1
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Lee EY, Hwang J, Kim MH. Phosphocode-dependent glutamyl-prolyl-tRNA synthetase 1 signaling in immunity, metabolism, and disease. Exp Mol Med 2023; 55:2116-2126. [PMID: 37779151 PMCID: PMC10618286 DOI: 10.1038/s12276-023-01094-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 10/03/2023] Open
Abstract
Ubiquitously expressed aminoacyl-tRNA synthetases play essential roles in decoding genetic information required for protein synthesis in every living species. Growing evidence suggests that they also function as crossover mediators of multiple biological processes required for homeostasis. In humans, eight cytoplasmic tRNA synthetases form a central machinery called the multi-tRNA synthetase complex (MSC). The formation of MSCs appears to be essential for life, although the role of MSCs remains unclear. Glutamyl-prolyl-tRNA synthetase 1 (EPRS1) is the most evolutionarily derived component within the MSC that plays a critical role in immunity and metabolism (beyond its catalytic role in translation) via stimulus-dependent phosphorylation events. This review focuses on the role of EPRS1 signaling in inflammation resolution and metabolic modulation. The involvement of EPRS1 in diseases such as cancer is also discussed.
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Affiliation(s)
- Eun-Young Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Jungwon Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
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2
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Sharaf A, Gruber A, Jiroutová K, Oborník M. Characterization of Aminoacyl-tRNA Synthetases in Chromerids. Genes (Basel) 2019; 10:E582. [PMID: 31370303 PMCID: PMC6723311 DOI: 10.3390/genes10080582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 01/24/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AaRSs) are enzymes that catalyze the ligation of tRNAs to amino acids. There are AaRSs specific for each amino acid in the cell. Each cellular compartment in which translation takes place (the cytosol, mitochondria, and plastids in most cases), needs the full set of AaRSs; however, individual AaRSs can function in multiple compartments due to dual (or even multiple) targeting of nuclear-encoded proteins to various destinations in the cell. We searched the genomes of the chromerids, Chromera velia and Vitrella brassicaformis, for AaRS genes: 48 genes encoding AaRSs were identified in C. velia, while only 39 AaRS genes were found in V. brassicaformis. In the latter alga, ArgRS and GluRS were each encoded by a single gene occurring in a single copy; only PheRS was found in three genes, while the remaining AaRSs were encoded by two genes. In contrast, there were nine cases for which C. velia contained three genes of a given AaRS (45% of the AaRSs), all of them representing duplicated genes, except AsnRS and PheRS, which are more likely pseudoparalogs (acquired via horizontal or endosymbiotic gene transfer). Targeting predictions indicated that AaRSs are not (or not exclusively), in most cases, used in the cellular compartment from which their gene originates. The molecular phylogenies of the AaRSs are variable between the specific types, and similar between the two investigated chromerids. While genes with eukaryotic origin are more frequently retained, there is no clear pattern of orthologous pairs between C. velia and V. brassicaformis.
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Affiliation(s)
- Abdoallah Sharaf
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ansgar Gruber
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Kateřina Jiroutová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic.
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3
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Wei Z, Xu Z, Liu X, Lo WS, Ye F, Lau CF, Wang F, Zhou JJ, Nangle LA, Yang XL, Zhang M, Schimmel P. Alternative splicing creates two new architectures for human tyrosyl-tRNA synthetase. Nucleic Acids Res 2016; 44:1247-55. [PMID: 26773056 PMCID: PMC4756856 DOI: 10.1093/nar/gkw002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/03/2016] [Indexed: 11/15/2022] Open
Abstract
Many human tRNA synthetases evolved alternative functions outside of protein synthesis. These functions are associated with over 200 splice variants (SVs), most of which are catalytic nulls that engender new biology. While known to regulate non-translational activities, little is known about structures resulting from natural internal ablations of any protein. Here, we report analysis of two closely related, internally deleted, SVs of homodimeric human tyrosyl-tRNA synthetase (TyrRS). In spite of both variants ablating a portion of the catalytic core and dimer-interface contacts of native TyrRS, each folded into a distinct stable structure. Biochemical and nuclear magnetic resonance (NMR) analysis showed that the internal deletion of TyrRSΔE2–4 SV gave an alternative, neomorphic dimer interface ‘orthogonal’ to that of native TyrRS. In contrast, the internal C-terminal splice site of TyrRSΔE2–3 prevented either dimerization interface from forming, and yielded a predominantly monomeric protein. Unlike ubiquitous TyrRS, the neomorphs showed clear tissue preferences, which were distinct from each other. The results demonstrate a sophisticated structural plasticity of a human tRNA synthetase for architectural reorganizations that are preferentially elicited in specific tissues.
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Affiliation(s)
- Zhiyi Wei
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Departmentof Biology, South University of Science and Technology of China, Shenzhen, Guangdong 518055, China
| | - Zhiwen Xu
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Pangu Biopharma, Edinburgh Tower, The landmark, 15 Queen'sRoad Central, Hong Kong, China
| | - Xiaotian Liu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Wing-Sze Lo
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Pangu Biopharma, Edinburgh Tower, The landmark, 15 Queen'sRoad Central, Hong Kong, China
| | - Fei Ye
- Division of Life Science, State Key Laboratory of Molecular Neuroscience Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ching-Fun Lau
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Pangu Biopharma, Edinburgh Tower, The landmark, 15 Queen'sRoad Central, Hong Kong, China
| | - Feng Wang
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Pangu Biopharma, Edinburgh Tower, The landmark, 15 Queen'sRoad Central, Hong Kong, China
| | - Jie J Zhou
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Pangu Biopharma, Edinburgh Tower, The landmark, 15 Queen'sRoad Central, Hong Kong, China
| | - Leslie A Nangle
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Xiang-Lei Yang
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China The Scripps Laboratories for tRNA Synthetase Research and the Departments of Chemical Physiology and of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mingjie Zhang
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Division of Life Science, State Key Laboratory of Molecular Neuroscience Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Paul Schimmel
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China The Scripps Laboratories for tRNA Synthetase Research and the Departments of Cell and Molecular Biology, and Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA The Scripps Laboratories for tRNA Synthetase Research and Departments of Metabolism & Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
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4
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Grant TD, Snell EH, Luft JR, Quartley E, Corretore S, Wolfley JR, Snell ME, Hadd A, Perona JJ, Phizicky EM, Grayhack EJ. Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase. Nucleic Acids Res 2011; 40:3723-31. [PMID: 22180531 PMCID: PMC3333875 DOI: 10.1093/nar/gkr1223] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In all organisms, aminoacyl tRNA synthetases covalently attach amino acids to their cognate tRNAs. Many eukaryotic tRNA synthetases have acquired appended domains, whose origin, structure and function are poorly understood. The N-terminal appended domain (NTD) of glutaminyl-tRNA synthetase (GlnRS) is intriguing since GlnRS is primarily a eukaryotic enzyme, whereas in other kingdoms Gln-tRNAGln is primarily synthesized by first forming Glu-tRNAGln, followed by conversion to Gln-tRNAGln by a tRNA-dependent amidotransferase. We report a functional and structural analysis of the NTD of Saccharomyces cerevisiae GlnRS, Gln4. Yeast mutants lacking the NTD exhibit growth defects, and Gln4 lacking the NTD has reduced complementarity for tRNAGln and glutamine. The 187-amino acid Gln4 NTD, crystallized and solved at 2.3 Å resolution, consists of two subdomains, each exhibiting an extraordinary structural resemblance to adjacent tRNA specificity-determining domains in the GatB subunit of the GatCAB amidotransferase, which forms Gln-tRNAGln. These subdomains are connected by an apparent hinge comprised of conserved residues. Mutation of these amino acids produces Gln4 variants with reduced affinity for tRNAGln, consistent with a hinge-closing mechanism proposed for GatB recognition of tRNA. Our results suggest a possible origin and function of the NTD that would link the phylogenetically diverse mechanisms of Gln-tRNAGln synthesis.
