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Fang Z, Lu Z, Han S, Zhou Y, Yang W, Zhang X, Zhou X. The Transcriptome-Wide Mapping of 2-Methylthio- N6-isopentenyladenosine at Single-Base Resolution. J Am Chem Soc 2023; 145:5467-5473. [PMID: 36820840 DOI: 10.1021/jacs.2c13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Hundreds of modified bases have been identified and enzymatically modified to transfer RNAs (tRNAs) to regulate RNA function in various organisms. 2-Methylthio-N6-isopentenyladenosine (ms2i6A), a hypermodified base found at tRNA position 37, exists in both prokaryotes and eukaryotes. ms2i6A is traditionally identified by separating and digesting each tRNA from total RNA using RNA mass spectrometry. A transcriptome-wide and single-base resolution method that enables absolute mapping of ms2i6A along with analysis of its distribution in different RNAs is lacking. Here, through chemoselective methylthio group bioconjugation, we introduce a new approach (redox activated chemical tagging sequencing, ReACT-seq) to detect ms2i6A transcriptome-wide at single-base resolution. Using the chemoselectivity between the methylthio group and oxaziridine group, ms2i6A is bio-orthogonally tagged with an azide group without interference of canonical nucleotides, advancing enrichment of methylthio group modified RNAs prior to sequencing. ReACT-seq was demonstrated on nine known tRNAs and proved to be highly accurate, and the reverse transcription stop (RT-stop) character enables ReACT-seq detection at single-base resolution. In addition, ReACT-seq identified that the modification of ms2i6A is conservative and may not exist in other RNAs.
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Affiliation(s)
- Zhentian Fang
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Yuanyuan Zhou
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Medicine, Wuhan 430071, People's Republic of China
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Xiaolian Zhang
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Medicine, Wuhan 430071, People's Republic of China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
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Amin USM, Parvez N, Rahman TA, Hasan MR, Das KC, Jahan S, Hasanat MA, Seraj ZI, Salimullah M. CDKAL1 gene rs7756992 A/G and rs7754840 G/C polymorphisms are associated with gestational diabetes mellitus in a sample of Bangladeshi population: implication for future T2DM prophylaxis. Diabetol Metab Syndr 2022; 14:18. [PMID: 35090536 PMCID: PMC8796445 DOI: 10.1186/s13098-021-00782-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Association of single nucleotide polymorphisms (SNP) rs7756992 A/G and rs7754840 G/C of cyclin-dependent kinase 5 regulatory subunit-associated protein 1-like 1 (CDKAL1) gene with the susceptibility of gestational diabetes mellitus (GDM) has been studied in a group of Bangladeshi women. METHODS In this case-control study, 212 GDM patients and 256 control subjects were genotyped for rs7756992 and rs7754840 by PCR-RFLP and TaqMan™ allelic discrimination assay method respectively. Genotyping results were confirmed by DNA sequencing and replicated TaqMan™ assay. The odds ratios and their 95% confidence interval were calculated by logistic regression to determine the associations between genotypes and GDM. RESULTS The genotype frequencies of rs7756992-AA/AG/GG in the GDM group and the control group were 37%/48%, 53%/45%, 10%/7% and those of rs7754840-CC/CG/GG were 51%/55%, 40.1%/39.8%, 9%/5% respectively. Under dominant and log additive models rs7756992 was revealed significantly associated with GDM after being adjusted for family history of diabetes (FHD) and gravidity. Conversely, rs7754840 was significantly associated (P = 0.047) with GDM only under the recessive model after the same adjustment. The risk allele frequency of both SNPs was higher in the GDM group but significantly (P = 0.029) increased prevalence was observed in the rs7756992 G allele. When positive FHD and risk alleles of these SNPs were synergistically present in any pregnant woman, the chance of developing GDM was augmented by many folds. The codominant model revealed 2.5 and 2.1 folds increase in odds by AG (rs7756992) and GC (rs7754840) genotypes and 3.7 and 4.5 folds by GG (rs7756992) and CC (rs7754840) genotypes respectively. A significant 2.7 folds (P = 0.038) increase in odds of GDM resulted from the interaction of rs7756992 and family history of diabetes under the dominant model. The cumulative effect of multigravidity and risk alleles of these SNPs increased the odds of GDM more than 1.5 folds in different genotypes. CONCLUSION This study not only revealed a significant association between rs7756992 and rs7754840 with GDM but also provided the possibility as potential markers for foretelling about GDM and type 2 diabetes mellitus in Bangladeshi women.
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Affiliation(s)
- U S Mahzabin Amin
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Nahid Parvez
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Tahia Anan Rahman
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Md Rakibul Hasan
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Sharmin Jahan
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Muhammad Abul Hasanat
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Zeba I Seraj
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.
