1
|
Bommisetti P, Bandarian V. Insights into the Mechanism of Installation of 5-Carboxymethylaminomethyl Uridine Hypermodification by tRNA-Modifying Enzymes MnmE and MnmG. J Am Chem Soc 2023; 145:26947-26961. [PMID: 38050996 PMCID: PMC10723064 DOI: 10.1021/jacs.3c10182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG (and their homologues in Eukarya) install a 5-carboxymethylaminomethyl (cmnm5) or a 5-taurinomethyl (τm5) group onto wobble uridines of several tRNA species. The Escherichia coli MnmE binds guanosine-5'-triphosphate (GTP) and methylenetetrahydrofolate (CH2THF), while MnmG binds flavin adenine dinucleotide (FAD) and a reduced nicotinamide adenine dinucleotide (NADH). Together with glycine, MnmEG catalyzes the installation of cmnm5 in a reaction that also requires hydrolysis of GTP. In this letter, we investigated key steps of the MnmEG reaction using a combination of biochemical techniques. We show multiple lines of evidence supporting flavin-iminium FADH[N5═CH2]+ as a central intermediate in the MnmEG reaction. Using a synthetic FADH[N5═CD2]+ analogue, the intermediacy of the FAD in the transfer of the methylene group from CH2THF to the C5 position of U34 was unambiguously demonstrated. Further, MnmEG reactions containing the deuterated flavin-iminium intermediate and alternate nucleophiles such as taurine and ammonia also led to the formation of the anticipated U34-modified tRNAs, showing FAD[N5═CH2]+ as the universal intermediate for all MnmEG homologues. Additionally, an RNA-protein complex stable to urea-denaturing polyacrylamide gel electrophoresis was identified. Studies involving a series of nuclease (RNase T1) and protease (trypsin) digestions along with reverse transcription experiments suggest that the complex may be noncovalent. While the conserved MnmG cysteine C47 and C277 mutant variants were shown to reduce FAD, they were unable to promote the modified tRNA formation. Overall, this study provides critical insights into the biochemical mechanism underlying tRNA modification by the MnmEG.
Collapse
Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
| |
Collapse
|
2
|
Bou-Nader C, Pecqueur L, de Crécy-Lagard V, Hamdane D. Integrative Approach to Probe Alternative Redox Mechanisms in RNA Modifications. Acc Chem Res 2023; 56:3142-3152. [PMID: 37916403 PMCID: PMC10999249 DOI: 10.1021/acs.accounts.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
RNA modifications found in most RNAs, particularly in tRNAs and rRNAs, reveal an abundance of chemical alterations of nucleotides. Over 150 distinct RNA modifications are known, emphasizing a remarkable diversity of chemical moieties in RNA molecules. These modifications play pivotal roles in RNA maturation, structural integrity, and the fidelity and efficiency of translation processes. The catalysts responsible for these modifications are RNA-modifying enzymes that use a striking array of chemistries to directly influence the chemical landscape of RNA. This diversity is further underscored by instances where the same modification is introduced by distinct enzymes that use unique catalytic mechanisms and cofactors across different domains of life. This phenomenon of convergent evolution highlights the biological importance of RNA modification and the vast potential within the chemical repertoire for nucleotide alteration. While shared RNA modifications can hint at conserved enzymatic pathways, a major bottleneck is to identify alternative routes within species that possess a modified RNA but are devoid of known RNA-modifying enzymes. To address this challenge, a combination of bioinformatic and experimental strategies proves invaluable in pinpointing new genes responsible for RNA modifications. This integrative approach not only unveils new chemical insights but also serves as a wellspring of inspiration for biocatalytic applications and drug design. In this Account, we present how comparative genomics and genome mining, combined with biomimetic synthetic chemistry, biochemistry, and anaerobic crystallography, can be judiciously implemented to address unprecedented and alternative chemical mechanisms in the world of RNA modification. We illustrate these integrative methodologies through the study of tRNA and rRNA modifications, dihydrouridine, 5-methyluridine, queuosine, 8-methyladenosine, 5-carboxymethylamino-methyluridine, or 5-taurinomethyluridine, each dependent on a diverse array of redox chemistries, often involving organic compounds, organometallic complexes, and metal coenzymes. We explore how vast genome and tRNA databases empower comparative genomic analyses and enable the identification of novel genes that govern RNA modification. Subsequently, we describe how the isolation of a stable reaction intermediate can guide the synthesis of a biomimetic to unveil new enzymatic pathways. We then discuss the usefulness of a biochemical "shunt" strategy to study catalytic mechanisms and to directly visualize reactive intermediates bound within active sites. While we primarily focus on various RNA-modifying enzymes studied in our laboratory, with a particular emphasis on the discovery of a SAM-independent methylation mechanism, the strategies and rationale presented herein are broadly applicable for the identification of new enzymes and the elucidation of their intricate chemistries. This Account offers a comprehensive glimpse into the evolving landscape of RNA modification research and highlights the pivotal role of integrated approaches to identify novel enzymatic pathways.
Collapse
Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, 32611, USA
- University of Florida, Genetics Institute, Gainesville, Florida, 32610, USA
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| |
Collapse
|
3
|
McGuffey JC, Jackson-Litteken CD, Di Venanzio G, Zimmer AA, Lewis JM, Distel JS, Kim KQ, Zaher HS, Alfonzo J, Scott NE, Feldman MF. The tRNA methyltransferase TrmB is critical for Acinetobacter baumannii stress responses and pulmonary infection. mBio 2023; 14:e0141623. [PMID: 37589464 PMCID: PMC10653896 DOI: 10.1128/mbio.01416-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023] Open
Abstract
IMPORTANCE As deficiencies in tRNA modifications have been linked to human diseases such as cancer and diabetes, much research has focused on the modifications' impacts on translational regulation in eukaryotes. However, the significance of tRNA modifications in bacterial physiology remains largely unexplored. In this paper, we demonstrate that the m7G tRNA methyltransferase TrmB is crucial for a top-priority pathogen, Acinetobacter baumannii, to respond to stressors encountered during infection, including oxidative stress, low pH, and iron deprivation. We show that loss of TrmB dramatically attenuates a murine pulmonary infection. Given the current efforts to use another tRNA methyltransferase, TrmD, as an antimicrobial therapeutic target, we propose that TrmB, and other tRNA methyltransferases, may also be viable options for drug development to combat multidrug-resistant A. baumannii.
Collapse
Affiliation(s)
- Jenna C. McGuffey
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Clay D. Jackson-Litteken
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Aubree A. Zimmer
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jessica M. Lewis
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kyusik Q. Kim
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Juan Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| |
Collapse
|
4
|
Tomoda E, Nagao A, Shirai Y, Asano K, Suzuki T, Battersby B, Suzuki T. Restoration of mitochondrial function through activation of hypomodified tRNAs with pathogenic mutations associated with mitochondrial diseases. Nucleic Acids Res 2023; 51:7563-7579. [PMID: 36928678 PMCID: PMC10415153 DOI: 10.1093/nar/gkad139] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/14/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Mutations in mitochondrial (mt-)tRNAs frequently cause mitochondrial dysfunction. Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), and myoclonus epilepsy associated with ragged red fibers (MERRF) are major clinical subgroups of mitochondrial diseases caused by pathogenic point mutations in tRNA genes encoded in mtDNA. We previously reported a severe reduction in the frequency of 5-taurinomethyluridine (τm5U) and its 2-thiouridine derivative (τm5s2U) in the anticodons of mutant mt-tRNAs isolated from the cells of patients with MELAS and MERRF, respectively. The hypomodified tRNAs fail to decode cognate codons efficiently, resulting in defective translation of respiratory chain proteins in mitochondria. To restore the mitochondrial activity of MELAS patient cells, we overexpressed MTO1, a τm5U-modifying enzyme, in patient-derived myoblasts. We used a newly developed primer extension method and showed that MTO1 overexpression almost completely restored the τm5U modification of the MELAS mutant mt-tRNALeu(UUR). An increase in mitochondrial protein synthesis and oxygen consumption rate suggested that the mitochondrial function of MELAS patient cells can be activated by restoring the τm5U of the mutant tRNA. In addition, we confirmed that MTO1 expression restored the τm5s2U of the mutant mt-tRNALys in MERRF patient cells. These findings pave the way for epitranscriptomic therapies for mitochondrial diseases.