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Affiliation(s)
- Thomas D Grant
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
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5
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Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M. Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis. Nucleic Acids Res 2011; 39:4475-89. [PMID: 21296757 PMCID: PMC3105412 DOI: 10.1093/nar/gkr027] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) belong to a newly defined family of enzymes that use aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesize the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with noteworthy biological activities. Here, we describe the crystal structure of AlbC, a CDPS from Streptomyces noursei. The AlbC structure consists of a monomer containing a Rossmann-fold domain. Strikingly, it is highly similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. AlbC contains a deep pocket, highly conserved among CDPSs. Site-directed mutagenesis studies indicate that this pocket accommodates the aminoacyl moiety of the aa-tRNA substrate in a way similar to that used by TyrRSs to recognize their tyrosine substrates. These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs. AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which l-Phe is shown to be transferred from Phe-tRNAPhe to an active serine. These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.
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Affiliation(s)
- Ludovic Sauguet
- CEA, IBITECS, Service d'Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France
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6
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Schimmel P. Development of tRNA synthetases and connection to genetic code and disease. Protein Sci 2008; 17:1643-52. [PMID: 18765819 DOI: 10.1110/ps.037242.108] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The genetic code is established by the aminoacylation reactions of aminoacyl tRNA synthetases, where amino acids are matched with triplet anticodons imbedded in the cognate tRNAs. The code established in this way is so robust that it gave birth to the entire tree of life. The tRNA synthetases are organized into two classes, based on their active site architectures. The details of this organization, and other considerations, suggest how the synthetases evolved by gene duplications, and how early proteins may have been statistical in nature, that is, products of a primitive code where one of several similar amino acids was used at a specific position in a polypeptide. The emergence of polypeptides with unique, defined sequences--true chemical entities--required extraordinary specificity of the aminoacylation reaction. This high specificity was achieved by editing activities that clear errors of aminoacylation and thereby prevent mistranslation. Defects in editing activities can be lethal and lead to pathologies in mammalian cells in culture. Even a mild defect in editing is casually associated with neurological disease in the mouse. Defects in editing are also mutagenic in an aging organism and suggest how mistranslation can lead to mutations that are fixed in the genome. Thus, clearance of mischarged tRNAs by the editing activities of tRNA synthetases was essential for development of the tree of life and has a role in the etiology of diseases that is just now being understood.
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Affiliation(s)
- Paul Schimmel
- The Scripps Research Institute, La Jolla, California 92037, USA.
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7
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Schimmel P. Alanine transfer RNA synthetase: structure-function relationships and molecular recognition of transfer RNA. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 63:233-70. [PMID: 2407064 DOI: 10.1002/9780470123096.ch4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- P Schimmel
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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8
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Gallant P, Finn J, Keith D, Wendler P. The identification of quality antibacterial drug discovery targets: a case study with aminoacyl-tRNA synthetases. ACTA ACUST UNITED AC 2005. [DOI: 10.1517/14728222.4.1.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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9
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Beebe K, Merriman E, Ribas De Pouplana L, Schimmel P. A domain for editing by an archaebacterial tRNA synthetase. Proc Natl Acad Sci U S A 2004; 101:5958-63. [PMID: 15079065 PMCID: PMC395905 DOI: 10.1073/pnas.0401530101] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rules of the genetic code are established by aminoacylations of transfer RNAs by aminoacyl tRNA synthetases. New codon assignments, and the introduction of new kinds of amino acids, are blocked by vigorous tRNA-dependent editing reactions occurring at hydrolytic sites embedded within specialized domains in the synthetases. For some synthetases, these domains were present at the time of the last common ancestor and were fixed in evolution through all three of the kingdoms of life. Significantly, a well characterized domain for editing found in bacterial and eukaryotic threonyl- and all alanyl-tRNA synthetases is missing from archaebacterial threonine enzymes. Here we show that the archaebacterial Methanosarcina mazei ThrRS efficiently misactivates serine, but does not fuse serine to tRNA. Consistent with this observation, the enzyme cleared serine that was linked to threonine-specific tRNAs. M. mazei and most other archaebacterial ThrRSs have a domain, N2(A), fused to the N terminus and not found in bacterial or eukaryotic orthologs. Mutations at conserved residues in this domain led to an inability to clear threonine-specific tRNA mischarged with serine. Thus, these results demonstrate a domain for editing that is distinct from all others, is restricted to just one branch of the tree of life, and was most likely added to archaebacterial ThrRSs after the eukaryote/archaebacteria split.
