1
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Aboelnga MM, Gauld JW. Screening a library of potential competitive inhibitors against bacterial threonyl-tRNA synthetase: DFT calculations. J Biomol Struct Dyn 2023:1-9. [PMID: 37909495 DOI: 10.1080/07391102.2023.2276878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
Due to the growing interest in directing aminoacyl-tRNA synthetases for antimicrobial therapies, evaluating the binding proficiency of potential inhibitors against this target holds significant importance. In this work, we proposed potential ligands that could properly bind to the crucial Zn(II) cofactor located in the active site of Threonyl-tRNA synthetases (ThrRS), potentially functioning as competitive inhibitors. Initially, detailed DFT quantum chemical study was conducted to examine the binding ability of threonine against unnatural amino acids to cofactor Zn(II). Then, the binding energy value for each suggested ligand has been determined and compared to the value determined for the native substrate, threonine. Our screening investigation showed that the native threonine should coordinate in a bidentate fashion to this Zn(II) which lead to the highest (binding energy) BE Thereby, the synthetic site of ThrRS rejects unnatural amino acids that cannot afford this type of coordination to Zn(II) ion which has been supported by our calculations. Moreover, based on their binding to the Zn(II) and the obtained BE values compared to the cognate threonine, many potent ligands have been suggested. Importantly, ligands with deprotonated warheads showed the highest binding ability amongst a list of potential hits. Further investigation on the selected ligands using molecular docking and QM/MM calculations confirmed our findings of the suggested ligands being able to bind efficiently in the active site of ThrRS. The suggested hits from this study should be valuable in paving routs for developing candidates as competitive inhibitors against the bacterial ThrRS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed M Aboelnga
- Department of Chemistry, Faculty of Science, Damietta University, New Damietta, Egypt
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
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2
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Zagrovic B, Adlhart M, Kapral TH. Coding From Binding? Molecular Interactions at the Heart of Translation. Annu Rev Biophys 2023; 52:69-89. [PMID: 36626765 DOI: 10.1146/annurev-biophys-090622-102329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The mechanism and the evolution of DNA replication and transcription, the key elements of the central dogma of biology, are fundamentally well explained by the physicochemical complementarity between strands of nucleic acids. However, the determinants that have shaped the third part of the dogma-the process of biological translation and the universal genetic code-remain unclear. We review and seek parallels between different proposals that view the evolution of translation through the prism of weak, noncovalent interactions between biological macromolecules. In particular, we focus on a recent proposal that there exists a hitherto unrecognized complementarity at the heart of biology, that between messenger RNA coding regions and the proteins that they encode, especially if the two are unstructured. Reflecting the idea that the genetic code evolved from intrinsic binding propensities between nucleotides and amino acids, this proposal promises to forge a link between the distant past and the present of biological systems.
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Affiliation(s)
- Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Marlene Adlhart
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Thomas H Kapral
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
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3
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Kanaji S, Chen W, Morodomi Y, Shapiro R, Kanaji T, Yang XL. Mechanistic perspectives on anti-aminoacyl-tRNA synthetase syndrome. Trends Biochem Sci 2023; 48:288-302. [PMID: 36280495 PMCID: PMC9974581 DOI: 10.1016/j.tibs.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 02/18/2023]
Abstract
Antisynthetase syndrome (ASSD) is an autoimmune disease characterized by circulating autoantibodies against one of eight aminoacyl-tRNA synthetases (aaRSs). Although these autoantibodies are believed to play critical roles in ASSD pathogenesis, the nature of their roles remains unclear. Here we describe ASSD pathogenesis and discuss ASSD-linked aaRSs - from the WHEP domain that may impart immunogenicity to the role of tRNA in eliciting the innate immune response and the secretion of aaRSs from cells. Through these explorations, we propose that ASSD pathogenesis involves the tissue-specific secretion of aaRSs and that extracellular tRNAs or tRNA fragments and their ability to engage Toll-like receptor signaling may be important disease factors.
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Affiliation(s)
- Sachiko Kanaji
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wenqian Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yosuke Morodomi
- 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
| | - Taisuke Kanaji
- 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.
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4
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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5
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Verdura E, Senger B, Raspall-Chaure M, Schlüter A, Launay N, Ruiz M, Casasnovas C, Rodriguez-Palmero A, Macaya A, Becker HD, Pujol A. Loss of seryl-tRNA synthetase ( SARS1) causes complex spastic paraplegia and cellular senescence. J Med Genet 2022; 59:1227-1233. [PMID: 36041817 PMCID: PMC9691831 DOI: 10.1136/jmg-2022-108529] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/25/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND Aminoacyl-tRNA synthetases (ARS) are key enzymes catalysing the first reactions in protein synthesis, with increasingly recognised pleiotropic roles in tumourgenesis, angiogenesis, immune response and lifespan. Germline mutations in several ARS genes have been associated with both recessive and dominant neurological diseases. Recently, patients affected with microcephaly, intellectual disability and ataxia harbouring biallelic variants in the seryl-tRNA synthetase encoded by seryl-tRNA synthetase 1 (SARS1) were reported. METHODS We used exome sequencing to identify the causal variant in a patient affected by complex spastic paraplegia with ataxia, intellectual disability, developmental delay and seizures, but without microcephaly. Complementation and serylation assays using patient's fibroblasts and an Saccharomyces cerevisiae model were performed to examine this variant's pathogenicity. RESULTS A de novo splice site deletion in SARS1 was identified in our patient, resulting in a 5-amino acid in-frame insertion near its active site. Complementation assays in S. cerevisiae and serylation assays in both yeast strains and patient fibroblasts proved a loss-of-function, dominant negative effect. Fibroblasts showed an abnormal cell shape, arrested division and increased beta-galactosidase staining along with a senescence-associated secretory phenotype (raised interleukin-6, p21, p16 and p53 levels). CONCLUSION We refine the phenotypic spectrum and modes of inheritance of a newly described, ultrarare neurodevelopmental disorder, while unveiling the role of SARS1 as a regulator of cell growth, division and senescence.
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Affiliation(s)
- Edgard Verdura
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Miquel Raspall-Chaure
- Pediatric Neurology Research Group, Vall d’Hebron University Hospital, Universitat Autònoma de Barcelona, 08035, Barcelona, Catalonia, Spain,Department of Paediatric Neurology, Vall d’Hebron University Hospital, 08035, Barcelona, Catalonia, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Nathalie Launay
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain,Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Agustí Rodriguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain,Pediatrics, Hospital Germans Trias i Pujol, Barcelona, Spain
| | - Alfons Macaya
- Pediatric Neurology Research Group, Vall d’Hebron University Hospital, Universitat Autònoma de Barcelona, 08035, Barcelona, Catalonia, Spain,Department of Paediatric Neurology, Vall d’Hebron University Hospital, 08035, Barcelona, Catalonia, Spain,Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Barcelona, Catalonia, Spain
| | | | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain,Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Catalonia, Spain
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6
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Formation of the Codon Degeneracy during Interdependent Development between Metabolism and Replication. Genes (Basel) 2021; 12:genes12122023. [PMID: 34946975 PMCID: PMC8701183 DOI: 10.3390/genes12122023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Nirenberg's genetic code chart shows a profound correspondence between codons and amino acids. The aim of this article is to try to explain the primordial formation of the codon degeneracy. It remains a puzzle how informative molecules arose from the supposed prebiotic random sequences. If introducing an initial driving force based on the relative stabilities of triplex base pairs, the prebiotic sequence evolution became innately nonrandom. Thus, the primordial assignment of the 64 codons to the 20 amino acids has been explained in detail according to base substitutions during the coevolution of tRNAs with aaRSs; meanwhile, the classification of aaRSs has also been explained.
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7
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Pang L, Weeks SD, Van Aerschot A. Aminoacyl-tRNA Synthetases as Valuable Targets for Antimicrobial Drug Discovery. Int J Mol Sci 2021; 22:1750. [PMID: 33578647 PMCID: PMC7916415 DOI: 10.3390/ijms22041750] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze the esterification of tRNA with a cognate amino acid and are essential enzymes in all three kingdoms of life. Due to their important role in the translation of the genetic code, aaRSs have been recognized as suitable targets for the development of small molecule anti-infectives. In this review, following a concise discussion of aaRS catalytic and proof-reading activities, the various inhibitory mechanisms of reported natural and synthetic aaRS inhibitors are discussed. Using the expanding repository of ligand-bound X-ray crystal structures, we classified these compounds based on their binding sites, focusing on their ability to compete with the association of one, or more of the canonical aaRS substrates. In parallel, we examined the determinants of species-selectivity and discuss potential resistance mechanisms of some of the inhibitor classes. Combined, this structural perspective highlights the opportunities for further exploration of the aaRS enzyme family as antimicrobial targets.
