1
|
Li ZH, Zhou XL. Eukaryotic AlaX provides multiple checkpoints for quality and quantity of aminoacyl-tRNAs in translation. Nucleic Acids Res 2024:gkae486. [PMID: 38869066 DOI: 10.1093/nar/gkae486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
Translational fidelity relies critically on correct aminoacyl-tRNA supply. The trans-editing factor AlaX predominantly hydrolyzes Ser-tRNAAla, functioning as a third sieve of alanyl-tRNA synthetase (AlaRS). Despite extensive studies in bacteria and archaea, the mechanism of trans-editing in mammals remains largely unknown. Here, we show that human AlaX (hAlaX), which is exclusively distributed in the cytoplasm, is an active trans-editing factor with strict Ser-specificity. In vitro, both hAlaX and yeast AlaX (ScAlaX) were capable of hydrolyzing nearly all Ser-mischarged cytoplasmic and mitochondrial tRNAs; and robustly edited cognate Ser-charged cytoplasmic and mitochondrial tRNASers. In vivo or cell-based studies revealed that loss of ScAlaX or hAlaX readily induced Ala- and Thr-to-Ser misincorporation. Overexpression of hAlaX impeded the decoding efficiency of consecutive Ser codons, implying its regulatory role in Ser codon decoding. Remarkably, yeast cells with ScAlaX deletion responded differently to translation inhibitor treatment, with a gain in geneticin resistance, but sensitivity to cycloheximide, both of which were rescued by editing-capable ScAlaX, alanyl- or threonyl-tRNA synthetase. Altogether, our results demonstrated the previously undescribed editing peculiarities of eukaryotic AlaXs, which provide multiple checkpoints to maintain the speed and fidelity of genetic decoding.
Collapse
Affiliation(s)
- Zi-Han Li
- Key Laboratory of RNA Innovation, Science and Engineering, 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Innovation, Science and Engineering, 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, 320 Yue Yang Road, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| |
Collapse
|
2
|
Tong Q, Miao Y, Yin H. Echocardiographic manifestations of mitochondrial disease with GTPBP3 gene mutations: A case report. Medicine (Baltimore) 2024; 103:e37847. [PMID: 38701254 PMCID: PMC11062751 DOI: 10.1097/md.0000000000037847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/20/2024] [Indexed: 05/05/2024] Open
Abstract
RATIONALE Mitochondrial diseases are a group of disorders in which mutations in mitochondrial DNA or nuclear DNA lead to dysfunctional oxidative phosphorylation of cells, with mutations in mitochondrial DNA being the most common cause of mitochondrial disease, and mutations in nuclear genes being rarely reported. The echocardiographic findings of mitochondrial diseases with nuclear gene mutations in children's hearts are even rarer. Even more valuable is that we followed up the patient for 4 years and dynamically observed the cardiac echocardiographic manifestations of mitochondrial disease. Provide ideas for the clinical diagnosis and prognosis of mitochondrial diseases. PATIENT CONCERNS The patient was seen in the pediatric outpatient clinic for poor strength and mental retardation. echocardiography: mild left ventricular (LV) enlargement and LV wall thickening. Nuclear genetic testing: uanosine triphosphate binding protein 3 (GTPBP3) gene mutation. Diagnosis of mitochondrial disease. DIAGNOSES Mitochondrial disease with GTPBP3 gene mutations. OUTCOMES After receiving drug treatment, the patient exhibited a reduction in lactate levels, an enhanced physical condition compared to prior assessments, and demonstrated average intellectual development. LESSONS SUBSECTIONS For echocardiographic indications of LV wall thickening and LV enlargement, one needs to be alert to the possibility of hereditary cardiomyopathy, especially in children.
