1
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de Moura MC, Miro F, Han JM, Kim S, Celada A, de Pouplana LR. Correction: Entamoeba lysyl-tRNA Synthetase Contains a Cytokine-Like Domain with Chemokine Activity towards Human Endothelial Cells. PLoS Negl Trop Dis 2024; 18:e0012047. [PMID: 38502641 PMCID: PMC10950210 DOI: 10.1371/journal.pntd.0012047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pntd.0001398.].
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2
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Lucas MC, Pryszcz LP, Medina R, Milenkovic I, Camacho N, Marchand V, Motorin Y, Ribas de Pouplana L, Novoa EM. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol 2024; 42:72-86. [PMID: 37024678 DOI: 10.1038/s41587-023-01743-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.
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Affiliation(s)
- Morghan C Lucas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Medina
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivan Milenkovic
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Virginie Marchand
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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3
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Alvarez-Carreño C, Arciniega M, Ribas de Pouplana L, Petrov AS, Hernández-González A, Dimas-Torres JU, Valencia-Sánchez MI, Williams LD, Torres-Larios A. Common evolutionary origins of the bacterial glycyl tRNA synthetase and alanyl tRNA synthetase. Protein Sci 2023; 33:e4844. [PMID: 38009704 PMCID: PMC10895455 DOI: 10.1002/pro.4844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/07/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) establish the genetic code. Each aaRS covalently links a given canonical amino acid to a cognate set of tRNA isoacceptors. Glycyl tRNA aminoacylation is unusual in that it is catalyzed by different aaRSs in different lineages of the Tree of Life. We have investigated the phylogenetic distribution and evolutionary history of bacterial glycyl tRNA synthetase (bacGlyRS). This enzyme is found in early diverging bacterial phyla such as Firmicutes, Acidobacteria, and Proteobacteria, but not in archaea or eukarya. We observe relationships between each of six domains of bacGlyRS and six domains of four different RNA-modifying proteins. Component domains of bacGlyRS show common ancestry with (i) the catalytic domain of class II tRNA synthetases; (ii) the HD domain of the bacterial RNase Y; (iii) the body and tail domains of the archaeal CCA-adding enzyme; (iv) the anti-codon binding domain of the arginyl tRNA synthetase; and (v) a previously unrecognized domain that we call ATL (Ancient tRNA latch). The ATL domain has been found thus far only in bacGlyRS and in the universal alanyl tRNA synthetase (uniAlaRS). Further, the catalytic domain of bacGlyRS is more closely related to the catalytic domain of uniAlaRS than to any other aminoacyl tRNA synthetase. The combined results suggest that the ATL and catalytic domains of these two enzymes are ancestral to bacGlyRS and uniAlaRS, which emerged from common protein ancestors by bricolage, stepwise accumulation of protein domains, before the last universal common ancestor of life.
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Affiliation(s)
- Claudia Alvarez-Carreño
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Marcelino Arciniega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Anton S Petrov
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Adriana Hernández-González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge-Uriel Dimas-Torres
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Marco Igor Valencia-Sánchez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Loren Dean Williams
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Alfredo Torres-Larios
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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4
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López-Soldado I, Torres AG, Ventura R, Martínez-Ruiz I, Díaz-Ramos A, Planet E, Cooper D, Pazderska A, Wanic K, O'Hanlon D, O'Gorman DJ, Carbonell T, de Pouplana LR, Nolan JJ, Zorzano A, Hernández-Alvarez MI. Decreased expression of mitochondrial aminoacyl-tRNA synthetases causes downregulation of OXPHOS subunits in type 2 diabetic muscle. Redox Biol 2023; 61:102630. [PMID: 36796135 PMCID: PMC9958393 DOI: 10.1016/j.redox.2023.102630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Type 2 diabetes mellitus (T2D) affects millions of people worldwide and is one of the leading causes of morbidity and mortality. The skeletal muscle (SKM) is one of the most important tissues involved in maintaining glucose homeostasis and substrate oxidation, and it undergoes insulin resistance in T2D. In this study, we identify the existence of alterations in the expression of mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in skeletal muscle from two different forms of T2D: early-onset type 2 diabetes (YT2) (onset of the disease before 30 years of age) and the classical form of the disease (OT2). GSEA analysis from microarray studies revealed the repression of mitochondrial mt-aaRSs independently of age, which was validated by real-time PCR assays. In agreement with this, a reduced expression of several encoding mt-aaRSs was also detected in skeletal muscle from diabetic (db/db) mice but not in obese ob/ob mice. In addition, the expression of the mt-aaRSs proteins most relevant in the synthesis of mitochondrial proteins, threonyl-tRNA, and leucyl-tRNA synthetases (TARS2 and LARS2) were also repressed in muscle from db/db mice. It is likely that these alterations participate in the reduced expression of proteins synthesized in the mitochondria detected in db/db mice. We also document an increased iNOS abundance in mitochondrial-enriched muscle fractions from diabetic mice that may inhibit aminoacylation of TARS2 and LARS2 by nitrosative stress. Our results indicate a reduced expression of mt-aaRSs in skeletal muscle from T2D patients, which may participate in the reduced expression of proteins synthesized in mitochondria. An enhanced mitochondrial iNOS could play a regulatory role in diabetes.
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Affiliation(s)
- Iliana López-Soldado
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institut de Biomedicina de la Universitat de Barcelona IBUB, Barcelona, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raúl Ventura
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institut de Biomedicina de la Universitat de Barcelona IBUB, Barcelona, Spain
| | - Inma Martínez-Ruiz
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institut de Biomedicina de la Universitat de Barcelona IBUB, Barcelona, Spain
| | - Angels Díaz-Ramos
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Spain
| | - Evarist Planet
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diane Cooper
- National Institute for Cellular Biotechnology, 3U Diabetes Partnership & School of Health and Human Performance, Dublin City University, Dublin, Ireland
| | - Agnieszka Pazderska
- Metabolic Research Unit, St James's Hospital, and Trinity College, Dublin, Ireland
| | - Krzysztof Wanic
- Metabolic Research Unit, St James's Hospital, and Trinity College, Dublin, Ireland
| | - Declan O'Hanlon
- Metabolic Research Unit, St James's Hospital, and Trinity College, Dublin, Ireland
| | - Donal J O'Gorman
- National Institute for Cellular Biotechnology, 3U Diabetes Partnership & School of Health and Human Performance, Dublin City University, Dublin, Ireland
| | - Teresa Carbonell
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biologia, 08028, Barcelona, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - John J Nolan
- Metabolic Research Unit, St James's Hospital, and Trinity College, Dublin, Ireland
| | - Antonio Zorzano
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Spain.
| | - María Isabel Hernández-Alvarez
- Department de Bioquímica i Biomedicina Molecular, Facultat de Biología, 08028, Spain; Institut de Biomedicina de la Universitat de Barcelona IBUB, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Spain.
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5
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Ribas de Pouplana L. Archeal tRNA meets biotechnology: From vaccines to genetic code expansion. J Biol Chem 2022; 299:102755. [PMID: 36455626 PMCID: PMC9800626 DOI: 10.1016/j.jbc.2022.102755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2022] [Indexed: 11/30/2022] Open
Abstract
Engineering new protein functionalities through the addition of noncoded amino acids is a major biotechnological endeavor that needs to overcome the natural firewalls that prevent misincorporation during protein synthesis. This field is in constant evolution driven by the discovery or design of new tools, many of which are based on archeal biology. In a recent article published in JBC, one such tool is characterized and its evolution studied, revealing unexpected details regarding the emergence of the universal genetic code machinery.
