1
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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.
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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.
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2
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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.
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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
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3
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Abstract
Ribonuclease P (RNase P) is an ancient and essential endonuclease that catalyses the cleavage of the 5' leader sequence from precursor tRNAs (pre-tRNAs). The enzyme is one of only two ribozymes which can be found in all kingdoms of life (Bacteria, Archaea, and Eukarya). Most forms of RNase P are ribonucleoproteins; the bacterial enzyme possesses a single catalytic RNA and one small protein. However, in archaea and eukarya the enzyme has evolved an increasingly more complex protein composition, whilst retaining a structurally related RNA subunit. The reasons for this additional complexity are not currently understood. Furthermore, the eukaryotic RNase P has evolved into several different enzymes including a nuclear activity, organellar activities, and the evolution of a distinct but closely related enzyme, RNase MRP, which has different substrate specificities, primarily involved in ribosomal RNA biogenesis. Here we examine the relationship between the bacterial and archaeal RNase P with the eukaryotic enzyme, and summarize recent progress in characterizing the archaeal enzyme. We review current information regarding the nuclear RNase P and RNase MRP enzymes in the eukaryotes, focusing on the relationship between these enzymes by examining their composition, structure and functions.
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Affiliation(s)
- Scott C Walker
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA
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4
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Williams D, Brown JW. In vitro selection of an archaeal RNase P RNA mimics natural variation. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2005; 1:241-5. [PMID: 15810433 PMCID: PMC2685577 DOI: 10.1155/2004/903283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Archaeal and bacterial RNase P RNAs are similar in sequence and secondary structure, but in the absence of protein, the archaeal RNAs are much less active and require extreme ionic conditions for activity. To assess how readily the activity of the archaeal RNA alone could be improved by small changes in sequence, in vitro selection was used to generate variants of a Methanobacterium formicicum RNase P RNA: Bacillus subtilus pre-tRNA(Asp) self-cleaving conjugate RNA. Functional variants were generated with a spectrum of mutations that were predominately consistent with natural variation in this RNA. Variants generated from the selection had cleavage rates comparable to that of wild type; variants with improved cleavage rates or lower ionic requirements were not obtained. This suggests that the RNase P RNAs of Bacteria and Archaea are globally optimized and the basis for the large biochemical differences between these two types of RNase P RNA is distributed in the molecule.
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Affiliation(s)
- Daniel Williams
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695-7615, USA
- V.A. Medical Center, Emory University Medical Research, Rm 5A188, 1670 Clarimont Rd., Decatur, GA 30033, USA
| | - James W. Brown
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695-7615, USA
- Corresponding author ()
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5
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Affiliation(s)
- T A Hall
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695, USA
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6
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Hall TA, Brown JW. Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins. RNA (NEW YORK, N.Y.) 2002; 8:296-306. [PMID: 12003490 PMCID: PMC1370252 DOI: 10.1017/s1355838202028492] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Although archaeal RNase P RNAs are similar in both sequence and structure to those of Bacteria rather than eukaryotes, and heterologous reconstitution between the Bacillus subtilis RNase P protein and some archaeal RNase P RNAs has been demonstrated, no archaeal protein sequences with similarity to any known bacterial RNase P protein subunit have been identified, and the density of Methanothermobacter thermoautotrophicus RNase P in Cs2SO4 (1.42 g/mL) is inconsistent with a single small bacterial-like protein subunit. Four hypothetical open reading frames (MTH11, MTH687, MTH688, and MTH1618) were identified in the genome of M. thermoautotrophicus that have sequence similarity to four of the nine Saccharomyces cerevisiae RNase P protein subunits: Pop4p, Pop5p, Rpp1p, and Rpr2p, respectively. Polyclonal antisera generated to recombinant Mth11p, Mth687p, Mth688p, and Mth1618p each recognized a protein of the predicted molecular weight in western blots of partially purified M. thermoautotrophicus RNase P, and immunoprecipitated RNase P activity from the same partially purified preparation. RNase P in Archaea is therefore composed of an RNA subunit similar to bacterial RNase P RNA and multiple protein subunits similar to those in the eukaryotic nucleus.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibody Formation
- Blotting, Western
