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Rhymes ER, Simkin RL, Qu J, Villarroel-Campos D, Surana S, Tong Y, Shapiro R, Burgess RW, Yang XL, Schiavo G, Sleigh JN. Boosting BDNF in muscle rescues impaired axonal transport in a mouse model of DI-CMTC peripheral neuropathy. Neurobiol Dis 2024; 195:106501. [PMID: 38583640 DOI: 10.1016/j.nbd.2024.106501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is a genetic peripheral neuropathy caused by mutations in many functionally diverse genes. The aminoacyl-tRNA synthetase (ARS) enzymes, which transfer amino acids to partner tRNAs for protein synthesis, represent the largest protein family genetically linked to CMT aetiology, suggesting pathomechanistic commonalities. Dominant intermediate CMT type C (DI-CMTC) is caused by YARS1 mutations driving a toxic gain-of-function in the encoded tyrosyl-tRNA synthetase (TyrRS), which is mediated by exposure of consensus neomorphic surfaces through conformational changes of the mutant protein. In this study, we first showed that human DI-CMTC-causing TyrRSE196K mis-interacts with the extracellular domain of the BDNF receptor TrkB, an aberrant association we have previously characterised for several mutant glycyl-tRNA synthetases linked to CMT type 2D (CMT2D). We then performed temporal neuromuscular assessments of YarsE196K mice modelling DI-CMT. We determined that YarsE196K homozygotes display a selective, age-dependent impairment in in vivo axonal transport of neurotrophin-containing signalling endosomes, phenocopying CMT2D mice. This impairment is replicated by injection of recombinant TyrRSE196K, but not TyrRSWT, into muscles of wild-type mice. Augmenting BDNF in DI-CMTC muscles, through injection of recombinant protein or muscle-specific gene therapy, resulted in complete axonal transport correction. Therefore, this work identifies a non-cell autonomous pathomechanism common to ARS-related neuropathies, and highlights the potential of boosting BDNF levels in muscles as a therapeutic strategy.
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Affiliation(s)
- Elena R Rhymes
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Rebecca L Simkin
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Ji Qu
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - David Villarroel-Campos
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; UK Dementia Research Institute at University College London, London WC1N 3BG, UK
| | - Sunaina Surana
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; UK Dementia Research Institute at University College London, London WC1N 3BG, UK
| | - Yao Tong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Shapiro
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; UK Dementia Research Institute at University College London, London WC1N 3BG, UK
| | - James N Sleigh
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; UK Dementia Research Institute at University College London, London WC1N 3BG, UK.
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2
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Sherlock ME, Langeberg CJ, Kieft JS. Diversity and modularity of tyrosine-accepting tRNA-like structures. RNA 2024; 30:213-222. [PMID: 38164607 PMCID: PMC10870377 DOI: 10.1261/rna.079768.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Certain positive-sense single-stranded RNA viruses contain elements at their 3' termini that structurally mimic tRNAs. These tRNA-like structures (TLSs) are classified based on which amino acid is covalently added to the 3' end by host aminoacyl-tRNA synthetase. Recently, a cryoEM reconstruction of a representative tyrosine-accepting tRNA-like structure (TLSTyr) from brome mosaic virus (BMV) revealed a unique mode of recognition of the viral anticodon-mimicking domain by tyrosyl-tRNA synthetase. Some viruses in the hordeivirus genus of Virgaviridae are also selectively aminoacylated with tyrosine, yet these TLS RNAs have a different architecture in the 5' domain that comprises the atypical anticodon loop mimic. Herein, we present bioinformatic and biochemical data supporting a distinct secondary structure for the 5' domain of the hordeivirus TLSTyr compared to those in Bromoviridae Despite forming a different secondary structure, the 5' domain is necessary to achieve robust in vitro aminoacylation. Furthermore, a chimeric RNA containing the 5' domain from the BMV TLSTyr and the 3' domain from a hordeivirus TLSTyr are aminoacylated, illustrating modularity in these structured RNA elements. We propose that the structurally distinct 5' domain of the hordeivirus TLSTyrs performs the same role in mimicking the anticodon loop as its counterpart in the BMV TLSTyr Finally, these structurally and phylogenetically divergent types of TLSTyr provide insight into the evolutionary connections between all classes of viral tRNA-like structures.
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Affiliation(s)
- Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Conner J Langeberg
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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3
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Jones JA, Wei N, Cui H, Shi Y, Fu G, Rauniyar N, Shapiro R, Morodomi Y, Berenst N, Dumitru CD, Kanaji S, Yates JR, Kanaji T, Yang XL. Nuclear translocation of an aminoacyl-tRNA synthetase may mediate a chronic "integrated stress response". Cell Rep 2023; 42:112632. [PMID: 37314928 PMCID: PMC10592355 DOI: 10.1016/j.celrep.2023.112632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 04/24/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Various stress conditions are signaled through phosphorylation of translation initiation factor eukaryotic initiation factor 2α (eIF2α) to inhibit global translation while selectively activating transcription factor ATF4 to aid cell survival and recovery. However, this integrated stress response is acute and cannot resolve lasting stress. Here, we report that tyrosyl-tRNA synthetase (TyrRS), a member of the aminoacyl-tRNA synthetase family that responds to diverse stress conditions through cytosol-nucleus translocation to activate stress-response genes, also inhibits global translation. However, it occurs at a later stage than eIF2α/ATF4 and mammalian target of rapamycin (mTOR) responses. Excluding TyrRS from the nucleus over-activates translation and increases apoptosis in cells under prolonged oxidative stress. Nuclear TyrRS transcriptionally represses translation genes by recruiting TRIM28 and/or NuRD complex. We propose that TyrRS, possibly along with other family members, can sense a variety of stress signals through intrinsic properties of this enzyme and strategically located nuclear localization signal and integrate them by nucleus translocation to effect protective responses against chronic stress.
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Affiliation(s)
- Julia A Jones
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Na Wei
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Haissi Cui
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yi Shi
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Guangsen Fu
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Navin Rauniyar
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Shapiro
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yosuke Morodomi
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nadine Berenst
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Calin Dan Dumitru
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sachiko Kanaji
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Taisuke Kanaji
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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4
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Zhao R, Cai K, Yang JJ, Zhou Q, Cao W, Xiang J, Shen YH, Cheng LL, Zang WD, Lin Y, Yuan YY, Xu W, Tao H, Zhao SM, Zhao JY. Nuclear ATR lysine-tyrosylation protects against heart failure by activating DNA damage response. Cell Rep 2023; 42:112400. [PMID: 37071536 DOI: 10.1016/j.celrep.2023.112400] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 01/12/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023] Open
Abstract
Dysregulated amino acid increases the risk for heart failure (HF) via unclear mechanisms. Here, we find that increased plasma tyrosine and phenylalanine levels are associated with HF. Increasing tyrosine or phenylalanine by high-tyrosine or high-phenylalanine chow feeding exacerbates HF phenotypes in transverse aortic constriction and isoproterenol infusion mice models. Knocking down phenylalanine dehydrogenase abolishes the effect of phenylalanine, indicating that phenylalanine functions by converting to tyrosine. Mechanistically, tyrosyl-tRNA synthetase (YARS) binds to ataxia telangiectasia and Rad3-related gene (ATR), catalyzes lysine tyrosylation (K-Tyr) of ATR, and activates the DNA damage response (DDR) in the nucleus. Increased tyrosine inhibits the nuclear localization of YARS, inhibits the ATR-mediated DDR, accumulates DNA damage, and elevates cardiomyocyte apoptosis. Enhancing ATR K-Tyr by overexpressing YARS, restricting tyrosine, or supplementing tyrosinol, a structural analog of tyrosine, promotes YARS nuclear localization and alleviates HF in mice. Our findings implicate facilitating YARS nuclear translocation as a potential preventive and/or interfering measure against HF.
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Affiliation(s)
- Rui Zhao
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China; Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Ke Cai
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Jing-Jing Yang
- Department of Cardiothoracic Surgery, Second Hospital of Anhui Medical University, and Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China
| | - Qian Zhou
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China; Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Wei Cao
- Department of Cardiothoracic Surgery, Second Hospital of Anhui Medical University, and Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China
| | - Jie Xiang
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Yi-Hui Shen
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Lei-Lei Cheng
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Wei-Dong Zang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yan Lin
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Yi-Yuan Yuan
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Wei Xu
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Hui Tao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China; Department of Cardiothoracic Surgery, Second Hospital of Anhui Medical University, and Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China.
| | - Shi-Min Zhao
- Obstetrics & Gynecology Hospital of Fudan University, Zhongshan Hospital of Fudan University, State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China.
| | - Jian-Yuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China; Department of Cardiothoracic Surgery, Second Hospital of Anhui Medical University, and Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China; School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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5
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Ermanoska B, Asselbergh B, Morant L, Petrovic-Erfurth ML, Hosseinibarkooie S, Leitão-Gonçalves R, Almeida-Souza L, Bervoets S, Sun L, Lee L, Atkinson D, Khanghahi A, Tournev I, Callaerts P, Verstreken P, Yang XL, Wirth B, Rodal AA, Timmerman V, Goode BL, Godenschwege TA, Jordanova A. Tyrosyl-tRNA synthetase has a noncanonical function in actin bundling. Nat Commun 2023; 14:999. [PMID: 36890170 PMCID: PMC9995517 DOI: 10.1038/s41467-023-35908-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/06/2023] [Indexed: 03/10/2023] Open
Abstract
Dominant mutations in tyrosyl-tRNA synthetase (YARS1) and six other tRNA ligases cause Charcot-Marie-Tooth peripheral neuropathy (CMT). Loss of aminoacylation is not required for their pathogenicity, suggesting a gain-of-function disease mechanism. By an unbiased genetic screen in Drosophila, we link YARS1 dysfunction to actin cytoskeleton organization. Biochemical studies uncover yet unknown actin-bundling property of YARS1 to be enhanced by a CMT mutation, leading to actin disorganization in the Drosophila nervous system, human SH-SY5Y neuroblastoma cells, and patient-derived fibroblasts. Genetic modulation of F-actin organization improves hallmark electrophysiological and morphological features in neurons of flies expressing CMT-causing YARS1 mutations. Similar beneficial effects are observed in flies expressing a neuropathy-causing glycyl-tRNA synthetase. Hence, in this work, we show that YARS1 is an evolutionary-conserved F-actin organizer which links the actin cytoskeleton to tRNA-synthetase-induced neurodegeneration.
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Affiliation(s)
- Biljana Ermanoska
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Bob Asselbergh
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, 2610, Antwerp, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
| | - Laura Morant
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
| | - Maria-Luise Petrovic-Erfurth
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
| | - Seyyedmohsen Hosseinibarkooie
- Institute of Human Genetics; Center for Molecular Medicine Cologne; Center for Rare Diseases Cologne, University Hospital of Cologne; University of Cologne, 50931, Cologne, Germany
- Division of Endocrinology and Metabolism and Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Ricardo Leitão-Gonçalves
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Frontiers Media SA, Lausanne, Switzerland
| | - Leonardo Almeida-Souza
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Helsinki Institute of Life Science, Institute of Biotechnology & Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Sven Bervoets
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Litao Sun
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangdong, China
| | - LaTasha Lee
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, 33458, USA
- Center for Social and Clinical Research, National Minority Quality Forum, Washington, DC, USA
| | - Derek Atkinson
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Akram Khanghahi
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
| | - Ivaylo Tournev
- Department of Neurology, Medical University-Sofia, 1431, Sofia, Bulgaria
- Department of Cognitive Science and Psychology, New Bulgarian University, 1618, Sofia, Bulgaria
| | | | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000, Leuven, Belgium
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Brunhilde Wirth
- Institute of Human Genetics; Center for Molecular Medicine Cologne; Center for Rare Diseases Cologne, University Hospital of Cologne; University of Cologne, 50931, Cologne, Germany
| | - Avital A Rodal
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Vincent Timmerman
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Tanja A Godenschwege
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, 33458, USA
| | - Albena Jordanova
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium.
