1
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Wulff TF, Hahnke K, Lécrivain AL, Schmidt K, Ahmed-Begrich R, Finstermeier K, Charpentier E. Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability. Nucleic Acids Res 2024:gkae629. [PMID: 39087550 DOI: 10.1093/nar/gkae629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 07/01/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing plays an important role in the post-transcriptional regulation of eukaryotic cell physiology. However, our understanding of the occurrence, function and regulation of A-to-I editing in bacteria remains limited. Bacterial mRNA editing is catalysed by the deaminase TadA, which was originally described to modify a single tRNA in Escherichia coli. Intriguingly, several bacterial species appear to perform A-to-I editing on more than one tRNA. Here, we provide evidence that in the human pathogen Streptococcus pyogenes, tRNA editing has expanded to an additional tRNA substrate. Using RNA sequencing, we identified more than 27 editing sites in the transcriptome of S. pyogenes SF370 and demonstrate that the adaptation of S. pyogenes TadA to a second tRNA substrate has also diversified the sequence context and recoding scope of mRNA editing. Based on the observation that editing is dynamically regulated in response to several infection-relevant stimuli, such as oxidative stress, we further investigated the underlying determinants of editing dynamics and identified mRNA stability as a key modulator of A-to-I editing. Overall, our findings reveal the presence and diversification of A-to-I editing in S. pyogenes and provide novel insights into the plasticity of the editome and its regulation in bacteria.
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Affiliation(s)
- Thomas F Wulff
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | | | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
- Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
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2
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Andac CA, Hornemann U, Noyanalpan N, Stringfellow TC. Synthesis, NMR kinetics and dynamic structure of a 17-mer heptaloop RNA hairpin carrying a 3- N-methyluridine nucleotide residue in the loop region. J Biomol Struct Dyn 2024; 42:3659-3681. [PMID: 37278223 DOI: 10.1080/07391102.2023.2214231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
A 17-mer RNA hairpin (5'GGGAGUXAGCGGCUCCC3') carrying 3-N-methyluridine (m3U) at position X (m3U7-RNA), designed to represent the anticodon stem-loop (ACSL) region of tRNAs to study an open loop state (O-state), was synthesized, purified by HPLC, and characterized by MALDI-ToF_MS and NMR methods. 1H-NMR data revealed primary (P-state in 56.1%), secondary (S-state in 43.9%) and tertiary (∼5-6%) ACSL conformations. Exchange rate constant (kex) for interconversion between P and S states is 112 sec-1 (<Δω ∼454 rad/sec), confirming a slow exchange regime between the two states. Forward (kPS) and backward (kSP) rate constants are 49.166 sec-1 and 62.792 sec-1, respectively, leading to a longer life-time (20.339 msec) for the P-state and a shorter life-time (15.926 msec) for the S-state. In accordance with conformational populations determined by 1H-NMR, dynamics of the P/S/tertiary states of m3U7-RNA and its wild-type counterpart (wt-RNA) were studied by three independent MD production simulations. Cluster analysis revealed that wt-RNA reflects the structural characteristics of the ACSL region of tRNAs. The P-state of m3U7-RNA was found to be structurally similar to wt-RNA but lacks an intraloop H-bond between m3U7 and C10 (U33 and nt36 in tRNAs). In the S-state of m3U7-RNA, m3U7 flips out of the loop region. O-state loop conformations of m3U7-RNA were also clustered (4.8%), wherein the loop nucleotides m3U7.A8.G9.C10.G11 stack one after another. We propose that the O-state of m3U7-RNA is the most suitable conformation that makes the loop accessible for complementary nucleotides and for non-enzymatic primordial replication of small circular RNAs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cenk A Andac
- Department of Medical Pharmacology, School of Medicine, Yeditepe University, Istanbul, Turkiye
| | - Ulfert Hornemann
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Ningur Noyanalpan
- Department of Medicinal Chemistry, School of Pharmacy, Gazi University, Ankara, Turkiye
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3
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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: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [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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4
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de Potter B, Vallee I, Camacho N, Filipe Costa Póvoas L, Bonsembiante A, Pons i Pons A, Eckhard U, Gomis-Rüth FX, Yang XL, Schimmel P, Kuhle B, Ribas de Pouplana L. Domain collapse and active site ablation generate a widespread animal mitochondrial seryl-tRNA synthetase. Nucleic Acids Res 2023; 51:10001-10010. [PMID: 37638745 PMCID: PMC10570016 DOI: 10.1093/nar/gkad696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Through their aminoacylation reactions, aminoacyl tRNA-synthetases (aaRS) establish the rules of the genetic code throughout all of nature. During their long evolution in eukaryotes, additional domains and splice variants were added to what is commonly a homodimeric or monomeric structure. These changes confer orthogonal functions in cellular activities that have recently been uncovered. An unusual exception to the familiar architecture of aaRSs is the heterodimeric metazoan mitochondrial SerRS. In contrast to domain additions or alternative splicing, here we show that heterodimeric metazoan mitochondrial SerRS arose from its homodimeric ancestor not by domain additions, but rather by collapse of an entire domain (in one subunit) and an active site ablation (in the other). The collapse/ablation retains aminoacylation activity while creating a new surface, which is necessary for its orthogonal function. The results highlight a new paradigm for repurposing a member of the ancient tRNA synthetase family.
