101
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Hurst T, Chen SJ. Deciphering nucleotide modification-induced structure and stability changes. RNA Biol 2021; 18:1920-1930. [PMID: 33586616 DOI: 10.1080/15476286.2021.1882179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nucleotide modification in RNA controls a bevy of biological processes, including RNA degradation, gene expression, and gene editing. In turn, misregulation of modified nucleotides is associated with a host of chronic diseases and disorders. However, the molecular mechanisms driving these processes remain poorly understood. To partially address this knowledge gap, we used alchemical and temperature replica exchange molecular dynamics (TREMD) simulations on an RNA duplex and an analogous hairpin to probe the structural effects of modified and/or mutant nucleotides. The simulations successfully predict the modification/mutation-induced relative free energy change for complementary duplex formation, and structural analyses highlight mechanisms driving stability changes. Furthermore, TREMD simulations for a hairpin-forming RNA with and without modification provide reliable estimations of the energy landscape. Illuminating the impact of methylated and/or mutated nucleotides on the structure-function relationship and the folding energy landscape, the simulations provide insights into modification-induced alterations to the folding mechanics of the hairpin. The results here may be biologically significant as hairpins are widespread structure motifs that play critical roles in gene expression and regulation. Specifically, the tetraloop of the probed hairpin is phylogenetically abundant, and the stem mirrors a miRNA seed region whose modification has been implicated in epilepsy pathogenesis.
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Affiliation(s)
- Travis Hurst
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
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102
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Jonkhout N, Cruciani S, Santos Vieira HG, Tran J, Liu H, Liu G, Pickford R, Kaczorowski D, Franco GR, Vauti F, Camacho N, Abedini SS, Najmabadi H, Ribas de Pouplana L, Christ D, Schonrock N, Mattick JS, Novoa EM. Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation. RNA Biol 2021; 18:1905-1919. [PMID: 33499731 DOI: 10.1080/15476286.2021.1881291] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory formation. However, whether additional RNA modifications may be playing a role in neuronal functions and in response to environmental queues is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m2,2G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNAAla(AGC) isodecoders at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes may play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.
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Affiliation(s)
- Nicky Jonkhout
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Sonia Cruciani
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Julia Tran
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Huanle Liu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Ganqiang Liu
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Current Address: School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, Australia
| | | | - Gloria R Franco
- Departamento De Bioquímica E Imunologia, Universidade Federal De Minas Gerais,Belo Horizonte,Minas Gerais, Brazil
| | - Franz Vauti
- Division of Cellular & Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Noelia Camacho
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain
| | - Seyedeh Sedigheh Abedini
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nicole Schonrock
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Eva Maria Novoa
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
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103
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Termathe M, Leidel SA. Urm1: A Non-Canonical UBL. Biomolecules 2021; 11:biom11020139. [PMID: 33499055 PMCID: PMC7911844 DOI: 10.3390/biom11020139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/10/2023] Open
Abstract
Urm1 (ubiquitin related modifier 1) is a molecular fossil in the class of ubiquitin-like proteins (UBLs). It encompasses characteristics of classical UBLs, such as ubiquitin or SUMO (small ubiquitin-related modifier), but also of bacterial sulfur-carrier proteins (SCP). Since its main function is to modify tRNA, Urm1 acts in a non-canonical manner. Uba4, the activating enzyme of Urm1, contains two domains: a classical E1-like domain (AD), which activates Urm1, and a rhodanese homology domain (RHD). This sulfurtransferase domain catalyzes the formation of a C-terminal thiocarboxylate on Urm1. Thiocarboxylated Urm1 is the sulfur donor for 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), a chemical nucleotide modification at the wobble position in tRNA. This thio-modification is conserved in all domains of life and optimizes translation. The absence of Urm1 increases stress sensitivity in yeast triggered by defects in protein homeostasis, a hallmark of neurological defects in higher organisms. In contrast, elevated levels of tRNA modifying enzymes promote the appearance of certain types of cancer and the formation of metastasis. Here, we summarize recent findings on the unique features that place Urm1 at the intersection of UBL and SCP and make Urm1 an excellent model for studying the evolution of protein conjugation and sulfur-carrier systems.
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Affiliation(s)
- Martin Termathe
- Institute of Biochemistry, Protein Biochemistry and Photobiocatalysis, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany;
| | - Sebastian A. Leidel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Correspondence:
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104
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Kimura S. Distinct evolutionary pathways for the synthesis and function of tRNA modifications. Brief Funct Genomics 2021; 20:125-134. [PMID: 33454776 DOI: 10.1093/bfgp/elaa027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022] Open
Abstract
Transfer ribonucleicacids (RNAs) (tRNAs) are essential adaptor molecules for translation. The functions and stability of tRNAs are modulated by their post-transcriptional modifications (tRNA modifications). Each domain of life has a specific set of modifications that include ones shared in multiple domains and ones specific to a domain. In some cases, different tRNA modifications across domains have similar functions to each other. Recent studies uncovered that distinct enzymes synthesize the same modification in different organisms, suggesting that such modifications are acquired through independent evolution. In this short review, I outline the mechanisms by which various modifications contribute to tRNA function, including modulation of decoding and tRNA stability, using recent findings. I also focus on modifications that are synthesized by distinct biosynthetic pathways.
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Affiliation(s)
- Satoshi Kimura
- Dr Matthew Waldor's lab at the Brigham and Women's Hospital. He completed his PhD and early postdoc work in Dr Tsutomu Suzuki's lab at the University of Tokyo
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105
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tRNA Biology in the Pathogenesis of Diabetes: Role of Genetic and Environmental Factors. Int J Mol Sci 2021; 22:ijms22020496. [PMID: 33419045 PMCID: PMC7825315 DOI: 10.3390/ijms22020496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 02/07/2023] Open
Abstract
The global rise in type 2 diabetes results from a combination of genetic predisposition with environmental assaults that negatively affect insulin action in peripheral tissues and impair pancreatic β-cell function and survival. Nongenetic heritability of metabolic traits may be an important contributor to the diabetes epidemic. Transfer RNAs (tRNAs) are noncoding RNA molecules that play a crucial role in protein synthesis. tRNAs also have noncanonical functions through which they control a variety of biological processes. Genetic and environmental effects on tRNAs have emerged as novel contributors to the pathogenesis of diabetes. Indeed, altered tRNA aminoacylation, modification, and fragmentation are associated with β-cell failure, obesity, and insulin resistance. Moreover, diet-induced tRNA fragments have been linked with intergenerational inheritance of metabolic traits. Here, we provide a comprehensive review of how perturbations in tRNA biology play a role in the pathogenesis of monogenic and type 2 diabetes.
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106
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Debiec K, Sochacka E. Efficient access to 3'- O-phosphoramidite derivatives of tRNA related N 6-threonylcarbamoyladenosine (t 6A) and 2-methylthio- N 6-threonylcarbamoyladenosine (ms 2t 6A). RSC Adv 2021; 11:1992-1999. [PMID: 35424152 PMCID: PMC8693639 DOI: 10.1039/d0ra09803e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
An efficient method of ureido linkage formation during epimerization-free one-pot synthesis of protected hypermodified N 6-threonylcarbamoyladenosine (t6A) and its 2-SMe analog (ms2t6A) was developed. The method is based on a Tf2O-mediated direct conversion of the N-Boc-protecting group of N-Boc-threonine into the isocyanate derivative, followed by reaction with the N 6 exo-amine function of the sugar protected nucleoside (yield 86-94%). Starting from 2',3',5'-tri-O-acetyl protected adenosine or 2-methylthioadenosine, the corresponding 3'-O-phosphoramidite monomers were obtained in 48% and 42% overall yield (5 step synthesis). In an analogous synthesis, using the 2'-O-(tert-butyldimethylsilyl)-3',5'-O-(di-tert-butylsilylene) protection system at the adenosine ribose moiety, the t6A-phosphoramidite monomer was obtained in a less laborious manner and in a remarkably better yield of 74%.
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Affiliation(s)
- Katarzyna Debiec
- Institute of Organic Chemistry, Lodz University of Technology Zeromskiego 116 90-924 Lodz Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology Zeromskiego 116 90-924 Lodz Poland
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107
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Haruehanroengra P, Vangaveti S, Ranganathan SV, Mao S, Su MD, Chen AA, Sheng J. Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex. iScience 2020; 23:101866. [PMID: 33319183 PMCID: PMC7726334 DOI: 10.1016/j.isci.2020.101866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/16/2020] [Accepted: 11/20/2020] [Indexed: 12/20/2022] Open
Abstract
Geranylation is a hydrophobic modification discovered in several bacteria tRNAs with the function of promoting codon bias during translation. However, why nature selects this C10-geranyl group remains a question. We conduct synthesis, UV-thermal denaturation, and molecular simulation studies in RNA duplexes and reveal possible reasons behind this natural selection. Among methyl-(C1), dimethylallyl-(C5), geranyl-(C10), and farnesyl-(C15) modified 2-thiouridines, only geranyl-group promotes U:G over U:A pair. Molecular simulation shows all the modified terpene groups point to the minor groove of RNA duplexes. The discrimination between U:G and U:A pairs derives from the difference in hydrogen bonding and interactions of the chain with the hydrophobic area in the minor groove. Geranyl group has perfect length to discriminate U:G and U:A pairs, whereas the others are either too long or too short to achieve the same behavior. This work indicates that geranyl group cannot be replaced by other terpene groups in promoting codon-specificity. Geranyl group on ges2U has perfect length to enhance binding to G over A in RNA Other ges2U analogues has no pairing preference between G or A MD shows the molecular dynamic behavior of different terpene chains in RNA duplex
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Affiliation(s)
- Phensinee Haruehanroengra
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | | | - Song Mao
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Max Daniel Su
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Alan A Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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108
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Bose S, Suescún AV, Song J, Castillo-González C, Aklilu BB, Branham E, Lynch R, Shippen DE. tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana. PLANT CELL REPORTS 2020; 39:1669-1685. [PMID: 32959123 PMCID: PMC7655638 DOI: 10.1007/s00299-020-02594-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE: tRNA Adenosine Deaminase 3 helps to sustain telomere tracts in a telomerase-independent fashion, likely through regulating cellular metabolism. Telomere length maintenance is influenced by a complex web of chromatin and metabolism-related factors. We previously reported that a lncRNA termed AtTER2 regulates telomerase activity in Arabidopsis thaliana in response to DNA damage. AtTER2 was initially shown to partially overlap with the 5' UTR of the tRNA ADENOSINE DEAMINASE 3 (TAD3) gene. However, updated genome annotation showed that AtTER2 was completely embedded in TAD3, raising the possibility that phenotypes ascribed to AtTER2 could be derived from TAD3. Here we show through strand-specific RNA-Seq, strand-specific qRT-PCR and bioinformatic analyses that AtTER2 does not encode a stable lncRNA. Further examination of the original tad3 (ter2-1/tad3-1) mutant revealed expression of an antisense transcript driven by a cryptic promoter in the T-DNA. Hence, a new hypomorphic allele of TAD3 (tad3-2) was examined. tad3-2 mutants showed hypersensitivity to DNA damage, but no deregulation of telomerase, suggesting that the telomerase phenotype of tad3-1 mutants reflects an off-target effect. Unexpectedly, however, tad3-2 plants displayed progressive loss of telomeric DNA over successive generations that was not accompanied by alteration of terminal architecture or end protection. The phenotype was exacerbated in plants lacking the telomerase processivity factor POT1a, indicating that TAD3 promotes telomere maintenance through a non-canonical, telomerase-independent pathway. The transcriptome of tad3-2 mutants revealed significant dysregulation of genes involved in auxin signaling and glucosinolate biosynthesis, pathways that intersect the stress response, cell cycle regulation and DNA metabolism. These findings indicate that the TAD3 locus indirectly contributes to telomere length homeostasis by altering the metabolic profile in Arabidopsis.
