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Yoshinaga M, Han K, Morgens DW, Horii T, Kobayashi R, Tsuruyama T, Hia F, Yasukura S, Kajiya A, Cai T, Cruz PHC, Vandenbon A, Suzuki Y, Kawahara Y, Hatada I, Bassik MC, Takeuchi O. The N 6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity. Nat Commun 2022; 13:6435. [PMID: 36307435 PMCID: PMC9616860 DOI: 10.1038/s41467-022-34078-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/12/2022] [Indexed: 02/07/2023] Open
Abstract
During erythroid differentiation, the maintenance of genome integrity is key for the success of multiple rounds of cell division. However, molecular mechanisms coordinating the expression of DNA repair machinery in erythroid progenitors are poorly understood. Here, we discover that an RNA N6-methyladenosine (m6A) methyltransferase, METTL16, plays an essential role in proper erythropoiesis by safeguarding genome integrity via the control of DNA-repair-related genes. METTL16-deficient erythroblasts exhibit defective differentiation capacity, DNA damage and activation of the apoptotic program. Mechanistically, METTL16 controls m6A deposition at the structured motifs in DNA-repair-related transcripts including Brca2 and Fancm mRNAs, thereby upregulating their expression. Furthermore, a pairwise CRISPRi screen revealed that the MTR4-nuclear RNA exosome complex is involved in the regulation of METTL16 substrate mRNAs in erythroblasts. Collectively, our study uncovers that METTL16 and the MTR4-nuclear RNA exosome act as essential regulatory machinery to maintain genome integrity and erythropoiesis.
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Affiliation(s)
- Masanori Yoshinaga
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Kyuho Han
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - David W. Morgens
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Takuro Horii
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan
| | - Ryosuke Kobayashi
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan
| | - Tatsuaki Tsuruyama
- grid.258799.80000 0004 0372 2033Department of Drug and Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Fabian Hia
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Shota Yasukura
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Asako Kajiya
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Ting Cai
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Pedro H. C. Cruz
- grid.136593.b0000 0004 0373 3971Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Alexis Vandenbon
- grid.258799.80000 0004 0372 2033Laboratory of Tissue Homeostasis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507 Japan
| | - Yutaka Suzuki
- grid.26999.3d0000 0001 2151 536XLaboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Yukio Kawahara
- grid.136593.b0000 0004 0373 3971Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Izuho Hatada
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan ,grid.256642.10000 0000 9269 4097Viral Vector Core, Gunma University Initiative for Advanced Research (GIAR), Gunma, 371-8512 Japan
| | - Michael C. Bassik
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Osamu Takeuchi
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
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2
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Yaku A, Inagaki T, Asano R, Okazawa M, Mori H, Sato A, Hia F, Masaki T, Manabe Y, Ishibashi T, Vandenbon A, Nakatsuka Y, Akaki K, Yoshinaga M, Uehata T, Mino T, Morita S, Ishibashi-Ueda H, Morinobu A, Tsujimura T, Ogo T, Nakaoka Y, Takeuchi O. Regnase-1 Prevents Pulmonary Arterial Hypertension Through mRNA Degradation of Interleukin-6 and Platelet-Derived Growth Factor in Alveolar Macrophages. Circulation 2022; 146:1006-1022. [PMID: 35997026 DOI: 10.1161/circulationaha.122.059435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a type of pulmonary hypertension (PH) characterized by obliterative pulmonary vascular remodeling, resulting in right-sided heart failure. Although the pathogenesis of PAH is not fully understood, inflammatory responses and cytokines have been shown to be associated with PAH, in particular, with connective tissue disease-PAH. In this sense, Regnase-1, an RNase that regulates mRNAs encoding genes related to immune reactions, was investigated in relation to the pathogenesis of PH. METHODS We first examined the expression levels of ZC3H12A (encoding Regnase-1) in peripheral blood mononuclear cells from patients with PH classified under various types of PH, searching for an association between the ZC3H12A expression and clinical features. We then generated mice lacking Regnase-1 in myeloid cells, including alveolar macrophages, and examined right ventricular systolic pressures and histological changes in the lung. We further performed a comprehensive analysis of the transcriptome of alveolar macrophages and pulmonary arteries to identify genes regulated by Regnase-1 in alveolar macrophages. RESULTS ZC3H12A expression in peripheral blood mononuclear cells was inversely correlated with the prognosis and severity of disease in patients with PH, in particular, in connective tissue disease-PAH. The critical role of Regnase-1 in controlling PAH was also reinforced by the analysis of mice lacking Regnase-1 in alveolar macrophages. These mice spontaneously developed severe PAH, characterized by the elevated right ventricular systolic pressures and irreversible pulmonary vascular remodeling, which recapitulated the pathology of patients with PAH. Transcriptomic analysis of alveolar macrophages and pulmonary arteries of these PAH mice revealed that Il6, Il1b, and Pdgfa/b are potential targets of Regnase-1 in alveolar macrophages in the regulation of PAH. The inhibition of IL-6 (interleukin-6) by an anti-IL-6 receptor antibody or platelet-derived growth factor by imatinib but not IL-1β (interleukin-1β) by anakinra, ameliorated the pathogenesis of PAH. CONCLUSIONS Regnase-1 maintains lung innate immune homeostasis through the control of IL-6 and platelet-derived growth factor in alveolar macrophages, thereby suppressing the development of PAH in mice. Furthermore, the decreased expression of Regnase-1 in various types of PH implies its involvement in PH pathogenesis and may serve as a disease biomarker, and a therapeutic target for PH as well.
