type mitochondrial genomes, and a significant portion of tRNA transcripts are processed. In contrast, precursor Rpm1r transcripts accumulate and mature Rpm1r is not made. These data show that one function of the deleted C-terminal region is in the maturation of Rpm1r, and that this region and mature Rpm1r are not absolutely required for RNase P activity. Finally, we demonstrate that full activity can be restored if the N-terminal and C-terminal domains of Rpm2p are supplied in trans.
Collapse
Affiliation(s)
- V Stribinskis
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Health Sciences Center, Louisville, KY 40292, USA
| | | | | | | | | |
Collapse
|
44
|
Kato Y, Kuwabara T, Warashina M, Toda H, Taira K. Relationships between the activities in vitro and in vivo of various kinds of ribozyme and their intracellular localization in mammalian cells. J Biol Chem 2001; 276:15378-85. [PMID: 11278700 DOI: 10.1074/jbc.m010570200] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nineteen different functional RNAs were synthesized for an investigation of the actions of ribozymes, in vitro and in vivo, under the control of two different promoters, tRNA or U6, which localize transcripts either in the cytoplasm or in the nucleus. No relationships were found between the activities of these RNAs in cultured cells and the kinetic parameters of their respective chemical cleavage reactions in vitro, indicating that in no case was chemical cleavage the rate-limiting step in vivo. For example, a hepatitis delta virus (HDV) ribozyme, whose activity in vitro was almost 3 orders of magnitude lower than that of a hammerhead ribozyme, still exhibited similar activity in cells when an appropriate expression system was used. As expected, external guide sequences, the actions of which depend on nuclear RNase P, were more active in the nucleus. Analysis of data obtained with cultured cells clearly demonstrated that the cytoplasmic ribozymes were significantly more active than the nuclear ribozymes, suggesting that mature mRNAs in the cytoplasm might be more accessible to antisense molecules than are pre-mRNAs in the nucleus. Our findings should be useful for the future design of intracellularly active functional molecules.
Collapse
Affiliation(s)
- Y Kato
- The Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology, 1-1-4 Higashi, Tsukuba Science City 305-8562, Japan
| | | | | | | | | |
Collapse
|
45
|
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.
Collapse
Affiliation(s)
- Y Takagi
- Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Science City 305-8562, Japan
| | | | | | | | | |
Collapse
|
46
|
XIAO SHAOHUA, HOUSER-SCOTT FELICIA, ENGELKE DAVIDR. Eukaryotic ribonuclease P: increased complexity to cope with the nuclear pre-tRNA pathway. J Cell Physiol 2001; 187:11-20. [PMID: 11241345 PMCID: PMC3758117 DOI: 10.1002/1097-4652(200104)187:1<11::aid-jcp1055>3.0.co;2-k] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ribonuclease P is an ancient enzyme that cleaves pre-tRNAs to generate mature 5' ends. It contains an essential RNA subunit in Bacteria, Archaea, and Eukarya, but the degree to which the RNA subunit relies on proteins to supplement catalysis is highly variable. The eukaryotic nuclear holoenzyme has recently been found to contain almost twenty times the protein content of the bacterial enzymes, in addition to having split into at least two related enzymes with distinct substrate specificity. In this review, recent progress in understanding the molecular architecture and functions of nuclear forms of RNase P will be considered.
Collapse
Affiliation(s)
| | | | - DAVID R. ENGELKE
- Correspondence: David R. Engelke, Department of Biological Chemistry, The University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA.
| |
Collapse
|
47
|
Vogel J, Hess WR. Complete 5' and 3' end maturation of group II intron-containing tRNA precursors. RNA (NEW YORK, N.Y.) 2001; 7:285-292. [PMID: 11233985 PMCID: PMC1370086 DOI: 10.1017/s1355838201001960] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Higher plant chloroplasts provide the only experimentally validated example of functional tRNA genes that are disrupted by group II introns. Here, precursor transcripts for tRNA(Gly)(UCC), tRNA(Val)(UAC), and tRNA(Ala)(UGC) were investigated for processing of 5' leader and 3' trailer sequences in vivo. Use of intron-specific primer pairs and inclusion of a barley chloroplast splicing mutant specifically allowed us to evaluate the potential effect of intervening sequences that disrupt tRNA secondary and tertiary structures. The data suggest that (1) neither integrity of the dihydrouridine nor the anticodon domain is required for the nucleotidyltransferase-mediated addition of 3'-terminal CCA; (2) interruption of these two structural elements by group II introns does not interfere with nucleotide-specific 5' maturation by RNase P; (3) processing intermediates of chloroplast tRNAs can be 3' polyadenylated; and (4) plastid DNA-encoded proteins are not required for 3' and 5' maturation of plastid tRNAs.
