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Schultz SK, Kothe U. RNA modifying enzymes shape tRNA biogenesis and function. J Biol Chem 2024:107488. [PMID: 38908752 DOI: 10.1016/j.jbc.2024.107488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Transfer RNAs (tRNAs) are the most highly modified cellular RNAs, both with respect to the proportion of nucleotides that are modified within the tRNA sequence and with respect to the extraordinary diversity in tRNA modification chemistry. However, the functions of many different tRNA modifications are only beginning to emerge. tRNAs have two general clusters of modifications. The first cluster is within the anticodon stem-loop including several modifications essential for protein translation. The second cluster of modifications is within the tRNA elbow, and roles for these modifications are less clear. In general, tRNA elbow modifications are typically not essential for cell growth, but nonetheless several tRNA elbow modifications have been highly conserved throughout all domains of life. In addition to forming modifications, many tRNA modifying enzymes have been demonstrated or hypothesized to additionally play an important role in folding tRNA acting as tRNA chaperones. In this review, we summarize the known functions of tRNA modifying enzymes throughout the lifecycle of a tRNA molecule, from transcription to degradation. Thereby, we describe how tRNA modification and folding by tRNA modifying enzymes enhance tRNA maturation, tRNA aminoacylation, and tRNA function during protein synthesis, ultimately impacting cellular phenotypes and disease.
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Affiliation(s)
- Sarah K Schultz
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
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2
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Yared MJ, Yoluç Y, Catala M, Tisné C, Kaiser S, Barraud P. Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs. Nucleic Acids Res 2023; 51:10653-10667. [PMID: 37650648 PMCID: PMC10602860 DOI: 10.1093/nar/gkad722] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
As essential components of the protein synthesis machinery, tRNAs undergo a tightly controlled biogenesis process, which include the incorporation of numerous posttranscriptional modifications. Defects in these tRNA maturation steps may lead to the degradation of hypomodified tRNAs by the rapid tRNA decay (RTD) and nuclear surveillance pathways. We previously identified m1A58 as a late modification introduced after modifications Ψ55 and T54 in yeast elongator tRNAPhe. However, previous reports suggested that m1A58 is introduced early during the tRNA modification process, in particular on primary transcripts of initiator tRNAiMet, which prevents its degradation by RNA decay pathways. Here, aiming to reconcile this apparent inconsistency on the temporality of m1A58 incorporation, we examined its introduction into yeast elongator and initiator tRNAs. We used specifically modified tRNAs to report on the molecular aspects controlling the Ψ55 → T54 → m1A58 modification circuit in elongator tRNAs. We also show that m1A58 is efficiently introduced on unmodified tRNAiMet, and does not depend on prior modifications. Finally, we show that m1A58 has major effects on the structural properties of initiator tRNAiMet, so that the tRNA elbow structure is only properly assembled when this modification is present. This observation provides a structural explanation for the degradation of hypomodified tRNAiMet lacking m1A58 by the nuclear surveillance and RTD pathways.
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Affiliation(s)
- Marcel-Joseph Yared
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Marjorie Catala
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Carine Tisné
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Stefanie Kaiser
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
| | - Pierre Barraud
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
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3
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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4
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Wolff P, Lechner A, Droogmans L, Grosjean H, Westhof E. Identification of U p47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium. RNA (NEW YORK, N.Y.) 2023; 29:551-556. [PMID: 36759127 PMCID: PMC10159004 DOI: 10.1261/rna.079546.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/19/2023] [Indexed: 05/06/2023]
Abstract
Analysis of the profile of the tRNA modifications in several Archaea allowed us to observe a novel modified uridine in the V-loop of several tRNAs from two species: Pyrococcus furiosus and Sulfolobus acidocaldarius Recently, Ohira and colleagues characterized 2'-phosphouridine (Up) at position 47 in tRNAs of thermophilic Sulfurisphaera tokodaii, as well as in several other archaea and thermophilic bacteria. From the presence of the gene arkI corresponding to the RNA kinase responsible for Up47 formation, they also concluded that Up47 should be present in tRNAs of other thermophilic Archaea Reanalysis of our earlier data confirms that the unidentified residue in tRNAs of both P. furiosus and S. acidocaldarius is indeed 2'-phosphouridine followed by m5C48. Moreover, we find this modification in several tRNAs of other Archaea and of the hyperthermophilic bacterium Aquifex aeolicus.
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Affiliation(s)
- Philippe Wolff
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Antony Lechner
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Louis Droogmans
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, Anderlecht B-1070, Belgium
| | - Henri Grosjean
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, Anderlecht B-1070, Belgium
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084 Strasbourg, France
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5
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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6
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Hori H. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Genes (Basel) 2023; 14:genes14020382. [PMID: 36833309 PMCID: PMC9957541 DOI: 10.3390/genes14020382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The existence of the thiouridine synthetase, methyltransferase and pseudouridine synthase (THUMP) domain was originally predicted by a bioinformatic study. Since the prediction of the THUMP domain more than two decades ago, many tRNA modification enzymes containing the THUMP domain have been identified. According to their enzymatic activity, THUMP-related tRNA modification enzymes can be classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase. In this review, I focus on the functions and structures of these tRNA modification enzymes and the modified nucleosides they produce. Biochemical, biophysical and structural studies of tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase have established the concept that the THUMP domain captures the 3'-end of RNA (in the case of tRNA, the CCA-terminus). However, in some cases, this concept is not simply applicable given the modification patterns observed in tRNA. Furthermore, THUMP-related proteins are involved in the maturation of other RNAs as well as tRNA. Moreover, the modified nucleosides, which are produced by the THUMP-related tRNA modification enzymes, are involved in numerous biological phenomena, and the defects of genes for human THUMP-related proteins are implicated in genetic diseases. In this review, these biological phenomena are also introduced.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
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7
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Antika TR, Nazilah KR, Lee YH, Lo YT, Yeh CS, Yeh FL, Chang TH, Wang TL, Wang CC. Human Thg1 displays tRNA-inducible GTPase activity. Nucleic Acids Res 2022; 50:10015-10025. [PMID: 36107775 PMCID: PMC9508852 DOI: 10.1093/nar/gkac768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
tRNAHis guanylyltransferase (Thg1) catalyzes the 3′-5′ incorporation of guanosine into position -1 (G-1) of tRNAHis. G-1 is unique to tRNAHis and is crucial for recognition by histidyl-tRNA synthetase (HisRS). Yeast Thg1 requires ATP for G-1 addition to tRNAHis opposite A73, whereas archaeal Thg1 requires either ATP or GTP for G-1 addition to tRNAHis opposite C73. Paradoxically, human Thg1 (HsThg1) can add G-1 to tRNAsHis with A73 (cytoplasmic) and C73 (mitochondrial). As N73 is immediately followed by a CCA end (positions 74–76), how HsThg1 prevents successive 3′-5′ incorporation of G-1/G-2/G-3 into mitochondrial tRNAHis (tRNAmHis) through a template-dependent mechanism remains a puzzle. We showed herein that mature native human tRNAmHis indeed contains only G-1. ATP was absolutely required for G-1 addition to tRNAmHis by HsThg1. Although HsThg1 could incorporate more than one GTP into tRNAmHisin vitro, a single-GTP incorporation prevailed when the relative GTP level was low. Surprisingly, HsThg1 possessed a tRNA-inducible GTPase activity, which could be inhibited by ATP. Similar activity was found in other high-eukaryotic dual-functional Thg1 enzymes, but not in yeast Thg1. This study suggests that HsThg1 may downregulate the level of GTP through its GTPase activity to prevent multiple-GTP incorporation into tRNAmHis.