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium.
- Department of Medical Chemistry and Biochemistry, Medical University-Sofia, 1431, Sofia, Bulgaria.
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6
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Averdunk L, Sticht H, Surowy H, Lüdecke HJ, Koch-Hogrebe M, Alsaif HS, Kahrizi K, Alzaidan H, Alawam BS, Tohary M, Kraus C, Endele S, Wadman E, Kaplan JD, Efthymiou S, Najmabadi H, Reis A, Alkuraya FS, Wieczorek D. The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype. J Mol Med (Berl) 2021; 99:1755-1768. [PMID: 34536092 PMCID: PMC8599376 DOI: 10.1007/s00109-021-02124-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 11/14/2022]
Abstract
Pathogenic variants in aminoacyl-tRNA synthetases (ARS1) cause a diverse spectrum of autosomal recessive disorders. Tyrosyl tRNA synthetase (TyrRS) is encoded by YARS1 (cytosolic, OMIM*603,623) and is responsible of coupling tyrosine to its specific tRNA. Next to the enzymatic domain, TyrRS has two additional functional domains (N-Terminal TyrRSMini and C-terminal EMAP-II-like domain) which confer cytokine-like functions. Mutations in YARS1 have been associated with autosomal-dominant Charcot-Marie-Tooth (CMT) neuropathy type C and a heterogenous group of autosomal recessive, multisystem diseases. We identified 12 individuals from 6 families with the recurrent homozygous missense variant c.1099C > T;p.(Arg367Trp) (NM_003680.3) in YARS1. This variant causes a multisystem disorder with developmental delay, microcephaly, failure to thrive, short stature, muscular hypotonia, ataxia, brain anomalies, microcytic anemia, hepatomegaly, and hypothyroidism. In silico analyses show that the p.(Arg367Trp) does not affect the catalytic domain responsible of enzymatic coupling, but destabilizes the cytokine-like C-terminal domain. The phenotype associated with p.(Arg367Trp) is distinct from the other biallelic pathogenic variants that reside in different functional domains of TyrRS which all show some common, but also divergent clinical signs [(e.g., p.(Phe269Ser)-retinal anomalies, p.(Pro213Leu)/p.(Gly525Arg)-mild ID, p.(Pro167Thr)-high fatality)]. The diverse clinical spectrum of ARS1-associated disorders is related to mutations affecting the various non-canonical domains of ARS1, and impaired protein translation is likely not the exclusive disease-causing mechanism of YARS1- and ARS1-associated neurodevelopmental disorders. KEY MESSAGES: The missense variant p.(Arg367Trp) in YARS1 causes a distinct multisystem disorder. p.(Arg367Trp) affects a non-canonical domain with cytokine-like functions. Phenotypic heterogeneity associates with the different affected YARS1 domains. Impaired protein translation is likely not the exclusive mechanism of ARS1-associated disorders.
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Affiliation(s)
- Luisa Averdunk
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Harald Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hermann-Josef Lüdecke
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | | | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hamad Alzaidan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bashayer S Alawam
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Tohary
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Cornelia Kraus
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sabine Endele
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Erin Wadman
- Division of Medical Genetics, Department of Pediatrics, Nemours Alfred I, DuPont Hospital for Children, Wilmington, Delaware, DE, USA
| | - Julie D Kaplan
- Division of Medical Genetics, Department of Pediatrics, Nemours Alfred I, DuPont Hospital for Children, Wilmington, Delaware, DE, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Hossein Najmabadi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - André Reis
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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7
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Datt M. Interplay of substrate polymorphism and conformational plasticity of Plasmodium tyrosyl-tRNA synthetase. Comput Biol Chem 2021; 95:107582. [PMID: 34571426 DOI: 10.1016/j.compbiolchem.2021.107582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/12/2021] [Accepted: 09/12/2021] [Indexed: 11/18/2022]
Abstract
Aminoacyl-tRNA synthetases are an indispensable component of ribosomal protein translational machinery and Plasmodium Tyrosyl-tRNA synthetase (PfTyrRS) is a validated drug target. This manuscript illustrates the dynamic conformational landscape of PfTyrRS in the context of substrate binding. Molecular dynamics simulations of PfTyrRS in the presence and absence of ligand show conformational heterogeneity for both the protein and the bound ligand. Diverse conformations for the evolutionarily conserved ATP binding motif (KMSKS) have been observed in both apo- and holo PfTyrRS. Further, the presented attributes of the tyrosyl-adenylate conformational sub-states in situ along with their implications on the strength of intermolecular interactions would be a pertinent benchmark for molecular design studies. In addition, an analysis of the ligand hydration pattern foregrounds the structurally conserved water-mediated inter-molecular interactions. The quantitative assessment of the conformational landscape, based on the fluctuations of the distance between the ligand binding pockets, of apo-PfTyrRS and holo-PfTyrRS highlights the nature of diversity in conformational sampling for the two cases. Evidently, the holo-PfTyrRS adopts a rather compact conformation compared to the apo-PfTyrRS. An intriguing asymmetry in the dynamics of the two monomers is contextualized with the functional asymmetry of the symmetrically dimeric PfTyrRS. Importantly, the network of non-bonded contacts in the apo- and holo- simulated ensembles has been analyzed. The graph-theoretic analysis-based novel insights concerning the nature of information flow as a function of ligation state would prove valuable in understanding PfTyrRS functions. The results presented here contend that understanding allostery in PfTyrRS is essential to astutely design structure-based inhibitors.
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Affiliation(s)
- Manish Datt
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat - 380009, India.
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8
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Spaulding EL, Hines TJ, Bais P, Tadenev ALD, Schneider R, Jewett D, Pattavina B, Pratt SL, Morelli KH, Stum MG, Hill DP, Gobet C, Pipis M, Reilly MM, Jennings MJ, Horvath R, Bai Y, Shy ME, Alvarez-Castelao B, Schuman EM, Bogdanik LP, Storkebaum E, Burgess RW. The integrated stress response contributes to tRNA synthetase-associated peripheral neuropathy. Science 2021; 373:1156-1161. [PMID: 34516839 PMCID: PMC8908546 DOI: 10.1126/science.abb3414] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Dominant mutations in ubiquitously expressed transfer RNA (tRNA) synthetase genes cause axonal peripheral neuropathy, accounting for at least six forms of Charcot-Marie-Tooth (CMT) disease. Genetic evidence in mouse and Drosophila models suggests a gain-of-function mechanism. In this study, we used in vivo, cell type–specific transcriptional and translational profiling to show that mutant tRNA synthetases activate the integrated stress response (ISR) through the sensor kinase GCN2 (general control nonderepressible 2). The chronic activation of the ISR contributed to the pathophysiology, and genetic deletion or pharmacological inhibition of Gcn2 alleviated the peripheral neuropathy. The activation of GCN2 suggests that the aberrant activity of the mutant tRNA synthetases is still related to translation and that inhibiting GCN2 or the ISR may represent a therapeutic strategy in CMT.
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Affiliation(s)
- E. L. Spaulding
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - T. J. Hines
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - P. Bais
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - A. L. D. Tadenev
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - R. Schneider
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - D. Jewett
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - B. Pattavina
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - S. L. Pratt
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Neuroscience Program, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, 02111 USA
| | - K. H. Morelli
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - M. G. Stum
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - D. P. Hill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - C. Gobet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - M. Pipis
- MRC Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - M. M. Reilly
- MRC Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - M. J. Jennings
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - R. Horvath
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Y. Bai
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - M. E. Shy
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | | | - E. M. Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - L. P. Bogdanik
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - E. Storkebaum
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - R. W. Burgess
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
- Neuroscience Program, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, 02111 USA
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9
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Estève C, Roman C, DeLeusse C, Baravalle M, Bertaux K, Blanc F, Bourgeois P, Bresson V, Cano A, Coste ME, Delteil C, Lacoste C, Loosveld M, De Paula AM, Monnier AS, Secq V, Levy N, Badens C, Fabre A. Novel partial loss-of-function variants in the tyrosyl-tRNA synthetase 1 (YARS1) gene involved in multisystem disease. Eur J Med Genet 2021; 64:104294. [PMID: 34352414 DOI: 10.1016/j.ejmg.2021.104294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 06/22/2021] [Accepted: 07/31/2021] [Indexed: 11/19/2022]
Abstract
Cytoplasmic aminoacyl-tRNA synthetases (ARSs) are emerging as a cause of numerous rare inherited diseases. Recently, biallelic variants in tyrosyl-tRNA synthetase 1 (YARS1) have been described in ten patients of three families with multi-systemic disease (failure to thrive, developmental delay, liver dysfunction, and lung cysts). Here, we report an additional subject with overlapping clinical findings, heterozygous for two novel variants in tyrosyl-tRNA synthetase 1 (NM_003680.3(YARS1):c.176T>C; p.(Ile59Thr) and NM_003680.3(YARS1):c.237C>G; p.(Tyr79*) identified by whole exome sequencing. The p.Ile59Thr variant is located in the highly conserved aminoacylation domain of the protein. Compared to subjects previously described, this patient presents a much more severe condition. Our findings support implication of two novel YARS1 variants in these disorders. Furthermore, we provide evidence for a reduced protein abundance in cells of the patient, in favor of a partial loss-of-function mechanism.
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Affiliation(s)
| | - Céline Roman
- Service de Pédiatrie Multidisciplinaire, Hôpital de La Timone Enfants, APHM, Marseille, France
| | - Cécile DeLeusse
- Service de Pédiatrie Multidisciplinaire, Hôpital de La Timone Enfants, APHM, Marseille, France
| | - Melissa Baravalle
- Service de Pneumologie Pédiatrique, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Karine Bertaux
- CRB TAC (CRB AP-HM TAC), [BIORESOURCES], Marseille, France
| | - Frédéric Blanc
- Service D'Anesthésie Réanimation Pédiatrique, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Patrice Bourgeois
- Aix Marseille Univ, INSERM, MMG, Marseille, France; Service de Génétique Médicale, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Violaine Bresson
- Service D'Urgences Pédiatriques, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Aline Cano
- Service de Pédiatrie Spécialisée & Médecine Infantile, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Marie-Edith Coste
- Service de Pédiatrie Multidisciplinaire, Hôpital de La Timone Enfants, APHM, Marseille, France
| | - Clémence Delteil
- Service de Médecine Légale, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Caroline Lacoste
- Service de Génétique Médicale, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Marie Loosveld
- Laboratoire D'Hématologie Biologique, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - André Maues De Paula
- Laboratoire D'Anatomie Pathologique, Hôpital de La Timone Enfants, APHM, Marseille, France
| | - Anne-Sophie Monnier
- Service de Pédiatrie Multidisciplinaire, Hôpital de La Timone Enfants, APHM, Marseille, France
| | - Véronique Secq
- U1068-CRCM, Aix Marseille Univ, APHM, Hôpital Nord, Service D'anatomo-pathologie, Marseille, France
| | - Nicolas Levy
- Aix Marseille Univ, INSERM, MMG, Marseille, France; Service de Génétique Médicale, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Catherine Badens
- Aix Marseille Univ, INSERM, MMG, Marseille, France; Service de Génétique Médicale, Assistance Publique des Hôpitaux de Marseille, Timone Enfant, Marseille, France
| | - Alexandre Fabre
- Aix Marseille Univ, INSERM, MMG, Marseille, France; Service de Pédiatrie Multidisciplinaire, Hôpital de La Timone Enfants, APHM, Marseille, France.