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Affiliation(s)
- Kirk Beebe
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Beckman Center, BCC379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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10
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Beebe K, Merriman E, Schimmel P. Structure-specific tRNA determinants for editing a mischarged amino acid. J Biol Chem 2003; 278:45056-61. [PMID: 12949076 DOI: 10.1074/jbc.m307080200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alanyl-tRNA synthetase efficiently aminoacylates tRNAAla and an RNA minihelix that comprises just one domain of the two-domain L-shaped tRNA structure. It also clears mischarged tRNAAla using a specialized domain in its C-terminal half. In contrast to full-length tRNAAla, minihelixAla was robustly mischarged and could not be edited. Addition in trans of the missing anticodon-containing domain did not activate editing of mischarged minihelixAla. To understand these differences between minihelixAla and tRNAAla, several chimeric full tRNAs were constructed. These had the acceptor stem of a non-cognate tRNA replaced with the stem of tRNAAla. The chimeric tRNAs collectively introduced multiple sequence changes in all parts but the acceptor stem. However, although the acceptor stem in isolation (as the minihelix) lacked determinants for editing, alanyl-tRNA synthetase effectively cleared a mischarged amino acid from each chimeric tRNA. Thus, a covalently continuous two-domain structure per se, not sequence, is a major determinant for clearance of errors of aminoacylation by alanyl-tRNA synthetase. Because errors of aminoacylation are known to be deleterious to cell growth, structure-specific determinants constitute a powerful selective pressure to retain the format of the two-domain L-shaped tRNA.
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Affiliation(s)
- Kirk Beebe
- Department of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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11
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Schimmel P, Ribas de Pouplana L. Formation of two classes of tRNA synthetases in relation to editing functions and genetic code. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:161-6. [PMID: 12762018 DOI: 10.1101/sqb.2001.66.161] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- P Schimmel
- Skaggs Institute for Chemical Biology, Scripps Research Institute, Beckman Center, La Jolla, California 92037, USA
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12
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Yang XL, Skene RJ, McRee DE, Schimmel P. Crystal structure of a human aminoacyl-tRNA synthetase cytokine. Proc Natl Acad Sci U S A 2002; 99:15369-74. [PMID: 12427973 PMCID: PMC137723 DOI: 10.1073/pnas.242611799] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2002] [Indexed: 11/18/2022] Open
Abstract
The 20 aminoacyl-tRNA synthetases catalyze the first step of protein synthesis and establish the rules of the genetic code through aminoacylation reactions. Biological fragments of two human enzymes, tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase, connect protein synthesis to cell-signaling pathways including angiogenesis. Alternative splicing or proteolysis produces these fragments. The proangiogenic N-terminal fragment mini-TyrRS has IL-8-like cytokine activity that, like other CXC cytokines, depends on a Glu-Leu-Arg motif. Point mutations in this motif abolish cytokine activity. The full-length native TyrRS lacks cytokine activity. No structure has been available for any mammalian tRNA synthetase that, in turn, might give insight into why mini-TyrRS and not TyrRS has cytokine activities. Here, the structure of human mini-TyrRS, which contains both the catalytic and the anticodon recognition domain, is reported to a resolution of 1.18 A. The critical Glu-Leu-Arg motif is located on an internal alpha-helix of the catalytic domain, where the guanidino side chain of R is part of a hydrogen-bonding network tethering the anticodon-recognition domain back to the catalytic site. Whereas the catalytic domains of the human and bacterial enzymes superimpose, the spatial disposition of the anticodon recognition domain relative to the catalytic domain is unique in mini-TyrRS relative to the bacterial orthologs. This unique orientation of the anticodon-recognition domain can explain why the fragment mini-TyrRS, and not full-length native TyrRS, is active in cytokine-signaling pathways.
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Affiliation(s)
- Xiang-Lei Yang
- The Skaggs Institute for Chemical Biology, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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13
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Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2001; 69:317-49. [PMID: 11550797 DOI: 10.1016/s0079-6603(01)69050-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Aminoacyl-tRNA synthetases are modular proteins, with domains that have distinct roles in the aminoacylation reaction. The catalytic core is responsible for aminoacyl adenylate formation and transfer of the amino acid to the 3' end of the bound transfer RNA (tRNA). Appended and inserted domains contact portions of the tRNA outside the acceptor site and contribute to the efficiency and specificity of aminoacylation. Some aminoacyl-tRNA synthetases also have distinct editing activities that are localized to unique domains. Efficient aminoacylation and editing require communication between RNA-binding and catalytic domains, and can be considered as a signal transduction system. Here, evidence for domain-domain communication in aminoacyl-tRNA synthetases is summarized, together with insights from structural analysis.
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Affiliation(s)
- R W Alexander
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, USA
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14
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Ribas de Pouplana L, Schimmel P. Aminoacyl-tRNA synthetases: potential markers of genetic code development. Trends Biochem Sci 2001; 26:591-6. [PMID: 11590011 DOI: 10.1016/s0968-0004(01)01932-6] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Aminoacylation of tRNAs, catalyzed by 20 aminoacyl-tRNA synthetases, is responsible for establishing the genetic code. The enzymes are divided into two classes on the basis of the architectures of their active sites. Members of the two classes also differ in that they bind opposite sides of the tRNA acceptor stem. Importantly, specific pairs of synthetases--one from each class--can be docked simultaneously onto the acceptor stem. This article relates these specific pairings to the organization of the table of codons that defines the universal genetic code.
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Affiliation(s)
- L Ribas de Pouplana
- Skaggs Institute for Chemical Biology and Depts of Molecular Biology and Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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15
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Fàbrega C, Farrow MA, Mukhopadhyay B, de Crécy-Lagard V, Ortiz AR, Schimmel P. An aminoacyl tRNA synthetase whose sequence fits into neither of the two known classes. Nature 2001; 411:110-4. [PMID: 11333988 DOI: 10.1038/35075121] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Aminoacyl transfer RNA synthetases catalyse the first step of protein synthesis and establish the rules of the genetic code through the aminoacylation of tRNAs. There is a distinct synthetase for each of the 20 amino acids and throughout evolution these enzymes have been divided into two classes of ten enzymes each. These classes are defined by the distinct architectures of their active sites, which are associated with specific and universal sequence motifs. Because the synthesis of aminoacyl-tRNAs containing each of the twenty amino acids is a universally conserved, essential reaction, the absence of a recognizable gene for cysteinyl tRNA synthetase in the genomes of Archae such as Methanococcus jannaschii and Methanobacterium thermoautotrophicum has been difficult to interpret. Here we describe a different cysteinyl-tRNA synthetase from M. jannaschii and Deinococcus radiodurans and its characterization in vitro and in vivo. This protein lacks the characteristic sequence motifs seen in the more than 700 known members of the two canonical classes of tRNA synthetase and may be of ancient origin. The existence of this protein contrasts with proposals that aminoacylation with cysteine in M. jannaschii is an auxiliary function of a canonical prolyl-tRNA synthetase.
