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Lin Y, Wang J, Zhuang X, Zhao Y, Wang W, Wang D, Zhao Y, Yan C, Ji K. Queuine ameliorates impaired mitochondrial function caused by mt-tRNA Asn variants. J Transl Med 2024; 22:780. [PMID: 39175050 PMCID: PMC11340107 DOI: 10.1186/s12967-024-05574-0] [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: 06/09/2024] [Accepted: 08/04/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Mitochondrial tRNA (mt-tRNA) variants have been found to cause disease. Post-transcriptional queuosine (Q) modifications of mt-tRNA can promote efficient mitochondrial mRNA translation. Q modifications of mt-tRNAAsn have recently been identified. Here, the therapeutic effectiveness of queuine was investigated in cells from patients with mt-tRNAAsn variants. METHODS Six patients (from four families) carrying mt-tRNAAsn variants were included in the study. Queuine levels were quantified by mass spectrometry. Clinical, genetic, histochemical, biochemical, and molecular analysis was performed on muscle tissues and lymphoblastoid cell lines (LCLs) from patients to investigate the pathogenicity of the novel m.5708 C > T variant. The use of queuine in mitigating mitochondrial dysfunction resulting from the mt-tRNAAsn variants was evaluated. RESULTS The variants included the m.5701 delA, m.5708 C > T, m.5709 C > T, and m.5698 G > A variants in mt-tRNAAsn. The pathogenicity of the novel m.5708 C > T variant was confirmed, as demonstrated by a decreased steady-state level of mt-tRNAAsn, mtDNA-encoded protein levels, oxygen consumption rate (OCR), and the respiratory complex activity. Notably, the serum queuine level was significantly reduced in these patients and in vitro queuine supplementation was found to restore the reductions in mitochondrial protein activities, mitochondrial membrane potential, OCR, and increases in reactive oxygen species. CONCLUSIONS The study not only confirmed the pathogenicity of the m.5708 C > T variant but also explored the therapeutic potential of queuine in individuals with mt-tRNAAsn variants. The recognition of the novel m.5708 C > T variant's pathogenic nature contributes to our comprehension of mitochondrial disorders. Furthermore, the results emphasize queuine supplementation as a promising approach to enhance the stability of mt-tRNAAsn and rescue mitochondrial dysfunction caused by mt-tRNAAsn variants, indicating potential implications for the development of targeted therapies for patients with mt-tRNAAsn variants.
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Affiliation(s)
- Yan Lin
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China
| | - Jiayin Wang
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China
| | - Xingyu Zhuang
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China
| | - Ying Zhao
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China
| | - Wei Wang
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China
| | - Dongdong Wang
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China
| | - Yuying Zhao
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China
| | - Chuanzhu Yan
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China.
- Qingdao Key Laboratory of Mitochondrial Medicine and Rare Disease, Qilu Hospital (Qingdao), Shandong University, Qingdao, Shandong, 266035, China.
| | - Kunqian Ji
- Department of Neurology, Shandong Key Laboratory of Mitochondrial Medicine and Rare Diseases, Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, No. 107 West Wenhua Road Jinan, Jinan, Shandong, 250012, China.
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2
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Yin X, Dong Q, Fan S, Yang L, Li H, Jin Y, Laurentinah MR, Chen X, Sysa A, Fang H, Lyu J, Yu Y, Wang Y. A novel pathogenic mitochondrial DNA variant m.4344T>C in tRNA Gln causes developmental delay. J Hum Genet 2024; 69:381-389. [PMID: 38730005 DOI: 10.1038/s10038-024-01254-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Mitochondrial diseases are a group of genetic diseases caused by mutations in mitochondrial DNA and nuclear DNA. However, the genetic spectrum of this disease is not yet complete. In this study, we identified a novel variant m.4344T>C in mitochondrial tRNAGln from a patient with developmental delay. The mutant loads of m.4344T>C were 95% and 89% in the patient's blood and oral epithelial cells, respectively. Multialignment analysis showed high evolutionary conservation of this nucleotide. TrRosettaRNA predicted that m.4344T>C variant would introduce an additional hydrogen bond and alter the conformation of the T-loop. The transmitochondrial cybrid-based study demonstrated that m.4344T>C variant impaired the steady-state level of mitochondrial tRNAGln and decreased the contents of mitochondrial OXPHOS complexes I, III, and IV, resulting in defective mitochondrial respiration, elevated mitochondrial ROS production, reduced mitochondrial membrane potential and decreased mitochondrial ATP levels. Altogether, this is the first report in patient carrying the m.4344T>C variant. Our data uncover the pathogenesis of the m.4344T>C variant and expand the genetic mutation spectrum of mitochondrial diseases, thus contributing to the clinical diagnosis of mitochondrial tRNAGln gene variants-associated mitochondrial diseases.