Collapse
Affiliation(s)
- Qiaoli Tong
- Department of Cardiac Ultrasound, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yajing Miao
- Department of Cardiac Ultrasound, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hongning Yin
- Department of Cardiac Ultrasound, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
3
|
Zhang Y, Zhou JB, Yin Y, Wang ED, Zhou XL. Multifaceted roles of t6A biogenesis in efficiency and fidelity of mitochondrial gene expression. Nucleic Acids Res 2024; 52:3213-3233. [PMID: 38227555 PMCID: PMC11014344 DOI: 10.1093/nar/gkae013] [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: 10/13/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
N 6-Threonylcarbamoyladenosine at A37 (t6A37) of ANN-decoding transfer RNAs (tRNAs) is a universal modification whose functions have been well documented in bacteria and lower eukaryotes; however, its role in organellar translation is not completely understood. In this study, we deleted the mitochondrial t6A37-modifying enzyme OSGEPL1 in HEK293T cells. OSGEPL1 is dispensable for cell viability. t6A37 hypomodification selectively stimulated N1-methyladenosine at A9 (m1A9) and N2-methylguanosine at G10 (m2G10) modifications and caused a substantial reduction in the aminoacylation of mitochondrial tRNAThr and tRNALys, resulting in impaired translation efficiency. Multiple types of amino acid misincorporation due to the misreading of near-cognate codons by t6A37-unmodified tRNAs were detected, indicating a triggered translational infidelity. Accordingly, the alterations in mitochondrial structure, function, and the activated mitochondrial unfolded protein response were observed. Mitochondrial function was efficiently restored by wild-type, but not by tRNA-binding-defective OSGEPL1. Lastly, in Osgepl1 deletion mice, disruption to mitochondrial translation was evident but resulted in no observable deficiency under physiological conditions in heart, which displays the highest Osgepl1 expression. Taken together, our data delineate the multifaceted roles of mitochondrial t6A37 modification in translation efficiency and quality control in mitochondria.
Collapse
Affiliation(s)
- Yong Zhang
- Key Laboratory of RNA Science and Engineering, 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Jing-Bo Zhou
- Key Laboratory of RNA Science and Engineering, 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, 333 Haike Road, Shanghai 201210, China
| | - En-Duo Wang
- Key Laboratory of RNA Science and Engineering, 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, 320 Yue Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, 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, 320 Yue Yang Road, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| |
Collapse
|
4
|
Wang Y, He J, Dong F, Shou W, Feng X, Yang Y, Li C, Wang J, Li B, Xiao S. A novel mutation in GTPBP3 causes combined oxidative phosphorylation deficiency 23 by affecting pre-mRNA splicing. Heliyon 2024; 10:e27199. [PMID: 38515655 PMCID: PMC10955198 DOI: 10.1016/j.heliyon.2024.e27199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
Background Combined Oxidative Phosphorylation Deficiency 23 (COXPD23) is a rare mitochondrial disease caused by mutations in the GTPBP3 gene. The rare incidence of the disease and the high clinical heterogeneity pose challenges in making a precise diagnosis. Investigations into the rare COXPD23 patients are of pathophysiological and etiological value. In this study, we investigated the genotype-phenotype relationship in a COXPD23 patient from a Manchu family, with GTPBP3 mutations. Methods Routine physical examinations, laboratory assays and imaging analyses were performed. The metabolic profiles of amino acids in blood, acylcarnitine in blood and organic acids in urine were used to determine the presence of inherited metabolic diseases. Genetic variations in the family were investigated using whole-exome sequencing and Sanger sequencing. Splicing disruption by a mutation was predicted and verified using a minigene assay. Results The patient presented with severe lactic acidosis, neurological symptoms, multiple symmetrical lesions in the brain and serious mitochondrial energy metabolism disturbances. The c.689A > C (p.Q230P) and c.809-1_809delinsA compound heterozygous mutations were detected in GTPBP3. The novel c.809-1_809delinsA mutation was located at the splicing site of exon 7 and intron 6 and multiple tools predicted that it would disrupt the normal splicing. The minigene assay proved that the novel mutation resulted in two aberrant transcripts that created premature termination codons. Conclusions The clinical manifestations, brain imaging change, mitochondrial metabolism disturbances and the detection and validation of the GTPBP3 mutations expand the profile of COXPD23 and the pathogenic mutation spectrum. Our study improves the understanding of the pathophysiology and etiology of COXPD23.