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Affiliation(s)
- C Fàbrega
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Beckman Center, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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16
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Ribas de Pouplana L, Schimmel P. Operational RNA code for amino acids in relation to genetic code in evolution. J Biol Chem 2001; 276:6881-4. [PMID: 11238440 DOI: 10.1074/jbc.r000032200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- L Ribas de Pouplana
- Department of Molecular Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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17
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Ribas de Pouplana L, Schimmel P. Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem. Cell 2001; 104:191-3. [PMID: 11269237 DOI: 10.1016/s0092-8674(01)00204-5] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Turner RJ, Lovato M, Schimmel P. One of two genes encoding glycyl-tRNA synthetase in Saccharomyces cerevisiae provides mitochondrial and cytoplasmic functions. J Biol Chem 2000; 275:27681-8. [PMID: 10874035 DOI: 10.1074/jbc.m003416200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, two genes (GRS1 and GRS2) encode glycyl-tRNA synthetase (GlyRS1 and GlyRS2, respectively). 59% of the sequence of GlyRS2 is identical to that of GlyRS1. Others have proposed that GRS1 and GRS2 encode the cytoplasmic and mitochondrial enzymes, respectively. In this work, we show that GRS1 encodes both functions, whereas GRS2 is dispensable. In addition, both cytoplasmic and mitochondrial phenotypes of the knockout allele of GRS1 in S. cerevisiae are complemented by the expression of the only known gene for glycyl-tRNA synthetase in Schizosaccharomyces pombe. Thus, a single gene for glycyl-tRNA synthetase likely encodes both cytoplasmic and mitochondrial activities in most or all yeast. Phylogenetic analysis shows that GlyRS2 is a predecessor of all yeast GlyRS homologues. Thus, GRS1 appears to be the result of a duplication of GRS2, which itself is pseudogene-like.
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Affiliation(s)
- R J Turner
- Skaggs Institute for Chemical Biology and Departments of Molecular Biology and Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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19
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Tumbula DL, Becker HD, Chang WZ, Söll D. Domain-specific recruitment of amide amino acids for protein synthesis. Nature 2000; 407:106-10. [PMID: 10993083 DOI: 10.1038/35024120] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The formation of aminoacyl-transfer RNA is a crucial step in ensuring the accuracy of protein synthesis. Despite the central importance of this process in all living organisms, it remains unknown how archaea and some bacteria synthesize Asn-tRNA and Gln-tRNA. These amide aminoacyl-tRNAs can be formed by the direct acylation of tRNA, catalysed by asparaginyl-tRNA synthetase and glutaminyl-tRNA synthetase, respectively. A separate, indirect pathway involves the formation of mis-acylated Asp-tRNA(Asn) or Glu-tRNA(Gln), and the subsequent amidation of these amino acids while they are bound to tRNA, which is catalysed by amidotransferases. Here we show that all archaea possess an archaea-specific heterodimeric amidotransferase (encoded by gatD and gatE) for Gln-tRNA formation. However, Asn-tRNA synthesis in archaea is divergent: some archaea use asparaginyl-tRNA synthetase, whereas others use a heterotrimeric amidotransferase (encoded by the gatA, gatB and gatC genes). Because bacteria primarily use transamidation, and the eukaryal cytoplasm uses glutaminyl-tRNA synthetase, it appears that the three domains use different mechanisms for Gln-tRNA synthesis; as such, this is the only known step in protein synthesis where all three domains have diverged. Closer inspection of the two amidotransferases reveals that each of them recruited a metabolic enzyme to aid its function; this provides direct evidence for a relationship between amino-acid metabolism and protein biosynthesis.
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Affiliation(s)
- D L Tumbula
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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20
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Tao J, Schimmel P. Inhibitors of aminoacyl-tRNA synthetases as novel anti-infectives. Expert Opin Investig Drugs 2000; 9:1767-75. [PMID: 11060775 DOI: 10.1517/13543784.9.8.1767] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Resistance to existing antibiotics has emerged as a major problem in healthcare. Novel antibiotics for which bacteria have not yet acquired resistance need to be developed to combat drug-resistant pathogens. Aminoacyl-tRNA synthetases are leading targets for novel anti-infectives. The validation of aminoacyl-tRNA synthetases as drug targets for anti-infectives has been established in an animal system. Using several conceptually distinct approaches, new inhibitors of synthetases have been developed as drug prototypes.
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Affiliation(s)
- J Tao
- Cubist Pharmaceuticals, Inc., Cambridge, MA 02139, USA
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21
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Wang CC, Morales AJ, Schimmel P. Functional redundancy in the nonspecific RNA binding domain of a class I tRNA synthetase. J Biol Chem 2000; 275:17180-6. [PMID: 10747983 DOI: 10.1074/jbc.m001057200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sequence of a 228-amino acid nonspecific RNA binding domain appended to the N terminus of a eukaryote tRNA synthetase is shown here to have two lysine-rich clusters (LRCs) that are functionally significant in vivo and in vitro. These two LRCs have unrelated sequences and are separated by a spacer of over 100 amino acids. By using a sensitive test for function in vivo, each LRC is shown to be sufficient in the absence of the other. This sufficiency requires fusion of the spacer to either of the LRCs. Experiments in vitro confirmed that the LRCs are each important for RNA binding. Thus, this nonspecific RNA binding domain has two dissimilar lysine-rich sequence elements that are functionally redundant. Further experiments suggest that this redundancy is not used to dock two molecules of RNA but rather to enhance the overall affinity for a single RNA molecule.
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Affiliation(s)
- C C Wang
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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22
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Ko YG, Kang YS, Kim EK, Park SG, Kim S. Nucleolar localization of human methionyl-tRNA synthetase and its role in ribosomal RNA synthesis. J Cell Biol 2000; 149:567-74. [PMID: 10791971 PMCID: PMC2174846 DOI: 10.1083/jcb.149.3.567] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human aminoacyl-tRNA synthetases (ARSs) are normally located in cytoplasm and are involved in protein synthesis. In the present work, we found that human methionyl-tRNA synthetase (MRS) was translocated to nucleolus in proliferative cells, but disappeared in quiescent cells. The nucleolar localization of MRS was triggered by various growth factors such as insulin, PDGF, and EGF. The presence of MRS in nucleoli depended on the integrity of RNA and the activity of RNA polymerase I in the nucleolus. The ribosomal RNA synthesis was specifically decreased by the treatment of anti-MRS antibody as determined by nuclear run-on assay and immunostaining with anti-Br antibody after incorporating Br-UTP into nascent RNA. Thus, human MRS plays a role in the biogenesis of rRNA in nucleoli, while it is catalytically involved in protein synthesis in cytoplasm.
