1
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Yermalovich AV, Mohsenin Z, Cowdin M, Giotti B, Gupta A, Feng A, Golomb L, Wheeler DB, Xu K, Tsankov A, Cleaver O, Meyerson M. An essential role for Cmtr2 in mammalian embryonic development. Dev Biol 2024; 516:47-58. [PMID: 39094818 DOI: 10.1016/j.ydbio.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
CMTR2 is an mRNA cap methyltransferase with poorly understood physiological functions. It catalyzes 2'-O-ribose methylation of the second transcribed nucleotide of mRNAs, potentially serving to mark RNAs as "self" to evade the cellular innate immune response. Here we analyze the consequences of Cmtr2 deficiency in mice. We discover that constitutive deletion of Cmtr2 results in mouse embryos that die during mid-gestation, exhibiting defects in embryo size, placental malformation and yolk sac vascularization. Endothelial cell deletion of Cmtr2 in mice results in vascular and hematopoietic defects, and perinatal lethality. Detailed characterization of the constitutive Cmtr2 KO phenotype shows an activation of the p53 pathway and decreased proliferation, but no evidence of interferon pathway activation. In summary, our study reveals the essential roles of Cmtr2 in mammalian cells beyond its immunoregulatory function.
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Affiliation(s)
- Alena V Yermalovich
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Zarin Mohsenin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Mitzy Cowdin
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Akansha Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Alice Feng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Lior Golomb
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Douglas B Wheeler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Kelly Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Alexander Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ondine Cleaver
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA; Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Departments of Genetics and Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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2
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Lukoszek R, Inesta-Vaquera F, Brett NJM, Liang S, Hepburn LA, Hughes DJ, Pirillo C, Roberts EW, Cowling VH. CK2 phosphorylation of CMTR1 promotes RNA cap formation and influenza virus infection. Cell Rep 2024; 43:114405. [PMID: 38923463 PMCID: PMC11290353 DOI: 10.1016/j.celrep.2024.114405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/12/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The RNA cap methyltransferase CMTR1 methylates the first transcribed nucleotide of RNA polymerase II transcripts, impacting gene expression mechanisms, including during innate immune responses. Using mass spectrometry, we identify a multiply phosphorylated region of CMTR1 (phospho-patch [P-Patch]), which is a substrate for the kinase CK2 (casein kinase II). CMTR1 phosphorylation alters intramolecular interactions, increases recruitment to RNA polymerase II, and promotes RNA cap methylation. P-Patch phosphorylation occurs during the G1 phase of the cell cycle, recruiting CMTR1 to RNA polymerase II during a period of rapid transcription and RNA cap formation. CMTR1 phosphorylation is required for the expression of specific RNAs, including ribosomal protein gene transcripts, and promotes cell proliferation. CMTR1 phosphorylation is also required for interferon-stimulated gene expression. The cap-snatching virus, influenza A, utilizes host CMTR1 phosphorylation to produce the caps required for virus production and infection. We present an RNA cap methylation control mechanism whereby CK2 controls CMTR1, enhancing co-transcriptional capping.
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Affiliation(s)
| | - Francisco Inesta-Vaquera
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Department of Biochemistry and Molecular Biology and Genetics, School of Sciences, Universidad de Extremadura, Avenida de Elvas, s/n, 06006 Badajoz, Spain
| | - Natasha J M Brett
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Shang Liang
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lydia A Hepburn
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David J Hughes
- School of Biology, University of St Andrews, Biomedical Sciences Research Complex, St Andrews KY16 9ST, UK
| | - Chiara Pirillo
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Edward W Roberts
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Victoria H Cowling
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK.
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3
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Jiang J, Duan M, Wang Z, Lai Y, Zhang C, Duan C. RNA epigenetics in pulmonary diseases: Insights into methylation modification of lncRNAs in lung cancer. Biomed Pharmacother 2024; 175:116704. [PMID: 38749181 DOI: 10.1016/j.biopha.2024.116704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 06/03/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are pivotal controllers of gene expression through epigenetic mechanisms, Methylation, a prominent area of study in epigenetics, significantly impacts cellular processes. Various RNA base methylations, including m6A, m5C, m1A, and 2'-O-methylation, profoundly influence lncRNA folding, interactions, and stability, thereby shaping their functionality. LncRNAs and methylation significantly contribute to tumor development, especially in lung cancer. Their roles encompass cell differentiation, proliferation, the generation of cancer stem cells, and modulation of immune responses. Recent studies have suggested that dysregulation of lncRNA methylation can contribute to lung cancer development. Furthermore, methylation modifications of lncRNAs hold potential for clinical application in lung cancer. Dysregulated lncRNA methylation can promote lung cancer progression and may offer insights into potential biomarker or therapeutic target. This review summarizes the current knowledge of lncRNA methylation in lung cancer and its implications for RNA epigenetics and pulmonary diseases.
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Affiliation(s)
- Junjie Jiang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Minghao Duan
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, 412017, Hunan, People's Republic of China
| | - Zheng Wang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Yuwei Lai
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China.
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4
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Li Y, Wang Q, Xu Y, Li Z. Structures of co-transcriptional RNA capping enzymes on paused transcription complex. Nat Commun 2024; 15:4622. [PMID: 38816438 PMCID: PMC11139899 DOI: 10.1038/s41467-024-48963-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
The 5'-end capping of nascent pre-mRNA represents the initial step in RNA processing, with evidence demonstrating that guanosine addition and 2'-O-ribose methylation occur in tandem with early steps of transcription by RNA polymerase II, especially at the pausing stage. Here, we determine the cryo-EM structures of the paused elongation complex in complex with RNGTT, as well as the paused elongation complex in complex with RNGTT and CMTR1. Our findings show the simultaneous presence of RNGTT and the NELF complex bound to RNA polymerase II. The NELF complex exhibits two conformations, one of which shows a notable rearrangement of NELF-A/D compared to that of the paused elongation complex. Moreover, CMTR1 aligns adjacent to RNGTT on the RNA polymerase II stalk. Our structures indicate that RNGTT and CMTR1 directly bind the paused elongation complex, illuminating the mechanism by which 5'-end capping of pre-mRNA during transcriptional pausing.
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Affiliation(s)
- Yan Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Ze Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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5
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Decombe A, El-Kazzi P, Nisole S, Decroly É. [How do 2'-O-methylations within Human Immunodeficiency Virus type 1 (HIV-1) genome regulate its replication?]. Med Sci (Paris) 2024; 40:421-427. [PMID: 38819277 DOI: 10.1051/medsci/2024046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Abstract
The genomic RNA of HIV-1 is modified by epitranscriptomic modifications, including 2'-O-methylations, which are found on 17 internal positions. These methylations are added by the cellular methyltransferase FTSJ3, and have pro-viral effects, since they shield the viral genome from the detection by the innate immune sensor MDA5. In turn, the production of interferons by infected cells is reduced, limiting the expression of interferon-stimulated genes (ISGs) with antiviral activities. Moreover, 2'-O-methylations protect the HIV-1 genome from its degradation by ISG20, an interferon-induced exonuclease. Conversely, these methylations also exhibit antiviral effects, as they impede reverse-transcription in vitro or in quiescent cells, which are known to contain low nucleotide concentrations. Altogether, these observations suggest a balance between the proviral effect of 2'-O-methylations, related to the protection of the viral genome from detection by MDA5 and degradation by ISG20, and the antiviral effect, associated with the negative impact of 2'-O-methylations on the viral replication. These findings pave the way for further optimization of therapeutic RNA, by selective methylation of specific nucleotides.