Collapse
Affiliation(s)
- Yanjun Wang
- Pediatric Intensive Care Unit, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Juan He
- Pediatric Intensive Care Unit, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Fangling Dong
- Pediatric Intensive Care Unit, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Weihua Shou
- Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children's Hospital, Kunming, China
| | - Xingxing Feng
- Department of Clinical Laboratory, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Ya Yang
- Pediatric Intensive Care Unit, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Cuifen Li
- Pediatric Intensive Care Unit, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Jingjing Wang
- Pediatric Intensive Care Unit, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Bin Li
- Pediatric Intensive Care Unit, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Shufang Xiao
- Pediatric Intensive Care Unit, Kunming Children's Hospital, Children's Hospital Affiliated to Kunming Medical University, Kunming, China
| |
Collapse
|
5
|
Nardecchia F, Carrozzo R, Innocenti A, Torraco A, Zaccaria V, Rizza T, Pisani F, Bertini E, Leuzzi V. Biallelic variants in GTPBP3: New patients, phenotypic spectrum, and outcome. Ann Clin Transl Neurol 2024; 11:819-825. [PMID: 38327089 DOI: 10.1002/acn3.51980] [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: 06/30/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 02/09/2024] Open
Abstract
INTRODUCTION COXPD23 is a rare mitochondrial disease caused by biallelic pathogenic variants in GTPBP3. We report on two siblings with a mild phenotype. CASE REPORTS The young boy presented with global developmental delay, ataxic gait and upper limbs tremor, and the older sister with absence seizures and hypertrophic cardiomyopathy. Respiratory chain impairment was confirmed in muscle. DISCUSSION Reviewed cases point toward clustering around two prevalent phenotypes: an early-onset presentation with severe fatal encephalopathy and a late milder presentation with global developmental delay/ID and cardiopathy, with the latter as, is the main feature. Our patients showed an intermediate phenotype with intrafamilial variability.
Collapse
Affiliation(s)
- Francesca Nardecchia
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Alice Innocenti
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Alessandra Torraco
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Valerio Zaccaria
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Teresa Rizza
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Francesco Pisani
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Enrico Bertini
- Neuromuscular Disorders Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Vincenzo Leuzzi
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
6
|
Ahmad RN, Zhang LT, Morita R, Tani H, Wu Y, Chujo T, Ogawa A, Harada R, Shigeta Y, Tomizawa K, Wei FY. Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP). Nucleic Acids Res 2024; 52:1341-1358. [PMID: 38113276 PMCID: PMC10853782 DOI: 10.1093/nar/gkad1197] [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: 05/19/2022] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
MTU1 controls intramitochondrial protein synthesis by catalyzing the 2-thiouridine modification of mitochondrial transfer RNAs (mt-tRNAs). Missense mutations in the MTU1 gene are associated with life-threatening reversible infantile hepatic failure. However, the molecular pathogenesis is not well understood. Here, we investigated 17 mutations associated with this disease, and our results showed that most disease-related mutations are partial loss-of-function mutations, with three mutations being particularly severe. Mutant MTU1 is rapidly degraded by mitochondrial caseinolytic peptidase (CLPP) through a direct interaction with its chaperone protein CLPX. Notably, knockdown of CLPP significantly increased mutant MTU1 protein expression and mt-tRNA 2-thiolation, suggesting that accelerated proteolysis of mutant MTU1 plays a role in disease pathogenesis. In addition, molecular dynamics simulations demonstrated that disease-associated mutations may lead to abnormal intermolecular interactions, thereby impairing MTU1 enzyme activity. Finally, clinical data analysis underscores a significant correlation between patient prognosis and residual 2-thiolation levels, which is partially consistent with the AlphaMissense predictions. These findings provide a comprehensive understanding of MTU1-related diseases, offering prospects for modification-based diagnostics and novel therapeutic strategies centered on targeting CLPP.