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Affiliation(s)
- Sreyashree Bose
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ana Victoria Suescún
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Facultad de Ciencias, Instituto de Ciencias Ambientales Y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | | | - Behailu Birhanu Aklilu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- KWS Gateway Research Center, LLC, 1005 N Warson Rd, BRDG Park, St. Louis, MO, 63132, USA
| | - Erica Branham
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ryan Lynch
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Department of Biochemistry and Biophysics, 300 Olsen Blvd, Room 413, College Station, TX, 77843-2128, USA.
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109
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Funk HM, Zhao R, Thomas M, Spigelmyer SM, Sebree NJ, Bales RO, Burchett JB, Mamaril JB, Limbach PA, Guy MP. Identification of the enzymes responsible for m2,2G and acp3U formation on cytosolic tRNA from insects and plants. PLoS One 2020; 15:e0242737. [PMID: 33253256 PMCID: PMC7704012 DOI: 10.1371/journal.pone.0242737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/06/2020] [Indexed: 11/18/2022] Open
Abstract
Posttranscriptional modification of tRNA is critical for efficient protein translation and proper cell growth, and defects in tRNA modifications are often associated with human disease. Although most of the enzymes required for eukaryotic tRNA modifications are known, many of these enzymes have not been identified and characterized in several model multicellular eukaryotes. Here, we present two related approaches to identify the genes required for tRNA modifications in multicellular organisms using primer extension assays with fluorescent oligonucleotides. To demonstrate the utility of these approaches we first use expression of exogenous genes in yeast to experimentally identify two TRM1 orthologs capable of forming N2,N2-dimethylguanosine (m2,2G) on residue 26 of cytosolic tRNA in the model plant Arabidopsis thaliana. We also show that a predicted catalytic aspartate residue is required for function in each of the proteins. We next use RNA interference in cultured Drosophila melanogaster cells to identify the gene required for m2,2G26 formation on cytosolic tRNA. Additionally, using these approaches we experimentally identify D. melanogaster gene CG10050 as the corresponding ortholog of human DTWD2, which encodes the protein required for formation of 3-amino-3-propylcarboxyuridine (acp3U) on residue 20a of cytosolic tRNA. We further show that A. thaliana gene AT2G41750 can form acp3U20b on an A. thaliana tRNA expressed in yeast cells, and that the aspartate and tryptophan residues in the DXTW motif of this protein are required for modification activity. These results demonstrate that these approaches can be used to study tRNA modification enzymes.
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Affiliation(s)
- Holly M. Funk
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Maggie Thomas
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Sarah M. Spigelmyer
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Nichlas J. Sebree
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Regan O. Bales
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Jamison B. Burchett
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Justen B. Mamaril
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Michael P. Guy
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
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110
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Ramos J, Proven M, Halvardson J, Hagelskamp F, Kuchinskaya E, Phelan B, Bell R, Kellner SM, Feuk L, Thuresson AC, Fu D. Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder. RNA (NEW YORK, N.Y.) 2020; 26:1654-1666. [PMID: 32763916 PMCID: PMC7566568 DOI: 10.1261/rna.076380.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The deamination of adenosine to inosine at the wobble position of tRNA is an essential post-transcriptional RNA modification required for wobble decoding in bacteria and eukaryotes. In humans, the wobble inosine modification is catalyzed by the heterodimeric ADAT2/3 complex. Here, we describe novel pathogenic ADAT3 variants impairing adenosine deaminase activity through a distinct mechanism that can be corrected through expression of the heterodimeric ADAT2 subunit. The variants were identified in a family in which all three siblings exhibit intellectual disability linked to biallelic variants in the ADAT3 locus. The biallelic ADAT3 variants result in a missense variant converting alanine to valine at a conserved residue or the introduction of a premature stop codon in the deaminase domain. Fibroblast cells derived from two ID-affected individuals exhibit a reduction in tRNA wobble inosine levels and severely diminished adenosine tRNA deaminase activity. Notably, the ADAT3 variants exhibit impaired interaction with the ADAT2 subunit and alterations in ADAT2-dependent nuclear localization. Based upon these findings, we find that tRNA adenosine deaminase activity and wobble inosine modification can be rescued in patient cells by overexpression of the ADAT2 catalytic subunit. These results uncover a key role for the inactive ADAT3 deaminase domain in proper assembly with ADAT2 and demonstrate that ADAT2/3 nuclear import is required for maintaining proper levels of the wobble inosine modification in tRNA.
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Affiliation(s)
- Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Melissa Proven
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | | | - Ekaterina Kuchinskaya
- Department of Clinical Genetics, and Department of Clinical Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Benjamin Phelan
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Ryan Bell
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | | | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | - Ann-Charlotte Thuresson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
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111
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Naseer MI, Abdulkareem AA, Jan MM, Chaudhary AG, Alharazy S, AlQahtani MH. Next generation sequencing reveals novel homozygous frameshift in PUS7 and splice acceptor variants in AASS gene leading to intellectual disability, developmental delay, dysmorphic feature and microcephaly. Saudi J Biol Sci 2020; 27:3125-3131. [PMID: 33100873 PMCID: PMC7569139 DOI: 10.1016/j.sjbs.2020.09.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/30/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022] Open
Abstract
Intellectual developmental disorder with abnormal behavior, microcephaly and short stature (IDDABS), (OMIM# 618342) is an autosomal recessive condition described as developmental delay, poor or absent speech, intellectual disability, short stature, mild to progressive microcephaly, delayed psychomotor development, hyperactivity, seizure, along with mild to swear aggressive behavior. Homozygous frameshift mutation in Pseudouridine Synthase 7, Putative; (PUS7) OMIM# 616,261 NM_019042.3 and splice acceptor variants in Alpha-Aminoadipic Semialdehyde Synthase; (AASS) OMIM# 605,113 NM_005763.3 was funded. Whole exome sequencing (WES) technique was used as tool to identify the molecular diagnostic test. Different bioinformatics analysis done for WES data and we identified two novel mutations one as frameshift mutation c.606_607delGA, p.Ser282CysfsTer9 in the PUS7 gene and splice acceptor variants c.1767–1 G > A in the AASS gene has been reported. The pattern of family segregation maintained the pathogenicity of this variation associated with abnormal behavior, intellectual developmental disorder, microcephaly along with short stature IDDABS. Further, the WES data was validated in the family having other affected individuals and healthy controls (n = 100) was done using Sanger sequencing. Finally, our results further explained the role of WES in the disease diagnosis and elucidated that the mutation in PUS7 and AASS genes may lead an important role for the development of IDDABS in Saudi family.
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Affiliation(s)
- Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | | | - Mohammed M Jan
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Box 80215, Jeddah 21589, Saudi Arabia
| | - Adeel G Chaudhary
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Genetics, King Fahad General Hospital, 21589 Jeddah, Saudi Arabia.,Center for Innovation in Personalized Medicine, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Shatha Alharazy
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad H AlQahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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112
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Liu J, An Z, Luo J, Li J, Li F, Zhang Z. Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite. Bioinformatics 2020; 36:2033-2039. [PMID: 31794005 PMCID: PMC7141862 DOI: 10.1093/bioinformatics/btz900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/07/2019] [Accepted: 11/29/2019] [Indexed: 01/17/2023] Open
Abstract
Motivation RNA 5-methylcytosine (m5C) is a type of post-transcriptional modification that may be involved in numerous biological processes and tumorigenesis. RNA m5C can be profiled at single-nucleotide resolution by high-throughput sequencing of RNA treated with bisulfite (RNA-BisSeq). However, the exploration of transcriptome-wide profile and potential function of m5C in splicing remains to be elucidated due to lack of isoform level m5C quantification tool. Results We developed a computational package to quantify Epitranscriptomal RNA m5C at the transcript isoform level (named Episo). Episo consists of three tools: mapper, quant and Bisulfitefq, for mapping, quantifying and simulating RNA-BisSeq data, respectively. The high accuracy of Episo was validated using an improved m5C-specific methylated RNA immunoprecipitation (meRIP) protocol, as well as a set of in silico experiments. By applying Episo to public human and mouse RNA-BisSeq data, we found that the RNA m5C is not evenly distributed among the transcript isoforms, implying the m5C may subject to be regulated at isoform level. Availability and implementation Episo is released under the GNU GPLv3+ license. The resource code Episo is freely accessible from https://github.com/liujunfengtop/Episo (with Tophat/cufflink) and https://github.com/liujunfengtop/Episo/tree/master/Episo_Kallisto (with Kallisto). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Junfeng Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ziyang An
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianjun Luo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Feifei Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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113
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Pabis M, Termathe M, Ravichandran KE, Kienast SD, Krutyhołowa R, Sokołowski M, Jankowska U, Grudnik P, Leidel SA, Glatt S. Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation. EMBO J 2020; 39:e105087. [PMID: 32901956 PMCID: PMC7527816 DOI: 10.15252/embj.2020105087] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/26/2022] Open
Abstract
The chemical modification of tRNA bases by sulfur is crucial to tune translation and to optimize protein synthesis. In eukaryotes, the ubiquitin‐related modifier 1 (Urm1) pathway is responsible for the synthesis of 2‐thiolated wobble uridine (U34). During the key step of the modification cascade, the E1‐like activating enzyme ubiquitin‐like protein activator 4 (Uba4) first adenylates and thiocarboxylates the C‐terminus of its substrate Urm1. Subsequently, activated thiocarboxylated Urm1 (Urm1‐COSH) can serve as a sulfur donor for specific tRNA thiolases or participate in ubiquitin‐like conjugation reactions. Structural and mechanistic details of Uba4 and Urm1 have remained elusive but are key to understand the evolutionary branch point between ubiquitin‐like proteins (UBL) and sulfur‐relay systems. Here, we report the crystal structures of full‐length Uba4 and its heterodimeric complex with its substrate Urm1. We show how the two domains of Uba4 orchestrate recognition, binding, and thiocarboxylation of the C‐terminus of Urm1. Finally, we uncover how the catalytic domains of Uba4 communicate efficiently during the reaction cycle and identify a mechanism that enables Uba4 to protect itself against self‐conjugation with its own product, namely activated Urm1‐COSH.