- Cell Nucleus/enzymology
- Centrifugation, Density Gradient
- Cesium/chemistry
- Chlorides/chemistry
- Chromatography, Affinity
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Eukaryotic Cells/enzymology
- Humans
- Methanobacterium/enzymology
- Molecular Sequence Data
- Precipitin Tests
- Protein Subunits
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/metabolism
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- Rabbits
- Recombinant Proteins/immunology
- Recombinant Proteins/isolation & purification
- Recombinant Proteins/metabolism
- Ribonuclease P
- Saccharomyces cerevisiae/enzymology
- Sequence Homology, Amino Acid
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Affiliation(s)
- Thomas A Hall
- Department of Microbiology, North Carolina State University, Raleigh 27695-7615, USA
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7
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Andrews AJ, Hall TA, Brown JW. Characterization of RNase P holoenzymes from Methanococcus jannaschii and Methanothermobacter thermoautotrophicus. Biol Chem 2001; 382:1171-7. [PMID: 11592398 DOI: 10.1515/bc.2001.147] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The partial purification and basic biochemical characterization of the RNase P holoenzymes of two species of methanogenic Archaea, Methanothermobacter thermoautotrophicus (previously Methanobacterium thermoautotrophicum strain deltaH) and Methanococcus jannaschii, are described. The properties of these enzymes, particularly buoyant density in Cs2SO4 and recent information about the subunit composition of the archaeal enzymes, suggest that RNase P enzymes in Archaea are much more alike than earlier studies in Sulfolobus acidocaldarius and Haloferax volcanii suggested.
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Affiliation(s)
- A J Andrews
- Department of Microbiology, North Carolina State University, Raleigh 27695-7615, USA
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8
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Harris JK, Haas ES, Williams D, Frank DN, Brown JW. New insight into RNase P RNA structure from comparative analysis of the archaeal RNA. RNA (NEW YORK, N.Y.) 2001; 7:220-32. [PMID: 11233979 PMCID: PMC1370080 DOI: 10.1017/s1355838201001777] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A detailed comparative analysis of archaeal RNase P RNA structure and a comparison of the resulting structural information with that of the bacterial RNA reveals that the archaeal RNase P RNAs are strikingly similar to those of Bacteria. The differences between the secondary structure models of archaeal and bacterial RNase P RNA have largely disappeared, and even variation in the sequence and structure of the RNAs are similar in extent and type. The structure of the cruciform (P7-11) has been reevaluated on the basis of a total of 321 bacterial and archaeal sequences, leading to a model for the structure of this region of the RNA that includes an extension to P11 that consistently organizes the cruciform and adjacent highly-conserved sequences.
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Affiliation(s)
- J K Harris
- Department of Microbiology, North Carolina State University, Raleigh 27695, USA
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9
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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
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Affiliation(s)
- S Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA.
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10
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Russell AG, Ebhardt H, Dennis PP. Substrate requirements for a novel archaeal endonuclease that cleaves within the 5' external transcribed spacer of Sulfolobus acidocaldarius precursor rRNA. Genetics 1999; 152:1373-85. [PMID: 10430568 PMCID: PMC1460720 DOI: 10.1093/genetics/152.4.1373] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During ribosome biogenesis in the hyperthermophilic archaeon Sulfolobus acidocaldarius, at least three separate precursor endonucleolytic cleavages occur within the 144-nucleotide-long 5' external transcribed spacer (5' ETS) region of the rRNA operon primary transcript. The 5' ETS sequence contains three regions of very stable helical structure. One cleavage (5' to position -98) is in the single-stranded region between the 5' and the central helical domains; a second cleavage (5' to position -31) is in the single-stranded region between the central and the 3' helical domains; and a third cleavage is at the 5' ETS-16S junction (5' to position +1). The three sites share a common consensus sequence around the position of cleavage. We have used an in vitro pre-RNA processing assay to define some of the sequence and structural recognition elements necessary for the two precursor cleavages 5' to positions -98 and -31. Surprisingly, none of the three predominant helical domains are required for recognition or targeting of the cleavages, although their removal reduces the rate of cleavage site utilization. We show that the sequence AAG downward arrow (CA)UU encompassing each site contains at least some of the essential features for recognition and efficient targeting of the cleavages. Cleavage depends on the presence of a purine 5' and a uracil two nucleotides 3' to the scissile phosphodiester bond. Mutations to other bases at these critical positions are either not cleaved or cleaved very poorly. Finally, on the basis of intermediates that are produced during a processing reaction, we can conclude that the cleavages at positions 98 and 31 are not ordered in vitro.