Collapse
Affiliation(s)
- Raja Norazireen Raja Ahmad
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Long-Teng Zhang
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Haruna Tani
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Yong Wu
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Akiko Ogawa
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Fan-Yan Wei
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| |
Collapse
|
7
|
Meng HH, Liu WY, Zhao WL, Zheng Q, Wang JS. Study on the acute toxicity of trichlorfon and its breakdown product dichlorvos to goldfish (Carassius auratus) based on 1H NMR metabonomics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:125664-125676. [PMID: 38001290 DOI: 10.1007/s11356-023-31012-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Trichlorfon, one of the most widely used organophosphate insecticides, is commonly employed in aquaculture and agriculture to combat parasitic infestations. However, its inherent instability leads to rapid decomposition into dichlorvos (DDVP), increasing its toxicity by eightfold. Therefore, the environmental effects of trichlorfon in real-world scenarios involve the combined effects of trichlorfon and its degradation product, DDVP. In this study, we systematically investigated the degradation of trichlorfon in tap water over time using HPLC and LC-MS/MS analysis. Subsequently, an experiment was conducted to assess the acute toxicity of trichlorfon and DDVP on goldfish (Carassius auratus), employing a 1H NMR-based metabolic approach in conjunction with serum biochemistry, histopathological inspection, and correlation network analysis. Exposure to trichlorfon and its degradation product DDVP leads to increased lipid peroxidation, reduced antioxidant activity, and severe hepatotoxicity and nephrotoxicity in goldfish. Based on the observed pathological changes and metabolite alterations, short-term exposure to trichlorfon significantly affected the liver and kidney functions of goldfish, while exerting minimal influence on the brain, potentially due to the presence of the blood-brain barrier. The changes in the metabolic profile indicated that trichlorfon and DDVP influenced several pathways, including oxidative stress, protein synthesis, energy metabolism, and nucleic acid metabolism. This study demonstrated the applicability and potential of 1H NMR-based metabonomics in pesticide environmental risk assessment, providing a feasible method for the comprehensive study of pesticide toxicity in water environments.
Collapse
Affiliation(s)
- Hui-Hui Meng
- Center of Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
| | - Wen-Ya Liu
- Center of Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
| | - Wen-Long Zhao
- Center of Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
| | - Qi Zheng
- Center of Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
| | - Jun-Song Wang
- Center of Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China.
| |
Collapse
|
8
|
Huang MH, Wang JT, Zhang JH, Mao XL, Peng GX, Lin X, Lv D, Yuan C, Lin H, Wang ED, Zhou XL. Mitochondrial RNA m 3C methyltransferase METTL8 relies on an isoform-specific N-terminal extension and modifies multiple heterogenous tRNAs. Sci Bull (Beijing) 2023; 68:2094-2105. [PMID: 37573249 DOI: 10.1016/j.scib.2023.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 08/14/2023]
Abstract
Methyltransferase-like 8 (METTL8) encodes a mitochondria-localized METTL8-Iso1 and a nucleolus-distributed METTL8-Iso4 isoform, which differ only in their N-terminal extension (N-extension), by mRNA alternative splicing. METTL8-Iso1 generates 3-methylcytidine at position 32 (m3C32) of mitochondrial tRNAThr and tRNASer(UCN). Whether METTL8-Iso4 is an active m3C32 methyltransferase and the role of the N-extension in mitochondrial tRNA m3C32 formation remain unclear. Here, we revealed that METTL8-Iso4 was inactive in m3C32 generation due to the lack of N-extension, which contains several absolutely conserved modification-critical residues; the counterparts were likewise essential in cytoplasmic m3C32 biogenesis by methyltransferase-like 2A (METTL2A) or budding yeasts tRNA N3-methylcytidine methyltransferase (Trm140), in vitro and in vivo. Cross-compartment/species tRNA modification assays unexpectedly found that METTL8-Iso1 efficiently introduced m3C32 to several cytoplasmic or even bacterial tRNAs in vitro. m3C32 did not influence tRNAThrN6-threonylcarbamoyladenosine (t6A) modification or aminoacylation. In addition to its interaction with mitochondrial seryl-tRNA synthetase (SARS2), we further discovered an interaction between mitochondrial threonyl-tRNA synthetase (TARS2) and METTL8-Iso1. METTL8-Iso1 substantially stimulated the aminoacylation activities of SARS2 and TARS2 in vitro, suggesting a functional connection between mitochondrial tRNA modification and charging. Altogether, our results deepen the mechanistic insights into mitochondrial m3C32 biogenesis and provide a valuable route to prepare cytoplasmic/bacterial tRNAs with only a m3C32 moiety, aiding in future efforts to investigate its effects on tRNA structure and function.
