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Wang Z, Xu X, Li X, Fang J, Huang Z, Zhang M, Liu J, Qiu X. Investigations of Single-Subunit tRNA Methyltransferases from Yeast. J Fungi (Basel) 2023; 9:1030. [PMID: 37888286 PMCID: PMC10608323 DOI: 10.3390/jof9101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
tRNA methylations, including base modification and 2'-O-methylation of ribose moiety, play critical roles in the structural stabilization of tRNAs and the fidelity and efficiency of protein translation. These modifications are catalyzed by tRNA methyltransferases (TRMs). Some of the TRMs from yeast can fully function only by a single subunit. In this study, after performing the primary bioinformatic analyses, the progress of the studies of yeast single-subunit TRMs, as well as the studies of their homologues from yeast and other types of eukaryotes and the corresponding TRMs from other types of organisms was systematically reviewed, which will facilitate the understanding of the evolutionary origin of functional diversity of eukaryotic single-subunit TRM.
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Affiliation(s)
- Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiangbin Xu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xinhai Li
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
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Li H, Dong H, Xu B, Xiong QP, Li CT, Yang WQ, Li J, Huang ZX, Zeng QY, Wang ED, Liu RJ. A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription. EMBO J 2021; 41:e108544. [PMID: 34850409 PMCID: PMC8922252 DOI: 10.15252/embj.2021108544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022] Open
Abstract
Since numerous RNAs and RBPs prevalently localize to active chromatin regions, many RNA-binding proteins (RBPs) may be potential transcriptional regulators. RBPs are generally thought to regulate transcription via noncoding RNAs. Here, we describe a distinct, dual mechanism of transcriptional regulation by the previously uncharacterized tRNA-modifying enzyme, hTrmt13. On one hand, hTrmt13 acts in the cytoplasm to catalyze 2'-O-methylation of tRNAs, thus regulating translation in a manner depending on its tRNA-modification activity. On the other hand, nucleus-localized hTrmt13 directly binds DNA as a transcriptional co-activator of key epithelial-mesenchymal transition factors, thereby promoting cell migration independent of tRNA-modification activity. These dual functions of hTrmt13 are mutually exclusive, as it can bind either DNA or tRNA through its CHHC zinc finger domain. Finally, we find that hTrmt13 expression is tightly associated with poor prognosis and survival in diverse cancer patients. Our discovery of the noncatalytic roles of an RNA-modifying enzyme provides a new perspective for understanding epitranscriptomic regulation.
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Affiliation(s)
- Hao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Han Dong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhi-Xuan Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Qi-Yu Zeng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - En-Duo Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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Ayadi L, Galvanin A, Pichot F, Marchand V, Motorin Y. RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:253-269. [PMID: 30572123 DOI: 10.1016/j.bbagrm.2018.11.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 01/01/2023]
Abstract
Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.
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Affiliation(s)
- Lilia Ayadi
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Adeline Galvanin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Florian Pichot
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Virginie Marchand
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Yuri Motorin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France.
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Wang Y, Li D, Gao J, Li X, Zhang R, Jin X, Hu Z, Zheng B, Persson S, Chen P. The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively regulates salt stress tolerance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1479-1491. [PMID: 28369540 PMCID: PMC5444449 DOI: 10.1093/jxb/erx061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stress induces changes of modified nucleosides in tRNA, and these changes can influence codon-anticodon interaction and therefore the translation of target proteins. Certain nucleoside modification genes are associated with regulation of stress tolerance and immune response in plants. In this study, we found a dramatic increase of 2'-O-methyladenosine (Am) nucleoside in rice seedlings subjected to salt stress and abscisic acid (ABA) treatment. We identified LOC_Os03g61750 (OsTRM13) as a rice candidate methyltransferase for the Am modification. OsTRM13 transcript levels increased significantly upon salt stress and ABA treatment, and the OsTrm13 protein was found to be located primarily to the nucleus. More importantly, OsTRM13 overexpression plants displayed improved salt stress tolerance, and vice versa, OsTRM13 RNA interference (RNAi) plants showed reduced tolerance. Furthermore, OsTRM13 complemented a yeast trm13Δ mutant, deficient in Am synthesis, and the purified OsTrm13 protein catalysed Am nucleoside formation on tRNA-Gly-GCC in vitro. Our results show that OsTRM13, encoding a rice tRNA nucleoside methyltransferase, is an important regulator of salt stress tolerance in rice.
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Affiliation(s)
- Youmei Wang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China
| | - Junbao Gao
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xukai Li
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Rui Zhang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xiaohuan Jin
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Zhen Hu
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Bo Zheng
- College of Horticulture and Forestry Sciences, HuaZhong Agricultural University, Wuhan 430070, China
| | - Staffan Persson
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
- School of Biosciences, University of Melbourne, Parkville 3010 VIC, Australia
| | - Peng Chen
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
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Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
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Maghsoudi S, Ashrafi-Kooshk MR, Shahlaei M, Ghadami SA, Ghobadi S, Mostafaie A, Khodarahmi R. Comparative evaluation of amphotericin B binding to the native and modified forms of rice lipid-transfer protein: a possible perspective on improving the drug-binding affinity and specificity. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2013. [DOI: 10.1007/s13738-013-0231-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Amyloid fibril formation by native and modified bovine β-lactoglobulins proceeds through unfolded form of proteins: A comparative study. Biophys Chem 2011; 159:311-20. [DOI: 10.1016/j.bpc.2011.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 11/16/2022]
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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