301
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Bage MG, Almohammed R, Cowling VH, Pisliakov A. A novel RNA pol II CTD interaction site on the mRNA capping enzyme is essential for its allosteric activation. Nucleic Acids Res 2021; 49:3109-3126. [PMID: 33684220 PMCID: PMC8034621 DOI: 10.1093/nar/gkab130] [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: 12/23/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 11/12/2022] Open
Abstract
Recruitment of the mRNA capping enzyme (CE/RNGTT) to the site of transcription is essential for the formation of the 5' mRNA cap, which in turn ensures efficient transcription, splicing, polyadenylation, nuclear export and translation of mRNA in eukaryotic cells. The CE GTase is recruited and activated by the Serine-5 phosphorylated carboxyl-terminal domain (CTD) of RNA polymerase II. Through the use of molecular dynamics simulations and enhanced sampling techniques, we provide a systematic and detailed characterization of the human CE-CTD interface, describing the effect of the CTD phosphorylation state, length and orientation on this interaction. Our computational analyses identify novel CTD interaction sites on the human CE GTase surface and quantify their relative contributions to CTD binding. We also identify, for the first time, allosteric connections between the CE GTase active site and the CTD binding sites, allowing us to propose a mechanism for allosteric activation. Through binding and activity assays we validate the novel CTD binding sites and show that the CDS2 site is essential for CE GTase activity stimulation. Comparison of the novel sites with cocrystal structures of the CE-CTD complex in different eukaryotic taxa reveals that this interface is considerably more conserved than previous structures have indicated.
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Affiliation(s)
- Marcus G Bage
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rajaei Almohammed
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Andrei V Pisliakov
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
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302
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Pietschmann M, Tempel G, Halladjian M, Krogh N, Nielsen H. Use of a Lariat Capping Ribozyme to Study Cap Function In Vivo. Methods Mol Biol 2021; 2167:271-285. [PMID: 32712925 DOI: 10.1007/978-1-0716-0716-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A lariat cap is a naturally occurring substitute of a conventional mRNA cap and is found in a particular genomic setting in a few eukaryotic microorganisms. It is installed by the lariat capping ribozyme acting in cis. In principle, any RNA molecule in any organism can be equipped with a lariat cap in vivo when expressed downstream of a lariat capping ribozyme. Lariat capping is thus a versatile tool for studying the importance of the 5' end structure of RNA molecules. In this chapter, we present protocols to validate the presence of the lariat cap and measure the efficiency of in vivo cleavage by the lariat capping ribozyme.
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Affiliation(s)
- Max Pietschmann
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Gregor Tempel
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Maral Halladjian
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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303
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Use of NAD tagSeq II to identify growth phase-dependent alterations in E. coli RNA NAD + capping. Proc Natl Acad Sci U S A 2021; 118:2026183118. [PMID: 33782135 PMCID: PMC8040648 DOI: 10.1073/pnas.2026183118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some RNAs in both prokaryotes and eukaryotes were recently found to contain the NAD+ cap, indicating a novel mechanism in gene regulation through noncanonical RNA capping. Copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry has been used to label NAD+-capped RNAs (NAD-RNAs) for their identification. However, copper-caused RNA fragmentation/degradation interferes with the analysis. We developed the NAD tagSeq II method for transcriptome-wide NAD-RNA analysis based on copper-free, strain-promoted azide-alkyne cycloaddition (SPAAC) click chemistry. This method was used to compare NAD-RNA and total transcriptome profiles in Escherichia coli. Our study reveals genome-wide alterations in E. coli RNA NAD+ capping in different growth phases and indicates that NAD-RNAs could be the primary form of transcripts from some genes under certain environments. Recent findings regarding nicotinamide adenine dinucleotide (NAD+)-capped RNAs (NAD-RNAs) indicate that prokaryotes and eukaryotes employ noncanonical RNA capping to regulate gene expression. Two methods for transcriptome-wide analysis of NAD-RNAs, NAD captureSeq and NAD tagSeq, are based on copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry to label NAD-RNAs. However, copper ions can fragment/degrade RNA, interfering with the analyses. Here we report development of NAD tagSeq II, which uses copper-free, strain-promoted azide-alkyne cycloaddition (SPAAC) for labeling NAD-RNAs, followed by identification of tagged RNA by single-molecule direct RNA sequencing. We used this method to compare NAD-RNA and total transcript profiles of Escherichia coli cells in the exponential and stationary phases. We identified hundreds of NAD-RNA species in E. coli and revealed genome-wide alterations of NAD-RNA profiles in the different growth phases. Although no or few NAD-RNAs were detected from some of the most highly expressed genes, the transcripts of some genes were found to be primarily NAD-RNAs. Our study suggests that NAD-RNAs play roles in linking nutrient cues with gene regulation in E. coli.
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304
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SPAAC-NAD-seq, a sensitive and accurate method to profile NAD +-capped transcripts. Proc Natl Acad Sci U S A 2021; 118:2025595118. [PMID: 33753511 DOI: 10.1073/pnas.2025595118] [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] [Indexed: 02/05/2023] Open
Abstract
Nicotinamide adenine diphosphate (NAD+) is a novel messenger RNA 5' cap in Escherichia coli, yeast, mammals, and Arabidopsis Transcriptome-wide identification of NAD+-capped RNAs (NAD-RNAs) was accomplished through NAD captureSeq, which combines chemoenzymatic RNA enrichment with high-throughput sequencing. NAD-RNAs are enzymatically converted to alkyne-RNAs that are then biotinylated using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Originally applied to E. coli RNA, which lacks the m7G cap, NAD captureSeq was then applied to eukaryotes without extensive verification of its specificity for NAD-RNAs vs. m7G-capped RNAs (m7G-RNAs). In addition, the Cu2+ ion in the CuAAC reaction causes RNA fragmentation, leading to greatly reduced yield and loss of full-length sequence information. We developed an NAD-RNA capture scheme utilizing the copper-free, strain-promoted azide-alkyne cycloaddition reaction (SPAAC). We examined the specificity of CuAAC and SPAAC reactions toward NAD-RNAs and m7G-RNAs and found that both prefer the former, but also act on the latter. We demonstrated that SPAAC-NAD sequencing (SPAAC-NAD-seq), when combined with immunodepletion of m7G-RNAs, enables NAD-RNA identification with accuracy and sensitivity, leading to the discovery of new NAD-RNA profiles in Arabidopsis Furthermore, SPAAC-NAD-seq retained full-length sequence information. Therefore, SPAAC-NAD-seq would enable specific and efficient discovery of NAD-RNAs in prokaryotes and, when combined with m7G-RNA depletion, in eukaryotes.