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Involvement of Cdkal1 in the etiology of type 2 diabetes mellitus and microvascular diabetic complications: a review. J Diabetes Metab Disord 2022; 21:991-1001. [PMID: 35673487 PMCID: PMC9167393 DOI: 10.1007/s40200-021-00953-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
Abstract
Diabetes Mellitus, being a polygenic disorder, have a set of risk genes involved in the onset of the insulin resistance, obesity and impaired insulin synthesis. Recent genome wide association studies (GWAS) shows the intimacy of CDK5 regulatory subunit Associated protein 1-Like 1 (Cdkal1) with the pathophysiology of the diabetes mellitus and its complications, although the exact molecular relation is still unknown. In this short review, we have summarized all the diverse biological roles of Cdkal1 in relation to the onset of diabetes mellitus. Variations in the Cdkal1 transcript are responsible for the accumulation of misfolded insulin and thus generating oxidative and ER stress in the pancreatic β-cells, leading to their destruction. Recent studies have shown that Cdkal1 has an intrinsic thiomethyl transferase activity, which is essential for proper posttranslational processing of pre-proinsulin to produce mature insulin. Moreover, Cdkal1 has also been claimed as an endogenous inhibitor of cdk5, which prevents the cdk5-induced interruption in insulin synthesis through PDX1 translocation from nucleus to cytosol. Recent clinical studies have identified the risk single nucleotide polymorphisms (SNPs) of Cdkal1 as one of the root causes for the onset of diabetic complications. To the best of our knowledge, it is the first comprehensive review which elaborates most of the potential Cdkal1-dependent molecular mechanisms studied yet. In this review, we present a compiled and concise summary about all the diverse roles of Cdkal1 in the context of type 2 diabetes mellitus and its associated complications. This review will be helpful to target Cdkal1 as a potential option for the management of type 2 diabetes mellitus in future. Graphical abstract
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Geng X, Li Z, Yang Y. Emerging Role of Epitranscriptomics in Diabetes Mellitus and Its Complications. Front Endocrinol (Lausanne) 2022; 13:907060. [PMID: 35692393 PMCID: PMC9184717 DOI: 10.3389/fendo.2022.907060] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/14/2022] [Indexed: 01/13/2023] Open
Abstract
Diabetes mellitus (DM) and its related complications are among the leading causes of disability and mortality worldwide. Substantial studies have explored epigenetic regulation that is involved in the modifications of DNA and proteins, but RNA modifications in diabetes are still poorly investigated. In recent years, posttranscriptional epigenetic modification of RNA (the so-called 'epitranscriptome') has emerged as an interesting field of research. Numerous modifications, mainly N6 -methyladenosine (m6A), have been identified in nearly all types of RNAs and have been demonstrated to have an indispensable effect in a variety of human diseases, such as cancer, obesity, and diabetes. Therefore, it is particularly important to understand the molecular basis of RNA modifications, which might provide a new perspective for the pathogenesis of diabetes mellitus and the discovery of new therapeutic targets. In this review, we aim to summarize the recent progress in the epitranscriptomics involved in diabetes and diabetes-related complications. We hope to provide some insights for enriching the understanding of the epitranscriptomic regulatory mechanisms of this disease as well as the development of novel therapeutic targets for future clinical benefit.
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Affiliation(s)
- Xinqian Geng
- Department of Endocrinology, The Affiliated Hospital of Yunnan University and the Second People’s Hospital of Yunnan Province, Kunming, China
| | - Zheng Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ying Yang
- Department of Endocrinology, The Affiliated Hospital of Yunnan University and the Second People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Ying Yang,
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Fradejas-Villar N, Bohleber S, Zhao W, Reuter U, Kotter A, Helm M, Knoll R, McFarland R, Taylor RW, Mo Y, Miyauchi K, Sakaguchi Y, Suzuki T, Schweizer U. The Effect of tRNA [Ser]Sec Isopentenylation on Selenoprotein Expression. Int J Mol Sci 2021; 22:ijms222111454. [PMID: 34768885 PMCID: PMC8583801 DOI: 10.3390/ijms222111454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 12/22/2022] Open
Abstract
Transfer RNA[Ser]Sec carries multiple post-transcriptional modifications. The A37G mutation in tRNA[Ser]Sec abrogates isopentenylation of base 37 and has a profound effect on selenoprotein expression in mice. Patients with a homozygous pathogenic p.R323Q variant in tRNA-isopentenyl-transferase (TRIT1) show a severe neurological disorder, and hence we wondered whether selenoprotein expression was impaired. Patient fibroblasts with the homozygous p.R323Q variant did not show a general decrease in selenoprotein expression. However, recombinant human TRIT1R323Q had significantly diminished activities towards several tRNA substrates in vitro. We thus engineered mice conditionally deficient in Trit1 in hepatocytes and neurons. Mass-spectrometry revealed that hypermodification of U34 to mcm5Um occurs independently of isopentenylation of A37 in tRNA[Ser]Sec. Western blotting and 75Se metabolic labeling showed only moderate effects on selenoprotein levels and 75Se incorporation. A detailed analysis of Trit1-deficient liver using ribosomal profiling demonstrated that UGA/Sec re-coding was moderately affected in Selenop, Txnrd1, and Sephs2, but not in Gpx1. 2′O-methylation of U34 in tRNA[Ser]Sec depends on FTSJ1, but does not affect UGA/Sec re-coding in selenoprotein translation. Taken together, our results show that a lack of isopentenylation of tRNA[Ser]Sec affects UGA/Sec read-through but differs from a A37G mutation.