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Affiliation(s)
- Young-Gyu Ko
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Young-Sun Kang
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Eun-Kyoung Kim
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Sang Gyu Park
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Sunghoon Kim
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
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23
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Affiliation(s)
- P Schimmel
- Skaggs Institute for Chemical Biology and Depts of Molecular Biology and Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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24
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Chihade JW, Schimmel P. Assembly of a catalytic unit for RNA microhelix aminoacylation using nonspecific RNA binding domains. Proc Natl Acad Sci U S A 1999; 96:12316-21. [PMID: 10535919 PMCID: PMC22914 DOI: 10.1073/pnas.96.22.12316] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An assembly of a catalytic unit for aminoacylation of an RNA microhelix is demonstrated here. This assembly may recapitulate a step in the historical development of tRNA synthetases. The class-defining domain of a tRNA synthetase is closely related to the primordial enzyme that catalyzed synthesis of aminoacyl adenylate. RNA binding elements are imagined to have been added so that early RNA substrates could be docked proximal to the activated amino acid. RNA microhelices that recapitulate the acceptor stem of modern tRNAs are potential examples of early substrates. In this work, we examined a fragment of Escherichia coli alanyl-tRNA synthetase, which catalyzes aminoacyl adenylate formation but is virtually inactive for catalysis of RNA microhelix aminoacylation. Fusion to the fragment of either of two unrelated nonspecific RNA binding domains activated microhelix aminoacylation. Although the fusion proteins lacked the RNA sequence specificity of the natural enzyme, their activity was within 1-2 kcal.mol(-1) of a truncated alanyl-tRNA synthetase that has aminoacylation activity sufficient to sustain cell growth. These results show that, starting with an activity for adenylate synthesis, barriers are relatively low for building catalytic units for aminoacylation of RNA helices.
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Affiliation(s)
- J W Chihade
- Skaggs Institute for Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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25
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Affiliation(s)
- Paul Schimmel
- The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteBeckman Center La Jolla California 92037 USA
| | - Jianshi Tao
- Cubist Pharmaceuticals Inc. Cambridge Massachusetts 02139 USA
| | - Jason Hill
- Cubist Pharmaceuticals Inc. Cambridge Massachusetts 02139 USA
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26
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Stoldt M, Wöhnert J, Görlach M, Brown LR. The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases. EMBO J 1998; 17:6377-84. [PMID: 9799245 PMCID: PMC1170962 DOI: 10.1093/emboj/17.21.6377] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The structure of the Escherichia coli ribosomal protein L25 has been determined to an r.m.s. displacement of backbone heavy atoms of 0.62 +/- 0.14 A by multi-dimensional heteronuclear NMR spectroscopy on protein samples uniformly labeled with 15N or 15N/13C. L25 shows a new topology for RNA-binding proteins consisting of a six-stranded beta-barrel and two alpha-helices. A putative RNA-binding surface for L25 has been obtained by comparison of backbone 15N chemical shifts for L25 with and without a bound cognate RNA containing the eubacterial E-loop that is the site for binding of L25 to 5S ribosomal RNA. Sequence comparisons with related proteins, including the general stress protein, CTC, show that the residues involved in RNA binding are highly conserved, thereby providing further confirmation of the binding surface. Tertiary structure comparisons indicate that the six-stranded beta-barrels of L25 and of the tRNA anticodon-binding domain of glutaminyl-tRNA synthetase are similar.
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Affiliation(s)
- M Stoldt
- Abteilung Molekulare Biophysik/NMR Spektroskopie, Institut für Molekulare Biotechnologie e. V., Postfach 100813, 07708 Jena, Germany
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27
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Shiba K, Motegi H, Schimmel P. Maintaining genetic code through adaptations of tRNA synthetases to taxonomic domains. Trends Biochem Sci 1997; 22:453-7. [PMID: 9433122 DOI: 10.1016/s0968-0004(97)01135-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The universal genetic code is determined by the aminoacylation of tRNAs. In spite of the universality of the code, there are barriers to aminoacylation across taxonomic domains. These barriers are thought to correlate with the co-segregation of sequences of synthetases and tRNAs into distinct taxonomic domains. By contrast, we show here examples of eukaryote-like synthetases that are found in certain prokaryotes. The associated tRNAs have retained their prokaryote-like character in each instance. Thus, co-segregation of domain-specific synthetases and tRNAs does not always occur. Instead, synthetases make adaptations of tRNA-protein contacts to cross taxonomic domains.
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Affiliation(s)
- K Shiba
- PRESTO, Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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28
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Cerini C, Semeriva M, Gratecos D. Evolution of the aminoacyl-tRNA synthetase family and the organization of the Drosophila glutamyl-prolyl-tRNA synthetase gene. Intron/exon structure of the gene, control of expression of the two mRNAs, selective advantage of the multienzyme complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:176-85. [PMID: 9063462 DOI: 10.1111/j.1432-1033.1997.00176.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In Drosophila, glutamyl-prolyl-tRNA synthetase is a multifunctional synthetase encoded by a unique gene and composed of three domains: the amino- and carboxy-terminal domains catalyze the aminoacylation of glutamic acid and proline tRNA species, respectively, and the central domain is made of 75 amino acids repeated six times amongst which 46 are highly conserved and constitute the repeated motifs [Cerini, C., Kerjan, P., Astier, M., Gratecos, D., Mirande, M. & Sémériva, M. (1991) EMBO J. 10, 4267-4277]. The intron/exon organization of the Drosophila gene reveals the presence of six exons among which four are in the 5'-end encoding glutamic acid activity. Only one exon encodes the repeated motifs. A comparison of introns positions, intron classes and intron/exon boundaries in the Drosophila gene and in its human counterpart is compatible with the intron-early hypothesis presiding, at least in part, to the evolution of the synthetases. The full-length fly protein is encoded by a 6.1-kb mRNA which is expressed throughout development. In addition, a shorter transcript encompasses the 3'-end of the cDNA and it is especially abundant in 5-10-h embryos until the first larval stage. Expression of these two mRNAs seems to be controlled by two independent promoters. The 6.1-kb mRNA promoter is probably localized in the 5'-end of the gene. The small mRNA promoter resides in the 4th intron and evidence is provided that the mRNA encodes only the domain corresponding to prolyl-tRNA synthetase and is functional in vivo. Finally, transgenic flies have been established by using constructs corresponding to the three domains of the protein. Overexpression of the repeated motifs leads to a sterility of the flies that suggests a role of these motifs in linking the multienzyme complex to an, as yet, unknown structure of the protein synthesis apparatus.
