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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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2
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Florentz C, Giegé R. History of tRNA research in strasbourg. IUBMB Life 2019; 71:1066-1087. [PMID: 31185141 DOI: 10.1002/iub.2079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/06/2019] [Indexed: 01/03/2023]
Abstract
The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl-tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two-way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health-focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1066-1087, 2019.
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Affiliation(s)
- Catherine Florentz
- Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, F-67084, 15 rue René Descartes, Strasbourg, France.,Direction de la Recherche et de la Valorisation, Université de Strasbourg, F-67084, 4 rue Blaise Pascal, Strasbourg, France
| | - Richard Giegé
- Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, F-67084, 15 rue René Descartes, Strasbourg, France
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3
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McShane A, Hok E, Tomberlin J, Eriani G, Geslain R. The Enzymatic Paradox of Yeast Arginyl-tRNA Synthetase: Exclusive Arginine Transfer Controlled by a Flexible Mechanism of tRNA Recognition. PLoS One 2016; 11:e0148460. [PMID: 26844776 PMCID: PMC4742068 DOI: 10.1371/journal.pone.0148460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/18/2016] [Indexed: 11/18/2022] Open
Abstract
Identity determinants are essential for the accurate recognition of transfer RNAs by aminoacyl-tRNA synthetases. To date, arginine determinants in the yeast Saccharomyces cerevisiae have been identified exclusively in vitro and only on a limited number of tRNA Arginine isoacceptors. In the current study, we favor a full cellular approach and expand the investigation of arginine determinants to all four tRNA Arg isoacceptors. More precisely, this work scrutinizes the relevance of the tRNA nucleotides at position 20, 35 and 36 in the yeast arginylation reaction. We built 21 mutants by site-directed mutagenesis and tested their functionality in YAL5, a previously engineered yeast knockout deficient for the expression of tRNA Arg CCG. Arginylation levels were also monitored using Northern blot. Our data collected in vivo correlate with previous observations. C35 is the prominent arginine determinant followed by G36 or U36 (G/U36). In addition, although there is no major arginine determinant in the D loop, the recognition of tRNA Arg ICG relies to some extent on the nucleotide at position 20. This work refines the existing model for tRNA Arg recognition. Our observations indicate that yeast Arginyl-tRNA synthetase (yArgRS) relies on distinct mechanisms to aminoacylate the four isoacceptors. Finally, according to our refined model, yArgRS is able to accommodate tRNA Arg scaffolds presenting N34, C/G35 and G/A/U36 anticodons while maintaining specificity. We discuss the mechanistic and potential physiological implications of these findings.
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Affiliation(s)
- Ariel McShane
- Laboratory of tRNA biology, Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
| | - Eveline Hok
- Laboratory of tRNA biology, Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
| | - Jensen Tomberlin
- Laboratory of tRNA biology, Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084, Strasbourg CEDEX, France
| | - Renaud Geslain
- Laboratory of tRNA biology, Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
- * E-mail:
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Eriani G, Karam J, Jacinto J, Morris Richard E, Geslain R. MIST, a Novel Approach to Reveal Hidden Substrate Specificity in Aminoacyl-tRNA Synthetases. PLoS One 2015; 10:e0130042. [PMID: 26067673 PMCID: PMC4465971 DOI: 10.1371/journal.pone.0130042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/15/2015] [Indexed: 11/17/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) constitute a family of RNA-binding proteins, that participate in the translation of the genetic code, by covalently linking amino acids to appropriate tRNAs. Due to their fundamental importance for cell life, AARSs are likely to be one of the most ancient families of enzymes and have therefore been characterized extensively. Paradoxically, little is known about their capacity to discriminate tRNAs mainly because of the practical challenges that represent precise and systematic tRNA identification. This work describes a new technical and conceptual approach named MIST (Microarray Identification of Shifted tRNAs) designed to study the formation of tRNA/AARS complexes independently from the aminoacylation reaction. MIST combines electrophoretic mobility shift assays with microarray analyses. Although MIST is a non-cellular assay, it fully integrates the notion of tRNA competition. In this study we focus on yeast cytoplasmic Arginyl-tRNA synthetase (yArgRS) and investigate in depth its ability to discriminate cellular tRNAs. We report that yArgRS in submicromolar concentrations binds cognate and non-cognate tRNAs with a wide range of apparent affinities. In particular, we demonstrate that yArgRS binds preferentially to type II tRNAs but does not support their misaminoacylation. Our results reveal important new trends in tRNA/AARS complex formation and potential deep physiological implications.