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Affiliation(s)
- Noelia Fradejas-Villar
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Simon Bohleber
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Wenchao Zhao
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Uschi Reuter
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany; (A.K.); (M.H.)
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany; (A.K.); (M.H.)
| | - Rainer Knoll
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (R.M.); (R.W.T.)
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (R.M.); (R.W.T.)
| | - Yufeng Mo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; (Y.M.); (K.M.); (Y.S.); (T.S.)
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; (Y.M.); (K.M.); (Y.S.); (T.S.)
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; (Y.M.); (K.M.); (Y.S.); (T.S.)
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; (Y.M.); (K.M.); (Y.S.); (T.S.)
| | - Ulrich Schweizer
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
- Correspondence:
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tRNA Biology in the Pathogenesis of Diabetes: Role of Genetic and Environmental Factors. Int J Mol Sci 2021; 22:ijms22020496. [PMID: 33419045 PMCID: PMC7825315 DOI: 10.3390/ijms22020496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 02/07/2023] Open
Abstract
The global rise in type 2 diabetes results from a combination of genetic predisposition with environmental assaults that negatively affect insulin action in peripheral tissues and impair pancreatic β-cell function and survival. Nongenetic heritability of metabolic traits may be an important contributor to the diabetes epidemic. Transfer RNAs (tRNAs) are noncoding RNA molecules that play a crucial role in protein synthesis. tRNAs also have noncanonical functions through which they control a variety of biological processes. Genetic and environmental effects on tRNAs have emerged as novel contributors to the pathogenesis of diabetes. Indeed, altered tRNA aminoacylation, modification, and fragmentation are associated with β-cell failure, obesity, and insulin resistance. Moreover, diet-induced tRNA fragments have been linked with intergenerational inheritance of metabolic traits. Here, we provide a comprehensive review of how perturbations in tRNA biology play a role in the pathogenesis of monogenic and type 2 diabetes.
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CDKAL1 (rs10946398) and TCF7L2 (rs7903146) gene polymorphisms and their association with risk of type-2 diabetes mellitus in population of Uttarakhand, India. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Yamamoto T, Fujimura A, Wei FY, Shinojima N, Kuroda JI, Mukasa A, Tomizawa K. 2-Methylthio Conversion of N6-Isopentenyladenosine in Mitochondrial tRNAs by CDK5RAP1 Promotes the Maintenance of Glioma-Initiating Cells. iScience 2019; 21:42-56. [PMID: 31654853 PMCID: PMC6820277 DOI: 10.1016/j.isci.2019.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 12/26/2022] Open
Abstract
2-Methylthio-N6-isopentenyl modification of adenosine (ms2i6A) is an evolutionally conserved modification found in mitochondrial (mt)-tRNAs. Cdk5 regulatory subunit-associated protein 1 (CDK5RAP1) specifically converts N6-isopentenyladenosine (i6A) to ms2i6A at position A37 of four mt-DNA-encoded tRNAs, and the modification regulates efficient mitochondrial translation and energy metabolism in mammals. Here, we report that the ms2 conversion mediated by CDK5RAP1 in mt-tRNAs is required to sustain glioma-initiating cell (GIC)-related traits. CDK5RAP1 maintained the self-renewal capacity, undifferentiated state, and tumorigenic potential of GICs. This regulation was not related to the translational control of mt-proteins. CDK5RAP1 abrogated the antitumor effect of i6A by converting i6A to ms2i6A and protected GICs from excessive autophagy triggered by i6A. The elevated activity of CDK5RAP1 contributed to the amelioration of the tumor-suppressive effect of i6A and promoted GIC maintenance. This work demonstrates that CDK5RAP1 is crucial for the detoxification of endogenous i6A and that GICs readily utilize this mechanism for survival. CDK5RAP1 is required to sustain the growth of GICs through ms2 modification of i6A Deficit of CDK5RAP1 inhibits the growth of GIC through i6A accumulation CDK5RAP1 detoxifies i6A by conversion into ms2i6A in the mitochondria of GICs Mitochondria serve as antidotal machinery against i6A in GICs
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Affiliation(s)
- Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Atsushi Fujimura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Neutron Therapy Research Center, Okayama University, Okayama 700-8558, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Naoki Shinojima
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Jun-Ichiro Kuroda
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Neutron Therapy Research Center, Okayama University, Okayama 700-8558, Japan.