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Affiliation(s)
- Bastiaan de Potter
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Utrecht University Faculty of Science, Department of Biology, Theoretical Biology and Bioinformatics Utrecht, Utrecht, The Netherlands
| | - Ingrid Vallee
- The Scripps Research Institute, Department of Molecular Medicine La Jolla, CA, USA
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Luís Filipe Costa Póvoas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Aureliano Bonsembiante
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Alba Pons i Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Ulrich Eckhard
- Molecular Biology Institute of Barcelona, Department of Structural Biology, Barcelona, Catalunya, Spain
| | | | - Xiang-Lei Yang
- The Scripps Research Institute, Department of Molecular Medicine La Jolla, CA, USA
| | - Paul Schimmel
- The Scripps Research Institute, Department of Molecular Medicine La Jolla, CA, USA
| | - Bernhard Kuhle
- The Scripps Research Institute, Department of Molecular Medicine La Jolla, CA, USA
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- ICREA, Catalan Institution for Research and Advanced Studies Barcelona, Catalonia, Spain
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5
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Kuhle B, Hirschi M, Doerfel LK, Lander GC, Schimmel P. Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition. Nat Commun 2023; 14:4794. [PMID: 37558671 PMCID: PMC10412605 DOI: 10.1038/s41467-023-40354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/22/2023] [Indexed: 08/11/2023] Open
Abstract
Animal mitochondrial gene expression relies on specific interactions between nuclear-encoded aminoacyl-tRNA synthetases and mitochondria-encoded tRNAs. Their evolution involves an antagonistic interplay between strong mutation pressure on mtRNAs and selection pressure to maintain their essential function. To understand the molecular consequences of this interplay, we analyze the human mitochondrial serylation system, in which one synthetase charges two highly divergent mtRNASer isoacceptors. We present the cryo-EM structure of human mSerRS in complex with mtRNASer(UGA), and perform a structural and functional comparison with the mSerRS-mtRNASer(GCU) complex. We find that despite their common function, mtRNASer(UGA) and mtRNASer(GCU) show no constrain to converge on shared structural or sequence identity motifs for recognition by mSerRS. Instead, mSerRS evolved a bimodal readout mechanism, whereby a single protein surface recognizes degenerate identity features specific to each mtRNASer. Our results show how the mutational erosion of mtRNAs drove a remarkable innovation of intermolecular specificity rules, with multiple evolutionary pathways leading to functionally equivalent outcomes.
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Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073, Göttingen, Germany.
| | - Marscha Hirschi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92121, USA
| | - Lili K Doerfel
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92121, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92121, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Scripps Florida Research Institute at the University of Florida, Jupiter, FL, 33458, USA
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6
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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] [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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7
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Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova K, Koonin E, Shen Y, Söll D, Fu X. The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism. Nucleic Acids Res 2022; 50:4601-4615. [PMID: 35466371 PMCID: PMC9071458 DOI: 10.1093/nar/gkac271] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 12/24/2022] Open
Abstract
Site-specific incorporation of distinct non-canonical amino acids into proteins via genetic code expansion requires mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs. Pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs are ideal for genetic code expansion and have been extensively engineered for developing mutually orthogonal pairs. Here, we identify two novel wild-type PylRS/tRNAPyl pairs simultaneously present in the deep-rooted extremely halophilic euryarchaeal methanogen Candidatus Methanohalarchaeum thermophilum HMET1, and show that both pairs are functional in the model halophilic archaeon Haloferax volcanii. These pairs consist of two different PylRS enzymes and two distinct tRNAs with dissimilar discriminator bases. Surprisingly, these two PylRS/tRNAPyl pairs display mutual orthogonality enabled by two unique features, the A73 discriminator base of tRNAPyl2 and a shorter motif 2 loop in PylRS2. In vivo translation experiments show that tRNAPyl2 charging by PylRS2 is defined by the enzyme's shortened motif 2 loop. Finally, we demonstrate that the two HMET1 PylRS/tRNAPyl pairs can simultaneously decode UAG and UAA codons for incorporation of two distinct noncanonical amino acids into protein. This example of a single base change in a tRNA leading to additional coding capacity suggests that the growth of the genetic code is not yet limited by the number of identity elements fitting into the tRNA structure.