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Affiliation(s)
- Luping Pang
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
- KU Leuven, Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Herestraat 49–box 822, 3000 Leuven, Belgium
| | | | - Arthur Van Aerschot
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
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8
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Chen H, Ercanbrack C, Wang T, Gan Q, Fan C. A Synthetic Reporter for Probing Mistranslation in Living Cells. Front Bioeng Biotechnol 2020; 8:623. [PMID: 32671035 PMCID: PMC7326783 DOI: 10.3389/fbioe.2020.00623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/21/2020] [Indexed: 01/13/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) play key roles in maintaining high fidelity of protein synthesis. They charge cognate tRNAs with corresponding amino acids and hydrolyze mischarged tRNAs by editing mechanisms. Impairment of AARS editing activities can reduce the accuracy of tRNA aminoacylation to produce mischarged tRNAs, which cause mistranslation and cell damages. To evaluate the mistranslation rate of threonine codons in living cells, in this study, we designed a quantitative reporter derived from the green fluorescent protein (GFP). The original GFP has multiple threonine codons which could affect the accuracy of measurement, so we generated a GFP variant containing only one threonine residue to specifically quantify mistranslation at the threonine codon. To validate, we applied this single-threonine GFP reporter to evaluate mistranslation at the threonine codon with mutations or modifications of threonine-tRNA synthetase and compared it with other methods of mistranslation evaluation, which showed that this reporter is reliable and facile to use.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Carson Ercanbrack
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Tony Wang
- Depratment of Biology, University of Arkansas, Fayetteville, AR, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States.,Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
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9
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Abstract
Aminoacyl-tRNA synthetases (ARSs) are a family of essential "housekeeping" enzymes ubiquitous in the three major domains of life. ARSs uniquely connect the essential minimal units of both major oligomer classes-the 3-nucleotide codons of oligonucleotides and the amino acids of proteins. They catalyze the esterification of amino acids to the 3'-end of cognate transfer RNAs (tRNAs) bearing the correct anticodon triplet to ensure accurate transfer of information from mRNA to protein according to the genetic code. As an essential translation factor responsible for the first biochemical reaction in protein biosynthesis, ARSs control protein production by catalyzing aminoacylation, and by editing of mischarged aminoacyl-tRNAs to maintain translational fidelity. In addition to their primary enzymatic activities, many ARSs have noncanonical functions unrelated to their catalytic activity in protein synthesis. Among the ARSs with "moonlighting" activities, several, including GluProRS (or EPRS), LeuRS, LysRS, SerRS, TyrRS, and TrpRS, exhibit cell signaling-related activities that sense environmental signals, regulate gene expression, and modulate cellular functions. ARS signaling functions generally depend on catalytically-inactive, appended domains not present in ancient enzyme forms, and are activated by stimulus-dependent post-translational modification. Activation often results in cellular re-localization and gain of new interacting partners. The newly formed ARS-bearing complexes conduct a host of signal transduction functions, including immune response, mTORC1 pathway signaling, and fibrogenic and angiogenic signaling, among others. Because noncanonical functions of ARSs in signal transduction are uncoupled from canonical aminoacylation functions, function-specific inhibitors can be developed, thus providing promising opportunities and therapeutic targets for treatment of human disease.
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Affiliation(s)
- Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine and Department of Biochemistry & Biophysics, The Center for RNA Biology, The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, United States.
| | - Paul L Fox
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States.
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10
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Yu Q, Mallory JD, Kolomeisky AB, Ling J, Igoshin OA. Trade-Offs between Speed, Accuracy, and Dissipation in tRNA Ile Aminoacylation. J Phys Chem Lett 2020; 11:4001-4007. [PMID: 32354218 PMCID: PMC7890467 DOI: 10.1021/acs.jpclett.0c01073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Living systems maintain a high fidelity in information processing through kinetic proofreading, a mechanism for preferentially removing incorrect substrates at the cost of energy dissipation and slower speed. Proofreading mechanisms must balance their demand for higher speed, fewer errors, and lower dissipation, but it is unclear how rates of individual reaction steps are evolutionarily tuned to balance these needs, especially when multiple proofreading mechanisms are present. Here, using a discrete-state stochastic model, we analyze the optimization strategies in Escherichia coli isoleucyl-tRNA synthetase. Surprisingly, this enzyme adopts an economic proofreading strategy and improves speed and dissipation as long as the error is tolerable. Through global parameter sampling, we reveal a fundamental dissipation-error relation that bounds the enzyme's optimal performance and explains the importance of the post-transfer editing mechanism. The proximity of native system parameters to this bound demonstrates the importance of energy dissipation as an evolutionary force affecting fitness.
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Affiliation(s)
- Qiwei Yu
- School of Physics, Peking University, Beijing 100871, China; Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Joel D. Mallory
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Anatoly B. Kolomeisky
- Center for Theoretical Biological Physics, Department of Chemistry, Department of Chemical and Biomolecular Engineering, and Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland 20742, United States
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11
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Liu Y, Hu XB, Zhang LZ, Wang Z, Fu R. Knockdown of Arginyl-tRNA Synthetase Attenuates Ischemia-Induced Cerebral Cortex Injury in Rats After Middle Cerebral Artery Occlusion. Transl Stroke Res 2020; 12:147-163. [PMID: 32221863 PMCID: PMC7803708 DOI: 10.1007/s12975-020-00809-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
Some researchers have previously shown that RNAi knockdown of arginyl-tRNA synthetase (ArgRS) before or after a hypoxic injury can rescue animals from death, based on the model organism, C. elegans. However, there has been no study on the application of arginyl-tRNA synthetase knockdown in treating mammalian ischemic stroke, and its potential mechanism and effect on ischemic brain damage are still unknown. Here, we focused on the Rars gene, which encodes an arginyl-tRNA synthetase, and examined the effects of Rars knockdown in a permanent middle cerebral artery occlusion model in rats. To achieve this aim, adult male Sprague-Dawley (SD) rats were given right cerebral cortex injections of short hairpin RNA (shRNA) adenovirus (AV) particles to knock down arginyl-tRNA synthetase, and a non-targeting control (NTC) vector or phosphate-buffered solution served as the controls. After 4 days, the rats were exposed to permanent middle cerebral artery occlusion (pMCAO). Then, the right cerebral cortex level of arginyl-tRNA synthetase was examined, and the effects of the Rars knockdown were evaluated by differences in infarction volume, oxidative stress, blood-brain barrier, mitochondrial function, and glucose metabolism at 1 day and 3 days after MCAO. The injection of shRNA adenovirus particles successfully suppressed the expression of arginyl-tRNA synthetase in the cerebral cortex. We observed an improvement in oxidative stress, mitochondrial function, and glucose utilization and a reduction in brain edema compared with the non-targeting control rats with suppressed expression of arginyl-tRNA synthetase mRNA in the ipsilateral ischemic cortex of the brain. Our findings indicate that knockdown of arginyl-tRNA synthetase in the cerebral cortex exerted neuroprotective effects, which were achieved not only by the improvement of oxidative stress and glucose utilization but also by the maintenance of mitochondrial morphological integrity and the preservation of mitochondrial function. Knockdown of ArgRS administration could be a promising approach to protect ischemic stroke.
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Affiliation(s)
- Yang Liu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Xue-Bin Hu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Li-Zhi Zhang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Zi Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Fu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China.
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12
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Weitzel CS, Li L, Zhang C, Eilts KK, Bretz NM, Gatten AL, Whitaker RJ, Martinis SA. Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions. J Biol Chem 2020; 295:4563-4576. [PMID: 32102848 DOI: 10.1074/jbc.ra118.006481] [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: 10/29/2018] [Revised: 02/25/2020] [Indexed: 12/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that play a fundamental role in protein synthesis. They catalyze the esterification of specific amino acids to the 3'-end of their cognate tRNAs and therefore play a pivotal role in protein synthesis. Although previous studies suggest that aaRS-dependent errors in protein synthesis can be beneficial to some microbial species, evidence that reduced aaRS fidelity can be adaptive is limited. Using bioinformatics analyses, we identified two distinct leucyl-tRNA synthetase (LeuRS) genes within all genomes of the archaeal family Sulfolobaceae. Remarkably, one copy, designated LeuRS-I, had key amino acid substitutions within its editing domain that would be expected to disrupt hydrolytic editing of mischarged tRNALeu and to result in variation within the proteome of these extremophiles. We found that another copy, LeuRS-F, contains canonical active sites for aminoacylation and editing. Biochemical and genetic analyses of the paralogs within Sulfolobus islandicus supported the hypothesis that LeuRS-F, but not LeuRS-I, functions as an essential tRNA synthetase that accurately charges leucine to tRNALeu for protein translation. Although LeuRS-I was not essential, its expression clearly supported optimal S. islandicus growth. We conclude that LeuRS-I may have evolved to confer a selective advantage under the extreme and fluctuating environmental conditions characteristic of the volcanic hot springs in which these archaeal extremophiles reside.
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Affiliation(s)
| | - Li Li
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
| | - Changyi Zhang
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Kristen K Eilts
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Nicholas M Bretz
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Alex L Gatten
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Susan A Martinis
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
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13
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Demongeot J, Seligmann H. Deamination gradients within codons after 1<->2 position swap predict amino acid hydrophobicity and parallel β-sheet conformational preference. Biosystems 2020; 191-192:104116. [PMID: 32081715 DOI: 10.1016/j.biosystems.2020.104116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/04/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022]
Abstract
Deaminations C->T and A->G are frequent mutations producing nucleotide content gradients across genomes proportional to singlestrandedness during replication/transcription. Hence, within single codons, deamination risks increase from first to third codon positions, while second codon positions are functionally most crucial. Here genetic codes are analyzed assuming that after anticodons protected codons from deaminations, first and second codon positions swapped (N2N1N3->N1N2N3), with lowest deamination risks for N2 in presumed primitive N2N1N3 codons. N2N1N3, not standard N1N2N3, codon structure minimizes deaminations inversely proportionally to cognate amino acid hydrophobicity and parallel betasheet conformational preference. For N1N2N3, deamination minimization increases with genetic code integration order of cognate amino acids: during the presumed N2N1N3->N1N2N3 codon structure transition, protein synthesis combined direct codon-amino acid interactions for late amino acids and tRNA-based translation for early amino acids. Hence N2N1N3 codons would correspond to tRNA-free translation by spontaneous codon-amino acid affinities, and tRNA-mediated translation presumably caused N2N1N3->N1N2N3 swaps. Results show that rational, not arbitrary rules link codon and amino acid structures. Some analyses detect mitochondrial RNAs and peptides in public data corresponding to systematic position swaps, suggesting occasional swapping polymerase activity.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700, La Tronche, France.
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700, La Tronche, France; The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel.