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Affiliation(s)
- Alice Decombe
- AFMB (Architecture et fonction des macromolécules biologiques), UMR 7257 - CNRS / Université Aix-Marseille, Marseille, France
| | - Priscila El-Kazzi
- AFMB (Architecture et fonction des macromolécules biologiques), UMR 7257 - CNRS / Université Aix-Marseille, Marseille, France
| | - Sébastien Nisole
- AFMB (Architecture et fonction des macromolécules biologiques), UMR 7257 - CNRS / Université Aix-Marseille, Marseille, France
| | - Étienne Decroly
- AFMB (Architecture et fonction des macromolécules biologiques), UMR 7257 - CNRS / Université Aix-Marseille, Marseille, France
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6
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Warminski M, Trepkowska E, Smietanski M, Sikorski PJ, Baranowski MR, Bednarczyk M, Kedzierska H, Majewski B, Mamot A, Papiernik D, Popielec A, Serwa RA, Shimanski BA, Sklepkiewicz P, Sklucka M, Sokolowska O, Spiewla T, Toczydlowska-Socha D, Warminska Z, Wolosewicz K, Zuberek J, Mugridge JS, Nowis D, Golab J, Jemielity J, Kowalska J. Trinucleotide mRNA Cap Analogue N6-Benzylated at the Site of Posttranscriptional m6A m Mark Facilitates mRNA Purification and Confers Superior Translational Properties In Vitro and In Vivo. J Am Chem Soc 2024; 146:8149-8163. [PMID: 38442005 PMCID: PMC10979456 DOI: 10.1021/jacs.3c12629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
Eukaryotic mRNAs undergo cotranscriptional 5'-end modification with a 7-methylguanosine cap. In higher eukaryotes, the cap carries additional methylations, such as m6Am─a common epitranscriptomic mark unique to the mRNA 5'-end. This modification is regulated by the Pcif1 methyltransferase and the FTO demethylase, but its biological function is still unknown. Here, we designed and synthesized a trinucleotide FTO-resistant N6-benzyl analogue of the m6Am-cap-m7GpppBn6AmpG (termed AvantCap) and incorporated it into mRNA using T7 polymerase. mRNAs carrying Bn6Am showed several advantages over typical capped transcripts. The Bn6Am moiety was shown to act as a reversed-phase high-performance liquid chromatography (RP-HPLC) purification handle, allowing the separation of capped and uncapped RNA species, and to produce transcripts with lower dsRNA content than reference caps. In some cultured cells, Bn6Am mRNAs provided higher protein yields than mRNAs carrying Am or m6Am, although the effect was cell-line-dependent. m7GpppBn6AmpG-capped mRNAs encoding reporter proteins administered intravenously to mice provided up to 6-fold higher protein outputs than reference mRNAs, while mRNAs encoding tumor antigens showed superior activity in therapeutic settings as anticancer vaccines. The biochemical characterization suggests several phenomena potentially underlying the biological properties of AvantCap: (i) reduced propensity for unspecific interactions, (ii) involvement in alternative translation initiation, and (iii) subtle differences in mRNA impurity profiles or a combination of these effects. AvantCapped-mRNAs bearing the Bn6Am may pave the way for more potent mRNA-based vaccines and therapeutics and serve as molecular tools to unravel the role of m6Am in mRNA.
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Affiliation(s)
- Marcin Warminski
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Edyta Trepkowska
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | | | - Pawel J. Sikorski
- Centre
of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
- Laboratory
of Epitranscriptomics, Department of Environmental Microbiology and
Biotechnology, Institute of Microbiology, Faculty of Biology, Biological
and Chemical Research Centre, University
of Warsaw, 02-089 Warsaw, Poland
| | | | - Marcelina Bednarczyk
- Centre
of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Hanna Kedzierska
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Bartosz Majewski
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Adam Mamot
- Centre
of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Diana Papiernik
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Agnieszka Popielec
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Remigiusz A. Serwa
- Proteomics
Core Facility, IMol Polish Academy of Sciences, 02-247 Warsaw, Poland
| | - Brittany A. Shimanski
- Department
of Chemistry & Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Piotr Sklepkiewicz
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Marta Sklucka
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Olga Sokolowska
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Tomasz Spiewla
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | | | - Zofia Warminska
- Centre
of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Karol Wolosewicz
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Zuberek
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Jeffrey S. Mugridge
- Department
of Chemistry & Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Dominika Nowis
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
- Laboratory
of Experimental Medicine, Faculty of Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Jakub Golab
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
- Laboratory
of Experimental Medicine, Faculty of Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Jacek Jemielity
- Centre
of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Kowalska
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Explorna
Therapeutics sp. z o.o. Zwirki i Wigury 93, 02-089 Warsaw, Poland
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7
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Pilotto S, Sýkora M, Cackett G, Dulson C, Werner F. Structure of the recombinant RNA polymerase from African Swine Fever Virus. Nat Commun 2024; 15:1606. [PMID: 38383525 PMCID: PMC10881513 DOI: 10.1038/s41467-024-45842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
African Swine Fever Virus is a Nucleo-Cytoplasmic Large DNA Virus that causes an incurable haemorrhagic fever in pigs with a high impact on global food security. ASFV replicates in the cytoplasm of the infected cell and encodes its own transcription machinery that is independent of cellular factors, however, not much is known about how this system works at a molecular level. Here, we present methods to produce recombinant ASFV RNA polymerase, functional assays to screen for inhibitors, and high-resolution cryo-electron microscopy structures of the ASFV RNAP in different conformational states. The ASFV RNAP bears a striking resemblance to RNAPII with bona fide homologues of nine of its twelve subunits. Key differences include the fusion of the ASFV assembly platform subunits RPB3 and RPB11, and an unusual C-terminal domain of the stalk subunit vRPB7 that is related to the eukaryotic mRNA cap 2´-O-methyltransferase 1. Despite the high degree of structural conservation with cellular RNA polymerases, the ASFV RNAP is resistant to the inhibitors rifampicin and alpha-amanitin. The cryo-EM structures and fully recombinant RNAP system together provide an important tool for the design, development, and screening of antiviral drugs in a low biosafety containment environment.
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Affiliation(s)
- Simona Pilotto
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Michal Sýkora
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Gwenny Cackett
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Christopher Dulson
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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8
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Monziani A, Ulitsky I. Noncoding snoRNA host genes are a distinct subclass of long noncoding RNAs. Trends Genet 2023; 39:908-923. [PMID: 37783604 DOI: 10.1016/j.tig.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Mammalian genomes are pervasively transcribed into different noncoding (nc)RNA classes, each one with its own hallmarks and exceptions. Some of them are nested into each other, such as host genes for small nucleolar RNAs (snoRNAs), which were long believed to simply act as molecular containers strictly facilitating snoRNA biogenesis. However, recent findings show that noncoding snoRNA host genes (ncSNHGs) display features different from those of 'regular' long ncRNAs (lncRNAs) and, more importantly, they can exert independent and unrelated functions to those of the encoded snoRNAs. Here, we review and summarize past and recent evidence that ncSNHGs form a defined subclass among the plethora of lncRNAs, and discuss future research that can further elucidate their biological relevance.
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Affiliation(s)
- Alan Monziani
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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9
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Chan SH, Molé CN, Nye D, Mitchell L, Dai N, Buss J, Kneller DW, Whipple JM, Robb GB. Biochemical characterization of mRNA capping enzyme from Faustovirus. RNA (NEW YORK, N.Y.) 2023; 29:1803-1817. [PMID: 37625853 PMCID: PMC10578482 DOI: 10.1261/rna.079738.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
The mammalian mRNA 5' cap structures play important roles in cellular processes such as nuclear export, efficient translation, and evading cellular innate immune surveillance and regulating 5'-mediated mRNA turnover. Hence, installation of the proper 5' cap is crucial in therapeutic applications of synthetic mRNA. The core 5' cap structure, Cap-0, is generated by three sequential enzymatic activities: RNA 5' triphosphatase, RNA guanylyltransferase, and cap N7-guanine methyltransferase. Vaccinia virus RNA capping enzyme (VCE) is a heterodimeric enzyme that has been widely used in synthetic mRNA research and manufacturing. The large subunit of VCE D1R exhibits a modular structure where each of the three structural domains possesses one of the three enzyme activities, whereas the small subunit D12L is required to activate the N7-guanine methyltransferase activity. Here, we report the characterization of a single-subunit RNA capping enzyme from an amoeba giant virus. Faustovirus RNA capping enzyme (FCE) exhibits a modular array of catalytic domains in common with VCE and is highly efficient in generating the Cap-0 structure without an activation subunit. Phylogenetic analysis suggests that FCE and VCE are descended from a common ancestral capping enzyme. We found that compared to VCE, FCE exhibits higher specific activity, higher activity toward RNA containing secondary structures and a free 5' end, and a broader temperature range, properties favorable for synthetic mRNA manufacturing workflows.
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Affiliation(s)
- S Hong Chan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Christa N Molé
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Dillon Nye
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Lili Mitchell
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Jackson Buss
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | | | | | - G Brett Robb
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
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10
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Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P. Structural insights into human co-transcriptional capping. Mol Cell 2023:S1097-2765(23)00424-0. [PMID: 37369200 DOI: 10.1016/j.molcel.2023.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/22/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryoelectron microscopy (cryo-EM) structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end. Addition of a GMP moiety can occur when the RNA is ∼22 nt long, sufficient to reach the active site of the guanylyltransferase. For subsequent cap(1) methylation, the methyltransferase CMTR1 binds the Pol II stalk and can receive RNA after it is grown to ∼29 nt in length. The observed rearrangements of capping factors on the Pol II surface may be triggered by the completion of catalytic reaction steps and are accommodated by domain movements in the elongation factor DRB sensitivity-inducing factor (DSIF).
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Affiliation(s)
- Gaurika Garg
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lucas Farnung
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Juliane Schwarz
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Andreas Linden
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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11
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Liang S, Almohammed R, Cowling VH. The RNA cap methyltransferases RNMT and CMTR1 co-ordinate gene expression during neural differentiation. Biochem Soc Trans 2023:233029. [PMID: 37145036 DOI: 10.1042/bst20221154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 04/03/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Regulation of RNA cap formation has potent impacts on gene regulation, controlling which transcripts are expressed, processed and translated into protein. Recently, the RNA cap methyltransferases RNA guanine-7 methyltransferase (RNMT) and cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 (CMTR1) have been found to be independently regulated during embryonic stem (ES) cell differentiation controlling the expression of overlapping and distinct protein families. During neural differentiation, RNMT is repressed and CMTR1 is up-regulated. RNMT promotes expression of the pluripotency-associated gene products; repression of the RNMT complex (RNMT-RAM) is required for repression of these RNAs and proteins during differentiation. The predominant RNA targets of CMTR1 encode the histones and ribosomal proteins (RPs). CMTR1 up-regulation is required to maintain the expression of histones and RPs during differentiation and to maintain DNA replication, RNA translation and cell proliferation. Thus the co-ordinate regulation of RNMT and CMTR1 is required for different aspects of ES cell differentiation. In this review, we discuss the mechanisms by which RNMT and CMTR1 are independently regulated during ES cell differentiation and explore how this influences the co-ordinated gene regulation required of emerging cell lineages.