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Affiliation(s)
| | | | | | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Huiming Zhang
- BGI-Shenzhen, Shenzhen, 518083, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuxing Zhang
- BGI-Shenzhen, Shenzhen, 518083, China,Sino-Danish College, University of the Chinese Academy of Sciences, Beijing, China
| | - Paul Wassel
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Julie Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yue Shen
- Correspondence may also be addressed to Yue Shen.
| | - Dieter Söll
- To whom correspondence should be addressed. Tel: +1 203 4326200;
| | - Xian Fu
- Correspondence may also be addressed to Xian Fu.
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8
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Jani J, Pappachan A. A review on quality control agents of protein translation - The role of Trans-editing proteins. Int J Biol Macromol 2022; 199:252-263. [PMID: 34995670 DOI: 10.1016/j.ijbiomac.2021.12.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Translation of RNA to protein is a key feature of cellular life. The fidelity of this process mainly depends on the availability of correctly charged tRNAs. Different domains of tRNA synthetase (aaRS) maintain translation quality by ensuring the proper attachment of particular amino acid with respective tRNA, thus it establishes the rule of genetic code. However occasional errors by aaRS generate mischarged tRNAs, which can become lethal to the cells. Accurate protein synthesis necessitates hydrolysis of mischarged tRNAs. Various cis and trans-editing proteins are identified which recognize these mischarged products and correct them by hydrolysis. Trans-editing proteins are homologs of cis-editing domains of aaRS. The trans-editing proteins work in close association with aaRS, Ef-Tu, and ribosome to prevent global mistranslation and ensures correct charging of tRNA. In this review, we discuss the major trans-editing proteins and compared them with their cis-editing counterparts. We also discuss their structural features, biochemical activity and role in maintaining cellular protein homeostasis.
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Affiliation(s)
- Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India.
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9
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Torres AG, Rodríguez-Escribà M, Marcet-Houben M, Santos Vieira H, Camacho N, Catena H, Murillo Recio M, Rafels-Ybern À, Reina O, Torres F, Pardo-Saganta A, Gabaldón T, Novoa E, 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: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [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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Srinivasan S, Torres AG, Ribas de Pouplana L. Inosine in Biology and Disease. Genes (Basel) 2021; 12:600. [PMID: 33921764 PMCID: PMC8072771 DOI: 10.3390/genes12040600] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
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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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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12
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Ehrlich R, Davyt M, López I, Chalar C, Marín M. On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? Front Mol Biosci 2021; 8:643701. [PMID: 33796548 PMCID: PMC8007984 DOI: 10.3389/fmolb.2021.643701] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Cellular tRNAs appear today as a diverse population of informative macromolecules with conserved general elements ensuring essential common functions and different and distinctive features securing specific interactions and activities. Their differential expression and the variety of post-transcriptional modifications they are subject to, lead to the existence of complex repertoires of tRNA populations adjusted to defined cellular states. Despite the tRNA-coding genes redundancy in prokaryote and eukaryote genomes, it is surprising to note the absence of genes coding specific translational-active isoacceptors throughout the phylogeny. Through the analysis of different releases of tRNA databases, this review aims to provide a general summary about those “missing tRNA genes.” This absence refers to both tRNAs that are not encoded in the genome, as well as others that show critical sequence variations that would prevent their activity as canonical translation adaptor molecules. Notably, while a group of genes are universally missing, others are absent in particular kingdoms. Functional information available allows to hypothesize that the exclusion of isodecoding molecules would be linked to: 1) reduce ambiguities of signals that define the specificity of the interactions in which the tRNAs are involved; 2) ensure the adaptation of the translational apparatus to the cellular state; 3) divert particular tRNA variants from ribosomal protein synthesis to other cellular functions. This leads to consider the “missing tRNA genes” as a source of putative non-canonical tRNA functions and to broaden the concept of adapter molecules in ribosomal-dependent protein synthesis.
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Affiliation(s)
- Ricardo Ehrlich
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay.,Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Davyt
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Ignacio López
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Cora Chalar
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Mónica Marín
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
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13
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Abstract
Diverse models have been advanced for the evolution of the genetic code. Here, models for tRNA, aminoacyl-tRNA synthetase (aaRS) and genetic code evolution were combined with an understanding of EF-Tu suppression of tRNA 3rd anticodon position wobbling. The result is a highly detailed scheme that describes the placements of all amino acids in the standard genetic code. The model describes evolution of 6-, 4-, 3-, 2- and 1-codon sectors. Innovation in column 3 of the code is explained. Wobbling and code degeneracy are explained. Separate distribution of serine sectors between columns 2 and 4 of the code is described. We conclude that very little chaos contributed to evolution of the genetic code and that the pattern of evolution of aaRS enzymes describes a history of the evolution of the code. A model is proposed to describe the biological selection for the earliest evolution of the code and for protocell evolution.