Collapse
Affiliation(s)
- Ena Tomoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuki Shirai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kana Asano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, 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
| |
Collapse
|
5
|
Chu M, Qin Y, Lin X, Ma L, Deng D, Lv D, Fu P, Lin H. A Preliminary Survey of Transfer RNA Modifications and Modifying Enzymes of the Tropical Plant Cocos nucifera L. Genes (Basel) 2023; 14:1287. [PMID: 37372467 PMCID: PMC10298058 DOI: 10.3390/genes14061287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The coconut (Cocos nucifera L.) is a commercial crop widely distributed among coastal tropical regions. It provides millions of farmers with food, fuel, cosmetics, folk medicine, and building materials. Among these, oil and palm sugar are representative extracts. However, this unique living species of Cocos has only been preliminarily studied at molecular levels. Benefiting from the genomic sequence data published in 2017 and 2021, we investigated the transfer RNA (tRNA) modifications and modifying enzymes of the coconut in this survey. An extraction method for the tRNA pool from coconut flesh was built. In total, 33 species of modified nucleosides and 66 homologous genes of modifying enzymes were confirmed using a nucleoside analysis using high-performance liquid chromatography combined with high-resolution mass spectrometry (HPLC-HRMS) and homologous protein sequence alignment. The positions of tRNA modifications, including pseudouridines, were preliminarily mapped using a oligonucleotide analysis, and the features of their modifying enzymes were summarized. Interestingly, we found that the gene encoding the modifying enzyme of 2'-O-ribosyladenosine at the 64th position of tRNA (Ar(p)64) was uniquely overexpressed under high-salinity stress. In contrast, most other tRNA-modifying enzymes were downregulated with mining transcriptomic sequencing data. According to previous physiological studies of Ar(p)64, the coconut appears to enhance the quality control of the translation process when subjected to high-salinity stress. We hope this survey can help advance research on tRNA modification and scientific studies of the coconut, as well as thinking of the safety and nutritional value of naturally modified nucleosides.
Collapse
Affiliation(s)
- Meng Chu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Yichao Qin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Xiuying Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Li Ma
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Dehai Deng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Daizhu Lv
- Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Huan Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| |
Collapse
|
6
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| |
Collapse
|
7
|
Yamagami R, Hori H. Application of mutational profiling: New functional analyses reveal the tRNA recognition mechanism of tRNA m 1A22 methyltransferase. J Biol Chem 2023; 299:102759. [PMID: 36462666 PMCID: PMC9801127 DOI: 10.1016/j.jbc.2022.102759] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Transfer RNAs undergo diverse posttranscriptional modifications to regulate a myriad of cellular events including translation, stress response, and viral replication. These posttranscriptional modifications are synthesized by site-specific modification enzymes. Recent RNA-seq techniques have revealed multiple features of tRNA such as tRNA abundance, tRNA modification, and tRNA structure. Here, we adapt a tRNA-sequencing technique and design a new functional analysis where we perform mutational profiling of tRNA modifications to gain mechanistic insights into how tRNA modification enzymes recognize substrate tRNA. Profiling of Geobacillus stearothermophilus tRNAs and protein orthology analysis predict the existence of natural modifications in 44 tRNA molecular species of G. stearothermophilus. We selected the 1-methyladenosine modification at position 22 (m1A22) and tRNA (m1A22) methyltransferase (TrmK) for further analysis. Relative quantification of m1A22 levels in 59 tRNA transcripts by mutational profiling reveals that TrmK selectively methylates a subset of tRNAs. Using 240 variants of tRNALeu transcripts, we demonstrate the conserved nucleosides including U8, A14, G15, G18, G19, U55, Purine57, and A58 are important for the methyl transfer reaction of TrmK. Additional biochemical experiments reveal that TrmK strictly recognizes U8, A14, G18, and U55 in tRNA. Furthermore, these findings from tRNALeu variants were crossvalidated using variants of three different tRNA species. Finally, a model of the TrmK-tRNA complex structure was constructed based on our findings and previous biochemical and structural studies by others. Collectively, our study expands functional analyses of tRNA modification enzyme in a high-throughput manner where our assay rapidly identifies substrates from a large pool of tRNAs.
Collapse
Affiliation(s)
- Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
| |
Collapse
|
8
|
Ferraz R, Coimbra S, Correia S, Canhoto J. RNA methyltransferases in plants: Breakthroughs in function and evolution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:449-460. [PMID: 36502609 DOI: 10.1016/j.plaphy.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Each day it is becoming increasingly difficult not to notice the completely new, fast growing, extremely intricate and challenging world of epitranscriptomics as the understanding of RNA methylation is expanding at a hasty rate. Writers (methyltransferases), erasers (demethylases) and readers (RNA-binding proteins) are responsible for adding, removing and recognising methyl groups on RNA, respectively. Several methyltransferases identified in plants are now being investigated and recent studies have shown a connection between RNA-methyltransferases (RNA-MTases) and stress and development processes. However, compared to their animal and bacteria counterparts, the understanding of RNA methyltransferases is still incipient, particularly those located in organelles. Comparative and systematic analyses allowed the tracing of the evolution of these enzymes suggesting the existence of several methyltransferases yet to be characterised. This review outlines the functions of plant nuclear and organellar RNA-MTases in plant development and stress responses and the comparative and evolutionary discoveries made on RNA-MTases across kingdoms.
Collapse
Affiliation(s)
- Ricardo Ferraz
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal; LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal.
| | - Sílvia Coimbra
- University of Porto, Faculty of Sciences, Portugal; LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal.
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
| |
Collapse
|
9
|
Bommisetti P, Young A, Bandarian V. Elucidation of the substrate of tRNA-modifying enzymes MnmEG leads to in vitro reconstitution of an evolutionarily conserved uridine hypermodification. J Biol Chem 2022; 298:102548. [PMID: 36181794 PMCID: PMC9626948 DOI: 10.1016/j.jbc.2022.102548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG collectively install a carboxymethylaminomethyl (cmnm) group at the fifth position of wobble uridines of several tRNA species. While the reaction catalyzed by MnmEG is one of the central steps in the biosynthesis of the methylaminomethyl (mnm) posttranscriptional tRNA modification, details of the reaction remain elusive. Glycine is known to be the source of the carboxy methylamino moiety of cmnm, and a tetrahydrofolate (THF) analog is thought to supply the one carbon that is appended to the fifth position of U. However, the nature of the folate analog remains unknown. This article reports the in vitro biochemical reconstitution of the MnmEG reaction. Using isotopically labeled methyl and methylene THF analogs, we demonstrate that methylene THF is the true substrate. We also show that reduced FAD is required for the reaction and that DTT can replace the NADH in its role as a reductant. We discuss the implications of these methylene-THF and reductant requirements on the mechanism of this key tRNA modification catalyzed by MnmEG.
Collapse
Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony Young
- Soliome Inc, 479 Jessie Street, San Francisco, CA 94103, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States.
| |
Collapse
|
10
|
Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
Collapse
Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| |
Collapse
|
11
|
Boulias K, Greer EL. Means, mechanisms and consequences of adenine methylation in DNA. Nat Rev Genet 2022; 23:411-428. [PMID: 35256817 PMCID: PMC9354840 DOI: 10.1038/s41576-022-00456-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2022] [Indexed: 12/29/2022]
Abstract
N6-methyl-2'-deoxyadenosine (6mA or m6dA) has been reported in the DNA of prokaryotes and eukaryotes ranging from unicellular protozoa and algae to multicellular plants and mammals. It has been proposed to modulate DNA structure and transcription, transmit information across generations and have a role in disease, among other functions. However, its existence in more recently evolved eukaryotes remains a topic of debate. Recent technological advancements have facilitated the identification and quantification of 6mA even when the modification is exceptionally rare, but each approach has limitations. Critical assessment of existing data, rigorous design of future studies and further development of methods will be required to confirm the presence and biological functions of 6mA in multicellular eukaryotes.