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Affiliation(s)
- A G Russell
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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11
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Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW. RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci U S A 1999; 96:7803-8. [PMID: 10393902 PMCID: PMC22142 DOI: 10.1073/pnas.96.14.7803] [Citation(s) in RCA: 177] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RNA subunits of RNase Ps of Archaea and eukaryotes have been thought to depend fundamentally on protein for activity, unlike those of Bacteria that are capable of efficient catalysis in the absence of protein. Although the eukaryotic RNase P RNAs are quite different than those of Bacteria in both sequence and structure, the archaeal RNAs generally contain the sequences and structures of the bacterial, phylogenetically conserved catalytic core. A spectrum of archaeal RNase P RNAs were therefore tested for activity in a wide range of conditions. Many remain inactive in ionically extreme conditions, but catalytic activity could be detected from those of the methanobacteria, thermococci, and halobacteria. Chimeric holoenzymes, reconstituted from the Methanobacterium RNase P RNA and the Bacillus subtilis RNase P protein subunits, were functional at low ionic strength. The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterial RNase P protein) are similar to synthetic RNase P RNAs that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements.
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Affiliation(s)
- J A Pannucci
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA
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12
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Cordier A, Schön A. Cyanelle RNase P: RNA structure analysis and holoenzyme properties of an organellar ribonucleoprotein enzyme. J Mol Biol 1999; 289:9-20. [PMID: 10339401 DOI: 10.1006/jmbi.1999.2762] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cyanelle of the primitive alga Cyanophora paradoxa is the only photosynthetic organelle where the ribonucleoprotein nature of ribonuclease P has been functionally proven. To increase our knowledge about RNA structure and overall composition of this enzyme, we have now determined relevant physical parameters and performed RNA accessibility experiments. Buoyant density and relative molecular mass of cyanelle RNase P were more similar to the eukaryotic (nuclear or mitochondrial) than to the bacterial enzyme type, despite the close phylogenetic relationship between plastids and cyanobacteria. Enzymatic and chemical probing was used to establish the secondary structure of cyanelle RNase P RNA. The results obtained with the naked transcript support the previously proposed, phylogenetically derived structure. Probing of the RNA in the holoenzyme resulted in reduced sensitivity at a large number of positions, indicating that these regions might be located in the interior of the ribonucleoprotein. Protection of the RNA in cyanelle RNase P was more extensive than reported for the Escherichia coli holoenzyme, but similar to the pattern observed in yeast nuclear RNase P. Taken together, these results indicate that the protein contribution in cyanelle RNase P is much larger than in the bacterial enzymes, and that the overall composition of the holoenzyme resembles that found in eukaryotes.
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Affiliation(s)
- A Cordier
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Biozentrum, Würzburg, 97074, Germany
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13
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Abstract
Ribonuclease P (RNase P) is the endoribonuclease that generates the mature 5'-ends of tRNA by removal of the 5'-leader elements of precursor-tRNAs. This enzyme has been characterized from representatives of all three domains of life (Archaea, Bacteria, and Eucarya) (1) as well as from mitochondria and chloroplasts. The cellular and mitochondrial RNase Ps are ribonucleoproteins, whereas the most extensively studied chloroplast RNase P (from spinach) is composed solely of protein. Remarkably, the RNA subunit of bacterial RNase P is catalytically active in vitro in the absence of the protein subunit (2). Although RNA-only activity has not been demonstrated for the archael, eucaryal, or mitochondrial RNAs, comparative sequence analysis has established that these RNAs are homologous (of common ancestry) to bacterial RNA. RNase P holoenzymes vary greatly in organizational complexity across the phylogenetic domains, primarily because of differences in the RNase P protein subunits: Mitochondrial, archaeal, and eucaryal holoenzymes contain larger, and perhaps more numerous, protein subunits than do the bacterial holoenzymes. However, that the nonbacterial RNase P RNAs retain significant structural similarity to their catalytically active bacterial counterparts indicates that the RNA remains the catalytic center of the enzyme.
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Affiliation(s)
- D N Frank
- Department of Plant and Microbial Biology, University of California, Berkeley 94720-3102, USA.