Collapse
Affiliation(s)
- Meng-Han Huang
- Key Laboratory of RNA Science and Engineering, 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 200031, China
| | - Jin-Tao Wang
- Key Laboratory of RNA Science and Engineering, 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 200031, China
| | - Jian-Hui Zhang
- Key Laboratory of RNA Science and Engineering, 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 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xue-Ling Mao
- Key Laboratory of RNA Science and Engineering, 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 200031, China
| | - Gui-Xin Peng
- Key Laboratory of RNA Science and Engineering, 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 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, 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
| | - Daizhu Lv
- Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chen Yuan
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Huan Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - En-Duo Wang
- Key Laboratory of RNA Science and Engineering, 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 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, 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 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| |
Collapse
|
9
|
Tsai PY, Shui B, Lee S, Liu Y, Qu Y, Cheng C, Edwards K, Wong C, Meng-Killeen R, Soloway PD, Barrow JJ. Ado-Mediated Depletion of Taurine Impairs Mitochondrial Respiratory Capacity and Alters the Chromatin Landscape of Inguinal Adipose Tissue. Nutrients 2023; 15:3532. [PMID: 37630723 PMCID: PMC10458711 DOI: 10.3390/nu15163532] [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: 06/16/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Non-shivering thermogenesis (NST) has strong potential to combat obesity; however, a safe molecular approach to activate this process has not yet been identified. The sulfur amino acid taurine has the ability to safely activate NST and confer protection against obesity and metabolic disease in both mice and humans, but the mechanism of this action is unknown. In this study, we discover that a suite of taurine biosynthetic enzymes, especially that of cysteamine dioxygenase (ADO), significantly increases in response to β3 adrenergic signaling in inguinal adipose tissue (IWAT) in order to increase intracellular concentrations of taurine. We further show that ADO is critical for thermogenic mitochondrial respiratory function as its ablation in adipocytes significantly reduces taurine levels, which leads to declines in mitochondrial oxygen consumption rates. Finally, we demonstrate via assay for transposase-accessible chromatin with sequencing (ATAC-seq) that taurine supplementation in beige adipocytes has the ability to remodel the chromatin landscape to increase the chromatin accessibility and transcription of genes, such as glucose-6-phosphate isomerase 1 (Gpi1), which are critical for NST. Taken together, our studies highlight a potential mechanism for taurine in the activation of NST that can be leveraged toward the treatment of obesity and metabolic disease.
Collapse
Affiliation(s)
- Pei-Yin Tsai
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Bo Shui
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Seoyeon Lee
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Yang Liu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Yue Qu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Chloe Cheng
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Kaydine Edwards
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Callie Wong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Ryan Meng-Killeen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Paul D. Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Joeva J. Barrow
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| |
Collapse
|
10
|
Boughanem H, Böttcher Y, Tomé-Carneiro J, López de Las Hazas MC, Dávalos A, Cayir A, Macias-González M. The emergent role of mitochondrial RNA modifications in metabolic alterations. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1753. [PMID: 35872632 DOI: 10.1002/wrna.1753] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 11/11/2022]
Abstract
Mitochondrial epitranscriptomics refers to the modifications occurring in all the different RNA types of mitochondria. Although the number of mitochondrial RNA modifications is less than those in cytoplasm, substantial evidence indicates that they play a critical role in accurate protein synthesis. Recent evidence supported those modifications in mitochondrial RNAs also have crucial implications in mitochondrial-related diseases. In the light of current knowledge about the involvement, the association between mitochondrial RNA modifications and diseases arises from studies focusing on mutations in both mitochondrial and nuclear DNA genes encoding enzymes involved in such modifications. Here, we review the current evidence available for mitochondrial RNA modifications and their role in metabolic disorders, and we also explore the possibility of using them as promising targets for prevention and early detection. Finally, we discuss future directions of mitochondrial epitranscriptomics in these metabolic alterations, and how these RNA modifications may offer a new diagnostic and theragnostic avenue for preventive purposes. This article is categorized under: RNA Processing > RNA Editing and Modification.