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305
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El Hassab MA, Ibrahim TM, Al-Rashood ST, Alharbi A, Eskandrani RO, Eldehna WM. In silico identification of novel SARS-COV-2 2'-O-methyltransferase (nsp16) inhibitors: structure-based virtual screening, molecular dynamics simulation and MM-PBSA approaches. J Enzyme Inhib Med Chem 2021; 36:727-736. [PMID: 33685335 PMCID: PMC7946047 DOI: 10.1080/14756366.2021.1885396] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The novel coronavirus disease COVID-19, caused by the virus SARS CoV-2, has exerted a significant unprecedented economic and medical crisis, in addition to its impact on the daily life and health care systems all over the world. Regrettably, no vaccines or drugs are currently available for this new critical emerging human disease. Joining the global fight against COVID-19, in this study we aim at identifying a potential novel inhibitor for SARS COV-2 2'-O-methyltransferase (nsp16) which is one of the most attractive targets in the virus life cycle, responsible for the viral RNA protection via a cap formation process. Firstly, nsp16 enzyme bound to Sinefungin was retrieved from the protein data bank (PDB ID: 6WKQ), then, a 3D pharmacophore model was constructed to be applied to screen 48 Million drug-like compounds of the Zinc database. This resulted in only 24 compounds which were subsequently docked into the enzyme. The best four score-ordered hits from the docking outcome exhibited better scores compared to Sinefungin. Finally, three molecular dynamics (MD) simulation experiments for 150 ns were carried out as a refinement step for our proposed approach. The MD and MM-PBSA outputs revealed compound 11 as the best potential nsp16 inhibitor herein identified, as it displayed a better stability and average binding free energy for the ligand-enzyme complex compared to Sinefungin.
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Affiliation(s)
- Mahmoud A El Hassab
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Egypt
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Sara T Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amal Alharbi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Razan O Eskandrani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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306
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Conti BJ, Leicht AS, Kirchdoerfer RN, Sussman MR. Mass spectrometric based detection of protein nucleotidylation in the RNA polymerase of SARS-CoV-2. Commun Chem 2021; 4:41. [PMID: 34189273 PMCID: PMC8238455 DOI: 10.1038/s42004-021-00476-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 02/22/2021] [Indexed: 02/08/2023] Open
Abstract
Coronaviruses, like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), encode a nucleotidyl transferase in the N-terminal (NiRAN) domain of the nonstructural protein (nsp) 12 protein within the RNA dependent RNA polymerase. Here we show the detection of guanosine monophosphate (GMP) and uridine monophosphate-modified amino acids in nidovirus proteins using heavy isotope-assisted mass spectrometry (MS) and MS/MS peptide sequencing. We identified lysine-143 in the equine arteritis virus (EAV) protein, nsp7, as a primary site of in vitro GMP attachment via a phosphoramide bond. In SARS-CoV-2 replicase proteins, we demonstrate nsp12-mediated nucleotidylation of nsp7 lysine-2. Our results demonstrate new strategies for detecting GMP-peptide linkages that can be adapted for higher throughput screening using mass spectrometric technologies. These data are expected to be important for a rapid and timely characterization of a new enzymatic activity in SARS-CoV-2 that may be an attractive drug target aimed at limiting viral replication in infected patients.
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Affiliation(s)
- Brian J. Conti
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI USA
| | - Andrew S. Leicht
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI USA
| | - Robert N. Kirchdoerfer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI USA
| | - Michael R. Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI USA
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307
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Campillo-Davo D, De Laere M, Roex G, Versteven M, Flumens D, Berneman ZN, Van Tendeloo VFI, Anguille S, Lion E. The Ins and Outs of Messenger RNA Electroporation for Physical Gene Delivery in Immune Cell-Based Therapy. Pharmaceutics 2021; 13:396. [PMID: 33809779 PMCID: PMC8002253 DOI: 10.3390/pharmaceutics13030396] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 01/02/2023] Open
Abstract
Messenger RNA (mRNA) electroporation is a powerful tool for transient genetic modification of cells. This non-viral method of genetic engineering has been widely used in immunotherapy. Electroporation allows fine-tuning of transfection protocols for each cell type as well as introduction of multiple protein-coding mRNAs at once. As a pioneering group in mRNA electroporation, in this review, we provide an expert overview of the ins and outs of mRNA electroporation, discussing the different parameters involved in mRNA electroporation as well as the production of research-grade and production and application of clinical-grade mRNA for gene transfer in the context of cell-based immunotherapies.
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Affiliation(s)
- Diana Campillo-Davo
- Tumor Immunology Group, Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium; (G.R.); (M.V.); (D.F.); (Z.N.B.); (V.F.I.V.T.); (S.A.)
| | - Maxime De Laere
- Center for Cell Therapy & Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium;
| | - Gils Roex
- Tumor Immunology Group, Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium; (G.R.); (M.V.); (D.F.); (Z.N.B.); (V.F.I.V.T.); (S.A.)
| | - Maarten Versteven
- Tumor Immunology Group, Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium; (G.R.); (M.V.); (D.F.); (Z.N.B.); (V.F.I.V.T.); (S.A.)
| | - Donovan Flumens
- Tumor Immunology Group, Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium; (G.R.); (M.V.); (D.F.); (Z.N.B.); (V.F.I.V.T.); (S.A.)
| | - Zwi N. Berneman
- Tumor Immunology Group, Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium; (G.R.); (M.V.); (D.F.); (Z.N.B.); (V.F.I.V.T.); (S.A.)