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10
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Abstract
Compared with green fluorescent protein-based biosensors, red fluorescent protein (RFP)-based biosensors are inherently advantageous because of reduced phototoxicity, decreased autofluorescence and enhanced tissue penetration. However, existing RFP-based biosensors often suffer from small dynamic ranges, mislocalization and undesired photoconversion. In addition, the choice of available RFP-based biosensors is limited, and development of each biosensor requires substantial effort. Herein, we describe a general and convenient method, which introduces a genetically encoded noncanonical amino acid, 3-aminotyrosine, to the chromophores of green fluorescent protein-like proteins and biosensors for spontaneous and efficient green-to-red conversion. We demonstrated that this method could be used to quickly expand the repertoire of RFP-based biosensors. With little optimization, the 3-aminotyrosine-modified biosensors preserved the molecular brightness, dynamic range and responsiveness of their green fluorescent predecessors. We further applied spectrally resolved biosensors for multiplexed imaging of metabolic dynamics in pancreatic β-cells.
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Affiliation(s)
- Shen Zhang
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, and the UVA Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Hui-Wang Ai
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, and the UVA Cancer Center, University of Virginia, Charlottesville, VA, USA.
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11
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He X, Chen Y, Beltran DG, Kelly M, Ma B, Lawrie J, Wang F, Dodds E, Zhang L, Guo J, Niu W. Functional genetic encoding of sulfotyrosine in mammalian cells. Nat Commun 2020; 11:4820. [PMID: 32973160 PMCID: PMC7515910 DOI: 10.1038/s41467-020-18629-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Protein tyrosine O-sulfation (PTS) plays a crucial role in extracellular biomolecular interactions that dictate various cellular processes. It also involves in the development of many human diseases. Regardless of recent progress, our current understanding of PTS is still in its infancy. To promote and facilitate relevant studies, a generally applicable method is needed to enable efficient expression of sulfoproteins with defined sulfation sites in live mammalian cells. Here we report the engineering, in vitro biochemical characterization, structural study, and in vivo functional verification of a tyrosyl-tRNA synthetase mutant for the genetic encoding of sulfotyrosine in mammalian cells. We further apply this chemical biology tool to cell-based studies on the role of a sulfation site in the activation of chemokine receptor CXCR4 by its ligand. Our work will not only facilitate cellular studies of PTS, but also paves the way for economical production of sulfated proteins as therapeutic agents in mammalian systems.
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Affiliation(s)
- Xinyuan He
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Yan Chen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Maia Kelly
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Bin Ma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Feng Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Limei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.
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12
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Gurtner C, Hug P, Kleiter M, Köhler K, Dietschi E, Jagannathan V, Leeb T. YARS2 Missense Variant in Belgian Shepherd Dogs with Cardiomyopathy and Juvenile Mortality. Genes (Basel) 2020; 11:genes11030313. [PMID: 32183361 PMCID: PMC7140874 DOI: 10.3390/genes11030313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 01/03/2023] Open
Abstract
Dog puppy loss by the age of six to eight weeks after normal development is relatively uncommon. Necropsy findings in two spontaneously deceased Belgian Shepherd puppies indicated an abnormal accumulation of material in several organs. A third deceased puppy exhibited mild signs of an inflammation in the central nervous system and an enteritis. The puppies were closely related, raising the suspicion of a genetic cause. Pedigree analysis suggested a monogenic autosomal recessive inheritance. Combined linkage and homozygosity mapping assigned the most likely position of a potential genetic defect to 13 genome segments totaling 82 Mb. The genome of an affected puppy was sequenced and compared to 645 control genomes. Three private protein changing variants were found in the linked and homozygous regions. Targeted genotyping in 96 Belgian Shepherd dogs excluded two of these variants. The remaining variant, YARS2:1054G>A or p.Glu352Lys, was perfectly associated with the phenotype in a cohort of 474 Belgian Shepherd dogs. YARS2 encodes the mitochondrial tyrosyl-tRNA synthetase 2 and the predicted amino acid change replaces a negatively charged and evolutionary conserved glutamate at the surface of the tRNA binding domain of YARS2 with a positively charged lysine. Human patients with loss-of-function variants in YARS2 suffer from myopathy, lactic acidosis, and sideroblastic anemia 2, a disease with clinical similarities to the phenotype of the studied dogs. The carrier frequency was 27.2% in the tested Belgian Shepherd dogs. Our data suggest YARS2:1054G>A as the candidate causative variant for the observed juvenile mortality.
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Affiliation(s)
- Corinne Gurtner
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland;
| | - Petra Hug
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (P.H.); (E.D.); (V.J.)
| | - Miriam Kleiter
- Department/Hospital for Companion Animals and Horses, University Clinic for Small Animals, Internal Medicine Small Animals, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Kernt Köhler
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, 35392 Giessen, Germany;
| | - Elisabeth Dietschi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (P.H.); (E.D.); (V.J.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (P.H.); (E.D.); (V.J.)
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (P.H.); (E.D.); (V.J.)
- Correspondence: ; Tel.: +41-31-631-23-26
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13
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Rybak MY, Rayevsky AV, Gudzera OI, Tukalo MA. Stereospecificity control in aminoacyl-tRNA-synthetases: new evidence of d-amino acids activation and editing. Nucleic Acids Res 2019; 47:9777-9788. [PMID: 31504788 PMCID: PMC6765224 DOI: 10.1093/nar/gkz756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/14/2019] [Accepted: 08/21/2019] [Indexed: 02/02/2023] Open
Abstract
The homochirality of amino acids is vital for the functioning of the translation apparatus. l-Amino acids predominate in proteins and d-amino acids usually represent diverse regulatory functional physiological roles in both pro- and eukaryotes. Aminoacyl-tRNA-synthetases (aaRSs) ensure activation of proteinogenic or nonproteinogenic amino acids and attach them to cognate or noncognate tRNAs. Although many editing mechanisms by aaRSs have been described, data about the protective role of aaRSs in d-amino acids incorporation remained unknown. Tyrosyl- and alanyl-tRNA-synthetases were represented as distinct members of this enzyme family. To study the potential to bind and edit noncognate substrates, Thermus thermophilus alanyl-tRNA-synthetase (AlaRS) and tyrosyl-tRNA-synthetase were investigated in the context of d-amino acids recognition. Here, we showed that d-alanine was effectively activated by AlaRS and d-Ala-tRNAAla, formed during the erroneous aminoacylation, was edited by AlaRS. On the other hand, it turned out that d-aminoacyl-tRNA-deacylase (DTD), which usually hydrolyzes d-aminoacyl-tRNAs, was inactive against d-Ala-tRNAAla. To support the finding about DTD, computational docking and molecular dynamics simulations were run. Overall, our work illustrates the novel function of the AlaRS editing domain in stereospecificity control during translation together with trans-editing factor DTD. Thus, we propose different evolutionary strategies for the maintenance of chiral selectivity during translation.
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Affiliation(s)
- Mariia Yu Rybak
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Street, 03143, Kyiv, Ukraine
| | - Alexey V Rayevsky
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Street, 03143, Kyiv, Ukraine
| | - Olga I Gudzera
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Street, 03143, Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Street, 03143, Kyiv, Ukraine
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14
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Cela M, Paulus C, Santos MAS, Moura GR, Frugier M, Rudinger-Thirion J. Plasmodium apicoplast tyrosyl-tRNA synthetase recognizes an unusual, simplified identity set in cognate tRNATyr. PLoS One 2018; 13:e0209805. [PMID: 30592748 PMCID: PMC6310243 DOI: 10.1371/journal.pone.0209805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/11/2018] [Indexed: 11/18/2022] Open
Abstract
The life cycle of Plasmodium falciparum, the agent responsible for malaria, depends on both cytosolic and apicoplast translation fidelity. Apicoplast aminoacyl-tRNA synthetases (aaRS) are bacterial-like enzymes devoted to organellar tRNA aminoacylation. They are all encoded by the nuclear genome and are translocated into the apicoplast only after cytosolic biosynthesis. Apicoplast aaRSs contain numerous idiosyncratic sequence insertions: An understanding of the roles of these insertions has remained elusive and they hinder efforts to heterologously overexpress these proteins. Moreover, the A/T rich content of the Plasmodium genome leads to A/U rich apicoplast tRNA substrates that display structural plasticity. Here, we focus on the P. falciparum apicoplast tyrosyl-tRNA synthetase (Pf-apiTyrRS) and its cognate tRNATyr substrate (Pf-apitRNATyr). Cloning and expression strategies used to obtain an active and functional recombinant Pf-apiTyrRS are reported. Functional analyses established that only three weak identity elements in the apitRNATyr promote specific recognition by the cognate Pf-apiTyrRS and that positive identity elements usually found in the tRNATyr acceptor stem are excluded from this set. This finding brings to light an unusual behavior for a tRNATyr aminoacylation system and suggests that Pf-apiTyrRS uses primarily negative recognition elements to direct tyrosylation specificity.
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Affiliation(s)
- Marta Cela
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
| | - Caroline Paulus
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
| | - Manuel A. S. Santos
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela R. Moura
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Magali Frugier
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
- * E-mail:
| | - Joëlle Rudinger-Thirion
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
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15
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Italia JS, Latour C, Wrobel CJJ, Chatterjee A. Resurrecting the Bacterial Tyrosyl-tRNA Synthetase/tRNA Pair for Expanding the Genetic Code of Both E. coli and Eukaryotes. Cell Chem Biol 2018; 25:1304-1312.e5. [PMID: 30078635 DOI: 10.1016/j.chembiol.2018.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/16/2018] [Accepted: 07/02/2018] [Indexed: 12/21/2022]
Abstract
The bacteria-derived tyrosyl-tRNA synthetase (TyrRS)/tRNA pair was first used for unnatural amino acid (Uaa) mutagenesis in eukaryotic cells over 15 years ago. It provides an ideal platform to genetically encode numerous useful Uaas in eukaryotes. However, this pair has been engineered to charge only a small collection of Uaas to date. Development of Uaa-selective variants of this pair has been limited by technical challenges associated with a yeast-based directed evolution platform, which is currently required to alter its substrate specificity. Here we overcome this limitation by enabling its directed evolution in an engineered strain of E. coli (ATMY), where the endogenous TyrRS/tRNA pair has been functionally replaced with an archaeal counterpart. The facile E. coli-based selection system enabled rapid engineering of this pair to develop variants that selectively incorporate various Uaas, including p-boronophenylalanine, into proteins expressed in mammalian cells as well as in the ATMY strain of E. coli.