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Affiliation(s)
- Titi Rindi Antika
- Department of Life Sciences, National Central University , Zhongli District, Taoyuan 320317, Taiwan
| | - Kun Rohmatan Nazilah
- Department of Life Sciences, National Central University , Zhongli District, Taoyuan 320317, Taiwan
| | - Yi-Hsueh Lee
- Department of Life Sciences, National Central University , Zhongli District, Taoyuan 320317, Taiwan
| | - Ya-Ting Lo
- Department of Life Sciences, National Central University , Zhongli District, Taoyuan 320317, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center , Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - Fu-Lung Yeh
- Genomics Research Center , Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - Tien-Hsien Chang
- Genomics Research Center , Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - Tzu-Ling Wang
- Graduate Institute of Mathematics and Science Education, National Tsing Hua University , Hsinchu City 30014, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University , Zhongli District, Taoyuan 320317, Taiwan
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Nishida Y, Ohmori S, Kakizono R, Kawai K, Namba M, Okada K, Yamagami R, Hirata A, Hori H. Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine- N2-) Methyltransferase (Trm11-Trm112 Complex). Int J Mol Sci 2022; 23:ijms23074046. [PMID: 35409407 PMCID: PMC8999500 DOI: 10.3390/ijms23074046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 12/10/2022] Open
Abstract
The Saccharomyces cerevisiae Trm11 and Trm112 complex (Trm11-Trm112) methylates the 2-amino group of guanosine at position 10 in tRNA and forms N2-methylguanosine. To determine the elements required in tRNA for methylation by Trm11-Trm112, we prepared 60 tRNA transcript variants and tested them for methylation by Trm11-Trm112. The results show that the precursor tRNA is not a substrate for Trm11-Trm112. Furthermore, the CCA terminus is essential for methylation by Trm11-Trm112, and Trm11-Trm112 also only methylates tRNAs with a regular-size variable region. In addition, the G10-C25 base pair is required for methylation by Trm11-Trm112. The data also demonstrated that Trm11-Trm112 recognizes the anticodon-loop and that U38 in tRNAAla acts negatively in terms of methylation. Likewise, the U32-A38 base pair in tRNACys negatively affects methylation. The only exception in our in vitro study was tRNAValAAC1. Our experiments showed that the tRNAValAAC1 transcript was slowly methylated by Trm11-Trm112. However, position 10 in this tRNA was reported to be unmodified G. We purified tRNAValAAC1 from wild-type and trm11 gene deletion strains and confirmed that a portion of tRNAValAAC1 is methylated by Trm11-Trm112 in S. cerevisiae. Thus, our study explains the m2G10 modification pattern of all S. cerevisiae class I tRNAs and elucidates the Trm11-Trm112 binding sites.
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9
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Wolff P, Villette C, Zumsteg J, Heintz D, Antoine L, Chane-Woon-Ming B, Droogmans L, Grosjean H, Westhof E. Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea. RNA (NEW YORK, N.Y.) 2020; 26:1957-1975. [PMID: 32994183 PMCID: PMC7668247 DOI: 10.1261/rna.077537.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/09/2020] [Indexed: 05/22/2023]
Abstract
To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.
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Affiliation(s)
- Philippe Wolff
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Laura Antoine
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Béatrice Chane-Woon-Ming
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Louis Droogmans
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, B-1070, Belgium
| | - Henri Grosjean
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, B-1070, Belgium
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
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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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11
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Wang C, van Tran N, Jactel V, Guérineau V, Graille M. Structural and functional insights into Archaeoglobus fulgidus m2G10 tRNA methyltransferase Trm11 and its Trm112 activator. Nucleic Acids Res 2020; 48:11068-11082. [PMID: 33035335 PMCID: PMC7641767 DOI: 10.1093/nar/gkaa830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 01/20/2023] Open
Abstract
tRNAs play a central role during the translation process and are heavily post-transcriptionally modified to ensure optimal and faithful mRNA decoding. These epitranscriptomics marks are added by largely conserved proteins and defects in the function of some of these enzymes are responsible for neurodevelopmental disorders and cancers. Here, we focus on the Trm11 enzyme, which forms N2-methylguanosine (m2G) at position 10 of several tRNAs in both archaea and eukaryotes. While eukaryotic Trm11 enzyme is only active as a complex with Trm112, an allosteric activator of methyltransferases modifying factors (RNAs and proteins) involved in mRNA translation, former studies have shown that some archaeal Trm11 proteins are active on their own. As these studies were performed on Trm11 enzymes originating from archaeal organisms lacking TRM112 gene, we have characterized Trm11 (AfTrm11) from the Archaeoglobus fulgidus archaeon, which genome encodes for a Trm112 protein (AfTrm112). We show that AfTrm11 interacts directly with AfTrm112 similarly to eukaryotic enzymes and that although AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. We finally describe the first crystal structures of the AfTrm11-Trm112 complex and of Trm11, alone or bound to the methyltransferase inhibitor sinefungin.