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Affiliation(s)
- Ai Yaku
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
- Department of Rheumatology and Clinical Immunology (A.Y., A.M.), Graduate School of Medicine, Kyoto University, Japan
| | - Tadakatsu Inagaki
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan (T. Inagaki, R.A., M.O., H.M., T. Masaki, Y.M., T. Ishibashi, Y. Nakaoka)
| | - Ryotaro Asano
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan (T. Inagaki, R.A., M.O., H.M., T. Masaki, Y.M., T. Ishibashi, Y. Nakaoka)
- Department of Advanced Medical Research for Pulmonary Hypertension (R.A., T.O.), National Cerebral and Cardiovascular Center, Suita, Japan
- Department of Cardiovascular Medicine (R.A., T.O.), National Cerebral and Cardiovascular Center, Suita, Japan
| | - Makoto Okazawa
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan (T. Inagaki, R.A., M.O., H.M., T. Masaki, Y.M., T. Ishibashi, Y. Nakaoka)
| | - Hiroyoshi Mori
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan (T. Inagaki, R.A., M.O., H.M., T. Masaki, Y.M., T. Ishibashi, Y. Nakaoka)
| | - Ayuko Sato
- Department of Pathology, Hyogo College of Medicine, Nishinomiya, Japan (A.S., T.T.)
| | - Fabian Hia
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
| | - Takeshi Masaki
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan (T. Inagaki, R.A., M.O., H.M., T. Masaki, Y.M., T. Ishibashi, Y. Nakaoka)
| | - Yusuke Manabe
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan (T. Inagaki, R.A., M.O., H.M., T. Masaki, Y.M., T. Ishibashi, Y. Nakaoka)
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan (Y.M.)
| | - Tomohiko Ishibashi
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan (T. Inagaki, R.A., M.O., H.M., T. Masaki, Y.M., T. Ishibashi, Y. Nakaoka)
| | - Alexis Vandenbon
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences (A.V.), Kyoto University, Japan
| | - Yoshinari Nakatsuka
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
| | - Kotaro Akaki
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
| | - Masanori Yoshinaga
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
| | - Takuya Uehata
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
| | - Takashi Mino
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
| | - Satoshi Morita
- Department of Biomedical Statistics and Bioinformatics, Graduate School of Medicine (S.M.), Kyoto University, Japan
| | - Hatsue Ishibashi-Ueda
- Department of Pathology (H.I.-U.), National Cerebral and Cardiovascular Center, Suita, Japan
| | - Akio Morinobu
- Department of Rheumatology and Clinical Immunology (A.Y., A.M.), Graduate School of Medicine, Kyoto University, Japan
| | - Tohru Tsujimura
- Department of Pathology, Hyogo College of Medicine, Nishinomiya, Japan (A.S., T.T.)