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Affiliation(s)
- Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain,For correspondence: Lluís Ribas de Pouplana
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6
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Murillo-Recio M, Martínez de Lejarza Samper IM, Tuñí I Domínguez C, Ribas de Pouplana L, Torres AG. tRNAstudio: facilitating the study of human mature tRNAs from deep sequencing datasets. Bioinformatics 2022; 38:2934-2936. [PMID: 35561195 DOI: 10.1093/bioinformatics/btac198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/17/2022] [Accepted: 04/06/2022] [Indexed: 11/14/2022] Open
Abstract
SUMMARY High-throughput sequencing of transfer RNAs (tRNA-Seq) is a powerful approach to characterize the cellular tRNA pool. Currently, however, analyzing tRNA-Seq datasets requires strong bioinformatics and programming skills. tRNAstudio facilitates the analysis of tRNA-Seq datasets and extracts information on tRNA gene expression, post-transcriptional tRNA modification levels, and tRNA processing steps. Users need only running a few simple bash commands to activate a graphical user interface that allows the easy processing of tRNA-Seq datasets in local mode. Output files include extensive graphical representations and associated numerical tables, and an interactive html summary report to help interpret the data. We have validated tRNAstudio using datasets generated by different experimental methods and derived from human cell lines and tissues that present distinct patterns of tRNA expression, modification and processing. AVAILABILITY AND IMPLEMENTATION Freely available at https://github.com/GeneTranslationLab-IRB/tRNAstudio under an open-source GNU GPL v3.0 license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marina Murillo-Recio
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | | | - Cristina Tuñí I Domínguez
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
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7
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Ros E, Bellido M, Matarin JA, Gallen A, Martínez M, Rodríguez L, Verdaguer X, Ribas de Pouplana L, Riera A. Amino acids with fluorescent tetrazine ethers as bioorthogonal handles for peptide modification. RSC Adv 2022; 12:14321-14327. [PMID: 35702248 PMCID: PMC9096626 DOI: 10.1039/d2ra02531k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022] Open
Abstract
A set of 3-bromo-1,2,4,5-tetrazines with three distinct substitutions have been used as reagents for late-stage functionalization of small molecules through nucleophilic aromatic substitution. Spectroscopic studies of the products obtained proved that tetrazine ethers are intrinsically fluorescent. This fluorescence is lost upon inverse Electron-Demand Diels–Alder (iEDDA) cycloaddition with strained alkenes. Tetrazine-phenol ethers are rather interesting because they can undergo rapid iEDDA reactions with a second order rate constant (k2) compatible with bioorthogonal ligations. As a showcase, l-tyrosine was derivatized with 3-bromo-6-methyl-1,2,4,5-tetrazine and coupled to the peptide drug octreotide. This peptide was detected in cellular flow cytometry, and its fluorescence turned off through a bioorthogonal iEDDA cycloaddition with a strained alkene, showing for the first time the detection and reactivity of intrinsically fluorescent tetrazines in a biologically relevant context. The synthesis and characterization of fluorescent tetrazine ethers with bioorthogonal applicability pave the way for the generation of useful compounds for both detection and bioconjugation in vivo. Octreotide derivatized with the fluorogenic amino acid 6-methyltetratrazinyl tryosine. Emission spectra before and after the iEDDA cycloaddition.![]()
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Affiliation(s)
- Enric Ros
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Marina Bellido
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Joan A Matarin
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain .,BCN Peptides S.A., Pol. Ind. Els Vinyets-Els Fogars Sector II, Ctra. Comarcal 244, Km. 22, 08777 Sant Quintí de Mediona Barcelona Spain
| | - Albert Gallen
- Departament de Química Inorgànica i Orgànica, Secció Química Inorgànica. Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain
| | - Manuel Martínez
- Departament de Química Inorgànica i Orgànica, Secció Química Inorgànica. Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain.,Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona 08028. Barcelona Spain
| | - Laura Rodríguez
- Departament de Química Inorgànica i Orgànica, Secció Química Inorgànica. Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain.,Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona 08028. Barcelona Spain
| | - Xavier Verdaguer
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain .,Departament de Química Inorgànica i Orgànica, Secció Química Orgànica. Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23 08010 Barcelona Spain
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain .,Departament de Química Inorgànica i Orgànica, Secció Química Orgànica. Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain
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8
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Tosar JP, Ivanov P, Ribas de Pouplana L, Torres AG. Editorial: Understanding the Importance of Non-Canonical tRNA Function. Front Mol Biosci 2021; 8:769784. [PMID: 34692774 PMCID: PMC8529061 DOI: 10.3389/fmolb.2021.769784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Juan Pablo Tosar
- Functional Genomics Unit, Institute Pasteur de Montevideo, Montevideo, Uruguay.,Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States.,The Broad Institute of Harvard and M.I.T., Cambridge, MA, United States
| | - Lluís Ribas de Pouplana
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain.,Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
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9
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Torres AG, Rodríguez-Escribà M, Marcet-Houben M, Santos Vieira HG, Camacho N, Catena H, Murillo Recio M, Rafels-Ybern À, Reina O, Torres FM, Pardo-Saganta A, Gabaldón T, Novoa EM, Ribas de Pouplana L. Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins. Nucleic Acids Res 2021; 49:7011-7034. [PMID: 34125917 PMCID: PMC8266599 DOI: 10.1093/nar/gkab461] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the transformation of the homodimeric bacterial enzyme TadA, which generates I34 in tRNAArg and tRNALeu, into the heterodimeric eukaryotic enzyme ADAT, which modifies up to eight different tRNAs. The emergence of ADAT and its larger set of substrates, strongly influenced the tRNA composition and codon usage of eukaryotic genomes. However, the selective advantages that drove the expansion of I34-tRNAs remain unknown. Here we investigate the functional relevance of I34-tRNAs in human cells and show that a full complement of these tRNAs is necessary for the translation of low-complexity protein domains enriched in amino acids cognate for I34-tRNAs. The coding sequences for these domains require codons translated by I34-tRNAs, in detriment of synonymous codons that use other tRNAs. I34-tRNA-dependent low-complexity proteins are enriched in functional categories related to cell adhesion, and depletion in I34-tRNAs leads to cellular phenotypes consistent with these roles. We show that the distribution of these low-complexity proteins mirrors the distribution of I34-tRNAs in the phylogenetic tree.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Marcet-Houben
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain
| | | | - Noelia Camacho
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Helena Catena
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Murillo Recio
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Àlbert Rafels-Ybern
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Francisco Miguel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Ana Pardo-Saganta
- Centre for Applied Medical Research (CIMA Universidad de Navarra), Pamplona 31008, Spain
| | - Toni Gabaldón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,University Pompeu Fabra, Barcelona, Catalonia 08003, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
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10
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Abstract
The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.
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Affiliation(s)
- Sundaramoorthy Srinivasan
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Catalonia, Spain
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11
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Jonkhout N, Cruciani S, Santos Vieira HG, Tran J, Liu H, Liu G, Pickford R, Kaczorowski D, Franco GR, Vauti F, Camacho N, Abedini SS, Najmabadi H, Ribas de Pouplana L, Christ D, Schonrock N, Mattick JS, Novoa EM. Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation. RNA Biol 2021; 18:1905-1919. [PMID: 33499731 DOI: 10.1080/15476286.2021.1881291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory formation. However, whether additional RNA modifications may be playing a role in neuronal functions and in response to environmental queues is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m2,2G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNAAla(AGC) isodecoders at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes may play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.
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Affiliation(s)
- Nicky Jonkhout
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Sonia Cruciani
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Julia Tran
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Huanle Liu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Ganqiang Liu
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Current Address: School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, Australia
| | | | - Gloria R Franco
- Departamento De Bioquímica E Imunologia, Universidade Federal De Minas Gerais,Belo Horizonte,Minas Gerais, Brazil
| | - Franz Vauti
- Division of Cellular & Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Noelia Camacho
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain
| | - Seyedeh Sedigheh Abedini
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nicole Schonrock
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Eva Maria Novoa
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
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12
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Ros E, Prades A, Forson D, Smyth J, Verdaguer X, Pouplana LRD, Riera A. Synthesis of 3-alkyl-6-methyl-1,2,4,5-tetrazines via a Sonogashira-type cross-coupling reaction. Chem Commun (Camb) 2020; 56:11086-11089. [PMID: 32812558 DOI: 10.1039/d0cc03482g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
1,2,4,5-Tetrazines have become extremely useful tools in chemical biology. However, the synthesis of some challenging substrates such as asymmetrically disubstituted alkyltetrazines is still a limitation for the widespread use of this class of compounds. Herein we describe an efficient route to these compounds based on the Sonogashira coupling of 3-bromo-6-methyl-1,2,4,5-tetrazine and 3-bromo-6-phenyl-1,2,4,5-tetrazine with terminal alkynes. The preparation of the starting reagents has also been optimized. The alkynyl products have been used as intermediates for the synthesis of dialkyl-tetrazines through a sequence of hydrogenation and re-oxidation with unprecedented yields. The synthetic applicability of this new approach is showcased through the preparation of several unnatural amino acids bearing alkynyl- and alkyl-1,2,4,5-tetrazine fragments.
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Affiliation(s)
- Enric Ros
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
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13
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Ros E, Torres AG, Ribas de Pouplana L. Learning from Nature to Expand the Genetic Code. Trends Biotechnol 2020; 39:460-473. [PMID: 32896440 DOI: 10.1016/j.tibtech.2020.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 01/14/2023]
Abstract
The genetic code is the manual that cells use to incorporate amino acids into proteins. It is possible to artificially expand this manual through cellular, molecular, and chemical manipulations to improve protein functionality. Strategies for in vivo genetic code expansion are under the same functional constraints as natural protein synthesis. Here, we review the approaches used to incorporate noncanonical amino acids (ncAAs) into designer proteins through the manipulation of the translation machinery and draw parallels between these methods and natural adaptations that improve translation in extant organisms. Following this logic, we propose new nature-inspired tactics to improve genetic code expansion (GCE) in synthetic organisms.
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Affiliation(s)
- Enric Ros
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, 08028, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, 08028, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, 08028, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, 08010, Spain.