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14
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Kosgodage US, Matewele P, Mastroianni G, Kraev I, Brotherton D, Awamaria B, Nicholas AP, Lange S, Inal JM. Peptidylarginine Deiminase Inhibitors Reduce Bacterial Membrane Vesicle Release and Sensitize Bacteria to Antibiotic Treatment. Front Cell Infect Microbiol 2019; 9:227. [PMID: 31316918 PMCID: PMC6610471 DOI: 10.3389/fcimb.2019.00227] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/11/2019] [Indexed: 12/25/2022] Open
Abstract
Outer membrane and membrane vesicles (OMV/MV) are released from bacteria and participate in cell communication, biofilm formation and host-pathogen interactions. Peptidylarginine deiminases (PADs) are phylogenetically conserved enzymes that catalyze post-translational deimination/citrullination of proteins, causing structural and functional changes in target proteins. PADs also play major roles in the regulation of eukaryotic extracellular vesicle release. Here we show phylogenetically conserved pathways of PAD-mediated OMV/MV release in bacteria and describe deiminated/citrullinated proteins in E. coli and their derived OMV/MVs. Furthermore, we show that PAD inhibitors can be used to effectively reduce OMV/MV release, both in Gram-negative and Gram-positive bacteria. Importantly, this resulted in enhanced antibiotic sensitivity of both E. coli and S. aureus to a range of antibiotics tested. Our findings reveal novel strategies for applying pharmacological OMV/MV-inhibition to reduce antibiotic resistance.
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Affiliation(s)
- Uchini S. Kosgodage
- Cellular and Molecular Immunology Research Centre, School of Human Sciences, London Metropolitan University, London, United Kingdom
| | - Paul Matewele
- Cellular and Molecular Immunology Research Centre, School of Human Sciences, London Metropolitan University, London, United Kingdom
| | - Giulia Mastroianni
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Igor Kraev
- School of Life, Health and Chemical Sciences, The Open University, London, United Kingdom
| | - Dominik Brotherton
- Bioscience Research Group, Extracellular Vesicle Research Unit, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Brigitte Awamaria
- Cellular and Molecular Immunology Research Centre, School of Human Sciences, London Metropolitan University, London, United Kingdom
| | - Anthony P. Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, United Kingdom
| | - Jameel M. Inal
- Bioscience Research Group, Extracellular Vesicle Research Unit, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
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15
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Demongeot J, Seligmann H. Bias for 3'-Dominant Codon Directional Asymmetry in Theoretical Minimal RNA Rings. J Comput Biol 2019; 26:1003-1012. [PMID: 31120344 DOI: 10.1089/cmb.2018.0256] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aminoacyl tRNA synthetases ligate tRNAs specifically with their cognate amino acid. These synthetases are among life's earliest proteins, class II tRNA synthetases (cognates A, D, F, G, H, K, N, P, S, and T) presumably preceding class I tRNA synthetases (cognates C, E, I, L, M, Q, R, V, W, and Y). Classification of codons into palindromic (structure XYX), 5'-dominant (YXX), and 3'-dominant (XXY) (Codon Directional Asymmetry [CDA]) shows that class II tRNA synthetases aminoacylate amino acids associated with XXY. Our working hypothesis expects bias for XXY codons in primordial RNAs, such as theoretical minimal RNA rings, designed in silico to mimic life's earliest RNAs. Twenty-five RNA rings have been computed, which code over a minimal length (22 nucleotides) for a start codon, stop codon, and one and only one codon for each of the 20 amino acids, and form stem-loop hairpins preventing degradation; these 25 minimal RNAs are the only ones matching these constraints and they seem homologous to consensus tRNA sequences. This similarity defined candidate RNA ring anticodons and corresponding cognate amino acids. Here, analyses of RNA ring codon contents confirm bias for XXY codons in 13 among 14 RNA rings with unequal XXY and YXX codon numbers. This bias increases with the genetic code integration order of the RNA ring's cognate amino acid across and within tRNA synthetase classes, suggesting that evolutionary processes, and not physicochemical constraints, produced the association between CDA and tRNA synthetase classes. The self-referential hypothesis for genetic code origin, a very complete genetic code evolutionary hypothesis integrating many translational machinery components, predicts best among genetic code evolutionary hypotheses CDA biases in RNA rings. The RNA rings' simple design inadvertently reproduces CDAs predicted by the genetic code's structure, confirming theoretical minimal RNA rings as good proxies for life's earliest RNAs.
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Affiliation(s)
- Jacques Demongeot
- Laboratory AGEIS EA 7407, Faculty of Medicine, Team Tools for e-Gnosis Medical, Université Grenoble Alpes, La Tronche, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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16
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Nyamai DW, Tastan Bishop Ö. Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study. Malar J 2019; 18:34. [PMID: 30728021 PMCID: PMC6366043 DOI: 10.1186/s12936-019-2665-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/27/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Treatment of parasitic diseases has been challenging due to evolution of drug resistant parasites, and thus there is need to identify new class of drugs and drug targets. Protein translation is important for survival of malarial parasite, Plasmodium, and the pathway is present in all of its life cycle stages. Aminoacyl tRNA synthetases are primary enzymes in protein translation as they catalyse amino acid addition to the cognate tRNA. This study sought to understand differences between Plasmodium and human aminoacyl tRNA synthetases through bioinformatics analysis. METHODS Plasmodium berghei, Plasmodium falciparum, Plasmodium fragile, Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale, Plasmodium vivax, Plasmodium yoelii and human aminoacyl tRNA synthetase sequences were retrieved from UniProt database and grouped into 20 families based on amino acid specificity. These families were further divided into two classes. Both families and classes were analysed. Motif discovery was carried out using the MEME software, sequence identity calculation was done using an in-house Python script, multiple sequence alignments were performed using PROMALS3D and TCOFFEE tools, and phylogenetic tree calculations were performed using MEGA vs 7.0 tool. Possible alternative binding sites were predicted using FTMap webserver and SiteMap tool. RESULTS Motif discovery revealed Plasmodium-specific motifs while phylogenetic tree calculations showed that Plasmodium proteins have different evolutionary history to the human homologues. Human aaRSs sequences showed low sequence identity (below 40%) compared to Plasmodium sequences. Prediction of alternative binding sites revealed potential druggable sites in PfArgRS, PfMetRS and PfProRS at regions that are weakly conserved when compared to the human homologues. Multiple sequence analysis, motif discovery, pairwise sequence identity calculations and phylogenetic tree analysis showed significant differences between parasite and human aaRSs proteins despite functional and structural conservation. These differences may provide a basis for further exploration of Plasmodium aminoacyl tRNA synthetases as potential drug targets. CONCLUSION This study showed that, despite, functional and structural conservation, Plasmodium aaRSs have key differences from the human homologues. These differences in Plasmodium aaRSs can be targeted to develop anti-malarial drugs with less toxicity to the host.
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Affiliation(s)
- Dorothy Wavinya Nyamai
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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17
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Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR, Fredrick K, Schimmel P, Ackerman SL. ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Nature 2018; 557:510-515. [PMID: 29769718 PMCID: PMC5973781 DOI: 10.1038/s41586-018-0137-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 04/09/2018] [Indexed: 11/29/2022]
Abstract
Editing domains of aminoacyl tRNA synthetases correct tRNA charging errors to maintain translational fidelity. A mutation in the editing domain of alanyl tRNA synthetase (AlaRS) in Aars sti mutant mice results in an increase in the production of serine-mischarged tRNAAla and the degeneration of cerebellar Purkinje cells. Here, using positional cloning, we identified Ankrd16, a gene that acts epistatically with the Aars sti mutation to attenuate neurodegeneration. ANKRD16, a vertebrate-specific protein that contains ankyrin repeats, binds directly to the catalytic domain of AlaRS. Serine that is misactivated by AlaRS is captured by the lysine side chains of ANKRD16, which prevents the charging of serine adenylates to tRNAAla and precludes serine misincorporation in nascent peptides. The deletion of Ankrd16 in the brains of Aarssti/sti mice causes widespread protein aggregation and neuron loss. These results identify an amino-acid-accepting co-regulator of tRNA synthetase editing as a new layer of the machinery that is essential to the prevention of severe pathologies that arise from defects in editing.
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Affiliation(s)
- My-Nuong Vo
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Section of Neurobiology, University of California San Diego, La Jolla, CA, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Jeong Woong Lee
- The Jackson Laboratory, Bar Harbor, ME, USA
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Litao Sun
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Hongjun Fu
- The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Qi Liu
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
- Sharklet Technologies, Aurora, CO, USA
| | | | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA.
- The Scripps Research Institute, Jupiter, FL, USA.
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Section of Neurobiology, University of California San Diego, La Jolla, CA, USA.
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.
- The Jackson Laboratory, Bar Harbor, ME, USA.
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18
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Branciamore S, Gogoshin G, Di Giulio M, Rodin AS. Intrinsic Properties of tRNA Molecules as Deciphered via Bayesian Network and Distribution Divergence Analysis. Life (Basel) 2018; 8:life8010005. [PMID: 29419741 PMCID: PMC5871937 DOI: 10.3390/life8010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/27/2022] Open
Abstract
The identity/recognition of tRNAs, in the context of aminoacyl tRNA synthetases (and other molecules), is a complex phenomenon that has major implications ranging from the origins and evolution of translation machinery and genetic code to the evolution and speciation of tRNAs themselves to human mitochondrial diseases to artificial genetic code engineering. Deciphering it via laboratory experiments, however, is difficult and necessarily time- and resource-consuming. In this study, we propose a mathematically rigorous two-pronged in silico approach to identifying and classifying tRNA positions important for tRNA identity/recognition, rooted in machine learning and information-theoretic methodology. We apply Bayesian Network modeling to elucidate the structure of intra-tRNA-molecule relationships, and distribution divergence analysis to identify meaningful inter-molecule differences between various tRNA subclasses. We illustrate the complementary application of these two approaches using tRNA examples across the three domains of life, and identify and discuss important (informative) positions therein. In summary, we deliver to the tRNA research community a novel, comprehensive methodology for identifying the specific elements of interest in various tRNA molecules, which can be followed up by the corresponding experimental work and/or high-resolution position-specific statistical analyses.