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Affiliation(s)
- C Cerini
- Laboratoire de Génétique et Physiologie du Développement, UMR 9943, CNRS Université de la Méditerranée, Marseille, France
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29
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30
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Madania A, Poch O, Tarassov I, Winsor B, Martin R. Analysis of a 22,956 bp region on the right arm of Saccharomyces cerevisiae chromosome XV. Yeast 1996; 12:1563-73. [PMID: 8972579 DOI: 10.1002/(sici)1097-0061(199612)12:15<1563::aid-yea44>3.0.co;2-m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We present here the sequence analysis of a DNA fragment (cosmid pUOA1258) located on the right arm of chromosome XV. The 22,956 bp sequence reveals 14 open reading frames (ORFs) longer than 300 bp and the 201 bp RPS33 gene. Among the 14 large ORFs, two overlapping frames are likely to be non-expressed and one corresponds to the known GLN4 gene encoding glutaminyl-tRNA synthetase. Two ORFs, O3571 and O3620, encode putative transcriptional regulators with a Zn(2)-Cys(6) DNA binding domain characteristic of members of the GAL4 family. Among the nine remaining ORFs, five (O3568, O3575, O3590, O3615 and O3625) present significant similarity to proteins of unknown function and four (O3580, O3595, O3630 and O3635) lack homology to sequences present in the databases screened.
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Affiliation(s)
- A Madania
- UPR 9005 MMDCD du CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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31
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Gagnon Y, Lacoste L, Champagne N, Lapointe J. Widespread use of the glu-tRNAGln transamidation pathway among bacteria. A member of the alpha purple bacteria lacks glutaminyl-trna synthetase. J Biol Chem 1996; 271:14856-63. [PMID: 8662929 DOI: 10.1074/jbc.271.25.14856] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The expression of the Rhizobium meliloti glutamyl-tRNA synthetase gene in Escherichia coli under the control of a trc promoter results in a toxic effect upon isopropyl-beta-D-thiogalactopyranoside induction, which is probably caused by a misacylation activity. To further investigate this unexpected result, we looked at the pathway of Gln-tRNAGln formation in R. meliloti. No glutaminyl-tRNA synthetase activity has been found in R. meliloti crude extract, but we detected a specific aminotransferase activity that changes Glu-tRNAGln to Gln-tRNAGln. Our results show that R. meliloti, a member of the alpha-subdivision of the purple bacteria, is the first Gram-negative bacteria reported to use a transamidation pathway for Gln-tRNAGln synthesis. A phylogenetic analysis of the contemporary glutamyl-tRNA synthetase and glutaminyl-tRNA synthetase amino acid sequences reveals that a close evolutionary relationship exists between R. meliloti and yeast mitochondrial glutamyl-tRNA synthetases, which is consistent with an origin of mitochondria in the alpha-subdivision of Gram-negative purple bacteria. A 256-amino acid open reading frame closely related to bacterial glutamyl-tRNA synthetases, which probably originates from a glutamyl-tRNA synthetase gene duplication, was found in the 4-min region of the E. coli chromosome. We suggest that this open reading frame is a relic of an ancient transamidation pathway that occurred in an E. coli ancestor before the horizontal transfer of a eukaryotic glutaminyl-tRNA synthetase (Lamour, V., Quevillon, S., Diriong, S., N'Guyen, V. C., Lipinski, M., and Mirande, M.(1994) Proc. Natl. Acad. Sci. U. S. A. 91, 8670-8674) and that it favored its stable acquisition. From these observations, a revisited model for the evolution of the contemporary glutamyl-tRNA synthetases and glutaminyl-tRNA synthetases that differs from the generally accepted model for the evolution of aminoacyl-tRNA synthetases is proposed.
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MESH Headings
- Amino Acid Sequence
- Amino Acyl-tRNA Synthetases/biosynthesis
- Amino Acyl-tRNA Synthetases/chemistry
- Amino Acyl-tRNA Synthetases/metabolism
- Chromatography, High Pressure Liquid
- Cloning, Molecular
- Confidence Intervals
- Enzyme Induction
- Escherichia coli/metabolism
- Genes, Bacterial
- Glutamate-tRNA Ligase/chemistry
- Isopropyl Thiogalactoside/pharmacology
- Molecular Sequence Data
- Phylogeny
- Promoter Regions, Genetic
- RNA, Transfer, Amino Acyl/isolation & purification
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Gln/metabolism
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/metabolism
- Sequence Homology, Amino Acid
- Sinorhizobium meliloti/enzymology
- Sinorhizobium meliloti/genetics
- Transferases/metabolism
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Affiliation(s)
- Y Gagnon
- Département de Biochimie, Faculté des Sciences et de Génie, Université Laval, Ste-Foy, Québec G1K 7P4, Canada
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32
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Gale AJ, Schimmel P. Affinity coelectrophoresis for dissecting protein-RNA domain-domain interactions in a tRNA synthetase system. PHARMACEUTICA ACTA HELVETIAE 1996; 71:45-50. [PMID: 8786999 DOI: 10.1016/0031-6865(95)00046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The class I methionyl tRNA synthetase has a conserved N-terminal nucleotide binding fold which contains the active site, and a largely non-conserved C-terminal anticodon binding domain. At the C-terminal end of the anticodon binding domain is a peptide which curls back into the N-terminal nucleotide binding fold near the active site. We showed that a mutation in this peptide disrupts aminoacylation and binding of a 7 base pair microhelix substrate based on the acceptor stem of tRNA(fMet). The novel technique of affinity coelectrophoresis was applied to this system for the first time to determine dissociation constants of wild-type and mutant MetRS for small RNA substrates. A description and evaluation of this technique for measuring weak protein-nucleic acid interactions is presented here, in the context of the methionyl tRNA synthetase system.
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Affiliation(s)
- A J Gale
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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33
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Nureki O, Vassylyev DG, Katayanagi K, Shimizu T, Sekine S, Kigawa T, Miyazawa T, Yokoyama S, Morikawa K. Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science 1995; 267:1958-65. [PMID: 7701318 DOI: 10.1126/science.7701318] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution. The amino-terminal half of GluRS shows a geometrical similarity with that of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) of the same subclass in class I, comprising the class I-specific Rossmann fold domain and the intervening subclass-specific alpha/beta domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then participated in the specific recognition of the D and acceptor stems of tRNA(Glu) as indicated by mutagenesis analyses based on the docking properties of GluRS and tRNA. In striking contrast to the beta-barrel structure of the GlnRS carboxyl-terminal half, the GluRS carboxyl-terminal half displayed an all-alpha-helix architecture, an alpha-helix cage, and mutagenesis analyses indicated that it had a role in the anticodon recognition.