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14
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Picchioni D, Antolin-Fontes A, Camacho N, Schmitz C, Pons-Pons A, Rodríguez-Escribà M, Machallekidou A, Güler MN, Siatra P, Carretero-Junquera M, Serrano A, Hovde SL, Knobel PA, Novoa EM, Solà-Vilarrubias M, Kaguni LS, Stracker TH, Ribas de Pouplana L. Mitochondrial Protein Synthesis and mtDNA Levels Coordinated through an Aminoacyl-tRNA Synthetase Subunit. Cell Rep 2020; 27:40-47.e5. [PMID: 30943413 DOI: 10.1016/j.celrep.2019.03.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/13/2019] [Accepted: 03/06/2019] [Indexed: 11/28/2022] Open
Abstract
The aminoacylation of tRNAs by aminoacyl-tRNA synthetases (ARSs) is a central reaction in biology. Multiple regulatory pathways use the aminoacylation status of cytosolic tRNAs to monitor and regulate metabolism. The existence of equivalent regulatory networks within the mitochondria is unknown. Here, we describe a functional network that couples protein synthesis to DNA replication in animal mitochondria. We show that a duplication of the gene coding for mitochondrial seryl-tRNA synthetase (SerRS2) generated in arthropods a paralog protein (SLIMP) that forms a heterodimeric complex with a SerRS2 monomer. This seryl-tRNA synthetase variant is essential for protein synthesis and mitochondrial respiration. In addition, SLIMP interacts with the substrate binding domain of the mitochondrial protease LON, thus stimulating proteolysis of the DNA-binding protein TFAM and preventing mitochondrial DNA (mtDNA) accumulation. Thus, mitochondrial translation is directly coupled to mtDNA levels by a network based upon a profound structural modification of an animal ARS.
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Affiliation(s)
- Daria Picchioni
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Albert Antolin-Fontes
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Claus Schmitz
- Structural MitoLab, Department of Structural Biology, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Alba Pons-Pons
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Antigoni Machallekidou
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Merve Nur Güler
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Panagiota Siatra
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Maria Carretero-Junquera
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Alba Serrano
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Stacy L Hovde
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain; Laboratory for Molecular Radiobiology, Clinic of Radiation Oncology, University of Zurich, 8057 Zurich, Switzerland
| | - Eva M Novoa
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003 Barcelona, Spain; Garvan Institute of Medical Research, 384 Victoria Street, 2010 Darlinghurst, NSW, Australia
| | - Maria Solà-Vilarrubias
- Structural MitoLab, Department of Structural Biology, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA; Institute of Biosciences and Medical Technology, University of Tampere, 33014 Tampere, Finland
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), P/Lluis Companys 23, 08010 Barcelona, Catalonia, Spain.
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15
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Ros E, Bellido M, Verdaguer X, Ribas de Pouplana L, Riera A. Synthesis and Application of 3-Bromo-1,2,4,5-Tetrazine for Protein Labeling to Trigger Click-to-Release Biorthogonal Reactions. Bioconjug Chem 2020; 31:933-938. [DOI: 10.1021/acs.bioconjchem.0c00052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Enric Ros
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marina Bellido
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Xavier Verdaguer
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament de Quı́mica Inorgànica i Orgànica, Secció Orgànica. Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament de Quı́mica Inorgànica i Orgànica, Secció Orgànica. Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
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16
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Ribas de Pouplana L, Kaguni LS. Preface. Enzymes 2020; 48:xiii. [PMID: 33837713 DOI: 10.1016/s1874-6047(20)30048-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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17
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Abstract
Since the origin of life, metabolism and protein synthesis have evolved together to balance the vast amounts of ATP and amino acids required for genetic translation with the rest of the cell's energy needs. A new study offers satisfying insights into a long-standing evolutionary mystery surrounding a fused, bifunctional aminoacyl-tRNA synthetase. To avoid depleting cells from an essential amino acid generated by the Krebs cycle, harvesting for Glu and Pro by the translation machinery was unified in animals, thus preventing a Pro-hungry translational apparatus from depleting the cell of essential Glu reserves.
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Affiliation(s)
- Lluís Ribas de Pouplana
- From the Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain and Catalan Institution for Research and Advanced Studies (ICREA), P/Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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18
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Rafels-Ybern À, Torres AG, Camacho N, Herencia-Ropero A, Roura Frigolé H, Wulff TF, Raboteg M, Bordons A, Grau-Bove X, Ruiz-Trillo I, Ribas de Pouplana L. The Expansion of Inosine at the Wobble Position of tRNAs, and Its Role in the Evolution of Proteomes. Mol Biol Evol 2019; 36:650-662. [PMID: 30590541 DOI: 10.1093/molbev/msy245] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The modification of adenosine to inosine at the first position of transfer RNA (tRNA) anticodons (I34) is widespread among bacteria and eukaryotes. In bacteria, the modification is found in tRNAArg and is catalyzed by tRNA adenosine deaminase A, a homodimeric enzyme. In eukaryotes, I34 is introduced in up to eight different tRNAs by the heterodimeric adenosine deaminase acting on tRNA. This substrate expansion significantly influenced the evolution of eukaryotic genomes in terms of codon usage and tRNA gene composition. However, the selective advantages driving this process remain unclear. Here, we have studied the evolution of I34, tRNA adenosine deaminase A, adenosine deaminase acting on tRNA, and their relevant codons in a large set of bacterial and eukaryotic species. We show that a functional expansion of I34 to tRNAs other than tRNAArg also occurred within bacteria, in a process likely initiated by the emergence of unmodified A34-containing tRNAs. In eukaryotes, we report on a large variability in the use of I34 in protists, in contrast to a more uniform presence in fungi, plans, and animals. Our data support that the eukaryotic expansion of I34-tRNAs was driven by the improvement brought by these tRNAs to the synthesis of proteins highly enriched in certain amino acids.
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Affiliation(s)
- Àlbert Rafels-Ybern
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Andrea Herencia-Ropero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Helena Roura Frigolé
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Thomas F Wulff
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Marina Raboteg
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Albert Bordons
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Xavier Grau-Bove
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiología i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiología i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain.,ICREA, Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.,ICREA, Barcelona, Catalonia, Spain
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19
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Roura Frigolé H, Camacho N, Castellví Coma M, Fernández-Lozano C, García-Lema J, Rafels-Ybern À, Canals A, Coll M, Ribas de Pouplana L. tRNA deamination by ADAT requires substrate-specific recognition mechanisms and can be inhibited by tRFs. RNA 2019; 25:607-619. [PMID: 30737359 PMCID: PMC6467012 DOI: 10.1261/rna.068189.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/28/2019] [Indexed: 05/30/2023]
Abstract
Adenosine deaminase acting on transfer RNA (ADAT) is an essential eukaryotic enzyme that catalyzes the deamination of adenosine to inosine at the first position of tRNA anticodons. Mammalian ADATs modify eight different tRNAs, having increased their substrate range from a bacterial ancestor that likely deaminated exclusively tRNAArg Here we investigate the recognition mechanisms of tRNAArg and tRNAAla by human ADAT to shed light on the process of substrate expansion that took place during the evolution of the enzyme. We show that tRNA recognition by human ADAT does not depend on conserved identity elements, but on the overall structural features of tRNA. We find that ancestral-like interactions are conserved for tRNAArg, while eukaryote-specific substrates use alternative mechanisms. These recognition studies show that human ADAT can be inhibited by tRNA fragments in vitro, including naturally occurring fragments involved in important regulatory pathways.
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MESH Headings
- Adenosine/metabolism
- Adenosine Deaminase/genetics
- Adenosine Deaminase/metabolism
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Base Sequence
- Deamination
- Evolution, Molecular
- Gene Expression
- Humans
- Inosine/metabolism
- Nucleic Acid Conformation
- RNA, Transfer, Ala/chemistry
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ala/metabolism
- RNA, Transfer, Arg/chemistry
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Arg/metabolism
- Sequence Alignment
- Substrate Specificity
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Affiliation(s)
- Helena Roura Frigolé
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Maria Castellví Coma
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Carla Fernández-Lozano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Jorge García-Lema
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Àlbert Rafels-Ybern
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Albert Canals
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Catalonia, Spain
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20
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Torres AG, Reina O, Stephan-Otto Attolini C, Ribas de Pouplana L. Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments. Proc Natl Acad Sci U S A 2019; 116:8451-8456. [PMID: 30962382 PMCID: PMC6486751 DOI: 10.1073/pnas.1821120116] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The human genome encodes hundreds of transfer RNA (tRNA) genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and posttranscriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. We find that sequencing caveats affect quantitation of only a subset of human tRNA genes. Unexpectedly, we detect several cases where the differences in tRNA expression among samples do not involve variations at the level of isoacceptor tRNA sets (tRNAs charged with the same amino acid but using different anticodons), but rather among tRNA genes within the same isodecoder set (tRNAs having the same anticodon sequence). Because isodecoder tRNAs are functionally equal in terms of genetic translation, their differential expression may be related to noncanonical tRNA functions. We show that several instances of differential tRNA gene expression result in changes in the abundance of tRNA-derived fragments (tRFs) but not of mature tRNAs. Examples of differentially expressed tRFs include PIWI-associated RNAs, tRFs present in tissue samples but not in cells cultured in vitro, and somatic tissue-specific tRFs. Our data support that differential expression of tRNA genes regulate noncanonical tRNA functions performed by tRFs.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain;
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Catalonia, Spain
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21
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Yang P, Beltramo DM, de Pouplana LR, Soria NW, Torres AG. Loss of the tRNA Lys CUU encoding gene, Chr-11 tRNA-Lys-CUU, is not associated with Type 2 diabetes mellitus. Biomark Med 2019; 13:259-266. [PMID: 30882233 DOI: 10.2217/bmm-2018-0322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate the presence/absence of the Chr-11 tRNA-Lys-CUU gene as a marker for genetic predisposition to Type 2 diabetes mellitus (T2DM). METHODS We enrolled 122 patients diagnosed with T2DM and 77 non-diabetic individuals. We evaluated clinical and biochemical parameters (body mass index, hypertension, cholesterol levels, glycosylated hemoglobin, triglycerides, etc.), and performed a genotypic profiling of Chr-11 tRNA-Lys-CUU by polymerase chain reaction analyses. RESULTS Approximately one third of the population lacked Chr-11 tRNA-Lys-CUU. We did not observe a statistically significant association between the presence/absence of Chr-11 tRNA-Lys-CUU and T2DM. CONCLUSION The genotypic distribution of Chr-11 tRNA-Lys-CUU in our population was consistent to that reported by others. This gene failed as a marker for T2DM predisposition.