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Affiliation(s)
- Xiaojie Yin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Qiyu Dong
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Shuanglong Fan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lina Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yijun Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Mahlatsi Refiloe Laurentinah
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiandan Chen
- International Sakharov Environmental Institute of Belarusian State University, Minsk, 220070, Republic of Belarus
| | - Aliaksei Sysa
- International Sakharov Environmental Institute of Belarusian State University, Minsk, 220070, Republic of Belarus
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, 200092, China.
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, 200092, China.
| | - Ya Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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3
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Cotter M, Quinn SM, Fearon U, Ansboro S, Rakovic T, Southern JM, Kelly VP, Connon SJ. A new class of 7-deazaguanine agents targeting autoimmune diseases: dramatic reduction of synovial fibroblast IL-6 production from human rheumatoid arthritis patients and improved performance against murine experimental autoimmune encephalomyelitis. RSC Med Chem 2024; 15:1556-1564. [PMID: 38784475 PMCID: PMC11110761 DOI: 10.1039/d4md00028e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/17/2024] [Indexed: 05/25/2024] Open
Abstract
A simple in vitro assay involving the measurement of IL-6 production in human synovial fibroblasts from rheumatoid arthritis patients has been utilised to select candidates from a targeted library of queuine tRNA ribosyltransferase (QTRT) substrates for subsequent in vivo screening in murine experimental autoimmune encephalomyelitis (EAE - a model of multiple sclerosis). The in vitro activity assay discriminated between poor and excellent 7-deazaguanine QTRT substrates and allowed the identification of several structures which subsequently outperformed the previous lead in EAE. Two molecules were of significant promise: one rigidified analogue of the lead, and another considerably simpler structure incorporating an oxime motif which differs structurally from the lead to a considerable extent. These studies provide data from human cells for the first time and have expanded both the chemical space and current understanding of the structure-activity relationship underpinning the remarkable potential of 7-deazguanines in a Multiple Sclerosis disease model.
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Affiliation(s)
- Michelle Cotter
- School of Chemistry, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Shauna M Quinn
- School of Biochemistry & Immunology, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Ursula Fearon
- School of Medicine, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Sharon Ansboro
- School of Medicine, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Tatsiana Rakovic
- School of Medicine, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - John M Southern
- School of Chemistry, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Stephen J Connon
- School of Chemistry, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
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4
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.31.565030. [PMID: 37961685 PMCID: PMC10635034 DOI: 10.1101/2023.10.31.565030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint particular residues in QueE that contribute distinctly to each of its functions - Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueEs secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of one gene, one enzyme, one function, which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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5
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Sievers K, Neumann P, Sušac L, Da Vela S, Graewert M, Trowitzsch S, Svergun D, Tampé R, Ficner R. Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Structure 2024; 32:316-327.e5. [PMID: 38181786 DOI: 10.1016/j.str.2023.12.006] [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: 04/14/2023] [Revised: 07/06/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAsAsp,Asn,His,Tyr for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding.
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Affiliation(s)
- Katharina Sievers
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Lukas Sušac
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany.