Collapse
Affiliation(s)
- Hatim Boughanem
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria and University of Málaga, Spain.,Instituto de Salud Carlos III (ISCIII), Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBERObn), Madrid, Spain
| | - Yvonne Böttcher
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway.,Akershus Universitetssykehus, Medical Department, Lørenskog, Norway
| | - João Tomé-Carneiro
- Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - María-Carmen López de Las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Akin Cayir
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey.,Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
| | - Manuel Macias-González
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria and University of Málaga, Spain.,Instituto de Salud Carlos III (ISCIII), Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBERObn), Madrid, Spain
| |
Collapse
|
11
|
Peng GX, Mao XL, Cao Y, Yao SY, Li QR, Chen X, Wang ED, Zhou XL. RNA granule-clustered mitochondrial aminoacyl-tRNA synthetases form multiple complexes with the potential to fine-tune tRNA aminoacylation. Nucleic Acids Res 2022; 50:12951-12968. [PMID: 36503967 PMCID: PMC9825176 DOI: 10.1093/nar/gkac1141] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/23/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial RNA metabolism is suggested to occur in identified compartmentalized foci, i.e. mitochondrial RNA granules (MRGs). Mitochondrial aminoacyl-tRNA synthetases (mito aaRSs) catalyze tRNA charging and are key components in mitochondrial gene expression. Mutations of mito aaRSs are associated with various human disorders. However, the suborganelle distribution, interaction network and regulatory mechanism of mito aaRSs remain largely unknown. Here, we found that all mito aaRSs partly colocalize with MRG, and this colocalization is likely facilitated by tRNA-binding capacity. A fraction of human mitochondrial AlaRS (hmtAlaRS) and hmtSerRS formed a direct complex via interaction between catalytic domains in vivo. Aminoacylation activities of both hmtAlaRS and hmtSerRS were fine-tuned upon complex formation in vitro. We further established a full spectrum of interaction networks via immunoprecipitation and mass spectrometry for all mito aaRSs and discovered interactions between hmtSerRS and hmtAsnRS, between hmtSerRS and hmtTyrRS and between hmtThrRS and hmtArgRS. The activity of hmtTyrRS was also influenced by the presence of hmtSerRS. Notably, hmtSerRS utilized the same catalytic domain in mediating several interactions. Altogether, our results systematically analyzed the suborganelle localization and interaction network of mito aaRSs and discovered several mito aaRS-containing complexes, deepening our understanding of the functional and regulatory mechanisms of mito aaRSs.
Collapse
Affiliation(s)
| | | | - Yating Cao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shi-Ying Yao
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Qing-Run Li
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Xin Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - En-Duo Wang
- Correspondence may also be addressed to En-Duo Wang. Tel: +86 21 5492 1241; Fax: +86 21 5492 1011;
| | - Xiao-Long Zhou
- To whom correspondence should be addressed. Tel: +86 21 5492 1247; Fax: +86 21 5492 1011;
| |
Collapse
|
12
|
Huang MH, Peng GX, Mao XL, Wang JT, Zhou JB, Zhang JH, Chen M, Wang ED, Zhou XL. OUP accepted manuscript. Nucleic Acids Res 2022; 50:4012-4028. [PMID: 35357504 PMCID: PMC9023283 DOI: 10.1093/nar/gkac184] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/06/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
METTL8 has recently been identified as the methyltransferase catalyzing 3-methylcytidine biogenesis at position 32 (m3C32) of mitochondrial tRNAs. METTL8 also potentially participates in mRNA methylation and R-loop biogenesis. How METTL8 plays multiple roles in distinct cell compartments and catalyzes mitochondrial tRNA m3C formation remain unclear. Here, we discovered that alternative mRNA splicing generated several isoforms of METTL8. One isoform (METTL8-Iso1) was targeted to mitochondria via an N-terminal pre-sequence, while another one (METTL8-Iso4) mainly localized to the nucleolus. METTL8-Iso1-mediated m3C32 modification of human mitochondrial tRNAThr (hmtRNAThr) was not reliant on t6A modification at A37 (t6A37), while that of hmtRNASer(UCN) critically depended on i6A modification at A37 (i6A37). We clarified the hmtRNAThr substrate recognition mechanism, which was obviously different from that of hmtRNASer(UCN), in terms of requiring a G35 determinant. Moreover, SARS2 (mitochondrial seryl-tRNA synthetase) interacted with METTL8-Iso1 in an RNA-independent manner and modestly accelerated m3C modification activity. We further elucidated how nonsubstrate tRNAs in human mitochondria were efficiently discriminated by METTL8-Iso1. In summary, our results established the expression pattern of METTL8, clarified the molecular basis for m3C32 modification by METTL8-Iso1 and provided the rationale for the involvement of METTL8 in tRNA modification, mRNA methylation or R-loop biogenesis.