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Affiliation(s)
- Pablo Yang
- Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Dante Miguel Beltramo
- Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science & Technology, 08028 Barcelona, Catalonia, Spain.,Catalan Institution for Research & Advanced Studies (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Néstor Walter Soria
- Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science & Technology, 08028 Barcelona, Catalonia, Spain
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22
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Torres AG, Wulff TF, Rodríguez-Escribà M, Camacho N, Ribas de Pouplana L. Detection of Inosine on Transfer RNAs without a Reverse Transcription Reaction. Biochemistry 2018; 57:5641-5647. [PMID: 30199619 DOI: 10.1021/acs.biochem.8b00718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inosine at the "wobble" position (I34) is one of the few essential posttranscriptional modifications in tRNAs (tRNAs). It results from the deamination of adenosine and occurs in bacteria on tRNAArgACG and in eukarya on six or seven additional tRNA substrates. Because inosine is structurally a guanosine analogue, reverse transcriptases recognize it as a guanosine. Most methods used to examine the presence of inosine rely on this phenomenon and detect the modified base as a change in the DNA sequence that results from the reverse transcription reaction. These methods, however, cannot always be applied to tRNAs because reverse transcription can be compromised by the presence of other posttranscriptional modifications. Here we present SL-ID (splinted ligation-based inosine detection), a reverse transcription-free method for detecting inosine based on an I34-dependent specific cleavage of tRNAs by endonuclease V, followed by a splinted ligation and polyacrylamide gel electrophoresis analysis. We show that the method can detect I34 on different tRNA substrates and can be applied to total RNA derived from different species, cell types, and tissues. Here we apply the method to solve previous controversies regarding the modification status of mammalian tRNAArgACG.
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Affiliation(s)
- Adrian G Torres
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Thomas F Wulff
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , P/Lluis Companys 23 , 08010 Barcelona , Catalonia , Spain
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23
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Charlton MH, Aleksis R, Saint-Leger A, Gupta A, Loza E, Ribas de Pouplana L, Kaula I, Gustina D, Madre M, Lola D, Jaudzems K, Edmund G, Randall CP, Kime L, O’Neill AJ, Goessens W, Jirgensons A, Finn PW. N-Leucinyl Benzenesulfonamides as Structurally Simplified Leucyl-tRNA Synthetase Inhibitors. ACS Med Chem Lett 2018; 9:84-88. [PMID: 29456792 DOI: 10.1021/acsmedchemlett.7b00374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/18/2018] [Indexed: 12/12/2022] Open
Abstract
N-Leucinyl benzenesulfonamides have been discovered as a novel class of potent inhibitors of E. coli leucyl-tRNA synthetase. The binding of inhibitors to the enzyme was measured by using isothermal titration calorimetry. This provided information on enthalpy and entropy contributions to binding, which, together with docking studies, were used for structure-activity relationship analysis. Enzymatic assays revealed that N-leucinyl benzenesulfonamides display remarkable selectivity for E. coli leucyl-tRNA synthetase compared to S. aureus and human orthologues. The simplest analogue of the series, N-leucinyl benzenesulfonamide (R = H), showed the highest affinity against E. coli leucyl-tRNA synthetase and also exhibited antibacterial activity against Gram-negative pathogens (the best MIC = 8 μg/mL, E. coli ATCC 25922), which renders it as a promising template for antibacterial drug discovery.
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Affiliation(s)
- Michael H. Charlton
- Oxford Drug Design Ltd., Oxford Centre for Innovation, New Road, Oxford, OX1 1BY. U.K
| | - Rihards Aleksis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Adélaïde Saint-Leger
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Catalonia, Spain
- ICREA, Pg. Lluís Company 23, 08010 Barcelona, Catalonia, Spain
| | - Arya Gupta
- Antimicrobial
Research Centre and School of Molecular and Cellular Biology, Faculty
of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Einars Loza
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Catalonia, Spain
- ICREA, Pg. Lluís Company 23, 08010 Barcelona, Catalonia, Spain
| | - Ilze Kaula
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Daina Gustina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Marina Madre
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Daina Lola
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Grace Edmund
- Oxford Drug Design Ltd., Oxford Centre for Innovation, New Road, Oxford, OX1 1BY. U.K
| | - Christopher P. Randall
- Antimicrobial
Research Centre and School of Molecular and Cellular Biology, Faculty
of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Louise Kime
- Antimicrobial
Research Centre and School of Molecular and Cellular Biology, Faculty
of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Alex J. O’Neill
- Antimicrobial
Research Centre and School of Molecular and Cellular Biology, Faculty
of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Wil Goessens
- Erasmus University Medical Center Rotterdam, Department
of Medical Microbiology and Infectious Diseases, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Paul W. Finn
- Oxford Drug Design Ltd., Oxford Centre for Innovation, New Road, Oxford, OX1 1BY. U.K
- Department
of Applied Computing, University of Buckingham, Hunter Street, Buckingham, MK18 1EG, U.K
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24
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Silva J, Aivio S, Knobel PA, Bailey LJ, Casali A, Vinaixa M, Garcia-Cao I, Coyaud É, Jourdain AA, Pérez-Ferreros P, Rojas AM, Antolin-Fontes A, Samino-Gené S, Raught B, González-Reyes A, Ribas de Pouplana L, Doherty AJ, Yanes O, Stracker TH. EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nat Cell Biol 2018; 20:162-174. [PMID: 29335528 DOI: 10.1038/s41556-017-0016-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/27/2017] [Indexed: 02/08/2023]
Abstract
Mitochondria are subcellular organelles that are critical for meeting the bioenergetic and biosynthetic needs of the cell. Mitochondrial function relies on genes and RNA species encoded both in the nucleus and mitochondria, and on their coordinated translation, import and respiratory complex assembly. Here, we characterize EXD2 (exonuclease 3'-5' domain-containing 2), a nuclear-encoded gene, and show that it is targeted to the mitochondria and prevents the aberrant association of messenger RNAs with the mitochondrial ribosome. Loss of EXD2 results in defective mitochondrial translation, impaired respiration, reduced ATP production, increased reactive oxygen species and widespread metabolic abnormalities. Depletion of the Drosophila melanogaster EXD2 orthologue (CG6744) causes developmental delays and premature female germline stem cell attrition, reduced fecundity and a dramatic extension of lifespan that is reversed with an antioxidant diet. Our results define a conserved role for EXD2 in mitochondrial translation that influences development and ageing.
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Affiliation(s)
- Joana Silva
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Suvi Aivio
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department for Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Laura J Bailey
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Andreu Casali
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maria Vinaixa
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Isabel Garcia-Cao
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexis A Jourdain
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pablo Pérez-Ferreros
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,EMBL Australia, University of New South Wales, Lowy Cancer Research Center, Single Molecule Science Node, Sydney and Arc Center of Excellence in Advance Molecular Imaging, Sydney, New South Wales, Australia
| | - Ana M Rojas
- Computational Biology and Bioinformatics Group, Institute of Biomedicine of Seville (IBIS/CSIC/US/JA), Campus Hospital Universitario Virgen del Rocio, Seville, Spain
| | - Albert Antolin-Fontes
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sara Samino-Gené
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Acaimo González-Reyes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Seville, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Oscar Yanes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
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25
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Rafels-Ybern À, Torres AG, Grau-Bove X, Ruiz-Trillo I, Ribas de Pouplana L. Codon adaptation to tRNAs with Inosine modification at position 34 is widespread among Eukaryotes and present in two Bacterial phyla. RNA Biol 2017; 15:500-507. [PMID: 28880718 DOI: 10.1080/15476286.2017.1358348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The modification of adenosine to inosine at position 34 of tRNA anticodons has a profound impact upon codon-anticodon recognition. In bacteria, I34 is thought to exist only in tRNAArg, while in eukaryotes the modification is present in eight different tRNAs. In eukaryotes, the widespread use of I34 strongly influenced the evolution of genomes in terms of tRNA gene abundance and codon usage. In humans, codon usage indicates that I34 modified tRNAs are preferred for the translation of highly repetitive coding sequences, suggesting that I34 is an important modification for the synthesis of proteins of highly skewed amino acid composition. Here we extend the analysis of distribution of codons that are recognized by I34 containing tRNAs to all phyla known to use this modification. We find that the preference for codons recognized by such tRNAs in genes with highly biased codon compositions is universal among eukaryotes, and we report that, unexpectedly, some bacterial phyla show a similar preference. We demonstrate that the genomes of these bacterial species contain previously undescribed tRNA genes that are potential substrates for deamination at position 34.