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Affiliation(s)
- Marta Pabis
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Martin Termathe
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Keerthiraju E Ravichandran
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Sandra D Kienast
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mikołaj Sokołowski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Przemysław Grudnik
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
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114
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Epigenetic loss of the transfer RNA-modifying enzyme TYW2 induces ribosome frameshifts in colon cancer. Proc Natl Acad Sci U S A 2020; 117:20785-20793. [PMID: 32778592 PMCID: PMC7456070 DOI: 10.1073/pnas.2003358117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Defects in transfer RNA (tRNA) modifications occur in human pathologies such as cancer; however, how these alterations contribute to the disease is poorly understood. One example is the tumor-specific hypomodification of position 37 of tRNAPhe, which was first described 45 y ago, although its cause and consequences have remained unknown. Here we report that the tRNAPhe hypomodification is due to promoter CpG island hypermethylation-associated transcriptional silencing of TYW2, a key enzyme in the synthesis of wybutosine derivatives. Furthermore, epigenetic loss of TYW2 in transformed cells provokes hypomodified tRNAPhe-mediated ribosome frameshifting, dysregulating mRNA abundance via nonsense-mediated decay. Importantly, TYW2 silencing in cancer cells confers enhanced migration and epithelial-to-mesenchymal features that are associated in early-stage colorectal cancer patients with poor clinical outcome. Transfer RNA (tRNA) activity is tightly regulated to provide a physiological protein translation, and tRNA chemical modifications control its function in a complex with ribosomes and messenger RNAs (mRNAs). In this regard, the correct hypermodification of position G37 of phenylalanine-tRNA, adjacent to the anticodon, is critical to prevent ribosome frameshifting events. Here we report that the tRNA-yW Synthesizing Protein 2 (TYW2) undergoes promoter hypermethylation-associated transcriptional silencing in human cancer, particularly in colorectal tumors. The epigenetic loss of TYW2 induces guanosine hypomodification in phenylalanine-tRNA, an increase in −1 ribosome frameshift events, and down-regulation of transcripts by mRNA decay, such as of the key cancer gene ROBO1. Importantly, TYW2 epigenetic inactivation is linked to poor overall survival in patients with early-stage colorectal cancer, a finding that could be related to the observed acquisition of enhanced migration properties and epithelial-to-mesenchymal features in the colon cancer cells that harbor TYW2 DNA methylation-associated loss. These findings provide an illustrative example of how epigenetic changes can modify the epitranscriptome and further support a role for tRNA modifications in cancer biology.
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115
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Ignatova VV, Kaiser S, Ho JSY, Bing X, Stolz P, Tan YX, Lee CL, Gay FPH, Lastres PR, Gerlini R, Rathkolb B, Aguilar-Pimentel A, Sanz-Moreno A, Klein-Rodewald T, Calzada-Wack J, Ibragimov E, Valenta M, Lukauskas S, Pavesi A, Marschall S, Leuchtenberger S, Fuchs H, Gailus-Durner V, de Angelis MH, Bultmann S, Rando OJ, Guccione E, Kellner SM, Schneider R. METTL6 is a tRNA m 3C methyltransferase that regulates pluripotency and tumor cell growth. SCIENCE ADVANCES 2020; 6:eaaz4551. [PMID: 32923617 PMCID: PMC7449687 DOI: 10.1126/sciadv.aaz4551] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Recently, covalent modifications of RNA, such as methylation, have emerged as key regulators of all aspects of RNA biology and have been implicated in numerous diseases, for instance, cancer. Here, we undertook a combination of in vitro and in vivo screens to test 78 potential methyltransferases for their roles in hepatocellular carcinoma (HCC) cell proliferation. We identified methyltransferase-like protein 6 (METTL6) as a crucial regulator of tumor cell growth. We show that METTL6 is a bona fide transfer RNA (tRNA) methyltransferase, catalyzing the formation of 3-methylcytidine at C32 of specific serine tRNA isoacceptors. Deletion of Mettl6 in mouse stem cells results in changes in ribosome occupancy and RNA levels, as well as impaired pluripotency. In mice, Mettl6 knockout results in reduced energy expenditure. We reveal a previously unknown pathway in the maintenance of translation efficiency with a role in maintaining stem cell self-renewal, as well as impacting tumor cell growth profoundly.
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Affiliation(s)
- Valentina V. Ignatova
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Steffen Kaiser
- Chemical Faculty, Ludwig-Maximilians Universität München, Munich, Germany
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xinyang Bing
- University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul Stolz
- Department of Biology II, Human Biology and BioImaging, Ludwig-Maximilians Universität München, Munich, Germany
| | - Ying Xim Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chee Leng Lee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Florence Pik Hoon Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Palma Rico Lastres
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Raffaele Gerlini
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University München, Munich, Germany
| | - Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Adrián Sanz-Moreno
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tanja Klein-Rodewald
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Julia Calzada-Wack
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Emil Ibragimov
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Magdalena Valenta
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Andrea Pavesi
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Susan Marschall
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Sebastian Bultmann
- Department of Biology II, Human Biology and BioImaging, Ludwig-Maximilians Universität München, Munich, Germany
| | - Oliver J. Rando
- University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Faculty of Biology, Ludwig-Maximilians Universität München, Munich, Germany
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116
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Wang L, Liang Y, Lin R, Xiong Q, Yu P, Ma J, Cheng M, Han H, Wang X, Wang G, Liang F, Pei Z, Chen D, Yuan Q, Jiang YZ, Lin S. Mettl5 mediated 18S rRNA N6-methyladenosine (m 6A) modification controls stem cell fate determination and neural function. Genes Dis 2020; 9:268-274. [PMID: 35005123 PMCID: PMC8720661 DOI: 10.1016/j.gendis.2020.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/11/2020] [Indexed: 02/08/2023] Open
Abstract
Ribosome RNA (rRNA) accounts for more than 80% of the cell's total RNA, while the physiological functions of rRNA modifications are poorly understood. Mutations of 18S rRNA m6A methyltransferase METTL5 cause intellectual disability, microcephaly, and facial dysmorphisms in patients, however, little is known about the underlying mechanisms. In this study, we identified METTL5 protein complex and revealed that METTL5 mainly interacts with RNA binding proteins and ribosome proteins. Functionally, we found that Mettl5 knockout in mESCs leads to the abnormal craniofacial and nervous development. Moreover, using Mettl5 knockout mouse model, we further demonstrated that Mettl5 knockout mice exhibit intellectual disability, recapitulating the human phenotype. Mechanistically, we found that Mettl5 maintains brain function and intelligence by regulating the myelination process. Our study uncovered the causal correlation between mis-regulated 18S rRNA m6A modification and neural function defects, supporting the important physiological functions of rRNA modifications in human diseases.
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Affiliation(s)
- Lu Wang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China.,Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, PR China
| | - Yu Liang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China.,Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, PR China
| | - Rongzhi Lin
- Department of Otorhinolaryngology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, PR China
| | - Qiuchan Xiong
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Peng Yu
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Jieyi Ma
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Maosheng Cheng
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Hui Han
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Xiaochen Wang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Ganping Wang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Fengyin Liang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, Guangdong 510080, PR China
| | - Zhong Pei
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, Guangdong 510080, PR China
| | - Demeng Chen
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yi-Zhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, PR China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
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Asada K, Bolatkan A, Takasawa K, Komatsu M, Kaneko S, Hamamoto R. Critical Roles of N6-Methyladenosine (m 6A) in Cancer and Virus Infection. Biomolecules 2020; 10:biom10071071. [PMID: 32709063 PMCID: PMC7408378 DOI: 10.3390/biom10071071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Studies have shown that epigenetic abnormalities are involved in various diseases, including cancer. In particular, in order to realize precision medicine, the integrated analysis of genetics and epigenetics is considered to be important; detailed epigenetic analysis in the medical field has been becoming increasingly important. In the epigenetics analysis, DNA methylation and histone modification analyses have been actively studied for a long time, and many important findings were accumulated. On the other hand, recently, attention has also been focused on RNA modification in the field of epigenetics; now it is known that RNA modification is associated with various biological functions, such as regulation of gene expression. Among RNA modifications, functional analysis of N6-methyladenosine (m6A), the most abundant RNA modification found from humans to plants is actively progressing, and it has also been known that m6A abnormality is involved in cancer and other diseases. Importantly, recent studies have shown that m6A is related to viral infections. Considering the current world situation under threat of viral infections, it is important to deepen knowledge of RNA modification from the viewpoint of viral diseases. Hence, in this review, we have summarized the recent findings regarding the roles of RNA modifications in biological functions, cancer biology, and virus infection, particularly focusing on m6A in mRNA.
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Affiliation(s)
- Ken Asada
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
- Correspondence: (K.A.); (R.H.); Tel.: +81-3-3547-5271 (R.H.)
| | - Amina Bolatkan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Ken Takasawa
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Masaaki Komatsu
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Ryuji Hamamoto
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
- Correspondence: (K.A.); (R.H.); Tel.: +81-3-3547-5271 (R.H.)
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118
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Mathlin J, Le Pera L, Colombo T. A Census and Categorization Method of Epitranscriptomic Marks. Int J Mol Sci 2020; 21:ijms21134684. [PMID: 32630140 PMCID: PMC7370119 DOI: 10.3390/ijms21134684] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, thorough investigation of chemical modifications operated in the cells on ribonucleic acid (RNA) molecules is gaining momentum. This new field of research has been dubbed “epitranscriptomics”, in analogy to best-known epigenomics, to stress the potential of ensembles of RNA modifications to constitute a post-transcriptional regulatory layer of gene expression orchestrated by writer, reader, and eraser RNA-binding proteins (RBPs). In fact, epitranscriptomics aims at identifying and characterizing all functionally relevant changes involving both non-substitutional chemical modifications and editing events made to the transcriptome. Indeed, several types of RNA modifications that impact gene expression have been reported so far in different species of cellular RNAs, including ribosomal RNAs, transfer RNAs, small nuclear RNAs, messenger RNAs, and long non-coding RNAs. Supporting functional relevance of this largely unknown regulatory mechanism, several human diseases have been associated directly to RNA modifications or to RBPs that may play as effectors of epitranscriptomic marks. However, an exhaustive epitranscriptome’s characterization, aimed to systematically classify all RNA modifications and clarify rules, actors, and outcomes of this promising regulatory code, is currently not available, mainly hampered by lack of suitable detecting technologies. This is an unfortunate limitation that, thanks to an unprecedented pace of technological advancements especially in the sequencing technology field, is likely to be overcome soon. Here, we review the current knowledge on epitranscriptomic marks and propose a categorization method based on the reference ribonucleotide and its rounds of modifications (“stages”) until reaching the given modified form. We believe that this classification scheme can be useful to coherently organize the expanding number of discovered RNA modifications.