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Takesue Y, Wei FY, Fukuda H, Tanoue Y, Yamamoto T, Chujo T, Shinojima N, Yano S, Morioka M, Mukasa A, Kuratsu J, Tomizawa K. Regulation of growth hormone biosynthesis by Cdk5 regulatory subunit associated protein 1-like 1 (CDKAL1) in pituitary adenomas. Endocr J 2019; 66:807-816. [PMID: 31189758 DOI: 10.1507/endocrj.ej18-0536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
CDK5 regulatory subunit associated protein 1-like 1 (CDKAL1) is a tRNA-modifying enzyme that catalyzes 2-methylthiolation (ms2) and has been implicated in the development of type 2 diabetes (T2D). CDKAL1-mediated ms2 is important for efficient protein translation and regulates insulin biosynthesis in pancreatic cells. Interestingly, an association between T2D and release of growth hormone (GH) has been reported in humans. However, it is unknown whether CDKAL1 is important for hormone production in the pituitary gland. The present study investigated the role of CDKAL1 in GH-producing pituitary adenomas (GHPAs). CDKAL1 activity was suppressed in GHPAs, as evidenced by a decrease in ms2, compared with non-functioning pituitary adenomas (NFPAs), which do not produce specific hormones. Downregulation of Cdkal1 using small interfering and short hairpin RNAs increased the biosynthesis and secretion of GH in rat GH3 cells. Depletion of Cdkal1 increased the cytosolic calcium level via downregulation of DnaJ heat shock protein family (Hsp40) member C10 (Dnajc10), which is an endoplasmic reticulum protein related to calcium homeostasis. This stimulated transcription of GH via upregulation of Pit-1. Moreover, CDKAL1 activity was highly sensitive to proteostatic stress and was upregulated by suppression of this stress. Taken together, these results suggest that dysregulation of CDKAL1 is involved in the pathogenesis of GHPAs, and that modulation of the proteostatic stress response might control CDKAL1 activity and facilitate treatment of GHPAs.
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Affiliation(s)
- Yoshihiro Takesue
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiroyuki Fukuda
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yuki Tanoue
- International Research Center for Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Naoki Shinojima
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Shigetoshi Yano
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Neurosurgery, Fukuoka Neurosurgical Hospital, Fukuoka 811-1313, Japan
| | - Motohiro Morioka
- Department of Neurosurgery, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Junichi Kuratsu
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Neurosurgery, Sakurajuji Hospital, Kumamoto 861-4173, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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Cosentino C, Cnop M, Igoillo-Esteve M. The tRNA Epitranscriptome and Diabetes: Emergence of tRNA Hypomodifications as a Cause of Pancreatic β-Cell Failure. Endocrinology 2019; 160:1262-1274. [PMID: 30907926 DOI: 10.1210/en.2019-00098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/15/2019] [Indexed: 01/26/2023]
Abstract
tRNAs are crucial noncoding RNA molecules that serve as amino acid carriers during protein synthesis. The transcription of tRNA genes is a highly regulated process. The tRNA pool is tissue and cell specific, it varies during development, and it is modulated by the environment. tRNAs are highly posttranscriptionally modified by specific tRNA-modifying enzymes. The tRNA modification signature of a cell determines the tRNA epitranscriptome. Perturbations in the tRNA epitranscriptome, as a consequence of mutations in tRNAs and tRNA-modifying enzymes or environmental exposure, have been associated with human disease, including diabetes. tRNA fragmentation induced by impaired tRNA modifications or dietary factors has been linked to pancreatic β-cell demise and paternal inheritance of metabolic traits. Herein, we review recent findings that associate tRNA epitranscriptome perturbations with diabetes.
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Affiliation(s)
- Cristina Cosentino
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
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Zhou Z, Sun B, Huang S, Jia W, Yu D. The tRNA-associated dysregulation in diabetes mellitus. Metabolism 2019; 94:9-17. [PMID: 30711570 DOI: 10.1016/j.metabol.2019.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/26/2019] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
Diabetes mellitus (DM) is a complex endocrine and metabolic disorder for human health and well-being. Deregulated glucose and lipid metabolism are the primary underlying manifestations associated with this disease. Transfer RNAs (tRNAs) are considered to mainly participate in protein translation and may contribute to complex human pathologies. Although the molecular mechanisms remain, for the most part, unknown, accumulating evidence indicates that tRNAs play a vital role in the pathogenesis of DM. This paper reviews different aspects of tRNA-associated dysregulation in DM, such as tRNA mutations, tRNA modifications, tRNA aminoacylation and tRNA derivatives, aiming at a better understanding of the pathogenesis of DM and providing new ideas for the personalized treatment of this metabolism-associated disease.
