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Ranea-Robles P, Pavlova NN, Bender A, Pereyra AS, Ellis JM, Stauffer B, Yu C, Thompson CB, Argmann C, Puchowicz M, Houten SM. A mitochondrial long-chain fatty acid oxidation defect leads to transfer RNA uncharging and activation of the integrated stress response in the mouse heart. Cardiovasc Res 2022; 118:3198-3210. [PMID: 35388887 PMCID: PMC9799058 DOI: 10.1093/cvr/cvac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/08/2022] [Accepted: 03/23/2022] [Indexed: 01/25/2023] Open
Abstract
AIMS Cardiomyopathy and arrhythmias can be severe presentations in patients with inherited defects of mitochondrial long-chain fatty acid β-oxidation (FAO). The pathophysiological mechanisms that underlie these cardiac abnormalities remain largely unknown. We investigated the molecular adaptations to a FAO deficiency in the heart using the long-chain acyl-CoA dehydrogenase (LCAD) knockout (KO) mouse model. METHODS AND RESULTS We observed enrichment of amino acid metabolic pathways and of ATF4 target genes among the upregulated genes in the LCAD KO heart transcriptome. We also found a prominent activation of the eIF2α/ATF4 axis at the protein level that was independent of the feeding status, in addition to a reduction of cardiac protein synthesis during a short period of food withdrawal. These findings are consistent with an activation of the integrated stress response (ISR) in the LCAD KO mouse heart. Notably, charging of several transfer RNAs (tRNAs), such as tRNAGln was decreased in LCAD KO hearts, reflecting a reduced availability of cardiac amino acids, in particular, glutamine. We replicated the activation of the ISR in the hearts of mice with muscle-specific deletion of carnitine palmitoyltransferase 2. CONCLUSIONS Our results show that perturbations in amino acid metabolism caused by long-chain FAO deficiency impact cardiac metabolic signalling, in particular the ISR. These results may serve as a foundation for investigating the role of the ISR in the cardiac pathology associated with long-chain FAO defects.Translational Perspective: The heart relies mainly on mitochondrial fatty acid β-oxidation (FAO) for its high energy requirements. The heart disease observed in patients with a genetic defect in this pathway highlights the importance of FAO for cardiac health. We show that the consequences of a FAO defect extend beyond cardiac energy homeostasis and include amino acid metabolism and associated signalling pathways such as the integrated stress response.
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Affiliation(s)
- Pablo Ranea-Robles
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Natalya N Pavlova
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aaron Bender
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Andrea S Pereyra
- Brody School of Medicine at East Carolina University, Department of Physiology, and East Carolina Diabetes and Obesity Institute, Greenville, NC 27858, USA
| | - Jessica M Ellis
- Brody School of Medicine at East Carolina University, Department of Physiology, and East Carolina Diabetes and Obesity Institute, Greenville, NC 27858, USA
| | - Brandon Stauffer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
- Mount Sinai Genomics, Inc, Stamford, CT 06902, USA
| | - Chunli Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
- Mount Sinai Genomics, Inc, Stamford, CT 06902, USA
| | - Craig B Thompson
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Michelle Puchowicz
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
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2
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Abstract
Most infectious pathogens have anecdotal evidence to support a link with stroke, but certain pathogens have more robust associations, in which causation is probable. Few dedicated prospective studies of stroke in the setting of infection have been done. The use of head imaging, a clinical standard of diagnostic care, to confirm stroke and stroke type is not universal. Data for stroke are scarce in locations where infections are probably most common, making it difficult to reach conclusions on how populations differ in terms of risk of infectious stroke. The treatment of infections and stroke, when concomitant, is based on almost no evidence and requires dedicated efforts to understand variations that might exist. We highlight the present knowledge and emphasise the need for stronger evidence to assist in the diagnosis, treatment, and secondary prevention of stroke in patients in whom an infectious cause for stroke is probable.