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Affiliation(s)
- Sergio Branciamore
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, 91010 CA, USA.
| | - Grigoriy Gogoshin
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, 91010 CA, USA.
| | - Massimo Di Giulio
- Early Evolution of Life Laboratory, Institute of Biosciences and Bioresources, CNR, 80131 Naples, Italy.
| | - Andrei S Rodin
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, 91010 CA, USA.
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19
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Hoffman KS, Berg MD, Shilton BH, Brandl CJ, O'Donoghue P. Genetic selection for mistranslation rescues a defective co-chaperone in yeast. Nucleic Acids Res 2017; 45:3407-3421. [PMID: 27899648 PMCID: PMC5389508 DOI: 10.1093/nar/gkw1021] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/18/2016] [Indexed: 12/22/2022] Open
Abstract
Despite the general requirement for translation fidelity, mistranslation can be an adaptive response. We selected spontaneous second site mutations that suppress the stress sensitivity caused by a Saccharomyces cerevisiae tti2 allele with a Leu to Pro mutation at residue 187, identifying a single nucleotide mutation at the same position (C70U) in four tRNAProUGG genes. Linkage analysis and suppression by SUF9G3:U70 expressed from a centromeric plasmid confirmed the causative nature of the suppressor mutation. Since the mutation incorporates the G3:U70 identity element for alanyl-tRNA synthetase into tRNAPro, we hypothesized that suppression results from mistranslation of Pro187 in Tti2L187P as Ala. A strain expressing Tti2L187A was not stress sensitive. In vitro, tRNAProUGG (C70U) was mis-aminoacylated with alanine by alanyl–tRNA synthetase, but was not a substrate for prolyl–tRNA synthetase. Mass spectrometry from protein expressed in vivo and a novel GFP reporter for mistranslation confirmed substitution of alanine for proline at a rate of ∼6%. Mistranslating cells expressing SUF9G3:U70 induce a partial heat shock response but grow nearly identically to wild-type. Introducing the same G3:U70 mutation in SUF2 (tRNAProAGG) suppressed a second tti2 allele (tti2L50P). We have thus identified a strategy that allows mistranslation to suppress deleterious missense Pro mutations in Tti2.
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Affiliation(s)
- Kyle S Hoffman
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew D Berg
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Brian H Shilton
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.,Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
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20
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Banerjee K, Kolomeisky AB, Igoshin OA. Elucidating interplay of speed and accuracy in biological error correction. Proc Natl Acad Sci U S A 2017; 114:5183-5188. [PMID: 28465435 PMCID: PMC5441828 DOI: 10.1073/pnas.1614838114] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
One of the most fascinating features of biological systems is the ability to sustain high accuracy of all major cellular processes despite the stochastic nature of underlying chemical processes. It is widely believed that such low error values are the result of the error-correcting mechanism known as kinetic proofreading. However, it is usually argued that enhancing the accuracy should result in slowing down the process, leading to the so-called speed-accuracy trade-off. We developed a discrete-state stochastic framework that allowed us to investigate the mechanisms of the proofreading using the method of first-passage processes. With this framework, we simultaneously analyzed the speed and accuracy of the two fundamental biological processes, DNA replication and tRNA selection during the translation. The results indicate that these systems tend to optimize speed rather than accuracy, as long as the error level is tolerable. Interestingly, for these processes, certain kinetic parameters lay in the suboptimal region where their perturbations can improve both speed and accuracy. Additional constraints due to the energetic cost of proofreading also play a role in the error correcting process. Our theoretical findings provide a microscopic picture of how complex biological processes are able to function so fast with high accuracy.
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Affiliation(s)
- Kinshuk Banerjee
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005;
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005;
- Department of Bioengineering, Rice University, Houston, TX 77005
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21
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Allenbach Y, Benveniste O, Goebel HH, Stenzel W. Integrated classification of inflammatory myopathies. Neuropathol Appl Neurobiol 2017; 43:62-81. [DOI: 10.1111/nan.12380] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/04/2017] [Accepted: 01/11/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Y. Allenbach
- Department of Internal Medicine and Clinical Immunology; Pitié-Salpêtrière Hospital; DHU I2B; AP-HP; Paris France
- INSERM U974; UPMC Sorbonne Universities; Paris France
| | - O. Benveniste
- Department of Internal Medicine and Clinical Immunology; Pitié-Salpêtrière Hospital; DHU I2B; AP-HP; Paris France
- INSERM U974; UPMC Sorbonne Universities; Paris France
| | - H-H. Goebel
- Department of Neuropathology; Charité - Universitätsmedizin; Berlin Germany
| | - W. Stenzel
- Department of Neuropathology; Charité - Universitätsmedizin; Berlin Germany
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22
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Kermgard E, Yang Z, Michel AM, Simari R, Wong J, Ibba M, Lazazzera BA. Quality Control by Isoleucyl-tRNA Synthetase of Bacillus subtilis Is Required for Efficient Sporulation. Sci Rep 2017; 7:41763. [PMID: 28139725 PMCID: PMC5282499 DOI: 10.1038/srep41763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/22/2016] [Indexed: 11/11/2022] Open
Abstract
Isoleucyl-tRNA synthetase (IleRS) is an aminoacyl-tRNA synthetase whose essential function is to aminoacylate tRNAIle with isoleucine. Like some other aminoacyl-tRNA synthetases, IleRS can mischarge tRNAIle and correct this misacylation through a separate post-transfer editing function. To explore the biological significance of this editing function, we created a ileS(T233P) mutant of Bacillus subtilis that allows tRNAIle mischarging while retaining wild-type Ile-tRNAIle synthesis activity. As seen in other species defective for aminoacylation quality control, the growth rate of the ileS(T233P) strain was not significantly different from wild-type. When the ileS(T233P) strain was assessed for its ability to promote distinct phenotypes in response to starvation, the ileS(T233P) strain was observed to exhibit a significant defect in formation of environmentally resistant spores. The sporulation defect ranged from 3-fold to 30-fold and was due to a delay in activation of early sporulation genes. The loss of aminoacylation quality control in the ileS(T233P) strain resulted in the inability to compete with a wild-type strain under selective conditions that required sporulation. These data show that the quality control function of IleRS is required in B. subtilis for efficient sporulation and suggests that editing by aminoacyl-tRNA synthetases may be important for survival under starvation/nutrient limitation conditions.
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Affiliation(s)
- Elizabeth Kermgard
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Zhou Yang
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Annika-Marisa Michel
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Technische Universität Braunschweig, Institut of Microbiology, Braunschweig, Germany
| | - Rachel Simari
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA
| | - Jacqueline Wong
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Michael Ibba
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, Ohio State University, Columbus, Ohio 43210, USA.,Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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23
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) ligate amino acids to their cognate tRNAs, allowing them to decode the triplet code during translation. Through different mechanisms aaRSs also perform several non-canonical functions in transcription, translation, apoptosis, angiogenesis and inflammation. Drosophila has become a preferred system to model human diseases caused by mutations in aaRS genes, to dissect effects of reduced translation or non-canonical activities, and to study aminoacylation and translational fidelity. However, the lack of a systematic annotation of this gene family has hampered such studies. Here, we report the identification of the entire set of aaRS genes in the fly genome and we predict their roles based on experimental evidence and/or orthology. Further, we propose a new, systematic and logical nomenclature for aaRSs. We also review the research conducted on Drosophila aaRSs to date. Together, our work provides the foundation for further research in the fly aaRS field.
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Affiliation(s)
- Jiongming Lu
- a Institute of Cell Biology; University of Bern ; Bern , Switzerland
| | - Steven J Marygold
- b FlyBase; Department of Genetics; University of Cambridge ; Cambridge , UK
| | - Walid H Gharib
- c Interfaculty Bioinformatics Unit; University of Bern ; Bern , Switzerland
| | - Beat Suter
- a Institute of Cell Biology; University of Bern ; Bern , Switzerland
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24
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Bais P, Beebe K, Morelli KH, Currie ME, Norberg SN, Evsikov AV, Miers KE, Seburn KL, Guergueltcheva V, Kremensky I, Jordanova A, Bult CJ, Burgess RW. Metabolite profile of a mouse model of Charcot-Marie-Tooth type 2D neuropathy: implications for disease mechanisms and interventions. Biol Open 2016; 5:908-20. [PMID: 27288508 PMCID: PMC4958279 DOI: 10.1242/bio.019273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Charcot–Marie–Tooth disease encompasses a genetically heterogeneous class of heritable polyneuropathies that result in axonal degeneration in the peripheral nervous system. Charcot–Marie–Tooth type 2D neuropathy (CMT2D) is caused by dominant mutations in glycyl tRNA synthetase (GARS). Mutations in the mouse Gars gene result in a genetically and phenotypically valid animal model of CMT2D. How mutations in GARS lead to peripheral neuropathy remains controversial. To identify putative disease mechanisms, we compared metabolites isolated from the spinal cord of Gars mutant mice and their littermate controls. A profile of altered metabolites that distinguish the affected and unaffected tissue was determined. Ascorbic acid was decreased fourfold in the spinal cord of CMT2D mice, but was not altered in serum. Carnitine and its derivatives were also significantly reduced in spinal cord tissue of mutant mice, whereas glycine was elevated. Dietary supplementation with acetyl-L-carnitine improved gross motor performance of CMT2D mice, but neither acetyl-L-carnitine nor glycine supplementation altered the parameters directly assessing neuropathy. Other metabolite changes suggestive of liver and kidney dysfunction in the CMT2D mice were validated using clinical blood chemistry. These effects were not secondary to the neuromuscular phenotype, as determined by comparison with another, genetically unrelated mouse strain with similar neuromuscular dysfunction. However, these changes do not seem to be causative or consistent metabolites of CMT2D, because they were not observed in a second mouse Gars allele or in serum samples from CMT2D patients. Therefore, the metabolite ‘fingerprint’ we have identified for CMT2D improves our understanding of cellular biochemical changes associated with GARS mutations, but identification of efficacious treatment strategies and elucidation of the disease mechanism will require additional studies. Summary: A metabolomics analysis of a mouse model of Charcot–Marie–Tooth type 2D neuropathy revealed a clear distinction between mutant and control samples, and the therapeutic potential of a subset of these changes was explored.