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6
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Rashad S, Al-Mesitef S, Mousa A, Zhou Y, Ando D, Sun G, Fukuuchi T, Iwasaki Y, Xiang J, Byrne SR, Sun J, Maekawa M, Saigusa D, Begley TJ, Dedon PC, Niizuma K. Translational response to mitochondrial stresses is orchestrated by tRNA modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580389. [PMID: 38405984 PMCID: PMC10888749 DOI: 10.1101/2024.02.14.580389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Mitochondrial stress and dysfunction play important roles in many pathologies. However, how cells respond to mitochondrial stress is not fully understood. Here, we examined the translational response to electron transport chain (ETC) inhibition and arsenite induced mitochondrial stresses. Our analysis revealed that during mitochondrial stress, tRNA modifications (namely f5C, hm5C, queuosine and its derivatives, and mcm5U) dynamically change to fine tune codon decoding, usage, and optimality. These changes in codon optimality drive the translation of many pathways and gene sets, such as the ATF4 pathway and selenoproteins, involved in the cellular response to mitochondrial stress. We further examined several of these modifications using targeted approaches. ALKBH1 knockout (KO) abrogated f5C and hm5C levels and led to mitochondrial dysfunction, reduced proliferation, and impacted mRNA translation rates. Our analysis revealed that tRNA queuosine (tRNA-Q) is a master regulator of the mitochondrial stress response. KO of QTRT1 or QTRT2, the enzymes responsible for tRNA-Q synthesis, led to mitochondrial dysfunction, translational dysregulation, and metabolic alterations in mitochondria-related pathways, without altering cellular proliferation. In addition, our analysis revealed that tRNA-Q loss led to a domino effect on various tRNA modifications. Some of these changes could be explained by metabolic profiling. Our analysis also revealed that utilizing serum deprivation or alteration with Queuine supplementation to study tRNA-Q or stress response can introduce various confounding factors by altering many other tRNA modifications. In summary, our data show that tRNA modifications are master regulators of the mitochondrial stress response by driving changes in codon decoding.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shadi Al-Mesitef
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Abdulrahman Mousa
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuan Zhou
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Daisuke Ando
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurology, Tohoku university Graduate school of Medicine, Sendai, Japan
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
| | - Tomoko Fukuuchi
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Yuko Iwasaki
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Jingdong Xiang
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
| | - Shane R Byrne
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Codomax Inc, 17 Briden St STE 219, Worcester, MA 01605
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Campus for Research Excellence and Technological Enterprise, Singapore
| | - Masamitsu Maekawa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, Albany, NY, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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7
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Cotter M, Varghese S, Chevot F, Fergus C, Kelly VP, Connon SJ, Southern JM. Queuine Analogues Incorporating the 7-Aminomethyl-7-deazaguanine Core: Structure-Activity Relationships in the Treatment of Experimental Autoimmune Encephalomyelitis. ChemMedChem 2023; 18:e202300207. [PMID: 37350546 DOI: 10.1002/cmdc.202300207] [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: 04/17/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023]
Abstract
A library of queuine analogues targeting the modification of tRNA isoacceptors for Asp, Asn, His and Tyr catalysed by queuine tRNA ribosyltransferase (QTRT, also known as TGT) was evaluated in the treatment of a chronic multiple sclerosis model: murine experimental autoimmune encephalomyelitis. Several active 7-deazaguanines emerged, together with a structure-activity relationship involving the necessity for a flexible alkyl chain of fixed length.
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Affiliation(s)
- Michelle Cotter
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Sreeja Varghese
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Franciane Chevot
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Claire Fergus
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - J Mike Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
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8
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Ren D, Mo Y, Yang M, Wang D, Wang Y, Yan Q, Guo C, Xiong W, Wang F, Zeng Z. Emerging roles of tRNA in cancer. Cancer Lett 2023; 563:216170. [PMID: 37054943 DOI: 10.1016/j.canlet.2023.216170] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Transfer RNAs (tRNAs) play pivotal roles in the transmission of genetic information, and abnormality of tRNAs directly leads to translation disorders and causes diseases, including cancer. The complex modifications enable tRNA to execute its delicate biological function. Alteration of appropriate modifications may affect the stability of tRNA, impair its ability to carry amino acids, and disrupt the pairing between anticodons and codons. Studies confirmed that dysregulation of tRNA modifications plays an important role in carcinogenesis. Furthermore, when the stability of tRNA is impaired, tRNAs are cleaved into small tRNA fragments (tRFs) by specific RNases. Though tRFs have been found to play vital regulatory roles in tumorigenesis, its formation process is far from clear. Understanding improper tRNA modifications and abnormal formation of tRFs in cancer is conducive to uncovering the role of metabolic process of tRNA under pathological conditions, which may open up new avenues for cancer prevention and treatment.