Collapse
Affiliation(s)
- Meng-Han Huang
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Gui-Xin Peng
- 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, 320 Yue Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Xue-Ling Mao
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Jin-Tao Wang
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Jing-Bo Zhou
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Jian-Hui Zhang
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Meirong Chen
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, Jiangsu, China
| | - En-Duo Wang
- Correspondence may also be addressed to Prof. En-Duo Wang. Tel: +86 21 5492 1241; Fax: +86 21 5492 1011;
| | - Xiao-Long Zhou
- To whom correspondence should be addressed. Tel: +86 21 5492 1247; Fax: +86 21 5492 1011;
| |
Collapse
|
13
|
tRNA modifications and their potential roles in pancreatic cancer. Arch Biochem Biophys 2021; 714:109083. [PMID: 34785212 DOI: 10.1016/j.abb.2021.109083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 12/23/2022]
Abstract
Since the breakthrough discovery of N6-methyladenosine (m6A), the field of RNA epitranscriptomics has attracted increasing interest in the biological sciences. Transfer RNAs (tRNAs) are extensively modified, and various modifications play a crucial role in the formation and stability of tRNA, which is universally required for accurate and efficient functioning of tRNA. Abnormal tRNA modification can lead to tRNA degradation or specific cleavage of tRNA into fragmented derivatives, thus affecting the translation process and frequently accompanying a variety of human diseases. Increasing evidence suggests that tRNA modification pathways are also misregulated in human cancers. In this review, we summarize tRNA modifications and their biological functions, describe the type and frequency of tRNA modification alterations in cancer, and highlight variations in tRNA-modifying enzymes and the multiple functions that they regulate in different types of cancers. Furthermore, the current implications and the potential role of tRNA modifications in the progression of pancreatic cancer are discussed. Collectively, this review describes recent advances in tRNA modification in cancers and its potential significance in pancreatic cancer. Further study of the mechanism of tRNA modifications in pancreatic cancer may provide possibilities for therapies targeting enzymes responsible for regulating tRNA modifications in pancreatic cancer.
Collapse
|
14
|
Zhou JB, Wang ED, Zhou XL. Modifications of the human tRNA anticodon loop and their associations with genetic diseases. Cell Mol Life Sci 2021; 78:7087-7105. [PMID: 34605973 PMCID: PMC11071707 DOI: 10.1007/s00018-021-03948-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022]
Abstract
Transfer RNAs (tRNAs) harbor the most diverse posttranscriptional modifications. Among such modifications, those in the anticodon loop, either on nucleosides or base groups, compose over half of the identified posttranscriptional modifications. The derivatives of modified nucleotides and the crosstalk of different chemical modifications further add to the structural and functional complexity of tRNAs. These modifications play critical roles in maintaining anticodon loop conformation, wobble base pairing, efficient aminoacylation, and translation speed and fidelity as well as mediating various responses to different stress conditions. Posttranscriptional modifications of tRNA are catalyzed mainly by enzymes and/or cofactors encoded by nuclear genes, whose mutations are firmly connected with diverse human diseases involving genetic nervous system disorders and/or the onset of multisystem failure. In this review, we summarize recent studies about the mechanisms of tRNA modifications occurring at tRNA anticodon loops. In addition, the pathogenesis of related disease-causing mutations at these genes is briefly described.
Collapse
Affiliation(s)
- Jing-Bo Zhou
- 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, 320 Yue Yang Road, Shanghai, 200031, China
| | - En-Duo Wang
- 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, 320 Yue Yang Road, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, 93 Middle Huaxia Road, Shanghai, 201210, China.
| | - Xiao-Long Zhou
- 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, 320 Yue Yang Road, Shanghai, 200031, China.