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Zhang X, Ling J, Barcia G, Jing L, Wu J, Barry BJ, Mochida GH, Hill RS, Weimer JM, Stein Q, Poduri A, Partlow JN, Ville D, Dulac O, Yu TW, Lam ATN, Servattalab S, Rodriguez J, Boddaert N, Munnich A, Colleaux L, Zon LI, Söll D, Walsh CA, Nabbout R. Mutations in QARS, encoding glutaminyl-tRNA synthetase, cause progressive microcephaly, cerebral-cerebellar atrophy, and intractable seizures. Am J Hum Genet 2014; 94:547-58. [PMID: 24656866 DOI: 10.1016/j.ajhg.2014.03.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/05/2014] [Indexed: 01/30/2023] Open
Abstract
Progressive microcephaly is a heterogeneous condition with causes including mutations in genes encoding regulators of neuronal survival. Here, we report the identification of mutations in QARS (encoding glutaminyl-tRNA synthetase [QARS]) as the causative variants in two unrelated families affected by progressive microcephaly, severe seizures in infancy, atrophy of the cerebral cortex and cerebellar vermis, and mild atrophy of the cerebellar hemispheres. Whole-exome sequencing of individuals from each family independently identified compound-heterozygous mutations in QARS as the only candidate causative variants. QARS was highly expressed in the developing fetal human cerebral cortex in many cell types. The four QARS mutations altered highly conserved amino acids, and the aminoacylation activity of QARS was significantly impaired in mutant cell lines. Variants p.Gly45Val and p.Tyr57His were located in the N-terminal domain required for QARS interaction with proteins in the multisynthetase complex and potentially with glutamine tRNA, and recombinant QARS proteins bearing either substitution showed an over 10-fold reduction in aminoacylation activity. Conversely, variants p.Arg403Trp and p.Arg515Trp, each occurring in a different family, were located in the catalytic core and completely disrupted QARS aminoacylation activity in vitro. Furthermore, p.Arg403Trp and p.Arg515Trp rendered QARS less soluble, and p.Arg403Trp disrupted QARS-RARS (arginyl-tRNA synthetase 1) interaction. In zebrafish, homozygous qars loss of function caused decreased brain and eye size and extensive cell death in the brain. Our results highlight the importance of QARS during brain development and that epilepsy due to impairment of QARS activity is unusually severe in comparison to other aminoacyl-tRNA synthetase disorders.
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Affiliation(s)
- Xiaochang Zhang
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute
| | - Jiqiang Ling
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Giulia Barcia
- Department of Pediatric Neurology, Centre de Reference Epilepsies Rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France; Institut National de la Santé et de la Recherche Médicale U1129, Université Paris Descartes, 75006 Paris, France; Institut National de la Santé et de la Recherche Médicale U1129, NeuroSpin, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, 91191 Gif-sur-Yvette, France
| | - Lili Jing
- Howard Hughes Medical Institute; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jiang Wu
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Brenda J Barry
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, MA 02115, USA; Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute
| | - Jill M Weimer
- Sanford Children's Health Research Center, Sanford Research, 2301 East 60(th) Street North, Sioux Falls, SD 57104, USA
| | - Quinn Stein
- Departments of Pediatrics and Ob/Gyn, Sanford School of Medicine, Sioux Falls, SD 57105, USA
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer N Partlow
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute
| | - Dorothée Ville
- Department of Pediatric Neurology, Centre Hospitalier Universitaire de Lyon, 69007 Lyon, France
| | - Olivier Dulac
- Department of Pediatric Neurology, Centre de Reference Epilepsies Rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France; Institut National de la Santé et de la Recherche Médicale U1129, Université Paris Descartes, 75006 Paris, France; Institut National de la Santé et de la Recherche Médicale U1129, NeuroSpin, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, 91191 Gif-sur-Yvette, France
| | - Tim W Yu
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Anh-Thu N Lam
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute
| | - Sarah Servattalab
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute
| | - Jacqueline Rodriguez
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute
| | - Nathalie Boddaert
- Institut National de la Santé et de la Recherche Médicale U781, Department of Pediatric Radiology, Hôpital Necker-Enfants Malades, Imagine institute, Université Paris Descartes, 75006 Paris, France
| | - Arnold Munnich
- Institut National de la Santé et de la Recherche Médicale U781, Department of Genetics, Hôpital Necker-Enfants Malades, Imagine institute, Université Paris Descartes, 75006 Paris, France
| | - Laurence Colleaux
- Institut National de la Santé et de la Recherche Médicale U781, Department of Genetics, Hôpital Necker-Enfants Malades, Imagine institute, Université Paris Descartes, 75006 Paris, France
| | - Leonard I Zon
- Howard Hughes Medical Institute; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute; Department of Pediatrics, Harvard Medical School, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Rima Nabbout
- Department of Pediatric Neurology, Centre de Reference Epilepsies Rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France; Institut National de la Santé et de la Recherche Médicale U1129, Université Paris Descartes, 75006 Paris, France; Institut National de la Santé et de la Recherche Médicale U1129, NeuroSpin, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, 91191 Gif-sur-Yvette, France.