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Affiliation(s)
- Àlbert Rafels-Ybern
- a Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac, Barcelona, Catalonia , Spain
| | - Adrian Gabriel Torres
- a Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac, Barcelona, Catalonia , Spain
| | - Xavier Grau-Bove
- b Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra) , Barcelona, Catalonia , Spain.,c Departament de Genètica, Microbiología i Estadística , Universitat de Barcelona , Catalonia , Spain
| | - Iñaki Ruiz-Trillo
- b Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra) , Barcelona, Catalonia , Spain.,c Departament de Genètica, Microbiología i Estadística , Universitat de Barcelona , Catalonia , Spain.,d ICREA , Pg. Lluís Companys 23, Barcelona , Catalonia , Spain
| | - Lluís Ribas de Pouplana
- a Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac, Barcelona, Catalonia , Spain.,d ICREA , Pg. Lluís Companys 23, Barcelona , Catalonia , Spain
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26
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Wulff TF, Argüello RJ, Molina Jordàn M, Roura Frigolé H, Hauquier G, Filonava L, Camacho N, Gatti E, Pierre P, Ribas de Pouplana L, Torres AG. Detection of a Subset of Posttranscriptional Transfer RNA Modifications in Vivo with a Restriction Fragment Length Polymorphism-Based Method. Biochemistry 2017; 56:4029-4038. [PMID: 28703578 DOI: 10.1021/acs.biochem.7b00324] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Transfer RNAs (tRNAs) are among the most heavily modified RNA species. Posttranscriptional tRNA modifications (ptRMs) play fundamental roles in modulating tRNA structure and function and are being increasingly linked to human physiology and disease. Detection of ptRMs is often challenging, expensive, and laborious. Restriction fragment length polymorphism (RFLP) analyses study the patterns of DNA cleavage after restriction enzyme treatment and have been used for the qualitative detection of modified bases on mRNAs. It is known that some ptRMs induce specific and reproducible base "mutations" when tRNAs are reverse transcribed. For example, inosine, which derives from the deamination of adenosine, is detected as a guanosine when an inosine-containing tRNA is reverse transcribed, amplified via polymerase chain reaction (PCR), and sequenced. ptRM-dependent base changes on reverse transcription PCR amplicons generated as a consequence of the reverse transcription reaction might create or abolish endonuclease restriction sites. The suitability of RFLP for the detection and/or quantification of ptRMs has not been studied thus far. Here we show that different ptRMs can be detected at specific sites of different tRNA types by RFLP. For the examples studied, we show that this approach can reliably estimate the modification status of the sample, a feature that can be useful in the study of the regulatory role of tRNA modifications in gene expression.
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Affiliation(s)
- Thomas F Wulff
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Rafael J Argüello
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université U2M, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Marc Molina Jordàn
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Helena Roura Frigolé
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Glenn Hauquier
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Liudmila Filonava
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Evelina Gatti
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université U2M, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France.,Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Philippe Pierre
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université U2M, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France.,Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , P/Lluis Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Adrian G Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
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27
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Saint-Léger A, Ribas de Pouplana L. A new set of assays for the discovery of aminoacyl-tRNA synthetase inhibitors. Methods 2016; 113:34-45. [PMID: 27989759 DOI: 10.1016/j.ymeth.2016.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 01/08/2023] Open
Abstract
Current biochemical methods available to monitor the activity of aminoacyl-tRNA synthetases (ARS) are ill-suited to high-throughput screening approaches for the identification of small-molecule inhibitors of these enzymes. In an attempt to improve the limitations of current assays we have developed a suite of new methods designed to streamline the discovery of new ARS antagonists. This set of assays includes approaches to monitor ARS activity in vitro, in human cells, and in bacteria. They are applicable to several ARSs from any given organism, can be easily adapted to very high-throughput set-ups, and allow for a multi-factorial selection of drug candidates.
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Affiliation(s)
- Adélaïde Saint-Léger
- Omnia Molecular S.L., c/ Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Omnia Molecular S.L., c/ Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c/ Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain.
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28
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Abstract
Cladosporin is an antimalarial drug that acts as an ATP-mimetic to selectively inhibit Plasmodium lysyl-tRNA synthetase. Using multiple crystal structures, Fang et al. (2015) reveal in this issue of Chemistry & Biology the fascinating mechanism responsible for cladosporin selectivity.
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Affiliation(s)
- Eva Maria Novoa
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA; The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain.
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29
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Saint-Léger A, Bello C, Dans PD, Torres AG, Novoa EM, Camacho N, Orozco M, Kondrashov FA, Ribas de Pouplana L. Saturation of recognition elements blocks evolution of new tRNA identities. Sci Adv 2016; 2:e1501860. [PMID: 27386510 PMCID: PMC4928997 DOI: 10.1126/sciadv.1501860] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/31/2016] [Indexed: 06/01/2023]
Abstract
Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure.
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Affiliation(s)
- Adélaïde Saint-Léger
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Carla Bello
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 88 Dr. Aiguader, 08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Pablo D. Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Joint BSC-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Eva Maria Novoa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02139, USA
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Joint BSC-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, 08028 Barcelona, Catalonia, Spain
| | - Fyodor A. Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 88 Dr. Aiguader, 08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain
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30
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Abstract
Malaria remains a major global health problem. Parasite resistance to existing drugs makes development of new antimalarials an urgency. The protein synthesis machinery is an excellent target for the development of new anti-infectives, and aminoacyl-tRNA synthetases (aaRS) have been validated as antimalarial drug targets. However, avoiding the emergence of drug resistance and improving selectivity to target aaRS in apicomplexan parasites, such as Plasmodium falciparum, remain crucial challenges. Here we discuss such issues using examples of known inhibitors of P. falciparum aaRS, namely halofuginone, cladosporin and borrelidin (inhibitors of ProRS, LysRS and ThrRS, respectively). Encouraging recent results provide useful guidelines to facilitate the development of novel drug candidates which are more potent and selective against these essential enzymes.
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Affiliation(s)
| | | | - Lluís Ribas de Pouplana
- a Omnia Molecular S.L. , Barcelona , Spain.,b Institute for Research in Biomedicine (IRB Barcelona) , Barcelona , Spain.,c Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona , Spain
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31
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Rovira-Graells N, Crowley VM, Bancells C, Mira-Martínez S, Ribas de Pouplana L, Cortés A. Deciphering the principles that govern mutually exclusive expression of Plasmodium falciparum clag3 genes. Nucleic Acids Res 2015. [PMID: 26202963 PMCID: PMC4787829 DOI: 10.1093/nar/gkv730] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The product of the Plasmodium falciparum genes clag3.1 and clag3.2 plays a fundamental role in malaria parasite biology by determining solute transport into infected erythrocytes. Expression of the two clag3 genes is mutually exclusive, such that a single parasite expresses only one of the two genes at a time. Here we investigated the properties and mechanisms of clag3 mutual exclusion using transgenic parasite lines with extra copies of clag3 promoters located either in stable episomes or integrated in the parasite genome. We found that the additional clag3 promoters in these transgenic lines are silenced by default, but under strong selective pressure parasites with more than one clag3 promoter simultaneously active are observed, demonstrating that clag3 mutual exclusion is strongly favored but it is not strict. We show that silencing of clag3 genes is associated with the repressive histone mark H3K9me3 even in parasites with unusual clag3 expression patterns, and we provide direct evidence for heterochromatin spreading in P. falciparum. We also found that expression of a neighbor ncRNA correlates with clag3.1 expression. Altogether, our results reveal a scenario where fitness costs and non-deterministic molecular processes that favor mutual exclusion shape the expression patterns of this important gene family.
