1
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Qiu Y, Kenana R, Beharry A, Wilhelm SDP, Hsu SY, Siu VM, Duennwald M, Heinemann IU. Histidine supplementation can escalate or rescue HARS deficiency in a Charcot-Marie-Tooth disease model. Hum Mol Genet 2023; 32:810-824. [PMID: 36164730 PMCID: PMC9941834 DOI: 10.1093/hmg/ddac239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/30/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Aminoacyl-tRNA synthetases are essential enzymes responsible for charging amino acids onto cognate tRNAs during protein synthesis. In histidyl-tRNA synthetase (HARS), autosomal dominant mutations V133F, V155G, Y330C and S356N in the HARS catalytic domain cause Charcot-Marie-Tooth disease type 2 W (CMT2W), while tRNA-binding domain mutation Y454S causes recessive Usher syndrome type IIIB. In a yeast model, all human HARS variants complemented a genomic deletion of the yeast ortholog HTS1 at high expression levels. CMT2W associated mutations, but not Y454S, resulted in reduced growth. We show mistranslation of histidine to glutamine and threonine in V155G and S356N but not Y330C mutants in yeast. Mistranslating V155G and S356N mutants lead to accumulation of insoluble proteins, which was rescued by histidine. Mutants V133F and Y330C showed the most significant growth defect and decreased HARS abundance in cells. Here, histidine supplementation led to insoluble protein aggregation and further reduced viability, indicating histidine toxicity associated with these mutants. V133F proteins displayed reduced thermal stability in vitro, which was rescued by tRNA. Our data will inform future treatment options for HARS patients, where histidine supplementation may either have a toxic or compensating effect depending on the nature of the causative HARS variant.
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Affiliation(s)
- Yi Qiu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Rosan Kenana
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sarah D P Wilhelm
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sung Yuan Hsu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Victoria M Siu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Martin Duennwald
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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2
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Towards a Cure for HARS Disease. Genes (Basel) 2023; 14:genes14020254. [PMID: 36833180 PMCID: PMC9956352 DOI: 10.3390/genes14020254] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Histidyl-tRNA synthetase (HARS) ligates histidine to its cognate transfer RNA (tRNAHis). Mutations in HARS cause the human genetic disorders Usher syndrome type 3B (USH3B) and Charcot-Marie-Tooth syndrome type 2W (CMT2W). Treatment for these diseases remains symptomatic, and no disease specific treatments are currently available. Mutations in HARS can lead to destabilization of the enzyme, reduced aminoacylation, and decreased histidine incorporation into the proteome. Other mutations lead to a toxic gain-of-function and mistranslation of non-cognate amino acids in response to histidine codons, which can be rescued by histidine supplementation in vitro. We discuss recent advances in characterizing HARS mutations and potential applications of amino acid and tRNA therapy for future gene and allele specific therapy.
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3
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Mullen P, Abbott JA, Wellman T, Aktar M, Fjeld C, Demeler B, Ebert AM, Francklyn CS. Neuropathy-associated histidyl-tRNA synthetase variants attenuate protein synthesis in vitro and disrupt axon outgrowth in developing zebrafish. FEBS J 2021; 288:142-159. [PMID: 32543048 PMCID: PMC7736457 DOI: 10.1111/febs.15449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/11/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022]
Abstract
Charcot-Marie-Tooth disease (CMT) encompasses a set of genetically and clinically heterogeneous neuropathies characterized by length-dependent dysfunction of the peripheral nervous system. Mutations in over 80 diverse genes are associated with CMT, and aminoacyl-tRNA synthetases (ARS) constitute a large gene family implicated in the disease. Despite considerable efforts to elucidate the mechanistic link between ARS mutations and the CMT phenotype, the molecular basis of the pathology is unknown. In this work, we investigated the impact of three CMT-associated substitutions (V155G, Y330C, and R137Q) in the cytoplasmic histidyl-tRNA synthetase (HARS1) on neurite outgrowth and peripheral nervous system development. The model systems for this work included a nerve growth factor-stimulated neurite outgrowth model in rat pheochromocytoma cells (PC12), and a zebrafish line with GFP/red fluorescent protein reporters of sensory and motor neuron development. The expression of CMT-HARS1 mutations led to attenuation of protein synthesis and increased phosphorylation of eIF2α in PC12 cells and was accompanied by impaired neurite and axon outgrowth in both models. Notably, these effects were phenocopied by histidinol, a HARS1 inhibitor, and cycloheximide, a protein synthesis inhibitor. The mutant proteins also formed heterodimers with wild-type HARS1, raising the possibility that CMT-HARS1 mutations cause disease through a dominant-negative mechanism. Overall, these findings support the hypothesis that CMT-HARS1 alleles exert their toxic effect in a neuronal context, and lead to dysregulated protein synthesis. These studies demonstrate the value of zebrafish as a model for studying mutant alleles associated with CMT, and for characterizing the processes that lead to peripheral nervous system dysfunction.