- Center for Cell Therapy & Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium;
- Division of Hematology, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Viggo F. I. Van Tendeloo
- Tumor Immunology Group, Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium; (G.R.); (M.V.); (D.F.); (Z.N.B.); (V.F.I.V.T.); (S.A.)
| | - Sébastien Anguille
- Tumor Immunology Group, Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium; (G.R.); (M.V.); (D.F.); (Z.N.B.); (V.F.I.V.T.); (S.A.)
- Center for Cell Therapy & Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium;
- Division of Hematology, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Eva Lion
- Tumor Immunology Group, Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium; (G.R.); (M.V.); (D.F.); (Z.N.B.); (V.F.I.V.T.); (S.A.)
- Center for Cell Therapy & Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium;
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308
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Interplay of mRNA capping and transcription machineries. Biosci Rep 2021; 40:221784. [PMID: 31904821 PMCID: PMC6981093 DOI: 10.1042/bsr20192825] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 12/31/2022] Open
Abstract
Early stages of transcription from eukaryotic promoters include two principal events: the capping of newly synthesized mRNA and the transition of RNA polymerase II from the preinitiation complex to the productive elongation state. The capping checkpoint model implies that these events are tightly coupled, which is necessary for ensuring the proper capping of newly synthesized mRNA. Recent findings also show that the capping machinery has a wider effect on transcription and the entire gene expression process. The molecular basis of these phenomena is discussed.
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309
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Dumoulin B, Ufer C, Kuhn H, Sofi S. Expression Regulation, Protein Chemistry and Functional Biology of the Guanine-Rich Sequence Binding Factor 1 (GRSF1). J Mol Biol 2021; 433:166922. [PMID: 33713675 DOI: 10.1016/j.jmb.2021.166922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 11/26/2022]
Abstract
In eukaryotic cells RNA-binding proteins have been implicated in virtually all post-transcriptional mechanisms of gene expression regulation. Based on the structural features of their RNA binding domains these proteins have been divided into several subfamilies. The presence of at least two RNA recognition motifs defines the group of heterogenous nuclear ribonucleoproteins H/F and one of its members is the guanine-rich sequence binding factor 1 (GRSF1). GRSF1 was first described 25 years ago and is widely distributed in eukaryotic cells. It is present in the nucleus, the cytoplasm and in mitochondria and has been implicated in a variety of physiological processes (embryogenesis, erythropoiesis, redox homeostasis, RNA metabolism) but also in the pathogenesis of various diseases. This review summarizes our current understanding on GRSF1 biology, critically discusses the literature reports and gives an outlook of future developments in the field.
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Affiliation(s)
- Bernhard Dumoulin
- Institute of Biochemistry, Charité - University Medicine Berlin, Corporate Member of Free University Berlin, Humboldt University Berlin and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Christoph Ufer
- Institute of Biochemistry, Charité - University Medicine Berlin, Corporate Member of Free University Berlin, Humboldt University Berlin and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Hartmut Kuhn
- Institute of Biochemistry, Charité - University Medicine Berlin, Corporate Member of Free University Berlin, Humboldt University Berlin and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Sajad Sofi
- University of York, Department of Biology, York YO10 5DD, United Kingdom
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310
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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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311
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Kim J, Eygeris Y, Gupta M, Sahay G. Self-assembled mRNA vaccines. Adv Drug Deliv Rev 2021; 170:83-112. [PMID: 33400957 PMCID: PMC7837307 DOI: 10.1016/j.addr.2020.12.014] [Citation(s) in RCA: 253] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 01/08/2023]
Abstract
mRNA vaccines have evolved from being a mere curiosity to emerging as COVID-19 vaccine front-runners. Recent advancements in the field of RNA technology, vaccinology, and nanotechnology have generated interest in delivering safe and effective mRNA therapeutics. In this review, we discuss design and self-assembly of mRNA vaccines. Self-assembly, a spontaneous organization of individual molecules, allows for design of nanoparticles with customizable properties. We highlight the materials commonly utilized to deliver mRNA, their physicochemical characteristics, and other relevant considerations, such as mRNA optimization, routes of administration, cellular fate, and immune activation, that are important for successful mRNA vaccination. We also examine the COVID-19 mRNA vaccines currently in clinical trials. mRNA vaccines are ready for the clinic, showing tremendous promise in the COVID-19 vaccine race, and have pushed the boundaries of gene therapy.
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Affiliation(s)
- Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Yulia Eygeris
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Mohit Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA; Department of Biomedical Engineering, Oregon Health & Science University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA; Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon 97239, USA.
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312
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Girardi E, Pfeffer S, Baumert TF, Majzoub K. Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell. Semin Cell Dev Biol 2021; 111:86-100. [PMID: 32847707 PMCID: PMC7443355 DOI: 10.1016/j.semcdb.2020.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
As obligate intracellular parasites with limited coding capacity, RNA viruses rely on host cells to complete their multiplication cycle. Viral RNAs (vRNAs) are central to infection. They carry all the necessary information for a virus to synthesize its proteins, replicate and spread and could also play essential non-coding roles. Regardless of its origin or tropism, vRNA has by definition evolved in the presence of host RNA Binding Proteins (RBPs), which resulted in intricate and complicated interactions with these factors. While on one hand some host RBPs recognize vRNA as non-self and mobilize host antiviral defenses, vRNA must also co-opt other host RBPs to promote viral infection. Focusing on pathogenic RNA viruses, we will review important scenarios of RBP-vRNA interactions during which host RBPs recognize, modify or degrade vRNAs. We will then focus on how vRNA hijacks the largest ribonucleoprotein complex (RNP) in the cell, the ribosome, to selectively promote the synthesis of its proteins. We will finally reflect on how novel technologies are helping in deepening our understanding of vRNA-host RBPs interactions, which can be ultimately leveraged to combat everlasting viral threats.
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Affiliation(s)
- Erika Girardi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Sebastien Pfeffer
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67000, Strasbourg, France; Pole Hépatodigestif, Institut Hopitalo-universitaire, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Karim Majzoub
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67000, Strasbourg, France.