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Affiliation(s)
- Núria Rovira-Graells
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Catalonia, Spain Institute for Research in Biomedicine (IRB), 08028 Barcelona, Catalonia, Spain
| | - Valerie M Crowley
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Catalonia, Spain
| | - Cristina Bancells
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Sofía Mira-Martínez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Alfred Cortés
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Catalonia, Spain Institute for Research in Biomedicine (IRB), 08028 Barcelona, Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Catalonia, Spain
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32
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Torres AG, Piñeyro D, Rodríguez-Escribà M, Camacho N, Reina O, Saint-Léger A, Filonava L, Batlle E, Ribas de Pouplana L. Inosine modifications in human tRNAs are incorporated at the precursor tRNA level. Nucleic Acids Res 2015; 43:5145-57. [PMID: 25916855 PMCID: PMC4446420 DOI: 10.1093/nar/gkv277] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/20/2015] [Indexed: 11/12/2022] Open
Abstract
Transfer RNAs (tRNAs) are key adaptor molecules of the genetic code that are heavily modified post-transcriptionally. Inosine at the first residue of the anticodon (position 34; I34) is an essential widespread tRNA modification that has been poorly studied thus far. The modification in eukaryotes results from a deamination reaction of adenine that is catalyzed by the heterodimeric enzyme adenosine deaminase acting on tRNA (hetADAT), composed of two subunits: ADAT2 and ADAT3. Using high-throughput small RNA sequencing (RNAseq), we show that this modification is incorporated to human tRNAs at the precursor tRNA level and during maturation. We also functionally validated the human genes encoding for hetADAT and show that the subunits of this enzyme co-localize in nucleus in an ADAT2-dependent manner. Finally, by knocking down HsADAT2, we demonstrate that variations in the cellular levels of hetADAT will result in changes in the levels of I34 modification in all its potential substrates. Altogether, we present RNAseq as a powerful tool to study post-transcriptional tRNA modifications at the precursor tRNA level and give the first insights on the biology of I34 tRNA modification in metazoans.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - David Piñeyro
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Adélaïde Saint-Léger
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Liudmila Filonava
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), P/Lluis Companys 23, Barcelona, 08010 Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), P/Lluis Companys 23, Barcelona, 08010 Catalonia, Spain
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33
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Novoa EM, Vargas-Rodriguez O, Lange S, Goto Y, Suga H, Musier-Forsyth K, Ribas de Pouplana L. Ancestral AlaX editing enzymes for control of genetic code fidelity are not tRNA-specific. J Biol Chem 2015; 290:10495-503. [PMID: 25724653 DOI: 10.1074/jbc.m115.640060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Indexed: 01/15/2023] Open
Abstract
Accurate protein synthesis requires the hydrolytic editing of tRNAs incorrectly aminoacylated by aminoacyl-tRNA synthetases (ARSs). Recognition of cognate tRNAs by ARS is less error-prone than amino acid recognition, and, consequently, editing domains are generally believed to act only on the tRNAs cognate to their related ARSs. For example, the AlaX family of editing domains, including the editing domain of alanyl-tRNA synthetase and the related free-standing trans-editing AlaX enzymes, are thought to specifically act on tRNA(Ala), whereas the editing domains of threonyl-tRNA synthetases are specific for tRNA(Thr). Here we show that, contrary to this belief, AlaX-S, the smallest of the extant AlaX enzymes, deacylates Ser-tRNA(Thr) in addition to Ser-tRNA(Ala) and that a single residue is important to determine this behavior. Our data indicate that promiscuous forms of AlaX are ancestral to tRNA-specific AlaXs. We propose that former AlaX domains were used to maintain translational fidelity in earlier stages of genetic code evolution when mis-serylation of several tRNAs was possible.
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Affiliation(s)
- Eva Maria Novoa
- From the Institute for Research in Biomedicine, c/ Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Oscar Vargas-Rodriguez
- the Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Stefanie Lange
- From the Institute for Research in Biomedicine, c/ Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Yuki Goto
- the Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
| | - Hiroaki Suga
- the Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
| | - Karin Musier-Forsyth
- the Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Lluís Ribas de Pouplana
- From the Institute for Research in Biomedicine, c/ Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain, the Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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34
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Ragionieri L, Vitorino R, Frommlet J, Oliveira JL, Gaspar P, Ribas de Pouplana L, Santos MAS, Moura GR. Improving the accuracy of recombinant protein production through integration of bioinformatics, statistical and mass spectrometry methodologies. FEBS J 2015; 282:769-87. [DOI: 10.1111/febs.13181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 10/09/2014] [Accepted: 12/16/2014] [Indexed: 02/05/2023]
Affiliation(s)
- Lapo Ragionieri
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
| | - Rui Vitorino
- Department of Chemistry; University of Aveiro; Portugal
| | - Joerg Frommlet
- Department of Biology and Centro de Estudos do Ambiente e do Mar; University of Aveiro; Portugal
| | - José L. Oliveira
- Department of Electronics; Telecommunications and Informatics and Instituto de Engenharia Electrónica e Telemática de Aveiro; University of Aveiro; Portugal
| | - Paulo Gaspar
- Department of Electronics; Telecommunications and Informatics and Instituto de Engenharia Electrónica e Telemática de Aveiro; University of Aveiro; Portugal
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine; Barcelona Spain
- Catalan Institution for Research and Advanced Studies; Barcelona Spain
| | - Manuel A. Silva Santos
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
| | - Gabriela Ribeiro Moura
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
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35
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Affiliation(s)
- Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), Barcelona Catalonia, Spain
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36
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Hoen R, Novoa EM, López A, Camacho N, Cubells L, Vieira P, Santos M, Marin-Garcia P, Bautista JM, Cortés A, Ribas de Pouplana L, Royo M. Selective inhibition of an apicoplastic aminoacyl-tRNA synthetase from Plasmodium falciparum. Chembiochem 2013; 14:499-509. [PMID: 23444099 DOI: 10.1002/cbic.201200620] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Indexed: 01/13/2023]
Abstract
The resistance of malaria parasites to available drugs continues to grow, and this makes the need for new antimalarial therapies pressing. Aminoacyl-tRNA synthetases (ARSs) are essential enzymes and well-established antibacterial targets and so constitute a promising set of targets for the development of new antimalarials. Despite their potential as drug targets, apicoplastic ARSs remain unexplored. We have characterized the lysylation system of Plasmodium falciparum, and designed, synthesized, and tested a set of inhibitors based on the structure of the natural substrate intermediate: lysyl-adenylate. Here we demonstrate that selective inhibition of apicoplastic ARSs is feasible and describe new compounds that that specifically inhibit Plasmodium apicoplastic lysyl-tRNA synthetase and show antimalarial activities in the micromolar range.
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Affiliation(s)
- Rob Hoen
- Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
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37
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Khan S, Garg A, Sharma A, Camacho N, Picchioni D, Saint-Léger A, de Pouplana LR, Yogavel M, Sharma A. An appended domain results in an unusual architecture for malaria parasite tryptophanyl-tRNA synthetase. PLoS One 2013; 8:e66224. [PMID: 23776638 PMCID: PMC3680381 DOI: 10.1371/journal.pone.0066224] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/02/2013] [Indexed: 01/03/2023] Open
Abstract
Specific activation of amino acids by aminoacyl-tRNA synthetases (aaRSs) is essential for maintaining fidelity during protein translation. Here, we present crystal structure of malaria parasite Plasmodium falciparum tryptophanyl-tRNA synthetase (Pf-WRS) catalytic domain (AAD) at 2.6 Å resolution in complex with L-tryptophan. Confocal microscopy-based localization data suggest cytoplasmic residency of this protein. Pf-WRS has an unusual N-terminal extension of AlaX-like domain (AXD) along with linker regions which together seem vital for enzymatic activity and tRNA binding. Pf-WRS is not proteolytically processed in the parasites and therefore AXD likely provides tRNA binding capability rather than editing activity. The N-terminal domain containing AXD and linker region is monomeric and would result in an unusual overall architecture for Pf-WRS where the dimeric catalytic domains have monomeric AXDs on either side. Our PDB-wide comparative analyses of 47 WRS crystal structures also provide new mechanistic insights into this enzyme family in context conserved KMSKS loop conformations.
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Affiliation(s)
- Sameena Khan
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Ankur Garg
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Arvind Sharma
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Catalonia, Spain
| | - Daria Picchioni
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Catalonia, Spain
| | - Adélaïde Saint-Léger
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
| | - Manickam Yogavel
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Amit Sharma
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- * E-mail:
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38
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Abstract
Recognition strategies for tRNA aminoacylation are ancient and highly conserved, having been selected very early in the evolution of the genetic code. In most cases, the trinucleotide anticodons of tRNA are important identity determinants for aminoacylation by cognate aminoacyl-tRNA synthetases. However, a degree of ambiguity exists in the recognition of certain tRNA(Ile) isoacceptors that are initially transcribed with the methionine-specifying CAU anticodon. In most organisms, the C34 wobble position in these tRNA(Ile) precursors is rapidly modified to lysidine to prevent recognition by methionyl-tRNA synthetase (MRS) and production of a chimeric Met-tRNA(Ile) that would compromise translational fidelity. In certain bacteria, however, lysidine modification is not required for MRS rejection, indicating that this recognition strategy is not universally conserved and may be relatively recent. To explore the actual distribution of lysidine-dependent tRNA(Ile) rejection by MRS, we have investigated the ability of bacterial MRSs from different clades to differentiate cognate tRNACAU(Met) from near-cognate tRNACAU(Ile). Discrimination abilities vary greatly and appear unrelated to phylogenetic or structural features of the enzymes or sequence determinants of the tRNA. Our data indicate that tRNA(Ile) identity elements were established late and independently in different bacterial groups. We propose that the observed variation in MRS discrimination ability reflects differences in the evolution of genetic code machineries of emerging bacterial clades.