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Affiliation(s)
- Patrick Mullen
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Jamie A Abbott
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Theresa Wellman
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
| | - Mahafuza Aktar
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Christian Fjeld
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Borries Demeler
- Department of Chemistry & Biochemistry, University of Lethbridge, Canada
| | - Alicia M Ebert
- Department of Biology, University of Vermont, Burlington, VT, USA
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4
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Pfab M, Kielkowski P, Krafczyk R, Volkwein W, Sieber SA, Lassak J, Jung K. Synthetic post-translational modifications of elongation factor P using the ligase EpmA. FEBS J 2020; 288:663-677. [PMID: 32337775 DOI: 10.1111/febs.15346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/24/2020] [Accepted: 04/23/2020] [Indexed: 12/20/2022]
Abstract
Canonically, tRNA synthetases charge tRNA. However, the lysyl-tRNA synthetase paralog EpmA catalyzes the attachment of (R)-β-lysine to the ε-amino group of lysine 34 of the translation elongation factor P (EF-P) in Escherichia coli. This modification is essential for EF-P-mediated translational rescue of ribosomes stalled at consecutive prolines. In this study, we determined the kinetics of EpmA and its variant EpmA_A298G to catalyze the post-translational modification of K34 in EF-P with eight noncanonical substrates. In addition, acetylated EF-P was generated using an amber suppression system. The impact of these synthetically modified EF-P variants on in vitro translation of a polyproline-containing NanoLuc luciferase reporter was analyzed. Our results show that natural (R)-β-lysylation was more effective in rescuing stalled ribosomes than any other synthetic modification tested. Thus, our work not only provides new biochemical insights into the function of EF-P, but also opens a new route to post-translationally modify proteins using EpmA.
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Affiliation(s)
- Miriam Pfab
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Pavel Kielkowski
- Organic Chemistry II, Technical University of Munich, Garching, Germany
| | - Ralph Krafczyk
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Wolfram Volkwein
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Stephan A Sieber
- Organic Chemistry II, Technical University of Munich, Garching, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
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5
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Pang L, Nautiyal M, De Graef S, Gadakh B, Zorzini V, Economou A, Strelkov SV, Van Aerschot A, Weeks SD. Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases. ACS Chem Biol 2020; 15:407-415. [PMID: 31869198 DOI: 10.1021/acschembio.9b00887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pyrimidine-containing Trojan horse antibiotics albomycin and a recently discovered cytidine-containing microcin C analog target the class II seryl- and aspartyl-tRNA synthetases (serRS and aspRS), respectively. The active components of these compounds are competitive inhibitors that mimic the aminoacyl-adenylate intermediate. How they effectively substitute for the interactions mediated by the canonical purine group is unknown. Employing nonhydrolyzable aminoacyl-sulfamoyl nucleosides substituting the base with cytosine, uracil, and N3-methyluracil the structure-activity relationship of the natural compounds was evaluated. In vitro using E. coli serRS and aspRS, the best compounds demonstrated IC50 values in the low nanomolar range, with a clear preference for cytosine or N3-methyluracil over uracil. X-ray crystallographic structures of K. pneumoniae serRS and T. thermophilus aspRS in complex with the compounds showed the contribution of structured waters and residues in the conserved motif-2 loop in defining base preference. Utilizing the N3-methyluracil bound serRS structure, MD simulations of the fully modified albomycin base were performed to identify the interacting network that drives stable association. This analysis pointed to key interactions with a methionine in the motif-2 loop. Interestingly, this residue is mutated to a glycine in a second serRS (serRS2) found in albomycin-producing actinobacteria possessing self-immunity to this antibiotic. A comparative study demonstrated that serRS2 is poorly inhibited by the pyrimidine-containing intermediate analogs, and an equivalent mutation in E. coli serRS significantly decreased the affinity of the cytosine congener. These findings highlight the crucial role of dynamics and solvation of the motif-2 loop in modulating the binding of the natural antibiotics.