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313
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Affiliation(s)
- Seung Hun Han
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
| | - Junho Choe
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
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314
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Qu X, Zhu K, Li Z, Zhang D, Hou L. The Alteration of M6A-Tagged Transcript Profiles in the Retina of Rats After Traumatic Optic Neuropathy. Front Genet 2021; 12:628841. [PMID: 33664770 PMCID: PMC7920991 DOI: 10.3389/fgene.2021.628841] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/25/2021] [Indexed: 12/27/2022] Open
Abstract
Messager RNA (mRNA) can be modified in a variety of ways, among which the modification of N6-methyladenosine (m6A) is one of the most common ones. Recent studies have found that the m6A modification in mRNA could functionally regulate the splicing, localization, translation, and stability of mRNA, which might be closely related to multiple diseases. However, the roles of m6A modification in traumatic optic neuropathy (TON) are unknown. Herein, we detected the expression of m6A-related genes via quantitative real-time PCR (qRT-PCR) and performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) as well as RNA-sequencing to analyze the alteration profiles of m6A modification after TON. The results showed that the expression of m6A-related genes (METTL3, WTAP, FTO, and ALKBH5) were all upregulated after TON. In all, 2,810 m6A peaks were differentially upregulated and 689 m6A peaks were downregulated. In addition, the hypermethylated and hypomethylated profiles of mRNA transcripts were also identified. To sum up, our study revealed the differentially expressed m6A modification in the early stage of TON, which may provide novel insights into the mechanism and treatment of TON.
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Affiliation(s)
- Xiaolin Qu
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Kaixin Zhu
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhenxing Li
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China.,Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Danfeng Zhang
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Lijun Hou
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
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315
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Henderson JM, Ujita A, Hill E, Yousif-Rosales S, Smith C, Ko N, McReynolds T, Cabral CR, Escamilla-Powers JR, Houston ME. Cap 1 Messenger RNA Synthesis with Co-transcriptional CleanCap ® Analog by In Vitro Transcription. Curr Protoc 2021; 1:e39. [PMID: 33524237 DOI: 10.1002/cpz1.39] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic messenger RNA (mRNA)-based therapeutics are an increasingly popular approach to gene and cell therapies, genome engineering, enzyme replacement therapy, and now, during the global SARS-CoV-2 pandemic, vaccine development. mRNA for such purposes can be synthesized through an enzymatic in vitro transcription (IVT) reaction and formulated for in vivo delivery. Mature mRNA requires a 5'-cap for gene expression and mRNA stability. There are two methods to add a cap in vitro: via a two-step multi-enzymatic reaction or co-transcriptionally. Co-transcriptional methods minimize reaction steps and enzymes needed to make mRNA when compared to enzymatic capping. CleanCap® AG co-transcriptional capping results in 5 mg/ml of IVT with 94% 5'-cap 1 structure. This is highly efficient compared to first-generation cap analogs, such as mCap and ARCA, that incorporate cap 0 structures at lower efficiency and reaction yield. This article describes co-transcriptional capping using TriLink Biotechnology's CleanCap® AG in IVT. © 2021 Wiley Periodicals LLC. Basic Protocol 1: IVT with CleanCap Basic Protocol 2: mRNA purification and analysis.
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Affiliation(s)
| | - Andrew Ujita
- TriLink Biotechnologies LLC, San Diego, California
| | | | | | - Cory Smith
- TriLink Biotechnologies LLC, San Diego, California
| | - Nicholas Ko
- TriLink Biotechnologies LLC, San Diego, California
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316
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Structure and Biochemical Characteristic of the Methyltransferase (MTase) Domain of RNA Capping Enzyme from African Swine Fever Virus. J Virol 2021; 95:JVI.02029-20. [PMID: 33268516 PMCID: PMC8092831 DOI: 10.1128/jvi.02029-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
African swine fever virus (ASFV) is a complex nucleocytoplasmic large DNA virus (NCLDV) that causes a devastating swine disease and it is urgently needed to develop effective anti-ASFV vaccines and drugs. The process of mRNA 5'-end capping is a common characteristic in eukaryotes and many viruses, and the cap structure is required for mRNA stability and efficient translation. The ASFV protein pNP868R was found to have guanylyltransferase (GTase) activity involved in mRNA capping. Here we report the crystal structure of pNP868R methyltransferase (MTase) domain (referred as pNP868RMT) in complex with S-adenosyl-L-methionine (AdoMet). The structure shows the characteristic core fold of the class I MTase family and the AdoMet is bound in a negative-deep groove. Remarkably, the N-terminal extension of pNP868RMT is ordered and keeps away from the AdoMet-binding site, distinct from the close conformation over the active site of poxvirus RNA capping D1 subunit or the largely disordered conformation in most cellular RNA capping MTases. Structure-based mutagenesis studies based on the pNP868RMT-cap analog complex model revealed essential residues involved in substrate recognition and binding. Functional studies suggest the N-terminal extension may play an essential role in substrate recognition instead of AdoMet-binding. A positively charged path stretching from the N-terminal extension to the region around the active site was suggested to provide a favorable electrostatic environment for the binding and approaching of substrate RNA into the active site. Our structure and biochemical studies provide novel insights into the methyltransfer process of mRNA cap catalyzed by pNP868R.IMPORTANCE African swine fever (ASF) is a highly contagious hemorrhagic viral disease in pigs that is caused by African swine fever virus (ASFV). There are no effective drugs or vaccines for protection against ASFV infection till now. The protein pNP868R was predicted to be responsible for process of mRNA 5'-end capping in ASFV, which is essential for mRNA stability and efficient translation. Here, we solved the high-resolution crystal structure of the methyltransferase (MTase) domain of pNP868R. The MTase domain structure shows a canonical class I MTase family fold and the AdoMet binds into a negative pocket. Structure-based mutagenesis studies revealed critical and conserved residues involved in AdoMet-binding and substrate RNA-binding. Notably, both the conformation and the role in MTase activities of the N-terminal extension are distinct from those of previously characterized poxvirus MTase domain. Our structure-function studies provide the basis for potential anti-ASFV inhibitor design targeting the critical enzyme.