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Affiliation(s)
- Shang Liang
- Cancer Research UK Beatson Institute, Glasgow, U.K
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, U.K
| | - Rajaei Almohammed
- Cancer Research UK Beatson Institute, Glasgow, U.K
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, U.K
| | - Victoria H Cowling
- Cancer Research UK Beatson Institute, Glasgow, U.K
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, U.K
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12
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Decombe A, El Kazzi P, Decroly E. Interplay of RNA 2'-O-methylations with viral replication. Curr Opin Virol 2023; 59:101302. [PMID: 36764118 DOI: 10.1016/j.coviro.2023.101302] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 02/11/2023]
Abstract
Viral RNAs (vRNAs) are decorated by post-transcriptional modifications, including methylation of nucleotides. Methylations regulate biological functions linked to the sequence, structure, and protein interactome of RNA. Several RNA viruses were found to harbor 2'-O-methylations, affecting the ribose moiety of RNA. This mark was initially shown to target the first and second nucleotides of the 5'-end cap structure of mRNA. More recently, nucleotides within vRNA were also reported to carry 2'-O-methylations. The consequences of such methylations are still puzzling since they were associated with both proviral and antiviral effects. Here, we focus on the mechanisms governing vRNA 2'-O-methylation and we explore the possible roles of this epitranscriptomic modification for viral replication.
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Affiliation(s)
- Alice Decombe
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Priscila El Kazzi
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France.
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13
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Despic V, Jaffrey SR. mRNA ageing shapes the Cap2 methylome in mammalian mRNA. Nature 2023; 614:358-366. [PMID: 36725932 PMCID: PMC9891201 DOI: 10.1038/s41586-022-05668-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 12/16/2022] [Indexed: 02/03/2023]
Abstract
The mRNA cap structure is a major site of dynamic mRNA methylation. mRNA caps exist in either the Cap1 or Cap2 form, depending on the presence of 2'-O-methylation on the first transcribed nucleotide or both the first and second transcribed nucleotides, respectively1,2. However, the identity of Cap2-containing mRNAs and the function of Cap2 are unclear. Here we describe CLAM-Cap-seq, a method for transcriptome-wide mapping and quantification of Cap2. We find that unlike other epitranscriptomic modifications, Cap2 can occur on all mRNAs. Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol. As a result, Cap2 is enriched on long-lived mRNAs. Large increases in the abundance of Cap1 leads to activation of RIG-I, especially in conditions in which expression of RIG-I is increased. The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind to and activate RIG-I. The slow methylation rate of Cap2 allows Cap2 to accumulate on host mRNAs, yet ensures that low levels of Cap2 occur on newly expressed viral RNAs. Overall, these results reveal an immunostimulatory role for Cap1, and that Cap2 functions to reduce activation of the innate immune response.
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Affiliation(s)
- Vladimir Despic
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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14
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Dix TC, Haussmann IU, Brivio S, Nallasivan MP, HadzHiev Y, Müller F, Müller B, Pettitt J, Soller M. CMTr mediated 2'- O-ribose methylation status of cap-adjacent nucleotides across animals. RNA (NEW YORK, N.Y.) 2022; 28:1377-1390. [PMID: 35970556 PMCID: PMC9479742 DOI: 10.1261/rna.079317.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Cap methyltransferases (CMTrs) O methylate the 2' position of the ribose (cOMe) of cap-adjacent nucleotides of animal, protist, and viral mRNAs. Animals generally have two CMTrs, whereas trypanosomes have three, and many viruses encode one in their genome. In the splice leader of mRNAs in trypanosomes, the first four nucleotides contain cOMe, but little is known about the status of cOMe in animals. Here, we show that cOMe is prominently present on the first two cap-adjacent nucleotides with species- and tissue-specific variations in Caenorhabditis elegans, honeybees, zebrafish, mouse, and human cell lines. In contrast, Drosophila contains cOMe primarily on the first cap-adjacent nucleotide. De novo RoseTTA modeling of CMTrs reveals close similarities of the overall structure and near identity for the catalytic tetrad, and for cap and cofactor binding for human, Drosophila and C. elegans CMTrs. Although viral CMTrs maintain the overall structure and catalytic tetrad, they have diverged in cap and cofactor binding. Consistent with the structural similarity, both CMTrs from Drosophila and humans methylate the first cap-adjacent nucleotide of an AGU consensus start. Because the second nucleotide is also methylated upon heat stress in Drosophila, these findings argue for regulated cOMe important for gene expression regulation.
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Affiliation(s)
- Thomas C Dix
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Irmgard U Haussmann
- Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City University, Birmingham, B15 3TN, United Kingdom
| | - Sarah Brivio
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Mohannakarthik P Nallasivan
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Yavor HadzHiev
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Ferenc Müller
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Berndt Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Jonathan Pettitt
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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15
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Wang M, Zhao Y, Liu J, Li T. SARS-CoV-2 modulation of RIG-I-MAVS signaling: Potential mechanisms of impairment on host antiviral immunity and therapeutic approaches. MEDCOMM - FUTURE MEDICINE 2022; 1:e29. [PMID: 37521851 PMCID: PMC9878249 DOI: 10.1002/mef2.29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 05/27/2023]
Abstract
The coronavirus disease 2019 (COVID-19) is a global infectious disease aroused by RNA virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients may suffer from severe respiratory failure or even die, posing a huge challenge to global public health. Retinoic acid-inducible gene I (RIG-I) is one of the major pattern recognition receptors, function to recognize RNA viruses and mediate the innate immune response. RIG-1 and melanoma differentiation-associated gene 5 contain an N-terminal caspase recruitment domain that is activated upon detection of viral RNA in the cytoplasm of virus-infected cells. Activated RIG-I and mitochondrial antiviral signaling (MAVS) protein trigger a series of corresponding immune responses such as the production of type I interferon against viral infection. In this review, we are summarizing the role of the structural, nonstructural, and accessory proteins from SARS-CoV-2 on the RIG-I-MAVS pathway, and exploring the potential mechanism how SARS-CoV-2 could evade the host antiviral response. We then proposed that modulation of the RIG-I-MAVS signaling pathway might be a novel and effective therapeutic strategy to against COVID-19 as well as the constantly mutating coronavirus.
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Affiliation(s)
- Mingming Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and HealthMacau University of Science and TechnologyMacauChina
| | - Yue Zhao
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and HealthMacau University of Science and TechnologyMacauChina
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Department of Clinical Immunology, Institute of Clinical Laboratory MedicineGuangdong Medical UniversityDongguanChina
| | - Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and HealthMacau University of Science and TechnologyMacauChina
| | - Ting Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and HealthMacau University of Science and TechnologyMacauChina
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16
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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17
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Tong J, Zhang W, Chen Y, Yuan Q, Qin NN, Qu G. The Emerging Role of RNA Modifications in the Regulation of Antiviral Innate Immunity. Front Microbiol 2022; 13:845625. [PMID: 35185855 PMCID: PMC8851159 DOI: 10.3389/fmicb.2022.845625] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Posttranscriptional modifications have been implicated in regulation of nearly all biological aspects of cellular RNAs, from stability, translation, splicing, nuclear export to localization. Chemical modifications also have been revealed for virus derived RNAs several decades before, along with the potential of their regulatory roles in virus infection. Due to the dynamic changes of RNA modifications during virus infection, illustrating the mechanisms of RNA epigenetic regulations remains a challenge. Nevertheless, many studies have indicated that these RNA epigenetic marks may directly regulate virus infection through antiviral innate immune responses. The present review summarizes the impacts of important epigenetic marks on viral RNAs, including N6-methyladenosine (m6A), 5-methylcytidine (m5C), 2ʹ-O-methylation (2ʹ-O-Methyl), and a few uncanonical nucleotides (A-to-I editing, pseudouridine), on antiviral innate immunity and relevant signaling pathways, while highlighting the significance of antiviral innate immune responses during virus infection.