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Affiliation(s)
- Luping Pang
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000 Leuven, Belgium
- Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 Box 1041, B-3000 Leuven, Belgium
| | - Manesh Nautiyal
- Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 Box 1041, B-3000 Leuven, Belgium
| | - Steff De Graef
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000 Leuven, Belgium
| | - Bharat Gadakh
- Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 Box 1041, B-3000 Leuven, Belgium
| | - Valentina Zorzini
- Laboratory for Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium
| | - Anastassios Economou
- Laboratory for Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium
| | - Sergei V. Strelkov
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000 Leuven, Belgium
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 Box 1041, B-3000 Leuven, Belgium
| | - Stephen D. Weeks
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000 Leuven, Belgium
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6
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Structural basis for tRNA-dependent cysteine biosynthesis. Nat Commun 2017; 8:1521. [PMID: 29142195 PMCID: PMC5688128 DOI: 10.1038/s41467-017-01543-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022] Open
Abstract
Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNACys followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNACys, respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNACys between SepRS and SepCysS distant active sites. This channeling mechanism could facilitate the consecutive reactions of the two-step indirect pathway of Cys-tRNACys synthesis (tRNA-dependent cysteine biosynthesis) to prevent challenge of translational fidelity, and may reflect the mechanism that cysteine was originally added into genetic code. tRNA-dependent cysteine biosynthesis is catalyzed by the transsulfursome protein complex. Here, the authors use a multidisciplinary approach to structurally characterize the archaeal transsulfursome and propose a model for tRNA channeling in the complex.
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7
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Abbott JA, Guth E, Kim C, Regan C, Siu VM, Rupar CA, Demeler B, Francklyn CS, Robey-Bond SM. The Usher Syndrome Type IIIB Histidyl-tRNA Synthetase Mutation Confers Temperature Sensitivity. Biochemistry 2017. [PMID: 28632987 DOI: 10.1021/acs.biochem.7b00114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histidyl-tRNA synthetase (HARS) is a highly conserved translation factor that plays an essential role in protein synthesis. HARS has been implicated in the human syndromes Charcot-Marie-Tooth (CMT) Type 2W and Type IIIB Usher (USH3B). The USH3B mutation, which encodes a Y454S substitution in HARS, is inherited in an autosomal recessive fashion and associated with childhood deafness, blindness, and episodic hallucinations during acute illness. The biochemical basis of the pathophysiologies linked to USH3B is currently unknown. Here, we present a detailed functional comparison of wild-type (WT) and Y454S HARS enzymes. Kinetic parameters for enzymes and canonical substrates were determined using both steady state and rapid kinetics. Enzyme stability was examined using differential scanning fluorimetry. Finally, enzyme functionality in a primary cell culture was assessed. Our results demonstrate that the Y454S substitution leaves HARS amino acid activation, aminoacylation, and tRNAHis binding functions largely intact compared with those of WT HARS, and the mutant enzyme dimerizes like the wild type does. Interestingly, during our investigation, it was revealed that the kinetics of amino acid activation differs from that of the previously characterized bacterial HisRS. Despite the similar kinetics, differential scanning fluorimetry revealed that Y454S is less thermally stable than WT HARS, and cells from Y454S patients grown at elevated temperatures demonstrate diminished levels of protein synthesis compared to those of WT cells. The thermal sensitivity associated with the Y454S mutation represents a biochemical basis for understanding USH3B.