Collapse
|
12
|
O’Brown ZK, Greer EL. N6-methyladenine: A Rare and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:177-210. [DOI: 10.1007/978-3-031-11454-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
13
|
Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1691. [PMID: 34913259 DOI: 10.1002/wrna.1691] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
Abstract
Among RNA modifications, transfer of methylgroups from the typical cofactor S-adenosyl-l-methionine by methyltransferases (MTases) to RNA is by far the most common reaction. Since our last review about a decade ago, the field has witnessed the re-emergence of mRNA methylation as an important mechanism in gene regulation. Attention has then spread to many other RNA species; all being included into the newly coined concept of the "epitranscriptome." The focus moved from prokaryotes and single cell eukaryotes as model organisms to higher eukaryotes, in particular to mammals. The perception of the field has dramatically changed over the past decade. A previous lack of phenotypes in knockouts in single cell organisms has been replaced by the apparition of MTases in numerous disease models and clinical investigations. Major driving forces of the field include methylation mapping techniques, as well as the characterization of the various MTases, termed "writers." The latter term has spilled over from DNA modification in the neighboring epigenetics field, along with the designations "readers," applied to mediators of biological effects upon specific binding to a methylated RNA. Furthermore "eraser" enzymes effect the newly discovered oxidative removal of methylgroups. A sense of reversibility and dynamics has replaced the older perception of RNA modification as a concrete-cast, irreversible part of RNA maturation. A related concept concerns incompletely methylated residues, which, through permutation of each site, lead to inhomogeneous populations of numerous modivariants. This review recapitulates the major developments of the past decade outlined above, and attempts a prediction of upcoming trends. This article is categorized under: RNA Processing > RNA Editing and Modification.
Collapse
Affiliation(s)
- Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Mainz, Germany
| |
Collapse
|
14
|
Graille M. Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases? WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1673. [PMID: 34044474 DOI: 10.1002/wrna.1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications.
Collapse
Affiliation(s)
- Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, IP Paris, Palaiseau Cedex, France
| |
Collapse
|
15
|
Photochemical processes in flavo-enzymes as a probe for active site dynamics: TrmFO of Thermus thermophilus. Photochem Photobiol Sci 2021; 20:663-670. [PMID: 33977512 DOI: 10.1007/s43630-021-00052-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
Quenching of flavin fluorescence by electron transfer from neighboring aromatic residues is ubiquitous in flavoproteins. Apart from constituting a functional process in specific light-active systems, time-resolved spectral characterization of the process can more generally be employed as a probe for the active site configuration and dynamics. In the C51A variant of the bacterial RNA-transforming flavoenzyme TrmFO from the bacterium Thermus thermophilus, fluorescence is very short-lived (~ 1 ps), and close-by Tyr343 is known to act as the main quencher, as confirmed here by the very similar dynamics observed in protein variants with modified other potential quenchers, Trp283 and Trp214. When Tyr343 is modified to redox-inactive phenylalanine, slower and highly multiphasic kinetics are observed on the picosecond-nanosecond timescale, reflecting heterogeneous electron donor-acceptor configurations. We demonstrate that Trp214, which is located on a potentially functional flexible loop, contributes to electron donor quenching in this variant. Contrasting with observations in other nucleic acid-transforming enzymes, these kinetics are strikingly temperature-independent. This indicates (a) near-barrierless electron transfer reactions and (b) no exchange between different configurations on the timescale up to at least 2 ns, despite the presumed flexibility of Trp214. Results of extensive molecular dynamics simulations are presented to explain this unexpected finding in terms of slowly exchanging protein configurations.
Collapse
|
16
|
Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution. Genes (Basel) 2021; 12:genes12020140. [PMID: 33499018 PMCID: PMC7912444 DOI: 10.3390/genes12020140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
The high conservation of nucleotides of the T-loop, including their chemical identity, are hallmarks of tRNAs from organisms belonging to the three Domains of Life. These structural characteristics allow the T-loop to adopt a peculiar intraloop conformation able to interact specifically with other conserved residues of the D-loop, which ultimately folds the mature tRNA in a unique functional canonical L-shaped architecture. Paradoxically, despite the high conservation of modified nucleotides in the T-loop, enzymes catalyzing their formation depend mostly on the considered organism, attesting for an independent but convergent evolution of the post-transcriptional modification processes. The driving force behind this is the preservation of a native conformation of the tRNA elbow that underlies the various interactions of tRNA molecules with different cellular components.
Collapse
|
17
|
Kimura S. Distinct evolutionary pathways for the synthesis and function of tRNA modifications. Brief Funct Genomics 2021; 20:125-134. [PMID: 33454776 DOI: 10.1093/bfgp/elaa027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022] Open
Abstract
Transfer ribonucleicacids (RNAs) (tRNAs) are essential adaptor molecules for translation. The functions and stability of tRNAs are modulated by their post-transcriptional modifications (tRNA modifications). Each domain of life has a specific set of modifications that include ones shared in multiple domains and ones specific to a domain. In some cases, different tRNA modifications across domains have similar functions to each other. Recent studies uncovered that distinct enzymes synthesize the same modification in different organisms, suggesting that such modifications are acquired through independent evolution. In this short review, I outline the mechanisms by which various modifications contribute to tRNA function, including modulation of decoding and tRNA stability, using recent findings. I also focus on modifications that are synthesized by distinct biosynthetic pathways.
Collapse
Affiliation(s)
- Satoshi Kimura
- Dr Matthew Waldor's lab at the Brigham and Women's Hospital. He completed his PhD and early postdoc work in Dr Tsutomu Suzuki's lab at the University of Tokyo
| |
Collapse
|
18
|
Rose S, Auxilien S, Havelund JF, Kirpekar F, Huber H, Grosjean H, Douthwaite S. The hyperthermophilic partners Nanoarchaeum and Ignicoccus stabilize their tRNA T-loops via different but structurally equivalent modifications. Nucleic Acids Res 2020; 48:6906-6918. [PMID: 32459340 PMCID: PMC7337903 DOI: 10.1093/nar/gkaa411] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/19/2020] [Accepted: 05/06/2020] [Indexed: 01/31/2023] Open
Abstract
The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis grow physically coupled under identical hyperthermic conditions. We report here two fundamentally different routes by which these archaea modify the key conserved nucleotide U54 within their tRNA T-loops. In N. equitans, this nucleotide is methylated by the S-adenosylmethionine-dependent enzyme NEQ053 to form m5U54, and a recombinant version of this enzyme maintains specificity for U54 in Escherichia coli. In N. equitans, m5U54 is subsequently thiolated to form m5s2U54. In contrast, I. hospitalis isomerizes U54 to pseudouridine prior to methylating its N1-position and thiolating the O4-position of the nucleobase to form the previously uncharacterized nucleotide m1s4Ψ. The methyl and thiol groups in m1s4Ψ and m5s2U are presented within the T-loop in a spatially identical manner that stabilizes the 3′-endo-anti conformation of nucleotide-54, facilitating stacking onto adjacent nucleotides and reverse-Hoogsteen pairing with nucleotide m1A58. Thus, two distinct structurally-equivalent solutions have evolved independently and convergently to maintain the tertiary fold of tRNAs under extreme hyperthermic conditions.
Collapse
Affiliation(s)
- Simon Rose
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Sylvie Auxilien
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jesper F Havelund
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Finn Kirpekar
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Harald Huber
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Henri Grosjean
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Stephen Douthwaite
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| |
Collapse
|
19
|
McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the "fifth" ribonucleotide in 1951. Since then, the ever-increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal-Hreidarsson syndrome, Bowen-Conradi syndrome, or Williams-Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under: RNA Processing > RNA Editing and Modification.