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4
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Grant TD, Luft JR, Wolfley JR, Snell ME, Tsuruta H, Corretore S, Quartley E, Phizicky EM, Grayhack EJ, Snell EH. The structure of yeast glutaminyl-tRNA synthetase and modeling of its interaction with tRNA. J Mol Biol 2013; 425:2480-93. [PMID: 23583912 DOI: 10.1016/j.jmb.2013.03.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 02/25/2013] [Accepted: 03/30/2013] [Indexed: 11/26/2022]
Abstract
Eukaryotic glutaminyl-tRNA synthetase (GlnRS) contains an appended N-terminal domain (NTD) whose precise function is unknown. Although GlnRS structures from two prokaryotic species are known, no eukaryotic GlnRS structure has been reported. Here we present the first crystallographic structure of yeast GlnRS, finding that the structure of the C-terminal domain is highly similar to Escherichia coli GlnRS but that 214 residues, including the NTD, are crystallographically disordered. We present a model of the full-length enzyme in solution, using the structures of the C-terminal domain, and the isolated NTD, with small-angle X-ray scattering data of the full-length molecule. We proceed to model the enzyme bound to tRNA, using the crystallographic structures of GatCAB and GlnRS-tRNA complex from bacteria. We contrast the tRNA-bound model with the tRNA-free solution state and perform molecular dynamics on the full-length GlnRS-tRNA complex, which suggests that tRNA binding involves the motion of a conserved hinge in the NTD.
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Affiliation(s)
- Thomas D Grant
- Hauptman Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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5
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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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6
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Chiu WC, Chang CP, Wen WL, Wang SW, Wang CC. Schizosaccharomyces pombe possesses two paralogous valyl-tRNA synthetase genes of mitochondrial origin. Mol Biol Evol 2010; 27:1415-24. [PMID: 20106903 DOI: 10.1093/molbev/msq025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Previous studies showed that VAS1 of Saccharomyces cerevisiae encodes both cytosolic and mitochondrial forms of valyl-tRNA synthetase (ValRS) through alternative initiation of translation. We show herein that except for Schizosaccharomyces pombe, all yeast species studied contained a single ValRS gene encoding both forms, and all of the mature protein forms deduced from those genes possessed an N-terminal appended domain (Ad) that was absent from their bacterial relatives. In contrast, S. pombe contained two distinct nuclear ValRS genes, one encoding the mitochondrial form and the other its cytosolic counterpart. Although the cytosolic form closely resembles other yeast ValRS sequences (approximately 60% identity), the mitochondrial form exhibits significant divergence from others (approximately 35% identity). Both genes are active and essential for the survival of the yeast. Most conspicuously, the mitochondrial form lacks the characteristic Ad. A phylogenetic analysis further suggested that both forms of S. pombe ValRS are of mitochondrial origin, and the mitochondrial form is ancestral to the cytoplasmic form.
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Affiliation(s)
- Wen-Chih Chiu
- Department of Life Science, National Central University, Jung-li, Taiwan
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7
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Chang CP, Lin G, Chen SJ, Chiu WC, Chen WH, Wang CC. Promoting the formation of an active synthetase/tRNA complex by a nonspecific tRNA-binding domain. J Biol Chem 2008; 283:30699-706. [PMID: 18755686 DOI: 10.1074/jbc.m805339200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previous studies showed that valyl-tRNA synthetase of Saccharomyces cerevisiae contains an N-terminal polypeptide extension of 97 residues, which is absent from its bacterial relatives, but is conserved in its mammalian homologues. We showed herein that this appended domain and its human counterpart are both nonspecific tRNA-binding domains (K(d) approximately 0.5 microm). Deletion of the appended domain from the yeast enzyme severely impaired its tRNA binding, aminoacylation, and complementation activities. This N-domain-deleted yeast valyl-tRNA synthetase mutant could be rescued by fusion of the equivalent domain from its human homologue. Moreover, fusion of the N-domain of the yeast enzyme or its human counterpart to Escherichia coli glutaminyl-tRNA synthetase enabled the otherwise "inactive" prokaryotic enzyme to function as a yeast enzyme in vivo. Different from the native yeast enzyme, which showed different affinities toward mixed tRNA populations, the fusion enzyme exhibited similar binding affinities for all yeast tRNAs. These results not only underscore the significance of nonspecific tRNA binding in aminoacylation, but also provide insights into the mechanism of the formation of aminoacyl-tRNAs.