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Affiliation(s)
- Preeti Bais
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA
| | | | - Kathryn H Morelli
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Graduate School of Biomedical Science and Engineering, University of Maine, Orono, 04469 ME, USA
| | | | | | - Alexei V Evsikov
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Department of Molecular Medicine, USF Health, University of South Florida, Tampa, 33620 FL, USA
| | | | | | | | - Ivo Kremensky
- National Genetics Laboratory, Department of Obstetrics and Gynecology, University Hospital of Obstetrics and Gynecology, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Albena Jordanova
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, 2610 Antwerpen, Belgium Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA
| | - Robert W Burgess
- The Jackson Laboratory, Bar Harbor, 04609 ME, USA Graduate School of Biomedical Science and Engineering, University of Maine, Orono, 04469 ME, USA
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25
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Wang X, Pan T. Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis. Adv Nutr 2016; 7:773S-9S. [PMID: 27422514 PMCID: PMC4942860 DOI: 10.3945/an.115.010991] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Translation of genetic information into functional proteins is critical for all cellular life. Accurate protein synthesis relies on proper aminoacylation of transfer RNAs (tRNAs) and decoding of mRNAs by the ribosome with the use of aminoacyl-tRNAs. Mistranslation can lead to pathologic consequences. All cells contain elaborate quality control mechanisms in translation, although translational fidelity may be regulated by various factors such as nutrient limitation or reactive oxygen species. Translation fidelity is maintained via the accuracy of tRNA aminoacylation by the aminoacyl-tRNA synthetases and matching of the mRNA codon with the tRNA anticodon by the ribosome. Stringent substrate discrimination and proofreading are critical in aminoacylating tRNAs with their cognate amino acid to maintain high accuracy of translation. Although the composition of the cellular proteome generally adheres to the genetic code, accumulating evidence indicates that cells can also deliberately mistranslate; they synthesize mutant proteins that deviate from the genetic code in response to stress or environmental changes. Mistranslation with tRNA charged with noncognate amino acids can expand the proteome to enhance stress response and help adaptation. Here, we review current knowledge on mistranslation through tRNA misacylation and describe advances in our understanding of translational control in the regulation of stress response and human diseases.
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Affiliation(s)
- Xiaoyun Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
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26
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Valencia-Sánchez MI, Rodríguez-Hernández A, Ferreira R, Santamaría-Suárez HA, Arciniega M, Dock-Bregeon AC, Moras D, Beinsteiner B, Mertens H, Svergun D, Brieba LG, Grøtli M, Torres-Larios A. Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases. J Biol Chem 2016; 291:14430-46. [PMID: 27226617 PMCID: PMC4938167 DOI: 10.1074/jbc.m116.730382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/09/2016] [Indexed: 11/06/2022] Open
Abstract
Glycyl tRNA synthetase (GlyRS) provides a unique case among class II aminoacyl tRNA synthetases, with two clearly widespread types of enzymes: a dimeric (α2) species present in some bacteria, archaea, and eukaryotes; and a heterotetrameric form (α2β2) present in most bacteria. Although the differences between both types of GlyRS at the anticodon binding domain level are evident, the extent and implications of the variations in the catalytic domain have not been described, and it is unclear whether the mechanism of amino acid recognition is also dissimilar. Here, we show that the α-subunit of the α2β2 GlyRS from the bacterium Aquifex aeolicus is able to perform the first step of the aminoacylation reaction, which involves the activation of the amino acid with ATP. The crystal structure of the α-subunit in the complex with an analog of glycyl adenylate at 2.8 Å resolution presents a conformational arrangement that properly positions the cognate amino acid. This work shows that glycine is recognized by a subset of different residues in the two types of GlyRS. A structural and sequence analysis of class II catalytic domains shows that bacterial GlyRS is closely related to alanyl tRNA synthetase, which led us to define a new subclassification of these ancient enzymes and to propose an evolutionary path of α2β2 GlyRS, convergent with α2 GlyRS and divergent from AlaRS, thus providing a possible explanation for the puzzling existence of two proteins sharing the same fold and function but not a common ancestor.
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Affiliation(s)
- Marco Igor Valencia-Sánchez
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México
| | - Annia Rodríguez-Hernández
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México, the Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 04510, México
| | - Ruben Ferreira
- the Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Hugo Aníbal Santamaría-Suárez
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México
| | - Marcelino Arciniega
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México
| | | | - Dino Moras
- the Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS UMR 7104, 1 Rue Laurent Fries, Illkirch, France, and
| | - Brice Beinsteiner
- the Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS UMR 7104, 1 Rue Laurent Fries, Illkirch, France, and
| | - Haydyn Mertens
- the European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany
| | - Dmitri Svergun
- the European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany
| | - Luis G Brieba
- the Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 04510, México
| | - Morten Grøtli
- the Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Alfredo Torres-Larios
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México,
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27
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Khan S. Recent advances in the biology and drug targeting of malaria parasite aminoacyl-tRNA synthetases. Malar J 2016; 15:203. [PMID: 27068331 PMCID: PMC4828885 DOI: 10.1186/s12936-016-1247-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/30/2016] [Indexed: 11/22/2022] Open
Abstract
Escalating drug resistance in malaria parasites and lack of vaccine entails the discovery of novel drug targets and inhibitor molecules. The multi-component protein translation machinery is a rich source of such drug targets. Malaria parasites contain three translational compartments: the cytoplasm, apicoplast and mitochondrion, of which the latter two are of the prokaryotic type. Recent explorations by many groups into the malaria parasite protein translation enzymes, aminoacyl-tRNA synthetases (aaRSs), have yielded many promising inhibitors. The understanding of the biology of this unique set of 36 enzymes has become much clearer in recent times. Current review discusses the advances made in understanding of crucial aaRSs from Plasmodium and also the specific inhibitors found against malaria aaRSs.
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Affiliation(s)
- Sameena Khan
- Drug Discovery Research Centre, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, India.
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28
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McKenney KM, Alfonzo JD. From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications. Life (Basel) 2016; 6:E13. [PMID: 26985907 PMCID: PMC4810244 DOI: 10.3390/life6010013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/27/2016] [Accepted: 03/07/2016] [Indexed: 12/13/2022] Open
Abstract
All nucleic acids in cells are subject to post-transcriptional chemical modifications. These are catalyzed by a myriad of enzymes with exquisite specificity and that utilize an often-exotic array of chemical substrates. In no molecule are modifications more prevalent than in transfer RNAs. In the present document, we will attempt to take a chemical rollercoaster ride from prebiotic times to the present, with nucleoside modifications as key players and tRNA as the centerpiece that drove the evolution of biological systems to where we are today. These ideas will be put forth while touching on several examples of tRNA modification enzymes and their modus operandi in cells. In passing, we submit that the choice of tRNA is not a whimsical one but rather highlights its critical function as an essential invention for the evolution of protein enzymes.
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Affiliation(s)
- Katherine M McKenney
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
| | - Juan D Alfonzo
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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29
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Malissovas N, Griffin LB, Antonellis A, Beis D. Dimerization is required for GARS-mediated neurotoxicity in dominant CMT disease. Hum Mol Genet 2016; 25:1528-42. [PMID: 27008886 DOI: 10.1093/hmg/ddw031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 02/01/2016] [Indexed: 01/25/2023] Open
Abstract
Charcot-Marie-Tooth (CMT) disease is a genetically heterogeneous group of peripheral neuropathies. Mutations in several aminoacyl-tRNA synthetase (ARS) genes have been implicated in inherited CMT disease. There are 12 reported CMT-causing mutations dispersed throughout the primary sequence of the human glycyl-tRNA synthetase (GARS). While there is strong genetic evidence linking GARS mutations to CMT disease, the molecular pathology underlying the neuromuscular and sensory phenotypes is still not fully understood. In particular, it is unclear whether the mutations result in a toxic gain of function, a partial loss of activity related to translation, or a combination of these mechanisms. We identified a zebrafish allele of gars (gars(s266)). Homozygous mutant embryos carry a C->A transversion, that changes a threonine to a lysine, in a residue next to a CMT-associated human mutation. We show that the neuromuscular phenotype observed in animals homozygous for T209K Gars (T130K in GARS) is due to a loss of dimerization of the mutated protein. Furthermore, we show that the loss of function, dimer-deficient and human disease-associated G319R Gars (G240R in GARS) mutant protein is unable to rescue the above phenotype. Finally, we demonstrate that another human disease-associated mutant G605R Gars (G526 in GARS) dimerizes with the remaining wild-type protein in animals heterozygous for the T209K Gars and reduces the function enough to elicit a neuromuscular phenotype. Our data indicate that dimerization is required for the dominant neurotoxicity of disease-associated GARS mutations and provide a rapid, tractable model for studying newly identified GARS variants for a role in human disease.