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Affiliation(s)
- Julia Mathlin
- Department of Life Sciences and Medicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Loredana Le Pera
- CNR-Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Teresa Colombo
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
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119
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Lyu X, Yang Q, Li L, Dang Y, Zhou Z, Chen S, Liu Y. Adaptation of codon usage to tRNA I34 modification controls translation kinetics and proteome landscape. PLoS Genet 2020; 16:e1008836. [PMID: 32479508 PMCID: PMC7289440 DOI: 10.1371/journal.pgen.1008836] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/11/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
Codon usage bias is a universal feature of all genomes and plays an important role in regulating protein expression levels. Modification of adenosine to inosine at the tRNA anticodon wobble position (I34) by adenosine deaminases (ADATs) is observed in all eukaryotes and has been proposed to explain the correlation between codon usage and tRNA pool. However, how the tRNA pool is affected by I34 modification to influence codon usage-dependent gene expression is unclear. Using Neurospora crassa as a model system, by combining molecular, biochemical and bioinformatics analyses, we show that silencing of adat2 expression severely impaired the I34 modification levels for the ADAT-related tRNAs, resulting in major ADAT-related tRNA profile changes and reprogramming of translation elongation kinetics on ADAT-related codons. adat2 silencing also caused genome-wide codon usage-biased ribosome pausing on mRNAs and proteome landscape changes, leading to selective translational repression or induction of different mRNAs. The induced expression of CPC-1, the Neurospora ortholog of yeast GCN4p, mediates the transcriptional response after adat2 silencing and amino acid starvation. Together, our results demonstrate that the tRNA I34 modification by ADAT plays a major role in driving codon usage-biased translation to shape proteome landscape. Modification of transfer RNA (tRNA) can have profound impacts on gene expression by shaping cellular tRNA pool. How codon usage bias and tRNA profiles synergistically regulate gene expression is unclear. By combining molecular, biochemical and bioinformatics analyses, we showed that the correlation between genome codon usage and tRNA I34 (inosine 34) modification modulates translation elongation kinetics and proteome landscape. Inhibition of tRNA I34 modification causes codon usage-dependent ribosome pausing on mRNAs during translation and changes cellular protein contents in a codon usage biased manner. Together, our results demonstrate that the tRNA I34 modification plays a major role in driving codon usage-dependent translation to determine proteome landscape in a eukaryotic organism.
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Affiliation(s)
- Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
| | - Qian Yang
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
| | - Lin Li
- National Institute of Biological Sciences, Changping District, Beijing, China
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Zhipeng Zhou
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - She Chen
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
- * E-mail:
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120
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Sajek MP, Woźniak T, Sprinzl M, Jaruzelska J, Barciszewski J. T-psi-C: user friendly database of tRNA sequences and structures. Nucleic Acids Res 2020; 48:D256-D260. [PMID: 31624839 PMCID: PMC7145666 DOI: 10.1093/nar/gkz922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/30/2019] [Accepted: 10/10/2019] [Indexed: 12/31/2022] Open
Abstract
tRNAs have been widely studied for their role as genetic code decoders in the ribosome during translation, but have recently received new attention due to the discovery of novel roles beyond decoding, often in connection with human diseases. Yet, existing tRNA databases have not been updated for more than a decade, so they do not contain this new functional information and have not kept pace with the rate of discovery in this field. Therefore, a regularly updated database that contains information about newly discovered characteristics of tRNA molecules and can be regularly updated is strongly needed. Here, we report the creation of the T-psi-C database (http://tpsic.igcz.poznan.pl), an up-to-date collection of tRNA sequences that contains data obtained from high-throughput tRNA sequencing, e.g. all isoacceptors and isodecoders for human HEK293 cells. This database also contains 3D tRNA structures obtained from Protein Data Bank and generated using homology modeling. The T-psi-C database can be continuously updated by any member of the scientific community, and contains its own application programming interface (API), which allows users to retrieve or upload data in JSON format. Altogether, T-psi-C is user-friendly, easy to develop and an up-to-date source of knowledge about tRNAs.
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Affiliation(s)
- Marcin Piotr Sajek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Tomasz Woźniak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | | | - Jadwiga Jaruzelska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61-704 Poznan, Poland.,NanoBioMedical Centre of the Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
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DALRD3 encodes a protein mutated in epileptic encephalopathy that targets arginine tRNAs for 3-methylcytosine modification. Nat Commun 2020; 11:2510. [PMID: 32427860 PMCID: PMC7237682 DOI: 10.1038/s41467-020-16321-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
In mammals, a subset of arginine tRNA isoacceptors are methylated in the anticodon loop by the METTL2 methyltransferase to form the 3-methylcytosine (m3C) modification. However, the mechanism by which METTL2 identifies specific tRNA arginine species for m3C formation as well as the biological role of m3C in mammals is unknown. Here, we show that human METTL2 forms a complex with DALR anticodon binding domain containing 3 (DALRD3) protein to recognize particular arginine tRNAs destined for m3C modification. DALRD3-deficient human cells exhibit nearly complete loss of the m3C modification in tRNA-Arg species. Notably, we identify a homozygous nonsense mutation in the DALRD3 gene that impairs m3C formation in human patients exhibiting developmental delay and early-onset epileptic encephalopathy. These findings uncover an unexpected function for the DALRD3 protein in the targeting of distinct arginine tRNAs for m3C modification and suggest a crucial biological role for DALRD3-dependent tRNA modification in proper neurological development.
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Begik O, Lucas MC, Liu H, Ramirez JM, Mattick JS, Novoa EM. Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures. Genome Biol 2020; 21:97. [PMID: 32375858 PMCID: PMC7204298 DOI: 10.1186/s13059-020-02009-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/03/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification-related proteins (RMPs) may be dysregulated in each cancer type. RESULTS Here, we perform a comprehensive annotation and evolutionary analysis of human RMPs, as well as an integrative analysis of their expression patterns across 32 tissues, 10 species, and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. We uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO are not significantly upregulated in most cancer types, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers. CONCLUSIONS Our analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviors that are orchestrated by RNA modifications.
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Affiliation(s)
- Oguzhan Begik
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- UNSW, Sydney, Sydney, NSW, 2052, Australia
| | - Morghan C Lucas
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Huanle Liu
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Jose Miguel Ramirez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- UNSW, Sydney, Sydney, NSW, 2052, Australia
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.
- UNSW, Sydney, Sydney, NSW, 2052, Australia.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Direct activation of tRNA methyltransferase-like 1 (Mettl1) gene by thyroid hormone receptor implicates a role in adult intestinal stem cell development and proliferation during Xenopus tropicalis metamorphosis. Cell Biosci 2020; 10:60. [PMID: 32391142 PMCID: PMC7197180 DOI: 10.1186/s13578-020-00423-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/25/2020] [Indexed: 12/12/2022] Open
Abstract
Background Thyroid hormone (T3) plays an important role in vertebrate development. Compared to the postembryonic development of uterus-enclosed mammalian embryos, T3-dependent amphibian metamorphosis is advantageous for studying the function of T3 and T3 receptors (TRs) during vertebrate development. The effects of T3 on the metamorphosis of anurans such as Xenopus tropicalis is known to be mediated by TRs. Many putative TR target genes have been identified previously. Among them is the tRNA methyltransferase Mettl1. Results We studied the regulation of Mettl1 gene by T3 during intestinal metamorphosis, a process involves near complete degeneration of the larval epithelial cells via apoptosis and de novo formation of adult epithelial stem cells and their subsequent proliferation and differentiation. We observed that Mettl1 was activated by T3 in the intestine during both natural and T3-induced metamorphosis and that its mRNA level peaks at the climax of intestinal remodeling. We further showed that Mettl1 promoter could be activated by liganded TR via a T3 response element upstream of the transcription start site in vivo. More importantly, we found that TR binding to the TRE region correlated with the increase in the level of H3K79 methylation, a transcription activation histone mark, and the recruitment of RNA polymerase II by T3 during metamorphosis. Conclusions Our findings suggest that Mettl1 is activated by liganded TR directly at the transcriptional level via the TRE in the promoter region in the intestine during metamorphosis. Mettl1 in turn regulate target tRNAs to affect translation, thus facilitating stem cell formation and/or proliferation during intestinal remodeling.
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Berthel E, Vincent A, Eberst L, Torres AG, Dacheux E, Rey C, Marcel V, Paraqindes H, Lachuer J, Catez F, de Pouplana LR, Treilleux I, Diaz JJ, Dalla Venezia N. Uncovering the Translational Regulatory Activity of the Tumor Suppressor BRCA1. Cells 2020; 9:cells9040941. [PMID: 32290274 PMCID: PMC7226996 DOI: 10.3390/cells9040941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/30/2020] [Accepted: 04/04/2020] [Indexed: 12/24/2022] Open
Abstract
BRCA1 inactivation is a hallmark of familial breast cancer, often associated with aggressive triple negative breast cancers. BRCA1 is a tumor suppressor with known functions in DNA repair, transcription regulation, cell cycle control, and apoptosis. In the present study, we demonstrate that BRCA1 is also a translational regulator. We previously showed that BRCA1 was implicated in translation regulation. Here, we asked whether translational control could be a novel function of BRCA1 that contributes to its tumor suppressive activity. A combination of RNA-binding protein immunoprecipitation, microarray analysis, and polysome profiling, was used to identify the mRNAs that were specifically deregulated under BRCA1 deficiency. Western blot analysis allowed us to confirm at the protein level the deregulated translation of a subset of mRNAs. A unique and dedicated cohort of patients with documented germ-line BRCA1 pathogenic variant statues was set up, and tissue microarrays with the biopsies of these patients were constructed and analyzed by immunohistochemistry for their content in each candidate protein. Here, we show that BRCA1 translationally regulates a subset of mRNAs with which it associates. These mRNAs code for proteins involved in major programs in cancer. Accordingly, the level of these key proteins is correlated with BRCA1 status in breast cancer cell lines and in patient breast tumors. ADAT2, one of these key proteins, is proposed as a predictive biomarker of efficacy of treatments recently recommended to patients with BRCA1 deficiency. This study proposes that translational control may represent a novel molecular mechanism with potential clinical impact through which BRCA1 is a tumor suppressor.
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Affiliation(s)
- Elise Berthel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Anne Vincent
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Lauriane Eberst
- Centre Léon Bérard, Medical Oncology Department, Université de Lyon 1, F-69008 Lyon, France;
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (A.G.T.); (L.R.d.P.)
| | - Estelle Dacheux
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Catherine Rey
- ProfileXpert, UNIV-US7 INSERM-UMS 3453 CNRS, F-69000 Lyon, France; (C.R.); (J.L.)
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Hermes Paraqindes
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Joël Lachuer
- ProfileXpert, UNIV-US7 INSERM-UMS 3453 CNRS, F-69000 Lyon, France; (C.R.); (J.L.)
| | - Frédéric Catez
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (A.G.T.); (L.R.d.P.)
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Isabelle Treilleux
- Department of Translational Research and Innovation, Centre Léon Bérard, F-69008 Lyon, France;
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Nicole Dalla Venezia
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
- Correspondence: ; Tel.: +33-426-556-745
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Alqasem MA, Fergus C, Southern JM, Connon SJ, Kelly VP. The eukaryotic tRNA-guanine transglycosylase enzyme inserts queuine into tRNA via a sequential bi-bi mechanism. Chem Commun (Camb) 2020; 56:3915-3918. [PMID: 32149287 DOI: 10.1039/c9cc09887a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eukaryotic tRNA-guanine transglycosylase (TGT) - an enzyme recently recognised to be of potential therapeutic importance - catalyses base-exchange of guanine for queuine at the wobble position of tRNAs associated with 4 amino acids via a distinct mechanism to that reported for its eubacterial homologue. The presence of queuine is unequivocally required as a trigger for reaction between the enzyme and tRNA and exhibits cooperativity not seen using guanine as a substrate.