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Affiliation(s)
- Chia-Pei Chang
- Department of Life Science, National Central University, Jung-li, 32001 Taiwan
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8
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Rinehart J, Krett B, Rubio MAT, Alfonzo JD, Söll D. Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion. Genes Dev 2005; 19:583-92. [PMID: 15706032 PMCID: PMC551578 DOI: 10.1101/gad.1269305] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Accepted: 01/06/2005] [Indexed: 11/25/2022]
Abstract
Aminoacyl-tRNA (aa-tRNA) formation, an essential process in protein biosynthesis, is generally achieved by direct attachment of an amino acid to tRNA by the aa-tRNA synthetases. An exception is Gln-tRNA synthesis, which in eukaryotes is catalyzed by glutaminyl-tRNA synthetase (GlnRS), while most bacteria, archaea, and chloroplasts employ the transamidation pathway, in which a tRNA-dependent glutamate modification generates Gln-tRNA. Mitochondrial protein synthesis is carried out normally by mitochondrial enzymes and organelle-encoded tRNAs that are different from their cytoplasmic counterparts. Early work suggested that mitochondria use the transamidation pathway for Gln-tRNA formation. We found no biochemical support for this in Saccharomyces cerevisiae mitochondria, but demonstrated the presence of the cytoplasmic GlnRS in the organelle and its involvement in mitochondrial Gln-tRNA synthesis. In addition, we showed in vivo localization of cytoplasmic tRNAGln in mitochondria and demonstrated its role in mitochondrial translation. We furthermore reconstituted in vitro cytoplasmic tRNAGln import into mitochondria by a novel mechanism. This tRNA import mechanism expands our knowledge of RNA trafficking in the eukaryotic cell. These findings change our view of the evolution of organellar protein synthesis.
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MESH Headings
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/metabolism
- Biological Transport, Active/genetics
- Biological Transport, Active/physiology
- Gene Expression Regulation, Fungal/genetics
- Gene Expression Regulation, Fungal/physiology
- Mitochondria/genetics
- Mitochondria/physiology
- Protein Biosynthesis/genetics
- Protein Biosynthesis/physiology
- Protein Transport/genetics
- Protein Transport/physiology
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Gln/genetics
- RNA, Transfer, Gln/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/physiology
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Jesse Rinehart
- Department of Molecular Biophysics and Biochemistry, and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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9
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Rinehart J, Horn EK, Wei D, Soll D, Schneider A. Non-canonical Eukaryotic Glutaminyl- and Glutamyl-tRNA Synthetases Form Mitochondrial Aminoacyl-tRNA in Trypanosoma brucei. J Biol Chem 2004; 279:1161-6. [PMID: 14563839 DOI: 10.1074/jbc.m310100200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glutaminyl-tRNA synthetase is thought to be absent from organelles. Instead, Gln-tRNA is formed via the transamidation pathway, the other route to this essential compound in protein biosynthesis. However, it was previously shown that glutaminyl-tRNA synthetase activity is present in Leishmania mitochondria. This work identifies genes encoding glutaminyl- and glutamyl-tRNA synthetase in the closely related organism Trypanosoma brucei. Down-regulation of their respective gene products by RNA interference showed that (i) they are essential for the growth of insect stage T. brucei and (ii) they are responsible for essentially all of the glutaminyl- and glutamyl-tRNA synthetase activity detected in both the cytosol and the mitochondria. In vitro aminoacylation experiments with the recombinant T. brucei enzymes and total tRNA confirmed the identity of the two aminoacyl-tRNA synthetases. Interestingly, T. brucei uses the same eukaryotic-type glutaminyl-tRNA synthetase to form mitochondrial and cytosolic Gln-tRNA. The formation of Glu-tRNA in mitochondria and the cytoplasm is catalyzed by a single eukaryotic-type discriminating glutamyl-tRNA synthetase. T. brucei, similar to Leishmania, imports all of its mitochondrial tRNAs from the cytosol. The use of these two eukaryotic-type enzymes in mitochondria may therefore reflect an adaptation to the situation in which the cytosol and mitochondria use the same set of tRNAs.