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Affiliation(s)
- Lei Lei
- Department of Biology, University of New England, Biddeford, ME, USA
| | - Zachary Frome Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, USA
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14
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Mukai T. Rational Design of Aptamer-Tagged tRNAs. Int J Mol Sci 2020; 21:ijms21207793. [PMID: 33096801 PMCID: PMC7590224 DOI: 10.3390/ijms21207793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Reprogramming of the genetic code system is limited by the difficulty in creating new tRNA structures. Here, I developed translationally active tRNA variants tagged with a small hairpin RNA aptamer, using Escherichia coli reporter assay systems. As the tRNA chassis for engineering, I employed amber suppressor variants of allo-tRNAs having the 9/3 composition of the 12-base pair amino-acid acceptor branch as well as a long variable arm (V-arm). Although their V-arm is a strong binding site for seryl-tRNA synthetase (SerRS), insertion of a bulge nucleotide in the V-arm stem region prevented allo-tRNA molecules from being charged by SerRS with serine. The SerRS-rejecting allo-tRNA chassis were engineered to have another amino-acid identity of either alanine, tyrosine, or histidine. The tip of the V-arms was replaced with diverse hairpin RNA aptamers, which were recognized by their cognate proteins expressed in E. coli. A high-affinity interaction led to the sequestration of allo-tRNA molecules, while a moderate-affinity aptamer moiety recruited histidyl-tRNA synthetase variants fused with the cognate protein domain. The new design principle for tRNA-aptamer fusions will enhance radical and dynamic manipulation of the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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15
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Pernod K, Schaeffer L, Chicher J, Hok E, Rick C, Geslain R, Eriani G, Westhof E, Ryckelynck M, Martin F. The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity. Nucleic Acids Res 2020; 48:6170-6183. [PMID: 32266934 PMCID: PMC7293025 DOI: 10.1093/nar/gkaa221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022] Open
Abstract
Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.
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Affiliation(s)
- Ketty Pernod
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Laure Schaeffer
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Johana Chicher
- Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg - Esplanade, CNRS FRC1589, Université de Strasbourg, 2, allée Konrad Roentgen Descartes, F-67084 Strasbourg, France
| | - Eveline Hok
- Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA
| | - Christian Rick
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Renaud Geslain
- Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Eric Westhof
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Michael Ryckelynck
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
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16
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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] [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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17
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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] [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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18
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Kuncha SK, Venkadasamy VL, Amudhan G, Dahate P, Kola SR, Pottabathini S, Kruparani SP, Shekar PC, Sankaranarayanan R. Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia. eLife 2020; 9:58118. [PMID: 32463355 PMCID: PMC7302879 DOI: 10.7554/elife.58118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
The emergence of multicellularity in Animalia is associated with increase in ROS and expansion of tRNA-isodecoders. tRNA expansion leads to misselection resulting in a critical error of L-Ala mischarged onto tRNAThr, which is proofread by Animalia-specific-tRNA Deacylase (ATD) in vitro. Here we show that in addition to ATD, threonyl-tRNA synthetase (ThrRS) can clear the error in cellular scenario. This two-tier functional redundancy for translation quality control breaks down during oxidative stress, wherein ThrRS is rendered inactive. Therefore, ATD knockout cells display pronounced sensitivity through increased mistranslation of threonine codons leading to cell death. Strikingly, we identify the emergence of ATD along with the error inducing tRNA species starting from Choanoflagellates thus uncovering an important genomic innovation required for multicellularity that occurred in unicellular ancestors of animals. The study further provides a plausible regulatory mechanism wherein the cellular fate of tRNAs can be switched from protein biosynthesis to non-canonical functions. The first animals evolved around 750 million years ago from single-celled ancestors that were most similar to modern-day organisms called the Choanoflagellates. As animals evolved they developed more complex body plans consisting of multiple cells organized into larger structures known as tissues and organs. Over time cells also evolved increased levels of molecules called reactive oxygen species, which are involved in many essential cell processes but are toxic at high levels. Animal cells also contain more types of molecules known as transfer ribonucleic acids, or tRNAs for short, than Choanoflagellate cells and other single-celled organisms. These molecules deliver building blocks known as amino acids to the machinery that produces new proteins. To ensure the proteins are made correctly, it is important that tRNAs deliver specific amino acids to the protein-building machinery in the right order. Each type of tRNA usually only pairs with a specific type of amino acid, but sometimes the enzymes involved in this process can make mistakes. Therefore, cells contain proofreading enzymes that help remove incorrect amino acids on tRNAs. One such enzyme – called ATD – is only found in animals. Experiments in test tubes reported that ATD removes an amino acid called alanine from tRNAs that are supposed to carry threonine, but its precise role in living cells remained unclear. To address this question, Kuncha et al. studied proofreading enzymes in human kidney cells. The experiments showed that, in addition to ATD, a second enzyme known as ThrRS was also able to correct alanine substitutions for threonines on tRNAs. However, reactive oxygen species inactivated the proofreading ability of ThrRS, suggesting ATD plays an essential role in correcting errors in cells containing high levels of reactive oxygen species. These findings suggest that as organisms evolved multiple cells and the levels of tRNA and oxidative stress increased, this led to the appearance of a new proofreading enzyme. Further studies found that ATD originated around 900 million years ago, before Choanoflagellates and animals diverged, indicating these enzymes might have helped to shape the evolution of animals. The next step following on from this work will be to understand the role of ATD in the cells of organs that are known to have particularly high levels of reactive oxygen species, such as testis and ovaries.