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Affiliation(s)
- Daixi Ren
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Yongzhen Mo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Mei Yang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Dan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qijia Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Fuyan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
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9
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Hung SH, Elliott GI, Ramkumar TR, Burtnyak L, McGrenaghan CJ, Alkuzweny S, Quaiyum S, Iwata-Reuyl D, Pan X, Green BD, Kelly VP, de Crécy-Lagard V, Swairjo M. Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate. Nucleic Acids Res 2023; 51:935-951. [PMID: 36610787 PMCID: PMC9881137 DOI: 10.1093/nar/gkac1231] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic life benefits from-and ofttimes critically relies upon-the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source of the nucleobase queuine, which once incorporated into the anticodon of tRNA contributes to translational efficiency and accuracy. Here, we report high-resolution, substrate-bound crystal structures of the Sphaerobacter thermophilus queuine salvage protein Qng1 (formerly DUF2419) and of its human ortholog QNG1 (C9orf64), which together with biochemical and genetic evidence demonstrate its function as the hydrolase releasing queuine from queuosine-5'-monophosphate as the biological substrate. We also show that QNG1 is highly expressed in the liver, with implications for Q salvage and recycling. The essential role of this family of hydrolases in supplying queuine in eukaryotes places it at the nexus of numerous (patho)physiological processes associated with queuine deficiency, including altered metabolism, proliferation, differentiation and cancer progression.
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Affiliation(s)
- Shr-Hau Hung
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
- The Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Gregory I Elliott
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
| | - Thakku R Ramkumar
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Lyubomyr Burtnyak
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Callum J McGrenaghan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Sana Alkuzweny
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Xiaobei Pan
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Brian D Green
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
- University of Florida Genetics Institute, Gainesville, FL 32610, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
- The Viral Information Institute, San Diego State University, San Diego, CA, USA
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10
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Katanski CD, Watkins CP, Zhang W, Reyer M, Miller S, Pan T. Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing. Nucleic Acids Res 2022; 50:e99. [PMID: 35713550 PMCID: PMC9508811 DOI: 10.1093/nar/gkac517] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/26/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas in mammals the substrate for Q-modification in tRNA is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing from biological RNA samples. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method periodate-dependent analysis of queuosine and sulfur modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.
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Affiliation(s)
- Christopher D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Christopher P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Reyer
- Program of Biophysics, University of Chicago, Chicago, IL 60637, USA
| | - Samuel Miller
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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11
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Sarid L, Ankri S. Are Metabolites From the Gut Microbiota Capable of Regulating Epigenetic Mechanisms in the Human Parasite Entamoeba histolytica? Front Cell Dev Biol 2022; 10:841586. [PMID: 35300430 PMCID: PMC8921869 DOI: 10.3389/fcell.2022.841586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
The unicellular parasite Entamoeba histolytica inhabits the human gut. It has to adapt to a complex environment that consists of the host microbiota, nutritional stress, oxidative stress, and nitrosative stress. Adaptation to this complex environment is vital for the survival of this parasite. Studies have shown that the host microbiota shapes virulence and stress adaptation in E. histolytica. Increasing evidence suggests that metabolites from the microbiota mediate communication between the parasite and microbiota. In this review, we discuss the bacterial metabolites that regulate epigenetic processes in E. histolytica and the implications that this knowledge may have for the development of new anti-amebic strategies.
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Affiliation(s)
- Lotem Sarid
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
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12
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Dannfald A, Favory JJ, Deragon JM. Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions. RNA Biol 2021; 18:4-18. [PMID: 34159889 PMCID: PMC8677040 DOI: 10.1080/15476286.2021.1931756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 01/27/2023] Open
Abstract
The timely reprogramming of gene expression in response to internal and external cues is essential to eukaryote development and acclimation to changing environments. Chemically modifying molecular receptors and transducers of these signals is one way to efficiently induce proper physiological responses. Post-translation modifications, regulating protein biological activities, are central to many well-known signal-responding pathways. Recently, messenger RNA (mRNA) chemical (i.e. epitranscriptomic) modifications were also shown to play a key role in these processes. In contrast, transfer RNA (tRNA) and ribosomal RNA (rRNA) chemical modifications, although critical for optimal function of the translation apparatus, and much more diverse and quantitatively important compared to mRNA modifications, were until recently considered as mainly static chemical decorations. We present here recent observations that are challenging this view and supporting the hypothesis that tRNA and rRNA modifications dynamically respond to various cell and environmental conditions and contribute to adapt translation to these conditions.