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Affiliation(s)
- James S Italia
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Christopher Latour
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Chester J J Wrobel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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16
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Tsukahara T, Yamagishi S, Neyama H, Ueda H. Tyrosyl-tRNA synthetase: A potential kyotorphin synthetase in mammals. Peptides 2018; 101:60-68. [PMID: 29289698 DOI: 10.1016/j.peptides.2017.12.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/17/2017] [Accepted: 12/27/2017] [Indexed: 11/24/2022]
Abstract
Kyotorphin (KTP; L-tyrosyl-l-arginine), an opioid-like analgesic discovered in the bovine brain, is potentially a neuromodulator because of its localization in synaptosomes, the existence of a specific KTP receptor, and the presence of its biosynthetic enzyme in the brain. KTP is formed in the brain from its constituent amino acids, L-tyrosine and L-arginine, by an enzyme termed KTP synthetase. However, the latter has never been identified. We aimed to test the hypothesis that tyrosyl-tRNA synthetase (TyrRS) is also KTP synthetase. We found that recombinant hTyrRS synthesizes KTP from tyrosine, arginine, and ATP, with Km = 1400 μM and 200 μM for arginine and tyrosine, respectively. TyrRS knockdown of PC12 cells with a small interfering RNA (siRNA) in the presence of 1.6 mM tyrosine, arginine, proline, or tryptophan significantly reduced the level of KTP, but not those of tyrosine-tyrosine, tyrosine-proline, or tyrosine-tryptophan. siRNA treatment did not affect cell survival or proliferation. In mice, TyrRS levels were found to be greater in the midbrain and medulla oblongata than in other brain regions. When arginine was administered 2 h prior to brain dissection, the KTP levels in these regions plus olfactory bulb significantly increased, although basal brain KTP levels remained relatively even. Our conclusion is further supported by a positive correlation across brain regions between TyrRS expression and arginine-accelerated KTP production.
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Affiliation(s)
- Tamotsu Tsukahara
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Shuhei Yamagishi
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Hiroyuki Neyama
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Hiroshi Ueda
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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17
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Venkat S, Gregory C, Gan Q, Fan C. Biochemical Characterization of the Lysine Acetylation of Tyrosyl-tRNA Synthetase in Escherichia coli. Chembiochem 2017; 18:1928-1934. [PMID: 28741290 PMCID: PMC5629106 DOI: 10.1002/cbic.201700343] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) play essential roles in protein synthesis. As a member of the aaRS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown in proteomic studies to be acetylated at multiple lysine residues. However, these putative acetylation targets have not yet been biochemically characterized. In this study, we applied a genetic-code-expansion strategy to site-specifically incorporate Nϵ -acetyl-l-lysine into selected positions of TyrRS for in vitro characterization. Enzyme assays demonstrated that acetylation at K85, K235, and K238 could impair the enzyme activity. In vitro deacetylation experiments showed that most acetylated lysine residues in TyrRS were sensitive to the E. coli deacetylase CobB but not YcgC. In vitro acetylation assays indicated that 25 members of the Gcn5-related N-acetyltransferase family in E. coli, including YfiQ, could not acetylate TyrRS efficiently, whereas TyrRS could be acetylated chemically by acetyl-CoA or acetyl-phosphate (AcP) only. Our in vitro characterization experiments indicated that lysine acetylation could be a possible mechanism for modulating aaRS enzyme activities, thus affecting translation.
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Affiliation(s)
- Sumana Venkat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Caroline Gregory
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 727011, USA
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
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18
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Sommerville EW, Ng YS, Alston CL, Dallabona C, Gilberti M, He L, Knowles C, Chin SL, Schaefer AM, Falkous G, Murdoch D, Longman C, de Visser M, Bindoff LA, Rawles JM, Dean JCS, Petty RK, Farrugia ME, Haack TB, Prokisch H, McFarland R, Turnbull DM, Donnini C, Taylor RW, Gorman GS. Clinical Features, Molecular Heterogeneity, and Prognostic Implications in YARS2-Related Mitochondrial Myopathy. JAMA Neurol 2017; 74:686-694. [PMID: 28395030 PMCID: PMC5822212 DOI: 10.1001/jamaneurol.2016.4357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/25/2016] [Indexed: 01/09/2023]
Abstract
Importance YARS2 mutations have been associated with a clinical triad of myopathy, lactic acidosis, and sideroblastic anemia in predominantly Middle Eastern populations. However, the identification of new patients expands the clinical and molecular spectrum of mitochondrial disorders. Objectives To review the clinical, molecular, and genetic features of YARS2-related mitochondrial disease and to demonstrate a new Scottish founder variant. Design, Setting, and Participants An observational case series study was conducted at a national diagnostic center for mitochondrial disease in Newcastle upon Tyne, England, and review of cases published in the literature. Six adults in a well-defined mitochondrial disease cohort and 11 additional cases described in the literature were identified with YARS2 variants between January 1, 2000, and January 31, 2015. Main Outcome and Measures The spectrum of clinical features and disease progression in unreported and reported patients with pathogenic YARS2 variants. Results Seventeen patients (median [interquartile range] age at onset, 1.5 [9.8] years) with YARS2-related mitochondrial myopathy were identified. Fifteen individuals (88%) exhibited an elevated blood lactate level accompanied by generalized myopathy; only 12 patients (71%) manifested with sideroblastic anemia. Hypertrophic cardiomyopathy (9 [53%]) and respiratory insufficiency (8 [47%]) were also prominent clinical features. Central nervous system involvement was rare. Muscle studies showed global cytochrome-c oxidase deficiency in all patients tested and severe, combined respiratory chain complex activity deficiencies. Microsatellite genotyping demonstrated a common founder effect shared between 3 Scottish patients with a p.Leu392Ser variant. Immunoblotting from fibroblasts and myoblasts of an affected Scottish patient showed normal YARS2 protein levels and mild respiratory chain complex defects. Yeast modeling of novel missense YARS2 variants closely correlated with the severity of clinical phenotypes. Conclusions and Relevance The p.Leu392Ser variant is likely a newly identified founder YARS2 mutation. Testing for pathogenic YARS2 variants should be considered in patients presenting with mitochondrial myopathy, characterized by exercise intolerance and muscle weakness even in the absence of sideroblastic anemia irrespective of ethnicity. Regular surveillance and early treatment for cardiomyopathy and respiratory muscle weakness is advocated because early treatment may mitigate the significant morbidity and mortality associated with this genetic disorder.
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Affiliation(s)
- Ewen W. Sommerville
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Yi Shiau Ng
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Charlotte L. Alston
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | | | - Micol Gilberti
- Department of Life Sciences, University of Parma, Parma, Italy
| | - Langping He
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Charlotte Knowles
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Sophie L. Chin
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Andrew M. Schaefer
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Gavin Falkous
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - David Murdoch
- Department of Cardiology, Queen Elizabeth University Hospital, Glasgow, Scotland
| | - Cheryl Longman
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow, Scotland
| | - Marianne de Visser
- Department of Neurology, Academic Medical Centre, Amsterdam, the Netherlands
| | - Laurence A. Bindoff
- Department of Clinical Medicine, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - John M. Rawles
- Department of Medicine, University of Aberdeen, Aberdeen, Scotland (retired)
| | - John C. S. Dean
- Department of Medical Genetics, Medical School Building, University of Aberdeen, Aberdeen, Scotland
| | - Richard K. Petty
- Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow, Scotland
| | - Maria E. Farrugia
- Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow, Scotland
| | - Tobias B. Haack
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Robert McFarland
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Douglass M. Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Claudia Donnini
- Department of Life Sciences, University of Parma, Parma, Italy
| | - Robert W. Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
| | - Gráinne S. Gorman
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, England
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19
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Lamech LT, Saoji M, Paukstelis PJ, Lambowitz AM. Structural Divergence of the Group I Intron Binding Surface in Fungal Mitochondrial Tyrosyl-tRNA Synthetases That Function in RNA Splicing. J Biol Chem 2016; 291:11911-27. [PMID: 27036943 PMCID: PMC4882457 DOI: 10.1074/jbc.m116.725390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 03/29/2016] [Indexed: 01/25/2023] Open
Abstract
The mitochondrial tyrosyl-tRNA synthetases (mtTyrRSs) of Pezizomycotina fungi, a subphylum that includes many pathogenic species, are bifunctional proteins that both charge mitochondrial tRNA(Tyr) and act as splicing cofactors for autocatalytic group I introns. Previous studies showed that one of these proteins, Neurospora crassa CYT-18, binds group I introns by using both its N-terminal catalytic and C-terminal anticodon binding domains and that the catalytic domain uses a newly evolved group I intron binding surface that includes an N-terminal extension and two small insertions (insertions 1 and 2) with distinctive features not found in non-splicing mtTyrRSs. To explore how this RNA binding surface diverged to accommodate different group I introns in other Pezizomycotina fungi, we determined x-ray crystal structures of C-terminally truncated Aspergillus nidulans and Coccidioides posadasii mtTyrRSs. Comparisons with previous N. crassa CYT-18 structures and a structural model of the Aspergillus fumigatus mtTyrRS showed that the overall topology of the group I intron binding surface is conserved but with variations in key intron binding regions, particularly the Pezizomycotina-specific insertions. These insertions, which arose by expansion of flexible termini or internal loops, show greater variation in structure and amino acids potentially involved in group I intron binding than do neighboring protein core regions, which also function in intron binding but may be more constrained to preserve mtTyrRS activity. Our results suggest a structural basis for the intron specificity of different Pezizomycotina mtTyrRSs, highlight flexible terminal and loop regions as major sites for enzyme diversification, and identify targets for therapeutic intervention by disrupting an essential RNA-protein interaction in pathogenic fungi.
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Affiliation(s)
- Lilian T Lamech
- From the Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 and
| | - Maithili Saoji
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Paul J Paukstelis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Alan M Lambowitz
- From the Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 and
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20
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Ren W, Truong TM, Ai HW. Study of the Binding Energies between Unnatural Amino Acids and Engineered Orthogonal Tyrosyl-tRNA Synthetases. Sci Rep 2015; 5:12632. [PMID: 26220470 PMCID: PMC4518261 DOI: 10.1038/srep12632] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/03/2015] [Indexed: 11/08/2022] Open
Abstract
We utilized several computational approaches to evaluate the binding energies of tyrosine (Tyr) and several unnatural Tyr analogs, to several orthogonal aaRSes derived from Methanocaldococcus jannaschii and Escherichia coli tyrosyl-tRNA synthetases. The present study reveals the following: (1) AutoDock Vina and ROSETTA were able to distinguish binding energy differences for individual pairs of favorable and unfavorable aaRS-amino acid complexes, but were unable to cluster together all experimentally verified favorable complexes from unfavorable aaRS-Tyr complexes; (2) MD-MM/PBSA provided the best prediction accuracy in terms of clustering favorable and unfavorable enzyme-substrate complexes, but also required the highest computational cost; and (3) MM/PBSA based on single energy-minimized structures has a significantly lower computational cost compared to MD-MM/PBSA, but still produced sufficiently accurate predictions to cluster aaRS-amino acid interactions. Although amino acid-aaRS binding is just the first step in a complex series of processes to acylate a tRNA with its corresponding amino acid, the difference in binding energy, as shown by MD-MM/PBSA, is important for a mutant orthogonal aaRS to distinguish between a favorable unnatural amino acid (unAA) substrate from unfavorable natural amino acid substrates. Our computational study should assist further designing and engineering of orthogonal aaRSes for the genetic encoding of novel unAAs.