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Affiliation(s)
- Mashael A Alqasem
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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Thakur P, Estevez M, Lobue PA, Limbach PA, Addepalli B. Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases. Analyst 2020; 145:816-827. [PMID: 31825413 PMCID: PMC7002195 DOI: 10.1039/c9an02111f] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Locating ribonucleoside modifications within an RNA sequence requires digestion of the RNA into oligoribonucleotides of amenable size for subsequent analysis by LC-MS (liquid chromatography-mass spectrometry). This approach, widely referred to as RNA modification mapping, is facilitated through ribonucleases (RNases) such as T1 (guanosine-specific), U2 (purine-selective) and A (pyrimidine-specific) among others. Sequence coverage by these enzymes depends on positioning of the recognized nucleobase (such as guanine or purine or pyrimidine) in the sequence and its ribonucleotide composition. Using E. coli transfer RNA (tRNA) and ribosomal RNA (rRNA) as model samples, we demonstrate the ability of complementary nucleobase-specific ribonucleases cusativin (C-specific) and MC1 (U-specific) to generate digestion products that facilitate confident mapping of modifications in regions such as G-rich and pyrimidine-rich segments of RNA, and to distinguish C to U sequence differences. These enzymes also increase the number of oligonucleotide digestion products that are unique to a specific RNA sequence. Further, with these additional RNases, multiple modifications can be localized with high confidence in a single set of experiments with minimal dependence on the individual tRNA abundance in a mixture. The sequence overlaps observed with these complementary digestion products and that of RNase T1 improved sequence coverage to 75% or above. A similar level of sequence coverage was also observed for the 2904 nt long 23S rRNA indicating their utility has no dependence on RNA size. Wide-scale adoption of these additional modification mapping tools could help expedite the characterization of modified RNA sequences to understand their structural and functional role in various living systems.
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Affiliation(s)
- Priti Thakur
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
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Zhang B, Arcinas AJ, Radle MI, Silakov A, Booker SJ, Krebs C. First Step in Catalysis of the Radical S-Adenosylmethionine Methylthiotransferase MiaB Yields an Intermediate with a [3Fe-4S] 0-Like Auxiliary Cluster. J Am Chem Soc 2020; 142:1911-1924. [PMID: 31899624 PMCID: PMC7008301 DOI: 10.1021/jacs.9b11093] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The enzyme MiaB catalyzes the attachment of a methylthio (-SCH3) group at the C2 position of N6-(isopentenyl)adenosine (i6A) in the final step of the biosynthesis of the hypermodified tRNA nucleotide 2-methythio-N6-(isopentenyl)adenosine (ms2i6A). MiaB belongs to the expanding subgroup of enzymes of the radical S-adenosylmethionine (SAM) superfamily that harbor one or more auxiliary [4Fe-4S] clusters in addition to the [4Fe-4S] cluster that all family members require for the reductive cleavage of SAM to afford the common 5'-deoxyadenosyl 5'-radical (5'-dA•) intermediate. While the role of the radical SAM cluster in generating the 5'-dA• is well understood, the detailed role of the auxiliary cluster, which is essential for MiaB catalysis, remains unclear. It has been proposed that the auxiliary cluster may serve as a coordination site for exogenously derived sulfur destined for attachment to the substrate or that the cluster itself provides the sulfur atom and is sacrificed during turnover. In this work, we report spectroscopic and biochemical evidence that the auxiliary [4Fe-4S]2+ cluster in Bacteroides thetaiotaomicron (Bt) MiaB is converted to a [3Fe-4S]0-like cluster during the methylation step of catalysis. Mössbauer characterization of the MiaB [3Fe-4S]0-like cluster revealed unusual spectroscopic properties compared to those of other well-characterized cuboidal [3Fe-4S]0 clusters. Specifically, the Fe sites of the mixed-valent moiety do not have identical Mössbauer parameters. Our results support a mechanism where the auxiliary [4Fe-4S] cluster is the direct sulfur source during catalysis.
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Varanda AS, Santos M, Soares AR, Vitorino R, Oliveira P, Oliveira C, Santos MAS. Human cells adapt to translational errors by modulating protein synthesis rate and protein turnover. RNA Biol 2020; 17:135-149. [PMID: 31570039 PMCID: PMC6948982 DOI: 10.1080/15476286.2019.1670039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 02/08/2023] Open
Abstract
Deregulation of tRNAs, aminoacyl-tRNA synthetases (aaRS) or tRNA modifying enzymes, increase the level of protein synthesis errors (PSE) and are associated with several diseases, but the cause-effect mechanisms of these pathologies remain elusive. To clarify the role of PSE in human biology, we have engineered a HEK293 cell line to overexpress a wild type (Wt) tRNASer and two tRNASer mutants that misincorporate serine at non-cognate codon sites. Then, we followed long-term adaptation to PSE of such recombinant cells by analysing cell viability, protein synthesis rate and activation of protein quality control mechanisms (PQC). Engineered cells showed higher level of misfolded and aggregated proteins; activated the ubiquitin-proteasome system (UPS) and the unfolded protein response (UPR), indicative of proteotoxic stress. Adaptation to PSE involved increased protein turnover, UPR up-regulation and altered protein synthesis rate. Gene expression analysis showed that engineered cells presented recurrent alterations in the endoplasmic reticulum, cell adhesion and calcium homeostasis. Herein, we unveil new phenotypic consequences of protein synthesis errors in human cells and identify the protein quality control processes that are necessary for long-term adaptation to PSE and proteotoxic stress. Our data provide important insight on how chronic proteotoxic stress may cause disease and highlight potential biological pathways that support the association of PSE with disease.
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Affiliation(s)
- Ana Sofia Varanda
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Mafalda Santos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Ana R. Soares
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Patrícia Oliveira
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Carla Oliveira
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Manuel A. S. Santos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
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Payea MJ, Hauke AC, De Zoysa T, Phizicky EM. Mutations in the anticodon stem of tRNA cause accumulation and Met22-dependent decay of pre-tRNA in yeast. RNA (NEW YORK, N.Y.) 2020; 26:29-43. [PMID: 31619505 PMCID: PMC6913130 DOI: 10.1261/rna.073155.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/11/2019] [Indexed: 05/20/2023]
Abstract
During tRNA maturation in yeast, aberrant pre-tRNAs are targeted for 3'-5' degradation by the nuclear surveillance pathway, and aberrant mature tRNAs are targeted for 5'-3' degradation by the rapid tRNA decay (RTD) pathway. RTD is catalyzed by the 5'-3' exonucleases Xrn1 and Rat1, which act on tRNAs with an exposed 5' end due to the lack of certain body modifications or the presence of destabilizing mutations in the acceptor stem, T-stem, or tRNA fold. RTD is inhibited by mutation of MET22, likely due to accumulation of the Met22 substrate adenosine 3',5' bis-phosphate, which inhibits 5'-3' exonucleases. Here we provide evidence for a new tRNA quality control pathway in which intron-containing pre-tRNAs with destabilizing mutations in the anticodon stem are targeted for Met22-dependent pre-tRNA decay (MPD). Multiple SUP4οc anticodon stem variants that are subject to MPD each perturb the bulge-helix-bulge structure formed by the anticodon stem-loop and intron, which is important for splicing, resulting in substantial accumulation of end-matured unspliced pre-tRNA as well as pre-tRNA decay. Mutations that restore exon-intron structure commensurately reduce pre-tRNA accumulation and MPD. The MPD pathway can contribute substantially to decay of anticodon stem variants, since pre-tRNA decay is largely suppressed by removal of the intron or by restoration of exon-intron structure, each also resulting in increased tRNA levels. The MPD pathway is general as it extends to variants of tRNATyr(GUA) and tRNASer(CGA) These results demonstrate that the integrity of the anticodon stem-loop and the efficiency of tRNA splicing are monitored by a quality control pathway.
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Affiliation(s)
- Matthew J Payea
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Alayna C Hauke
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Thareendra De Zoysa
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
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130
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Qin C, Xu PP, Zhang X, Zhang C, Liu CB, Yang DG, Gao F, Yang ML, Du LJ, Li JJ. Pathological significance of tRNA-derived small RNAs in neurological disorders. Neural Regen Res 2020; 15:212-221. [PMID: 31552886 PMCID: PMC6905339 DOI: 10.4103/1673-5374.265560] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs (tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cleaved into a heterogeneous population of ncRNAs with lengths of 18–40 nucleotides, known as tRNA-derived small RNAs (tsRNAs). There are two main types of tsRNA, based on their length and the number of cleavage sites that they contain: tRNA-derived fragments and tRNA-derived stress-induced RNAs. These RNA species were first considered to be byproducts of tRNA random cleavage. However, mounting evidence has demonstrated their critical functional roles as regulatory factors in the pathophysiological processes of various diseases, including neurological diseases. However, the underlying mechanisms by which tsRNAs affect specific cellular processes are largely unknown. Therefore, this study comprehensively summarizes the following points: (1) The biogenetics of tsRNA, including their discovery, classification, formation, and the roles of key enzymes. (2) The main biological functions of tsRNA, including its miRNA-like roles in gene expression regulation, protein translation regulation, regulation of various cellular activities, immune mediation, and response to stress. (3) The potential mechanisms of pathophysiological changes in neurological diseases that are regulated by tsRNA, including neurodegeneration and neurotrauma. (4) The identification of the functional diversity of tsRNA may provide valuable information regarding the physiological and pathophysiological mechanisms of neurological disorders, thus providing a new reference for the clinical treatment of neurological diseases. Research into tsRNAs in neurological diseases also has the following challenges: potential function and mechanism studies, how to accurately quantify expression, and the exact relationship between tsRNA and miRNA. These challenges require future research efforts.
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Affiliation(s)
- Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Pei-Pei Xu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xin Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chang-Bin Liu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - De-Gang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Ming-Liang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liang-Jie Du
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jian-Jun Li
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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131
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O'Keefe H, Queen R, Lord P, Elson JL. What can a comparative genomics approach tell us about the pathogenicity of mtDNA mutations in human populations? Evol Appl 2019; 12:1912-1930. [PMID: 31700535 PMCID: PMC6824070 DOI: 10.1111/eva.12851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial disorders are heterogeneous, showing variable presentation and penetrance. Over the last three decades, our ability to recognize mitochondrial patients and diagnose these mutations, linking genotype to phenotype, has greatly improved. However, it has become increasingly clear that these strides in diagnostics have not benefited all population groups. Recent studies have demonstrated that patients from genetically understudied populations, in particular those of black African heritage, are less likely to receive a diagnosis of mtDNA disease. It has been suggested that haplogroup context might influence the presentation and penetrance of mtDNA disease; thus, the spectrum of mutations that are associated with disease in different populations. However, to date there is only one well-established example of such an effect: the increased penetrance of two Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducted the most extensive investigation to date into the importance of haplogroup context on the pathogenicity of mtDNA mutations. We searched for proven human point mutations across 726 multiple sequence alignments derived from 33 non-human species absent of disease. A total of 58 pathogenic point mutations arise in the sequences of these species. We assessed the sequence context and found evidence of population variants that could modulate the phenotypic expression of these point mutations masking the pathogenic effects seen in humans. This supports the theory that sequence context is influential in the presentation of mtDNA disease and has implications for diagnostic practices. We have shown that our current understanding of the pathogenicity of mtDNA point mutations, primarily built on studies of individuals with haplogroups HVUKTJ, will not present a complete picture. This will have the effect of creating a diagnostic inequality, whereby individuals who do not belong to these lineages are less likely to receive a genetic diagnosis.