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Affiliation(s)
- Jie Tong
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yuran Chen
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Qiaoling Yuan
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Ning-Ning Qin
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Guosheng Qu
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
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18
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Jiang Y, Liu L, Manning M, Bonahoom M, Lotvola A, Yang Z, Yang ZQ. Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus. J Biomol Struct Dyn 2022; 40:1331-1346. [PMID: 33016237 PMCID: PMC7544923 DOI: 10.1080/07391102.2020.1828172] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/12/2020] [Indexed: 12/14/2022]
Abstract
SARS-CoV-2, an emerging coronavirus, has spread rapidly around the world, resulting in over ten million cases and more than half a million deaths as of July 1, 2020. Effective treatments and vaccines for SARS-CoV-2 infection do not currently exist. Previous studies demonstrated that nonstructural protein 16 (nsp16) of coronavirus is an S-adenosyl methionine (SAM)-dependent 2'-O-methyltransferase (2'-O-MTase) that has an important role in viral replication and prevents recognition by the host innate immune system. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2'-O-MTase of SARS-CoV-2. Comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs defined the key residues for nsp16 2-O'-MTase functions. Virtual screening and docking analysis ranked the potential inhibitors of nsp16 from more than 4,500 clinically investigated and approved drugs. Furthermore, molecular dynamics simulations were carried out on eight top candidates, including Hesperidin, Rimegepant, Gs-9667, and Sonedenoson, to calculate various structural parameters and understand the dynamic behavior of the drug-protein complexes. Our studies provided the foundation to further test and repurpose these candidate drugs experimentally and/or clinically for COVID-19 treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuanyuan Jiang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Lanxin Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Morenci Manning
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Madison Bonahoom
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Aaron Lotvola
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Zhe Yang
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
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19
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Liang S, Silva JC, Suska O, Lukoszek R, Almohammed R, Cowling V. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2905-2922. [PMID: 35212377 PMCID: PMC8934662 DOI: 10.1093/nar/gkac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 01/09/2022] [Accepted: 02/09/2022] [Indexed: 11/29/2022] Open
Abstract
CMTR1 (cap methyltransferase 1) catalyses methylation of the first transcribed nucleotide of RNAPII transcripts (N1 2′-O-Me), creating part of the mammalian RNA cap structure. In addition to marking RNA as self, N1 2′-O-Me has ill-defined roles in RNA expression and translation. Here, we investigated the gene specificity of CMTR1 and its impact on RNA expression in embryonic stem cells. Using chromatin immunoprecipitation, CMTR1 was found to bind to transcription start sites (TSS) correlating with RNAPII levels, predominantly binding at histone genes and ribosomal protein (RP) genes. Repression of CMTR1 expression resulted in repression of RNAPII binding at the TSS and repression of RNA expression, particularly of histone and RP genes. In correlation with regulation of histones and RP genes, CMTR1 repression resulted in repression of translation and induction of DNA replication stress and damage. Indicating a direct role for CMTR1 in transcription, addition of recombinant CMTR1 to purified nuclei increased transcription of the histone and RP genes. CMTR1 was found to be upregulated during neural differentiation and there was an enhanced requirement for CMTR1 for gene expression and proliferation during this process. We highlight the distinct roles of the cap methyltransferases RNMT and CMTR1 in target gene expression and differentiation.
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Affiliation(s)
- Shang Liang
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Joana C Silva
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Olga Suska
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Radoslaw Lukoszek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Rajaei Almohammed
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Victoria H Cowling
- To whom correspondence should be addressed. Tel: +44 1382 386997; Fax: +44 1382 386997;
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20
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Staller E, Barclay WS. Host Cell Factors That Interact with Influenza Virus Ribonucleoproteins. Cold Spring Harb Perspect Med 2021; 11:a038307. [PMID: 32988980 PMCID: PMC8559542 DOI: 10.1101/cshperspect.a038307] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Influenza viruses hijack host cell factors at each stage of the viral life cycle. After host cell entry and endosomal escape, the influenza viral ribonucleoproteins (vRNPs) are released into the cytoplasm where the classical cellular nuclear import pathway is usurped for nuclear translocation of the vRNPs. Transcription takes place inside the nucleus at active host transcription sites, and cellular mRNA export pathways are subverted for export of viral mRNAs. Newly synthesized RNP components cycle back into the nucleus using various cellular nuclear import pathways and host-encoded chaperones. Replication of the negative-sense viral RNA (vRNA) into complementary RNA (cRNA) and back into vRNA requires complex interplay between viral and host factors. Progeny vRNPs assemble at the host chromatin and subsequently exit from the nucleus-processes orchestrated by sets of host and viral proteins. Finally, several host pathways appear to play a role in vRNP trafficking from the nuclear envelope to the plasma membrane for egress.
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Affiliation(s)
- Ecco Staller
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
| | - Wendy S Barclay
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
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21
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Thompson MG, Sacco MT, Horner SM. How RNA modifications regulate the antiviral response. Immunol Rev 2021; 304:169-180. [PMID: 34405413 PMCID: PMC8616813 DOI: 10.1111/imr.13020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 12/25/2022]
Abstract
Induction of the antiviral innate immune response is highly regulated at the RNA level, particularly by RNA modifications. Recent discoveries have revealed how RNA modifications play key roles in cellular surveillance of nucleic acids and in controlling gene expression in response to viral infection. These modifications have emerged as being essential for a functional antiviral response and maintaining cellular homeostasis. In this review, we will highlight these and other discoveries that describe how the antiviral response is controlled by modifications to both viral and cellular RNA, focusing on how mRNA cap modifications, N6-methyladenosine, and RNA editing all contribute to coordinating an efficient response that properly controls viral infection.
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Affiliation(s)
- Matthew G Thompson
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Matthew T Sacco
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Stacy M Horner
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
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22
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O’Donoghue SI, Schafferhans A, Sikta N, Stolte C, Kaur S, Ho BK, Anderson S, Procter JB, Dallago C, Bordin N, Adcock M, Rost B. SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms. Mol Syst Biol 2021; 17:e10079. [PMID: 34519429 PMCID: PMC8438690 DOI: 10.15252/msb.202010079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/18/2023] Open
Abstract
We modeled 3D structures of all SARS-CoV-2 proteins, generating 2,060 models that span 69% of the viral proteome and provide details not available elsewhere. We found that ˜6% of the proteome mimicked human proteins, while ˜7% was implicated in hijacking mechanisms that reverse post-translational modifications, block host translation, and disable host defenses; a further ˜29% self-assembled into heteromeric states that provided insight into how the viral replication and translation complex forms. To make these 3D models more accessible, we devised a structural coverage map, a novel visualization method to show what is-and is not-known about the 3D structure of the viral proteome. We integrated the coverage map into an accompanying online resource (https://aquaria.ws/covid) that can be used to find and explore models corresponding to the 79 structural states identified in this work. The resulting Aquaria-COVID resource helps scientists use emerging structural data to understand the mechanisms underlying coronavirus infection and draws attention to the 31% of the viral proteome that remains structurally unknown or dark.
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MESH Headings
- Amino Acid Transport Systems, Neutral/chemistry
- Amino Acid Transport Systems, Neutral/genetics
- Amino Acid Transport Systems, Neutral/metabolism
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Binding Sites
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/virology
- Computational Biology/methods
- Coronavirus Envelope Proteins/chemistry
- Coronavirus Envelope Proteins/genetics
- Coronavirus Envelope Proteins/metabolism
- Coronavirus Nucleocapsid Proteins/chemistry
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Mitochondrial Membrane Transport Proteins/chemistry
- Mitochondrial Membrane Transport Proteins/genetics
- Mitochondrial Membrane Transport Proteins/metabolism
- Mitochondrial Precursor Protein Import Complex Proteins
- Models, Molecular
- Molecular Mimicry
- Neuropilin-1/chemistry
- Neuropilin-1/genetics
- Neuropilin-1/metabolism
- Phosphoproteins/chemistry
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Interaction Mapping/methods
- Protein Multimerization
- Protein Processing, Post-Translational
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Matrix Proteins/chemistry
- Viral Matrix Proteins/genetics
- Viral Matrix Proteins/metabolism
- Viroporin Proteins/chemistry
- Viroporin Proteins/genetics
- Viroporin Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Seán I O’Donoghue
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- CSIRO Data61CanberraACTAustralia
- School of Biotechnology and Biomolecular Sciences (UNSW)KensingtonNSWAustralia
| | - Andrea Schafferhans
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- Department of Bioengineering SciencesWeihenstephan‐Tr. University of Applied SciencesFreisingGermany
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
| | - Neblina Sikta
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | | | - Sandeep Kaur
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Biotechnology and Biomolecular Sciences (UNSW)KensingtonNSWAustralia
| | - Bosco K Ho
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | | | | | - Christian Dallago
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
| | - Nicola Bordin
- Institute of Structural and Molecular BiologyUniversity College LondonLondonUK
| | | | - Burkhard Rost
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
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23
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Kasprzyk R, Jemielity J. Enzymatic Assays to Explore Viral mRNA Capping Machinery. Chembiochem 2021; 22:3236-3253. [PMID: 34291555 PMCID: PMC8426721 DOI: 10.1002/cbic.202100291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/21/2021] [Indexed: 12/25/2022]
Abstract
In eukaryotes, mRNA is modified by the addition of the 7-methylguanosine (m7 G) 5' cap to protect mRNA from premature degradation, thereby enhancing translation and enabling differentiation between self (endogenous) and non-self RNAs (e. g., viral ones). Viruses often develop their own mRNA capping pathways to augment the expression of their proteins and escape host innate immune response. Insights into this capping system may provide new ideas for therapeutic interventions and facilitate drug discovery, e. g., against viruses that cause pandemic outbreaks, such as beta-coronaviruses SARS-CoV (2002), MARS-CoV (2012), and the most recent SARS-CoV-2. Thus, proper methods for the screening of large compound libraries are required to identify lead structures that could serve as a basis for rational antiviral drug design. This review summarizes the methods that allow the monitoring of the activity and inhibition of enzymes involved in mRNA capping.