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Affiliation(s)
- Wei Ren
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Tan M. Truong
- Cell, Molecular, and Developmental Biology Graduate Program, University of California-Riverside, Riverside, California 92521, United States
| | - Hui-wang Ai
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, California 92521, United States
- Cell, Molecular, and Developmental Biology Graduate Program, University of California-Riverside, Riverside, California 92521, United States
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21
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Hoekstra LA, Siddiq MA, Montooth KL. Pleiotropic effects of a mitochondrial-nuclear incompatibility depend upon the accelerating effect of temperature in Drosophila. Genetics 2013; 195:1129-39. [PMID: 24026098 PMCID: PMC3813842 DOI: 10.1534/genetics.113.154914] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 08/29/2013] [Indexed: 12/21/2022] Open
Abstract
Interactions between mitochondrial and nuclear gene products that underlie eukaryotic energy metabolism can cause the fitness effects of mutations in one genome to be conditional on variation in the other genome. In ectotherms, the effects of these interactions are likely to depend upon the thermal environment, because increasing temperature accelerates molecular rates. We find that temperature strongly modifies the pleiotropic phenotypic effects of an incompatible interaction between a Drosophila melanogaster polymorphism in the nuclear-encoded, mitochondrial tyrosyl-transfer (t)RNA synthetase and a D. simulans polymorphism in the mitochondrially encoded tRNA(Tyr). The incompatible mitochondrial-nuclear genotype extends development time, decreases larval survivorship, and reduces pupation height, indicative of decreased energetic performance. These deleterious effects are ameliorated when larvae develop at 16° and exacerbated at warmer temperatures, leading to complete sterility in both sexes at 28°. The incompatible genotype has a normal metabolic rate at 16° but a significantly elevated rate at 25°, consistent with the hypothesis that inefficient energy metabolism extends development in this genotype at warmer temperatures. Furthermore, the incompatibility decreases metabolic plasticity of larvae developed at 16°, indicating that cooler development temperatures do not completely mitigate the deleterious effects of this genetic interaction. Our results suggest that the epistatic fitness effects of metabolic mutations may generally be conditional on the thermal environment. The expression of epistatic interactions in some environments, but not others, weakens the efficacy of selection in removing deleterious epistatic variants from populations and may promote the accumulation of incompatibilities whose fitness effects will depend upon the environment in which hybrids occur.
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MESH Headings
- Animals
- Base Sequence
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- DNA, Mitochondrial/genetics
- Drosophila/genetics
- Drosophila/growth & development
- Drosophila/physiology
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Drosophila melanogaster/genetics
- Drosophila melanogaster/growth & development
- Drosophila melanogaster/physiology
- Epistasis, Genetic
- Evolution, Molecular
- Female
- Fertility/genetics
- Fertility/physiology
- Genes, Insect
- Genetic Fitness
- Hot Temperature
- Larva/genetics
- Larva/growth & development
- Larva/metabolism
- Male
- Mitochondria/genetics
- Mitochondria/metabolism
- Mutation
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/genetics
- RNA, Transfer, Tyr/metabolism
- Selection, Genetic
- Species Specificity
- Tyrosine-tRNA Ligase/genetics
- Tyrosine-tRNA Ligase/metabolism
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Affiliation(s)
- Luke A. Hoekstra
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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22
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Shahni R, Wedatilake Y, Cleary MA, Lindley KJ, Sibson KR, Rahman S. A distinct mitochondrial myopathy, lactic acidosis and sideroblastic anemia (MLASA) phenotype associates with YARS2 mutations. Am J Med Genet A 2013; 161A:2334-8. [PMID: 23918765 PMCID: PMC3884767 DOI: 10.1002/ajmg.a.36065] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/02/2013] [Indexed: 01/19/2023]
Abstract
Nuclear-encoded disorders of mitochondrial translation are clinically and genetically heterogeneous. Genetic causes include defects of mitochondrial aminoacyl-tRNA synthetases, and factors required for initiation, elongation and termination of protein synthesis as well as ribosome recycling. We report on a new case of myopathy, lactic acidosis and sideroblastic anemia (MLASA) syndrome caused by defective mitochondrial tyrosyl aminoacylation. The patient presented at 1 year with anemia initially attributed to iron deficiency. Bone marrow aspirate at 5 years revealed ringed sideroblasts but transfusion dependency did not occur until 11 years. Other clinical features included lactic acidosis, poor weight gain, hypertrophic cardiomyopathy and severe myopathy leading to respiratory failure necessitating ventilatory support. Long-range PCR excluded mitochondrial DNA rearrangements. Clinical diagnosis of MLASA prompted direct sequence analysis of the YARS2 gene encoding the mitochondrial tyrosyl-tRNA synthetase, which revealed homozygosity for a known pathogenic mutation, c.156C>G;p.F52L. Comparison with four previously reported cases demonstrated remarkable clinical homogeneity. First line investigation of MLASA should include direct sequence analysis of YARS2 and PUS1 (encoding a tRNA modification factor) rather than muscle biopsy. Early genetic diagnosis is essential for counseling and to facilitate appropriate supportive therapy. Reasons for segregation of specific clinical phenotypes with particular mitochondrial aminoacyl tRNA-synthetase defects remain unknown. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- Rojeen Shahni
- Mitochondrial Research Group, Clinical and Molecular Genetics Unit, UCL Institute of Child HealthLondon, UK
| | - Yehani Wedatilake
- Mitochondrial Research Group, Clinical and Molecular Genetics Unit, UCL Institute of Child HealthLondon, UK
| | | | - Keith J Lindley
- Gastroenterology Unit, Great Ormond Street HospitalLondon, UK
| | - Keith R Sibson
- Haematology Unit, Great Ormond Street HospitalLondon, UK
| | - Shamima Rahman
- Mitochondrial Research Group, Clinical and Molecular Genetics Unit, UCL Institute of Child HealthLondon, UK
- Metabolic Unit, Great Ormond Street HospitalLondon, UK
- *Correspondence to:, Dr. Shamima Rahman, Mitochondrial Research Group, Clinical and Molecular Genetics Unit, UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK., E-mail:
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23
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Lee PS, Zhang HM, Marshall AG, Yang XL, Schimmel P. Uncovering of a short internal peptide activates a tRNA synthetase procytokine. J Biol Chem 2012; 287:20504-8. [PMID: 22549774 PMCID: PMC3370235 DOI: 10.1074/jbc.c112.369439] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 04/28/2012] [Indexed: 11/06/2022] Open
Abstract
In higher organisms, aminoacyl-tRNA synthetases developed receptor-mediated ex-translational functions that are activated by various natural mechanisms. Hydrogen-deuterium exchange combined with mass spectrometry and small-angle x-ray scattering showed that activation of the cytokine function of the 528-amino acid human tyrosyl-tRNA synthetase was associated with pinpointed uncovering of a miniature internal ELR tripeptide that triggers receptor signaling. The results reveal the structural simplicity of how the ex-translational function is implemented.
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Affiliation(s)
| | - Hui-Min Zhang
- the National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Alan G. Marshall
- the National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Xiang-Lei Yang
- From the Departments of Molecular Biology and
- Chemical Physiology and
| | - Paul Schimmel
- From the Departments of Molecular Biology and
- The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La, Jolla, California 92037 and
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24
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Shadwick JDL, Ruiz-Trillo I. A genomic survey shows that the haloarchaeal type tyrosyl tRNA synthetase is not a synapomorphy of opisthokonts. Eur J Protistol 2011; 48:89-93. [PMID: 22209425 DOI: 10.1016/j.ejop.2011.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 10/04/2011] [Accepted: 10/25/2011] [Indexed: 01/28/2023]
Abstract
The haloarchaeal-type tyrosyl tRNA synthetase (tyrRS) have previously been proposed to be a molecular synapomorphy of the opisthokonts. To re-evaluate this we have performed a taxon-wide genomic survey of tyrRS in eukaryotes and prokaryotes. Our phylogenetic trees group eukaryotes with archaea, with all opisthokonts sharing the haloarchaeal-type tyrRS. However, this type of tyrRS is not exclusive to opisthokonts, since it also encoded by two amoebozoans. Whether this is a consequence of lateral gene transfer or lineage sorting remains unsolved, but in any case haloarchaeal-type tyrRS is not a synapomorphy of opisthokonts. This demonstrates that molecular markers should be re-evaluated once a better taxon sampling becomes available.
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Affiliation(s)
- John D L Shadwick
- Departament de Genètica & Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
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25
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Shen B, Xiang Z, Miller B, Louie G, Wang W, Noel JP, Gage FH, Wang L. Genetically encoding unnatural amino acids in neural stem cells and optically reporting voltage-sensitive domain changes in differentiated neurons. Stem Cells 2011; 29:1231-40. [PMID: 21681861 PMCID: PMC3209808 DOI: 10.1002/stem.679] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although unnatural amino acids (Uaas) have been genetically encoded in bacterial, fungal, and mammalian cells using orthogonal transfer RNA (tRNA)/aminoacyl-tRNA synthetase pairs, applications of this method to a wider range of specialized cell types, such as stem cells, still face challenges. While relatively straightforward in stem cells, transient expression lacks sufficient temporal resolution to afford reasonable levels of Uaa incorporation and to allow for the study of the longer term differentiation process of stem cells. Moreover, Uaa incorporation may perturb differentiation. Here, we describe a lentiviral-based gene delivery method to stably incorporate Uaas into proteins expressed in neural stem cells, specifically HCN-A94 cells. The transduced cells differentiated into neural progenies in the same manner as the wild-type cells. By genetically incorporating a fluorescent Uaa into a voltage-dependent membrane lipid phosphatase, we show that this Uaa optically reports the conformational change of the voltage-sensitive domain in response to membrane depolarization. The method described here should be generally applicable to other stem cells and membrane proteins.
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Affiliation(s)
- Bin Shen
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
| | - Zheng Xiang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
| | - Barbara Miller
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
| | - Gordon Louie
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
| | - Wenyuan Wang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
| | - Joseph P. Noel
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
| | - Lei Wang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California, 92037, U.S.A
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Leitão-Gonçalves R, Ermanoska B, Jacobs A, De Vriendt E, Timmerman V, Lupski JR, Callaerts P, Jordanova A. Drosophila as a platform to predict the pathogenicity of novel aminoacyl-tRNA synthetase mutations in CMT. Amino Acids 2011; 42:1661-8. [PMID: 21384131 DOI: 10.1007/s00726-011-0868-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Accepted: 02/17/2011] [Indexed: 01/06/2023]
Abstract
Charcot-Marie-Tooth disease (CMT) is the major form of inherited peripheral neuropathy in humans. CMT is clinically and genetically heterogeneous and four aminoacyl-tRNA synthetases have been implicated in disease etiology. Mutations in the YARS gene encoding a tyrosyl-tRNA synthetase (TyrRS) lead to Dominant Intermediate CMT type C (DI-CMTC). Three dominant YARS mutations were so far associated with DI-CMTC. To further expand the spectrum of CMT causing genetic defects in this tRNA synthetase, we performed DNA sequencing of YARS coding regions in a cohort of 181 patients with various types of peripheral neuropathy. We identified a novel K265N substitution that in contrast to all previously described mutations is located at the anticodon recognition domain of the enzyme. Further genetic analysis revealed that this variant represents a benign substitution. Using our recently developed DI-CMTC Drosophila model, we tested in vivo the pathogenicity of this new YARS variant. We demonstrated that the developmental and behavioral defects induced by all DI-CMTC causing mutations were not present upon ubiquitous or panneuronal TyrRS K265N expression. Thus, in line with our genetic studies, functional analysis confirmed that the K265N substitution does not induce toxicity signs in Drosophila. The consistency observed throughout this work underscores the robustness of our DI-CMTC animal model and identifies Drosophila as a valid read-out platform to ascertain the pathogenicity of novel mutations to be identified in the future.