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Affiliation(s)
- Nikos Malissovas
- Developmental Biology, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 11527 Athens, Greece, Medical School, University of Crete, Greece
| | - Laurie B Griffin
- Cellular and Molecular Biology Program, Medical Scientist Training Program
| | - Anthony Antonellis
- Cellular and Molecular Biology Program, Department of Human Genetics, and Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dimitris Beis
- Developmental Biology, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 11527 Athens, Greece,
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30
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Park SJ, Ahn HS, Kim JS, Lee C. Evaluation of Multi-tRNA Synthetase Complex by Multiple Reaction Monitoring Mass Spectrometry Coupled with Size Exclusion Chromatography. PLoS One 2015; 10:e0142253. [PMID: 26544075 PMCID: PMC4636271 DOI: 10.1371/journal.pone.0142253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/20/2015] [Indexed: 11/19/2022] Open
Abstract
Eight aminoacyl-tRNA synthetases (M, K, Q, D, R, I, EP and LARS) and three auxiliary proteins (AIMP1, 2 and 3) are known to form a multi-tRNA synthetase complex (MSC) in mammalian cells. We combined size exclusion chromatography (SEC) with reversed-phase liquid chromatography multiple reaction monitoring mass spectrometry (RPLC-MRM-MS) to characterize MSC components and free ARS proteins in human embryonic kidney (HEK 293T) cells. Crude cell extract and affinity-purified proteins were fractionated by SEC in non-denaturing state and ARSs were monitored in each fraction by MRM-MS. The eleven MSC components appeared mostly in earlier SEC fractions demonstrating their participation in complex formation. TARSL2 and AIMP2-DX2, despite their low abundance, were co-purified with KARS and detected in the SEC fractions, where MSC appeared. Moreover, other large complex-forming ARS proteins, such as VARS and FARS, were detected in earlier fractions. The MRM-MS results were further confirmed by western blot analysis. Our study demonstrates usefulness of combined SEC-MRM analysis for the characterization of protein complexes and in understanding the behavior of minor isoforms or variant proteins.
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Affiliation(s)
- Seong-Jun Park
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136–791, Republic of Korea
| | - Hee-Sung Ahn
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136–791, Republic of Korea
- Department of Biological Chemistry, University of Science and Technology, Daejeon 305–333, Republic of Korea
| | - Jun Seok Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136–791, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136–791, Republic of Korea
- Department of Biological Chemistry, University of Science and Technology, Daejeon 305–333, Republic of Korea
- * E-mail:
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31
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Vermulst M, Denney AS, Lang MJ, Hung CW, Moore S, Moseley MA, Mosely AM, Thompson JW, Thompson WJ, Madden V, Gauer J, Wolfe KJ, Summers DW, Schleit J, Sutphin GL, Haroon S, Holczbauer A, Caine J, Jorgenson J, Cyr D, Kaeberlein M, Strathern JN, Duncan MC, Erie DA. Transcription errors induce proteotoxic stress and shorten cellular lifespan. Nat Commun 2015; 6:8065. [PMID: 26304740 DOI: 10.1038/ncomms9065] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/14/2015] [Indexed: 11/09/2022] Open
Abstract
Transcription errors occur in all living cells; however, it is unknown how these errors affect cellular health. To answer this question, we monitor yeast cells that are genetically engineered to display error-prone transcription. We discover that these cells suffer from a profound loss in proteostasis, which sensitizes them to the expression of genes that are associated with protein-folding diseases in humans; thus, transcription errors represent a new molecular mechanism by which cells can acquire disease phenotypes. We further find that the error rate of transcription increases as cells age, suggesting that transcription errors affect proteostasis particularly in aging cells. Accordingly, transcription errors accelerate the aggregation of a peptide that is implicated in Alzheimer's disease, and shorten the lifespan of cells. These experiments reveal a previously unappreciated role for transcriptional fidelity in cellular health and aging.
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Affiliation(s)
- Marc Vermulst
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Ashley S Denney
- School of Medicine, University of Colorado, Denver, Colorado 80217, USA
| | - Michael J Lang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Chao-Wei Hung
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Stephanie Moore
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - M Arthur Moseley
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - Arthur M Mosely
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - J Will Thompson
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - William J Thompson
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - Victoria Madden
- Microscopy Services Laboratory, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jacob Gauer
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Katie J Wolfe
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Daniel W Summers
- Department of Developmental Biology, and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Suraiya Haroon
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Agnes Holczbauer
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Joanne Caine
- CSIRO, Department of Materials Science and Engineering, Parkville 3052, Australia
| | - James Jorgenson
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Douglas Cyr
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Jeffrey N Strathern
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Chemistry, Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Fournier GP, Andam CP, Gogarten JP. Ancient horizontal gene transfer and the last common ancestors. BMC Evol Biol 2015; 15:70. [PMID: 25897759 PMCID: PMC4427996 DOI: 10.1186/s12862-015-0350-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 04/14/2015] [Indexed: 01/22/2023] Open
Abstract
Background The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated in lineages that have since gone extinct. Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life. Results Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages. If these other lineages persisted for some time, HGT with the descendants of LUCA could have continued into the bacterial and archaeal lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein families support the hypothesis that the molecular common ancestors of the most ancient gene families did not all coincide in space and time. This is most apparent in the evolutionary histories of seryl-tRNA synthetase and threonyl-tRNA synthetase protein families, each containing highly divergent “rare” forms, as well as the sparse phylogenetic distributions of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of glycyl-tRNA synthetase. These topologies and phyletic distributions are consistent with horizontal transfers from ancient, likely extinct branches of the tree of life. Conclusions Of all the organisms that may have existed at the time of LUCA, by definition only one lineage is survived by known progeny; however, this lineage retains a genomic record of heterogeneous genetic origins. The evolutionary histories of aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting this signal, as they perform primordial biological functions, have undergone several ancient HGT events, and contain many sites with low substitution rates allowing deep phylogenetic reconstruction. We conclude that some aaRS families contain groups that diverge before LUCA. We propose that these ancient gene variants be described by the term “hypnologs”, reflecting their ancient, reticulate origin from a time in life history that has been all but erased”. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0350-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Cheryl P Andam
- Department of Epidemiology, School of Public Health, Harvard University, Boston, MA, 02115, USA.
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, and the Institute for Systems Genomics, University of Connecticut, 91 North Eagleville Road, Storrs, CT, 06269-3125, USA.
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Giordano C, Morea V, Perli E, d'Amati G. The phenotypic expression of mitochondrial tRNA-mutations can be modulated by either mitochondrial leucyl-tRNA synthetase or the C-terminal domain thereof. Front Genet 2015; 6:113. [PMID: 25852750 PMCID: PMC4370040 DOI: 10.3389/fgene.2015.00113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/04/2015] [Indexed: 11/23/2022] Open
Abstract
Mutations in mitochondrial (mt) DNA determine important human diseases. The majority of the known pathogenic mutations are located in transfer RNA (tRNA) genes and are responsible for a wide range of currently untreatable disorders. Experimental evidence both in yeast and in human cells has shown that the detrimental effects of mt-tRNA point mutations can be attenuated by increasing the expression of the cognate mt-aminoacyl-tRNA synthetases (aaRSs). In addition, constitutive high levels of isoleucyl-tRNA syntethase have been shown to reduce the penetrance of a homoplasmic mutation in mt-tRNAIle in a small kindred. More recently, we showed that the isolated carboxy-terminal domain of human mt-leucyl tRNA synthetase (LeuRS-Cterm) localizes to mitochondria and ameliorates the energetic defect in transmitochondrial cybrids carrying mutations either in the cognate mt-tRNALeu(UUR) or in the non-cognate mt-tRNAIle gene. Since the mt-LeuRS-Cterm does not possess catalytic activity, its rescuing ability is most likely mediated by a chaperon-like effect, consisting in the stabilization of the tRNA structure altered by the mutation. All together, these observations open potential therapeutic options for mt-tRNA mutations-associated diseases.
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Affiliation(s)
- Carla Giordano
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome Rome, Italy
| | - Veronica Morea
- National Research Council of Italy, Institute of Molecular Biology and Pathology, Department of Biochemical Sciences, Sapienza University of Rome Rome, Italy
| | - Elena Perli
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome Rome, Italy
| | - Giulia d'Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome Rome, Italy ; Pasteur Institute-Cenci Bolognetti Foundation Rome, Italy
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Abstract
An RNA World that predated the modern world of polypeptide and polynucleotide is one of the most widely accepted models in origin of life research. In this model, the translation system shepherded the RNA World into the extant biology of DNA, RNA, and protein. Here, we examine the RNA World Hypothesis in the context of increasingly detailed information available about the origins, evolution, functions, and mechanisms of the translation system. We conclude that the translation system presents critical challenges to RNA World Hypotheses. Firstly, a timeline of the RNA World is problematic when the ribosome is incorporated. The mechanism of peptidyl transfer of the ribosome appears distinct from evolved enzymes, signaling origins in a chemical rather than biological milieu. Secondly, we have no evidence that the basic biochemical toolset of life is subject to substantive change by Darwinian evolution, as required for the transition from the RNA world to extant biology. Thirdly, we do not see specific evidence for biological takeover of ribozyme function by protein enzymes. Finally, we can find no basis for preservation of the ribosome as ribozyme or the universality of translation, if it were the case that other information transducing ribozymes, such as ribozyme polymerases, were replaced by protein analogs and erased from the phylogenetic record. We suggest that an updated model of the RNA World should address the current state of knowledge of the translation system.
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35
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The place of RNA in the origin and early evolution of the genetic machinery. Life (Basel) 2014; 4:1050-91. [PMID: 25532530 PMCID: PMC4284482 DOI: 10.3390/life4041050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/02/2014] [Accepted: 12/09/2014] [Indexed: 11/17/2022] Open
Abstract
The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that life began as an autotrophic metabolism in hot volcanic-hydrothermal fluids and evolved with organic products turning into ligands for transition metal catalysts thereby eliciting feedback and feed-forward effects. In this latter context it is posited that the three polymers of the genetic machinery essentially coevolved from monomers through oligomers to polymers, operating functionally first as ligands for ligand-accelerated transition metal catalysis with later addition of base stacking and base pairing, whereby the functional dichotomy between hereditary DNA with stability on geologic time scales and transient, catalytic RNA with stability on metabolic time scales existed since the dawn of the genetic machinery. Both approaches are assessed comparatively for chemical soundness.