Collapse
Affiliation(s)
- Phillip J. McCown
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Agnieszka Ruszkowska
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
- Present address:
Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
| | - Charlotte N. Kunkler
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Kurtis Breger
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jacob P. Hulewicz
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew C. Wang
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Noah A. Springer
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jessica A. Brown
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| |
Collapse
|
20
|
de Crécy-Lagard V, Jaroch M. Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. Trends Microbiol 2020; 29:41-53. [PMID: 32718697 DOI: 10.1016/j.tim.2020.06.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/21/2023]
Abstract
Modified nucleotides in tRNA are critical components of the translation apparatus, but their importance in the process of translational regulation had until recently been greatly overlooked. Two breakthroughs have recently allowed a fuller understanding of the importance of tRNA modifications in bacterial physiology. One is the identification of the full set of tRNA modification genes in model organisms such as Escherichia coli K12. The second is the improvement of available analytical tools to monitor tRNA modification patterns. The role of tRNA modifications varies greatly with the specific modification within a given tRNA and with the organism studied. The absence of these modifications or reductions can lead to cell death or pleiotropic phenotypes or may have no apparent visible effect. By linking translation through their decoding functions to metabolism through their biosynthetic pathways, tRNA modifications are emerging as important components of the bacterial regulatory toolbox.
Collapse
Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Marshall Jaroch
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
21
|
Danchin A, Sekowska A, You C. One-carbon metabolism, folate, zinc and translation. Microb Biotechnol 2020; 13:899-925. [PMID: 32153134 PMCID: PMC7264889 DOI: 10.1111/1751-7915.13550] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells. Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.
Collapse
Affiliation(s)
- Antoine Danchin
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
- School of Biomedical SciencesLi Ka Shing Faculty of MedicineThe University of Hong KongS.A.R. Hong KongChina
| | - Agnieszka Sekowska
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen University1066 Xueyuan Rd518055ShenzhenChina
| |
Collapse
|
22
|
de Crécy-Lagard V, Ross RL, Jaroch M, Marchand V, Eisenhart C, Brégeon D, Motorin Y, Limbach PA. Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168. Biomolecules 2020; 10:E977. [PMID: 32629984 PMCID: PMC7408541 DOI: 10.3390/biom10070977] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/14/2022] Open
Abstract
Extensive knowledge of both the nature and position of tRNA modifications in all cellular tRNAs has been limited to two bacteria, Escherichia coli and Mycoplasma capricolum. Bacillus subtilis sp subtilis strain 168 is the model Gram-positive bacteria and the list of the genes involved in tRNA modifications in this organism is far from complete. Mass spectrometry analysis of bulk tRNA extracted from B. subtilis, combined with next generation sequencing technologies and comparative genomic analyses, led to the identification of 41 tRNA modification genes with associated confidence scores. Many differences were found in this model Gram-positive bacteria when compared to E. coli. In general, B. subtilis tRNAs are less modified than those in E. coli, even if some modifications, such as m1A22 or ms2t6A, are only found in the model Gram-positive bacteria. Many examples of non-orthologous displacements and of variations in the most complex pathways are described. Paralog issues make uncertain direct annotation transfer from E. coli to B. subtilis based on homology only without further experimental validation. This difficulty was shown with the identification of the B. subtilis enzyme that introduces ψ at positions 31/32 of the tRNAs. This work presents the most up to date list of tRNA modification genes in B. subtilis, identifies the gaps in knowledge, and lays the foundation for further work to decipher the physiological role of tRNA modifications in this important model organism and other bacteria.
Collapse
Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA;
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Robert L. Ross
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45221, USA;
| | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA;
| | - Virginie Marchand
- UMR7365 IMoPA CNRS-UL and UMS2008 CNRS-UL-INSERM, Université de Lorraine, Biopôle UL, 54000 Nancy, France; (V.M.); (Y.M.)
| | - Christina Eisenhart
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (C.E.); (P.A.L.)
| | - Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne University, 7 Quai Saint Bernard, CEDEX 05, F-75252 Paris, France;
| | - Yuri Motorin
- UMR7365 IMoPA CNRS-UL and UMS2008 CNRS-UL-INSERM, Université de Lorraine, Biopôle UL, 54000 Nancy, France; (V.M.); (Y.M.)
| | - Patrick A. Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (C.E.); (P.A.L.)
| |
Collapse
|
23
|
Zou M, Mu Y, Chai X, Ouyang M, Yu LJ, Zhang L, Meurer J, Chi W. The critical function of the plastid rRNA methyltransferase, CMAL, in ribosome biogenesis and plant development. Nucleic Acids Res 2020; 48:3195-3210. [PMID: 32095829 PMCID: PMC7102989 DOI: 10.1093/nar/gkaa129] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. The formation of methylated nucleotides is performed by a variety of RNA-methyltransferases. Chloroplasts of plant cells result from an endosymbiotic event and possess their own genome and ribosomes. However, enzymes responsible for rRNA methylation and the function of modified nucleotides in chloroplasts remain to be determined. Here, we identified an rRNA methyltransferase, CMAL (Chloroplast MraW-Like), in the Arabidopsis chloroplast and investigated its function. CMAL is the Arabidopsis ortholog of bacterial MraW/ RsmH proteins and accounts to the N4-methylation of C1352 in chloroplast 16S rRNA, indicating that CMAL orthologs and this methyl-modification nucleotide is conserved between bacteria and the endosymbiont-derived eukaryotic organelle. The knockout of CMAL in Arabidopsis impairs the chloroplast ribosome accumulation and accordingly reduced the efficiency of mRNA translation. Interestingly, the loss of CMAL leads not only to defects in chloroplast function, but also to abnormal leaf and root development and overall plant morphology. Further investigation showed that CMAL is involved in the plant development probably by modulating auxin derived signaling pathways. This study uncovered the important role of 16S rRNA methylation mediated by CMAL in chloroplast ribosome biogenesis and plant development.
Collapse
Affiliation(s)
- Meijuan Zou
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ying Mu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin Chai
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University, Munich, D-82152 Planegg-Martinsried, Germany
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
24
|
Sirand-Pugnet P, Brégeon D, Béven L, Goyenvalle C, Blanchard A, Rose S, Grosjean H, Douthwaite S, Hamdane D, de Crécy-Lagard V. Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes. Biomolecules 2020; 10:E587. [PMID: 32290235 PMCID: PMC7226160 DOI: 10.3390/biom10040587] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 01/17/2023] Open
Abstract
The C5-methylation of uracil to form 5-methyluracil (m5U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Here, we investigate the evolution of 5-methyluracil synthase families in Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m5U methyltransferases present in their common ancestor. Cases of duplication and subsequent shift of function are also described. For example, most members of the Spiroplasma subgroup use the ancestral tetrahydrofolate-dependent TrmFO enzyme to catalyze the formation of m5U54 in tRNA, while a TrmFO paralog (termed RlmFO) is responsible for m5U1939 formation in 23S rRNA. RlmFO has replaced the S-adenosyl-L-methionine (SAM)-enzyme RlmD that adds the same modification in the ancestor and which is still present in mollicutes from the Hominis subgroup. Another paralog of this family, the TrmFO-like protein, has a yet unidentified function that differs from the TrmFO and RlmFO homologs. Despite having evolved towards minimal genomes, the mollicutes possess a repertoire of m5U-modifying enzymes that is highly dynamic and has undergone horizontal transfer.