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317
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Chen H, Yao J, Bao R, Dong Y, Zhang T, Du Y, Wang G, Ni D, Xun Z, Niu X, Ye Y, Li HB. Cross-talk of four types of RNA modification writers defines tumor microenvironment and pharmacogenomic landscape in colorectal cancer. Mol Cancer 2021; 20:29. [PMID: 33557837 PMCID: PMC7869236 DOI: 10.1186/s12943-021-01322-w] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/22/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The four major RNA adenosine modifications, i.e., m6A, m1A, alternative polyadenylation, and adenosine-to-inosine RNA editing, are mediated mostly by the "writer" enzymes and constitute critical mechanisms of epigenetic regulation in immune response and tumorigenesis. However, the cross-talk and potential roles of these "writers" in the tumor microenvironment (TME), drug sensitivity, and immunotherapy remain unknown. METHODS We systematically characterized mRNA expression and genetic alterations of 26 RNA modification "writers" in colorectal cancer (CRC), and evaluated their expression pattern in 1697 CRC samples from 8 datasets. We used an unsupervised clustering method to assign the samples into two patterns of expression of RNA modification "writers". Subsequently, we constructed the RNA modification "writer" Score (WM_Score) model based on differentially expressed genes (DEGs) responsible for the RNA modification patterns to quantify the RNA modification-related subtypes of individual tumors. Furthermore, we performed association analysis for WM_Score and characteristics of TME, consensus molecular subtypes (CMSs), clinical features, transcriptional and post-transcriptional regulation, drug response, and the efficacy of immunotherapy. RESULTS We demonstrated that multi-layer alterations of RNA modification "writer" are associated with patient survival and TME cell-infiltrating characteristics. We identified two distinct RNA modification patterns, characterized by a high and a low WM_Score. The WM_Score-high group was associated with worse patient overall survival and with the infiltration of inhibitory immune cells, such as M2 macrophages, EMT activation, and metastasis, while the WM_Score-low group was associated with a survival advantage, apoptosis, and cell cycle signaling pathways. WM_Score correlated highly with the regulation of transcription and post-transcriptional events contributing to the development of CRC. In response to anti-cancer drugs, WM_Score highly negatively correlated (drug sensitive) with drugs which targeted oncogenic related pathways, such as MAPK, EGFR, and mTOR signaling pathways, positively correlated (drug resistance) with drugs which targeted in apoptosis and cell cycle. Importantly, the WM_Score was associated with the therapeutic efficacy of PD-L1 blockade, suggesting that the development of potential drugs targeting these "writers" to aid the clinical benefits of immunotherapy. CONCLUSIONS Our study is the first to provide a comprehensive analysis of four RNA modifications in CRC. We revealed the potential function of these writers in TME, transcriptional and post-transcriptional events, and identified their therapeutic liability in targeted therapy and immunotherapy. This work highlights the cross-talk and potential clinical utility of RNA modification "writers" in cancer therapy.
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Affiliation(s)
- Huifang Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Jiameng Yao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Rujuan Bao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yu Dong
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Ting Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yanhua Du
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Gaoyang Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, NSW 2006 Australia
| | - Zhenzhen Xun
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Xiaoyin Niu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
- Department of Liver Surgery, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 China
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318
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Han SH, Choe J. Deciphering the molecular mechanisms of epitranscriptome regulation in cancer. BMB Rep 2021; 54:89-97. [PMID: 33298243 PMCID: PMC7907739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/13/2020] [Accepted: 11/25/2020] [Indexed: 08/08/2024] Open
Abstract
Post-transcriptional regulation is an indispensable cellular mechanism of gene expression control that dictates various cellular functions and cell fate decisions. Recently, various chemical RNA modifications, termed the "epitranscriptome," have been proposed to play crucial roles in the regulation of post-transcriptional gene expression. To date, more than 170 RNA modifications have been identified in almost all types of RNA. As with DNA modification-mediated control of gene expression, regulation of gene expression via RNA modification is also accomplished by three groups of proteins: writers, readers, and erasers. Several emerging studies have revealed that dysregulation in RNA modification is closely associated with tumorigenesis. Notably, the molecular outcomes of specific RNA modifications often have opposite cellular consequences. In this review, we highlight the current progress in the elucidation of the mechanisms of cancer development due to chemical modifications of various RNA species. [BMB Reports 2021; 54(2): 89-97].
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Affiliation(s)
- Seung Hun Han
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
| | - Junho Choe
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
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319
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Deal CE, Carfi A, Plante OJ. Advancements in mRNA Encoded Antibodies for Passive Immunotherapy. Vaccines (Basel) 2021; 9:vaccines9020108. [PMID: 33572679 PMCID: PMC7910832 DOI: 10.3390/vaccines9020108] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/28/2022] Open
Abstract
Monoclonal antibodies are the fastest growing therapeutic class in medicine today. They hold great promise for a myriad of indications, including cancer, allergy, autoimmune and infectious diseases. However, the wide accessibility of these therapeutics is hindered by manufacturing and purification challenges that result in high costs and long lead times. Efforts are being made to find alternative ways to produce and deliver antibodies in more expedient and cost-effective platforms. The field of mRNA has made significant progress in the last ten years and has emerged as a highly attractive means of encoding and producing any protein of interest in vivo. Through the natural role of mRNA as a transient carrier of genetic information for translation into proteins, in vivo expression of mRNA-encoded antibodies offer many advantages over recombinantly produced antibodies. In this review, we examine both preclinical and clinical studies that demonstrate the feasibility of mRNA-encoded antibodies and discuss the remaining challenges ahead.