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Affiliation(s)
- Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | | | - Priyanka Dahate
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sankara Rao Kola
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - P Chandra Shekar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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19
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Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code. Life (Basel) 2020; 10:life10030021. [PMID: 32131473 PMCID: PMC7151597 DOI: 10.3390/life10030021] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/13/2020] [Accepted: 02/27/2020] [Indexed: 02/07/2023] Open
Abstract
Life on Earth and the genetic code evolved around tRNA and the tRNA anticodon. We posit that the genetic code initially evolved to synthesize polyglycine as a cross-linking agent to stabilize protocells. We posit that the initial amino acids to enter the code occupied larger sectors of the code that were then invaded by incoming amino acids. Displacements of amino acids follow selection rules. The code sectored from a glycine code to a four amino acid code to an eight amino acid code to an ~16 amino acid code to the standard 20 amino acid code with stops. The proposed patterns of code sectoring are now most apparent from patterns of aminoacyl-tRNA synthetase evolution. The Elongation Factor-Tu GTPase anticodon-codon latch that checks the accuracy of translation appears to have evolved at about the eight amino acid to ~16 amino acid stage. Before evolution of the EF-Tu latch, we posit that both the 1st and 3rd anticodon positions were wobble positions. The genetic code evolved via tRNA charging errors and via enzymatic modifications of amino acids joined to tRNAs, followed by tRNA and aminoacyl-tRNA synthetase differentiation. Fidelity mechanisms froze the code by inhibiting further innovation.
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20
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Ślęczkowski ML, Segers I, Liu Y, Palmans ARA. Sequence-defined l-glutamamide oligomers with pendant supramolecular motifs via iterative synthesis and orthogonal post-functionalization. Polym Chem 2020. [DOI: 10.1039/d0py01157f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
One of the great challenges in polymer chemistry is to achieve discrete and sequence-defined synthetic polymers that fold in defined conformations and form well-defined three-dimensional structured particles.
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Affiliation(s)
- Marcin L. Ślęczkowski
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Laboratory of Macromolecular and Organic Chemistry
| | - Ian Segers
- Laboratory of Macromolecular and Organic Chemistry
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
| | - Yiliu Liu
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Laboratory of Macromolecular and Organic Chemistry
| | - Anja R. A. Palmans
- Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
- Laboratory of Macromolecular and Organic Chemistry
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21
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The evolution of aminoacyl-tRNA synthetases: From dawn to LUCA. BIOLOGY OF AMINOACYL-TRNA SYNTHETASES 2020; 48:11-37. [DOI: 10.1016/bs.enz.2020.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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22
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Formation of tRNA Wobble Inosine in Humans Is Disrupted by a Millennia-Old Mutation Causing Intellectual Disability. Mol Cell Biol 2019; 39:MCB.00203-19. [PMID: 31263000 PMCID: PMC6751630 DOI: 10.1128/mcb.00203-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022] Open
Abstract
The formation of inosine at the wobble position of eukaryotic tRNAs is an essential modification catalyzed by the ADAT2/ADAT3 complex. In humans, a valine-to-methionine mutation (V144M) in ADAT3 that originated ∼1,600 years ago is the most common cause of autosomal recessive intellectual disability (ID) in Arabia. While the mutation is predicted to affect protein structure, the molecular and cellular effects of the V144M mutation are unknown. The formation of inosine at the wobble position of eukaryotic tRNAs is an essential modification catalyzed by the ADAT2/ADAT3 complex. In humans, a valine-to-methionine mutation (V144M) in ADAT3 that originated ∼1,600 years ago is the most common cause of autosomal recessive intellectual disability (ID) in Arabia. While the mutation is predicted to affect protein structure, the molecular and cellular effects of the V144M mutation are unknown. Here, we show that cell lines derived from ID-affected individuals expressing only ADAT3-V144M exhibit decreased wobble inosine in certain tRNAs. Moreover, extracts from the same cell lines of ID-affected individuals display a severe reduction in tRNA deaminase activity. While ADAT3-V144M maintains interactions with ADAT2, the purified ADAT2/3-V144M complexes exhibit defects in activity. Notably, ADAT3-V144M exhibits an increased propensity to form aggregates associated with cytoplasmic chaperonins that can be suppressed by ADAT2 overexpression. These results identify a key role for ADAT2-dependent folding of ADAT3 in wobble inosine modification and indicate that proper formation of an active ADAT2/3 complex is crucial for proper neurodevelopment.