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Affiliation(s)
- O Nureki
- Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan
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34
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Shiba K, Schimmel P, Motegi H, Noda T. Human glycyl-tRNA synthetase. Wide divergence of primary structure from bacterial counterpart and species-specific aminoacylation. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43986-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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35
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Conley J, Sherman J, Thomann HU, Söill D. Domains ofE. ColiGlutaminyl-tRNA Synthetase Disordered in the Crystal Structure Are Essential for Function or Stability. ACTA ACUST UNITED AC 1994. [DOI: 10.1080/15257779408012173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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36
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Schimmel P, Landro JA, Schmidt E. Evidence for distinct locations for metal binding sites in two closely related class I tRNA synthetases. J Biomol Struct Dyn 1993; 11:571-81. [PMID: 8129874 DOI: 10.1080/07391102.1993.10508016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Of the ten class I tRNA synthetases, those for methionine and isoleucine are among the most closely related. In recent work we showed that the 676 amino acid E. coli methionine tRNA synthetase has one zinc bound per polypeptide. Zinc may be replaced by spectroscopically observable cobalt with retention of full activity. Bound zinc has been localized to a cysteine cluster within an insertion into the nucleotide binding fold that characterizes all class I enzymes. Mutations which interfere with metal ligation to these cysteines yield proteins that are defective in activity. Additional data presented here show that change of the cobalt oxidation state and coordination geometry of the Co(II)-substituted enzyme results in a complete loss in activity, and that mutations which replace any one of the zinc-binding cysteine sulfhydryls have a small but measurable effect on protein stability. These results further support the importance of the metal for the active site. We also show that, in contrast to methionine tRNA synthetase, the closely related but larger 939 amino acid E. coli isoleucine tRNA synthetase contains 1.5 to 2 molecules of zinc bound per polypeptide. The cobalt-substituted enzyme is active and shows the expected spectrum for tetrahedral coordination to sulfur ligands. Although the site(s) for metal coordination in isoleucine tRNA synthetase has not been rigorously established, one likely sequence element is in a region of the primary structure different from the known metal binding site in methionine tRNA synthetase. Thus, these two closely related proteins have incorporated metal binding sites into distinct parts of their related sequences.
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Affiliation(s)
- P Schimmel
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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37
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38
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Chemical modification and mutagenesis studies on zinc binding of aminoacyl-tRNA synthetases. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)82266-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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39
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Buechter DD, Schimmel P. Dissection of a class II tRNA synthetase: determinants for minihelix recognition are tightly associated with domain for amino acid activation. Biochemistry 1993; 32:5267-72. [PMID: 8494904 DOI: 10.1021/bi00070a039] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The ten class II aminoacyl-tRNA synthetases are large homo- and hetero-oligomeric proteins that share three conserved sequence motifs. Within this class, Escherichia coli alanyl-tRNA synthetase is the only homotetramer and is comprised of subunits of 875 amino acids. The enzyme aminoacylates sequence-specific RNA oligonucleotides that recreate as few as four base pairs of the acceptor stem of tRNA(Ala). A monomeric 461 amino acid N-terminal fragment (461N) was previously shown to have full adenylate synthesis activity. However, fragment 461N has significant, but reduced, efficiency of charging of tRNA(Ala), when compared to native enzyme [Ho, C., Jasin, M., & Schimmel, P. (1985) Science 229, 389-393]. We show here that, in contrast, the fragment and the native enzyme aminoacylate a 12 base pair acceptor-T psi C stem minihelix and a four base pair RNA tetraloop with the same efficiency. We also show that fragment 461N makes footprint contacts both on and outside the acceptor helix of bound tRNA(Ala). With one possible exception, the contacts observed with fragment 461N are identical to those seen with the native enzyme. In spite of contacts outside the acceptor helix, fragment 461N charges the native tRNA, minihelix, and tetraloop with similar efficiency. Thus, all minihelix contacts required for activation for charging are tightly associated with the adenylate synthesis domain and, at least in the fragment, are not influenced by additional RNA-protein contacts outside the minihelix domain.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- D D Buechter
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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40
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Ludmerer S, Wright D, Schimmel P. Purification of glutamine tRNA synthetase from Saccharomyces cerevisiae. A monomeric aminoacyl-tRNA synthetase with a large and dispensable NH2-terminal domain. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53351-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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41
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Buechter DD, Schimmel P. Aminoacylation of RNA minihelices: implications for tRNA synthetase structural design and evolution. Crit Rev Biochem Mol Biol 1993; 28:309-22. [PMID: 7691478 DOI: 10.3109/10409239309078438] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The genetic code is based on the aminoacylation of tRNA with amino acids catalyzed by the aminoacyl-tRNA synthetases. The synthetases are constructed from discrete domains and all synthetases possess a core catalytic domain that catalyzes amino acid activation, binds the acceptor stem of tRNA, and transfers the amino acid to tRNA. Fused to the core domain are additional domains that mediate RNA interactions distal to the acceptor stem. Several synthetases catalyze the aminoacylation of RNA oligonucleotide substrates that recreate only the tRNA acceptor stems. In one case, a relatively small catalytic domain catalyzes the aminoacylation of these substrates independent of the rest of the protein. Thus, the active site domain may represent a primordial synthetase in which polypeptide insertions that mediate RNA acceptor stem interactions are tightly integrated with determinants for aminoacyl adenylate synthesis. The relationship between nucleotide sequences in small RNA oligonucleotides and the specific amino acids that are attached to these oligonucleotides could constitute a second genetic code.