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Affiliation(s)
- Hannah O'Keefe
- Institute of Genetic MedicineNewcastle UniversityNewcastle‐upon‐TyneUK
- School of ComputingNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel Queen
- Bioinformatics Core FacilityNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Phillip Lord
- School of ComputingNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Joanna L. Elson
- Institute of Genetic MedicineNewcastle UniversityNewcastle‐upon‐TyneUK
- Centre for Human MetabonomicsNorth‐West UniversityPotchefstroomSouth Africa
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132
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Lee MY, Leonardi A, Begley TJ, Melendez JA. Loss of epitranscriptomic control of selenocysteine utilization engages senescence and mitochondrial reprogramming ☆. Redox Biol 2019; 28:101375. [PMID: 31765888 PMCID: PMC6904832 DOI: 10.1016/j.redox.2019.101375] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 11/17/2022] Open
Abstract
Critically important to the maintenance of the glutathione (GSH) redox cycle are the activities of many selenocysteine-containing GSH metabolizing enzymes whose translation is controlled by the epitranscriptomic writer alkylation repair homolog 8 (ALKBH8). ALKBH8 is a tRNA methyltransferase that methylates the wobble uridine of specific tRNAs to regulate the synthesis of selenoproteins. Here we demonstrate that a deficiency in the writer ALKBH8 (Alkbh8def), alters selenoprotein levels and engages senescence, regulates stress response genes and promotes mitochondrial reprogramming. Alkbh8def mouse embryonic fibroblasts (MEFs) increase many hallmarks of senescence, including senescence associated β-galactosidase, heterocromatic foci, the cyclin dependent kinase inhibitor p16Ink4a, markers of mitochondrial dynamics as well as the senescence associated secretory phenotype (SASP). Alkbh8def cells also acquire a stress resistance phenotype that is accompanied by an increase in a number redox-modifying transcripts. In addition, Alkbh8def MEFs undergo a metabolic shift that is highlighted by a striking increase in the level of uncoupling protein 2 (UCP2) which enhances oxygen consumption and promotes a reliance on glycolytic metabolism. Finally, we have shown that the Alkbh8 deficiency can be exploited and corresponding MEFs are killed by glycolytic inhibition. Our work demonstrates that defects in an epitransciptomic writer promote senescence and mitochondrial reprogramming and unveils a novel adaptive mechanism for coping with defects in selenocysteine utilization. Deficiencies in selenocysteine utilization engages cellular senescence and the senescence associated secretory phenotype. Alkbh8 deficiency promotes mitochondrial elongation, increased oxygen consumption and a reliance on glycolytic metabolism. Cellular adaptions to Alkbh8 deficiency confer stress resistance.
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Affiliation(s)
- May Y Lee
- Nanobioscience Constellation, Colleges of Nanoscale Science & Engineering, SUNY Polytechnic Institute, 257 Fuller Rd., Albany, NY, 12203, USA
| | - Andrea Leonardi
- Nanobioscience Constellation, Colleges of Nanoscale Science & Engineering, University at Albany, 257 Fuller Rd., Albany, NY, 12203, USA
| | - Thomas J Begley
- Nanobioscience Constellation, Colleges of Nanoscale Science & Engineering, SUNY Polytechnic Institute, 257 Fuller Rd., Albany, NY, 12203, USA; Nanobioscience Constellation, Colleges of Nanoscale Science & Engineering, University at Albany, 257 Fuller Rd., Albany, NY, 12203, USA; The RNA Institute, College of Arts & Sciences, University at Albany, 1400 Washington Ave., Albany, NY, 12222, USA
| | - J Andrés Melendez
- Nanobioscience Constellation, Colleges of Nanoscale Science & Engineering, SUNY Polytechnic Institute, 257 Fuller Rd., Albany, NY, 12203, USA.
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133
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Lin S, Liu Q, Jiang YZ, Gregory RI. Nucleotide resolution profiling of m 7G tRNA modification by TRAC-Seq. Nat Protoc 2019; 14:3220-3242. [PMID: 31619810 DOI: 10.1038/s41596-019-0226-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/08/2019] [Indexed: 01/27/2023]
Abstract
Precise identification of sites of RNA modification is key to studying the functional role of such modifications in the regulation of gene expression and for elucidating relevance to diverse physiological processes. tRNA reduction and cleavage sequencing (TRAC-Seq) is a chemically based approach for the unbiased global mapping of 7-methylguansine (m7G) modification of tRNAs at single-nucleotide resolution throughout the tRNA transcriptome. m7G TRAC-Seq involves the treatment of size-selected (<200 nt) RNAs with the demethylase AlkB to remove major tRNA modifications, followed by sodium borohydride (NaBH4) reduction of m7G sites and subsequent aniline-mediated cleavage of the RNA chain at the resulting abasic sites. The cleaved sites are subsequently ligated with adaptors for the construction of libraries for high-throughput sequencing. The m7G modification sites are identified using a bioinformatic pipeline that calculates the cleavage scores at individual sites on all tRNAs. Unlike antibody-based methods, such as methylated RNA immunoprecipitation and sequencing (meRIP-Seq) for enrichment of methylated RNA sequences, chemically based approaches, including TRAC-Seq, can provide nucleotide-level resolution of modification sites. Compared to the related method AlkAniline-Seq (alkaline hydrolysis and aniline cleavage sequencing), TRAC-Seq incorporates small RNA selection, AlkB demethylation, and sodium borohydride reduction steps to achieve specific and efficient single-nucleotide resolution profiling of m7G sites in tRNAs. The m7G TRAC-Seq protocol could be adapted to chemical cleavage-mediated detection of other RNA modifications. The protocol can be completed within ~9 d for four biological replicates of input and treated samples.
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Affiliation(s)
- Shuibin Lin
- Department of Neurology and Stroke Center, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Qi Liu
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yi-Zhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, USA. .,Harvard Initiative for RNA Medicine, Boston, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
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134
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Sun L, Xu Y, Bai S, Bai X, Zhu H, Dong H, Wang W, Zhu X, Hao F, Song CP. Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5089-5600. [PMID: 31173101 PMCID: PMC6793436 DOI: 10.1093/jxb/erz273] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 05/29/2019] [Indexed: 05/18/2023]
Abstract
Pseudouridine (Ψ) is widely distributed in mRNA and various non-coding RNAs in yeast and mammals, and the specificity of its distribution has been determined. However, knowledge about Ψs in the RNAs of plants, particularly in mRNA, is lacking. In this study, we performed genome-wide pseudouridine-sequencing in Arabidopsis and for the first time identified hundreds of Ψ sites in mRNA and multiple Ψ sites in non-coding RNAs. Many predicted and novel Ψ sites in rRNA and tRNA were detected. mRNA was extensively pseudouridylated, but with Ψs being under-represented in 3'-untranslated regions and enriched at position 1 of triple codons. The phenylalanine codon UUC was the most frequently pseudouridylated site. Some Ψs present in chloroplast 23S, 16S, and 4.5S rRNAs in wild-type Col-0 were absent in plants with a mutation of SVR1 (Suppressor of variegation 1), a chloroplast pseudouridine synthase gene. Many plastid ribosomal proteins and photosynthesis-related proteins were significantly reduced in svr1 relative to the wild-type, indicating the roles of SVR1 in chloroplast protein biosynthesis in Arabidopsis. Our results provide new insights into the occurrence of pseudouridine in Arabidopsis RNAs and the biological functions of SVR1, and will pave the way for further exploiting the mechanisms underlying Ψ modifications in controlling gene expression and protein biosynthesis in plants.
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Affiliation(s)
- Lirong Sun
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yuxing Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shenglong Bai
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xue Bai
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Huijie Zhu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Huan Dong
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Wei Wang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaohong Zhu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Fushun Hao
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- Correspondence:
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135
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Chen Z, Qi M, Shen B, Luo G, Wu Y, Li J, Lu Z, Zheng Z, Dai Q, Wang H. Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs. Nucleic Acids Res 2019; 47:2533-2545. [PMID: 30541109 PMCID: PMC6411830 DOI: 10.1093/nar/gky1250] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/16/2018] [Accepted: 12/03/2018] [Indexed: 12/11/2022] Open
Abstract
Transfer RNA is heavily modified and plays a central role in protein synthesis and cellular functions. Here we demonstrate that ALKBH3 is a 1-methyladenosine (m1A) and 3-methylcytidine (m3C) demethylase of tRNA. ALKBH3 can promote cancer cell proliferation, migration and invasion. In vivo study confirms the regulation effects of ALKBH3 on growth of tumor xenograft. The m1A demethylated tRNA is more sensitive to angiogenin (ANG) cleavage, followed by generating tRNA-derived small RNAs (tDRs) around the anticodon regions. tDRs are conserved among species, which strengthen the ribosome assembly and prevent apoptosis triggered by cytochrome c (Cyt c). Our discovery opens a potential and novel paradigm of tRNA demethylase, which regulates biological functions via generation of tDRs.
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Affiliation(s)
- Zhuojia Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Meijie Qi
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Guanzheng Luo
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingmin Wu
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiexin Li
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhike Lu
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Zhong Zheng
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Hongsheng Wang
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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136
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Liu H, Begik O, Lucas MC, Ramirez JM, Mason CE, Wiener D, Schwartz S, Mattick JS, Smith MA, Novoa EM. Accurate detection of m 6A RNA modifications in native RNA sequences. Nat Commun 2019; 10:4079. [PMID: 31501426 PMCID: PMC6734003 DOI: 10.1038/s41467-019-11713-9] [Citation(s) in RCA: 256] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/29/2019] [Indexed: 12/12/2022] Open
Abstract
The epitranscriptomics field has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here, we show that using direct RNA sequencing, N6-methyladenosine (m6A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Specifically, we find that our algorithm, trained with m6A-modified and unmodified synthetic sequences, can predict m6A RNA modifications with ~90% accuracy. We then extend our findings to yeast data sets, finding that our method can identify m6A RNA modifications in vivo with an accuracy of 87%. Moreover, we further validate our method by showing that these 'errors' are typically not observed in yeast ime4-knockout strains, which lack m6A modifications. Our results open avenues to investigate the biological roles of RNA modifications in their native RNA context.