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Affiliation(s)
- Jamie A Abbott
- Department of Biochemistry, University of Vermont , Burlington, Vermont 05405, United States
| | - Ethan Guth
- Chemistry & Biochemistry Department, Norwich University , Northfield, Vermont 05663, United States
| | | | | | | | | | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio , San Antonio, Texas 78229, United States
| | - Christopher S Francklyn
- Department of Biochemistry, University of Vermont , Burlington, Vermont 05405, United States
| | - Susan M Robey-Bond
- Department of Biochemistry, University of Vermont , Burlington, Vermont 05405, United States
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8
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Hagimori M, Hatabe E, Sano K, Miyazaki H, Sasaki H, Saji H, Mukai T. An Activatable Fluorescent γ-Polyglutamic Acid Complex for Sentinel Lymph Node Imaging. Biol Pharm Bull 2017; 40:297-302. [DOI: 10.1248/bpb.b16-00773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masayori Hagimori
- Department of Biophysical Chemistry, Kobe Pharmaceutical University
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University
| | - Eri Hatabe
- Department of Biophysical Chemistry, Kobe Pharmaceutical University
| | - Kohei Sano
- Department of Biophysical Chemistry, Kobe Pharmaceutical University
- Radioisotopes Research Laboratory, Kyoto University Hospital
- Department of Patho-Functional Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University
| | | | - Hitoshi Sasaki
- Hospital Pharmacy, Nagasaki University Hospital of Medicine and Dentistry
| | - Hideo Saji
- Department of Patho-Functional Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Takahiro Mukai
- Department of Biophysical Chemistry, Kobe Pharmaceutical University
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9
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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10
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French RL, Gupta N, Copeland PR, Simonović M. Structural asymmetry of the terminal catalytic complex in selenocysteine synthesis. J Biol Chem 2014; 289:28783-94. [PMID: 25190812 DOI: 10.1074/jbc.m114.597955] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Selenocysteine (Sec), the 21(st) amino acid, is synthesized from a serine precursor in a series of reactions that require selenocysteine tRNA (tRNA(Sec)). In archaea and eukaryotes, O-phosphoseryl-tRNA(Sec):selenocysteinyl-tRNA(Sec) synthase (SepSecS) catalyzes the terminal synthetic reaction during which the phosphoseryl intermediate is converted into the selenocysteinyl moiety while being attached to tRNA(Sec). We have previously shown that only the SepSecS tetramer is capable of binding to and recognizing the distinct fold of tRNA(Sec). Because only two of the four tRNA-binding sites were occupied in the crystal form, a question was raised regarding whether the observed arrangement and architecture faithfully recapitulated the physiologically relevant ribonucleoprotein complex important for selenoprotein formation. Herein, we determined the stoichiometry of the human terminal synthetic complex of selenocysteine by using small angle x-ray scattering, multi-angle light scattering, and analytical ultracentrifugation. In addition, we provided the first estimate of the ratio between SepSecS and tRNA(Sec) in vivo. We show that SepSecS preferentially binds one or two tRNA(Sec) molecules at a time and that the enzyme is present in large molar excess over the substrate tRNA in vivo. Moreover, we show that in a complex between SepSecS and two tRNAs, one enzyme homodimer plays a role of the noncatalytic unit that positions CCA ends of two tRNA(Sec) molecules into the active site grooves of the other, catalytic, homodimer. Finally, our results demonstrate that the previously determined crystal structure represents the physiologically and catalytically relevant complex and suggest that allosteric regulation of SepSecS might play an important role in regulation of selenocysteine and selenoprotein synthesis.