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Affiliation(s)
- Jesse Rinehart
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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10
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Kim T, Park SG, Kim JE, Seol W, Ko YG, Kim S. Catalytic peptide of human glutaminyl-tRNA synthetase is essential for its assembly to the aminoacyl-tRNA synthetase complex. J Biol Chem 2000; 275:21768-72. [PMID: 10801842 DOI: 10.1074/jbc.m002404200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human glutaminyl-tRNA synthetase (QRS) is one of several mammalian aminoacyl-tRNA synthetases (ARSs) that form a macromolecular protein complex. To understand the mechanism of QRS targeting to the multi-ARS complex, we analyzed both exogenous and endogenous QRSs by immunoprecipitation after overexpression of various Myc-tagged QRS mutants in human embryonic kidney 293 cells. Whereas a deletion mutant containing only the catalytic domain (QRS-C) was targeted to the multi-ARS complex, a mutant QRS containing only the N-terminal appended domain (QRS-N) was not. Deletion mapping showed that the ATP-binding Rossman fold was necessary for targeting of QRS to the multi-ARS complex. Furthermore, exogenous Myc-tagged QRS-C was co-immunoprecipitated with endogenous QRS. Since glutaminylation of tRNA was dramatically increased in cells transfected with the full-length QRS, but not with either QRS-C or QRS-N, both the QRS catalytic domain and the N-terminal appended domain were required for full aminoacylation activity. When QRS-C was overexpressed, arginyl-tRNA synthetase and p43 were released from the multi-ARS complex along with endogenous QRS, suggesting that the N-terminal appendix of QRS is required to keep arginyl-tRNA synthetase and p43 within the complex. Thus, the eukaryote-specific N-terminal appendix of QRS appears to stabilize the association of other components in the multi-ARS complex, whereas the C-terminal catalytic domain is necessary for QRS association with the multi-ARS complex.
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Affiliation(s)
- T Kim
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Suwon, Kyunggido 440-746, Korea
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11
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Liu DR, Schultz PG. Progress toward the evolution of an organism with an expanded genetic code. Proc Natl Acad Sci U S A 1999; 96:4780-5. [PMID: 10220370 PMCID: PMC21768 DOI: 10.1073/pnas.96.9.4780] [Citation(s) in RCA: 143] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several significant steps have been completed toward a general method for the site-specific incorporation of unnatural amino acids into proteins in vivo. An "orthogonal" suppressor tRNA was derived from Saccharomyces cerevisiae tRNA2Gln. This yeast orthogonal tRNA is not a substrate in vitro or in vivo for any Escherichia coli aminoacyl-tRNA synthetase, including E. coli glutaminyl-tRNA synthetase (GlnRS), yet functions with the E. coli translational machinery. Importantly, S. cerevisiae GlnRS aminoacylates the yeast orthogonal tRNA in vitro and in E. coli, but does not charge E. coli tRNAGln. This yeast-derived suppressor tRNA together with yeast GlnRS thus represents a completely orthogonal tRNA/synthetase pair in E. coli suitable for the delivery of unnatural amino acids into proteins in vivo. A general method was developed to select for mutant aminoacyl-tRNA synthetases capable of charging any ribosomally accepted molecule onto an orthogonal suppressor tRNA. Finally, a rapid nonradioactive screen for unnatural amino acid uptake was developed and applied to a collection of 138 amino acids. The majority of glutamine and glutamic acid analogs under examination were found to be uptaken by E. coli. Implications of these results are discussed.