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Affiliation(s)
- Gilbert Eriani
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 67084, Strasbourg, CEDEX, France
| | - Joseph Karam
- Laboratory of tRNA Biology, Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
| | - Jomel Jacinto
- Laboratory of tRNA Biology, Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
| | - Erin Morris Richard
- Laboratory of tRNA Biology, Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
| | - Renaud Geslain
- Laboratory of tRNA Biology, Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
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5
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Jakó É, Ittzés P, Szenes Á, Kun Á, Szathmáry E, Pál G. In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership. Nucleic Acids Res 2007; 35:5593-609. [PMID: 17704131 PMCID: PMC2018626 DOI: 10.1093/nar/gkm598] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaRS. Although some aaRS–tRNA interactions are not extremely specific and require editing mechanisms to avoid misaminoacylation, most aaRS–tRNA interactions are rather stereospecific. Thus, class-specific aaRS features could be mirrored by class-specific tRNA features. However, previous investigations failed to detect conserved class-specific nucleotides. Here we introduce a discrete mathematical approach that evaluates not only class-specific ‘strictly present’, but also ‘strictly absent’ nucleotides. The disjoint subsets of these elements compose a unique partition, named extended consensus partition (ECP). By analyzing the ECP for both Class I and II tDNA sets from 50 (13 archaeal, 30 bacterial and 7 eukaryotic) species, we could demonstrate that class-specific tRNA sequence features do exist, although not in terms of strictly conserved nucleotides as it had previously been anticipated. This finding demonstrates that important information was hidden in tRNA sequences inaccessible for traditional statistical methods. The ECP analysis might contribute to the understanding of tRNA evolution and could enrich the sequence analysis tool repertoire.
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Affiliation(s)
- Éena Jakó
- Theoretical Biology and Ecology Research Group of the Hungarian Academy of Sciences, Department of Plant Taxonomy and Ecology, eScience Regional Knowledge Center, at Eötvös Loránd University, Collegium Budapest, Institute for Advanced Study, Budapest, Hungary, Department of Biochemistry and Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Budapest, Hungary
| | - Péter Ittzés
- Theoretical Biology and Ecology Research Group of the Hungarian Academy of Sciences, Department of Plant Taxonomy and Ecology, eScience Regional Knowledge Center, at Eötvös Loránd University, Collegium Budapest, Institute for Advanced Study, Budapest, Hungary, Department of Biochemistry and Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Budapest, Hungary
| | - Áron Szenes
- Theoretical Biology and Ecology Research Group of the Hungarian Academy of Sciences, Department of Plant Taxonomy and Ecology, eScience Regional Knowledge Center, at Eötvös Loránd University, Collegium Budapest, Institute for Advanced Study, Budapest, Hungary, Department of Biochemistry and Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Budapest, Hungary
| | - Ádám Kun
- Theoretical Biology and Ecology Research Group of the Hungarian Academy of Sciences, Department of Plant Taxonomy and Ecology, eScience Regional Knowledge Center, at Eötvös Loránd University, Collegium Budapest, Institute for Advanced Study, Budapest, Hungary, Department of Biochemistry and Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Budapest, Hungary
| | - Eörs Szathmáry
- Theoretical Biology and Ecology Research Group of the Hungarian Academy of Sciences, Department of Plant Taxonomy and Ecology, eScience Regional Knowledge Center, at Eötvös Loránd University, Collegium Budapest, Institute for Advanced Study, Budapest, Hungary, Department of Biochemistry and Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Pál
- Theoretical Biology and Ecology Research Group of the Hungarian Academy of Sciences, Department of Plant Taxonomy and Ecology, eScience Regional Knowledge Center, at Eötvös Loránd University, Collegium Budapest, Institute for Advanced Study, Budapest, Hungary, Department of Biochemistry and Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Budapest, Hungary
- *To whom correspondence should be addressed. +36 1 2090555/8577+36 1 3812172
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Vasil'eva IA, Moor NA. Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition. BIOCHEMISTRY (MOSCOW) 2007; 72:247-63. [PMID: 17447878 DOI: 10.1134/s0006297907030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review summarizes results of numerous (mainly functional) studies that have been accumulated over recent years on the problem of tRNA recognition by aminoacyl-tRNA synthetases. Development and employment of approaches that use synthetic mutant and chimeric tRNAs have demonstrated general principles underlying highly specific interaction in different systems. The specificity of interaction is determined by a certain number of nucleotides and structural elements of tRNA (constituting the set of recognition elements or specificity determinants), which are characteristic of each pair. Crystallographic structures available for many systems provide the details of the molecular basis of selective interaction. Diversity and identity of biochemical functions of the recognition elements make substantial contribution to the specificity of such interactions.