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Affiliation(s)
- Rachel L French
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and
| | - Nirupama Gupta
- the Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Paul R Copeland
- the Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Miljan Simonović
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and
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11
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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12
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Alba ANR, Valero G, Calbet T, Font-Bardía M, Moyano A, Rios R. Enantioselective addition of oxazolones to maleimides. An easy entry to quaternary aminoacids. NEW J CHEM 2012. [DOI: 10.1039/c1nj20659a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Yadavalli SS, Ibba M. Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:1-43. [PMID: 22243580 DOI: 10.1016/b978-0-12-386497-0.00001-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Accurate translation of mRNA into protein is vital for maintenance of cellular integrity. Translational fidelity is achieved by two key events: synthesis of correctly paired aminoacyl-tRNAs by aminoacyl-tRNA synthetases (aaRSs) and stringent selection of aminoacyl-tRNAs (aa-tRNAs) by the ribosome. AaRSs define the genetic code by catalyzing the formation of precise aminoacyl ester-linked tRNAs via a two-step reaction. AaRSs ensure faithful aa-tRNA synthesis via high substrate selectivity and/or by proofreading (editing) of noncognate products. About half of the aaRSs rely on proofreading mechanisms to achieve high levels of accuracy in aminoacylation. Editing functions in aaRSs contribute to the overall low error rate in protein synthesis. Over 40 years of research on aaRSs using structural, biochemical, and kinetic approaches has expanded our knowledge of their cellular roles and quality control mechanisms. Here, we review aaRS editing with an emphasis on the mechanistic and kinetic details of the process.
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Affiliation(s)
- Srujana S Yadavalli
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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14
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Alba AN, Valero G, Calbet T, Font-Bardía M, Moyano A, Rios R. Enantioselective Organocatalytic Addition of Azlactones to Maleimides: A Highly Stereocontrolled Entry to 2,2-Disubstituted-2H-oxazol-5-ones. Chemistry 2010; 16:9884-9. [DOI: 10.1002/chem.201000239] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Minajigi A, Francklyn CS. Aminoacyl transfer rate dictates choice of editing pathway in threonyl-tRNA synthetase. J Biol Chem 2010; 285:23810-7. [PMID: 20504770 DOI: 10.1074/jbc.m110.105320] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases hydrolyze aminoacyl adenylates and aminoacyl-tRNAs formed from near-cognate amino acids, thereby increasing translational fidelity. The contributions of pre- and post-transfer editing pathways to the fidelity of Escherichia coli threonyl-tRNA synthetase (ThrRS) were investigated by rapid kinetics. In the pre-steady state, asymmetric activation of cognate threonine and noncognate serine was observed in the active sites of dimeric ThrRS, with similar rates of activation. In the absence of tRNA, seryl-adenylate was hydrolyzed 29-fold faster by the ThrRS catalytic domain than threonyl-adenylate. The rate of seryl transfer to cognate tRNA was only 2-fold slower than threonine. Experiments comparing the rate of ATP consumption to the rate of aminoacyl-tRNA(AA) formation demonstrated that pre-transfer hydrolysis contributes to proofreading only when the rate of transfer is slowed significantly. Thus, the relative contributions of pre- and post-transfer editing in ThrRS are subject to modulation by the rate of aminoacyl transfer.
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Affiliation(s)
- Anand Minajigi
- Cell and Molecular Biology Program, University of Vermont, Burlington, VT 05405, USA
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Christian T, Lahoud G, Liu C, Hou YM. Control of catalytic cycle by a pair of analogous tRNA modification enzymes. J Mol Biol 2010; 400:204-17. [PMID: 20452364 DOI: 10.1016/j.jmb.2010.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 04/13/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
Enzymes that use distinct active site structures to perform identical reactions are known as analogous enzymes. The isolation of analogous enzymes suggests the existence of multiple enzyme structural pathways that can catalyze the same chemical reaction. A fundamental question concerning analogous enzymes is whether their distinct active-site structures would confer the same or different kinetic constraints to the chemical reaction, particularly with respect to the control of enzyme turnover. Here, we address this question with the analogous enzymes of bacterial TrmD and its eukaryotic and archaeal counterpart Trm5. TrmD and Trm5 catalyze methyl transfer to synthesize the m1G37 base at the 3' position adjacent to the tRNA anticodon, using S-adenosyl methionine (AdoMet) as the methyl donor. TrmD features a trefoil-knot active-site structure whereas Trm5 features the Rossmann fold. Pre-steady-state analysis revealed that product synthesis by TrmD proceeds linearly with time, whereas that by Trm5 exhibits a rapid burst followed by a slower and linear increase with time. The burst kinetics of Trm5 suggests that product release is the rate-limiting step of the catalytic cycle, consistent with the observation of higher enzyme affinity to the products of tRNA and AdoMet. In contrast, the lack of burst kinetics of TrmD suggests that its turnover is controlled by a step required for product synthesis. Although TrmD exists as a homodimer, it showed half-of-the-sites reactivity for tRNA binding and product synthesis. The kinetic differences between TrmD and Trm5 are parallel with those between the two classes of aminoacyl-tRNA synthetases, which use distinct active site structures to catalyze tRNA aminoacylation. This parallel suggests that the findings have a fundamental importance for enzymes that catalyze both methyl and aminoacyl transfer to tRNA in the decoding process.