| | - Takeshi Ogo
- Department of Advanced Medical Research for Pulmonary Hypertension (R.A., T.O.), National Cerebral and Cardiovascular Center, Suita, Japan
- Department of Cardiovascular Medicine (R.A., T.O.), National Cerebral and Cardiovascular Center, Suita, Japan
| | - Yoshikazu Nakaoka
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan (T. Inagaki, R.A., M.O., H.M., T. Masaki, Y.M., T. Ishibashi, Y. Nakaoka)
- Department of Cardiovascular Medicine (Y. Nakaoka), Osaka University Graduate School of Medicine, Suita, Japan
- Department of Molecular Imaging in Cardiovascular Medicine (Y. Nakaoka), Osaka University Graduate School of Medicine, Suita, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry (A.Y., F.H., Y. Nakatsuka, K.A., M.Y., T.U., T. Mino, O.T.), Graduate School of Medicine, Kyoto University, Japan
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3
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Tse KM, Vandenbon A, Cui X, Mino T, Uehata T, Yasuda K, Sato A, Tsujimura T, Hia F, Yoshinaga M, Kinoshita M, Okuno T, Takeuchi O. Enhancement of Regnase-1 expression with stem loop-targeting antisense oligonucleotides alleviates inflammatory diseases. Sci Transl Med 2022; 14:eabo2137. [PMID: 35544597 DOI: 10.1126/scitranslmed.abo2137] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Regnase-1 is an ribonuclease that plays essential roles in restricting inflammation through degrading messenger RNAs (mRNAs) involved in immune reactions via the recognition of stem-loop (SL) structures in the 3' untranslated regions (3'UTRs). Dysregulated expression of Regnase-1 is associated with the pathogenesis of inflammatory and autoimmune diseases in mice and humans. Here, we developed a therapeutic strategy to suppress inflammatory responses by blocking Regnase-1 self-regulation, which was mediated by the simultaneous use of two antisense phosphorodiamidate morpholino oligonucleotides (MOs) to alter the binding of Regnase-1 toward the SL structures in its 3'UTR. Regnase-1-targeting MOs not only enhanced Regnase-1 expression by stabilizing mRNAs but also effectively reduced the expression of multiple proinflammatory transcripts that were controlled by Regnase-1 in macrophages. Intratracheal administration of Regnase-1-targeting MOs ameliorated acute respiratory distress syndrome and chronic fibrosis through suppression of inflammatory cascades. In addition, intracranial treatment with Regnase-1-targeting MOs attenuated the development of experimental autoimmune encephalomyelitis by promoting the expansion of homeostatic microglia and regulatory T cell populations. Regnase-1 expression was inversely correlated with disease severity in patients with multiple sclerosis, and MOs targeting human Regnase-1 SL structures were effective in mitigating cytokine production in human immune cells. Collectively, MO-mediated disruption of the Regnase-1 self-regulation pathway is a potential therapeutic strategy to enhance Regnase-1 abundance, which, in turn, provides therapeutic benefits for treating inflammatory diseases by suppressing inflammation.
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Affiliation(s)
- Ka Man Tse
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Alexis Vandenbon
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Xiaotong Cui
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Keiko Yasuda
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Ayuko Sato
- Department of Pathology, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Tohru Tsujimura
- Department of Pathology, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Makoto Kinoshita
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tatsusada Okuno
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
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4
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Chong YK, Tartey S, Yoshikawa Y, Imami K, Li S, Yoshinaga M, Hirabayashi A, Liu G, Vandenbon A, Hia F, Uehata T, Mino T, Suzuki Y, Noda T, Ferrandon D, Standley DM, Ishihama Y, Takeuchi O. Cyclin J-CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism. Sci Signal 2022; 15:eabm5011. [PMID: 35412849 DOI: 10.1126/scisignal.abm5011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Toll-like receptor (TLR) stimulation induces glycolysis and the production of mitochondrial reactive oxygen species (ROS), both of which are critical for inflammatory responses in macrophages. Here, we demonstrated that cyclin J, a TLR-inducible member of the cyclin family, reduced cytokine production in macrophages by coordinately controlling glycolysis and mitochondrial functions. Cyclin J interacted with cyclin-dependent kinases (CDKs), which increased the phosphorylation of a subset of CDK substrates, including the transcription factor FoxK1 and the GTPase Drp1. Cyclin J-dependent phosphorylation of FoxK1 decreased the transcription of glycolytic genes and Hif-1α activation, whereas hyperactivation of Drp1 by cyclin J-dependent phosphorylation promoted mitochondrial fragmentation and impaired the production of mitochondrial ROS. In mice, cyclin J in macrophages limited the growth of tumor xenografts and protected against LPS-induced shock but increased the susceptibility to bacterial infection. Collectively, our findings indicate that cyclin J-CDK signaling promotes antitumor immunity and the resolution of inflammation by opposing the metabolic changes that drive inflammatory responses in macrophages.