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Affiliation(s)
- Can Wang
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Nhan van Tran
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Vincent Jactel
- Laboratoire de Synthèse Organique (LSO), CNRS, Ecole polytechnique, ENSTA, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Vincent Guérineau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
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12
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Durán-Aranguren D, Chiriví-Salomón J, Anaya L, Durán-Sequeda D, Cruz L, Serrano J, Sarmiento L, Restrepo S, Sanjuan T, Sierra R. Effect of bioactive compounds extracted from Cordyceps nidus ANDES-F1080 on laccase activity of Pleurotus ostreatus ANDES-F515. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 26:e00466. [PMID: 32617265 PMCID: PMC7322798 DOI: 10.1016/j.btre.2020.e00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Laccases are ligninolytic enzymes produced by different microorganisms, especially by fungi such as the white-rot fungus Pleurotus ostreatus. Chemical inductors have been used to promote laccase secretion due to the application of these enzymes in lignocellulosic biomass pretreatment. Cordyceps nidus ANDES-F1080 was previously described as a source of bioactive compounds that could influence the enzymatic production system of other fungi. For that reason, this study evaluates the effect of C. nidus' ANDES-F1080 extracts on the laccase activity of P. ostreatus ANDES-F515. To achieve this objective, C. nidus ANDES-F1080 was grown in four different substrates: two artificial-based and two natural-based culture media. Metabolites were extracted from C. nidus ANDES-F1080 using water and methanol as solvents. Biochemical characterization of these extracts was performed to complement the analysis of their effect on laccase activity. Our results revealed an enhancement on the laccase activity of P. ostreatus ANDES-F515 grown in natural-based cultures when C. nidus' ANDES-F1080 extracts were supplemented. The best laccase activities registered values around 10,575 ± 813 U·L-1.
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Affiliation(s)
- D. Durán-Aranguren
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - J.S. Chiriví-Salomón
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
- Conservación, Bioprospección y Desarrollo Sostenible, Escuela de Ciencias Agrícolas, Pecuarias y del Medio Ambiente, Universidad Nacional Abierta y a Distancia, Bogotá, Colombia
| | - L. Anaya
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - D. Durán-Sequeda
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - L.J. Cruz
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - J.D. Serrano
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - L. Sarmiento
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - S. Restrepo
- Laboratory of Mycology and Plant Diseases, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - T. Sanjuan
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - R. Sierra
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
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13
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Distinct Modified Nucleosides in tRNA Trp from the Hyperthermophilic Archaeon Thermococcus kodakarensis and Requirement of tRNA m 2G10/m 2 2G10 Methyltransferase (Archaeal Trm11) for Survival at High Temperatures. J Bacteriol 2019; 201:JB.00448-19. [PMID: 31405913 DOI: 10.1128/jb.00448-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022] Open
Abstract
tRNA m2G10/m2 2G10 methyltransferase (archaeal Trm11) methylates the 2-amino group in guanosine at position 10 in tRNA and forms N 2,N 2-dimethylguanosine (m2 2G10) via N 2-methylguanosine (m2G10). We determined the complete sequence of tRNATrp, one of the substrate tRNAs for archaeal Trm11 from Thermococcus kodakarensis, a hyperthermophilic archaeon. Liquid chromatography/mass spectrometry following enzymatic digestion of tRNATrp identified 15 types of modified nucleoside at 21 positions. Several modifications were found at novel positions in tRNA, including 2'-O-methylcytidine at position 6, 2-thiocytidine at position 17, 2'-O-methyluridine at position 20, 5,2'-O-dimethylcytidine at position 32, and 2'-O-methylguanosine at position 42. Furthermore, methylwyosine was found at position 37 in this tRNATrp, although 1-methylguanosine is generally found at this location in tRNATrp from other archaea. We constructed trm11 (Δtrm11) and some gene disruptant strains and compared their tRNATrp with that of the wild-type strain, which confirmed the absence of m2 2G10 and other corresponding modifications, respectively. The lack of 2-methylguanosine (m2G) at position 67 in the trm11 trm14 double disruptant strain suggested that this methylation is mediated by Trm14, which was previously identified as an m2G6 methyltransferase. The Δtrm11 strain grew poorly at 95°C, indicating that archaeal Trm11 is required for T. kodakarensis survival at high temperatures. The m2 2G10 modification might have effects on stabilization of tRNA and/or correct folding of tRNA at the high temperatures. Collectively, these results provide new clues to the function of modifications and the substrate specificities of modification enzymes in archaeal tRNA, enabling us to propose a strategy for tRNA stabilization of this archaeon at high temperatures.IMPORTANCE Thermococcus kodakarensis is a hyperthermophilic archaeon that can grow at 60 to 100°C. The sequence of tRNATrp from this archaeon was determined by liquid chromatography/mass spectrometry. Fifteen types of modified nucleoside were observed at 21 positions, including 5 modifications at novel positions; in addition, methylwyosine at position 37 was newly observed in an archaeal tRNATrp The construction of trm11 (Δtrm11) and other gene disruptant strains confirmed the enzymes responsible for modifications in this tRNA. The lack of 2-methylguanosine (m2G) at position 67 in the trm11 trm14 double disruptant strain suggested that this position is methylated by Trm14, which was previously identified as an m2G6 methyltransferase. The Δtrm11 strain grew poorly at 95°C, indicating that archaeal Trm11 is required for T. kodakarensis survival at high temperatures.
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14
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Abstract
Ribonucleic acid (RNA) is involved in translation and transcription, which are the mechanisms in which cells express genes (Alberts et al., 2002). The three classes of RNA discussed are transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). mRNA is the transcript encoded from DNA, rRNA is associated with ribosomes, and tRNA is associated with amino acids and is used to read mRNA transcripts to make proteins (Lodish, Berk, Zipursky, et al., 2000). Interestingly, the function of tRNA, rRNA, and mRNA can be significantly altered by chemical modifications at the co-transcriptional and post-transcriptional levels, and there are over 171 of these modifications identified thus far (Boccaletto et al., 2018; Modomics-Modified bases, 2017). Several of these modifications are linked to diseases such as cancer, diabetes, and neurological disorders. In this review, we will introduce a few RNA modifications with biological functions and how dysregulation of these RNA modifications is linked to human disease.