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23
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A tRNA-mimic Strategy to Explore the Role of G34 of tRNA Gly in Translation and Codon Frameshifting. Int J Mol Sci 2019; 20:ijms20163911. [PMID: 31405256 PMCID: PMC6720975 DOI: 10.3390/ijms20163911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/20/2022] Open
Abstract
Decoding of the 61 sense codons of the genetic code requires a variable number of tRNAs that establish codon-anticodon interactions. Thanks to the wobble base pairing at the third codon position, less than 61 different tRNA isoacceptors are needed to decode the whole set of codons. On the tRNA, a subtle distribution of nucleoside modifications shapes the anticodon loop structure and participates to accurate decoding and reading frame maintenance. Interestingly, although the 61 anticodons should exist in tRNAs, a strict absence of some tRNAs decoders is found in several codon families. For instance, in Eukaryotes, G34-containing tRNAs translating 3-, 4- and 6-codon boxes are absent. This includes tRNA specific for Ala, Arg, Ile, Leu, Pro, Ser, Thr, and Val. tRNAGly is the only exception for which in the three kingdoms, a G34-containing tRNA exists to decode C3 and U3-ending codons. To understand why G34-tRNAGly exists, we analysed at the genome wide level the codon distribution in codon +1 relative to the four GGN Gly codons. When considering codon GGU, a bias was found towards an unusual high usage of codons starting with a G whatever the amino acid at +1 codon. It is expected that GGU codons are decoded by G34-containing tRNAGly, decoding also GGC codons. Translation studies revealed that the presence of a G at the first position of the downstream codon reduces the +1 frameshift by stabilizing the G34•U3 wobble interaction. This result partially explains why G34-containing tRNAGly exists in Eukaryotes whereas all the other G34-containing tRNAs for multiple codon boxes are absent.
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24
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Southworth J, Armitage P, Fallon B, Dawson H, Bryk J, Carr M. Patterns of Ancestral Animal Codon Usage Bias Revealed through Holozoan Protists. Mol Biol Evol 2019; 35:2499-2511. [PMID: 30169693 PMCID: PMC6188563 DOI: 10.1093/molbev/msy157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Choanoflagellates and filastereans are the closest known single celled relatives of Metazoa within Holozoa and provide insight into how animals evolved from their unicellular ancestors. Codon usage bias has been extensively studied in metazoans, with both natural selection and mutation pressure playing important roles in different species. The disparate nature of metazoan codon usage patterns prevents the reconstruction of ancestral traits. However, traits conserved across holozoan protists highlight characteristics in the unicellular ancestors of Metazoa. Presented here are the patterns of codon usage in the choanoflagellates Monosiga brevicollis and Salpingoeca rosetta, as well as the filasterean Capsaspora owczarzaki. Codon usage is shown to be remarkably conserved. Highly biased genes preferentially use GC-ending codons, however there is limited evidence this is driven by local mutation pressure. The analyses presented provide strong evidence that natural selection, for both translational accuracy and efficiency, dominates codon usage bias in holozoan protists. In particular, the signature of selection for translational accuracy can be detected even in the most weakly biased genes. Biased codon usage is shown to have coevolved with the tRNA species, with optimal codons showing complementary binding to the highest copy number tRNA genes. Furthermore, tRNA modification is shown to be a common feature for amino acids with higher levels of degeneracy and highly biased genes show a strong preference for using modified tRNAs in translation. The translationally optimal codons defined here will be of benefit to future transgenics work in holozoan protists, as their use should maximise protein yields from edited transgenes.