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Affiliation(s)
- Yee Kien Chong
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sarang Tartey
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,IGM Biosciences Inc., Mountain View, CA, USA
| | - Yuki Yoshikawa
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Songling Li
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ai Hirabayashi
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Guohao Liu
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Alexis Vandenbon
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | | | - Daron M Standley
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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5
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Akaki K, Ogata K, Yamauchi Y, Iwai N, Tse KM, Hia F, Mochizuki A, Ishihama Y, Mino T, Takeuchi O. IRAK1-dependent Regnase-1-14-3-3 complex formation controls Regnase-1-mediated mRNA decay. eLife 2021; 10:71966. [PMID: 34636324 PMCID: PMC8553338 DOI: 10.7554/elife.71966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/08/2021] [Indexed: 01/14/2023] Open
Abstract
Regnase-1 is an endoribonuclease crucial for controlling inflammation by degrading mRNAs encoding cytokines and inflammatory mediators in mammals. However, it is unclear how Regnase-1-mediated mRNA decay is controlled in interleukin (IL)-1β- or Toll-like receptor (TLR) ligand-stimulated cells. Here, by analyzing the Regnase-1 interactome, we found that IL-1β or TLR stimulus dynamically induced the formation of Regnase-1-β-transducin repeat-containing protein (βTRCP) complex. Importantly, we also uncovered a novel interaction between Regnase-1 and 14-3-3 in both mouse and human cells. In IL-1R/TLR-stimulated cells, the Regnase-1-14-3-3 interaction is mediated by IRAK1 through a previously uncharacterized C-terminal structural domain. Phosphorylation of Regnase-1 at S494 and S513 is critical for Regnase-1-14-3-3 interaction, while a different set of phosphorylation sites of Regnase-1 is known to be required for the recognition by βTRCP and proteasome-mediated degradation. We found that Regnase-1-14-3-3 and Regnase-1-βTRCP interactions are not sequential events. Rather, 14-3-3 protects Regnase-1 from βTRCP-mediated degradation. On the other hand, 14-3-3 abolishes Regnase-1-mediated mRNA decay by inhibiting Regnase-1-mRNA association. In addition, nuclear-cytoplasmic shuttling of Regnase-1 is abrogated by 14-3-3 interaction. Taken together, the results suggest that a novel inflammation-induced interaction of 14-3-3 with Regnase-1 stabilizes inflammatory mRNAs by sequestering Regnase-1 in the cytoplasm to prevent mRNA recognition.
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Affiliation(s)
- Kotaro Akaki
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kosuke Ogata
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yuhei Yamauchi
- Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Noriki Iwai
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ka Man Tse
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Mochizuki
- Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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6
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Hia F, Takeuchi O. The effects of codon bias and optimality on mRNA and protein regulation. Cell Mol Life Sci 2021; 78:1909-1928. [PMID: 33128106 PMCID: PMC11072601 DOI: 10.1007/s00018-020-03685-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022]
Abstract
The central dogma of molecular biology entails that genetic information is transferred from nucleic acid to proteins. Notwithstanding retro-transcribing genetic elements, DNA is transcribed to RNA which in turn is translated into proteins. Recent advancements have shown that each stage is regulated to control protein abundances for a variety of essential physiological processes. In this regard, mRNA regulation is essential in fine-tuning or calibrating protein abundances. In this review, we would like to discuss one of several mRNA-intrinsic features of mRNA regulation that has been gaining traction of recent-codon bias and optimality. Specifically, we address the effects of codon bias with regard to codon optimality in several biological processes centred on translation, such as mRNA stability and protein folding among others. Finally, we examine how different organisms or cell types, through this system, are able to coordinate physiological pathways to respond to a variety of stress or growth conditions.