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Affiliation(s)
- Huanle Liu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, New South Wales, 2010, Australia
| | - Oguzhan Begik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, New South Wales, 2010, Australia
- St-Vincent's Clinical School, UNSW Sydney, Darlinghurst, New South Wales, 2010, Australia
| | - Morghan C Lucas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Miguel Ramirez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- The Feil Family Brain and Mind Institute, Weill Cornell Medicine, New York, NY, 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA
| | - David Wiener
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - John S Mattick
- Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, New South Wales, 2010, Australia
- St-Vincent's Clinical School, UNSW Sydney, Darlinghurst, New South Wales, 2010, Australia
- Green templeton College, Oxford, OX2 6HG, UK
| | - Martin A Smith
- St-Vincent's Clinical School, UNSW Sydney, Darlinghurst, New South Wales, 2010, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, 2010, Australia
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.
- Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, New South Wales, 2010, Australia.
- St-Vincent's Clinical School, UNSW Sydney, Darlinghurst, New South Wales, 2010, Australia.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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137
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Konno M, Koseki J, Asai A, Yamagata A, Shimamura T, Motooka D, Okuzaki D, Kawamoto K, Mizushima T, Eguchi H, Takiguchi S, Satoh T, Mimori K, Ochiya T, Doki Y, Ofusa K, Mori M, Ishii H. Distinct methylation levels of mature microRNAs in gastrointestinal cancers. Nat Commun 2019; 10:3888. [PMID: 31467274 PMCID: PMC6715669 DOI: 10.1038/s41467-019-11826-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
The biological significance of micro (mi)RNAs has traditionally been evaluated according to their RNA expression levels based on the assumption that miRNAs recognize and regulate their targets in an unvarying fashion. Here we show that a fraction of mature miRNAs including miR-17-5p, -21-5p, and -200c-3p and let-7a-5p harbor methyl marks that potentially alter their stability and target recognition. Importantly, methylation of these miRNAs was significantly increased in cancer tissues as compared to paired normal tissues. Furthermore, miR-17-5p methylation level in serum samples distinguished early pancreatic cancer patients from healthy controls with extremely high sensitivity and specificity. These findings provide a basis for diagnostic strategies for early-stage cancer and add a dimension to our understanding of miRNA biology. In cancer it is assumed that microRNAs recognise and regulate their targets uniformly. Here, the authors show that in gastrointestinal cancers methylation of microRNAs may impact their stability, and that levels of microRNA methylation are distinct in pancreatic cancer patients compared to healthy controls with potential diagnostic implications.
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Affiliation(s)
- Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Jun Koseki
- Department of Cancer Profiling Discovery/ Medical Data Science, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Ayumu Asai
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.,Department of Cancer Profiling Discovery/ Medical Data Science, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Akira Yamagata
- Prophoenix Division, Food and Life-Science Laboratory, Idea Consultants, Inc., Osaka-city, Osaka, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Koichi Kawamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Shuji Takiguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.,Department of Gastroenterological Surgery, Nagoya City University Graduate School of Medical Sciences and Medical School, Nagoya, Aichi, Japan
| | - Taroh Satoh
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita, Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Ken Ofusa
- Prophoenix Division, Food and Life-Science Laboratory, Idea Consultants, Inc., Osaka-city, Osaka, Japan.
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hideshi Ishii
- Department of Cancer Profiling Discovery/ Medical Data Science, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
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138
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Debiec K, Matuszewski M, Podskoczyj K, Leszczynska G, Sochacka E. Chemical Synthesis of Oligoribonucleotide (ASL of tRNA Lys T. brucei) Containing a Recently Discovered Cyclic Form of 2-Methylthio-N 6 -threonylcarbamoyladenosine (ms 2 ct 6 A). Chemistry 2019; 25:13309-13317. [PMID: 31328310 DOI: 10.1002/chem.201902411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/16/2019] [Indexed: 01/25/2023]
Abstract
The synthesis of the protected form of 2-methylthio-N6 -threonylcarbamoyl adenosine (ms2 t6 A) was developed starting from adenosine or guanosine by using the optimized carbamate method and, for the first time, an isocyanate route. The hypermodified nucleoside was subsequently transformed into the protected ms2 t6 A-phosphoramidite monomer and used in a large-scale synthesis of the precursor 17nt ms2 t6 A-oligonucleotide (the anticodon stem and loop fragment of tRNALys from T. brucei). Finally, stereochemically secure ms2 t6 A→ms2 ct6 A cyclization at the oligonucleotide level efficiently afforded a tRNA fragment bearing the ms2 ct6 A unit. The applied post-synthetic approach provides two sequentially homologous ms2 t6 A- and ms2 ct6 A-oligonucleotides that are suitable for further comparative structure-activity relationship studies.
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Affiliation(s)
- Katarzyna Debiec
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
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139
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Valdez F, Salvador J, Palermo PM, Mohl JE, Hanley KA, Watts D, Llano M. Schlafen 11 Restricts Flavivirus Replication. J Virol 2019; 93:e00104-19. [PMID: 31118262 PMCID: PMC6639263 DOI: 10.1128/jvi.00104-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/14/2019] [Indexed: 02/07/2023] Open
Abstract
Schlafen 11 (Slfn11) is an interferon-stimulated gene that controls the synthesis of proteins by regulating tRNA abundance. Likely through this mechanism, Slfn11 has previously been shown to impair human immunodeficiency virus type 1 (HIV-1) infection and the expression of codon-biased open reading frames. Because replication of positive-sense single-stranded RNA [(+)ssRNA] viruses requires the immediate translation of the incoming viral genome, whereas negative-sense single-stranded RNA [(-)ssRNA] viruses carry at infection an RNA replicase that makes multiple translation-competent copies of the incoming viral genome, we reasoned that (+)ssRNA viruses will be more sensitive to the effect of Slfn11 on protein synthesis than (-)ssRNA viruses. To evaluate this hypothesis, we tested the effects of Slfn11 on the replication of a panel of ssRNA viruses in the human glioblastoma cell line A172, which naturally expresses Slfn11. Depletion of Slfn11 significantly increased the replication of (+)ssRNA viruses from the Flavivirus genus, including West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV), but had no significant effect on the replication of the (-)ssRNA viruses vesicular stomatitis virus (VSV) (Rhabdoviridae family) and Rift Valley fever virus (RVFV) (Phenuiviridae family). Quantification of the ratio of genome-containing viral particles to PFU indicated that Slfn11 impairs WNV infectivity. Intriguingly, Slfn11 prevented WNV-induced downregulation of a subset of tRNAs implicated in the translation of 11.8% of the viral polyprotein. Low-abundance tRNAs might promote optimal protein folding and enhance viral infectivity, as previously reported. In summary, this study demonstrates that Slfn11 restricts flavivirus replication by impairing viral infectivity.IMPORTANCE We provide evidence that the cellular protein Schlafen 11 (Slfn11) impairs replication of flaviviruses, including West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV). However, replication of single-stranded negative RNA viruses was not affected. Specifically, Slfn11 decreases the infectivity of WNV potentially by preventing virus-induced modifications of the host tRNA repertoire that could lead to enhanced viral protein folding. Furthermore, we demonstrate that Slfn11 is not the limiting factor of this novel broad antiviral pathway.
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Affiliation(s)
- Federico Valdez
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Julienne Salvador
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Pedro M Palermo
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Jonathon E Mohl
- Department of Bioinformatics, The University of Texas at El Paso, El Paso, Texas, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - Douglas Watts
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Manuel Llano
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
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140
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Barraud P, Tisné C. To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs. IUBMB Life 2019; 71:1126-1140. [PMID: 30932315 PMCID: PMC6850298 DOI: 10.1002/iub.2041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/10/2019] [Indexed: 12/12/2022]
Abstract
Transfer RNAs (tRNAs) are essential components of the cellular protein synthesis machineries, but are also implicated in many roles outside translation. To become functional, tRNAs, initially transcribed as longer precursor tRNAs, undergo a tightly controlled biogenesis process comprising the maturation of their extremities, removal of intronic sequences if present, addition of the 3'-CCA amino-acid accepting sequence, and aminoacylation. In addition, the most impressive feature of tRNA biogenesis consists in the incorporation of a large number of posttranscriptional chemical modifications along its sequence. The chemical nature of these modifications is highly diverse, with more than hundred different modifications identified in tRNAs to date. All functions of tRNAs in cells are controlled and modulated by modifications, making the understanding of the mechanisms that determine and influence nucleotide modifications in tRNAs an essential point in tRNA biology. This review describes the different aspects that determine whether a certain position in a tRNA molecule is modified or not. We describe how sequence and structural determinants, as well as the presence of prior modifications control modification processes. We also describe how environmental factors and cellular stresses influence the level and/or the nature of certain modifications introduced in tRNAs, and report situations where these dynamic modulations of tRNA modification levels are regulated by active demodification processes. © 2019 IUBMB Life, 71(8):1126-1140, 2019.
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Affiliation(s)
- Pierre Barraud
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
| | - Carine Tisné
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
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141
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Ranjan N, Leidel SA. The epitranscriptome in translation regulation: mRNA and tRNA modifications as the two sides of the same coin? FEBS Lett 2019; 593:1483-1493. [PMID: 31206634 DOI: 10.1002/1873-3468.13491] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022]
Abstract
Translation of mRNA is a highly regulated process that is tightly coordinated with cotranslational protein maturation. Recently, mRNA modifications and tRNA modifications - the so called epitranscriptome - have added a new layer of regulation that is still poorly understood. Both types of modifications can affect codon-anticodon interactions, thereby affecting mRNA translation and protein synthesis in similar ways. Here, we describe an updated view on how the different types of modifications can be mapped, how they affect translation, how they trigger phenotypes and discuss how the combined action of mRNA and tRNA modifications coordinate translation in health and disease.
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Affiliation(s)
- Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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142
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Bornelöv S, Selmi T, Flad S, Dietmann S, Frye M. Codon usage optimization in pluripotent embryonic stem cells. Genome Biol 2019; 20:119. [PMID: 31174582 PMCID: PMC6555954 DOI: 10.1186/s13059-019-1726-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/23/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The uneven use of synonymous codons in the transcriptome regulates the efficiency and fidelity of protein translation rates. Yet, the importance of this codon bias in regulating cell state-specific expression programmes is currently debated. Here, we ask whether different codon usage controls gene expression programmes in self-renewing and differentiating embryonic stem cells. RESULTS Using ribosome and transcriptome profiling, we identify distinct codon signatures during human embryonic stem cell differentiation. We find that cell state-specific codon bias is determined by the guanine-cytosine (GC) content of differentially expressed genes. By measuring the codon frequencies at the ribosome active sites interacting with transfer RNAs (tRNA), we further discover that self-renewing cells optimize translation of codons that depend on the inosine tRNA modification in the anticodon wobble position. Accordingly, inosine levels are highest in human pluripotent embryonic stem cells. This effect is conserved in mice and is independent of the differentiation stimulus. CONCLUSIONS We show that GC content influences cell state-specific mRNA levels, and we reveal how translational mechanisms based on tRNA modifications change codon usage in embryonic stem cells.