Collapse
Affiliation(s)
- Pascal Sirand-Pugnet
- INRAE, UMR BFP, University Bordeaux, 33882 Bordeaux Villenave D’Ornon, France; (L.B.); (A.B.)
| | - Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne University, 7 quai Saint Bernard, CEDEX 05, F-75252 Paris, France; (D.B.); (C.G.)
| | - Laure Béven
- INRAE, UMR BFP, University Bordeaux, 33882 Bordeaux Villenave D’Ornon, France; (L.B.); (A.B.)
| | - Catherine Goyenvalle
- IBPS, Biology of Aging and Adaptation, Sorbonne University, 7 quai Saint Bernard, CEDEX 05, F-75252 Paris, France; (D.B.); (C.G.)
| | - Alain Blanchard
- INRAE, UMR BFP, University Bordeaux, 33882 Bordeaux Villenave D’Ornon, France; (L.B.); (A.B.)
| | - Simon Rose
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (S.R.); (S.D.)
| | - Henri Grosjean
- Institute for Integrative Biology of the Cell (I2BC), French Atomic Energy and Energy Commission Alternatives, CNRS, Paris-Sud University, Paris-Saclay University, Gif-sur-Yvette CEDEX, 91198 Paris, France;
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (S.R.); (S.D.)
| | - Djemel Hamdane
- Laboratory of Biological Process Chemistry, CNRS-UMR 8229, College De France, Sorbonne University, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| |
Collapse
|
25
|
Laptev I, Shvetsova E, Levitskii S, Serebryakova M, Rubtsova M, Bogdanov A, Kamenski P, Sergiev P, Dontsova O. Mouse Trmt2B protein is a dual specific mitochondrial metyltransferase responsible for m 5U formation in both tRNA and rRNA. RNA Biol 2020; 17:441-450. [PMID: 31736397 PMCID: PMC7237156 DOI: 10.1080/15476286.2019.1694733] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/27/2019] [Accepted: 11/14/2019] [Indexed: 10/25/2022] Open
Abstract
RNA molecules of all species contain modified nucleotides and particularly m5U residues. The vertebrate mitochondrial small subunit rRNA contains m5U nucleotide in a unique site. In this work we found an enzyme, TRMT2B, responsible for the formation of this nucleotide and m5U residues in a number of mitochondrial tRNA species. Inactivation of the Trmt2B gene leads to a reduction of the activity of respiratory chain complexes I, III and IV, containing the subunits synthesized by the mitochondrial protein synthesis apparatus. Comparative sequence analysis of m5U-specific RNA methyltransferases revealed an unusual evolutionary pathway of TRMT2B formation which includes consecutive substrate specificity switches from the large subunit rRNA to tRNA and then to the small subunit rRNA.
Collapse
Affiliation(s)
- Ivan Laptev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Shvetsova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey Levitskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Marina Serebryakova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Rubtsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
| | - Olga Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| |
Collapse
|
26
|
Meyer B, Immer C, Kaiser S, Sharma S, Yang J, Watzinger P, Weiß L, Kotter A, Helm M, Seitz HM, Kötter P, Kellner S, Entian KD, Wöhnert J. Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs. Nucleic Acids Res 2020; 48:1435-1450. [PMID: 31863583 PMCID: PMC7026641 DOI: 10.1093/nar/gkz1191] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
tRNAs from all domains of life contain modified nucleotides. However, even for the experimentally most thoroughly characterized model organism Escherichia coli not all tRNA modification enzymes are known. In particular, no enzyme has been found yet for introducing the acp3U modification at position 47 in the variable loop of eight E. coli tRNAs. Here we identify the so far functionally uncharacterized YfiP protein as the SAM-dependent 3-amino-3-carboxypropyl transferase catalyzing this modification and thereby extend the list of known tRNA modification enzymes in E. coli. Similar to the Tsr3 enzymes that introduce acp modifications at U or m1Ψ nucleotides in rRNAs this protein contains a DTW domain suggesting that acp transfer reactions to RNA nucleotides are a general function of DTW domain containing proteins. The introduction of the acp3U-47 modification in E. coli tRNAs is promoted by the presence of the m7G-46 modification as well as by growth in rich medium. However, a deletion of the enzymes responsible for the modifications at position 46 and 47 in the variable loop of E. coli tRNAs did not lead to a clearly discernible phenotype suggesting that these two modifications play only a minor role in ensuring the proper function of tRNAs in E. coli.
Collapse
Affiliation(s)
- Britta Meyer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Carina Immer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Steffen Kaiser
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Sunny Sharma
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Jun Yang
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Peter Watzinger
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Lena Weiß
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Hans-Michael Seitz
- Institute for Geosciences, Research Unit Mineralogy, and Frankfurt Isotope and Element Research Center (FIERCE), Goethe-Universität Frankfurt, Altenhöferallee 1, 60438 Frankfurt/M., Germany
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| |
Collapse
|
27
|
Dozova N, Lacombat F, Bou-Nader C, Hamdane D, Plaza P. Ultrafast photoinduced flavin dynamics in the unusual active site of the tRNA methyltransferase TrmFO. Phys Chem Chem Phys 2019; 21:8743-8756. [PMID: 30968076 DOI: 10.1039/c8cp06072j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flavoproteins often stabilize their flavin coenzyme by stacking interactions involving the isoalloxazine moiety of the flavin and an aromatic residue from the apoprotein. The bacterial FAD and folate-dependent tRNA methyltransferase TrmFO has the unique property of stabilizing its FAD coenzyme by an unusual H-bond-assisted π-π stacking interaction, involving a conserved tyrosine (Y346 in Bacillus subtilis TrmFO, BsTrmFO), the isoalloxazine of FAD and the backbone of a catalytic cysteine (C53). Here, the interaction between FAD and Y346 has been investigated by measuring the photoinduced flavin dynamics of BsTrmFO in the wild-type (WT) protein, C53A and several Y346 mutants by ultrafast transient absorption spectroscopy. In C53A, the excited FAD very rapidly (0.43 ps) abstracts an electron from Y346, yielding the FAD˙-/Y346OH˙+ radical pair, while relaxation of the local environment (1.3 ps) of the excited flavin produces a slight Stokes shift of its stimulated emission band. The radical pair then decays via charge recombination, mostly in 3-4 ps, without any deprotonation of the Y346OH˙+ radical. Presumably, the H-bond between Y346 and the amide group of C53 increases the pKa of Y346OH˙+ and slows down its deprotonation. The dynamics of WT BsTrmFO shows additional slow decay components (43 and 700 ps), absent in the C53A mutant, assigned to excited FADox populations not undergoing fast photoreduction. Their presence is likely due to a more flexible structure of the WT protein, favored by the presence of C53. Interestingly, mutations of Y346 canceling its electron donating character lead to multiple slower quenching channels in the ps-ns regime. These channels are proposed to be due to electron abstraction either (i) from the adenine moiety of FAD, a distribution of the isoalloxazine-adenine distance in the absence of Y346 explaining the multiexponential decay, or (ii) from the W286 residue, possibly accounting for one of the decays. This work supports the idea that H-bond-assisted π-π stacking controls TrmFO's active site dynamics, required for competent orientation of the reactive centers during catalysis.
Collapse
Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | | | | | | | | |
Collapse
|
28
|
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.
Collapse
|
29
|
Barraud P, Tisné C. To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs. IUBMB Life 2019; 71:1126-1140. [PMID: 30932315 PMCID: PMC6850298 DOI: 10.1002/iub.2041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/10/2019] [Indexed: 12/12/2022]
Abstract
Transfer RNAs (tRNAs) are essential components of the cellular protein synthesis machineries, but are also implicated in many roles outside translation. To become functional, tRNAs, initially transcribed as longer precursor tRNAs, undergo a tightly controlled biogenesis process comprising the maturation of their extremities, removal of intronic sequences if present, addition of the 3'-CCA amino-acid accepting sequence, and aminoacylation. In addition, the most impressive feature of tRNA biogenesis consists in the incorporation of a large number of posttranscriptional chemical modifications along its sequence. The chemical nature of these modifications is highly diverse, with more than hundred different modifications identified in tRNAs to date. All functions of tRNAs in cells are controlled and modulated by modifications, making the understanding of the mechanisms that determine and influence nucleotide modifications in tRNAs an essential point in tRNA biology. This review describes the different aspects that determine whether a certain position in a tRNA molecule is modified or not. We describe how sequence and structural determinants, as well as the presence of prior modifications control modification processes. We also describe how environmental factors and cellular stresses influence the level and/or the nature of certain modifications introduced in tRNAs, and report situations where these dynamic modulations of tRNA modification levels are regulated by active demodification processes. © 2019 IUBMB Life, 71(8):1126-1140, 2019.