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Affiliation(s)
- Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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24
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Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophys J 2021; 120:2880-2889. [PMID: 33794150 PMCID: PMC8007187 DOI: 10.1016/j.bpj.2021.03.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/17/2021] [Accepted: 03/25/2021] [Indexed: 01/12/2023] Open
Abstract
Coronaviruses have caused multiple epidemics in the past two decades, in addition to the current COVID-19 pandemic that is severely damaging global health and the economy. Coronaviruses employ between 20 and 30 proteins to carry out their viral replication cycle, including infection, immune evasion, and replication. Among these, nonstructural protein 16 (Nsp16), a 2'-O-methyltransferase, plays an essential role in immune evasion. Nsp16 achieves this by mimicking its human homolog, CMTr1, which methylates mRNA to enhance translation efficiency and distinguish self from other. Unlike human CMTr1, Nsp16 requires a binding partner, Nsp10, to activate its enzymatic activity. The requirement of this binding partner presents two questions that we investigate in this manuscript. First, how does Nsp10 activate Nsp16? Although experimentally derived structures of the active Nsp16/Nsp10 complex exist, structures of inactive, monomeric Nsp16 have yet to be solved. Therefore, it is unclear how Nsp10 activates Nsp16. Using over 1 ms of molecular dynamics simulations of both Nsp16 and its complex with Nsp10, we investigate how the presence of Nsp10 shifts Nsp16's conformational ensemble to activate it. Second, guided by this activation mechanism and Markov state models, we investigate whether Nsp16 adopts inactive structures with cryptic pockets that, if targeted with a small molecule, could inhibit Nsp16 by stabilizing its inactive state. After identifying such a pocket in SARS-CoV2 Nsp16, we show that this cryptic pocket also opens in SARS-CoV1 and MERS but not in human CMTr1. Therefore, it may be possible to develop pan-coronavirus antivirals that target this cryptic pocket.
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Affiliation(s)
- Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri
| | - Michael D Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri
| | - Borna Novak
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri; Medical Scientist Training Program, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Jonathan H Borowsky
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri.
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25
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Minasov G, Rosas-Lemus M, Shuvalova L, Inniss NL, Brunzelle JS, Daczkowski CM, Hoover P, Mesecar AD, Satchell KJF. Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O-methyl transfer by SARS-CoV-2 nsp16. Sci Signal 2021; 14:scisignal.abh2071. [PMID: 34131072 PMCID: PMC8432954 DOI: 10.1126/scisignal.abh2071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Virally encoded 2′-O-methyltransferases catalyze the last step in the capping of viral RNAs, which protects the RNAs from degradation and prevents them from triggering host defenses. Minasov et al. report structures of the SARS-CoV-2 methyltransferase, a heterodimeric complex of the enzyme nsp16 and its coactivator nsp10, in complex with a short, capped RNA (instead of the RNA cap analogs used to generate previous structures), the methyl donor SAM, and divalent metal cations. The metal ions and a four-residue insert of nsp16 were important for precisely aligning the RNA substrate in the active site for efficient catalysis. This insert is present in coronavirus but not in mammalian methyltransferases, suggesting this site as a potential target for the design of coronavirus-specific methyltransferase inhibitors. Capping of viral messenger RNAs is essential for efficient translation, for virus replication, and for preventing detection by the host cell innate response system. The SARS-CoV-2 genome encodes the 2′-O-methyltransferase nsp16, which, when bound to the coactivator nsp10, uses S-adenosylmethionine (SAM) as a donor to transfer a methyl group to the first ribonucleotide of the mRNA in the final step of viral mRNA capping. Here, we provide biochemical and structural evidence that this reaction requires divalent cations, preferably Mn2+, and a coronavirus-specific four-residue insert. We determined the x-ray structures of the SARS-CoV-2 2′-O-methyltransferase (the nsp16-nsp10 heterodimer) in complex with its reaction substrates, products, and divalent metal cations. These structural snapshots revealed that metal ions and the insert stabilize interactions between the capped RNA and nsp16, resulting in the precise alignment of the ribonucleotides in the active site. Comparison of available structures of 2′-O-methyltransferases with capped RNAs from different organisms revealed that the four-residue insert unique to coronavirus nsp16 alters the backbone conformation of the capped RNA in the binding groove, thereby promoting catalysis. This insert is highly conserved across coronaviruses, and its absence in mammalian methyltransferases makes this region a promising site for structure-guided drug design of selective coronavirus inhibitors.
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Affiliation(s)
- George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Courtney M Daczkowski
- Department of Biochemistry and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Paul Hoover
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA
| | - Andrew D Mesecar
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.,Department of Biochemistry and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine,,Chicago, IL 60611, USA. .,Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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26
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Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
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Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
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27
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Destefanis E, Avşar G, Groza P, Romitelli A, Torrini S, Pir P, Conticello SG, Aguilo F, Dassi E. A mark of disease: how mRNA modifications shape genetic and acquired pathologies. RNA (NEW YORK, N.Y.) 2021; 27:367-389. [PMID: 33376192 PMCID: PMC7962492 DOI: 10.1261/rna.077271.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA modifications have recently emerged as a widespread and complex facet of gene expression regulation. Counting more than 170 distinct chemical modifications with far-reaching implications for RNA fate, they are collectively referred to as the epitranscriptome. These modifications can occur in all RNA species, including messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). In mRNAs the deposition, removal, and recognition of chemical marks by writers, erasers and readers influence their structure, localization, stability, and translation. In turn, this modulates key molecular and cellular processes such as RNA metabolism, cell cycle, apoptosis, and others. Unsurprisingly, given their relevance for cellular and organismal functions, alterations of epitranscriptomic marks have been observed in a broad range of human diseases, including cancer, neurological and metabolic disorders. Here, we will review the major types of mRNA modifications and editing processes in conjunction with the enzymes involved in their metabolism and describe their impact on human diseases. We present the current knowledge in an updated catalog. We will also discuss the emerging evidence on the crosstalk of epitranscriptomic marks and what this interplay could imply for the dynamics of mRNA modifications. Understanding how this complex regulatory layer can affect the course of human pathologies will ultimately lead to its exploitation toward novel epitranscriptomic therapeutic strategies.
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Affiliation(s)
- Eliana Destefanis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- The EPITRAN COST Action Consortium, COST Action CA16120
| | - Gülben Avşar
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Paula Groza
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Center for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Antonia Romitelli
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Department of Medical Biotechnologies, Università di Siena, 53100 Siena, Italy
| | - Serena Torrini
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Department of Medical Biotechnologies, Università di Siena, 53100 Siena, Italy
| | - Pınar Pir
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Silvestro G Conticello
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - Francesca Aguilo
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Center for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- The EPITRAN COST Action Consortium, COST Action CA16120
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28
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Borbolis F, Syntichaki P. Biological implications of decapping: beyond bulk mRNA decay. FEBS J 2021; 289:1457-1475. [PMID: 33660392 DOI: 10.1111/febs.15798] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/21/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022]
Abstract
It is well established that mRNA steady-state levels do not directly correlate with transcription rate. This is attributed to the multiple post-transcriptional mechanisms, which control both mRNA turnover and translation within eukaryotic cells. One such mechanism is the removal of the 5' end cap structure of RNAs (decapping). This 5' cap plays a fundamental role in cellular functions related to mRNA processing, transport, translation, quality control, and decay, while its chemical modifications influence the fate of cytoplasmic mRNAs. Decapping is a highly controlled process, performed by multiple decapping enzymes, and regulated by complex cellular networks. In this review, we provide an updated synopsis of 5' end modifications and functions, and give an overview of mRNA decapping enzymes, presenting their enzymatic properties. Focusing on DCP2 decapping enzyme, a major component on the 5'-3' mRNA decay pathway, we describe cis-elements and trans-acting factors that affect its activity, substrate specificity, and cellular localization. Finally, we discuss current knowledge on the biological functions of mRNA decapping and decay factors, highlighting the major questions that remain to be addressed.