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36
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Kumar M, Kumar SAP, Dimkovikj A, Baykal LN, Banton MJ, Outlaw MM, Polivka KE, Hellmann-Whitaker RA. Zinc is the molecular "switch" that controls the catalytic cycle of bacterial leucyl-tRNA synthetase. J Inorg Biochem 2014; 142:59-67. [PMID: 25450019 DOI: 10.1016/j.jinorgbio.2014.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/12/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
The Escherichia coli (E. coli) leucyl-tRNA synthetase (LeuRS) enzyme is part of the aminoacyl-tRNA synthetase (aaRS) family. LeuRS is an essential enzyme that relies on specialized domains to facilitate the aminoacylation reaction. Herein, we have biochemically characterized a specialized zinc-binding domain 1 (ZN-1). We demonstrate that the ZN-1 domain plays a central role in the catalytic cycle of E. coli LeuRS. The ZN-1 domain, when associated with Zn(2+), assumes a rigid architecture that is stabilized by thiol groups from the residues C159, C176 and C179. When LeuRS is in the aminoacylation complex, these cysteine residues form an equilateral planar triangular configuration with Zn(2+), but when LeuRS transitions to the editing conformation, this geometric configuration breaks down. By generating a homology model of LeuRS while in the editing conformation, we conclude that structural changes within the ZN-1 domain play a central role in LeuRS's catalytic cycle. Additionally, we have biochemically shown that C159, C176 and C179 coordinate Zn(2+) and that this interaction is essential for leucylation to occur, but is not essential for deacylation. Furthermore, calculated Kd values indicate that the wild-type enzyme binds Zn(2+) to a greater extent than any of the mutant LeuRSs. Lastly, we have shown through secondary structural analysis of our LeuRS enzymes that Zn(2+) is an architectural cornerstone of the ZN-1 domain and that without its geometric coordination the domain collapses. We believe that future research on the ZN-1 domain may reveal a possible Zn(2+) dependent translocation mechanism for charged tRNA(Leu).
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Affiliation(s)
- Manonmani Kumar
- Department of Computer Science and Information Systems, Coastal Carolina University, 301 Allied Drive, Conway, SC 29526, USA
| | - Sathish A P Kumar
- Department of Computer Science and Information Systems, Coastal Carolina University, 301 Allied Drive, Conway, SC 29526, USA
| | - Aleksandar Dimkovikj
- Department of Chemistry and Physics, Coastal Carolina University, Smith Science Center, Room 216, 109 Chanticleer Dr. East, Conway, SC 29526, USA
| | - Layla N Baykal
- Department of Chemistry and Physics, Coastal Carolina University, Smith Science Center, Room 216, 109 Chanticleer Dr. East, Conway, SC 29526, USA
| | - Mallory J Banton
- Department of Chemistry and Physics, Coastal Carolina University, Smith Science Center, Room 216, 109 Chanticleer Dr. East, Conway, SC 29526, USA
| | - Maya M Outlaw
- Department of Chemistry and Physics, Coastal Carolina University, Smith Science Center, Room 216, 109 Chanticleer Dr. East, Conway, SC 29526, USA
| | - Kristen E Polivka
- Department of Chemistry and Physics, Coastal Carolina University, Smith Science Center, Room 216, 109 Chanticleer Dr. East, Conway, SC 29526, USA
| | - Rachel A Hellmann-Whitaker
- Department of Chemistry and Physics, Coastal Carolina University, Smith Science Center, Room 216, 109 Chanticleer Dr. East, Conway, SC 29526, USA.
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37
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Deficiencies in tRNA synthetase editing activity cause cardioproteinopathy. Proc Natl Acad Sci U S A 2014; 111:17570-5. [PMID: 25422440 DOI: 10.1073/pnas.1420196111] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Misfolded proteins are an emerging hallmark of cardiac diseases. Although some misfolded proteins, such as desmin, are associated with mutations in the genes encoding these disease-associated proteins, little is known regarding more general mechanisms that contribute to the generation of misfolded proteins in the heart. Reduced translational fidelity, caused by a hypomorphic mutation in the editing domain of alanyl-tRNA synthetase (AlaRS), resulted in accumulation of misfolded proteins in specific mouse neurons. By further genetic modulation of the editing activity of AlaRS, we generated mouse models with broader phenotypes, the severity of which was directly related to the degree of compromised editing. Severe disruption of the editing activity of AlaRS caused embryonic lethality, whereas an intermediate reduction in AlaRS editing efficacy resulted in ubiquitinated protein aggregates and mitochondrial defects in cardiomyocytes that were accompanied by progressive cardiac fibrosis and dysfunction. In addition, autophagic vacuoles accumulated in mutant cardiomyocytes, suggesting that autophagy is insufficient to eliminate misfolded proteins. These findings demonstrate that the pathological consequences of diminished tRNA synthetase editing activity, and thus translational infidelity, are dependent on the cell type and the extent of editing disruption, and provide a previously unidentified mechanism underlying cardiac proteinopathy.
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38
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Bhattacharyya M, Bhat CR, Vishveshwara S. An automated approach to network features of protein structure ensembles. Protein Sci 2014; 22:1399-416. [PMID: 23934896 DOI: 10.1002/pro.2333] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/12/2013] [Indexed: 12/14/2022]
Abstract
Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of β2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.
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39
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In silico discovery of aminoacyl-tRNA synthetase inhibitors. Int J Mol Sci 2014; 15:1358-73. [PMID: 24447926 PMCID: PMC3907873 DOI: 10.3390/ijms15011358] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/02/2014] [Accepted: 01/07/2014] [Indexed: 11/17/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNA. They play a pivotal role in protein synthesis and are essential for cell growth and survival. The aaRSs are one of the leading targets for development of antibiotic agents. In this review, we mainly focused on aaRS inhibitor discovery and development using in silico methods including virtual screening and structure-based drug design. These computational methods are relatively fast and cheap, and are proving to be of great benefit for the rational development of more potent aaRS inhibitors and other pharmaceutical agents that may usher in a much needed generation of new antibiotics.
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40
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Abstract
The composition of the cellular proteome is commonly thought to strictly adhere to the genetic code. However, accumulating evidence indicates that cells also regulate the synthesis of mutant protein molecules that deviate from the genetic code. Production of mutant proteins generally occurs when cells are stressed or when they undergo environmental adaptation, but production varies in amounts and specificity. The deliberate synthesis of mutant proteins suggests that some of these proteins can be useful in cellular stress response and adaptation. This review describes the occurrence of, the translation mechanisms for, and the functional hypotheses on regulated synthesis of mutant proteins.
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Affiliation(s)
- Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
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41
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Zhou X, Wang E. Transfer RNA: a dancer between charging and mis-charging for protein biosynthesis. SCIENCE CHINA-LIFE SCIENCES 2013; 56:921-32. [PMID: 23982864 DOI: 10.1007/s11427-013-4542-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/13/2013] [Indexed: 01/17/2023]
Abstract
Transfer RNA plays a fundamental role in the protein biosynthesis as an adaptor molecule by functioning as a biological link between the genetic nucleotide sequence in the mRNA and the amino acid sequence in the protein. To perform its role in protein biosynthesis, it has to be accurately recognized by aminoacyl-tRNA synthetases (aaRSs) to generate aminoacyl-tRNAs (aa-tRNAs). The correct pairing between an amino acid with its cognate tRNA is crucial for translational quality control. Production and utilization of mis-charged tRNAs are usually detrimental for all the species, resulting in cellular dysfunctions. Correct aa-tRNAs formation is collectively controlled by aaRSs with distinct mechanisms and/or other trans-factors. However, in very limited instances, mis-charged tRNAs are intermediate for specific pathways or essential components for the translational machinery. Here, from the point of accuracy in tRNA charging, we review our understanding about the mechanism ensuring correct aa-tRNA generation. In addition, some unique mis-charged tRNA species necessary for the organism are also briefly described.
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Affiliation(s)
- Xiaolong Zhou
- Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
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42
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Yao P, Fox PL. Aminoacyl-tRNA synthetases in medicine and disease. EMBO Mol Med 2013; 5:332-43. [PMID: 23427196 PMCID: PMC3598075 DOI: 10.1002/emmm.201100626] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 11/30/2012] [Accepted: 01/15/2013] [Indexed: 12/12/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential and ubiquitous 'house-keeping' enzymes responsible for charging amino acids to their cognate tRNAs and providing the substrates for global protein synthesis. Recent studies have revealed a role of multiple ARSs in pathology, and their potential use as pharmacological targets and therapeutic reagents. The ongoing discovery of genetic mutations in human ARSs is increasing exponentially and can be considered an important determinant of disease etiology. Several chemical compounds target bacterial, fungal and human ARSs as antibiotics or disease-targeting medicines. Remarkably, ongoing exploration of noncanonical functions of ARSs has shown important contributions to control of angiogenesis, inflammation, tumourigenesis and other important physiopathological processes. Here, we summarize the roles of ARSs in human diseases and medicine, focusing on the most recent and exciting discoveries.
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Affiliation(s)
- Peng Yao
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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43
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Klipcan L, Safro M, Schimmel P. Anticodon G recognition by tRNA synthetases mimics the tRNA core. Trends Biochem Sci 2012; 38:229-32. [PMID: 23266103 DOI: 10.1016/j.tibs.2012.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 11/04/2012] [Accepted: 11/07/2012] [Indexed: 10/27/2022]
Abstract
Ancient mechanisms for nucleotide base recognition in the RNA world are candidates for mimicking by early proteins like tRNA synthetases. In the core of the tRNA, conserved G22 interacts with two internal bases in a complex further stabilized by stacking interactions. This particular tRNA format for G recognition is shown here to be adapted by nine different and even nonhomologous anticodon binding domains (ABDs) of tRNA synthetases, in which amino acid side chains mimic all of the tRNA G22 base interactions. We offer the possibility that mimicking this RNA-based mechanism for guanine recognition is perhaps one of the selective pressures for choosing amino acids for the genetic code.