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Affiliation(s)
- Amber Yanas
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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15
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Orita I, Futatsuishi R, Adachi K, Ohira T, Kaneko A, Minowa K, Suzuki M, Tamura T, Nakamura S, Imanaka T, Suzuki T, Fukui T. Random mutagenesis of a hyperthermophilic archaeon identified tRNA modifications associated with cellular hyperthermotolerance. Nucleic Acids Res 2019; 47:1964-1976. [PMID: 30605516 PMCID: PMC6393311 DOI: 10.1093/nar/gky1313] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 12/05/2018] [Accepted: 12/22/2018] [Indexed: 12/20/2022] Open
Abstract
Random mutagenesis for the hyperthermophilic archaeon Thermococcus kodakarensis was established by the insertion of an artificial transposon designed to allow easy identification of the transposon-inserted locus. The phenotypic screening was applied for the isolation of thermosensitive mutants of T. kodakarensis, which resulted in the isolation of 16 mutants showing defective growth at the supraoptimal temperature 93°C. The high occurrence of the mutants suggested that the high thermotolerance of hyperthermophiles was achieved by a combination of diverse gene functions. The transposon insertion sites in two-thirds of the mutants were identified in a group of genes responsible for tRNA modifications including 7-formamidino-7-deaza-guanosine (archaeosine), N1-methyladenosine/N1-methylinosine, N4-acetylcytidine, and N2-dimethylguanosine/N2,N2-dimethylguanosine. LC–MS/MS analyses of tRNA nucleosides and fragments exhibited disappearance of the corresponding modifications in the mutants. The melting temperature of total tRNA fraction isolated from the mutants lacking archaeosine or N1-methyladenosine/N1-methylinosine decreased significantly, suggesting that the thermosensitive phenotype of these mutants was attributed to low stability of the hypomodified tRNAs. Genes for metabolism, transporters, and hypothetical proteins were also identified in the thermosensitive mutants. The present results demonstrated the usefulness of random mutagenesis for the studies on the hyperthermophile, as well as crucial roles of tRNA modifications in cellular thermotolerance.
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Affiliation(s)
- Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Ryohei Futatsuishi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Kyoko Adachi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akira Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Keiichi Minowa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Miho Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Takeshi Tamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
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16
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The emerging impact of tRNA modifications in the brain and nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:412-428. [PMID: 30529455 DOI: 10.1016/j.bbagrm.2018.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023]
Abstract
A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. In particular, we describe how the structure and location of a tRNA modification influences tRNA folding, stability, and function. We then highlight how modifications in tRNA can impact multiple aspects of protein translation that are instrumental for maintaining proper cellular proteostasis. Importantly, we describe how perturbations in tRNA modification lead to a spectrum of deleterious biological outcomes that can disturb neurodevelopment and neurological function. Finally, we summarize the biological themes shared by the different tRNA modifications linked to cognitive disorders and offer insight into the future questions that remain to decipher the role of tRNA modifications. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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17
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Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
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18
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Dewe JM, Fuller BL, Lentini JM, Kellner SM, Fu D. TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. Mol Cell Biol 2017; 37:e00214-17. [PMID: 28784718 PMCID: PMC5640816 DOI: 10.1128/mcb.00214-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/17/2017] [Accepted: 07/29/2017] [Indexed: 02/07/2023] Open
Abstract
Mutations in the tRNA methyltransferase 1 (TRMT1) gene have been identified as the cause of certain forms of autosomal-recessive intellectual disability (ID). However, the molecular pathology underlying ID-associated TRMT1 mutations is unknown, since the biological role of the encoded TRMT1 protein remains to be determined. Here, we have elucidated the molecular targets and function of TRMT1 to uncover the cellular effects of ID-causing TRMT1 mutations. Using human cells that have been rendered deficient in TRMT1, we show that TRMT1 is responsible for catalyzing the dimethylguanosine (m2,2G) base modification in both nucleus- and mitochondrion-encoded tRNAs. TRMT1-deficient cells exhibit decreased proliferation rates, alterations in global protein synthesis, and perturbations in redox homeostasis, including increased endogenous ROS levels and hypersensitivity to oxidizing agents. Notably, ID-causing TRMT1 variants are unable to catalyze the formation of m2,2G due to defects in RNA binding and cannot rescue oxidative stress sensitivity. Our results uncover a biological role for TRMT1-catalyzed tRNA modification in redox metabolism and show that individuals with TRMT1-associated ID are likely to have major perturbations in cellular homeostasis due to the lack of m2,2G modifications.
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Affiliation(s)
- Joshua M Dewe
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | - Benjamin L Fuller
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | - Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | | | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
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19
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Tomikawa C, Takai K, Hori H. Kinetic characterization of substrate-binding sites of thermostable tRNA methyltransferase (TrmB). J Biochem 2017; 163:133-142. [DOI: 10.1093/jb/mvx068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/01/2017] [Indexed: 11/13/2022] Open
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20
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Lorenz C, Lünse CE, Mörl M. tRNA Modifications: Impact on Structure and Thermal Adaptation. Biomolecules 2017; 7:E35. [PMID: 28375166 PMCID: PMC5485724 DOI: 10.3390/biom7020035] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 12/27/2022] Open
Abstract
Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots-the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation.
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Affiliation(s)
- Christian Lorenz
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Christina E Lünse
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Mario Mörl
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
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21
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Hirata A, Nishiyama S, Tamura T, Yamauchi A, Hori H. Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules. Nucleic Acids Res 2016; 44:6377-90. [PMID: 27325738 PMCID: PMC5291279 DOI: 10.1093/nar/gkw561] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/09/2016] [Indexed: 12/30/2022] Open
Abstract
N(2)-methylguanosine is one of the most universal modified nucleosides required for proper function in transfer RNA (tRNA) molecules. In archaeal tRNA species, a specific S-adenosyl-L-methionine (SAM)-dependent tRNA methyltransferase (MTase), aTrm11, catalyzes formation of N(2)-methylguanosine and N(2),N(2)-dimethylguanosine at position 10. Here, we report the first X-ray crystal structures of aTrm11 from Thermococcus kodakarensis (Tko), of the apo-form, and of its complex with SAM. The structures show that TkoTrm11 consists of three domains: an N-terminal ferredoxinlike domain (NFLD), THUMP domain and Rossmann-fold MTase (RFM) domain. A linker region connects the THUMP-NFLD and RFM domains. One SAM molecule is bound in the pocket of the RFM domain, suggesting that TkoTrm11 uses a catalytic mechanism similar to that of other tRNA MTases containing an RFM domain. Furthermore, the conformation of NFLD and THUMP domains in TkoTrm11 resembles that of other tRNA-modifying enzymes specifically recognizing the tRNA acceptor stem. Our docking model of TkoTrm11-SAM in complex with tRNA, combined with biochemical analyses and pre-existing evidence, provides insights into the substrate tRNA recognition mechanism: The THUMP domain recognizes a 3'-ACCA end, and the linker region and RFM domain recognize the T-stem, acceptor stem and V-loop of tRNA, thereby causing TkoTrm11 to specifically identify its methylation site.