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Affiliation(s)
- Thomas Christian
- Thomas Jefferson University, Department of Biochemistry and Molecular Biology, 233 South 10th Street, BLSB 220, Philadelphia, PA 19107, USA
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17
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Merritt EA, Arakaki TL, Gillespie JR, Larson ET, Kelley A, Mueller N, Napuli AJ, Kim J, Zhang L, Verlinde CLMJ, Fan E, Zucker F, Buckner FS, Van Voorhis WC, Hol WGJ. Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs. J Mol Biol 2010; 397:481-94. [PMID: 20132829 PMCID: PMC2834879 DOI: 10.1016/j.jmb.2010.01.051] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/11/2010] [Accepted: 01/24/2010] [Indexed: 01/07/2023]
Abstract
Crystal structures of histidyl-tRNA synthetase (HisRS) from the eukaryotic parasites Trypanosoma brucei and Trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme and reveal differences from bacterial homologs. HisRSs in general contain an extra domain inserted between conserved motifs 2 and 3 of the Class II aminoacyl-tRNA synthetase catalytic core. The current structures show that the three-dimensional topology of this domain is very different in bacterial and archaeal/eukaryotic forms of the enzyme. Comparison of apo and histidine-bound trypanosomal structures indicates substantial active-site rearrangement upon histidine binding but relatively little subsequent rearrangement after reaction of histidine with ATP to form the enzyme's first reaction product, histidyladenylate. The specific residues involved in forming the binding pocket for the adenine moiety differ substantially both from the previously characterized binding site in bacterial structures and from the homologous residues in human HisRSs. The essentiality of the single HisRS gene in T. brucei is shown by a severe depression of parasite growth rate that results from even partial suppression of expression by RNA interference.
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Affiliation(s)
- Ethan A Merritt
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA,Corresponding author: Phone: 206-543-1421 Fax: 206-685-7002,
| | - Tracy L Arakaki
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - J Robert Gillespie
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Eric T Larson
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Angela Kelley
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Natascha Mueller
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Alberto J Napuli
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Jessica Kim
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Li Zhang
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Christophe L M J Verlinde
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Erkang Fan
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Frank Zucker
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Frederick S Buckner
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Wesley C Van Voorhis
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Wim G J Hol
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
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Francklyn CS, Minajigi A. tRNA as an active chemical scaffold for diverse chemical transformations. FEBS Lett 2009; 584:366-75. [PMID: 19925795 DOI: 10.1016/j.febslet.2009.11.045] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/11/2009] [Accepted: 11/11/2009] [Indexed: 10/20/2022]
Abstract
During protein synthesis, tRNA serves as the intermediary between cognate amino acids and their corresponding RNA trinucleotide codons. Aminoacyl-tRNA is also a biosynthetic precursor and amino acid donor for other macromolecules. AA-tRNAs allow transformations of acidic amino acids into their amide-containing counterparts, and seryl-tRNA(Ser) donates serine for antibiotic synthesis. Aminoacyl-tRNA is also used to cross-link peptidoglycan, to lysinylate the lipid bilayer, and to allow proteolytic turnover via the N-end rule. These alternative functions may signal the use of RNA in early evolution as both a biological scaffold and a catalyst to achieve a wide variety of chemical transformations.
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Affiliation(s)
- Christopher S Francklyn
- Cell and Molecular Biology Program, University of Vermont, Burlington, VT 05405, United States.
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