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Affiliation(s)
- Arnaud Dannfald
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Jacques Favory
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Marc Deragon
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
- Institut Universitaire de France, Paris, France
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13
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Shaukat AN, Kaliatsi EG, Stamatopoulou V, Stathopoulos C. Mitochondrial tRNA-Derived Fragments and Their Contribution to Gene Expression Regulation. Front Physiol 2021; 12:729452. [PMID: 34539450 PMCID: PMC8446549 DOI: 10.3389/fphys.2021.729452] [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: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 01/14/2023] Open
Abstract
Mutations in human mitochondrial tRNAs (mt-tRNAs) are responsible for several and sometimes severe clinical phenotypes, classified among mitochondrial diseases. In addition, post-transcriptional modifications of mt-tRNAs in correlation with several stress signals can affect their stability similarly to what has been described for their nuclear-encoded counterparts. Many of the perturbations related to either point mutations or aberrant modifications of mt-tRNAs can lead to specific cleavage and the production of mitochondrial tRNA-derived fragments (mt-tRFs). Although mt-tRFs have been detected in several studies, the exact biogenesis steps and biological role remain, to a great extent, unexplored. Several mt-tRFs are produced because of the excessive oxidative stress which predominantly affects mitochondrial DNA integrity. In addition, mt-tRFs have been detected in various diseases with possible detrimental consequences, but also their production may represent a response mechanism to external stimuli, including infections from pathogens. Finally, specific point mutations on mt-tRNAs have been reported to impact the pool of the produced mt-tRFs and there is growing evidence suggesting that mt-tRFs can be exported and act in the cytoplasm. In this review, we summarize current knowledge on mitochondrial tRNA-deriving fragments and their possible contribution to gene expression regulation.
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Affiliation(s)
| | - Eleni G Kaliatsi
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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14
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Richard P, Kozlowski L, Guillorit H, Garnier P, McKnight NC, Danchin A, Manière X. Queuine, a bacterial-derived hypermodified nucleobase, shows protection in in vitro models of neurodegeneration. PLoS One 2021; 16:e0253216. [PMID: 34379627 PMCID: PMC8357117 DOI: 10.1371/journal.pone.0253216] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/29/2021] [Indexed: 11/26/2022] Open
Abstract
Growing evidence suggests that human gut bacteria, which comprise the microbiome, are linked to several neurodegenerative disorders. An imbalance in the bacterial population in the gut of Parkinson's disease (PD) and Alzheimer's disease (AD) patients has been detected in several studies. This dysbiosis very likely decreases or increases microbiome-derived molecules that are protective or detrimental, respectively, to the human body and those changes are communicated to the brain through the so-called 'gut-brain-axis'. The microbiome-derived molecule queuine is a hypermodified nucleobase enriched in the brain and is exclusively produced by bacteria and salvaged by humans through their gut epithelium. Queuine replaces guanine at the wobble position (position 34) of tRNAs with GUN anticodons and promotes efficient cytoplasmic and mitochondrial mRNA translation. Queuine depletion leads to protein misfolding and activation of the endoplasmic reticulum stress and unfolded protein response pathways in mice and human cells. Protein aggregation and mitochondrial impairment are often associated with neural dysfunction and neurodegeneration. To elucidate whether queuine could facilitate protein folding and prevent aggregation and mitochondrial defects that lead to proteinopathy, we tested the effect of chemically synthesized queuine, STL-101, in several in vitro models of neurodegeneration. After neurons were pretreated with STL-101 we observed a significant decrease in hyperphosphorylated alpha-synuclein, a marker of alpha-synuclein aggregation in a PD model of synucleinopathy, as well as a decrease in tau hyperphosphorylation in an acute and a chronic model of AD. Additionally, an associated increase in neuronal survival was found in cells pretreated with STL-101 in both AD models as well as in a neurotoxic model of PD. Measurement of queuine in the plasma of 180 neurologically healthy individuals suggests that healthy humans maintain protective levels of queuine. Our work has identified a new role for queuine in neuroprotection uncovering a therapeutic potential for STL-101 in neurological disorders.
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Affiliation(s)
- Patricia Richard
- Stellate Therapeutics Inc., JLABS @ NYC, New York, New York, United States of America
| | | | - Hélène Guillorit
- Stellate Therapeutics SAS, Paris, France
- Institut de Génomique Fonctionnelle, Montpellier, France
| | | | - Nicole C. McKnight
- Stellate Therapeutics Inc., JLABS @ NYC, New York, New York, United States of America
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15
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Abstract
Queuosine (Q) in humans is a microbiome-dependent modification in the wobble anticodon position of tRNATyr, tRNAHis, tRNAAsn, and tRNAAsp. These tRNAs share a G34U35N36 anticodon consensus. In humans, the Q base in tRNATyr and tRNAAsp is further glycosylated to generate galactosyl-Q (galQ) and mannosyl-Q (manQ) modifications. Q-tRNA modification is known to regulate translation in a codon dependent manner, but the function of Q glycosylation is unknown. A sensitive and quantitative detection method for Q-glycosylation in tRNA is essential to investigate its biological function. Although LC/MS was used in the characterization of glyco-Q tRNA, the requirements of large amount of input material and LC/MS expertise limit its application. We recently developed an acid denaturing gel and Northern blot method to sensitively detect galQ and manQ-tRNA modification and quantify their modification fractions using just microgram amounts of total RNA. This method uses the same acid denaturing gel system for separating charged from uncharged tRNA; however, deacylated, galQ and manQ modified tRNAs are also separated from unmodified tRNAs because of the positive charge carried by the secondary amine and the large chemical moiety of the glyco-Q base. Our method enables rapid investigation of glycosylated Q modification in tRNA, and also has the potential to investigate other large tRNA modifications that carry a positive charge under acid denaturing gel conditions.