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Affiliation(s)
- Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Seiji Nishiyama
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Toshihiro Tamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Ayano Yamauchi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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22
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Structural effects of modified ribonucleotides and magnesium in transfer RNAs. Bioorg Med Chem 2016; 24:4826-4834. [PMID: 27364608 DOI: 10.1016/j.bmc.2016.06.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 11/20/2022]
Abstract
Modified nucleotides are ubiquitous and important to tRNA structure and function. To understand their effect on tRNA conformation, we performed a series of molecular dynamics simulations on yeast tRNAPhe and tRNAinit, Escherichia coli tRNAinit and HIV tRNALys. Simulations were performed with the wild type modified nucleotides, using the recently developed CHARMM compatible force field parameter set for modified nucleotides (J. Comput. Chem.2016, 37, 896), or with the corresponding unmodified nucleotides, and in the presence or absence of Mg2+. Results showed a stabilizing effect associated with the presence of the modifications and Mg2+ for some important positions, such as modified guanosine in position 37 and dihydrouridines in 16/17 including both structural properties and base interactions. Some other modifications were also found to make subtle contributions to the structural properties of local domains. While we were not able to investigate the effect of adenosine 37 in tRNAinit and limitations were observed in the conformation of E. coli tRNAinit, the presence of the modified nucleotides and of Mg2+ better maintained the structural features and base interactions of the tRNA systems than in their absence indicating the utility of incorporating the modified nucleotides in simulations of tRNA and other RNAs.
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23
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Chawla M, Oliva R, Bujnicki JM, Cavallo L. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. Nucleic Acids Res 2015; 43:6714-29. [PMID: 26117545 PMCID: PMC4538814 DOI: 10.1093/nar/gkv606] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/28/2015] [Indexed: 01/08/2023] Open
Abstract
Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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24
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Domingo O, Hellmuth I, Jäschke A, Kreutz C, Helm M. Intermolecular 'cross-torque': the N4-cytosine propargyl residue is rotated to the 'CH'-edge as a result of Watson-Crick interaction. Nucleic Acids Res 2015; 43:5275-83. [PMID: 25934805 PMCID: PMC4477647 DOI: 10.1093/nar/gkv285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/24/2015] [Indexed: 12/13/2022] Open
Abstract
Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being frequent in natural nucleotide modifications. To understand under which circumstances propargyl-containing oligodeoxynucleotides preserve base pairing, we focused on the exocyclic amine of cytidine. Residues attached to the exocyclic N4 may orient away from or toward the Watson-Crick face, ensuing dramatic alteration of base pairing properties. ROESY-NMR experiments suggest a uniform orientation toward the Watson-Crick face of N(4)-propargyl residues in derivatives of both deoxycytidine and 5-methyl-deoxycytidine. In oligodeoxynucleotides, however, UV-melting indicated that N(4)-propargyl-deoxycytidine undergoes standard base pairing. This implies a rotation of the propargyl moiety toward the 'CH'-edge as a result of base pairing on the Watson-Crick face. In oligonucleotides containing the corresponding 5-methyl-deoxycytidine derivative, dramatically reduced melting temperatures indicate impaired Watson-Crick base pairing. This was attributed to a steric clash of the propargyl moiety with the 5-methyl group, which prevents back rotation to the 'CH'-edge, consequently preventing Watson-Crick geometry. Our results emphasize the tendency of an opposing nucleic acid strand to mechanically rotate single N(4)-substituents to make way for Watson-Crick base pairing, providing no steric hindrance is present on the 'CH'-edge.
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Affiliation(s)
- Olwen Domingo
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55128 Mainz, Rhineland-Palatinate, Germany
| | - Isabell Hellmuth
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55128 Mainz, Rhineland-Palatinate, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Baden-Wuerttemberg, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Tyrol, Austria
| | - Mark Helm
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55128 Mainz, Rhineland-Palatinate, Germany
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25
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Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
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Roovers M, Oudjama Y, Fislage M, Bujnicki JM, Versées W, Droogmans L. The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N²-methylguanosine at position 6 in tRNA. RNA (NEW YORK, N.Y.) 2012; 18:815-24. [PMID: 22337946 PMCID: PMC3312568 DOI: 10.1261/rna.030411.111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 12/22/2011] [Indexed: 05/31/2023]
Abstract
N(2)-methylguanosine (m(2)G) is found at position 6 in the acceptor stem of Thermus thermophilus tRNA(Phe). In this article, we describe the cloning, expression, and characterization of the T. thermophilus HB27 methyltransferase (MTase) encoded by the TTC1157 open reading frame that catalyzes the formation of this modified nucleoside. S-adenosyl-L-methionine is used as donor of the methyl group. The enzyme behaves as a monomer in solution. It contains an N-terminal THUMP domain predicted to bind RNA and contains a C-terminal Rossmann-fold methyltransferase (RFM) domain predicted to be responsible for catalysis. We propose to rename the TTC1157 gene trmN and the corresponding protein TrmN, according to the bacterial nomenclature of tRNA methyltransferases. Inactivation of the trmN gene in the T. thermophilus HB27 chromosome led to a total absence of m(2)G in tRNA but did not affect cell growth or the formation of other modified nucleosides in tRNA(Phe). Archaeal homologs of TrmN were identified and characterized. These proteins catalyze the same reaction as TrmN from T. thermophilus. Individual THUMP and RFM domains of PF1002 from Pyrococcus furiosus were produced. These separate domains were inactive and did not bind tRNA, reinforcing the idea that the THUMP domain acts in concert with the catalytic domain to target a particular position of the tRNA molecule.
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Affiliation(s)
- Martine Roovers
- Institut de Recherches Microbiologiques Jean-Marie Wiame, B-1070 Bruxelles, Belgium
| | - Yamina Oudjama
- Institut de Recherches Microbiologiques Jean-Marie Wiame, B-1070 Bruxelles, Belgium
| | - Marcus Fislage
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB Department of Structural Biology, 1050 Brussels, Belgium
| | - Janusz M. Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, PL-61-614 Poznan, Poland
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB Department of Structural Biology, 1050 Brussels, Belgium
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université Libre de Bruxelles (ULB), B-1070 Bruxelles, Belgium
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Menezes S, Gaston KW, Krivos KL, Apolinario EE, Reich NO, Sowers KR, Limbach PA, Perona JJ. Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14. Nucleic Acids Res 2011; 39:7641-55. [PMID: 21693558 PMCID: PMC3177210 DOI: 10.1093/nar/gkr475] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The modified nucleosides N2-methylguanosine and N22-dimethylguanosine in transfer RNA occur at five positions in the D and anticodon arms, and at positions G6 and G7 in the acceptor stem. Trm1 and Trm11 enzymes are known to be responsible for several of the D/anticodon arm modifications, but methylases catalyzing post-transcriptional m2G synthesis in the acceptor stem are uncharacterized. Here, we report that the MJ0438 gene from Methanocaldococcus jannaschii encodes a novel S-adenosylmethionine-dependent methyltransferase, now identified as Trm14, which generates m2G at position 6 in tRNACys. The 381 amino acid Trm14 protein possesses a canonical RNA recognition THUMP domain at the amino terminus, followed by a γ-class Rossmann fold amino-methyltransferase catalytic domain featuring the signature NPPY active site motif. Trm14 is associated with cluster of orthologous groups (COG) 0116, and most closely resembles the m2G10 tRNA methylase Trm11. Phylogenetic analysis reveals a canonical archaeal/bacterial evolutionary separation with 20–30% sequence identities between the two branches, but it is likely that the detailed functions of COG 0116 enzymes differ between the archaeal and bacterial domains. In the archaeal branch, the protein is found exclusively in thermophiles. More distantly related Trm14 homologs were also identified in eukaryotes known to possess the m2G6 tRNA modification.