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Affiliation(s)
- Fivos Borbolis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
| | - Popi Syntichaki
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
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29
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Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. PLoS One 2021; 16:e0246181. [PMID: 33596235 PMCID: PMC7888625 DOI: 10.1371/journal.pone.0246181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/18/2023] Open
Abstract
The 2019 emergence of, SARS-CoV-2 has tragically taken an immense toll on human life and far reaching impacts on society. There is a need to identify effective antivirals with diverse mechanisms of action in order to accelerate preclinical development. This study focused on five of the most established drug target proteins for direct acting small molecule antivirals: Nsp5 Main Protease, Nsp12 RNA-dependent RNA polymerase, Nsp13 Helicase, Nsp16 2'-O methyltransferase and the S2 subunit of the Spike protein. A workflow of solvent mapping and free energy calculations was used to identify and characterize favorable small-molecule binding sites for an aromatic pharmacophore (benzene). After identifying the most favorable sites, calculated ligand efficiencies were compared utilizing computational fragment screening. The most favorable sites overall were located on Nsp12 and Nsp16, whereas the most favorable sites for Nsp13 and S2 Spike had comparatively lower ligand efficiencies relative to Nsp12 and Nsp16. Utilizing fragment screening on numerous possible sites on Nsp13 helicase, we identified a favorable allosteric site on the N-terminal zinc binding domain (ZBD) that may be amenable to virtual or biophysical fragment screening efforts. Recent structural studies of the Nsp12:Nsp13 replication-transcription complex experimentally corroborates ligand binding at this site, which is revealed to be a functional Nsp8:Nsp13 protein-protein interaction site in the complex. Detailed structural analysis of Nsp13 ZBD conformations show the role of induced-fit flexibility in this ligand binding site and identify which conformational states are associated with efficient ligand binding. We hope that this map of over 200 possible small-molecule binding sites for these drug targets may be of use for ongoing discovery, design, and drug repurposing efforts. This information may be used to prioritize screening efforts or aid in the process of deciphering how a screening hit may bind to a specific target protein.
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30
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Functional and computational identification of a rescue mutation near the active site of an mRNA methyltransferase. Sci Rep 2020; 10:21841. [PMID: 33318548 PMCID: PMC7736282 DOI: 10.1038/s41598-020-79026-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/03/2020] [Indexed: 11/08/2022] Open
Abstract
RNA-based drugs are an emerging class of therapeutics combining the immense potential of DNA gene-therapy with the absence of genome integration-associated risks. While the synthesis of such molecules is feasible, large scale in vitro production of humanised mRNA remains a biochemical and economical challenge. Human mRNAs possess two post-transcriptional modifications at their 5' end: an inverted methylated guanosine and a unique 2'O-methylation on the ribose of the penultimate nucleotide. One strategy to precisely methylate the 2' oxygen is to use viral mRNA methyltransferases that have evolved to escape the host's cell immunity response following virus infection. However, these enzymes are ill-adapted to industrial processes and suffer from low turnovers. We have investigated the effects of homologous and orthologous active-site mutations on both stability and transferase activity, and identified new functional motifs in the interaction network surrounding the catalytic lysine. Our findings suggest that despite their low catalytic efficiency, the active-sites of viral mRNA methyltransferases have low mutational plasticity, while mutations in a defined third shell around the active site have strong effects on folding, stability and activity in the variant enzymes, mostly via network-mediated effects.
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31
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Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.10.420109. [PMID: 33330873 PMCID: PMC7743098 DOI: 10.1101/2020.12.10.420109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Coronaviruses have caused multiple epidemics in the past two decades, in addition to the current COVID-19 pandemic that is severely damaging global health and the economy. Coronaviruses employ between twenty and thirty proteins to carry out their viral replication cycle including infection, immune evasion, and replication. Among these, nonstructural protein 16 (Nsp16), a 2'-O-methyltransferase, plays an essential role in immune evasion. Nsp16 achieves this by mimicking its human homolog, CMTr1, which methylates mRNA to enhance translation efficiency and distinguish self from other. Unlike human CMTr1, Nsp16 requires a binding partner, Nsp10, to activate its enzymatic activity. The requirement of this binding partner presents two questions that we investigate in this manuscript. First, how does Nsp10 activate Nsp16? While experimentally-derived structures of the active Nsp16/Nsp10 complex exist, structures of inactive, monomeric Nsp16 have yet to be solved. Therefore, it is unclear how Nsp10 activates Nsp16. Using over one millisecond of molecular dynamics simulations of both Nsp16 and its complex with Nsp10, we investigate how the presence of Nsp10 shifts Nsp16's conformational ensemble in order to activate it. Second, guided by this activation mechanism and Markov state models (MSMs), we investigate if Nsp16 adopts inactive structures with cryptic pockets that, if targeted with a small molecule, could inhibit Nsp16 by stabilizing its inactive state. After identifying such a pocket in SARS-CoV-2 Nsp16, we show that this cryptic pocket also opens in SARS-CoV-1 and MERS, but not in human CMTr1. Therefore, it may be possible to develop pan-coronavirus antivirals that target this cryptic pocket. STATEMENT OF SIGNIFICANCE Coronaviruses are a major threat to human health. These viruses employ molecular machines, called proteins, to infect host cells and replicate. Characterizing the structure and dynamics of these proteins could provide a basis for designing small molecule antivirals. In this work, we use computer simulations to understand the moving parts of an essential SARS-CoV-2 protein, understand how a binding partner turns it on and off, and identify a novel pocket that antivirals could target to shut this protein off. The pocket is also present in other coronaviruses but not in the related human protein, so it could be a valuable target for pan-coronavirus antivirals.
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Affiliation(s)
- Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael D. Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Maxwell I. Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Borna Novak
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Medical Scientist Training Program, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, United States
| | - Jonathan H. Borowsky
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Gregory R. Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
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32
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Pelletier J, Schmeing TM, Sonenberg N. The multifaceted eukaryotic cap structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1636. [PMID: 33300197 DOI: 10.1002/wrna.1636] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022]
Abstract
The 5' cap structure is added onto RNA polymerase II transcripts soon after initiation of transcription and modulates several post-transcriptional regulatory events involved in RNA maturation. It is also required for stimulating translation initiation of many cytoplasmic mRNAs and serves to protect mRNAs from degradation. These functional properties of the cap are mediated by several cap binding proteins (CBPs) involved in nuclear and cytoplasmic gene expression steps. The role that CBPs play in gene regulation, as well as the biophysical nature by which they recognize the cap, is quite intricate. Differences in mechanisms of capping as well as nuances in cap recognition speak to the potential of targeting these processes for drug development. In this review, we focus on recent findings concerning the cap epitranscriptome, our understanding of cap binding by different CBPs, and explore therapeutic targeting of CBP-cap interaction. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > Capping and 5' End Modifications Translation > Translation Mechanisms.
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Affiliation(s)
- Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
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33
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CMTR1-Catalyzed 2'-O-Ribose Methylation Controls Neuronal Development by Regulating Camk2α Expression Independent of RIG-I Signaling. Cell Rep 2020; 33:108269. [PMID: 33086056 PMCID: PMC7574844 DOI: 10.1016/j.celrep.2020.108269] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/10/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic mRNAs are 5′ end capped with a 7-methylguanosine, which is important for processing and translation of mRNAs. Cap methyltransferase 1 (CMTR1) catalyzes 2′-O-ribose methylation of the first transcribed nucleotide (N1 2′-O-Me) to mask mRNAs from innate immune surveillance by retinoic-acid-inducible gene-I (RIG-I). Nevertheless, whether this modification regulates gene expression for neuronal functions remains unexplored. Here, we find that knockdown of CMTR1 impairs dendrite development independent of secretory cytokines and RIG-I signaling. Using transcriptomic analyses, we identify altered gene expression related to dendrite morphogenesis instead of RIG-I-activated interferon signaling, such as decreased calcium/calmodulin-dependent protein kinase 2α (Camk2α). In line with these molecular changes, dendritic complexity in CMTR1-insufficient neurons is rescued by ectopic expression of CaMK2α but not by inactivation of RIG-I signaling. We further generate brain-specific CMTR1-knockout mice to validate these findings in vivo. Our study reveals the indispensable role of CMTR1-catalyzed N1 2′-O-Me in gene regulation for brain development. Every mRNA molecule in neurons is N1 2′-O methylated by CMTR1 CMTR1 is essential for neuromorphogenesis and brain development CMTR1 deficiency does not activate RIG-I and interferon signaling CMTR1 promotes Camk2α expression to support dendrite development
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34
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Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Brunzelle J, Satchell KJF. High-resolution structures of the SARS-CoV-2 2'- O-methyltransferase reveal strategies for structure-based inhibitor design. Sci Signal 2020; 13:eabe1202. [PMID: 32994211 PMCID: PMC8028745 DOI: 10.1126/scisignal.abe1202] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There are currently no antiviral therapies specific for SARS-CoV-2, the virus responsible for the global pandemic disease COVID-19. To facilitate structure-based drug design, we conducted an x-ray crystallographic study of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase complex, which methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. We determined the structures for nsp16-nsp10 heterodimers bound to the methyl donor S-adenosylmethionine (SAM), the reaction product S-adenosylhomocysteine (SAH), or the SAH analog sinefungin (SFG). We also solved structures for nsp16-nsp10 in complex with the methylated Cap-0 analog m7GpppA and either SAM or SAH. Comparative analyses between these structures and published structures for nsp16 from other betacoronaviruses revealed flexible loops in open and closed conformations at the m7GpppA-binding pocket. Bound sulfates in several of the structures suggested the location of the ribonucleic acid backbone phosphates in the ribonucleotide-binding groove. Additional nucleotide-binding sites were found on the face of the protein opposite the active site. These various sites and the conserved dimer interface could be exploited for the development of antiviral inhibitors.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Olga Kiryukhina
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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Abstract
Chemical modifications of viral RNA are an integral part of the viral life cycle and are present in most classes of viruses. To date, more than 170 RNA modifications have been discovered in all types of cellular RNA. Only a few, however, have been found in viral RNA, and the function of most of these has yet to be elucidated. Those few we have discovered and whose functions we understand have a varied effect on each virus. They facilitate RNA export from the nucleus, aid in viral protein synthesis, recruit host enzymes, and even interact with the host immune machinery. The most common methods for their study are mass spectrometry and antibody assays linked to next-generation sequencing. However, given that the actual amount of modified RNA can be very small, it is important to pair meticulous scientific methodology with the appropriate detection methods and to interpret the results with a grain of salt. Once discovered, RNA modifications enhance our understanding of viruses and present a potential target in combating them. This review provides a summary of the currently known chemical modifications of viral RNA, the effects they have on viral machinery, and the methods used to detect them.