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Affiliation(s)
- D D Buechter
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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42
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Shiba K, Schimmel P. Tripartite functional assembly of a large class I aminoacyl tRNA synthetase. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)50003-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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43
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Kim S, Schimmel P. Function independence of microhelix aminoacylation from anticodon binding in a class I tRNA synthetase. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)49573-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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44
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Burbaum JJ, Schimmel P. Amino acid binding by the class I aminoacyl-tRNA synthetases: role for a conserved proline in the signature sequence. Protein Sci 1992; 1:575-81. [PMID: 1304356 PMCID: PMC2142228 DOI: 10.1002/pro.5560010503] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although partial or complete three-dimensional structures are known for three Class I aminoacyl-tRNA synthetases, the amino acid-binding sites in these proteins remain poorly characterized. To explore the methionine binding site of Escherichia coli methionyl-tRNA synthetase, we chose to study a specific, randomly generated methionine auxotroph that contains a mutant methionyl-tRNA synthetase whose defect is manifested in an elevated Km for methionine (Barker, D.G., Ebel, J.-P., Jakes, R.C., & Bruton, C.J., 1982, Eur. J. Biochem. 127, 449-457), and employed the polymerase chain reaction to sequence this mutant synthetase directly. We identified a Pro 14 to Ser replacement (P14S), which accounts for a greater than 300-fold elevation in Km for methionine and has little effect on either the Km for ATP or the kcat of the amino acid activation reaction. This mutation destabilizes the protein in vivo, which may partly account for the observed auxotrophy. The altered proline is found in the "signature sequence" of the Class I synthetases and is conserved. This sequence motif is 1 of 2 found in the 10 Class I aminoacyl-tRNA synthetases and, in the known structures, it is in the nucleotide-binding fold as part of a loop between the end of a beta-strand and the start of an alpha-helix. The phenotype of the mutant and the stability and affinity for methionine of the wild-type and mutant enzymes are influenced by the amino acid that is 25 residues beyond the C-terminus of the signature sequence.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J J Burbaum
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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45
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Kaiser E, Eberhard D, Knippers R. Exons encoding the highly conserved part of human glutaminyl-tRNA synthetase. J Mol Evol 1992; 34:45-53. [PMID: 1556743 DOI: 10.1007/bf00163851] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aminoacyl-tRNA synthetases are important components of the genetic apparatus. In spite of common catalytic properties, synthetases with different amino acid specificities are widely diverse in their primary structures, subunit sizes, and subunit composition. However, synthetases with given amino acid specificities are well conserved throughout evolution. We have been studying the human glutaminyl-tRNA synthetase possessing a sequence of about 400 amino acid residues (the core region) that is very similar to sequences in the corresponding enzymes from bacteria and yeast. The conserved sequence appears to be essential for the basic function of the enzyme, the charging of tRNA with glutamine. As a first step to a better understanding of the evolution of this enzyme, we determined the coding region for the conserved part of the human glutaminyl-tRNA synthetase. The coding region is composed of eight exons. It appears that individual exons encode defined secondary structural elements as parts of functionally important domains of the enzyme. Evolution of the gene by assembly of individual exons seems to be a viable hypothesis; alternative pathways are discussed.
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Affiliation(s)
- E Kaiser
- Fakultät für Biologie, Universität Konstanz, Germany
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46
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Englisch-Peters S, Conley J, Plumbridge J, Leptak C, Söll D, Rogers MJ. Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNA(Gln) interaction. Biochimie 1991; 73:1501-8. [PMID: 1725262 DOI: 10.1016/0300-9084(91)90184-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This paper focuses on several aspects of the specificity of mutants of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) and tRNA(Gln). Temperature-sensitive mutants located in glnS, the gene for GlnRS, have been described previously. The mutations responsible for the temperature-sensitive phenotype were analyzed, and pseudorevertants of these mutants isolated and characterized. The nature of these mutations is discussed in terms of their location in the three-dimensional structure of the tRNA(Gln).GlnRS complex. In order to characterize the specificity of the aminoacylation reaction, mutant tRNA(Gln) species were synthesized with either a 2'-deoxy AMP or 3'-deoxy AMP as their 3'-terminal nucleotide. Subsequent assays for aminoacylation and ATP/PPi exchange activity established the esterification of glutamine to the 2'-hydroxyl of the terminal adenosine; there is no glutaminylation of the 3'-OH group. This correlates with the classification of GlnRS as a class I aminoacyl-tRNA synthetase. Mutations in tRNA(Gln) are discussed which affect the recognition of GlnRS and the current concept of glutamine identity in E coli is reviewed.
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Affiliation(s)
- S Englisch-Peters
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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47
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Eriani G, Prevost G, Kern D, Vincendon P, Dirheimer G, Gangloff J. Cytoplasmic aspartyl-tRNA synthetase from Saccharomyces cerevisiae. Study of its functional organisation by deletion analysis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 200:337-43. [PMID: 1889402 DOI: 10.1111/j.1432-1033.1991.tb16190.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aspartyl-tRNA synthetase (AspRS) from yeast, a homodimer of 125 kDa, was shortened by several residues from the C- and N-termini, via site-directed mutagenesis, to examine the contribution of the removed peptides to the enzyme properties. This study showed that the N-terminal sequence up to amino acid 70 (which confers peculiar ionic properties to the protein) is dispensable for activity. Domains located beyond amino acid 70 appeared to have increasing catalytic importance; the removal of 80 or 90 residues affected the Km values for ATP and deletions of 101 or 140 amino acids profoundly modified the physiochemical properties of AspRS, and by consequence, its structural organisation (extraction of the mutated proteins out of the cells required the presence of SDS). On the C-terminal side, very limited modifications readily affected the enzyme properties. Deletion of as few as three residues increased the Km for ATP and reduced the aminoacylation kcat as well as the thermostability of the adenylate synthesis activity; the kcat of this step was impaired after deletion of two further residues. Finally, shortening the C-terminal decapeptide completely inactivated AspRS, whilst affecting neither its affinity for tRNAAsp nor its dimerisation capacity. These data reveal the role of the C-terminal decapeptide as a determinant in both reactions catalysed by AspRS. This peptide is involved in ATP binding, stabilising the functional conformation of the amino-acid-activating domain and probably maintaining the tRNA-acceptor end in a reactive position with regard to the activated amino acid.
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Affiliation(s)
- G Eriani
- Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Strasbourg, France
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48
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Nureki O, Muramatsu T, Suzuki K, Kohda D, Matsuzawa H, Ohta T, Miyazawa T, Yokoyama S. Methionyl-tRNA synthetase gene from an extreme thermophile, Thermus thermophilus HB8. Molecular cloning, primary-structure analysis, expression in Escherichia coli, and site-directed mutagenesis. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)49984-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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49
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Mirande M. Aminoacyl-tRNA synthetase family from prokaryotes and eukaryotes: structural domains and their implications. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1991; 40:95-142. [PMID: 2031086 DOI: 10.1016/s0079-6603(08)60840-5] [Citation(s) in RCA: 200] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- M Mirande
- Laboratoire d'Enzymologie, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
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50
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Fett R, Knippers R. The primary structure of human glutaminyl-tRNA synthetase. A highly conserved core, amino acid repeat regions, and homologies with translation elongation factors. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)52315-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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