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Affiliation(s)
- Liron Klipcan
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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44
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Durrenberger PF, Fernando FS, Magliozzi R, Kashefi SN, Bonnert TP, Ferrer I, Seilhean D, Nait-Oumesmar B, Schmitt A, Gebicke-Haerter PJ, Falkai P, Grünblatt E, Palkovits M, Parchi P, Capellari S, Arzberger T, Kretzschmar H, Roncaroli F, Dexter DT, Reynolds R. Selection of novel reference genes for use in the human central nervous system: a BrainNet Europe Study. Acta Neuropathol 2012; 124:893-903. [PMID: 22864814 DOI: 10.1007/s00401-012-1027-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/15/2012] [Accepted: 07/24/2012] [Indexed: 01/17/2023]
Abstract
The use of an appropriate reference gene to ensure accurate normalisation is crucial for the correct quantification of gene expression using qPCR assays and RNA arrays. The main criterion for a gene to qualify as a reference gene is a stable expression across various cell types and experimental settings. Several reference genes are commonly in use but more and more evidence reveals variations in their expression due to the presence of on-going neuropathological disease processes, raising doubts concerning their use. We conducted an analysis of genome-wide changes of gene expression in the human central nervous system (CNS) covering several neurological disorders and regions, including the spinal cord, and were able to identify a number of novel stable reference genes. We tested the stability of expression of eight novel (ATP5E, AARS, GAPVD1, CSNK2B, XPNPEP1, OSBP, NAT5 and DCTN2) and four more commonly used (BECN1, GAPDH, QARS and TUBB) reference genes in a smaller cohort using RT-qPCR. The most stable genes out of the 12 reference genes were tested as normaliser to validate increased levels of a target gene in CNS disease. We found that in human post-mortem tissue the novel reference genes, XPNPEP1 and AARS, were efficient in replicating microarray target gene expression levels and that XPNPEP1 was more efficient as a normaliser than BECN1, which has been shown to change in expression as a consequence of neuronal cell loss. We provide herein one more suitable novel reference gene, XPNPEP1, with no current neuroinflammatory or neurodegenerative associations that can be used for gene quantitative gene expression studies with human CNS post-mortem tissue and also suggest a list of potential other candidates. These data also emphasise the importance of organ/tissue-specific stably expressed genes as reference genes for RNA studies.
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Affiliation(s)
- Pascal F Durrenberger
- Wolfson Neuroscience Laboratories, Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
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45
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Guo M, Schimmel P. Structural analyses clarify the complex control of mistranslation by tRNA synthetases. Curr Opin Struct Biol 2011; 22:119-26. [PMID: 22155179 DOI: 10.1016/j.sbi.2011.11.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/13/2011] [Accepted: 11/15/2011] [Indexed: 12/24/2022]
Abstract
Proteins are precisely assembled with amino acids by matching the anticodons of charged transfer RNAs to nucleotide triplets in mRNA sequences. Accurate translation depends on the specific coupling of cognate amino acids and tRNAs - a step carried out by aminoacyl-tRNA synthetases (aaRSs) and that generates the genetic code. Owing to their intrinsic similarity, aaRSs developed highly differentiated structures to discriminate between amino acids at the active site for aminoacylation. Because this discrimination is not sufficient to prevent toxic mistranslation, aaRSs developed separate structures to further refine recognition by proofreading. From comprehensive structural studies on aaRSs, many of the molecular details have been elucidated for the recognition of cognate amino acids and for the misactivation and editing of noncognate amino acids, Here we review recent advances in the structural description of the binding, activation and editing of amino acids, which collectively reveal many aspects of the fine-tuned systems that resulted in a robust and universal genetic code.
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Affiliation(s)
- Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, United States
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46
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Fournier GP, Andam CP, Alm EJ, Gogarten JP. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. ORIGINS LIFE EVOL B 2011; 41:621-32. [PMID: 22200905 DOI: 10.1007/s11084-011-9261-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/06/2011] [Indexed: 01/02/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.
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Affiliation(s)
- Gregory P Fournier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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47
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Jakubowski H. Quality control in tRNA charging. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:295-310. [PMID: 22095844 DOI: 10.1002/wrna.122] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Faithful translation of the genetic code during protein synthesis is fundamental to the growth, development, and function of living organisms. Aminoacyl-tRNA synthetases (AARSs), which define the genetic code by correctly pairing amino acids with their cognate tRNAs, are responsible for 'quality control' in the flow of information from a gene to a protein. When differences in binding energies of amino acids to an AARS are inadequate, editing is used to achieve high selectivity. Editing occurs at the synthetic active site by hydrolysis of noncognate aminoacyl-adenylates (pretransfer editing) and at a dedicated editing site located in a separate domain by deacylation of mischarged aminoacyl-tRNA (posttransfer editing). Access of nonprotein amino acids, such as homocysteine or ornithine, to the genetic code is prevented by the editing function of AARSs, which functionally partitions amino acids present in living cells into protein and nonprotein amino acids. Continuous editing is part of the tRNA aminoacylation process in living organisms from bacteria to human beings. Preventing mistranslation by the clearance of misactivated amino acids is crucial to cellular homeostasis and has a role in etiology of disease. Although there is a strong selective pressure to minimize mistranslation, some organisms possess error-prone AARSs that cause mistranslation. Elevated levels of mistranslation and the synthesis of statistical proteins can be beneficial for pathogens by increasing phenotypic variation essential for the evasion of host defenses.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, International Center for Public Health, Newark, NJ, USA.
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48
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Panwar B, Raghava GPS. Predicting sub-cellular localization of tRNA synthetases from their primary structures. Amino Acids 2011; 42:1703-13. [DOI: 10.1007/s00726-011-0872-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 02/21/2011] [Indexed: 11/25/2022]
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49
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Rodin AS, Szathmáry E, Rodin SN. On origin of genetic code and tRNA before translation. Biol Direct 2011; 6:14. [PMID: 21342520 PMCID: PMC3050877 DOI: 10.1186/1745-6150-6-14] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 02/22/2011] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental veto on "foresight evolution", 2) modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3) the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. RESULTS The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code) the anticodon(2-3)/codon(1-2) tetramers to their anticodon(1-2)/codon(2-3) counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other) needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator) to the eventual 76 base-long cloverleaf-shaped molecule. CONCLUSION Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ''fit'' the (likely already defined) genetic code, rather than the opposite way around. Coding triplets in this primal pre-translational code were likely similar to the anticodons, with second and third nucleotides being more important than the less specific first one. Later, when the code was expanding in co-evolution with the translation apparatus, the importance of 2-3 nucleotides of coding triplets "transferred" to the 1-2 nucleotides of their complements, thus distinguishing anticodons from codons. This evolutionary primacy of anticodons in genetic coding makes the hypothesis of primal stereo-chemical affinity between amino acids and cognate triplets, the hypothesis of coding coenzyme handles for amino acids, the hypothesis of tRNA-like genomic 3' tags suggesting that tRNAs originated in replication, and the hypothesis of ancient ribozymes-mediated operational code of tRNA aminoacylation not mutually contradicting but rather co-existing in harmony.
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Affiliation(s)
- Andrei S Rodin
- Human Genetics Center, School of Public Health, University of Texas, Houston, TX 77225, USA
- Collegium Budapest (Institute for Advanced Study), Szentháromság u. 2, H-1014 Budapest, Hungary
| | - Eörs Szathmáry
- Collegium Budapest (Institute for Advanced Study), Szentháromság u. 2, H-1014 Budapest, Hungary
- Parmenides Center for the Study of Thinking, Kirchplatz 1, D-82049 Munich/Pullach, Germany
- Institute of Biology, Eötvös University, 1c Pázmány Péter sétány, H-1117 Budapest, Hungary
| | - Sergei N Rodin
- Collegium Budapest (Institute for Advanced Study), Szentháromság u. 2, H-1014 Budapest, Hungary
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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50
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Vo MN, Yang XL, Schimmel P. Dissociating quaternary structure regulates cell-signaling functions of a secreted human tRNA synthetase. J Biol Chem 2011; 286:11563-8. [PMID: 21310955 DOI: 10.1074/jbc.c110.213876] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many tRNA synthetases are homodimers that are catalytically inactive as monomers. An example is the 528-amino acid human tyrosyl-tRNA synthetase, which is made up of an N-terminal catalytic unit (TyrRS(Mini)) and a 164-amino acid C-domain. Although native TyrRS has no known cytokine functions, natural proteolysis of secreted TyrRS releases TyrRS(Mini), which not only has the same aminoacylation activity as native TyrRS but also has strong activity for stimulating migration of polymorphonuclear leukocytes. The migration-stimulating activity is dependent on an ELR tripeptide motif, similar to that in CXC cytokines like IL-8, and also has the familiar bell-shaped concentration dependence seen for CXC cytokines. Here we show that in contrast to IL-8, where the bell-shaped dependence arises from the effects of CXCR1/2 receptor internalization, TyrRS(Mini) does not induce internalization of CXCR1/2. A rationally designed non-associating monomer and a non-dissociating dimer were constructed. With these constructs, the bell-shaped concentration dependence of leukocyte migration was shown to arise from the agonist (for migration) activity of the catalytically inactive monomer and the antagonist activity of the catalytically active dimer. Thus, the dissociating quaternary structure of TyrRS(Mini) regulates two opposing cytokine activities and suggests the possibility of dissociating quaternary structures regulating novel functions of other tRNA synthetases.
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Affiliation(s)
- My-Nuong Vo
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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