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Affiliation(s)
- Thomas E Jones
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109-7486, USA
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39
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Guitart T, Picchioni D, Piñeyro D, Ribas de Pouplana L. Human mitochondrial disease-like symptoms caused by a reduced tRNA aminoacylation activity in flies. Nucleic Acids Res 2013; 41:6595-608. [PMID: 23677612 PMCID: PMC3711456 DOI: 10.1093/nar/gkt402] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The translation of genes encoded in the mitochondrial genome requires specific machinery that functions in the organelle. Among the many mutations linked to human disease that affect mitochondrial translation, several are localized to nuclear genes coding for mitochondrial aminoacyl-transfer RNA synthetases. The molecular significance of these mutations is poorly understood, but it is expected to be similar to that of the mutations affecting mitochondrial transfer RNAs. To better understand the molecular features of diseases caused by these mutations, and to improve their diagnosis and therapeutics, we have constructed a Drosophila melanogaster model disrupting the mitochondrial seryl-tRNA synthetase by RNA interference. At the molecular level, the knockdown generates a reduction in transfer RNA serylation, which correlates with the severity of the phenotype observed. The silencing compromises viability, longevity, motility and tissue development. At the cellular level, the knockdown alters mitochondrial morphology, biogenesis and function, and induces lactic acidosis and reactive oxygen species accumulation. We report that administration of antioxidant compounds has a palliative effect of some of these phenotypes. In conclusion, the fly model generated in this work reproduces typical characteristics of pathologies caused by mutations in the mitochondrial aminoacylation system, and can be useful to assess therapeutic approaches.
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Affiliation(s)
- Tanit Guitart
- Institute for Research in Biomedicine (IRB Barcelona), Gene Translation Laboratory, c/Baldiri Reixac 10, Barcelona, 08028, Catalonia, Spain
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40
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Mateus DD, Paredes JA, Español Y, Ribas de Pouplana L, Moura GR, Santos MAS. Molecular reconstruction of a fungal genetic code alteration. RNA Biol 2013; 10:969-80. [PMID: 23619021 DOI: 10.4161/rna.24683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fungi of the CTG clade translate the Leu CUG codon as Ser. This genetic code alteration is the only eukaryotic sense-to-sense codon reassignment known to date, is mediated by an ambiguous serine tRNA (tRNACAG(Ser)), exposes unanticipated flexibility of the genetic code and raises major questions about its selection and fixation in this fungal lineage. In particular, the origin of the tRNACAG(Ser) and the evolutionary mechanism of CUG reassignment from Leu to Ser remain poorly understood. In this study, we have traced the origin of the tDNACAG(Ser) gene and studied critical mutations in the tRNACAG(Ser) anticodon-loop that modulated CUG reassignment. Our data show that the tRNACAG(Ser) emerged from insertion of an adenosine in the middle position of the 5'-CGA-3'anticodon of a tRNACGA(Ser) ancestor, producing the 5'-CAG-3' anticodon of the tRNACAG(Ser), without altering its aminoacylation properties. This mutation initiated CUG reassignment while two additional mutations in the anticodon-loop resolved a structural conflict produced by incorporation of the Leu 5'-CAG-3'anticodon in the anticodon-arm of a tRNA(Ser). Expression of the mutant tRNACAG(Ser) in yeast showed that it cannot be expressed at physiological levels and we postulate that such downregulation was essential to maintain Ser misincorporation at sub-lethal levels during the initial stages of CUG reassignment. We demonstrate here that such low level CUG ambiguity is advantageous in specific ecological niches and we propose that misreading tRNAs are targeted for degradation by an unidentified tRNA quality control pathway.
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Affiliation(s)
- Denisa D Mateus
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
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41
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Novoa EM, Ribas de Pouplana L. Speeding with control: codon usage, tRNAs, and ribosomes. Trends Genet 2012; 28:574-81. [PMID: 22921354 DOI: 10.1016/j.tig.2012.07.006] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/19/2012] [Accepted: 07/20/2012] [Indexed: 11/26/2022]
Abstract
Codon usage and tRNA abundance are critical parameters for gene synthesis. However, the forces determining codon usage bias within genomes and between organisms, as well as the functional roles of biased codon compositions, remain poorly understood. Similarly, the composition and dynamics of mature tRNA populations in cells in terms of isoacceptor abundances, and the prevalence and function of base modifications are not well understood. As we begin to decipher some of the rules that govern codon usage and tRNA abundances, it is becoming clear that these parameters are a way to not only increase gene expression, but also regulate the speed of ribosomal translation, the efficiency of protein folding, and the coordinated expression of functionally related gene families. Here, we discuss the importance of codon-anticodon interactions in translation regulation and highlight the contribution of non-random codon distributions and post-transcriptional base modifications to this regulation.
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Affiliation(s)
- Eva Maria Novoa
- Institute for Research in Biomedicine (IRB), c/Baldiri Reixac 15-21 08028, Barcelona, Catalonia, Spain
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42
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Novoa EM, Pavon-Eternod M, Pan T, Ribas de Pouplana L. A role for tRNA modifications in genome structure and codon usage. Cell 2012; 149:202-13. [PMID: 22464330 DOI: 10.1016/j.cell.2012.01.050] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 11/23/2011] [Accepted: 01/12/2012] [Indexed: 11/17/2022]
Abstract
Transfer RNA (tRNA) gene content is a differentiating feature of genomes that contributes to the efficiency of the translational apparatus, but the principles shaping tRNA gene copy number and codon composition are poorly understood. Here, we report that the emergence of two specific tRNA modifications shaped the structure and composition of all extant genomes. Through the analysis of more than 500 genomes, we identify two kingdom-specific tRNA modifications as major contributors that separated archaeal, bacterial, and eukaryal genomes in terms of their tRNA gene composition. We show that, contrary to prior observations, genomic codon usage and tRNA gene frequencies correlate in all kingdoms if these two modifications are taken into account and that presence or absence of these modifications explains patterns of gene expression observed in previous studies. Finally, we experimentally demonstrate that human gene expression levels correlate well with genomic codon composition if these identified modifications are considered.
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Affiliation(s)
- Eva Maria Novoa
- Institute for Research in Biomedicine, c/ Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
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43
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Rovira-Graells N, Gupta AP, Planet E, Crowley VM, Mok S, Ribas de Pouplana L, Preiser PR, Bozdech Z, Cortés A. Transcriptional variation in the malaria parasite Plasmodium falciparum. Genome Res 2012; 22:925-38. [PMID: 22415456 PMCID: PMC3337437 DOI: 10.1101/gr.129692.111] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Malaria genetic variation has been extensively characterized, but the level of epigenetic plasticity remains largely unexplored. Here we provide a comprehensive characterization of transcriptional variation in the most lethal malaria parasite, Plasmodium falciparum, based on highly accurate transcriptional analysis of isogenic parasite lines grown under homogeneous conditions. This analysis revealed extensive transcriptional heterogeneity within genetically homogeneous clonal parasite populations. We show that clonally variant expression controlled at the epigenetic level is an intrinsic property of specific genes and gene families, the majority of which participate in host–parasite interactions. Intrinsic transcriptional variability is not restricted to genes involved in immune evasion, but also affects genes linked to lipid metabolism, protein folding, erythrocyte remodeling, or transcriptional regulation, among others, indicating that epigenetic variation results in both antigenic and functional variation. We observed a general association between heterochromatin marks and clonally variant expression, extending previous observations for specific genes to essentially all variantly expressed gene families. These results suggest that phenotypic variation of functionally unrelated P. falciparum gene families is mediated by a common mechanism based on reversible formation of H3K9me3-based heterochromatin. In changing environments, diversity confers fitness to a population. Our results support the idea that P. falciparum uses a bet-hedging strategy, as an alternative to directed transcriptional responses, to adapt to common fluctuations in its environment. Consistent with this idea, we found that transcriptionally different isogenic parasite lines markedly differed in their survival to heat-shock mimicking febrile episodes and adapted to periodic heat-shock with a pattern consistent with natural selection of pre-existing parasites.
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44
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Castro de Moura M, Miro F, Han JM, Kim S, Celada A, Ribas de Pouplana L. Entamoeba lysyl-tRNA synthetase contains a cytokine-like domain with chemokine activity towards human endothelial cells. PLoS Negl Trop Dis 2011; 5:e1398. [PMID: 22140588 PMCID: PMC3226552 DOI: 10.1371/journal.pntd.0001398] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 09/30/2011] [Indexed: 11/18/2022] Open
Abstract
Immunological pressure encountered by protozoan parasites drives the selection of strategies to modulate or avoid the immune responses of their hosts. Here we show that the parasite Entamoeba histolytica has evolved a chemokine that mimics the sequence, structure, and function of the human cytokine HsEMAPII (Homo sapiens endothelial monocyte activating polypeptide II). This Entamoeba EMAPII-like polypeptide (EELP) is translated as a domain attached to two different aminoacyl-tRNA synthetases (aaRS) that are overexpressed when parasites are exposed to inflammatory signals. EELP is dispensable for the tRNA aminoacylation activity of the enzymes that harbor it, and it is cleaved from them by Entamoeba proteases to generate a standalone cytokine. Isolated EELP acts as a chemoattractant for human cells, but its cell specificity is different from that of HsEMAPII. We show that cell specificity differences between HsEMAPII and EELP can be swapped by site directed mutagenesis of only two residues in the cytokines' signal sequence. Thus, Entamoeba has evolved a functional mimic of an aaRS-associated human cytokine with modified cell specificity.