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Affiliation(s)
- Ricardo Leitão-Gonçalves
- Department of Molecular Genetics, VIB, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
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Riley LG, Cooper S, Hickey P, Rudinger-Thirion J, McKenzie M, Compton A, Lim SC, Thorburn D, Ryan MT, Giegé R, Bahlo M, Christodoulou J. Mutation of the mitochondrial tyrosyl-tRNA synthetase gene, YARS2, causes myopathy, lactic acidosis, and sideroblastic anemia--MLASA syndrome. Am J Hum Genet 2010; 87:52-9. [PMID: 20598274 DOI: 10.1016/j.ajhg.2010.06.001] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Revised: 05/26/2010] [Accepted: 06/08/2010] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial respiratory chain disorders are a heterogeneous group of disorders in which the underlying genetic defect is often unknown. We have identified a pathogenic mutation (c.156C>G [p.F52L]) in YARS2, located at chromosome 12p11.21, by using genome-wide SNP-based homozygosity analysis of a family with affected members displaying myopathy, lactic acidosis, and sideroblastic anemia (MLASA). We subsequently identified the same mutation in another unrelated MLASA patient. The YARS2 gene product, mitochondrial tyrosyl-tRNA synthetase (YARS2), was present at lower levels in skeletal muscle whereas fibroblasts were relatively normal. Complex I, III, and IV were dysfunctional as indicated by enzyme analysis, immunoblotting, and immunohistochemistry. A mitochondrial protein-synthesis assay showed reduced levels of respiratory chain subunits in myotubes generated from patient cell lines. A tRNA aminoacylation assay revealed that mutant YARS2 was still active; however, enzyme kinetics were abnormal compared to the wild-type protein. We propose that the reduced aminoacylation activity of mutant YARS2 enzyme leads to decreased mitochondrial protein synthesis, resulting in mitochondrial respiratory chain dysfunction. MLASA has previously been associated with PUS1 mutations; hence, the YARS2 mutation reported here is an alternative cause of MLASA.
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Affiliation(s)
- Lisa G Riley
- Genetic Metabolic Disorders Research Unit, Children's Hospital at Westmead, Sydney 2145, Australia
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28
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Iraha F, Oki K, Kobayashi T, Ohno S, Yokogawa T, Nishikawa K, Yokoyama S, Sakamoto K. Functional replacement of the endogenous tyrosyl-tRNA synthetase-tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion. Nucleic Acids Res 2010; 38:3682-91. [PMID: 20159998 PMCID: PMC2887954 DOI: 10.1093/nar/gkq080] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Non-natural amino acids have been genetically encoded in living cells, using aminoacyl-tRNA synthetase-tRNA pairs orthogonal to the host translation system. In the present study, we engineered Escherichia coli cells with a translation system orthogonal to the E. coli tyrosyl-tRNA synthetase (TyrRS)-tRNA(Tyr) pair, to use E. coli TyrRS variants for non-natural amino acids in the cells without interfering with tyrosine incorporation. We showed that the E. coli TyrRS-tRNA(Tyr) pair can be functionally replaced by the Methanocaldococcus jannaschii and Saccharomyces cerevisiae tyrosine pairs, which do not cross-react with E. coli TyrRS or tRNA(Tyr). The endogenous TyrRS and tRNA(Tyr) genes were then removed from the chromosome of the E. coli cells expressing the archaeal TyrRS-tRNA(Tyr) pair. In this engineered strain, 3-iodo-L-tyrosine and 3-azido-L-tyrosine were each successfully encoded with the amber codon, using the E. coli amber suppressor tRNATyr and a TyrRS variant, which was previously developed for 3-iodo-L-tyrosine and was also found to recognize 3-azido-L-tyrosine. The structural basis for the 3-azido-L-tyrosine recognition was revealed by X-ray crystallography. The present engineering allows E. coli TyrRS variants for non-natural amino acids to be developed in E. coli, for use in both eukaryotic and bacterial cells for genetic code expansion.
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Affiliation(s)
- Fumie Iraha
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Kenji Oki
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Takatsugu Kobayashi
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Satoshi Ohno
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Takashi Yokogawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Kazuya Nishikawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
- *To whom correspondence should be addressed. Tel: +81 45 503 9196; Fax: +81 45 503 9195;
| | - Kensaku Sakamoto
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
- *To whom correspondence should be addressed. Tel: +81 45 503 9196; Fax: +81 45 503 9195;
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Wang F, Robbins S, Guo J, Shen W, Schultz PG. Genetic incorporation of unnatural amino acids into proteins in Mycobacterium tuberculosis. PLoS One 2010; 5:e9354. [PMID: 20179771 PMCID: PMC2825273 DOI: 10.1371/journal.pone.0009354] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 01/28/2010] [Indexed: 11/26/2022] Open
Abstract
New tools are needed to study the intracellular pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), to facilitate new drug discovery and vaccine development. We have developed methodology to genetically incorporate unnatural amino acids into proteins in Mycobacterium smegmatis, BCG and Mtb, grown both extracellularly in culture and inside host cells. Orthogonal mutant tRNATyr/tyrosyl-tRNA synthetase pairs derived from Methanococcus jannaschii and evolved in Escherichia coli incorporate a variety of unnatural amino acids (including photocrosslinking, chemically reactive, heavy atom containing, and immunogenic amino acids) into proteins in response to the amber nonsense codon. By taking advantage of the fidelity and suppression efficiency of the MjtRNA/pIpaRS pair in mycobacteria, we are also able to use p-iodophenylalanine to induce the expression of proteins in mycobacteria both extracellularly in culture and inside of mammalian host cells. This provides a new approach to regulate the expression of reporter genes or mycobacteria endogenous genes of interest. The establishment of the unnatural amino acid expression system in Mtb, an intracellular pathogen, should facilitate studies of TB biology and vaccine development.
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Affiliation(s)
- Feng Wang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Scott Robbins
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Jiantao Guo
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Weijun Shen
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Peter G. Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * E-mail:
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30
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Do T, Gilbert SC, Clark D, Ali F, Fatturi Parolo CC, Maltz M, Russell RR, Holbrook P, Wade WG, Beighton D. Generation of diversity in Streptococcus mutans genes demonstrated by MLST. PLoS One 2010; 5:e9073. [PMID: 20140210 PMCID: PMC2816709 DOI: 10.1371/journal.pone.0009073] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 12/17/2009] [Indexed: 11/19/2022] Open
Abstract
Streptococcus mutans, consisting of serotypes c, e, f and k, is an oral aciduric organism associated with the initiation and progression of dental caries. A total of 135 independent Streptococcus mutans strains from caries-free and caries-active subjects isolated from various geographical locations were examined in two versions of an MLST scheme consisting of either 6 housekeeping genes [accC (acetyl-CoA carboxylase biotin carboxylase subunit), gki (glucokinase), lepA (GTP-binding protein), recP (transketolase), sodA (superoxide dismutase), and tyrS (tyrosyl-tRNA synthetase)] or the housekeeping genes supplemented with 2 extracellular putative virulence genes [gtfB (glucosyltransferase B) and spaP (surface protein antigen I/II)] to increase sequence type diversity. The number of alleles found varied between 20 (lepA) and 37 (spaP). Overall, 121 sequence types (STs) were defined using the housekeeping genes alone and 122 with all genes. However pi, nucleotide diversity per site, was low for all loci being in the range 0.019-0.007. The virulence genes exhibited the greatest nucleotide diversity and the recombination/mutation ratio was 0.67 [95% confidence interval 0.3-1.15] compared to 8.3 [95% confidence interval 5.0-14.5] for the 6 concatenated housekeeping genes alone. The ML trees generated for individual MLST loci were significantly incongruent and not significantly different from random trees. Analysis using ClonalFrame indicated that the majority of isolates were singletons and no evidence for a clonal structure or evidence to support serotype c strains as the ancestral S. mutans strain was apparent. There was also no evidence of a geographical distribution of individual isolates or that particular isolate clusters were associated with caries. The overall low sequence diversity suggests that S. mutans is a newly emerged species which has not accumulated large numbers of mutations but those that have occurred have been shuffled as a consequence of intra-species recombination generating genotypes which can be readily distinguished by sequence analysis.
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Affiliation(s)
- Thuy Do
- Infection Research Group, Dental Institute, King's College London, London, United Kingdom
| | - Steven C. Gilbert
- Infection Research Group, Dental Institute, King's College London, London, United Kingdom
| | - Douglas Clark
- Infection Research Group, Dental Institute, King's College London, London, United Kingdom
| | - Farida Ali
- Infection Research Group, Dental Institute, King's College London, London, United Kingdom
| | - Clarissa C. Fatturi Parolo
- Faculty of Dentistry, Department of Social and Preventive Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Marisa Maltz
- Faculty of Dentistry, Department of Social and Preventive Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Roy R. Russell
- School of Dental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Peter Holbrook
- Faculty of Odontology, University of Iceland, Reykjavik, Iceland
| | - William G. Wade
- Infection Research Group, Dental Institute, King's College London, London, United Kingdom
| | - David Beighton
- Infection Research Group, Dental Institute, King's College London, London, United Kingdom
- * E-mail:
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31
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Melançon CE, Schultz PG. One plasmid selection system for the rapid evolution of aminoacyl-tRNA synthetases. Bioorg Med Chem Lett 2009; 19:3845-7. [PMID: 19398201 PMCID: PMC2714362 DOI: 10.1016/j.bmcl.2009.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/02/2009] [Accepted: 04/03/2009] [Indexed: 11/18/2022]
Abstract
We have developed a rapid, straightforward, one plasmid dual positive/negative selection system for the evolution of aminoacyl-tRNA synthetases with altered specificities in Escherichia coli. This system utilizes an amber stop codon containing chloramphenicol acetyltransferase/uracil phosphoribosyltransferase fusion gene. We demonstrate the utility of the system by identifying a variant of the Methanococcus jannaschii tyrosyl synthetase from a library of 10(9) variants that selectively incorporates para-iodophenylalanine in response to an amber stop codon.
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Affiliation(s)
- Charles E Melançon
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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32
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Abstract
Although horizontal gene transfer (HGT) is often considered as a disruptive force in reconstructing organismal phylogeny, it can also be a valuable phylogenetic tool. A gene in the net of life is often horizontally transferred to the ancestor of a major lineage. If the gene is retained in the recipient and its descendants, it will constitute a shared derived character and mark the recipient and all descendants as a monophyletic group. Additionally, phylogenetically informative HGTs also provide information about the sequence of emergence of involved taxa, because the donor organism must have emerged at least as early as the recipient. Here we review the recent applications of ancient HGT events in reconstructing organismal phylogeny as well as the promise and potential pitfalls of this approach.
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Affiliation(s)
- Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
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33
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Abstract
Although horizontal gene transfer (HGT) is often considered as a disruptive force in reconstructing organismal phylogeny, it can also be a valuable phylogenetic tool. A gene in the net of life is often horizontally transferred to the ancestor of a major lineage. If the gene is retained in the recipient and its descendants, it will constitute a shared derived character and mark the recipient and all descendants as a monophyletic group. Additionally, phylogenetically informative HGTs also provide information about the sequence of emergence of involved taxa, because the donor organism must have emerged at least as early as the recipient. Here we review the recent applications of ancient HGT events in reconstructing organismal phylogeny as well as the promise and potential pitfalls of this approach.
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Affiliation(s)
- Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
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34
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Bonnefond L, Frugier M, Touzé E, Lorber B, Florentz C, Giegé R, Sauter C, Rudinger-Thirion J. Crystal structure of human mitochondrial tyrosyl-tRNA synthetase reveals common and idiosyncratic features. Structure 2008; 15:1505-16. [PMID: 17997975 DOI: 10.1016/j.str.2007.09.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 09/11/2007] [Accepted: 09/13/2007] [Indexed: 12/20/2022]
Abstract
We report the structure of a strictly mitochondrial human synthetase, namely tyrosyl-tRNA synthetase (mt-TyrRS), in complex with an adenylate analog at 2.2 A resolution. The structure is that of an active enzyme deprived of the C-terminal S4-like domain and resembles eubacterial TyrRSs with a canonical tyrosine-binding pocket and adenylate-binding residues typical of class I synthetases. Two bulges at the enzyme surface, not seen in eubacterial TyrRSs, correspond to conserved sequences in mt-TyrRSs. The synthetase electrostatic surface potential differs from that of other TyrRSs, including the human cytoplasmic homolog and the mitochondrial one from Neurospora crassa. The homodimeric human mt-TyrRS shows an asymmetry propagating from the dimer interface toward the two catalytic sites and extremities of each subunit. Mutagenesis of the catalytic domain reveals functional importance of Ser200 in line with an involvement of A73 rather than N1-N72 in tyrosine identity.