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Affiliation(s)
- Jiří František Potužník
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Cahová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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36
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Lee S, Hong JS, Lim DH, Lee YS. Roles for Drosophila cap1 2'-O-ribose methyltransferase in the small RNA silencing pathway associated with Argonaute 2. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 123:103415. [PMID: 32504809 DOI: 10.1016/j.ibmb.2020.103415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Cap1 2'-O-ribose methyltransferase (CMTR1) modifies RNA transcripts containing the 7-methylguanosine cap via 2'-O-ribose methylation of the first transcribed nucleotide, yielding cap1 structures. However, the role of CMTR1 in small RNA-mediated gene silencing remains unknown. Here, we identified and characterized a Drosophila CMTR1 gene (dCMTR1) mutation. We found that the catalytic activity of dCMTR1 was involved in the biogenesis of small interfering RNAs (siRNAs) but not microRNAs. Additionally, dCMTR1 interacted with R2D2, a key component for the assembly of the RNA-induced silencing complex (RISC) containing Argonaute 2 (Ago2). Consistent with this finding, loss of dCMTR1 function impaired RISC assembly by inhibiting the unwinding of Ago2-bound siRNA duplexes, thus preventing the retention of the guide strand. Moreover, dCMTR1 is unlikely to modify siRNAs during RISC assembly. Collectively, our data indicate that dCMTR1 is a positive regulator of the small RNA pathway associated with Ago2 with roles in both siRNA biogenesis and RISC assembly.
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Affiliation(s)
- Seungjae Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea; Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jae-Sang Hong
- College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea; Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Do-Hwan Lim
- College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea; Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Young Sik Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea; Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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37
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Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nat Commun 2020; 11:3717. [PMID: 32709887 PMCID: PMC7381658 DOI: 10.1038/s41467-020-17495-9] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/01/2020] [Indexed: 11/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the COVID-19 pandemic. 2′-O-RNA methyltransferase (MTase) is one of the enzymes of this virus that is a potential target for antiviral therapy as it is crucial for RNA cap formation; an essential process for viral RNA stability. This MTase function is associated with the nsp16 protein, which requires a cofactor, nsp10, for its proper activity. Here we show the crystal structure of the nsp10-nsp16 complex bound to the pan-MTase inhibitor sinefungin in the active site. Our structural comparisons reveal low conservation of the MTase catalytic site between Zika and SARS-CoV-2 viruses, but high conservation of the MTase active site between SARS-CoV-2 and SARS-CoV viruses; these data suggest that the preparation of MTase inhibitors targeting several coronaviruses - but not flaviviruses - should be feasible. Together, our data add to important information for structure-based drug discovery. SARS-CoV-2 expresses a 2′-O RNA methyltransferase (MTase) that is involved in the viral RNA cap formation and therefore a target for antiviral therapy. Here the authors provide the structure of nsp10-nsp16 with the panMTase inhibitor sinefungin and report that the development of MTase inhibitor therapies that target multiple coronoaviruses is feasible.
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38
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Höfler S, Carlomagno T. Structural and functional roles of 2'-O-ribose methylations and their enzymatic machinery across multiple classes of RNAs. Curr Opin Struct Biol 2020; 65:42-50. [PMID: 32610226 DOI: 10.1016/j.sbi.2020.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 01/27/2023]
Abstract
RNA complexity is augmented by numerous post-transcriptional modifications, which influence RNA function by modulating its structure and interactome. One prominent modification is methylation at the ribose 2'-hydroxyl group. 2'-O-methylation has been found in all RNA classes, with rRNA and tRNA being extensively modified. The exact function of 2'-O-methylation at specific RNA sites is still not understood, with a few notable exceptions. The relevance of 2'-O-methylation for cell survival and well-being is proven by the large effort that the cell spends in maintaining a diverse and highly regulated methylation machinery. Here, we review the current knowledge on the impact of 2'-O-methylation on structure and function of different RNAs as well as on the factors determining substrate specificity in the enzymatic machinery.
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Affiliation(s)
- Simone Höfler
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Teresa Carlomagno
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Helmholz Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig, Germany.
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39
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Li B, Clohisey SM, Chia BS, Wang B, Cui A, Eisenhaure T, Schweitzer LD, Hoover P, Parkinson NJ, Nachshon A, Smith N, Regan T, Farr D, Gutmann MU, Bukhari SI, Law A, Sangesland M, Gat-Viks I, Digard P, Vasudevan S, Lingwood D, Dockrell DH, Doench JG, Baillie JK, Hacohen N. Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection. Nat Commun 2020; 11:164. [PMID: 31919360 PMCID: PMC6952391 DOI: 10.1038/s41467-019-13965-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
Host dependency factors that are required for influenza A virus infection may serve as therapeutic targets as the virus is less likely to bypass them under drug-mediated selection pressure. Previous attempts to identify host factors have produced largely divergent results, with few overlapping hits across different studies. Here, we perform a genome-wide CRISPR/Cas9 screen and devise a new approach, meta-analysis by information content (MAIC) to systematically combine our results with prior evidence for influenza host factors. MAIC out-performs other meta-analysis methods when using our CRISPR screen as validation data. We validate the host factors, WDR7, CCDC115 and TMEM199, demonstrating that these genes are essential for viral entry and regulation of V-type ATPase assembly. We also find that CMTR1, a human mRNA cap methyltransferase, is required for efficient viral cap snatching and regulation of a cell autonomous immune response, and provides synergistic protection with the influenza endonuclease inhibitor Xofluza. Here, Li et al. perform a genome-wide CRISPR screen to identify host dependency factors for influenza A virus infection and show that the host mRNA cap methyltransferase CMTR1 is important for viral cap snatching and that it affects expression of antiviral genes.
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Affiliation(s)
- Bo Li
- Harvard University Virology Program, Harvfvard Medical School, Boston, MA02142, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Sara M Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Bing Shao Chia
- Harvard University Virology Program, Harvfvard Medical School, Boston, MA02142, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Ang Cui
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - Thomas Eisenhaure
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | | | - Paul Hoover
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | | | - Aharon Nachshon
- School of Molecular Cell Biology and Biotechnology, Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nikki Smith
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Tim Regan
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - David Farr
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Michael U Gutmann
- School of informatics, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | - Syed Irfan Bukhari
- Center for Cancer Research, Massachusetts General hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew Law
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - Irit Gat-Viks
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,School of Molecular Cell Biology and Biotechnology, Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Paul Digard
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Shobha Vasudevan
- Center for Cancer Research, Massachusetts General hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - David H Dockrell
- MRC Center for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - John G Doench
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK. .,Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, EH16 5SA, UK.
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA. .,Massachusetts General Hospital Cancer Center, Boston, MA, 02129, USA.
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40
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Yang Z, Liu F, Steeves AH, Kulik HJ. Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases. J Phys Chem Lett 2019; 10:3779-3787. [PMID: 31244268 DOI: 10.1021/acs.jpclett.9b01555] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the SN2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Fang Liu
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Adam H Steeves
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Heather J Kulik
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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41
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Muthmann N, Guez T, Vasseur JJ, Jaffrey SR, Debart F, Rentmeister A. Combining Chemical Synthesis and Enzymatic Methylation to Access Short RNAs with Various 5' Caps. Chembiochem 2019; 20:1693-1700. [PMID: 30768827 PMCID: PMC6755138 DOI: 10.1002/cbic.201900037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Indexed: 12/31/2022]
Abstract
Eukaryotic RNAs are heavily processed, including co- and post-transcriptional formation of various 5' caps. In small nuclear RNAs (snRNAs) or small nucleolar RNAs (snoRNAs), the canonical 7m G cap is hypermethylated at the N2 -position, whereas in higher eukaryotes and viruses 2'-O-methylation of the first transcribed nucleotide yields the cap1 structure. The function and potential dynamics of several RNA cap modifications have not been fully elucidated, which necessitates preparative access to these caps. However, the introduction of these modifications during chemical solid-phase synthesis is challenging and enzymatic production of defined short and uniform RNAs also faces difficulties. In this work, the chemical synthesis of RNA is combined with site-specific enzymatic methylation by using the methyltransferases human trimethylguanosine synthase 1 (hTgs1), trimethylguanosine synthase from Giardia lamblia (GlaTgs2), and cap methyltransferase 1 (CMTR1). It is shown that RNAs with di-and trimethylated caps, as well as RNAs with caps methylated at the 2'-O-position of the first transcribed nucleotide, can be conveniently prepared. These highly modified RNAs, with a defined and uniform sequence, are hard to access by in vitro transcription or chemical synthesis alone.