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Affiliation(s)
- Sheena Menezes
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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Motorin Y, Helm M. RNA nucleotide methylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:611-31. [PMID: 21823225 DOI: 10.1002/wrna.79] [Citation(s) in RCA: 332] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Methylation of RNA occurs at a variety of atoms, nucleotides, sequences and tertiary structures. Strongly related to other posttranscriptional modifications, methylation of different RNA species includes tRNA, rRNA, mRNA, tmRNA, snRNA, snoRNA, miRNA, and viral RNA. Different catalytic strategies are employed for RNA methylation by a variety of RNA-methyltransferases which fall into four superfamilies. This review outlines the different functions of methyl groups in RNA, including biophysical, biochemical and metabolic stabilization of RNA, quality control, resistance to antibiotics, mRNA reading frame maintenance, deciphering of normal and altered genetic code, selenocysteine incorporation, tRNA aminoacylation, ribotoxins, splicing, intracellular trafficking, immune response, and others. Connections to other fields including gene regulation, DNA repair, stress response, and possibly histone acetylation and exocytosis are pointed out. WIREs RNA 2011 2 611-631 DOI: 10.1002/wrna.79 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), Université Henri Poincaré, Vandoeuvre-les-Nancy, France
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Abstract
Post-transcriptional ribonucleotide modification is a phenomenon best studied in tRNA, where it occurs most frequently and in great chemical diversity. This paper reviews the intrinsic network of modifications in the structural core of the tRNA, which governs structural flexibility and rigidity to fine-tune the molecule to peak performance and to regulate its steady-state level. Structural effects of RNA modifications range from nanometer-scale rearrangements to subtle restrictions of conformational space on the angstrom scale. Structural stabilization resulting from nucleotide modification results in increased thermal stability and translates into protection against unspecific degradation by bases and nucleases. Several mechanisms of specific degradation of hypomodified tRNA, which were only recently discovered, provide a link between structural and metabolic stability.
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Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), UMR 7214 CNRS-UHP Faculté des Sciences et Techniques, Université Henri Poincaré, Nancy 1, Bld des Aiguillettes, BP 70239, 54506 Vandoeuvre-les-Nancy, France
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Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L. New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Nucleic Acids Res 2010; 38:6533-43. [PMID: 20525789 PMCID: PMC2965216 DOI: 10.1093/nar/gkq451] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Two archaeal tRNA methyltransferases belonging to the SPOUT superfamily and displaying unexpected activities are identified. These enzymes are orthologous to the yeast Trm10p methyltransferase, which catalyses the formation of 1-methylguanosine at position 9 of tRNA. In contrast, the Trm10p orthologue from the crenarchaeon Sulfolobus acidocaldarius forms 1-methyladenosine at the same position. Even more surprisingly, the Trm10p orthologue from the euryarchaeon Thermococcus kodakaraensis methylates the N1-atom of either adenosine or guanosine at position 9 in different tRNAs. This is to our knowledge the first example of a tRNA methyltransferase with a broadened nucleoside recognition capability. The evolution of tRNA methyltransferases methylating the N1 atom of a purine residue is discussed.
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Affiliation(s)
- Morgane Kempenaers
- Laboratoire de Microbiologie, Université Libre de Bruxelles, Institut de Recherches Microbiologiques Jean-Marie Wiame, Avenue E Gryson 1, B-1070 Bruxelles, Belgium
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Awai T, Kimura S, Tomikawa C, Ochi A, Ihsanawati, Bessho Y, Yokoyama S, Ohno S, Nishikawa K, Yokogawa T, Suzuki T, Hori H. Aquifex aeolicus tRNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA. J Biol Chem 2009; 284:20467-78. [PMID: 19491098 PMCID: PMC2742811 DOI: 10.1074/jbc.m109.020024] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 05/13/2009] [Indexed: 11/06/2022] Open
Abstract
Transfer RNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes N2,N2-dimethylguanine formation at position 26 (m(2)(2)G26) in tRNA. In the reaction, N2-guanine at position 26 (m(2)G26) is generated as an intermediate. The trm1 genes are found only in archaea and eukaryotes, although it has been reported that Aquifex aeolicus, a hyper-thermophilic eubacterium, has a putative trm1 gene. To confirm whether A. aeolicus Trm1 has tRNA methyltransferase activity, we purified recombinant Trm1 protein. In vitro methyl transfer assay revealed that the protein has a strong tRNA methyltransferase activity. We confirmed that this gene product is expressed in living A. aeolicus cells and that the enzymatic activity exists in cell extract. By preparing 22 tRNA transcripts and testing their methyl group acceptance activities, it was demonstrated that this Trm1 protein has a novel tRNA specificity. Mass spectrometry analysis revealed that it catalyzes methyl transfers not only to G26 but also to G27 in substrate tRNA. Furthermore, it was confirmed that native tRNA(Cys) has an m(2)(2)G26m(2)G27 or m(2)(2)G26m(2)(2)G27 sequence, demonstrating that these modifications occur in living cells. Kinetic studies reveal that the m2G26 formation is faster than the m(2)G27 formation and that disruption of the G27-C43 base pair accelerates velocity of the G27 modification. Moreover, we prepared an additional 22 mutant tRNA transcripts and clarified that the recognition sites exist in the T-arm structure. This long distance recognition results in multisite recognition by the enzyme.