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Affiliation(s)
- Susanne Bornelöv
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Tommaso Selmi
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Sophia Flad
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Sabine Dietmann
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Michaela Frye
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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143
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Monies D, Vågbø CB, Al-Owain M, Alhomaidi S, Alkuraya FS. Recessive Truncating Mutations in ALKBH8 Cause Intellectual Disability and Severe Impairment of Wobble Uridine Modification. Am J Hum Genet 2019; 104:1202-1209. [PMID: 31079898 DOI: 10.1016/j.ajhg.2019.03.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/26/2019] [Indexed: 01/17/2023] Open
Abstract
The wobble hypothesis was proposed to explain the presence of fewer tRNAs than possible codons. The wobble nucleoside position in the anticodon stem-loop undergoes a number of modifications that help maintain the efficiency and fidelity of translation. AlkB homolog 8 (ALKBH8) is an atypical member of the highly conserved AlkB family of dioxygenases and is involved in the formation of mcm5s2U, (S)-mchm5U, (R)-mchm5U, mcm5U, and mcm5Um at the anticodon wobble uridines of specific tRNAs. In two multiplex consanguineous families, we identified two homozygous truncating ALKBH8 mutations causing intellectual disability. Analysis of tRNA derived from affected individuals showed the complete absence of these modifications, consistent with the presumptive loss of function of the variants. Our results highlight the sensitivity of the brain to impaired wobble modification and expand the list of intellectual-disability syndromes caused by mutations in genes related to tRNA modification.
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144
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Chen Y, Bai B, Yan H, Wen F, Qin D, Jander G, Xia Q, Wang G. Systemic disruption of the homeostasis of transfer RNA isopentenyltransferase causes growth and development abnormalities in Bombyx mori. INSECT MOLECULAR BIOLOGY 2019; 28:380-391. [PMID: 30548717 DOI: 10.1111/imb.12561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isopentenylation at A37 (i6 A37) of some transfer RNAs (tRNAs) plays a vital role in regulating the efficiency and fidelity of protein synthesis. However, whether insects, which are well known for their highly efficient protein synthesis machinery, employ this regulatory mechanism remains uninvestigated. In the current study, a candidate tRNA isopentenyltransferase (IPT) gene with three alternative splicing isoforms (BmIPT1-BmIPT3) was identified in Bombyx mori (silkworm). Only BmIPT1 could complement a yeast mutant lacking tRNA IPT. Phylogenetic analysis showed that silkworm tRNA IPT is conserved in the Lepidoptera. BmIPT was expressed in all B. mori tissues and organs that were investigated, but was expressed at a significantly higher level in silk glands of the fourth instar compared to the first day of the fifth instar. Interestingly, BmIPT was expressed at a significantly higher level in the domesticated silkworm, B. mori, than in wild Bombyx mandarina in multiple tissues and organs. Knock-down of BmIPT by RNA interference caused severe abnormalities in silk spinning and metamorphosis. Constitutive overexpression of BmIPT1 using a cytoplasmic actin 4 promoter in B. mori raised its messenger RNA level more than sixfold compared with nontransgenic insects and led to significant decreases in the body weight and cocoon shell ratio. Together, these results confirm the first functional tRNA IPT in insects and show that a suitable expression level of tRNA IPT is vital for silk spinning, normal growth, and metamorphosis. Thus, i6 A modification at position A37 in tRNA probably plays an important role in B. mori protein synthesis.
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Affiliation(s)
- Y Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - B Bai
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - H Yan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - F Wen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - D Qin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - G Jander
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Q Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - G Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
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145
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Charging the code - tRNA modification complexes. Curr Opin Struct Biol 2019; 55:138-146. [PMID: 31102979 DOI: 10.1016/j.sbi.2019.03.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/08/2019] [Indexed: 02/06/2023]
Abstract
All types of cellular RNAs are post-transcriptionally modified, constituting the so called 'epitranscriptome'. In particular, tRNAs and their anticodon stem loops represent major modification hotspots. The attachment of small chemical groups at the heart of the ribosomal decoding machinery can directly affect translational rates, reading frame maintenance, co-translational folding dynamics and overall proteome stability. The variety of tRNA modification patterns is driven by the activity of specialized tRNA modifiers and large modification complexes. Notably, the absence or dysfunction of these cellular machines is correlated with several human pathophysiologies. In this review, we aim to highlight the most recent scientific progress and summarize currently available structural information of the most prominent eukaryotic tRNA modifiers.
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146
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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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147
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Delaunay S, Frye M. RNA modifications regulating cell fate in cancer. Nat Cell Biol 2019; 21:552-559. [PMID: 31048770 DOI: 10.1038/s41556-019-0319-0] [Citation(s) in RCA: 209] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/26/2019] [Indexed: 02/02/2023]
Abstract
The deposition of chemical modifications into RNA is a crucial regulator of temporal and spatial gene expression programs during development. Accordingly, altered RNA modification patterns are widely linked to developmental diseases. Recently, the dysregulation of RNA modification pathways also emerged as a contributor to cancer. By modulating cell survival, differentiation, migration and drug resistance, RNA modifications add another regulatory layer of complexity to most aspects of tumourigenesis.
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Affiliation(s)
- Sylvain Delaunay
- Department of Genetics, University of Cambridge, Cambridge, UK
- German Cancer Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Michaela Frye
- Department of Genetics, University of Cambridge, Cambridge, UK.
- German Cancer Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany.
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148
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Cosentino C, Cnop M, Igoillo-Esteve M. The tRNA Epitranscriptome and Diabetes: Emergence of tRNA Hypomodifications as a Cause of Pancreatic β-Cell Failure. Endocrinology 2019; 160:1262-1274. [PMID: 30907926 DOI: 10.1210/en.2019-00098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/15/2019] [Indexed: 01/26/2023]
Abstract
tRNAs are crucial noncoding RNA molecules that serve as amino acid carriers during protein synthesis. The transcription of tRNA genes is a highly regulated process. The tRNA pool is tissue and cell specific, it varies during development, and it is modulated by the environment. tRNAs are highly posttranscriptionally modified by specific tRNA-modifying enzymes. The tRNA modification signature of a cell determines the tRNA epitranscriptome. Perturbations in the tRNA epitranscriptome, as a consequence of mutations in tRNAs and tRNA-modifying enzymes or environmental exposure, have been associated with human disease, including diabetes. tRNA fragmentation induced by impaired tRNA modifications or dietary factors has been linked to pancreatic β-cell demise and paternal inheritance of metabolic traits. Herein, we review recent findings that associate tRNA epitranscriptome perturbations with diabetes.
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Affiliation(s)
- Cristina Cosentino
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
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149
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Ohsawa Y, Hagiwara H, Nishimatsu SI, Hirakawa A, Kamimura N, Ohtsubo H, Fukai Y, Murakami T, Koga Y, Goto YI, Ohta S, Sunada Y. Taurine supplementation for prevention of stroke-like episodes in MELAS: a multicentre, open-label, 52-week phase III trial. J Neurol Neurosurg Psychiatry 2019; 90:529-536. [PMID: 29666206 PMCID: PMC6581075 DOI: 10.1136/jnnp-2018-317964] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/29/2022]
Abstract
OBJECTIVE The aim of this study was to evaluate the efficacy and safety of high-dose taurine supplementation for prevention of stroke-like episodes of MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes), a rare genetic disorder caused by point mutations in the mitochondrial DNA that lead to a taurine modification defect at the first anticodon nucleotide of mitochondrial tRNALeu(UUR), resulting in failure to decode codons accurately. METHODS After the nationwide survey of MELAS, we conducted a multicentre, open-label, phase III trial in which 10 patients with recurrent stroke-like episodes received high-dose taurine (9 g or 12 g per day) for 52 weeks. The primary endpoint was the complete prevention of stroke-like episodes during the evaluation period. The taurine modification rate of mitochondrial tRNALeu(UUR) was measured before and after the trial. RESULTS The proportion of patients who reached the primary endpoint (100% responder rate) was 60% (95% CI 26.2% to 87.8%). The 50% responder rate, that is, the number of patients achieving a 50% or greater reduction in frequency of stroke-like episodes, was 80% (95% CI 44.4% to 97.5%). Taurine reduced the annual relapse rate of stroke-like episodes from 2.22 to 0.72 (P=0.001). Five patients showed a significant increase in the taurine modification of mitochondrial tRNALeu(UUR) from peripheral blood leukocytes (P<0.05). No severe adverse events were associated with taurine. CONCLUSIONS The current study demonstrates that oral taurine supplementation can effectively reduce the recurrence of stroke-like episodes and increase taurine modification in mitochondrial tRNALeu(UUR) in MELAS. TRIAL REGISTRATION NUMBER UMIN000011908.
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Affiliation(s)
- Yutaka Ohsawa
- Department of Neurology, Kawasaki Medical School, Kurashiki, Japan
| | - Hiroki Hagiwara
- Department of Medical Science, Teikyo University of Science, Adachi-ku, Japan
| | | | - Akihiro Hirakawa
- Center for Advanced Medicine and Clinical Research, Statistical Analysis Section, Nagoya University Hospital, Nagoya, Japan.,Graduate School of Medicine, Department of Biostatistics and Bioinformatics, The University of Tokyo, Tokyo, Japan
| | - Naomi Kamimura
- Department of Biochemistry and Cell Biology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Hideaki Ohtsubo
- Department of Neurology, Kawasaki Medical School, Kurashiki, Japan
| | - Yuta Fukai
- Department of Neurology, Kawasaki Medical School, Kurashiki, Japan
| | | | - Yasutoshi Koga
- Department of Pediatrics and Child Health, Kurume University Graduate School of Medicine, Kurume, Japan
| | - Yu-Ichi Goto
- The Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Shigeo Ohta
- Department of Biochemistry and Cell Biology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.,Department of Neurology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Yoshihide Sunada
- Department of Neurology, Kawasaki Medical School, Kurashiki, Japan
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150
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Zhou Z, Sun B, Huang S, Jia W, Yu D. The tRNA-associated dysregulation in diabetes mellitus. Metabolism 2019; 94:9-17. [PMID: 30711570 DOI: 10.1016/j.metabol.2019.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/26/2019] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
Diabetes mellitus (DM) is a complex endocrine and metabolic disorder for human health and well-being. Deregulated glucose and lipid metabolism are the primary underlying manifestations associated with this disease. Transfer RNAs (tRNAs) are considered to mainly participate in protein translation and may contribute to complex human pathologies. Although the molecular mechanisms remain, for the most part, unknown, accumulating evidence indicates that tRNAs play a vital role in the pathogenesis of DM. This paper reviews different aspects of tRNA-associated dysregulation in DM, such as tRNA mutations, tRNA modifications, tRNA aminoacylation and tRNA derivatives, aiming at a better understanding of the pathogenesis of DM and providing new ideas for the personalized treatment of this metabolism-associated disease.
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Affiliation(s)
- Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Bao Sun
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410000, China; Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410000, China
| | - Shiqiong Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410000, China; Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410000, China
| | - Wenrui Jia
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
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