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Affiliation(s)
- Nils Muthmann
- Department of Chemistry and Pharmacy, Institute for Biochemistry, University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany
| | - Théo Guez
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Campus Triolet UM, Place Eugène Bataillon, 34095, Montpellier, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Campus Triolet UM, Place Eugène Bataillon, 34095, Montpellier, France
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, 1300 York Avenue, Box 70, New York, NY, 10065, USA
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Campus Triolet UM, Place Eugène Bataillon, 34095, Montpellier, France
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute for Biochemistry, University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany
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42
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Bohnsack MT, Sloan KE. Modifications in small nuclear RNAs and their roles in spliceosome assembly and function. Biol Chem 2019; 399:1265-1276. [PMID: 29908124 DOI: 10.1515/hsz-2018-0205] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/28/2018] [Indexed: 01/27/2023]
Abstract
Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2'-O-methylated nucleotides, which are largely introduced by small Cajal body-specific ribonucleoproteins (scaRNPs). Modified nucleotides typically cluster in functionally important regions of the snRNAs, suggesting that their presence could optimise the interactions of snRNAs with each other or with pre-mRNAs, or may affect the binding of spliceosomal proteins. snRNA modifications appear to play important roles in snRNP biogenesis and spliceosome assembly, and have also been proposed to influence the efficiency and fidelity of pre-mRNA splicing. Interestingly, alterations in the modification status of snRNAs have recently been observed in different cellular conditions, implying that some snRNA modifications are dynamic and raising the possibility that these modifications may fine-tune the spliceosome for particular functions. Here, we review the current knowledge on the snRNA modification machinery and discuss the timing, functions and dynamics of modifications in snRNAs.
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Affiliation(s)
- Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany.,Göttingen Centre for Molecular Biosciences, Georg August University, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
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43
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Galloway A, Cowling VH. mRNA cap regulation in mammalian cell function and fate. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:270-279. [PMID: 30312682 PMCID: PMC6414751 DOI: 10.1016/j.bbagrm.2018.09.011] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/13/2018] [Accepted: 09/30/2018] [Indexed: 12/17/2022]
Abstract
In this review we explore the regulation of mRNA cap formation and its impact on mammalian cells. The mRNA cap is a highly methylated modification of the 5' end of RNA pol II-transcribed RNA. It protects RNA from degradation, recruits complexes involved in RNA processing, export and translation initiation, and marks cellular mRNA as "self" to avoid recognition by the innate immune system. The mRNA cap can be viewed as a unique mark which selects RNA pol II transcripts for specific processing and translation. Over recent years, examples of regulation of mRNA cap formation have emerged, induced by oncogenes, developmental pathways and during the cell cycle. These signalling pathways regulate the rate and extent of mRNA cap formation, resulting in changes in gene expression, cell physiology and cell function.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Dimitrova DG, Teysset L, Carré C. RNA 2'-O-Methylation (Nm) Modification in Human Diseases. Genes (Basel) 2019; 10:E117. [PMID: 30764532 PMCID: PMC6409641 DOI: 10.3390/genes10020117] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/24/2022] Open
Abstract
Nm (2'-O-methylation) is one of the most common modifications in the RNA world. It has the potential to influence the RNA molecules in multiple ways, such as structure, stability, and interactions, and to play a role in various cellular processes from epigenetic gene regulation, through translation to self versus non-self recognition. Yet, building scientific knowledge on the Nm matter has been hampered for a long time by the challenges in detecting and mapping this modification. Today, with the latest advancements in the area, more and more Nm sites are discovered on RNAs (tRNA, rRNA, mRNA, and small non-coding RNA) and linked to normal or pathological conditions. This review aims to synthesize the Nm-associated human diseases known to date and to tackle potential indirect links to some other biological defects.
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Affiliation(s)
- Dilyana G Dimitrova
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Laure Teysset
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Clément Carré
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
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Yang Y, Eichhorn CD, Wang Y, Cascio D, Feigon J. Structural basis of 7SK RNA 5'-γ-phosphate methylation and retention by MePCE. Nat Chem Biol 2019; 15:132-140. [PMID: 30559425 PMCID: PMC6339579 DOI: 10.1038/s41589-018-0188-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/06/2018] [Indexed: 01/28/2023]
Abstract
Among RNA 5'-cap structures, γ-phosphate monomethylation is unique to a small subset of noncoding RNAs, 7SK and U6 in humans. 7SK is capped by methylphosphate capping enzyme (MePCE), which has a second nonenzymatic role as a core component of the 7SK ribonuclear protein (RNP), an essential regulator of RNA transcription. We report 2.0- and 2.1-Å X-ray crystal structures of the human MePCE methyltransferase domain bound to S-adenosylhomocysteine (SAH) and uncapped or capped 7SK substrates, respectively. 7SK recognition is achieved by protein contacts to a 5'-hairpin-single-stranded RNA region, thus explaining MePCE's specificity for 7SK and U6. The structures reveal SAH and product RNA in a near-transition-state geometry. Unexpectedly, binding experiments showed that MePCE has higher affinity for capped versus uncapped 7SK, and kinetic data support a model of slow product release. This work reveals the molecular mechanism of methyl transfer and 7SK retention by MePCE for subsequent assembly of 7SK RNP.
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Affiliation(s)
- Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yaqiang Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
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46
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GAPDH as a model non-canonical AU-rich RNA binding protein. Semin Cell Dev Biol 2019; 86:162-173. [DOI: 10.1016/j.semcdb.2018.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
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Ayadi L, Galvanin A, Pichot F, Marchand V, Motorin Y. RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:253-269. [PMID: 30572123 DOI: 10.1016/j.bbagrm.2018.11.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 01/01/2023]
Abstract
Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.
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Affiliation(s)
- Lilia Ayadi
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Adeline Galvanin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Florian Pichot
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Virginie Marchand
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Yuri Motorin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France.
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Fenwick MK, Ealick SE. Towards the structural characterization of the human methyltransferome. Curr Opin Struct Biol 2018; 53:12-21. [DOI: 10.1016/j.sbi.2018.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/06/2018] [Indexed: 10/17/2022]
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49
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Toczydlowska-Socha D, Zielinska MM, Kurkowska M, Astha, Almeida CF, Stefaniak F, Purta E, Bujnicki JM. Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5' termini. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0161. [PMID: 30397098 PMCID: PMC6232587 DOI: 10.1098/rstb.2018.0161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2018] [Indexed: 11/23/2022] Open
Abstract
The 5′-cap structure, characteristic for RNA polymerase II-transcribed RNAs, plays important roles in RNA metabolism. In humans, RNA cap formation includes post-transcriptional modification of the first transcribed nucleotide by RNA cap1 methyltransferase (CMTr1). Here, we report that CMTr1 activity is hindered towards RNA substrates with highly structured 5′ termini. We found that CMTr1 binds ATP-dependent RNA DHX15 helicase and that this interaction, mediated by the G-patch domain of CMTr1, has an advantageous effect on CMTr1 activity towards highly structured RNA substrates. The effect of DHX15 helicase activity is consistent with the strength of the secondary structure that has to be removed for CMTr1 to access the 5′-terminal residues in a single-stranded conformation. This is, to our knowledge, the first demonstration of the involvement of DHX15 in post-transcriptional RNA modification, and the first example of a molecular process in which DHX15 directly affects the activity of another enzyme. Our findings suggest a new mechanism underlying the regulatory role of DHX15 in the RNA capping process. RNAs with highly structured 5′ termini constitute a significant fraction of the human transcriptome. Hence, CMTr1–DHX15 cooperation is likely to be important for the metabolism of RNA polymerase II-transcribed RNAs. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
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Affiliation(s)
- Diana Toczydlowska-Socha
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Magdalena M Zielinska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Malgorzata Kurkowska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Astha
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Catarina F Almeida
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Elzbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland .,Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland
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Simabuco FM, Pavan ICB, Pestana NF, Carvalho PC, Basei FL, Campos Granato D, Paes Leme AF, Zanchin NIT. Interactome analysis of the human Cap‐specific mRNA (nucleoside‐2′‐O‐)‐methyltransferase 1 (hMTr1) protein. J Cell Biochem 2018; 120:5597-5611. [DOI: 10.1002/jcb.27843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/14/2018] [Indexed: 01/28/2023]
Affiliation(s)
- Fernando Moreira Simabuco
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais Campinas SP Brazil
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas Limeira SP Brazil
| | | | - Nathalie Fortes Pestana
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas Limeira SP Brazil
- Centro Universitário da Fundação Hermínio Ometto‐FHO Araras SP Brazil
| | | | | | - Daniela Campos Granato
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais Campinas SP Brazil
| | - Adriana Franco Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais Campinas SP Brazil
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