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Affiliation(s)
- D R Liu
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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Motorin Y, Le Caer JP, Waller JP. Cysteinyl-tRNA synthetase from Saccharomyces cerevisiae. Purification, characterization and assignment to the genomic sequence YNL247w. Biochimie 1997; 79:731-40. [PMID: 9523015 DOI: 10.1016/s0300-9084(97)86931-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cysteinyl-tRNA synthetase (CRS) from Saccharomyces cerevisiae was purified 2300-fold with a yield of 33%, to a high specific activity (kcat4.3 s-1 at 25 degrees C for the aminoacylation of yeast tRNACys). SDS-PAGE revealed a single polypeptide corresponding to a molecular mass of 86 kDa. Polyclonal antibodies to the purified protein inactivated CRS activity and detected only one polypeptide of 86 kDa in a yeast extract subjected to SDS-PAGE followed by immunoblotting. In contrast to bacterial CRS which is a monomer of about 50 kDa, the native yeast enzyme behaved as a dimer, as assessed by gel filtration and cross-linking. Its subunit molecular mass is in good agreement with the value of 87.5 kDa calculated for the protein encoded by the yeast genomic sequence YNL247w. The latter was previously tentatively assigned to CRS, based on limited sequence similarities to the corresponding enzyme from other sources. Determination of the amino acid sequence of internal polypeptides derived from the purified yeast enzyme confirmed this assignment. Alignment of the primary sequences of prokaryotic and yeast CRS reveals that the larger size of the latter is accounted for mostly by several insertions within the sequence.
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Affiliation(s)
- Y Motorin
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France
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Agou F, Waller JP, Mirande M. Expression of rat aspartyl-tRNA synthetase in Saccharomyces cerevisiae. Role of the NH2-terminal polypeptide extension on enzyme activity and stability. J Biol Chem 1996; 271:29295-303. [PMID: 8910590 DOI: 10.1074/jbc.271.46.29295] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cytoplasmic aspartyl-tRNA synthetase from mammals is one of the components of a multienzyme complex comprising nine synthetase activities. The presence of an amino-terminal extension composed of about 40 residues is a characteristic of the eukaryotic enzyme. We report here the expression in the yeast Saccharomyces cerevisiae of a native form of rat aspartyl-tRNA synthetase and of two truncated derivatives lacking 20 or 36 amino acid residues from their amino-terminal polypeptide extension. The three recombinant enzyme species were purified to homogeneity. They behave as alpha2 dimers and display catalytic parameters in the tRNA aminoacylation reaction identical to those determined for the native, complex-associated form of aspartyl-tRNA synthetase isolated from rat liver. Because the dimer dissociation constant of rat AspRS is much higher than that of its bacterial and yeast counterparts, we could establish a direct correlation between dissociation of the dimer and inactivation of the enzyme. Our results clearly show that the monomer is devoid of amino acid activation and tRNA aminoacylation activities, indicating that dimerization is essential to confer an active conformation on the catalytic site. The two NH2-terminal truncated derivatives were fully active, but proved to be more unstable than the recombinant native enzyme, suggesting that the polypeptide extension fulfills structural rather than catalytic requirements.
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Affiliation(s)
- F Agou
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France.
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Weygand-Durasević I, Lenhard B, Filipić S, Söll D. The C-terminal extension of yeast seryl-tRNA synthetase affects stability of the enzyme and its substrate affinity. J Biol Chem 1996; 271:2455-61. [PMID: 8576207 DOI: 10.1074/jbc.271.5.2455] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Saccharomyces cerevisiae seryl-tRNA synthetase (SerRS) contains a 20-amino acid C-terminal extension, which is not found in prokaryotic SerRS enzymes. A truncated yeast SES1 gene, lacking the 60 base pairs that encode this C-terminal domain, is able to complement a yeast SES1 null allele strain; thus, the C-terminal extension in SerRS is dispensable for the viability of the cell. However, the removal of the C-terminal peptide affects both stability of the enzyme and its affinity for the substrates. The truncation mutant binds tRNA with 3.6-fold higher affinity, while the Km for serine is 4-fold increased relative to the wild-type SerRS. This indicates the importance of the C-terminal extension in maintaining the overall structure of SerRS.
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Affiliation(s)
- I Weygand-Durasević
- Department of Molecular Genetics, Rudjer Bosković Institute, Zagreb, Croatia
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Affiliation(s)
- D C Yang
- Department of Chemistry, Georgetown University, Washington DC 20057, USA
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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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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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