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Affiliation(s)
- Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Bao Sun
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410000, China; Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410000, China
| | - Shiqiong Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410000, China; Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410000, China
| | - Wenrui Jia
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
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12
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Yang P, Beltramo DM, de Pouplana LR, Soria NW, Torres AG. Loss of the tRNA Lys CUU encoding gene, Chr-11 tRNA-Lys-CUU, is not associated with Type 2 diabetes mellitus. Biomark Med 2019; 13:259-266. [PMID: 30882233 DOI: 10.2217/bmm-2018-0322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate the presence/absence of the Chr-11 tRNA-Lys-CUU gene as a marker for genetic predisposition to Type 2 diabetes mellitus (T2DM). METHODS We enrolled 122 patients diagnosed with T2DM and 77 non-diabetic individuals. We evaluated clinical and biochemical parameters (body mass index, hypertension, cholesterol levels, glycosylated hemoglobin, triglycerides, etc.), and performed a genotypic profiling of Chr-11 tRNA-Lys-CUU by polymerase chain reaction analyses. RESULTS Approximately one third of the population lacked Chr-11 tRNA-Lys-CUU. We did not observe a statistically significant association between the presence/absence of Chr-11 tRNA-Lys-CUU and T2DM. CONCLUSION The genotypic distribution of Chr-11 tRNA-Lys-CUU in our population was consistent to that reported by others. This gene failed as a marker for T2DM predisposition.
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Affiliation(s)
- Pablo Yang
- Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Dante Miguel Beltramo
- Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science & Technology, 08028 Barcelona, Catalonia, Spain.,Catalan Institution for Research & Advanced Studies (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Néstor Walter Soria
- Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science & Technology, 08028 Barcelona, Catalonia, Spain
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13
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Cosentino C, Toivonen S, Diaz Villamil E, Atta M, Ravanat JL, Demine S, Schiavo A, Pachera N, Deglasse JP, Jonas JC, Balboa D, Otonkoski T, Pearson ER, Marchetti P, Eizirik DL, Cnop M, Igoillo-Esteve M. Pancreatic β-cell tRNA hypomethylation and fragmentation link TRMT10A deficiency with diabetes. Nucleic Acids Res 2018; 46:10302-10318. [PMID: 30247717 PMCID: PMC6212784 DOI: 10.1093/nar/gky839] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/17/2018] [Accepted: 09/10/2018] [Indexed: 12/20/2022] Open
Abstract
Transfer RNAs (tRNAs) are non-coding RNA molecules essential for protein synthesis. Post-transcriptionally they are heavily modified to improve their function, folding and stability. Intronic polymorphisms in CDKAL1, a tRNA methylthiotransferase, are associated with increased type 2 diabetes risk. Loss-of-function mutations in TRMT10A, a tRNA methyltransferase, are a monogenic cause of early onset diabetes and microcephaly. Here we confirm the role of TRMT10A as a guanosine 9 tRNA methyltransferase, and identify tRNAGln and tRNAiMeth as two of its targets. Using RNA interference and induced pluripotent stem cell-derived pancreatic β-like cells from healthy controls and TRMT10A-deficient patients we demonstrate that TRMT10A deficiency induces oxidative stress and triggers the intrinsic pathway of apoptosis in β-cells. We show that tRNA guanosine 9 hypomethylation leads to tRNAGln fragmentation and that 5'-tRNAGln fragments mediate TRMT10A deficiency-induced β-cell death. This study unmasks tRNA hypomethylation and fragmentation as a hitherto unknown mechanism of pancreatic β-cell demise relevant to monogenic and polygenic forms of diabetes.