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Affiliation(s)
- Jade Southworth
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Paul Armitage
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Brandon Fallon
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Holly Dawson
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Jaroslaw Bryk
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Martin Carr
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, United Kingdom
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25
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A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code. Life (Basel) 2019; 9:life9020037. [PMID: 31060233 PMCID: PMC6616430 DOI: 10.3390/life9020037] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 11/25/2022] Open
Abstract
Pathways of standard genetic code evolution remain conserved and apparent, particularly upon analysis of aminoacyl-tRNA synthetase (aaRS) lineages. Despite having incompatible active site folds, class I and class II aaRS are homologs by sequence. Specifically, structural class IA aaRS enzymes derive from class IIA aaRS enzymes by in-frame extension of the protein N-terminus and by an alternate fold nucleated by the N-terminal extension. The divergence of aaRS enzymes in the class I and class II clades was analyzed using the Phyre2 protein fold recognition server. The class I aaRS radiated from the class IA enzymes, and the class II aaRS radiated from the class IIA enzymes. The radiations of aaRS enzymes bolster the coevolution theory for evolution of the amino acids, tRNAomes, the genetic code, and aaRS enzymes and support a tRNA anticodon-centric perspective. We posit that second- and third-position tRNA anticodon sequence preference (C>(U~G)>A) powerfully selected the sectoring pathway for the code. GlyRS-IIA appears to have been the primordial aaRS from which all aaRS enzymes evolved, and glycine appears to have been the primordial amino acid around which the genetic code evolved.
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26
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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 (NEW YORK, N.Y.) 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] [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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27
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Dans PD, Gallego D, Balaceanu A, Darré L, Gómez H, Orozco M. Modeling, Simulations, and Bioinformatics at the Service of RNA Structure. Chem 2019. [DOI: 10.1016/j.chempr.2018.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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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] [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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29
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Pak D, Kim Y, Burton ZF. Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code. Transcription 2018; 9:205-224. [PMID: 29727262 PMCID: PMC6104698 DOI: 10.1080/21541264.2018.1467718] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/13/2018] [Indexed: 02/08/2023] Open
Abstract
The genetic code sectored via tRNA charging errors, and the code progressed toward closure and universality because of evolution of aminoacyl-tRNA synthetase (aaRS) fidelity and translational fidelity mechanisms. Class I and class II aaRS folds are identified as homologs. From sequence alignments, a structurally conserved Zn-binding domain common to class I and class II aaRS was identified. A model for the class I and class II aaRS alternate folding pathways is posited. Five mechanisms toward code closure are highlighted: 1) aaRS proofreading to remove mischarged amino acids from tRNA; 2) accurate aaRS active site specification of amino acid substrates; 3) aaRS-tRNA anticodon recognition; 4) conformational coupling proofreading of the anticodon-codon interaction; and 5) deamination of tRNA wobble adenine to inosine. In tRNA anticodons there is strong wobble sequence preference that results in a broader spectrum of contacts to synonymous mRNA codon wobble bases. Adenine is excluded from the anticodon wobble position of tRNA unless it is modified to inosine. Uracil is generally preferred to cytosine in the tRNA anticodon wobble position. Because of wobble ambiguity when tRNA reads mRNA, the maximal coding capacity of the three nucleotide code read by tRNA is 31 amino acids + stops.
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Affiliation(s)
- Daewoo Pak
- Center for Statistical Training and Consulting, Michigan State University, E. Lansing, MI 48824, USA
| | | | - Zachary F. Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, E. Lansing, MI 48824-1319, USA
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30
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Abstract
We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code.
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Affiliation(s)
- Daewoo Pak
- a Center for Statistical Training and Consulting , Michigan State University , E. Lansing , MI 48824 , USA
| | - Nan Du
- b Computer Science and Engineering , Michigan State University , E. Lansing , MI 48824
| | | | - Yanni Sun
- b Computer Science and Engineering , Michigan State University , E. Lansing , MI 48824
| | - Zachary F Burton
- d Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI 48824-1319
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31
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A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia. Nat Commun 2018; 9:511. [PMID: 29410408 PMCID: PMC5802732 DOI: 10.1038/s41467-017-02204-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/13/2017] [Indexed: 01/07/2023] Open
Abstract
D-aminoacyl-tRNA deacylase (DTD), a bacterial/eukaryotic trans-editing factor, removes D-amino acids mischarged on tRNAs and achiral glycine mischarged on tRNAAla. An invariant cross-subunit Gly-cisPro motif forms the mechanistic basis of L-amino acid rejection from the catalytic site. Here, we present the identification of a DTD variant, named ATD (Animalia-specific tRNA deacylase), that harbors a Gly-transPro motif. The cis-to-trans switch causes a "gain of function" through L-chiral selectivity in ATD resulting in the clearing of L-alanine mischarged on tRNAThr(G4•U69) by eukaryotic AlaRS. The proofreading activity of ATD is conserved across diverse classes of phylum Chordata. Animalia genomes enriched in tRNAThr(G4•U69) genes are in strict association with the presence of ATD, underlining the mandatory requirement of a dedicated factor to proofread tRNA misaminoacylation. The study highlights the emergence of ATD during genome expansion as a key event associated with the evolution of Animalia.