Collapse
Affiliation(s)
- Pierre Barraud
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
| | - Carine Tisné
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
| |
Collapse
|
30
|
Sergiev PV, Aleksashin NA, Chugunova AA, Polikanov YS, Dontsova OA. Structural and evolutionary insights into ribosomal RNA methylation. Nat Chem Biol 2019; 14:226-235. [PMID: 29443970 DOI: 10.1038/nchembio.2569] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/02/2018] [Indexed: 01/24/2023]
Abstract
Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. Identification of all enzymes responsible for rRNA methylation, as well as mapping of all modified rRNA residues, is now complete for a number of model species, such as Escherichia coli and Saccharomyces cerevisiae. Recent high-resolution structures of bacterial ribosomes provided the first direct visualization of methylated nucleotides. The structures of ribosomes from various organisms and organelles have also lately become available, enabling comparative structure-based analysis of rRNA methylation sites in various taxonomic groups. In addition to the conserved core of modified residues in ribosomes from the majority of studied organisms, structural analysis points to the functional roles of some of the rRNA methylations, which are discussed in this Review in an evolutionary context.
Collapse
Affiliation(s)
- Petr V Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Anastasia A Chugunova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Olga A Dontsova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
31
|
Hori H. Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus. Front Genet 2019; 10:204. [PMID: 30906314 PMCID: PMC6418473 DOI: 10.3389/fgene.2019.00204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/26/2019] [Indexed: 01/02/2023] Open
Abstract
Thermus thermophilus is an extreme-thermophilic bacterium that can grow at a wide range of temperatures (50-83°C). To enable T. thermophilus to grow at high temperatures, several biomolecules including tRNA and tRNA modification enzymes show extreme heat-resistance. Therefore, the modified nucleosides in tRNA from T. thermophilus have been studied mainly from the view point of tRNA stabilization at high temperatures. Such studies have shown that several modifications stabilize the structure of tRNA and are essential for survival of the organism at high temperatures. Together with tRNA modification enzymes, the modified nucleosides form a network that regulates the extent of different tRNA modifications at various temperatures. In this review, I describe this network, as well as the tRNA recognition mechanism of individual tRNA modification enzymes. Furthermore, I summarize the roles of other tRNA stabilization factors such as polyamines and metal ions.
Collapse
Affiliation(s)
- Hiroyuki Hori
- Department of Materials Sciences and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis. Nat Chem Biol 2018; 14:1010-1020. [PMID: 30150682 DOI: 10.1038/s41589-018-0119-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/09/2018] [Indexed: 11/08/2022]
Abstract
Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N4-acetylcytidine (ac4C) is present at the anticodon first position (position 34) of bacterial elongator tRNAMet. Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac4C34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes ac4C34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of ac4C34 formation. The ΔtmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNAIle to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the ΔtmcAL strain upon tilS repression suggests that ac4C34 modification of tRNAMet and L34 modification of tRNAIle act cooperatively to prevent misdecoding of the AUA codon.
Collapse
|
34
|
Yamagami R, Miyake R, Fukumoto A, Nakashima M, Hori H. Consumption of N5, N10-methylenetetrahydrofolate in Thermus thermophilus under nutrient-poor condition. J Biochem 2018. [PMID: 29538705 DOI: 10.1093/jb/mvy037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
TrmFO catalyzes the formation of 5-methyluridine at position 54 in tRNA and uses N5, N10-methylenetetrahydrofolate (CH2THF) as the methyl group donor. We found that the trmFO gene-disruptant strain of Thermus thermophilus, an extremely thermophilic eubacterium, can grow faster than the wild-type strain in the synthetic medium at 70°C (optimal growth temperature). Nucleoside analysis revealed that the majority of modifications were appropriately introduced into tRNA, showing that the limited nutrients are preferentially consumed in the tRNA modification systems. CH2THF is consumed not only for tRNA methylation by TrmFO but also for dTMP synthesis by ThyX and methionine synthesis by multiple steps including MetF reaction. In vivo experiment revealed that methylene group derived from serine was rapidly incorporated into DNA in the absence of TrmFO. Furthermore, the addition of thymidine to the medium accelerated growth speed of the wild-type strain. Moreover, in vitro experiments showed that TrmFO interfered with ThyX through consumption of CH2THF. Addition of methionine to the medium accelerated growth speed of wild-type strain and the activity of TrmFO was disturbed by MetF. Thus, the consumption of CH2THF by TrmFO has a negative effect on dTMP and methionine syntheses and results in the slow growth under a nutrient-poor condition.
Collapse
Affiliation(s)
- Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Ryota Miyake
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Ayaka Fukumoto
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Misa Nakashima
- 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
| |
Collapse
|
35
|
Myllykallio H, Sournia P, Heliou A, Liebl U. Unique Features and Anti-microbial Targeting of Folate- and Flavin-Dependent Methyltransferases Required for Accurate Maintenance of Genetic Information. Front Microbiol 2018; 9:918. [PMID: 29867829 PMCID: PMC5954106 DOI: 10.3389/fmicb.2018.00918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
Comparative genome analyses have led to the discovery and characterization of novel flavin- and folate-dependent methyltransferases that mainly function in DNA precursor synthesis and post-transcriptional RNA modification by forming (ribo) thymidylate and its derivatives. Here we discuss the recent literature on the novel mechanistic features of these enzymes sometimes referred to as “uracil methyltransferases,” albeit we prefer to refer to them as (ribo) thymidylate synthases. These enzyme families attest to the convergent evolution of nucleic acid methylation. Special focus is given to describing the unique characteristics of these flavin- and folate-dependent enzymes that have emerged as new models for studying the non-canonical roles of reduced flavin co-factors (FADH2) in relaying carbon atoms between enzyme substrates. This ancient enzymatic methylation mechanism with a very wide phylogenetic distribution may be more commonly used for biological methylation reactions than previously anticipated. This notion is exemplified by the recent discovery of additional substrates for these enzymes. Moreover, similar reaction mechanisms can be reversed by demethylases, which remove methyl groups e.g., from human histones. Future work is now required to address whether the use of different methyl donors facilitates the regulation of distinct methylation reactions in the cell. It will also be of great interest to address whether the low activity flavin-dependent thymidylate synthases ThyX represent ancestral enzymes that were eventually replaced by the more active thymidylate synthases of the ThyA family to facilitate the maintenance of larger genomes in fast-growing microbes. Moreover, we discuss the recent efforts from several laboratories to identify selective anti-microbial compounds that target flavin-dependent thymidylate synthase ThyX. Altogether we underline how the discovery of the alternative flavoproteins required for methylation of DNA and/or RNA nucleotides, in addition to providing novel targets for antibiotics, has provided new insight into microbial physiology and virulence.
Collapse
Affiliation(s)
- Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
| | - Pierre Sournia
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
| | - Alice Heliou
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France.,Laboratoire d'Informatique de l'École Polytechnique, Ecole Polytechnique, Centre National de la Recherche Scientifique, Université Paris-Saclay, Palaiseau, France
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
| |
Collapse
|
36
|
Wang Y, Pang C, Li X, Hu Z, Lv Z, Zheng B, Chen P. Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis. BMC PLANT BIOLOGY 2017; 17:261. [PMID: 29268705 PMCID: PMC5740945 DOI: 10.1186/s12870-017-1206-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/06/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Modification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding. RESULTS In this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants-O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, m1A and m7G, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, m5U and m5C, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, m1A and m7G MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, m5U and m5C modifications and corresponding methylation genes in different tissues during different developmental stages. CONCLUSIONS We identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, m1A and m7G) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, m5U and m5C) that might be important during development.