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Affiliation(s)
- Cristina Cosentino
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Sanna Toivonen
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Esteban Diaz Villamil
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Mohamed Atta
- CEA/Grenoble, DRF/BIG/LCBM UMR5249, Grenoble, France
| | - Jean-Luc Ravanat
- Université Grenoble Alpes, CEA, CNRS INAC, SyMMES UMR 5819, Grenoble, France
| | - Stéphane Demine
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Andrea Alex Schiavo
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Nathalie Pachera
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Jean-Philippe Deglasse
- Université Catholique de Louvain, Institut de Recherche Expérimentale et Clinique, Pôle d’ Endocrinologie, Diabète et Nutrition, Brussels, Belgium
| | - Jean-Christophe Jonas
- Université Catholique de Louvain, Institut de Recherche Expérimentale et Clinique, Pôle d’ Endocrinologie, Diabète et Nutrition, Brussels, Belgium
| | - Diego Balboa
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ewan R Pearson
- Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, UK
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Décio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, 1070 Brussels, Belgium
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium
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14
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Fakruddin M, Wei FY, Emura S, Matsuda S, Yasukawa T, Kang D, Tomizawa K. Cdk5rap1-mediated 2-methylthio-N6-isopentenyladenosine modification is absent from nuclear-derived RNA species. Nucleic Acids Res 2017; 45:11954-11961. [PMID: 28981754 PMCID: PMC5714233 DOI: 10.1093/nar/gkx819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/05/2017] [Indexed: 11/30/2022] Open
Abstract
2-Methylthio-N6-isopentenyl modification of adenosine (ms2i6A) is an evolutionally conserved modification that is found in transfer RNAs (tRNAs). We have recently shown that Cdk5 regulatory subunit-associated protein 1 (Cdk5rap1) specifically converts i6A to ms2i6A at position A37 of four mitochondrial DNA-encoded tRNAs, and that the modification regulates efficient mitochondrial translation and energy metabolism in mammals. Curiously, a previous study reported that ms2i6A is present abundantly in nuclear-derived RNA species such as microRNAs, but not in tRNA fractions. To fully understand the molecular property of ms2i6A, the existence of non-canonical ms2i6A must be carefully validated. In the present study, we examined ms2i6A in total RNA purified from human and murine ρ0 cells, in which mitochondrial DNA-derived tRNAs were completely depleted. The ms2i6A was not detected in these cells at all. We generated a monoclonal antibody against ms2i6A and examined ms2i6A in murine RNAs using the antibody. The anti-ms2i6A antibody only reacted with the tRNA fractions and not in other RNA species. Furthermore, immunocytochemistry analysis using the antibody showed the predominant localization of ms2i6A in mitochondria and co-localization with the mitochondrial elongation factor Tu. Taken together, we propose that ms2i6A is a mitochondrial tRNA-specific modification and is absent from nuclear-encoded RNA species.
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Affiliation(s)
- Md Fakruddin
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjyo, Kumamoto 860-8556, Japan
| | - Fan Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjyo, Kumamoto 860-8556, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Shohei Emura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjyo, Kumamoto 860-8556, Japan
| | - Shigeru Matsuda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjyo, Kumamoto 860-8556, Japan
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15
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Take K, Waki H, Sun W, Wada T, Yu J, Nakamura M, Aoyama T, Yamauchi T, Kadowaki T. CDK5 Regulatory Subunit-Associated Protein 1-like 1 Negatively Regulates Adipocyte Differentiation through Activation of Wnt Signaling Pathway. Sci Rep 2017; 7:7326. [PMID: 28779110 PMCID: PMC5544666 DOI: 10.1038/s41598-017-06469-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 06/13/2017] [Indexed: 12/04/2022] Open
Abstract
CDK5 Regulatory Subunit-Associated Protein 1-like 1 (CDKAL1) was identified as a susceptibility gene for type 2 diabetes and body mass index in genome-wide association studies. Although it was reported that CDKAL1 is a methylthiotransferase essential for tRNALys(UUU) and faithful translation of proinsulin generated in pancreatic β cells, the role of CDKAL1 in adipocytes has not been understood well. In this study, we found that CDKAL1 is expressed in adipose tissue and its expression is increased during differentiation. Stable overexpression of CDKAL1, however, inhibited adipocyte differentiation of 3T3-L1 cells, whereas knockdown of CDKAL1 promoted differentiation. CDKAL1 increased protein levels of β-catenin and its active unphosphorylated form in the nucleus, thereby promoting Wnt target gene expression, suggesting that CDKAL1 activated the Wnt/β-catenin pathway—a well-characterized inhibitory regulator of adipocyte differentiation. Mutant experiments show that conserved cysteine residues of Fe-S clusters of CDKAL1 are essential for its anti-adipogenic action. Our results identify CDKAL1 as novel negative regulator of adipocyte differentiation and provide insights into the link between CDKAL1 and metabolic diseases such as type 2 diabetes and obesity.