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320
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Cheng MY, Tao WB, Yuan BF, Feng YQ. Methods for isolation of messenger RNA from biological samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:289-298. [PMID: 33300893 DOI: 10.1039/d0ay01912g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
RNA molecules contain many chemical modifications that can regulate a variety of biological processes. Messenger RNA (mRNA) molecules are critical components in the central dogma of molecular biology. The discovery of reversible chemical modifications in eukaryotic mRNA brings forward a new research field in RNA modification-mediated regulation of gene expression. The modifications in mRNA generally exist in low abundance. The use of highly pure mRNA is critical for the confident identification of new modifications as well as for the accurate quantification of existing modifications in mRNA. In addition, isolation of highly pure mRNA is the first step in many biological research studies. Therefore, the methods for isolating highly pure mRNA are important for mRNA-based downstream studies. A variety of methods for isolating mRNA have been developed in the past few decades and new methods continuously emerge. This review focuses on the methodologies and protocols for isolating mRNA populations. In addition, we discuss the advantages and limitations of these methods. We hope this paper will provide a general view of mRNA isolation strategies and facilitate studies that involve mRNA modifications and functions.
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Affiliation(s)
- Ming-Yu Cheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.
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321
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Lin MH, Cho CC, Chiu YC, Chien CY, Huang YP, Chang CF, Hsu CH. Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites. Commun Biol 2021; 4:123. [PMID: 33504944 PMCID: PMC7840908 DOI: 10.1038/s42003-020-01633-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
The macro domain is an ADP-ribose (ADPR) binding module, which is considered to act as a sensor to recognize nicotinamide adenine dinucleotide (NAD) metabolites, including poly ADPR (PAR) and other small molecules. The recognition of macro domains with various ligands is important for a variety of biological functions involved in NAD metabolism, including DNA repair, chromatin remodeling, maintenance of genomic stability, and response to viral infection. Nevertheless, how the macro domain binds to moieties with such structural obstacles using a simple cleft remains a puzzle. We systematically investigated the Middle East respiratory syndrome-coronavirus (MERS-CoV) macro domain for its ligand selectivity and binding properties by structural and biophysical approaches. Of interest, NAD, which is considered not to interact with macro domains, was co-crystallized with the MERS-CoV macro domain. Further studies at physiological temperature revealed that NAD has similar binding ability with ADPR because of the accommodation of the thermal-tunable binding pocket. This study provides the biochemical and structural bases of the detailed ligand-binding mode of the MERS-CoV macro domain. In addition, our observation of enhanced binding affinity of the MERS-CoV macro domain to NAD at physiological temperature highlights the need for further study to reveal the biological functions.
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Affiliation(s)
- Meng-Hsuan Lin
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chao-Cheng Cho
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Chih Chiu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chia-Yu Chien
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Ping Huang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Hua Hsu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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322
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Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export.
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323
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Sauter D, Kirchhoff F. Evolutionary conflicts and adverse effects of antiviral factors. eLife 2021; 10:e65243. [PMID: 33450175 PMCID: PMC7811402 DOI: 10.7554/elife.65243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Human cells are equipped with a plethora of antiviral proteins protecting them against invading viral pathogens. In contrast to apoptotic or pyroptotic cell death, which serves as ultima ratio to combat viral infections, these cell-intrinsic restriction factors may prevent or at least slow down viral spread while allowing the host cell to survive. Nevertheless, their antiviral activity may also have detrimental effects on the host. While the molecular mechanisms underlying the antiviral activity of restriction factors are frequently well investigated, potential undesired effects of their antiviral functions on the host cell are hardly explored. With a focus on antiretroviral proteins, we summarize in this review how individual restriction factors may exert adverse effects as trade-off for efficient defense against attacking pathogens.
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Affiliation(s)
- Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical CenterUlmGermany
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital TübingenTübingenGermany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical CenterUlmGermany
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324
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Moya-Ramírez I, Bouton C, Kontoravdi C, Polizzi K. High resolution biosensor to test the capping level and integrity of mRNAs. Nucleic Acids Res 2021; 48:e129. [PMID: 33152073 PMCID: PMC7736790 DOI: 10.1093/nar/gkaa955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/22/2020] [Accepted: 10/08/2020] [Indexed: 11/21/2022] Open
Abstract
5′ Cap structures are ubiquitous on eukaryotic mRNAs, essential for post-transcriptional processing, translation initiation and stability. Here we describe a biosensor designed to detect the presence of cap structures on mRNAs that is also sensitive to mRNA degradation, so uncapped or degraded mRNAs can be detected in a single step. The biosensor is based on a chimeric protein that combines the recognition and transduction roles in a single molecule. The main feature of this sensor is its simplicity, enabling semi-quantitative analyses of capping levels with minimal instrumentation. The biosensor was demonstrated to detect the capping level on several in vitro transcribed mRNAs. Its sensitivity and dynamic range remained constant with RNAs ranging in size from 250 nt to approximately 2700 nt and the biosensor was able to detect variations in the capping level in increments of at least 20%, with a limit of detection of 2.4 pmol. Remarkably, it also can be applied to more complex analytes, such mRNA vaccines and mRNAs transcribed in vivo. This biosensor is an innovative example of a technology able to detect analytically challenging structures such as mRNA caps. It could find application in a variety of scenarios, from quality analysis of mRNA-based products such as vaccines to optimization of in vitro capping reactions.
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Affiliation(s)
- Ignacio Moya-Ramírez
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Clement Bouton
- Department of Infectious Disease, Imperial College London, London W2 1NY, UK
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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325
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Liu XM, Zhou J. Multifaceted regulation of translation by the epitranscriptomic modification N 6-methyladenosine. Crit Rev Biochem Mol Biol 2021; 56:137-148. [PMID: 33412937 DOI: 10.1080/10409238.2020.1869174] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Translation occurring on cytoplasmic mRNA is precisely governed at three consecutive stages, including initiation, elongation and termination. A growing body of evidence has revealed that an emerging epitranscriptomic code N6-methyladenosine (m6A), asymmetrically present in a large subset of coding and non-coding transcripts, is crucially required for mediating the translatomic stability. Through recruiting translation machinery proteins, serving as a physical barrier, or directing RNA structural rearrangement and mRNA looping formation, m6A has been decoded to modulate translational dynamics through potentially influencing the progress of different stages, thereby forming an additional layer of complexity to the regulation of translation. In this review, we summarize the current understanding of how m6A guides mRNA translation under normal and stress conditions, highlighting the divergent molecular mechanisms of multifarious regulation of m6A-mediated translation.