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Affiliation(s)
- I A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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7
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Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H. The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 2006; 34:1816-35. [PMID: 16600899 PMCID: PMC1447645 DOI: 10.1093/nar/gkl085] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 02/03/2006] [Accepted: 03/03/2006] [Indexed: 01/09/2023] Open
Abstract
We present the first comprehensive analysis of RNA polymerase III (Pol III) transcribed genes in ten yeast genomes. This set includes all tRNA genes (tDNA) and genes coding for SNR6 (U6), SNR52, SCR1 and RPR1 RNA in the nine hemiascomycetes Saccharomyces cerevisiae, Saccharomyces castellii, Candida glabrata, Kluyveromyces waltii, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii, Candida albicans, Yarrowia lipolytica and the archiascomycete Schizosaccharomyces pombe. We systematically analysed sequence specificities of tRNA genes, polymorphism, variability of introns, gene redundancy and gene clustering. Analysis of decoding strategies showed that yeasts close to S.cerevisiae use bacterial decoding rules to read the Leu CUN and Arg CGN codons, in contrast to all other known Eukaryotes. In D.hansenii and C.albicans, we identified a novel tDNA-Leu (AAG), reading the Leu CUU/CUC/CUA codons with an unusual G at position 32. A systematic 'p-distance tree' using the 60 variable positions of the tRNA molecule revealed that most tDNAs cluster into amino acid-specific sub-trees, suggesting that, within hemiascomycetes, orthologous tDNAs are more closely related than paralogs. We finally determined the bipartite A- and B-box sequences recognized by TFIIIC. These minimal sequences are nearly conserved throughout hemiascomycetes and were satisfactorily retrieved at appropriate locations in other Pol III genes.
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MESH Headings
- Ascomycota/enzymology
- Ascomycota/genetics
- Base Sequence
- Codon
- Conserved Sequence
- DNA, Fungal/chemistry
- Evolution, Molecular
- Genes, Fungal
- Genome, Fungal
- Genomics
- Introns
- Molecular Sequence Data
- Multigene Family
- Polymorphism, Genetic
- Promoter Regions, Genetic
- RNA Polymerase III/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Untranslated/genetics
- Transcription Factors, TFIII/metabolism
- Transcription, Genetic
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Affiliation(s)
- Christian Marck
- Service de Biochimie et de Génétique Moléculaire, Bât 144. CEA/Saclay, 91191 Gif-sur-Yvette, France.
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8
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Copela LA, Chakshusmathi G, Sherrer RL, Wolin SL. The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability. RNA (NEW YORK, N.Y.) 2006; 12:644-54. [PMID: 16581807 PMCID: PMC1421099 DOI: 10.1261/rna.2307206] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Although the La protein stabilizes nascent pre-tRNAs from nucleases, influences the pathway of pre-tRNA maturation, and assists correct folding of certain pre-tRNAs, it is dispensable for growth in both budding and fission yeast. Here we show that the Saccharomyces cerevisiae La shares functional redundancy with both tRNA modification enzymes and other proteins that contact tRNAs during their biogenesis. La is important for growth in the presence of mutations in either the arginyl tRNA synthetase or the tRNA modification enzyme Trm1p. In addition, two pseudouridine synthases, PUS3 and PUS4, are important for growth in strains carrying a mutation in tRNA(Arg)(CCG) and are essential when La is deleted in these strains. Depletion of Pus3p results in accumulation of the aminoacylated mutant tRNA(Arg)(CCG) in nuclei, while depletion of Pus4p results in decreased stability of the mutant tRNA. Interestingly, the degradation of mutant unstable forms of tRNA(Arg)(CCG) does not require the Trf4p poly(A) polymerase, suggesting that yeast cells possess multiple pathways for tRNA decay. These data demonstrate that La functions redundantly with both tRNA modifications and proteins that associate with tRNAs to achieve tRNA structural stability and efficient biogenesis.
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Affiliation(s)
- Laura A Copela
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, Connecticut 06536, USA
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9
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Current awareness on yeast. Yeast 2005; 22:503-10. [PMID: 15918233 DOI: 10.1002/yea.1162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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