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32
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The evolution of the genetic code: Impasses and challenges. Biosystems 2018; 164:217-225. [DOI: 10.1016/j.biosystems.2017.10.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 01/17/2023]
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33
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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: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [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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34
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The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat Rev Mol Cell Biol 2017; 19:45-58. [PMID: 28875994 DOI: 10.1038/nrm.2017.77] [Citation(s) in RCA: 277] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The discovery of the genetic code and tRNAs as decoders of the code transformed life science. However, after establishing the role of tRNAs in protein synthesis, the field moved to other parts of the RNA world. Now, tRNA research is blooming again, with demonstration of the involvement of tRNAs in various other pathways beyond translation and in adapting translation to environmental cues. These roles are linked to the presence of tRNA sequence variants known as isoacceptors and isodecoders, various tRNA base modifications, the versatility of protein binding partners and tRNA fragmentation events, all of which collectively create an incalculable complexity. This complexity provides a vast repertoire of tRNA species that can serve various functions in cellular homeostasis and in adaptation of cellular functions to changing environments, and it likely arose from the fundamental role of RNAs in early evolution.
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35
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What Froze the Genetic Code? Life (Basel) 2017; 7:life7020014. [PMID: 28379164 PMCID: PMC5492136 DOI: 10.3390/life7020014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 03/27/2017] [Accepted: 04/03/2017] [Indexed: 11/16/2022] Open
Abstract
The frozen accident theory of the Genetic Code was a proposal by Francis Crick that attempted to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. Fifty years later, it is clear that variations to the universal Genetic Code exist in nature and that translation is not limited to twenty amino acids. However, given the astonishing diversity of life on earth, and the extended evolutionary time that has taken place since the emergence of the extant Genetic Code, the idea that the translation apparatus is for the most part immobile remains true. Here, we will offer a potential explanation to the reason why the code has remained mostly stable for over three billion years, and discuss some of the mechanisms that allow species to overcome the intrinsic functional limitations of the protein synthesis machinery.
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36
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Nemzer LR. A binary representation of the genetic code. Biosystems 2017; 155:10-19. [PMID: 28300609 DOI: 10.1016/j.biosystems.2017.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/23/2022]
Abstract
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA bases is assigned a unique 2-bit identifier, so that the 64 triplet codons are each indexed by a 6-bit label. The ordering of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. In this system, transition and transversion mutations are naturally expressed as binary operations, and the severities of the different point mutations can be analyzed. Using a principal component analysis, it is shown that the physicochemical properties of amino acids related to protein folding also correlate with certain bit positions of their respective labels. Thus, the likelihood for a point mutation to be conservative, and less likely to cause a change in protein functionality, can be estimated.
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Affiliation(s)
- Louis R Nemzer
- Department of Chemistry and Physics, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
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37
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Maraia RJ, Arimbasseri AG. Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon-Codon Use. Biomolecules 2017; 7:biom7010026. [PMID: 28282871 PMCID: PMC5372738 DOI: 10.3390/biom7010026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/24/2017] [Indexed: 01/24/2023] Open
Abstract
Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias. Here, we review convergent evidence that suggest that expansion of the eukaryotic tRNAome was supported by its dedicated RNA polymerase III transcription system and coupling to the precursor-tRNA chaperone, La protein. We also review aspects of eukaryotic tRNAome evolution involving G34/A34 anticodon-sparing, relation to A34 modification to inosine, biased codon use and regulatory information in the redundancy (synonymous) component of the genetic code. We then review interdependent anticodon loop modifications involving position 37 in eukaryotes. This includes the eukaryote-specific tRNA modification, 3-methylcytidine-32 (m3C32) and the responsible gene, TRM140 and homologs which were duplicated and subspecialized for isoacceptor-specific substrates and dependence on i6A37 or t6A37. The genetics of tRNA function is relevant to health directly and as disease modifiers.
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Affiliation(s)
- Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
- Commissioned Corps, U.S. Public Health Service, Rockville, MD, 20016, USA.
| | - Aneeshkumar G Arimbasseri
- Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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38
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Darré L, Ivani I, Dans PD, Gómez H, Hospital A, Orozco M. Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA. J Am Chem Soc 2016; 138:16355-16363. [DOI: 10.1021/jacs.6b09471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Leonardo Darré
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Ivan Ivani
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Pablo D. Dans
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Hansel Gómez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
- Department
of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
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