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Affiliation(s)
- Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
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326
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Sacco MT, Horner SM. Flipping the script: viral capitalization of RNA modifications. Brief Funct Genomics 2021; 20:86-93. [PMID: 33401298 DOI: 10.1093/bfgp/elaa025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023] Open
Abstract
RNA encoded by RNA viruses is highly regulated so that it can function in multiple roles during the viral life cycle. These roles include serving as the mRNA template for translation or the genetic material for replication as well as being packaged into progeny virions. RNA modifications provide an emerging regulatory dimension to the RNA of viruses. Modification of the viral RNA can increase the functional genomic capacity of the RNA viruses without the need to encode and translate additional genes. Further, RNA modifications can facilitate interactions with host or viral RNA-binding proteins that promote replication or can prevent interactions with antiviral RNA-binding proteins. The mechanisms by which RNA viruses facilitate modification of their RNA are diverse. In this review, we discuss some of these mechanisms, including exploring the unknown mechanism by which the RNA of viruses that replicate in the cytoplasm could acquire the RNA modification N6-methyladenosine.
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327
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Detecting Internal N7-Methylguanosine mRNA Modifications by Differential Enzymatic Digestion Coupled with Mass Spectrometry Analysis. Methods Mol Biol 2021; 2298:247-259. [PMID: 34085250 DOI: 10.1007/978-1-0716-1374-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The recent discovery of reversible chemical modifications on mRNA has opened a new era of post-transcriptional gene regulation in eukaryotes. Among these modifications identified in eukaryotic mRNA, N7-methylguanosine (m7G) is unique owing to its presence in the 5' cap structure. Recently, it has been reported that m7G also exists internally in mRNA. Here, we describe a protocol of combining differential enzymatic digestion with liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis to detect internal m7G modification in mRNA. This protocol can also be used to quantify the level of m7G at both the 5' cap and internal positions of mRNA.
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328
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Yang H, Rao Z. Structural biology of SARS-CoV-2 and implications for therapeutic development. Nat Rev Microbiol 2021; 19:685-700. [PMID: 34535791 PMCID: PMC8447893 DOI: 10.1038/s41579-021-00630-8] [Citation(s) in RCA: 242] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an unprecedented global health crisis. However, therapeutic options for treatment are still very limited. The development of drugs that target vital proteins in the viral life cycle is a feasible approach for treating COVID-19. Belonging to the subfamily Orthocoronavirinae with the largest RNA genome, SARS-CoV-2 encodes a total of 29 proteins. These non-structural, structural and accessory proteins participate in entry into host cells, genome replication and transcription, and viral assembly and release. SARS-CoV-2 proteins can individually perform essential physiological roles, be components of the viral replication machinery or interact with numerous host cellular factors. In this Review, we delineate the structural features of SARS-CoV-2 from the whole viral particle to the individual viral proteins and discuss their functions as well as their potential as targets for therapeutic interventions.
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Affiliation(s)
- Haitao Yang
- grid.440637.20000 0004 4657 8879Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zihe Rao
- grid.440637.20000 0004 4657 8879Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.12527.330000 0001 0662 3178Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China ,grid.216938.70000 0000 9878 7032State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China ,grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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329
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Abstract
The mRNA epitranscriptome imparts diversity to gene expression by installing chemical modifications. Advances in detection methods have identified chemical modifications in eukaryotic, bacterial, and viral messenger RNAs (mRNAs). The biological functions of modifications in mRNAs still remain to be understood. Chemical modifications are introduced in synthetic mRNAs meant for therapeutic applications to maximize expression from the synthetic mRNAs and to evade the host immune response. This overview provides a background of chemical modifications found in mRNAs, with an emphasis on pseudouridine and its known effects on the mRNA life cycle, its potential applications in synthetic mRNA, and the methods used to assess its effects on mRNA translation.
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Affiliation(s)
- Bijoyita Roy
- RNA and Genome Editing, New England Biolabs Inc, Ipswich, MA, USA.
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330
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El Hassab MA, Ibrahim TM, Shoun AA, Al-Rashood ST, Alkahtani HM, Alharbi A, Eskandrani RO, Eldehna WM. In silico identification of potential SARS COV-2 2′-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations. RSC Adv 2021; 11:16026-16033. [PMID: 35481212 PMCID: PMC9029993 DOI: 10.1039/d1ra01809d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
In the present era, there are many efforts trying to face the emerging and successive waves of the COVID-19 pandemic. This has led to considering new and unusual targets for SARS CoV-2. 2′-O-Methyltransferase (nsp16) is a key and attractive target in the SARS CoV-2 life cycle since it is responsible for the viral RNA protection via a cap formation process. In this study, we propose a new potential inhibitor for SARS COV-2 2′-O-methyltransferase (nsp16). A fragment library was screened against the co-crystal structure of the SARS COV-2 2′-O-methyltransferase complexed with Sinefungin (nsp16 – PDB ID: 6WKQ), and consequently the best proposed fragments were linked via a de novo approach to build molecule AP-20. Molecule AP-20 displayed a superior docking score to Sinefungin and reproduced the key interactions in the binding site of 2′-O-methyltransferase. Three molecular dynamic simulations of the 2′-O-methyltransferase apo structure and its complexed forms with AP-20 and Sinefungin were performed for 150 nano-seconds to provide insights on the dynamic nature of such setups and to assess the stability of the proposed AP-20/enzyme complex. AP-20/enzyme complex demonstrated better stability for the ligand–enzyme complex compared to Sinefungin in a respective setup. Furthermore, MM-PBSA binding free energy calculations showed a better profile for AP-20/enzyme complex compared to Sinefungin/enzyme complex emphasizing the potential inhibitory effect of AP-20 on SARS COV-2 2′-O-methyltransferase. We endorse our designed molecule AP-20 to be further explored via experimental evaluations to confront the spread of the emerging COVID-19. Also, in silico ADME profiling has ascribed to AP-20 an excellent safety and metabolic stability profile. The identification of AP-20 as a potential SARS COV-2 2′-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations.![]()