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Affiliation(s)
- Luc Bonnefond
- Département Machineries Traductionnelles, Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
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35
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Abergel C, Rudinger-Thirion J, Giegé R, Claverie JM. Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS. J Virol 2007; 81:12406-17. [PMID: 17855524 PMCID: PMC2169003 DOI: 10.1128/jvi.01107-07] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 09/04/2007] [Indexed: 11/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. As such, they fulfill a key role in a process universally conserved in all cellular organisms from their most complex to their most reduced parasitic forms. In contrast, even complex viruses were not found to encode much translation machinery, with the exception of isolated components such as tRNAs. In this context, the discovery of four aminoacyl-tRNA synthetases encoded in the genome of mimivirus together with a full set of translation initiation, elongation, and termination factors appeared to blur what was once a clear frontier between the cellular and viral world. Functional studies of two mimivirus tRNA synthetases confirmed the MetRS specificity for methionine and the TyrRS specificity for tyrosine and conformity with the identity rules for tRNA(Tyr) for archea/eukarya. The atomic structure of the mimivirus tyrosyl-tRNA synthetase in complex with tyrosinol exhibits the typical fold and active-site organization of archaeal-type TyrRS. However, the viral enzyme presents a unique dimeric conformation and significant differences in its anticodon binding site. The present work suggests that mimivirus aminoacyl-tRNA synthetases function as regular translation enzymes in infected amoebas. Their phylogenetic classification does not suggest that they have been acquired recently by horizontal gene transfer from a cellular host but rather militates in favor of an intricate evolutionary relationship between large DNA viruses and ancestral eukaryotes.
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MESH Headings
- Acanthamoeba/virology
- Animals
- Anticodon/chemistry
- Anticodon/metabolism
- Crystallography, X-Ray
- DNA Viruses/enzymology
- Methionine-tRNA Ligase/chemistry
- Methionine-tRNA Ligase/classification
- Methionine-tRNA Ligase/genetics
- Phylogeny
- Protein Structure, Secondary
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/metabolism
- Tyrosine-tRNA Ligase/chemistry
- Tyrosine-tRNA Ligase/classification
- Tyrosine-tRNA Ligase/genetics
- Viral Proteins/chemistry
- Viral Proteins/classification
- Viral Proteins/genetics
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Affiliation(s)
- Chantal Abergel
- Structural and Genomic Information Laboratory, CNRS-UPR2589, IBSM-IFR88, 163 Avenue de Luminy, Case 934, 13288, Marseille Cedex 9, France.
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Abstract
The unnatural amino acid p-nitrophenylalanine (pNO2-Phe) was genetically introduced into proteins in Escherichia coli in response to the amber nonsense codon with high fidelity and efficiency by means of an evolved tRNA/aminoacyl-tRNA synthetase pair from Methanocuccus jannaschii. It was shown that pNO2-Phe efficiently quenches the intrinsic fluorescence of Trp in a distance-dependent manner in a model GCN4 basic region leucine zipper (bZIP) protein. Thus, the pNO2-Phe/Trp pair should be a useful biophysical probe of protein structure and function.
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Affiliation(s)
- Meng-Lin Tsao
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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37
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Nangle LA, Zhang W, Xie W, Yang XL, Schimmel P. Charcot-Marie-Tooth disease-associated mutant tRNA synthetases linked to altered dimer interface and neurite distribution defect. Proc Natl Acad Sci U S A 2007; 104:11239-44. [PMID: 17595294 PMCID: PMC2040883 DOI: 10.1073/pnas.0705055104] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Charcot-Marie-Tooth (CMT) diseases are the most common heritable peripheral neuropathy. At least 10 different mutant alleles of GARS (the gene for glycyl-tRNA synthetase) have been reported to cause a dominant axonal form of CMT (type 2D). A unifying connection between these mutations and CMT has been unclear. Here, mapping mutations onto the recently determined crystal structure of human GlyRS showed them within a band encompassing both sides of the dimer interface, with two CMT-causing mutations being at sites that are complementary partners of a "kissing" contact across the dimer interface. The CMT phenotype is shown here to not correlate with aminoacylation activity. However, most mutations affect dimer formation (to enhance or weaken). Seven CMT-causing variants and the wild-type protein were expressed in transfected neuroblastoma cells that sprout primitive neurites. Wild-type GlyRS distributed into the nascent neurites and was associated with normal neurite sprouting. In contrast, all mutant proteins were distribution-defective. Thus, CMT-causing mutations of GlyRS share a common defect in localization. This defect may be connected in some way to a change in the surfaces at the dimer interface.
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Affiliation(s)
- Leslie A. Nangle
- The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Wei Zhang
- The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Wei Xie
- The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Xiang-Lei Yang
- The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037
- *To whom correspondence may be addressed. E-mail: or
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037
- *To whom correspondence may be addressed. E-mail: or
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38
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Kordysh M, Kornelyuk A. Conformational Flexibility of Cytokine-Like C-Module of Tyrosyl-tRNA Synthetase Monitored by Trp144 Intrinsic Fluorescence. J Fluoresc 2006; 16:705-11. [PMID: 16955364 DOI: 10.1007/s10895-006-0113-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2006] [Accepted: 07/21/2006] [Indexed: 10/24/2022]
Abstract
The non-catalytic COOH-terminal module formed after proteolytic cleavage of full-length mammalian tyrosyl-tRNA synthetase displays dual function: tRNA binding ability and cytokine activity. With the aim to explore the intramolecular dynamics of C-module in solution we used fluorescence spectroscopy to study conformational changes of isolated protein. We used information from fluorescence spectra and computational model for characterization of a microenvironment of a single tryptophan residue (Trp144). Its fluorescence parameters and protection from quenching by Cs+ ions indicate the internal localization--buried into protein globule. The fluorescence quenching of Trp144 by acrylamide suggests rapid conformation dynamics of the C-module in nanosecond time scale. The temperature-induced conformational changes in the C-module were monitored by the fluorescence measurements of Trp144 emission and by red-edge excitation shift. An emission maximum shift up to approximately 349 nm and significant decrease of the red-edge shift effect at 37-52 degrees C indicated a major conformational transition of Trp144 from buried native state into highly relaxing polar solvent environment.
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Affiliation(s)
- Mariya Kordysh
- Department of Protein Engineering, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, 150, Acad. Zabolotnogo Str., Kiev, Kyiv 03143, Ukraine.
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39
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Abstract
Recently, tRNA aminoacyl-tRNA synthetase pairs have been evolved that allow one to genetically encode a large array of unnatural amino acids in both prokaryotic and eukaryotic organisms. We have determined the crystal structures of two substrate-bound Methanococcus jannaschii tyrosyl aminoacyl-tRNA synthetases that charge the unnatural amino acids p-bromophenylalanine and 3-(2-naphthyl)alanine (NpAla). A comparison of these structures with the substrate-bound WT synthetase, as well as a mutant synthetase that charges p-acetylphenylalanine, shows that altered specificity is due to both side-chain and backbone rearrangements within the active site that modify hydrogen bonds and packing interactions with substrate, as well as disrupt the alpha8-helix, which spans the WT active site. The high degree of structural plasticity that is observed in these aminoacyl-tRNA synthetases is rarely found in other mutant enzymes with altered specificities and provides an explanation for the surprising adaptability of the genetic code to novel amino acids.
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Affiliation(s)
- James M. Turner
- *Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; and
| | - James Graziano
- *Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; and
| | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121
- To whom correspondence may be addressed. E-mail:
or
| | - Peter G. Schultz
- *Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; and
- To whom correspondence may be addressed. E-mail:
or
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40
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Ryu Y, Schultz PG. Efficient incorporation of unnatural amino acids into proteins in Escherichia coli. Nat Methods 2006; 3:263-5. [PMID: 16554830 DOI: 10.1038/nmeth864] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Accepted: 02/09/2006] [Indexed: 11/09/2022]
Abstract
We have developed a single-plasmid system for the efficient bacterial expression of mutant proteins containing unnatural amino acids at specific sites designated by amber nonsense codons. In this system, multiple copies of a gene encoding an amber suppressor tRNA derived from a Methanocaldococcus jannaschii tyrosyl-tRNA (MjtRNATyrCUA) are expressed under control of the proK promoter and terminator, and a gene encoding the desired mutant M. jannaschii tyrosyl-tRNA synthetase (MjTyrRS) is expressed under control of a mutant glnS (glnS') promoter.
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Affiliation(s)
- Youngha Ryu
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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41
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Jordanova A, Irobi J, Thomas FP, Van Dijck P, Meerschaert K, Dewil M, Dierick I, Jacobs A, De Vriendt E, Guergueltcheva V, Rao CV, Tournev I, Gondim FAA, D'Hooghe M, Van Gerwen V, Callaerts P, Van Den Bosch L, Timmermans JP, Robberecht W, Gettemans J, Thevelein JM, De Jonghe P, Kremensky I, Timmerman V. Disrupted function and axonal distribution of mutant tyrosyl-tRNA synthetase in dominant intermediate Charcot-Marie-Tooth neuropathy. Nat Genet 2006; 38:197-202. [PMID: 16429158 DOI: 10.1038/ng1727] [Citation(s) in RCA: 280] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Accepted: 12/13/2005] [Indexed: 01/30/2023]
Abstract
Charcot-Marie-Tooth (CMT) neuropathies are common disorders of the peripheral nervous system caused by demyelination or axonal degeneration, or a combination of both features. We previously assigned the locus for autosomal dominant intermediate CMT neuropathy type C (DI-CMTC) to chromosome 1p34-p35. Here we identify two heterozygous missense mutations (G41R and E196K) and one de novo deletion (153-156delVKQV) in tyrosyl-tRNA synthetase (YARS) in three unrelated families affected with DI-CMTC. Biochemical experiments and genetic complementation in yeast show partial loss of aminoacylation activity of the mutant proteins, and mutations in YARS, or in its yeast ortholog TYS1, reduce yeast growth. YARS localizes to axonal termini in differentiating primary motor neuron and neuroblastoma cultures. This specific distribution is significantly reduced in cells expressing mutant YARS proteins. YARS is the second aminoacyl-tRNA synthetase found to be involved in CMT, thereby linking protein-synthesizing complexes with neurodegeneration.
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Affiliation(s)
- Albena Jordanova
- Department of Molecular Genetics, Flanders Interuniversity Institute for Biotechnology, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium
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42
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Iwaki J, Suzuki R, Fujimoto Z, Momma M, Kuno A, Hasegawa T. Overexpression, purification and crystallization of tyrosyl-tRNA synthetase from the hyperthermophilic archaeon Aeropyrum pernix K1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1003-5. [PMID: 16511219 PMCID: PMC1978129 DOI: 10.1107/s1744309105033245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 10/17/2005] [Indexed: 11/10/2022]
Abstract
Hyperthermophilic archaeal tyrosyl-tRNA synthetase from Aeropyrum pernix K1 was cloned and overexpressed in Escherichia coli. The expressed protein was purified by Cibacron Blue affinity chromatography following heat treatment at 363 K. Crystals suitable for X-ray diffraction studies were obtained under optimized crystallization conditions in the presence of 1.5 M ammonium sulfate using the hanging-drop vapour-diffusion method. The crystals belonged to the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 66.1, c = 196.2 A, and diffracted to beyond 2.15 A resolution at 100 K.