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Affiliation(s)
- Takako Awai
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
| | - Satoshi Kimura
- the Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656
| | - Chie Tomikawa
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
| | - Anna Ochi
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
| | - Ihsanawati
- the Systems and Structural Biology Center, Yokohama Institute, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045
| | - Yoshitaka Bessho
- the Systems and Structural Biology Center, Yokohama Institute, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045
- the RIKEN SPring-8 Center, Harima Institute, Kouto 1-1-1, Sayo, Hyogo 679-5148
| | - Shigeyuki Yokoyama
- the Systems and Structural Biology Center, Yokohama Institute, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045
- the RIKEN SPring-8 Center, Harima Institute, Kouto 1-1-1, Sayo, Hyogo 679-5148
- the Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033
| | - Satoshi Ohno
- the Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu, Gifu 501-1193, and
| | - Kazuya Nishikawa
- the Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu, Gifu 501-1193, and
| | - Takashi Yokogawa
- the Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu, Gifu 501-1193, and
| | - Tsutomu Suzuki
- the Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656
| | - Hiroyuki Hori
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
- the Systems and Structural Biology Center, Yokohama Institute, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045
- the Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan
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32
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Iida K, Jin H, Zhu JK. Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana. BMC Genomics 2009; 10:155. [PMID: 19358740 PMCID: PMC2674459 DOI: 10.1186/1471-2164-10-155] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 04/09/2009] [Indexed: 11/10/2022] Open
Abstract
Background Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. Results In the current work, we carried out a bioinformatics analysis of RNA base modifications in tRNAs and miRNAs using large numbers of cDNA sequences of small RNAs (sRNAs) generated with the 454 technology and the massively parallel signature sequencing (MPSS) method. We looked for sRNAs that map to the genome sequence with one-base mismatch (OMM), which indicate candidate modified nucleotides. We obtained 1,187 sites with possible RNA base modifications supported by both 454 and MPSS sequences. Seven hundred and three of these sites were within tRNA loci. Nucleotide substitutions were frequently located in the T arm (substitutions from A to U or G), upstream of the D arm (from G to C, U, or A), and downstream of the D arm (from G to U). The positions of major substitution sites corresponded with the following known RNA base modifications in tRNAs: N1-methyladenosine (m1A), N2-methylguanosine (m2G), and N2-N2-methylguanosine (m22G). Conclusion These results indicate that our bioinformatics method successfully detected modified nucleotides in tRNAs. Using this method, we also found 147 substitution sites in miRNA loci. As with tRNAs, substitutions from A to U or G and from G to C, U, or A were common, suggesting that base modifications might be similar in tRNAs and miRNAs. We suggest that miRNAs contain modified bases and such modifications might be important for miRNA maturation and/or function.
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Affiliation(s)
- Kei Iida
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
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Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii. J Mol Biol 2008; 383:871-84. [PMID: 18789948 DOI: 10.1016/j.jmb.2008.08.068] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 08/21/2008] [Indexed: 11/21/2022]
Abstract
Trm1 catalyzes a two-step reaction, leading to mono- and dimethylation of guanosine at position 26 in most eukaryotic and archaeal tRNAs. We report the crystal structures of Trm1 from Pyrococcus horikoshii liganded with S-adenosyl-l-methionine or S-adenosyl-l-homocysteine. The protein comprises N-terminal and C-terminal domains with class I methyltransferase and novel folds, respectively. The methyl moiety of S-adenosyl-l-methionine points toward the invariant Phe27 and Phe140 within a narrow pocket, where the target G26 might flip in. Mutagenesis of Phe27 or Phe140 to alanine abolished the enzyme activity, indicating their role in methylating G26. Structural analyses revealed that the movements of Phe140 and the loop preceding Phe27 may be involved in dissociation of the monomethylated tRNA*Trm1 complex prior to the second methylation. Moreover, the catalytic residues Asp138, Pro139, and Phe140 are in a different motif from that in DNA 6-methyladenosine methyltransferases, suggesting a different methyl transfer mechanism in the Trm1 family.
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Targanski I, Cherkasova V. Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon-codon hydrogen bonds as a major determinant of tRNA compositional variations. RNA (NEW YORK, N.Y.) 2008; 14:1095-109. [PMID: 18441051 PMCID: PMC2390787 DOI: 10.1261/rna.896108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Analysis of 100 complete sets of the cytoplasmic elongator tRNA genes from Bacteria, Archaea, and Eukarya pointed to correspondences between types of anticodon and composition of the rest of the tRNA body. The number of the hydrogen bonds formed between the complementary nucleotides in the anticodon-codon duplex appeared as a major quantitative parameter determining covariations in all three domains of life. Our analysis has supported and advanced the "extended anticodon" concept that is based on the argument that the decoding performance of the anticodon is enhanced by selection of a matching anticodon stem-loop sequence, as reported by Yarus in 1982. In addition to the anticodon stem-loop, we have found covariations between the anticodon nucleotides and the composition of the distant regions of their respective tRNAs that include dihydrouridine (D) and thymidyl (T) stem-loops. The majority of the covariable tRNA positions were found at the regions with the increased dynamic potential--such as stem-loop and stem-stem junctions. The consistent occurrences of the covariations on the multigenomic level suggest that the number and pattern of the hydrogen bonds in the anticodon-codon duplex constitute a major factor in the course of translation that is reflected in the fine-tuning of the tRNA composition and structure.
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Gabant G, Augier J, Armengaud J. Assessment of solvent residues accessibility using three Sulfo-NHS-biotin reagents in parallel: application to footprint changes of a methyltransferase upon binding its substrate. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:360-370. [PMID: 17968972 DOI: 10.1002/jms.1328] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
NHS-biotin modification as a specific lysine probe coupled to mass spectrometry detection is increasingly used over the past years for assessing amino acid accessibility of proteins or complexes as an alternative when well-established methods are challenged. We present a strategy based on usage in parallel of three commercially available reagents (Sulfo-NHS-biotin, Sulfo-NHS-LC-biotin, and Sulfo-NHS-LC-LC-biotin) to efficiently assess the solvent accessibility of amino acids using MALDI-TOF mass spectrometry. The same qualitative pattern of reactivity was observed for these three reagents on the THUMPalpha protein at four reagent/polypeptide molar ratios (2 : 1, 6 : 1, 13 : 1, and 26 : 1). Peptide assignment of the detected ions gains in accuracy because of the triple redundancy due to specific increments of monoisotopic mass. These reagents are a good alternative to isotope labeling when using only a single MALDI-TOF mass spectrometer. We observed that hydroxyl groups of serine and tyrosine residues were also modified by these Sulfo-NHS-biotin reagents. The low amount of protein required and the method's simplicity make this procedure accessible and affordable in order to obtain topological information on proteins difficult to purify. This method was used to identify two lysine residues of the TrmG10 methyltransferase from Pyrococcus abyssi that were differentially reactive, modified in the protein but not in the tRNA-protein complex.