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45
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Krog JS, Español Y, Giessing AMB, Dziergowska A, Malkiewicz A, Ribas de Pouplana L, Kirpekar F. 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine is one of two novel post-transcriptional modifications in tRNALys(UUU) from Trypanosoma brucei. FEBS J 2011; 278:4782-96. [PMID: 22040320 DOI: 10.1111/j.1742-4658.2011.08379.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
tRNA is the most heavily modified of all RNA types, with typically 10-20% of the residues being post-transcriptionally altered. Unravelling the modification pattern of a tRNA is a challenging task; there are 92 currently known tRNA modifications, many of which are chemically similar. Furthermore, the tRNA has to be investigated with single-nucleotide resolution in order to ensure complete mapping of all modifications. In the present work, we characterized tRNA(Lys)(UUU) from Trypanosoma brucei, and provide a complete overview of its post-transcriptional modifications. The first step was MALDI-TOF MS of two independent digests of the tRNA, with RNase A and RNase T1, respectively. This revealed digestion products harbouring mass-changing modifications. Next, the modifications were mapped at the nucleotide level in the RNase products by tandem MS. Comparison with the sequence of the unmodified tRNA revealed the modified residues. The modifications were further characterized at the nucleoside level by chromatographic retention time and fragmentation pattern upon higher-order tandem MS. Phylogenetic comparison with modifications in tRNA(Lys) from other organisms was used through the entire analysis. We identified modifications on 12 nucleosides in tRNA(Lys)(UUU), where U47 exhibited a novel modification, 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine, based on identical chromatographic retention and MS fragmentation as the synthetic nucleoside. A37 was observed in two versions: a minor fraction with the previously described 2-methylthio-N(6)-threonylcarbamoyl-modification, and a major fraction with A37 being modified by a 294.0-Da moiety. The latter product is the largest adenosine modification reported so far, and we discuss its nature and origin.
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Affiliation(s)
- Jesper S Krog
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Crowley VM, Rovira-Graells N, Ribas de Pouplana L, Cortés A. Heterochromatin formation in bistable chromatin domains controls the epigenetic repression of clonally variant Plasmodium falciparum genes linked to erythrocyte invasion. Mol Microbiol 2011; 80:391-406. [PMID: 21306446 DOI: 10.1111/j.1365-2958.2011.07574.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Clonally variant gene expression is a common survival strategy used by many pathogens, including the malaria parasite Plasmodium falciparum. Among the genes that show variant expression in this parasite are several members of small gene families linked to erythrocyte invasion, including the clag and eba families. The active or repressed state of these genes is clonally transmitted by epigenetic mechanisms. Here we characterized the promoters of clag3.1, clag3.2 and eba-140, and compared nuclease accessibility and post-translational histone modifications between their active and repressed states. Activity of these promoters in an episomal context is similar between parasite subclones characterized by different patterns of expression of the endogenous genes. Variant expression is controlled by the euchromatic or heterochromatic state of bistable chromatin domains. Repression is mediated by H3K9me3-based heterochromatin, whereas the active state is characterized by H3K9ac. These marks are maintained throughout the asexual blood cycle to transmit the epigenetic memory. Furthermore, eba-140 is organized in two distinct chromatin domains, probably separated by a barrier insulator located within its ORF. The 5' chromatin domain controls expression of the gene, whereas the 3' domain shares the chromatin conformation with the upstream region of the neighbouring phista family gene, which also shows variant expression.
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Affiliation(s)
- Valerie M Crowley
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Catalonia, Spain
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Guitart T, Leon Bernardo T, Sagalés J, Stratmann T, Bernués J, Ribas de Pouplana L. New aminoacyl-tRNA synthetase-like protein in insecta with an essential mitochondrial function. J Biol Chem 2010; 285:38157-66. [PMID: 20870726 PMCID: PMC2992249 DOI: 10.1074/jbc.m110.167486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 09/22/2010] [Indexed: 12/24/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARS) are modular enzymes that aminoacylate transfer RNAs (tRNA) for their use by the ribosome during protein synthesis. ARS are essential and universal components of the genetic code that were almost completely established before the appearance of the last common ancestor of all living species. This long evolutionary history explains the growing number of functions being discovered for ARS, and for ARS homologues, beyond their canonical role in gene translation. Here we present a previously uncharacterized paralogue of seryl-tRNA synthetase named SLIMP (seryl-tRNA synthetase-like insect mitochondrial protein). SLIMP is the result of a duplication of a mitochondrial seryl-tRNA synthetase (SRS) gene that took place in early metazoans and was fixed in Insecta. Here we show that SLIMP is localized in the mitochondria, where it carries out an essential function that is unrelated to the aminoacylation of tRNA. The knockdown of SLIMP by RNA interference (RNAi) causes a decrease in respiration capacity and an increase in mitochondrial mass in the form of aberrant mitochondria.
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Affiliation(s)
- Tanit Guitart
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
| | - Teresa Leon Bernardo
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
| | - Jessica Sagalés
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
| | - Thomas Stratmann
- the Department of Physiology, University of Barcelona (Biology), Avinguda Diagonal 645, 08028 Barcelona, Catalonia
| | - Jordi Bernués
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
- the Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Parc Cientific de Barcelona, Carrer Baldiri Reixac 12, 08028 Barcelona, Catalonia, and
| | - Lluís Ribas de Pouplana
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
- the Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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Novoa EM, Castro de Moura M, Orozco M, Ribas de Pouplana L. A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins. FEBS Lett 2010; 584:460-6. [PMID: 19913539 DOI: 10.1016/j.febslet.2009.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/03/2009] [Accepted: 11/08/2009] [Indexed: 02/05/2023]
Abstract
During their extended evolution genes coding for aminoacyl-tRNA synthetases (ARS) have experienced numerous instances of duplication, insertion and deletion of domains. The ARS-related proteins that have resulted from these genetic events are generally known as aminoacyl-tRNA synthetase-like proteins (ARS-like). This heterogeneous group of polypeptides carries out an equally varied number of functions that need not be related to gene translation. Several of these proteins remain uncharacterized. At least 16 different ARS-like proteins have been identified to date, but their functions remain incompletely understood. Here we review the individual phylogenetic distribution of these proteins in bacteria, and apply a new genomics method to determine their potential implication in pathogenicity.
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Affiliation(s)
- Eva Maria Novoa
- Institute for Research in Biomedicine (IRB), c/ Baldiri Reixac 15-21, 08028 Barcelona, Spain
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Geslain R, Cubells L, Bori-Sanz T, Alvarez-Medina R, Rossell D, Martí E, Ribas de Pouplana L. Chimeric tRNAs as tools to induce proteome damage and identify components of stress responses. Nucleic Acids Res 2009; 38:e30. [PMID: 20007146 PMCID: PMC2836549 DOI: 10.1093/nar/gkp1083] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Misfolded proteins are caused by genomic mutations, aberrant splicing events, translation errors or environmental factors. The accumulation of misfolded proteins is a phenomenon connected to several human disorders, and is managed by stress responses specific to the cellular compartments being affected. In wild-type cells these mechanisms of stress response can be experimentally induced by expressing recombinant misfolded proteins or by incubating cells with large concentrations of amino acid analogues. Here, we report a novel approach for the induction of stress responses to protein aggregation. Our method is based on engineered transfer RNAs that can be expressed in cells or tissues, where they actively integrate in the translation machinery causing general proteome substitutions. This strategy allows for the introduction of mutations of increasing severity randomly in the proteome, without exposing cells to unnatural compounds. Here, we show that this approach can be used for the differential activation of the stress response in the Endoplasmic Reticulum (ER). As an example of the applications of this method, we have applied it to the identification of human microRNAs activated or repressed during unfolded protein stress.
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Affiliation(s)
- Renaud Geslain
- Institute for Research in Biomedicine, Omnia Molecular, Barcelona Science Park, Instituto de Biología Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, c/Baldiri Reixac 15-21, Barcelona 08028, Spain
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Farrera-Sinfreu J, Español Y, Geslain R, Guitart T, Albericio F, Ribas de Pouplana L, Royo M. Solid-Phase Combinatorial Synthesis of a Lysyl-tRNA Synthetase (LysRS) Inhibitory Library. ACTA ACUST UNITED AC 2008; 10:391-400. [DOI: 10.1021/cc700157j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josep Farrera-Sinfreu
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Yaiza Español
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Renaud Geslain
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Tanit Guitart
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Miriam Royo
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
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