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14
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Hartmann RK, Krupp G, Hardt WD. Towards a new concept of gene inactivation: specific RNA cleavage by endogenous ribonuclease P. BIOTECHNOLOGY ANNUAL REVIEW 1998; 1:215-65. [PMID: 9704090 DOI: 10.1016/s1387-2656(08)70053-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the first part of this chapter, general concepts for gene inactivation, antisense techniques and catalytic RNAs (ribozymes) are presented. The requirements for modified oligonucleotides are discussed with their effects on the stability of base-paired hybrids and on resistance against nuclease attack. This also includes the problems in the choice of an optimal target sequence within the inactivated RNA and the options of cellular delivery systems. The second part describes the recently introduced antisense concept based on the ubiquitous cellular enzyme ribonuclease P. This system is unique, since the substrate recognition requires the proper tertiary structure of the cleaved RNA. General properties and possible advantages of this approach are discussed.
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Affiliation(s)
- R K Hartmann
- Institut für Biochemie, Freie Universität Berlin, Germany
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15
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Rossmanith W, Karwan RM. Characterization of human mitochondrial RNase P: novel aspects in tRNA processing. Biochem Biophys Res Commun 1998; 247:234-41. [PMID: 9642109 DOI: 10.1006/bbrc.1998.8766] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human mitochondrial RNase P does not distinguish itself from other RNase P enzymes by most of its basic properties. 5' phosphates on tRNA products, strict dependence on a divalent cation, independence of ATP or other cofactors, and sensitivity to puromycin are generally characteristic for RNase P. Slow sedimentation of human mitochondrial RNase P in glycerol gradients suggests a molecular weight considerably lower than that of bacterial or nuclear RNase P. In contrast to fungi, all putative components of mammalian mitochondrial RNase P are encoded by the nucleus. Intriguingly, no indication of the involvement of a trans-acting RNA was found in mammalian mitochondrial tRNA processing. Mitochondrial RNase P is resistant to rigorous treatments with nucleases and exhibits a protein-like density in Cs2SO4 gradients. Moreover, an analysis of copurifying RNAs revealed no putative RNase P RNA candidates. These data suggest that mammalian mitochondrial RNase P, unlike its nuclear counterpart or its bacterial relatives, is not a ribonucleoprotein but a protein enzyme.
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Affiliation(s)
- W Rossmanith
- Institut für Tumorbiologie-Krebsforschung der Universität Wien, Borschkegasse 8a, Vienna, A-1090, Austria.
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16
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Zuker M, Jacobson AB. Using reliability information to annotate RNA secondary structures. RNA (NEW YORK, N.Y.) 1998; 4:669-79. [PMID: 9622126 PMCID: PMC1369649 DOI: 10.1017/s1355838298980116] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A number of heuristic descriptors have been developed previously in conjunction with the mfold package that describe the propensity of individual bases to participate in base pairs and whether or not a predicted helix is "well-determined." They were developed for the "energy dot plot" output of mfold. Two descriptors, P-num and H-num, are used to measure the level of promiscuity in the association of any given nucleotide or helix with alternative complementary pairs. The third descriptor, S-num, measures the propensity of bases to be single-stranded. In the current work, we describe a series of programs that were developed in order to annotate individual structures with "well-definedness" information. We use color annotation to present the information. The programs can annotate PostScript files that are created by the mfold package or the PostScript secondary structure plots produced by the Weiser and Noller program XRNA (Weiser B, Noller HF, 1995, XRNA: Auto-interactive program for modeling RNA, The Center for Molecular Biology of RNA, Santa Cruz, California: University of California; Internet: ftp://fangio.ucsc.edu/pub/XRNA). In addition, these programs can annotate ss files that serve as input to XRNA. The annotation package can also handle structure comparison with a reference structure. This feature can be used to compare predicted structure with a phylogenetically deduced model, to compare two different predicted foldings, and to identify conformational changes that are predicted between wild-type and mutant RNAs. We provide several examples of application. Predicted structures of two RNase P RNAs were colored with P-num information and further annotated with comparative information. The comparative model of a 16S rRNA was annotated with P-num information from mfold and with base pair probabilities obtained from the Vienna RNA folding package. Further annotation adds comparisons with the optimal foldings obtained from mfold and the Vienna package, respectively. The results of all of these analyses are discussed in the context of the reliability of structure prediction.
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Affiliation(s)
- M Zuker
- Institute for Biomedical Computing, Washington University, St. Louis, Missouri 63110, USA.