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Affiliation(s)
- Guillaume Gabant
- CEA VALRHO, DSV, iBEB, SBTN, LBSP, Institut de Biologie environnementale et Biotechnologie, Service de Biochimie et Toxicologie Nucléaire, Laboratoire de Biochimie des Systèmes Perturbés, F-30207 Bagnols-sur-Cèze, France
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Grosjean H, Droogmans L, Roovers M, Keith G. Detection of enzymatic activity of transfer RNA modification enzymes using radiolabeled tRNA substrates. Methods Enzymol 2007; 425:55-101. [PMID: 17673079 DOI: 10.1016/s0076-6879(07)25003-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The presence of modified ribonucleotides derived from adenosine, guanosine, cytidine, and uridine is a hallmark of almost all cellular RNA, and especially tRNA. The objective of this chapter is to describe a few simple methods that can be used to identify the presence or absence of a modified nucleotide in tRNA and to reveal the enzymatic activity of particular tRNA-modifying enzymes in vitro and in vivo. The procedures are based on analysis of prelabeled or postlabeled nucleotides (mainly with [(32)P] but also with [(35)S], [(14)C] or [(3)H]) generated after complete digestion with selected nucleases of modified tRNA isolated from cells or incubated in vitro with modifying enzyme(s). Nucleotides of the tRNA digests are separated by two-dimensional (2D) thin-layer chromatography on cellulose plates (TLC), which allows establishment of base composition and identification of the nearest neighbor nucleotide of a given modified nucleotide in the tRNA sequence. This chapter provides useful maps for identification of migration of approximately 70 modified nucleotides on TLC plates by use of two different chromatographic systems. The methods require only a few micrograms of purified tRNA and can be run at low cost in any laboratory.
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Affiliation(s)
- Henri Grosjean
- Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
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Gabant G, Auxilien S, Tuszynska I, Locard M, Gajda MJ, Chaussinand G, Fernandez B, Dedieu A, Grosjean H, Golinelli-Pimpaneau B, Bujnicki JM, Armengaud J. THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain. Nucleic Acids Res 2006; 34:2483-94. [PMID: 16687654 PMCID: PMC1459410 DOI: 10.1093/nar/gkl145] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 02/13/2006] [Accepted: 03/16/2006] [Indexed: 11/14/2022] Open
Abstract
The tRNA:m2(2)G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N2,N2-dimethylation of guanosine at position 10 in tRNA. Boundaries of its THUMP (THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases)--containing N-terminal domain [1-152] and C-terminal catalytic domain [157-329] were assessed by trypsin limited proteolysis. An inter-domain flexible region of at least six residues was revealed. The N-terminal domain was then produced as a standalone protein (THUMPalpha) and further characterized. This autonomously folded unit exhibits very low affinity for tRNA. Using protein fold-recognition (FR) methods, we identified the similarity between THUMPalpha and a putative RNA-recognition module observed in the crystal structure of another THUMP-containing protein (ThiI thiolase of Bacillus anthracis). A comparative model of THUMPalpha structure was generated, which fulfills experimentally defined restraints, i.e. chemical modification of surface exposed residues assessed by mass spectrometry, and identification of an intramolecular disulfide bridge. A model of the whole PAB1283 enzyme docked onto its tRNA(Asp) substrate suggests that the THUMP module specifically takes support on the co-axially stacked helices of T-arm and acceptor stem of tRNA and, together with the catalytic domain, screw-clamp structured tRNA. We propose that this mode of interactions may be common to other THUMP-containing enzymes that specifically modify nucleotides in the 3D-core of tRNA.
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Affiliation(s)
- Guillaume Gabant
- CEA VALRHO, DSV-DIEP—SBTN, Service de Biochimie post-génomique & Toxicologie NucléaireF-30207 Bagnols-sur-Cèze, France
| | - Sylvie Auxilien
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRSBld 34, avenue de la Terrasse 1, F-91198 Gif-sur-Yvette, France
| | - Irina Tuszynska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell BiologyTrojdena 4, 02-109, Warsaw, Poland
| | - Marie Locard
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRSBld 34, avenue de la Terrasse 1, F-91198 Gif-sur-Yvette, France
| | - Michal J. Gajda
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell BiologyTrojdena 4, 02-109, Warsaw, Poland
| | - Guylaine Chaussinand
- CEA VALRHO, DSV-DIEP—SBTN, Service de Biochimie post-génomique & Toxicologie NucléaireF-30207 Bagnols-sur-Cèze, France
| | - Bernard Fernandez
- CEA VALRHO, DSV-DIEP—SBTN, Service de Biochimie post-génomique & Toxicologie NucléaireF-30207 Bagnols-sur-Cèze, France
| | - Alain Dedieu
- CEA VALRHO, DSV-DIEP—SBTN, Service de Biochimie post-génomique & Toxicologie NucléaireF-30207 Bagnols-sur-Cèze, France
| | - Henri Grosjean
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRSBld 34, avenue de la Terrasse 1, F-91198 Gif-sur-Yvette, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRSBld 34, avenue de la Terrasse 1, F-91198 Gif-sur-Yvette, France
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell BiologyTrojdena 4, 02-109, Warsaw, Poland
| | - Jean Armengaud
- CEA VALRHO, DSV-DIEP—SBTN, Service de Biochimie post-génomique & Toxicologie NucléaireF-30207 Bagnols-sur-Cèze, France
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Abstract
Alternative foldings are an inherent property of RNA and a ubiquitous problem in scientific investigations. To a living organism, alternative foldings can be a blessing or a problem, and so nature has found both, ways to harness this property and ways to avoid the drawbacks. A simple and effective method employed by nature to avoid unwanted folding is the modulation of conformation space through post-transcriptional base modification. Modified nucleotides occur in almost all classes of natural RNAs in great chemical diversity. There are about 100 different base modifications known, which may perform a plethora of functions. The presumably most ancient and simple nucleotide modifications, such as methylations and uridine isomerization, are able to perform structural tasks on the most basic level, namely by blocking or reinforcing single base-pairs or even single hydrogen bonds in RNA. In this paper, functional, genomic and structural evidence on cases of folding space alteration by post-transcriptional modifications in native RNA are reviewed.
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Affiliation(s)
- Mark Helm
- Department of Chemistry, Institute for Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
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