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Affiliation(s)
- Jun Iwaki
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Ryuichiro Suzuki
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Research Centre for Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Zui Fujimoto
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Mitsuru Momma
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Atsushi Kuno
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
- Research Centre for Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Tsunemi Hasegawa
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
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43
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Ivakhno SS, Kornelyuk AI. Bioinformatic analysis of changes in expression level of tyrosyl-tRNA synthetase during sporulation process in Saccharomyces cerevisiae. Mikrobiol Z 2005; 67:37-49. [PMID: 16396110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Study of tyrosyl-tRNA synthetases (TyrRS) gene expression during sporulation cycle in Saccharomyces cerevisiae by bioinformatic analysis of microarray data showed high correlation of TyrRS expression to genes that participate in cell wall assembly. Furthermore, the cell wall biogenesis protein KNR4 which physically interacts with TyrRS and cooperates in beta-1,3 glucan biosynthesis falls into a single gene cluster with TyrRS. One third of genes (13 from 42) in TyrRS gene cluster are responsible for the functions directly related to cell wall assembly and maintenance during sporulation. Putative transcription factor binding site on TyrRS upstream sequences was localized with expectation maximization algorithm. The site could be involved in the control of TyrRS expression during sporulation. Absence of correlation in gene expression between KNR4 and TyrRS in S. cerevisiae and their homologues in Schizosaccharomyces pombe--genes SPBC30D10.17 and TYR1 as well as the lack of correlation in the expression level of TyrRS with other sporulation cycle genes indicates that participation of TyrRS in cell wall assembly in S. cerevisiae appeared later in evolution after divergence of S. pombe and S. cerevisiae.
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Affiliation(s)
- S S Ivakhno
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Acad. Zabolotny St., Kyiv 03143, Ukraine
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44
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Bonnefond L, Giegé R, Rudinger-Thirion J. Evolution of the tRNATyr/TyrRS aminoacylation systems. Biochimie 2005; 87:873-83. [PMID: 16164994 DOI: 10.1016/j.biochi.2005.03.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 02/18/2005] [Accepted: 03/17/2005] [Indexed: 11/29/2022]
Abstract
The tRNA identity rules ensuring fidelity of translation are globally conserved throughout evolution except for tyrosyl-tRNA synthetases (TyrRSs) that display species-specific tRNA recognition. This discrimination originates from the presence of a conserved identity pair, G1-C72, located at the top of the acceptor stem of tRNA(Tyr) from eubacteria that is invariably replaced by an unusual C1-G72 pair in archaeal and eubacterial tRNA(Tyr). In addition to the key role of pair 1-72 in tyrosylation, discriminator base A73, the anticodon triplet and the large variable region (present in eubacterial tRNA(Tyr) but not found in eukaryal tRNA(Tyr)) contribute to tyrosylation with variable strengths. Crystallographic structures of two tRNA(Tyr)/TyrRS complexes revealed different interaction modes in accordance with the phylum-specificity. Recent functional studies on the human mitochondrial tRNA(Tyr)/TyrRS system indicates strong deviations from the canonical tyrosylation rules. These differences are discussed in the light of the present knowledge on TyrRSs.
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Affiliation(s)
- Luc Bonnefond
- Département Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15, rue René Descartes, 67084 Strasbourg cedex, France
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45
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Abstract
Lateral gene transfer plays an important role in the evolution of life. Events of ancient gene transfer can transmit genetic novelties to descendent lineages and subsequently shape their genetic systems. We here present the analyses of the gene encoding tyrosyl-tRNA synthetase (tyrRS), which reveal two eukaryotic tyrRS lineages, one including the opisthokonts and the other the remaining eukaryotes. The different origins of tyrRS lineages between the opisthokonts and the remaining eukaryotes indicate a likely case of ancient lateral gene transfer of tyrRS from an archaeon to the opisthokonts, which lends further support for the monophyly of the latter group. Ancient paralogy followed by differential gene loss is an alternative, albeit less parsimonious explanation for the distribution of the two eukaryotic tyrRS types. In either case, the presence of a haloarchaeal tyrRS type in the opisthokonts marks this group as monophyletic. This finding also points to the potential utility of ancient gene transfer events as molecular markers for major organismal lineages.
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46
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Abstract
The T box transcription antitermination regulatory system, found in Gram-positive bacteria, is dependent on a complex set of interactions between uncharged tRNA and the 5'-untranslated mRNA leader region of the regulated gene. One of these interactions involves the base pairing of the acceptor end of cognate tRNA with four bases in a 7 nt bulge of the antiterminator RNA. In vitro selection of randomized tRNA binding to Bacillus subtilis tyrS antiterminator model RNAs was used to determine what, if any, sequence trends there are for binding beyond the known base pair complementarity. The model antiterminator RNAs were selected for the wild-type tertiary fold of tRNA. While there were no obvious sequence correlations between the selected tRNAs, there were correlations between certain tertiary structural elements and binding efficiency to different antiterminator model RNAs. In addition, one antiterminator model selected primarily for a kissing tRNA T loop-antiterminator bulge interaction, while another antiterminator model resulted in no such selection. The selection results indicate that, at the level of tertiary structure, there are ideal matches between tRNAs and antiterminator model RNAs consistent with in vivo observations and that additional recognition features, beyond base pair complementarity, may play a role in the formation of the complex.
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Affiliation(s)
| | | | - Jennifer V. Hines
- To whom correspondence should be addressed. Tel: +1 740 517 8482; Fax: +1 740 593 0148;
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47
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Paukstelis PJ, Coon R, Madabusi L, Nowakowski J, Monzingo A, Robertus J, Lambowitz AM. A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface. Mol Cell 2005; 17:417-28. [PMID: 15694342 DOI: 10.1016/j.molcel.2004.12.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2004] [Revised: 12/01/2004] [Accepted: 12/07/2004] [Indexed: 11/13/2022]
Abstract
We determined a 1.95 A X-ray crystal structure of a C-terminally truncated Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) that functions in splicing group I introns. CYT-18's nucleotide binding fold and intermediate alpha-helical domains superimpose on those of bacterial TyrRSs, except for an N-terminal extension and two small insertions not found in nonsplicing bacterial enzymes. These additions surround the cyt-18-1 mutation site and are sites of suppressor mutations that restore splicing, but not synthetase activity. Highly constrained models based on directed hydroxyl radical cleavage assays show that the group I intron binds at a site formed in part by the three additions on the nucleotide binding fold surface opposite that which binds tRNATyr. Our results show how essential proteins can progressively evolve new functions.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Catalytic Domain/genetics
- Crystallography, X-Ray
- Genes, Fungal
- Hydroxyl Radical/metabolism
- Introns
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutagenesis, Site-Directed
- Neurospora crassa/enzymology
- Neurospora crassa/genetics
- Nucleic Acid Conformation
- Protein Structure, Tertiary
- RNA Splicing
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Sequence Homology, Amino Acid
- Static Electricity
- Tyrosine-tRNA Ligase/chemistry
- Tyrosine-tRNA Ligase/genetics
- Tyrosine-tRNA Ligase/metabolism
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Affiliation(s)
- Paul J Paukstelis
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas, Austin, TX 78712, USA
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48
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Deiters A, Schultz PG. In vivo incorporation of an alkyne into proteins in Escherichia coli. Bioorg Med Chem Lett 2005; 15:1521-4. [PMID: 15713420 DOI: 10.1016/j.bmcl.2004.12.065] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 11/18/2004] [Accepted: 12/21/2004] [Indexed: 11/21/2022]
Abstract
Using a genetic selection we identified mutants of the M. janaschii tyrosyl-tRNA synthetase that selectively charge an amber suppressor tRNA with para-propargyloxyphenylalanine in Escherichia coli. These evolved tRNA-synthetase pairs were used to site-specifically incorporate an alkynyl group into a protein, which was subsequently conjugated with fluorescent dyes by a [3+2]-cycloaddition reaction under mild reaction conditions.
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Affiliation(s)
- Alexander Deiters
- Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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49
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Bonnefond L, Fender A, Rudinger-Thirion J, Giegé R, Florentz C, Sissler M. Toward the Full Set of Human Mitochondrial Aminoacyl-tRNA Synthetases: Characterization of AspRS and TyrRS†. Biochemistry 2005; 44:4805-16. [PMID: 15779907 DOI: 10.1021/bi047527z] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The human mitochondrion possesses a translational machinery devoted to the synthesis of 13 proteins. While the required tRNAs and rRNAs are produced by transcription of the mitochondrial genome, all other factors needed for protein synthesis are synthesized in the cytosol and imported. This is the case for aminoacyl-tRNA synthetases, the enzymes which esterify their cognate tRNA with the specific amino acid. The genes for the full set of cytosolic aaRSs are well defined, but only nine genes for mitochondrial synthetases are known. Here we describe the genes for human mitochondrial aspartyl- and tyrosyl-tRNA synthetases and the initial characterization of the enzymes. Both belong to the expected class of synthetases, have a dimeric organization, and aminoacylate Escherichia coli tRNAs as well as in vitro transcribed human mitochondrial tRNAs. Genes for the remaining missing synthetases were also found with the exception of glutaminyl-tRNA synthetase. Their sequence analysis confirms and further extends the view that, except for lysyl- and glycyl-tRNA synthetases, human mitochondrial and cytosolic enzymes are coded by two different sets of genes.
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Affiliation(s)
- Luc Bonnefond
- Department Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
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50
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Kobayashi T, Sakamoto K, Takimura T, Sekine R, Kelly VP, Vincent K, Kamata K, Nishimura S, Yokoyama S. Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion. Proc Natl Acad Sci U S A 2005; 102:1366-71. [PMID: 15671170 PMCID: PMC547826 DOI: 10.1073/pnas.0407039102] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Accepted: 12/21/2004] [Indexed: 11/18/2022] Open
Abstract
The genetic code in a eukaryotic system has been expanded by the engineering of Escherichia coli tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically recognize 3-iodo-L-tyrosine rather than L-tyrosine. In the present study, we determined the 3-iodo-L-tyrosine- and L-tyrosine-bound structures of the 37V195C mutant of the E. coli TyrRS catalytic domain at 2.0-A resolution. The gamma-methyl group of Val-37 and the sulfur atom of Cys-195 make van der Waals contacts with the iodine atom of 3-iodo-L-tyrosine. The Val-37 and Cys-195 side chains are rigidly fixed by the neighboring residues forming the hydrophobic core of the TyrRS. The major roles of the two mutations are different for the 3-iodo-L-tyrosine-selective recognition in the first step of the aminoacylation reaction (the amino acid activation step): the Y37V mutation eliminates the fatal steric repulsion with the iodine atom, and the Q195C mutation reduces the L-tyrosine misrecognition. The structure of the 37V195C mutant TyrRS complexed with an L-tyrosyladenylate analogue was also solved, indicating that the 3-iodo-L-tyrosine and L-tyrosine side chains are similarly discriminated in the second step (the aminoacyl transfer step). These results demonstrate that the amino acid-binding pocket on the 37V195C mutant is optimized for specific 3-iodo-L-tyrosine recognition.
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Affiliation(s)
- Takatsugu Kobayashi
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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