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Affiliation(s)
- Kazumi Take
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hironori Waki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan. .,Functional Regulation of Adipocytes, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan. .,Department of Molecular Sciences on Diabetes, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Wei Sun
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Takahito Wada
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Jing Yu
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Masahiro Nakamura
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tomohisa Aoyama
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
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16
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Takahashi N, Wei FY, Watanabe S, Hirayama M, Ohuchi Y, Fujimura A, Kaitsuka T, Ishii I, Sawa T, Nakayama H, Akaike T, Tomizawa K. Reactive sulfur species regulate tRNA methylthiolation and contribute to insulin secretion. Nucleic Acids Res 2016; 45:435-445. [PMID: 27568003 PMCID: PMC5224495 DOI: 10.1093/nar/gkw745] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/16/2016] [Indexed: 12/22/2022] Open
Abstract
The 2-methylthio (ms2) modification at A37 of tRNAs is critical for accurate decoding, and contributes to metabolic homeostasis in mammals. However, the regulatory mechanism of ms2 modification remains largely unknown. Here, we report that cysteine hydropersulfide (CysSSH), a newly identified reactive sulfur species, is involved in ms2 modification in cells. The suppression of intracellular CysSSH production rapidly reduced ms2 modification, which was rescued by the application of an exogenous CysSSH donor. Using a unique and stable isotope-labeled CysSSH donor, we show that CysSSH was capable of specifically transferring its reactive sulfur atom to the cysteine residues of ms2-modifying enzymes as well as ms2 modification. Furthermore, the suppression of CysSSH production impaired insulin secretion and caused glucose intolerance in both a pancreatic β-cell line and mouse model. These results demonstrate that intracellular CysSSH is a novel sulfur source for ms2 modification, and that it contributes to insulin secretion.
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Affiliation(s)
- Nozomu Takahashi
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Japan
| | - Sayaka Watanabe
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Mayumi Hirayama
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yuya Ohuchi
- Dojindo Laboratories, 2025-5 Tabaru Kamimashikigun, Mashikimachi, Kumamoto 861-2202, Japan
| | - Atsushi Fujimura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Isao Ishii
- Department of Health Chemistry, Showa Pharmaceutical University, Tokyo 194-8543, Japan
| | - Tomohiro Sawa
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556,Japan
| | - Hideki Nakayama
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology,Tohoku University Graduate School of Medicine, Sendai 980-8577, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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17
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Wei FY, Tomizawa K. Measurement of 2-methylthio Modifications in Mitochondrial Transfer RNAs by Reverse-transcription Quantitative PCR. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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18
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Shigi N. Sulfur Modifications in tRNA: Function and Implications for Human Disease. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Wei FY, Zhou B, Suzuki T, Miyata K, Ujihara Y, Horiguchi H, Takahashi N, Xie P, Michiue H, Fujimura A, Kaitsuka T, Matsui H, Koga Y, Mohri S, Suzuki T, Oike Y, Tomizawa K. Cdk5rap1-mediated 2-methylthio modification of mitochondrial tRNAs governs protein translation and contributes to myopathy in mice and humans. Cell Metab 2015; 21:428-42. [PMID: 25738458 DOI: 10.1016/j.cmet.2015.01.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/24/2014] [Accepted: 01/26/2015] [Indexed: 12/20/2022]
Abstract
Transfer RNAs (tRNAs) contain a wide variety of posttranscriptional modifications that are important for accurate decoding. Mammalian mitochondrial tRNAs (mt-tRNAs) are modified by nuclear-encoded tRNA-modifying enzymes; however, the physiological roles of these modifications remain largely unknown. In this study, we report that Cdk5 regulatory subunit-associated protein 1 (Cdk5rap1) is responsible for 2-methylthio (ms(2)) modifications of mammalian mt-tRNAs for Ser(UCN), Phe, Tyr, and Trp codons. Deficiency in ms(2) modification markedly impaired mitochondrial protein synthesis, which resulted in respiratory defects in Cdk5rap1 knockout (KO) mice. The KO mice were highly susceptive to stress-induced mitochondrial remodeling and exhibited accelerated myopathy and cardiac dysfunction under stressed conditions. Furthermore, we demonstrate that the ms(2) modifications of mt-tRNAs were sensitive to oxidative stress and were reduced in patients with mitochondrial disease. These findings highlight the fundamental role of ms(2) modifications of mt-tRNAs in mitochondrial protein synthesis and their pathological consequences in mitochondrial disease.