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17
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Arends S, Schon A. Partial purification and characterization of nuclear ribonuclease P from wheat. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:635-45. [PMID: 9119034 DOI: 10.1111/j.1432-1033.1997.t01-1-00635.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ribonuclease P (RNase P) from wheat nuclei has been purified over 1000-fold, using wheat germ extract as starting material and a combination of poly(ethylenglycol) precipitation and column chromatography. The enzyme was shown to be of nuclear origin by its characteristic ionic requirements; for optimum activity it requires 0.5-1.5 mM Mg2+, which can be partly replaced by Mn2+. With about 100 kDa, wheat nuclear RNase P has the lowest molecular mass reported so far for a eukaryotic RNase P. The enzyme has an isoelectric point of 5.0 and a buoyant density of 1.34 g/ml in CsCl, suggesting the presence of a nucleic acid component; it is, however, insensitive against treatment with micrococcal nuclease. Wheat germ RNase P requires an intact tertiary structure of the pre-tRNA substrate; its cleavage efficiency is also influenced by the presence of an intron, and by the nature of the 3' terminus of the substrate. The apparent Km and Vmax for an intronless plant pre-tRNA(Tyr) are 10.3 nM and 1.12 fmol/min, respectively.
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MESH Headings
- Base Sequence
- Cell Nucleus/enzymology
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Isoelectric Point
- Kinetics
- Micrococcal Nuclease
- Molecular Sequence Data
- Molecular Structure
- Molecular Weight
- Nucleic Acid Conformation
- Oligodeoxyribonucleotides/genetics
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/genetics
- RNA, Transfer, Tyr/metabolism
- Ribonuclease P
- Substrate Specificity
- Triticum/enzymology
- Triticum/genetics
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Affiliation(s)
- S Arends
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Biozentrum, Würzburg, Germany
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18
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Herrmann B, Winqvist O, Mattsson JG, Kirsebom LA. Differentiation of Chlamydia spp. by sequence determination and restriction endonuclease cleavage of RNase P RNA genes. J Clin Microbiol 1996; 34:1897-902. [PMID: 8818877 PMCID: PMC229149 DOI: 10.1128/jcm.34.8.1897-1902.1996] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The amplification of DNA from Chlamydia trachomatis by PCR with degenerated primers yielded a 345-bp fragment of the putative RNase P RNA gene. From the deduced DNA sequence of this gene in C. trachomatis, a modified primer pair was designed. The primer pair was subsequently used to obtain the corresponding gene products from Chlamydia pneumoniae and Chlamydia psittaci. Sequence comparisons revealed similarities of 76.6% between C. trachomatis and C. pneumoniae, 79.5% between C. trachomatis and C. psittaci, and 84.7% between C. pneumoniae and C. psittaci. Furthermore, the three species were differentiated by fragment length polymorphism analysis after restriction enzyme cleavage of the PCR products. Sequence variations among 14 serotypes of C. trachomatis were confined to one purine base substitution in the putative RNase P RNA gene of lymphogranuloma venereum strains L1 to L3. Complete sequence similarity was found for nine strains of C. pneumoniae of different geographic origins. Taken together, our results indicate a possibility of the general application of this method in clinical bacteriology. Analysis of the secondary structures of the putative RNase P RNA genes from the different Chlamydia species suggested that a novel structural element in the domain of RNase P RNA is involved in base pairing with the 3'-terminal CCA motif of a tRNA precursor. This structure has not previously been found among RNase P RNAs of members of the division Bacteria.
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Affiliation(s)
- B Herrmann
- Department of Clinical Microbiology, University Hospital, Uppsala, Sweden.
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19
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Abstract
A deletion mutant of the catalytic RNA component of Escherichia coli RNase P missing residues 87-241 retains the ability to interact with the protein component to form a functional catalyst. The deletion of this phylogenetically conserved region significantly increases the Km, indicating that the deleted structures may be important for binding to the precursor tRNA substrate but not for the cleavage reaction. Under some reaction conditions, this RNase P deletion mutant can become a relatively non-specific nuclease, indicating that this RNA's catalytic center may be more exposed. The catalytic core of the RNase P is formed by less than one third of the 377 residues of the RNase P RNA.