| |
Collapse
|
15
|
Mao XL, Li ZH, Huang MH, Wang JT, Zhou JB, Li QR, Xu H, Wang XJ, Zhou XL. Mutually exclusive substrate selection strategy by human m3C RNA transferases METTL2A and METTL6. Nucleic Acids Res 2021; 49:8309-8323. [PMID: 34268557 PMCID: PMC8373065 DOI: 10.1093/nar/gkab603] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/27/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
tRNAs harbor the most diverse posttranscriptional modifications. The 3-methylcytidine (m3C) is widely distributed at position C32 (m3C32) of eukaryotic tRNAThr and tRNASer species. m3C32 is decorated by the single methyltransferase Trm140 in budding yeasts; however, two (Trm140 and Trm141 in fission yeasts) or three enzymes (METTL2A, METTL2B and METTL6 in mammals) are involved in its biogenesis. The rationale for the existence of multiple m3C32 methyltransferases and their substrate discrimination mechanism is hitherto unknown. Here, we revealed that both METTL2A and METTL2B are expressed in vivo. We purified human METTL2A, METTL2B, and METTL6 to high homogeneity. We successfully reconstituted m3C32 modification activity for tRNAThr by METT2A and for tRNASer(GCU) by METTL6, assisted by seryl-tRNA synthetase (SerRS) in vitro. Compared with METTL2A, METTL2B exhibited dramatically lower activity in vitro. Both G35 and t6A at position 37 (t6A37) are necessary but insufficient prerequisites for tRNAThr m3C32 formation, while the anticodon loop and the long variable arm, but not t6A37, are key determinants for tRNASer(GCU) m3C32 biogenesis, likely being recognized synergistically by METTL6 and SerRS, respectively. Finally, we proposed a mutually exclusive substrate selection model to ensure correct discrimination among multiple tRNAs by multiple m3C32 methyltransferases.
Collapse
Affiliation(s)
- Xue-Ling Mao
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Zi-Han Li
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Meng-Han Huang
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Jin-Tao Wang
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Jing-Bo Zhou
- 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Qing-Run Li
- CAS Key Laboratory of Systems 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, 320 Yue Yang Road, Shanghai 200031, China
| | - Hong Xu
- Shanghai Key Laboratory of Embryo Original Diseases, the International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Heng Shan Road, Shanghai 200030, China
| | - Xi-Jin Wang
- Department of Neurology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 1665 Kong Jiang Road, Shanghai 200092, China
| | - Xiao-Long Zhou
- 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, 320 Yue Yang Road, Shanghai 200031, China
| |
Collapse
|
16
|
Mechanistic insights into mitochondrial tRNA Ala 3'-end metabolism deficiency. J Biol Chem 2021; 297:100816. [PMID: 34023389 PMCID: PMC8212662 DOI: 10.1016/j.jbc.2021.100816] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial tRNA 3’-end metabolism is critical for the formation of functional tRNAs. Deficient mitochondrial tRNA 3’-end metabolism is linked to an array of human diseases, including optic neuropathy, but their pathophysiology remains poorly understood. In this report, we investigated the molecular mechanism underlying the Leber’s hereditary optic neuropathy (LHON)-associated tRNAAla 5587A>G mutation, which changes a highly conserved adenosine at position 73 (A73) to guanine (G73) on the 3’-end of the tRNA acceptor stem. The m.5587A>G mutation was identified in three Han Chinese families with suggested maternal inheritance of LHON. We hypothesized that the m.5587A>G mutation altered tRNAAla 3’-end metabolism and mitochondrial function. In vitro processing experiments showed that the m.5587A>G mutation impaired the 3’-end processing of tRNAAla precursors by RNase Z and inhibited the addition of CCA by tRNA nucleotidyltransferase (TRNT1). Northern blot analysis revealed that the m.5587A>G mutation perturbed tRNAAla aminoacylation, as evidenced by decreased efficiency of aminoacylation and faster electrophoretic mobility of mutated tRNAAla in these cells. The impact of m.5587A>G mutation on tRNAAla function was further supported by increased melting temperature, conformational changes, and reduced levels of this tRNA. Failures in tRNAAla metabolism impaired mitochondrial translation, perturbed assembly and activity of oxidative phosphorylation complexes, diminished ATP production and membrane potential, and increased production of reactive oxygen species. These pleiotropic defects elevated apoptotic cell death and promoted mitophagy in cells carrying the m.5587A>G mutation, thereby contributing to visual impairment. Our findings may provide new insights into the pathophysiology of LHON arising from mitochondrial tRNA 3’-end metabolism deficiency.
Collapse
|