Collapse
Affiliation(s)
- Youmei Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chaoqun Pang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xukai Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi Province 030801 China
| | - Zhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhengyi Lv
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
37
|
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
|
38
|
Bou‐Nader C, Cornu D, Guerineau V, Fogeron T, Fontecave M, Hamdane D. Enzyme Activation with a Synthetic Catalytic Co‐enzyme Intermediate: Nucleotide Methylation by Flavoenzymes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Charles Bou‐Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229 Collège De France Université Pierre et Marie Curie 11 place Marcelin Berthelot 75231 Paris Cedex 05 France
| | - David Cornu
- Institut de Biologie Intégrative de la Cellule CNRS CEA Université Paris-Saclay Gif-sur-Yvette France
| | - Vincent Guerineau
- Institut de Chimie des Substances Naturelles Centre de Recherche de Gif CNRS 1 avenue de la Terrasse 91198 Gif-sur-Yvette France
| | - Thibault Fogeron
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229 Collège De France Université Pierre et Marie Curie 11 place Marcelin Berthelot 75231 Paris Cedex 05 France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229 Collège De France Université Pierre et Marie Curie 11 place Marcelin Berthelot 75231 Paris Cedex 05 France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229 Collège De France Université Pierre et Marie Curie 11 place Marcelin Berthelot 75231 Paris Cedex 05 France
| |
Collapse
|
39
|
|
40
|
Bou-Nader C, Cornu D, Guerineau V, Fogeron T, Fontecave M, Hamdane D. Enzyme Activation with a Synthetic Catalytic Co-enzyme Intermediate: Nucleotide Methylation by Flavoenzymes. Angew Chem Int Ed Engl 2017; 56:12523-12527. [PMID: 28796306 DOI: 10.1002/anie.201706219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/25/2017] [Indexed: 12/11/2022]
Abstract
To facilitate production of functional enzymes and to study their mechanisms, especially in the complex cases of coenzyme-dependent systems, activation of an inactive apoenzyme preparation with a catalytically competent coenzyme intermediate is an attractive strategy. This is illustrated with the simple chemical synthesis of a flavin-methylene iminium compound previously proposed as a key intermediate in the catalytic cycle of several important flavoenzymes involved in nucleic acid metabolism. Reconstitution of both flavin-dependent RNA methyltransferase and thymidylate synthase apoproteins with this synthetic compound led to active enzymes for the C5-uracil methylation within their respective transfer RNA and dUMP substrate. This strategy is expected to be of general application in enzymology.
Collapse
Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231, Paris Cedex 05, France
| | - David Cornu
- Institut de Biologie Intégrative de la Cellule, CNRS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Vincent Guerineau
- Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Thibault Fogeron
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231, Paris Cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231, Paris Cedex 05, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231, Paris Cedex 05, France
| |
Collapse
|
41
|
TrmFO, a Fibronectin-Binding Adhesin of Mycoplasma bovis. Int J Mol Sci 2017; 18:ijms18081732. [PMID: 28792486 PMCID: PMC5578122 DOI: 10.3390/ijms18081732] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 07/24/2017] [Accepted: 08/02/2017] [Indexed: 11/17/2022] Open
Abstract
Mycoplasma bovis is an important pathogenic mycoplasma, causing the cattle industry serious economic losses. Adhesion is a crucial step in the mycoplasmas' infection and colonization process; fibronectin (Fn), an extracellular matrix glycoprotein, is a molecular bridge between the bacterial adhesins and host cell receptors. The present study was designed to characterize the Fn-binding ability of methylenetetrahydrofolate-tRNA-(uracil-5-)-methyltransferase (TrmFO) and its role in M. bovis cytoadherence. The trmFO (MBOV_RS00785) gene was cloned and expressed in E. coli BL21, and polyclonal antibodies against the recombinant TrmFO (rTrmFO) were raised in rabbits. Immunoblotting demonstrated that TrmFO was an immunogenic component, and the TrmFO expression was conserved in different M. bovis isolates. The mycoplasmacidal assay further showed that in the presence of complement, rabbit anti-recombinant TrmFO serum exhibited remarkable mycoplasmacidal efficacy. TrmFO was detected in both the M. bovis membrane and cytoplasm. By ligand dot blot and enzyme-linked immunosorbent assay (ELISA) binding assay, we found that rTrmFO bound Fn in a dose-dependent manner. Immunostaining visualized by confocal laser scanning microscopy showed that rTrmFO had capacity to adhere to the embryonic bovine lung (EBL) cells. In addition, the adhesion of M. bovis and rTrmFO to EBL cells could be inhibited by anti-rTrmFO antibodies. To the best of our knowledge, this is the first report to characterize the Fn-binding ability of TrmFO and its role in the bacterial adhesion to host cells.
Collapse
|
42
|
Nag L, Sournia P, Myllykallio H, Liebl U, Vos MH. Identification of the TyrOH •+ Radical Cation in the Flavoenzyme TrmFO. J Am Chem Soc 2017; 139:11500-11505. [PMID: 28745052 DOI: 10.1021/jacs.7b04586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tyrosine (TyrOH) and tryptophan radicals play important roles as intermediates in biochemical charge-transfer reactions. Tryptophanyl radicals have been observed both in their protonated cation form and in their unprotonated neutral form, but to date, tyrosyl radicals have only been observed in their unprotonated form. With a genetically modified form of the flavoenzyme TrmFO as a suitable model system and using ultrafast fluorescence and absorption spectroscopy, we characterize its protonated precursor TyrOH•+, and we show this species to have a distinct visible absorption band and a transition moment that we suggest to lie close to the phenol symmetry axis. TyrOH•+ is formed in ∼1 ps by electron transfer to excited flavin and decays in ∼3 ps by charge recombination. These findings imply that TyrOH oxidation does not necessarily induce its concerted deprotonation. Our results will allow disentangling of photoproduct states in flavoproteins in often-encountered complex situations and more generally are important for understanding redox chains relying on tyrosyl intermediates.
Collapse
Affiliation(s)
- Lipsa Nag
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Pierre Sournia
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Hannu Myllykallio
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Ursula Liebl
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| |
Collapse
|
43
|
Motorin Y, Seidu-Larry S, Helm M. DNA and RNA Pyrimidine Nucleobase Alkylation at the Carbon-5 Position. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 945:19-33. [PMID: 27826833 DOI: 10.1007/978-3-319-43624-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modification in both DNA and RNA. The simplest modification of uridine at this position is methylation leading to thymine. Thymine is an integral part of the standard nucleobase repertoire of DNA that is synthesized at the nucleotide level. However, it also occurs in RNA, where it is synthesized posttranscriptionally at the polynucleotide level. The cytidine analogue 5-methylcytidine also occurs in both DNA and RNA, but is introduced at the polynucleotide level in both cases. The same applies to a plethora of additional derivatives found in nature, resulting either from a direct modification of the 5-position by electrophiles or by further derivatization of the 5-methylpyrimidines. Here, we review the structural diversity of these modified bases, the variety of cofactors that serve as carbon donors, and the common principles shared by enzymatic mechanisms generating them.