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Affiliation(s)
- C J Green
- SRI International, Menlo Park, CA 94025-3493, USA
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20
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Haas ES, Armbruster DW, Vucson BM, Daniels CJ, Brown JW. Comparative analysis of ribonuclease P RNA structure in Archaea. Nucleic Acids Res 1996; 24:1252-9. [PMID: 8614627 PMCID: PMC145784 DOI: 10.1093/nar/24.7.1252] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Although the structure of the catalytic RNA component of ribonuclease P has been well characterized in Bacteria, it has been little studied in other organisms, such as the Archaea. We have determined the sequences encoding RNase P RNA in eight euryarchaeal species: Halococcus morrhuae, Natronobacterium gregoryi, Halobacterium cutirubrum, Halobacteriurn trapanicum, Methanobacterium thermoautotrophicum strains deltaH and Marburg, Methanothermus fervidus and Thermococcus celer strain AL-1. On the basis of these and previously available sequences from Sulfolobus acidocaldarius, Haloferax volcanii and Methanosarcina barkeri the secondary structure of RNase P RNA in Archaea has been analyzed by phylogenetic comparative analysis. The archaeal RNAs are similar in both primary and secondary structure to bacterial RNase P RNAs, but unlike their bacterial counterparts these archaeal RNase P RNAs are not by themselves catalytically proficient in vitro.
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Affiliation(s)
- E S Haas
- Department of Microbiology, North Carolina State University, Raleigh 27695, USA
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21
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Abstract
An important approach to understanding RNA-based catalytic function by ribonuclease P is the investigation of its evolutionary diversity in structure and function. Because RNase P enzymes from all organisms are thought to share common ancestry, the fundamental features of structure and biochemistry should be conserved in all of its modern forms. In contrast to the bacterial enzyme, the RNase P enzymes from Eucarya, organelles, and Archaea are poorly understood. This review describes our nascent understanding of the structure and function of RNase P in Archaea, and how this enzyme compares to its homologs in the other evolutionary Domains.
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Affiliation(s)
- J W Brown
- Department of Microbiology, North Carolina State University, Raleigh 27695, USA
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22
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Abstract
Molecular investigations in mitochondria of higher plants have to take in account the complicated genomic structure of these organelles and their complex mode of gene expression. Recently tRNA processing activities and particularly RNase P-like activities have been described for mitochondria of mono- and dicot plants. The determined biochemical characteristics of these plant mitochondrial tRNA processing enzymes now allow a comparison to the bacterial prototype from which they evolved. The substrate specificity of the plant mitochondrial RNase P in particular has unique selection parameters distinct from the E. coli RNase P.
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23
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Abstract
RNase P consists of both protein and RNA subunits in all organisms and organelles investigated so far, with the exception of chloroplasts and plant nuclei where no enzyme-associated RNA has been detected to date. Studies on substrate specificity revealed that cleavage by plant nuclear RNase P is critically dependent on a complete and intact structure of the substrate. No clearcut answer is yet possible regarding the order of processing events at the 5' or 3' end of tRNAs in the case of nuclear or chloroplast processing enzymes. RNase P from a phylogenetically ancient photosynthetic organelle will be discussed in greater detail: The enzyme from the Cyanophora paradoxa cyanelle is the first RNase P from a photosynthetic organelle which has been shown to contain an essential RNA subunit. This RNA is strikingly similar to its counterpart from cyanobacteria, yet it lacks catalytic activity. Properties of the holoenzyme suggest an intermediate position in RNA enzyme evolution, with an Eukaryotic-type, inactive RNA and a prokaryotic-type small protein subunit. The possible presence of an RNA component in RNase P from plant nuclei and modern chloroplasts will be discussed, including a critical evaluation of some criteria that have been frequently applied to elucidate the subunit composition of RNase P from different organisms.
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Affiliation(s)
- A Schön
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Würzburg, Germany
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24
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Abstract
The ubiquitous occurrence of ribonuclease P (RNase P) as a ribonucleoprotein and the catalytic properties of bacterial RNase P RNAs indicate that RNA fulfills an ancient and important role in the function of this enzyme. This review focuses on efforts to determine the structure of the bacterial RNase P RNA ribozyme. Phylogenetic comparative analysis of a library of bacterial RNase P RNA sequences has resulted in a well-developed secondary structure model and allowed identification of some elements of tertiary structure. The native structure has been redesigned by circular permutation to facilitate intra- and inter-molecular crosslinking experiments in order to gain further structural information. The crosslinking constraints, together with the constraints provided by comparative analyses, have been incorporated into a first-order model of the structure of of the ribozyme-substrate complex. The developing structural perspective allows the design of self-cleaving pre-tRNA-RNase P RNA conjugates which are useful tools for additional structure-probing experiments.