Collapse
Affiliation(s)
- J Vogel
- University of Uppsala, Institute of Cellular and Molecular Biology, Department of Microbiology, Sweden.
| | | |
Collapse
|
48
|
Houser-Scott F, Ziehler WA, Engelke DR. Saccharomyces cerevisiae nuclear ribonuclease P: structure and function. Methods Enzymol 2001; 342:101-17. [PMID: 11586886 DOI: 10.1016/s0076-6879(01)42539-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- F Houser-Scott
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | | | | |
Collapse
|
49
|
Altman S, Gopalan V, Vioque A. Varieties of RNase P: a nomenclature problem? RNA (NEW YORK, N.Y.) 2000; 6:1689-94. [PMID: 11142368 PMCID: PMC1370038 DOI: 10.1017/s1355838200001783] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
MESH Headings
- Archaea/enzymology
- Archaea/genetics
- Archaeal Proteins/chemistry
- Archaeal Proteins/classification
- Archaeal Proteins/genetics
- Archaeal Proteins/isolation & purification
- Bacteria/enzymology
- Bacteria/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/classification
- Bacterial Proteins/genetics
- Bacterial Proteins/isolation & purification
- Base Sequence
- Chloroplasts/enzymology
- Endoribonucleases/chemistry
- Endoribonucleases/classification
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Evolution, Molecular
- Fungal Proteins/chemistry
- Fungal Proteins/classification
- Fungal Proteins/genetics
- Fungal Proteins/isolation & purification
- HeLa Cells/enzymology
- Humans
- Molecular Sequence Data
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/classification
- Neoplasm Proteins/genetics
- Neoplasm Proteins/isolation & purification
- Nucleic Acid Conformation
- Organelles/enzymology
- Plant Proteins/chemistry
- Plant Proteins/classification
- Plant Proteins/isolation & purification
- Protein Subunits
- RNA, Archaeal/chemistry
- RNA, Archaeal/classification
- RNA, Archaeal/genetics
- RNA, Archaeal/isolation & purification
- RNA, Bacterial/chemistry
- RNA, Bacterial/classification
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Catalytic/chemistry
- RNA, Catalytic/classification
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Fungal/chemistry
- RNA, Fungal/classification
- RNA, Fungal/genetics
- RNA, Fungal/isolation & purification
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/classification
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Ribonuclease P
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/classification
- Ribonucleoproteins/genetics
- Ribonucleoproteins/isolation & purification
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Terminology as Topic
- Zea mays/enzymology
Collapse
Affiliation(s)
- S Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA.
| | | | | |
Collapse
|
50
|
Thomas BC, Chamberlain J, Engelke DR, Gegenheimer P. Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P. RNA (NEW YORK, N.Y.) 2000; 6:554-62. [PMID: 10786846 PMCID: PMC1369936 DOI: 10.1017/s1355838200991477] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ribonuclease P is the enzyme responsible for removing the 5'-leader segment of precursor transfer RNAs in all organisms. All eukaryotic nuclear RNase Ps are ribonucleoproteins in which multiple protein components and a single RNA species are required for activity in vitro as well as in vivo. It is not known, however, which subunits participate directly in phosphodiester-bond hydrolysis. The RNA subunit of nuclear RNase P is evolutionarily related to its catalytically active bacterial counterpart, prompting speculation that in eukaryotes the RNA may be the catalytic component. In the bacterial RNase P reaction, Mg(II) is required to coordinate the nonbridging phosphodiester oxygen(s) of the scissile bond. As a consequence, bacterial RNase P cannot cleave pre-tRNA in which the pro-Rp nonbridging oxygen of the scissile bond is replaced by sulfur. In contrast, the RNase P reaction in plant chloroplasts is catalyzed by a protein enzyme whose mechanism does not involve Mg(II) coordinated by the pro-Rp oxygen. To determine whether the mechanism of nuclear RNase P resembles more closely an RNA- or a protein-catalyzed reaction, we analyzed the ability of Saccharomyces cerevisiae nuclear RNase P to cleave pre-tRNA containing a sulfur substitution of the pro-Rp oxygen at the cleavage site. Sulfur substitution at this position prohibits correct cleavage of pre-tRNA. Cleavage by eukaryotic RNase P thus depends on the presence of a thio-sensitive ligand to the pro-Rp oxygen of the scissile bond, and is consistent with a common, RNA-based mechanism for the bacterial and eukaryal enzymes.
Collapse
MESH Headings
- Base Sequence
- Catalysis
- Cell Nucleus/enzymology
- Chlorides/metabolism
- Endoribonucleases/chemistry
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Escherichia coli/enzymology
- Escherichia coli Proteins
- Eukaryotic Cells/cytology
- Eukaryotic Cells/enzymology
- Eukaryotic Cells/metabolism
- Magnesium/metabolism
- Manganese Compounds/metabolism
- Mutation/genetics
- Nucleic Acid Conformation
- Organothiophosphorus Compounds/metabolism
- Oxygen/metabolism
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- Ribonuclease P
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Substrate Specificity
Collapse
Affiliation(s)
- B C Thomas
- Department of Molecular Biosciences, The University of Kansas, Lawrence 66045-2106, USA
| | | | | | | |
Collapse
|