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Affiliation(s)
- Wen Zhang
- Department of Chemistry, University of Chicago, Chicago, IL, United States
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States.
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16
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Fergus C, Al-Qasem M, Cotter M, McDonnell CM, Sorrentino E, Chevot F, Hokamp K, Senge MO, Southern JM, Connon SJ, Kelly VP. The human tRNA-guanine transglycosylase displays promiscuous nucleobase preference but strict tRNA specificity. Nucleic Acids Res 2021; 49:4877-4890. [PMID: 34009357 PMCID: PMC8136771 DOI: 10.1093/nar/gkab289] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/12/2022] Open
Abstract
Base-modification can occur throughout a transfer RNA molecule; however, elaboration is particularly prevalent at position 34 of the anticodon loop (the wobble position), where it functions to influence protein translation. Previously, we demonstrated that the queuosine modification at position 34 can be substituted with an artificial analogue via the queuine tRNA ribosyltransferase enzyme to induce disease recovery in an animal model of multiple sclerosis. Here, we demonstrate that the human enzyme can recognize a very broad range of artificial 7-deazaguanine derivatives for transfer RNA incorporation. By contrast, the enzyme displays strict specificity for transfer RNA species decoding the dual synonymous NAU/C codons, determined using a novel enzyme-RNA capture-release method. Our data highlight the broad scope and therapeutic potential of exploiting the queuosine incorporation pathway to intentionally engineer chemical diversity into the transfer RNA anticodon.
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Affiliation(s)
- Claire Fergus
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Mashael Al-Qasem
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Michelle Cotter
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Ciara M McDonnell
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Emiliano Sorrentino
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Franciane Chevot
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Karsten Hokamp
- School of Genetics and Microbiology, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Mathias O Senge
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - John M Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
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17
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Suzuki T, Yashiro Y, Kikuchi I, Ishigami Y, Saito H, Matsuzawa I, Okada S, Mito M, Iwasaki S, Ma D, Zhao X, Asano K, Lin H, Kirino Y, Sakaguchi Y, Suzuki T. Complete chemical structures of human mitochondrial tRNAs. Nat Commun 2020; 11:4269. [PMID: 32859890 PMCID: PMC7455718 DOI: 10.1038/s41467-020-18068-6] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
Mitochondria generate most cellular energy via oxidative phosphorylation. Twenty-two species of mitochondrial (mt-)tRNAs encoded in mtDNA translate essential subunits of the respiratory chain complexes. mt-tRNAs contain post-transcriptional modifications introduced by nuclear-encoded tRNA-modifying enzymes. They are required for deciphering genetic code accurately, as well as stabilizing tRNA. Loss of tRNA modifications frequently results in severe pathological consequences. Here, we perform a comprehensive analysis of post-transcriptional modifications of all human mt-tRNAs, including 14 previously-uncharacterized species. In total, we find 18 kinds of RNA modifications at 137 positions (8.7% in 1575 nucleobases) in 22 species of human mt-tRNAs. An up-to-date list of 34 genes responsible for mt-tRNA modifications are provided. We identify two genes required for queuosine (Q) formation in mt-tRNAs. Our results provide insight into the molecular mechanisms underlying the decoding system and could help to elucidate the molecular pathogenesis of human mitochondrial diseases caused by aberrant tRNA modifications.
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Affiliation(s)
- Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuka Yashiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ittoku Kikuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuma Ishigami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hironori Saito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Ikuya Matsuzawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba, 278-0022, Japan
| | - Mari Mito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Ding Ma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Xuewei Zhao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kana Asano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Huan Lin
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, Hainan, P.R. China
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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