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Affiliation(s)
- M E Harris
- Department of Biology, Indiana University, Bloomington 47402, USA
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25
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Abstract
Ribonuclease P (RNase P) is a key enzyme involved in tRNA biosynthesis. It catalyses the endonucleolytic cleavage of nearly all tRNA precursors to produce 5'-end matured tRNA. RNase P activity has been found in all organisms examined, from bacteria to mammals. Eubacterial RNase RNA is the only known RNA enzyme which functions in trans in nature. Similar behaviour has not been demonstrated in RNase P enzymes examined from archaebacteria or eukaryotes. Characterisation of RNase P enzymes from more diverse eukaryotic species, including the slime mold Dictyostelium discoideum, is useful for comparative analysis of the structure and function of eukaryotic RNase P.
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Affiliation(s)
- D Drainas
- Department of Biochemistry, School of Medicine, University of Patras, Greece
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26
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Moll R, Schmidtke S, Schäfer G. Nucleotide sequence of a gene cluster encoding ribosomal proteins in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1261:315-8. [PMID: 7711082 DOI: 10.1016/0167-4781(95)00024-b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A 1.6 kb genomic DNA fragment derived from the extremely thermoacidophilic archaeon Sulfolobus acidocaldarius (DSM 639) comprises four open reading frames. The sequence contains three genes encoding crenarchaeal ribosomal proteins with apparent molecular masses of 6.3 kDa, 15.2 kDa and 9.9 kDa, which all represent strongly basic properties. These were identified by sequence comparison as RL46, RL31 and RL33. One open reading frame encodes a new polypeptide (22.1 kDa, pI = 7.3) with no homology to known proteins. The latter is transcribed as a common mRNA with RL46 and RL31. This gene cluster immediately precedes another cluster including genes encoding the putative SRP receptor alpha subunit as well as the putative secEp.
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Affiliation(s)
- R Moll
- Institute of Biochemistry, Medical University of Lübeck, Germany
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27
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Pace NR, Brown JW. Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J Bacteriol 1995; 177:1919-28. [PMID: 7536728 PMCID: PMC176831 DOI: 10.1128/jb.177.8.1919-1928.1995] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- N R Pace
- Department of Biology, Indiana University, Bloomington 47405, USA
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28
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Abstract
This is an update containing small RNA sequences deposited in GenBank recently. Over four hundred small RNA sequences are available in this and earlier complications.
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Affiliation(s)
- J Gu
- Baylor College of Medicine, Pharmacology Department, Houston, TX 77030
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29
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Lygerou Z, Mitchell P, Petfalski E, Séraphin B, Tollervey D. The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins. Genes Dev 1994; 8:1423-33. [PMID: 7926742 DOI: 10.1101/gad.8.12.1423] [Citation(s) in RCA: 160] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two forms of the yeast 5.8S rRNA are generated from a large precursor by distinct processing pathways. Cleavage at site A3 is required for synthesis of the major, short form, designated 5.8S(S), but not for synthesis of the long form, 5.8S(L). To identify components required for A3 cleavage, a bank of temperature-sensitive lethal mutants was screened for those with a reduced ratio of 5.8S(S):5.8S(L). The pop1-1 mutation (for processing of precursor RNAs) shows this phenotype and also inhibits A3 cleavage. The pre-rRNA processing defect of pop1-1 strains is similar to that reported for mutations in the RNA component of RNase MRP; we show that a mutation in the RNase MRP RNA also inhibits cleavage at site A3. This is the first site shown to require RNase MRP for cleavage in vivo. The pop1-1 mutation also leads to a block in the processing of pre-tRNA that is identical to that reported for mutations in the RNA component of RNase P. The RNA components of both RNase MRP and RNase P are underaccumulated in pop1-1 strains at the nonpermissive temperature, and immunoprecipitation demonstrates that POP1p is a component of both ribonucleoproteins. The POP1 gene encodes a protein with a predicted molecular mass of 100.5 kD and is essential for viability. POP1p is the first protein component of the nuclear RNase P or RNase MRP for which the gene has been cloned.
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Affiliation(s)
- Z Lygerou
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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