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Affiliation(s)
- Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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7
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Mino T, Iwai N, Endo M, Inoue K, Akaki K, Hia F, Uehata T, Emura T, Hidaka K, Suzuki Y, Standley DM, Okada-Hatakeyama M, Ohno S, Sugiyama H, Yamashita A, Takeuchi O. Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs. Nucleic Acids Res 2019; 47:8838-8859. [PMID: 31329944 PMCID: PMC7145602 DOI: 10.1093/nar/gkz628] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 01/14/2023] Open
Abstract
Regnase-1-mediated mRNA decay (RMD), in which inflammatory mRNAs harboring specific stem–loop structures are degraded, is a critical part of proper immune homeostasis. Prior to initial translation, Regnase-1 associates with target stem–loops but does not carry out endoribonucleolytic cleavage. Single molecule imaging revealed that UPF1 is required to first unwind the stem–loops, thus licensing Regnase-1 to proceed with RNA degradation. Following translation, Regnase-1 physically associates with UPF1 using two distinct points of interaction: The Regnase-1 RNase domain binds to SMG1-phosphorylated residue T28 in UPF1; in addition, an intrinsically disordered segment in Regnase-1 binds to the UPF1 RecA domain, enhancing the helicase activity of UPF1. The SMG1-UPF1–Regnase-1 axis targets pioneer rounds of translation and is critical for rapid resolution of inflammation through restriction of the number of proteins translated by a given mRNA. Furthermore, small-molecule inhibition of SMG1 prevents RNA unwinding in dendritic cells, allowing post-transcriptional control of innate immune responses.
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Affiliation(s)
- Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Noriki Iwai
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kentaro Inoue
- Department of Computer Science and Systems Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Kotaro Akaki
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yutaka Suzuki
- Laboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Daron M Standley
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan
| | - Mariko Okada-Hatakeyama
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory of Cell Systems, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Shigeo Ohno
- Department of Molecular Biology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Akio Yamashita
- Department of Molecular Biology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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8
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Hia F, Yang SF, Shichino Y, Yoshinaga M, Murakawa Y, Vandenbon A, Fukao A, Fujiwara T, Landthaler M, Natsume T, Adachi S, Iwasaki S, Takeuchi O. Codon bias confers stability to human mRNAs. EMBO Rep 2019; 20:e48220. [PMID: 31482640 DOI: 10.15252/embr.201948220] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/08/2019] [Accepted: 08/19/2019] [Indexed: 11/09/2022] Open
Abstract
Codon bias has been implicated as one of the major factors contributing to mRNA stability in several model organisms. However, the molecular mechanisms of codon bias on mRNA stability remain unclear in humans. Here, we show that human cells possess a mechanism to modulate RNA stability through a unique codon bias. Bioinformatics analysis showed that codons could be clustered into two distinct groups-codons with G or C at the third base position (GC3) and codons with either A or T at the third base position (AT3): the former stabilizing while the latter destabilizing mRNA. Quantification of codon bias showed that increased GC3-content entails proportionately higher GC-content. Through bioinformatics, ribosome profiling, and in vitro analysis, we show that decoupling the effects of codon bias reveals two modes of mRNA regulation, one GC3- and one GC-content dependent. Employing an immunoprecipitation-based strategy, we identify ILF2 and ILF3 as RNA-binding proteins that differentially regulate global mRNA abundances based on codon bias. Our results demonstrate that codon bias is a two-pronged system that governs mRNA abundance.
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Affiliation(s)
- Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sheng Fan Yang
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Murakawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
| | - Alexis Vandenbon
- Laboratory of Infection and Prevention, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Akira Fukao
- Laboratory of Biochemistry, Department of Pharmacy, Kindai University, Higashiosaka City, Japan
| | - Toshinobu Fujiwara
- Laboratory of Biochemistry, Department of Pharmacy, Kindai University, Higashiosaka City, Japan
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine Berlin, Berlin Institute for Molecular Systems Biology, Berlin, Germany.,IRI Life Sciences, Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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9
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Cui X, Mino T, Yoshinaga M, Nakatsuka Y, Hia F, Yamasoba D, Tsujimura T, Tomonaga K, Suzuki Y, Uehata T, Takeuchi O. Regnase-1 and Roquin Nonredundantly Regulate Th1 Differentiation Causing Cardiac Inflammation and Fibrosis. J I 2017; 199:4066-4077. [DOI: 10.4049/jimmunol.1701211] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022]
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10
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Cai WM, Chionh YH, Hia F, Gu C, Kellner S, McBee ME, Ng CS, Pang YLJ, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. Methods Enzymol 2015; 560:29-71. [PMID: 26253965 DOI: 10.1016/bs.mie.2015.03.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications.