Collapse
Affiliation(s)
- Yuri Motorin
- IMoPA UMR7365 CNRS-UL, BioPole de l'Université de Lorraine, 9 avenue de la Foret de Haye, 54505, Vandoeuvre-les-Nancy, France.
| | - Salifu Seidu-Larry
- Department of Biochemistry, University of Cape Coast, College of Agriculture and Natural Sciences, School of Biological Sciences, Cape Coast, Ghana
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany.
| |
Collapse
|
44
|
Piano V, Palfey BA, Mattevi A. Flavins as Covalent Catalysts: New Mechanisms Emerge. Trends Biochem Sci 2017; 42:457-469. [DOI: 10.1016/j.tibs.2017.02.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
|
45
|
Nakashima M, Yamagami R, Tomikawa C, Ochi Y, Moriya T, Asahara H, Fourmy D, Yoshizawa S, Oshima T, Hori H. Long and branched polyamines are required for maintenance of the ribosome, tRNAHisand tRNATyrinThermus thermophiluscells at high temperatures. Genes Cells 2017; 22:628-645. [DOI: 10.1111/gtc.12502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Misa Nakashima
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Yuki Ochi
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Toshiyuki Moriya
- Institute of Environmental Microbiology; Kyowa Kako Co. Ltd.; Tadao 2-15-5 Machida 194-0035 Japan
| | - Haruichi Asahara
- New England Biolabs, Inc; 240 County Road Ipswich Massachusetts 01938 USA
| | - Dominique Fourmy
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS; Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Satoko Yoshizawa
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS; Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Tairo Oshima
- Institute of Environmental Microbiology; Kyowa Kako Co. Ltd.; Tadao 2-15-5 Machida 194-0035 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
| |
Collapse
|
46
|
Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA. Biomolecules 2017; 7:biom7010023. [PMID: 28264529 PMCID: PMC5372735 DOI: 10.3390/biom7010023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/23/2017] [Indexed: 11/22/2022] Open
Abstract
The existence of SpoU-TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics. SpoU is the previous name of TrmH, which catalyzes the 2’-O-methylation of ribose of G18 in tRNA; TrmD catalyzes the formation of N1-methylguanosine at position 37 in tRNA. Although SpoU (TrmH) and TrmD were originally considered to be unrelated, the bioinformatics study suggested that they might share a common evolution origin and form a single superfamily. The common feature of SPOUT RNA methyltransferases is the formation of a deep trefoil knot in the catalytic domain. In the past decade, the SPOUT RNA methyltransferase superfamily has grown; furthermore, knowledge concerning the functions of their modified nucleosides in tRNA has also increased. Some enzymes are potential targets in the design of anti-bacterial drugs. In humans, defects in some genes may be related to carcinogenesis. In this review, recent findings on the tRNA methyltransferases with a SPOUT fold and their methylated nucleosides in tRNA, including classification of tRNA methyltransferases with a SPOUT fold; knot structures, domain arrangements, subunit structures and reaction mechanisms; tRNA recognition mechanisms, and functions of modified nucleosides synthesized by this superfamily, are summarized. Lastly, the future perspective for studies on tRNA modification enzymes are considered.
Collapse
|
47
|
Fislage M, Wauters L, Versées W. Invited review: MnmE, a GTPase that drives a complex tRNA modification reaction. Biopolymers 2017; 105:568-79. [PMID: 26832457 DOI: 10.1002/bip.22813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/19/2016] [Accepted: 01/27/2016] [Indexed: 01/30/2023]
Abstract
MnmE is a multi-domain GTPase that is conserved from bacteria to man. Together with its partner protein MnmG it is involved in the synthesis of a tRNA wobble uridine modification. The orthologues of these proteins in eukaryotes are targeted to mitochondria and mutations in the encoding genes are associated with severe mitochondrial diseases. While classical small GTP-binding proteins are regulated via auxiliary GEFs and GAPs, the GTPase activity of MnmE is activated via potassium-dependent homodimerization of its G domains. In this review we focus on the catalytic mechanism of GTP hydrolysis by MnmE and the large scale conformational changes that are triggered throughout the GTPase cycle. We also discuss how these conformational changes might be used to drive and tune the complex tRNA modification reaction. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 568-579, 2016.
Collapse
Affiliation(s)
- Marcus Fislage
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032.,Howard Hughes Medical Institute, Columbia University, New York, NY, 10032
| | - Lina Wauters
- Department of Cell Biochemistry, University of Groningen, Nijenborgh 7, Groningen, 9747 AG, Netherlands.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussel, 1050, Belgium.,Structural Biology Research Center, VIB, Pleinlaan 2, Brussel, 1050, Belgium
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussel, 1050, Belgium.,Structural Biology Research Center, VIB, Pleinlaan 2, Brussel, 1050, Belgium
| |
Collapse
|
48
|
Flavin-Dependent Methylation of RNAs: Complex Chemistry for a Simple Modification. J Mol Biol 2016; 428:4867-4881. [PMID: 27825927 DOI: 10.1016/j.jmb.2016.10.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 12/28/2022]
Abstract
RNA methylation is the most abundant and evolutionarily conserved chemical modification of bases or ribose in noncoding and coding RNAs. This rather simple modification has nevertheless major consequences on the function of maturated RNA molecules and ultimately on their cellular fates. The methyl group employed in the methylation is almost universally derived from S-adenosyl-L-methionine via a simple SN2 displacement reaction. However, in some rare cases, the carbon originates from N5,N10-methylenetetrahydrofolate (CH2=THF). Here, a methylene group is transferred first and requires a subsequent reduction step (2e-+H+) via the flavin adenine dinucleotide hydroquinone (FADH-) to form the final methylated derivative. This FAD/folate-dependent mode of chemical reaction, called reductive methylation, is thus far more complex than the usual simple S-adenosyl-L-methionine-dependent one. This reaction is catalyzed by flavoenzymes, now named TrmFO and RlmFO, which respectively modify transfer and ribosomal RNAs. In this review, we briefly recount how these new RNA methyltransferases were discovered and describe a novel aspect of the chemistry of flavins, wherein this versatile biological cofactor is not just a simple redox catalyst but is also a new methyl transfer agent acting via a critical CH2=(N5)FAD iminium intermediate. The enigmatic structural reorganization of these enzymes that needs to take place during catalysis in order to build their active center is also discussed. Finally, recent findings demonstrated that this flavin-dependent mechanism is also employed by enzymatic systems involved in DNA synthesis, suggesting that the use of this cofactor as a methylating agent of biomolecules could be far more usual than initially anticipated.
Collapse
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
Yamagami R, Tomikawa C, Shigi N, Kazayama A, Asai SI, Takuma H, Hirata A, Fourmy D, Asahara H, Watanabe K, Yoshizawa S, Hori H. Folate-/FAD-dependent tRNA methyltransferase from Thermus thermophilus regulates other modifications in tRNA at low temperatures. Genes Cells 2016; 21:740-54. [PMID: 27238446 DOI: 10.1111/gtc.12376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/19/2016] [Indexed: 11/29/2022]
Abstract
TrmFO is a N(5) , N(10) -methylenetetrahydrofolate (CH2 THF)-/FAD-dependent tRNA methyltransferase, which synthesizes 5-methyluridine at position 54 (m(5) U54) in tRNA. Thermus thermophilus is an extreme-thermophilic eubacterium, which grows in a wide range of temperatures (50-83 °C). In T. thermophilus, modified nucleosides in tRNA and modification enzymes form a network, in which one modification regulates the degrees of other modifications and controls the flexibility of tRNA. To clarify the role of m(5) U54 and TrmFO in the network, we constructed the trmFO gene disruptant (∆trmFO) strain of T. thermophilus. Although this strain did not show any growth retardation at 70 °C, it showed a slow-growth phenotype at 50 °C. Nucleoside analysis showed increase in 2'-O-methylguanosine at position 18 and decrease in N(1) -methyladenosine at position 58 in the tRNA mixture from the ∆trmFO strain at 50 °C. These in vivo results were reproduced by in vitro experiments with purified enzymes. Thus, we concluded that the m(5) U54 modification have effects on the other modifications in tRNA through the network at 50 °C. (35) S incorporations into proteins showed that the protein synthesis activity of ∆trmFO strain was inferior to the wild-type strain at 50 °C, suggesting that the growth delay at 50 °C was caused by the inferior protein synthesis activity.
Collapse
Affiliation(s)
- Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ai Kazayama
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Shin-Ichi Asai
- Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), Tokyo, 135-0064, Japan
| | - Hiroyuki Takuma
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Dominique Fourmy
- Institute for Integrative Biology of the Cell (I2BC), UMR9198, CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, Gif-sur-Yvette, Cedex, 91198, France
| | - Haruichi Asahara
- New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
| | - Kimitsuna Watanabe
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Satoko Yoshizawa
- Institute for Integrative Biology of the Cell (I2BC), UMR9198, CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, Gif-sur-Yvette, Cedex, 91198, France
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| |
Collapse
|