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Affiliation(s)
- Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Bo Zhou
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Keishi Miyata
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yoshihiro Ujihara
- First Department of Physiology, Kawasaki Medical School, Okayama 701-0192, Japan
| | - Haruki Horiguchi
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Nozomu Takahashi
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Peiyu Xie
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiroyuki Michiue
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Atsushi Fujimura
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hideki Matsui
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Yasutoshi Koga
- Department of Pediatrics and Child Health, Kurume University Graduate School of Medicine, Fukuoka 830-0011, Japan
| | - Satoshi Mohri
- First Department of Physiology, Kawasaki Medical School, Okayama 701-0192, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yuichi Oike
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
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20
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Adaptive human CDKAL1 variants underlie hormonal response variations at the enteroinsular axis. PLoS One 2014; 9:e105410. [PMID: 25222615 PMCID: PMC4164438 DOI: 10.1371/journal.pone.0105410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 07/22/2014] [Indexed: 11/19/2022] Open
Abstract
Recent analyses have identified positively selected loci that explain differences in immune responses, body forms, and adaptations to extreme climates, but variants that describe adaptations in energy-balance regulation remain underexplored. To identify variants that confer adaptations in energy-balance regulation, we explored the evolutionary history and functional associations of candidate variants in 207 genes. We screened single nucleotide polymorphisms in genes that had been associated with energy-balance regulation for unusual genetic patterns in human populations, followed by studying associations among selected variants and serum levels of GIP, insulin, and C-peptide in pregnant women after an oral glucose tolerance test. Our analysis indicated that 5′ variants in CDKAL1, CYB5R4, GAD2, and PPARG are marked with statistically significant signals of gene–environment interactions. Importantly, studies of serum hormone levels showed that variants in CDKAL1 are associated with glucose-induced GIP and insulin responses (p<0.05). On the other hand, a GAD2 variant exhibited a significant association with glucose-induced C-peptide response. In addition, simulation analysis indicated that a type 2 diabetes risk variant in CDKAL1 (rs7754840) was selected in East Asians ∼6,900 years ago. Taken together, these data indicated that variants in CDKAL1 and GAD2 were targets of prior environmental selection. Because the selection of the CDKAL1 variant overlapped with the selection of a cluster of GIP variants in the same population ∼11,800 to 2,000 years ago, we speculate that these regulatory genes at the human enteroinsular axis could be highly responsive to environmental selection in recent human history.
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21
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Zhou B, Wei FY, Kanai N, Fujimura A, Kaitsuka T, Tomizawa K. Identification of a splicing variant that regulates type 2 diabetes risk factor CDKAL1 level by a coding-independent mechanism in human. Hum Mol Genet 2014; 23:4639-50. [PMID: 24760768 DOI: 10.1093/hmg/ddu184] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) in CDKAL1 have been associated with the development of type 2 diabetes (T2D). CDKAL1 catalyzes 2-methylthio modification of adenosine at position 37 of tRNA(Lys)(UUU). A deficit of this modification causes aberrant protein synthesis, and is associated with impairment of insulin secretion in both mouse model and human. However, it is unknown whether the T2D-associated SNPs in CDKAL1 are associated with downregulation of CDKAL1 by regulating the gene expression. Here, we report a specific splicing variant of CDKAL1 termed CDKAL1-v1 that is markedly lower in individuals carrying risk SNPs of CDKAL1. Interestingly, CDKAL1-v1 is a non-coding transcript, which regulates the CDKAL1 level by competitive binding to a CDKAL1-targeting miRNA. By direct editing of the genome, we further show that the nucleotides around the SNP regions are critical for the alternative splicing of CDKAL1-v1. These findings reveal that the T2D-associated SNPs in CDKAL1 reduce CDKAL1-v1 levels by impairing splicing, which in turn increases miRNA-mediated suppression of CDKAL1. Our results suggest that CDKAL1-v1-mediated suppression of CDKAL1 might underlie the pathogenesis of T2D in individuals carrying the risk SNPs.
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Affiliation(s)
- Bo Zhou
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Narumi Kanai
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Atsushi Fujimura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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22
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Sarin LP, Leidel SA. Modify or die?--RNA modification defects in metazoans. RNA Biol 2014; 11:1555-67. [PMID: 25692999 PMCID: PMC4615230 DOI: 10.4161/15476286.2014.992279] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 12/21/2022] Open
Abstract
Chemical RNA modifications are present in all kingdoms of life and many of these post-transcriptional modifications are conserved throughout evolution. However, most of the research has been performed on single cell organisms, whereas little is known about how RNA modifications contribute to the development of metazoans. In recent years, the identification of RNA modification genes in genome wide association studies (GWAS) has sparked new interest in previously neglected genes. In this review, we summarize recent findings that connect RNA modification defects and phenotypes in higher eukaryotes. Furthermore, we discuss the implications of aberrant tRNA modification in various human diseases including metabolic defects, mitochondrial dysfunctions, neurological disorders, and cancer. As the molecular mechanisms of these diseases are being elucidated, we will gain first insights into the functions of RNA modifications in higher eukaryotes and finally understand their roles during development.
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MESH Headings
- Amyotrophic Lateral Sclerosis/genetics
- Amyotrophic Lateral Sclerosis/metabolism
- Amyotrophic Lateral Sclerosis/pathology
- Animals
- Dysautonomia, Familial/genetics
- Dysautonomia, Familial/metabolism
- Dysautonomia, Familial/pathology
- Epilepsy, Rolandic/genetics
- Epilepsy, Rolandic/metabolism
- Epilepsy, Rolandic/pathology
- Genome-Wide Association Study
- Humans
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Mutation
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Nucleic Acid Conformation
- Phenotype
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Mitochondrial
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- L Peter Sarin
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
- Faculty of Medicine; University of Münster; Münster, Germany
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