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Affiliation(s)
- Weiling Maggie Cai
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yok Hian Chionh
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chee Sheng Ng
- Singapore-MIT Alliance for Research and Technology, Singapore; School of Biological Sciences, Nanyang Technological Institute, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kok Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - I Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Thomas J Begley
- College of Nanoscale Engineering and Science, State University of New York, Albany, New York, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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11
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Hia F, Chionh YH, Pang YLJ, DeMott MS, McBee ME, Dedon PC. Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides. Nucleic Acids Res 2014; 43:e32. [PMID: 25539917 PMCID: PMC4357692 DOI: 10.1093/nar/gku1317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria.
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Affiliation(s)
- Fabian Hia
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Yok Hian Chionh
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore Department of Microbiology and Immunology Programme, National University of Singapore, 117456, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Megan E McBee
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Peter C Dedon
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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12
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Chionh YH, Ho CH, Pruksakorn D, Ramesh Babu I, Ng CS, Hia F, McBee ME, Su D, Pang YLJ, Gu C, Dong H, Prestwich EG, Shi PY, Preiser PR, Alonso S, Dedon PC. A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Res 2013; 41:e168. [PMID: 23907385 PMCID: PMC3783195 DOI: 10.1093/nar/gkt668] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.
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Affiliation(s)
- Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Applied Biological Science Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand, Division of Molecular Genetics & Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Immunology Programme, Life Science Institute, Centre for Life Science, Singapore 117456 and Novartis Institute for Tropical Disease, Singapore 138670
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13
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Dong H, Chang DC, Hua MHC, Lim SP, Chionh YH, Hia F, Lee YH, Kukkaro P, Lok SM, Dedon PC, Shi PY. 2'-O methylation of internal adenosine by flavivirus NS5 methyltransferase. PLoS Pathog 2012; 8:e1002642. [PMID: 22496660 PMCID: PMC3320599 DOI: 10.1371/journal.ppat.1002642] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Accepted: 02/27/2012] [Indexed: 01/20/2023] Open
Abstract
RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 2′-O methyltransferase activities that are required for the formation of 5′ type I cap (m7GpppAm) of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4) specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 2′-O-methyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N6-methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 2′-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 2′-O-methyladenosine. Importantly, genomic RNA purified from DENV virion contains 2′-O-methyladenosine. The 2′-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine) pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 2′-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 2′-O methylation of internal adenosine of viral RNA in vivo and host ribosomal RNAs in vitro. We report that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant proteins of NS5 and its N-terminal methyltransferase domain of West Nile virus and Dengue virus (DENV) specifically methylates polyA, but not polyG, polyC, or polyU. RNAs with internal adenosines substituted with 2′-O-methyladenosines are not active substrates for internal methylation, suggesting that the internal methylation occurs at the 2′-OH position of adenosine. Mass spectroscopic analysis confirmed that the internal methylation product is 2′-O-methyladenosine. Furthermore, the 2′-O-methyladenosine could also be detected in DENV genomic RNA. The 2′-O methylation of internal adenosine does not require specific RNA sequence context because the DENV methyltransferase can methylate RNAs spanning different regions of viral genome and host ribosomal RNAs at equal efficiencies. Mutagenesis analysis showed that K61-D146-K181-E217 motif of the DENV methyltransferase forms the active site of internal methylation activity; in addition, distinct residues on the surface of the enzyme are critical for the internal methylation activity. Functional analysis showed that internal methylation attenuated viral RNA translation and replication. Overall, our results demonstrate that flavivirus NS5 performs 2′-O methylation of internal adenosine of viral RNA in vivo and host ribosomal RNA in vitro. Such 2′-O-methyladenosine modification may modulate virus-host interaction.
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Affiliation(s)
- Hongping Dong
- Novartis Institute for Tropical Diseases, Singapore
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | | | - Maggie Ho Chia Hua
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | | | - Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | - Yie Hou Lee
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | | | | | - Peter C. Dedon
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Pei-Yong Shi
- Novartis Institute for Tropical Diseases, Singapore
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail:
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