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Affiliation(s)
- Mahmoud A. El Hassab
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- Badr University in Cairo (BUC)
- Cairo
- Egypt
| | - Tamer M. Ibrahim
- Department of Pharmaceutical Chemistry
- Faculty of Pharmacy
- Kafrelsheikh University
- Kafrelsheikh
- Egypt
| | - Aly A. Shoun
- Department of Microbiology & Immunology
- Faculty of Pharmacy
- Sinai University
- North Sinai
- Egypt
| | - Sara T. Al-Rashood
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Hamad M. Alkahtani
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Amal Alharbi
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Razan O. Eskandrani
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry
- Faculty of Pharmacy
- Kafrelsheikh University
- Kafrelsheikh
- Egypt
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331
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Ciuman RR. Understanding Human Body Maintenance, Protection, and Modification: Antibodies, Genetics, Stem Cells and Connected Artificial Intelligence Applications—Where Are We? Health (London) 2021. [DOI: 10.4236/health.2021.137059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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332
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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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333
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Lu Q, Ren F, Yan J, Zhang Y, Awais M, He J, Sun J. Alkaline phosphatase can promote the replication of Bombyx mori cypovirus 1 by interaction with its turret protein. Virus Res 2020; 292:198261. [PMID: 33316354 DOI: 10.1016/j.virusres.2020.198261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 11/28/2020] [Accepted: 12/06/2020] [Indexed: 11/25/2022]
Abstract
Bombyx mori cypovirus 1 (BmCPV1) is a member of the Reoviridae family which is characterized by its single-layered capsid. Similar with other turreted viruses in the Reoviridae, transcription of BmCPV1 occurs inside the capsid, and the nascent mRNA is released to the turret which consists of five turret proteins (TPs) and located at the 5-fold axis of the outer capsid, then the capping enzyme TP will guanylate and methylate the nascent viral mRNA to produce a matured mRNA. However, during these processes, how the BmCPV1 draws other cellular proteins to facilitate its replication is still lesser-known. Here we used an ELISA to investigate the interaction between ALP and BmCPV1. A co-immunoprecipitation technique was employed to detect the interaction of ALP with the Methylase domain of TP. We further studied whether ALP affects the replication of BmCPV1 inside the cell, results show that reducing the expression of ALP through RNAi reduced the transcription level of the BmCPV1 VP1 gene, which was increased by overexpression of ALP. In summary, our data demonstrate an interaction between ALP and BmCPV1 and that ALP promoted the replication of BmCPV1, and support our hypothesis of the ALP is an RTPase to facilitate the capping process of BmCPV1.
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Affiliation(s)
- Qiuyuan Lu
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Feifei Ren
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jiming Yan
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yinong Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Mian Awais
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jian He
- Public Experimental Teaching Center, Sun Yat-sen University, Guangzhou, Guangdong, 510642, China.
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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334
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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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335
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Processing of coding and non-coding RNAs in plant development and environmental responses. Essays Biochem 2020; 64:931-945. [DOI: 10.1042/ebc20200029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]
Abstract
Abstract
Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5′ capping, 3′-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant–environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.
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336
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Deaver JW, López SM, Ryan PJ, Nghiem PP, Riechman SE, Fluckey JD. Regulation of cellular anabolism by mTOR: or how I learned to stop worrying and love translation. SPORTS MEDICINE AND HEALTH SCIENCE 2020; 2:195-201. [PMID: 35782997 PMCID: PMC9219308 DOI: 10.1016/j.smhs.2020.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- J. William Deaver
- Department of Health and Kinesiology, 107 Gilchrist Building, 2929 Research Parkway, Texas A&M University, College Station, TX, USA
| | - Sara Mata López
- Department of Veterinary Integrative Biosciences, 402 Raymond Stotzer Pkwy Building 2, Texas A&M University, College Station, TX, USA
| | - Patrick J. Ryan
- Department of Health and Kinesiology, 107 Gilchrist Building, 2929 Research Parkway, Texas A&M University, College Station, TX, USA
| | - Peter P. Nghiem
- Department of Veterinary Integrative Biosciences, 402 Raymond Stotzer Pkwy Building 2, Texas A&M University, College Station, TX, USA
| | - Steven E. Riechman
- Department of Health and Kinesiology, 107 Gilchrist Building, 2929 Research Parkway, Texas A&M University, College Station, TX, USA
| | - James D. Fluckey
- Department of Health and Kinesiology, 107 Gilchrist Building, 2929 Research Parkway, Texas A&M University, College Station, TX, USA
- Corresponding author. Department of Health and Kinesiology, 107 Gilchrist Building, Room 313, 2929 Research Parkway, Texas A&M University, College Station, TX, 77843-4243, USA.
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337
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Leitão MIPS, Gonzalez C, Francescato G, Filipiak Z, Petronilho A. On the reactivity of mRNA Cap0: C-H oxidative addition of 7-methylguanosine to Pt 0 and base pairing studies. Chem Commun (Camb) 2020; 56:13365-13368. [PMID: 33030477 DOI: 10.1039/d0cc06075e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
7-Methylguanosine, whose lability to form an ylide/NHC has been known for decades, reacts with [Pt(PPh3)4] via C-H oxidative addition to yield a hydrido-PtII carbene complex. 1H NMR studies on Watson-Crick base-pairs showed no significant effect of metallation.
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Affiliation(s)
- Maria Inês P S Leitão
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Carmen Gonzalez
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Giulia Francescato
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Zuzanna Filipiak
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Ana Petronilho
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
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338
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Bell PJ. Evidence supporting a viral origin of the eukaryotic nucleus. Virus Res 2020; 289:198168. [DOI: 10.1016/j.virusres.2020.198168] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022]
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339
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Agana BA, Wysocki VH, Schoenberg DR. Cytoplasmic mRNA recapping has limited impact on proteome complexity. Open Biol 2020; 10:200313. [PMID: 33234072 PMCID: PMC7729026 DOI: 10.1098/rsob.200313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/26/2020] [Indexed: 01/25/2023] Open
Abstract
The m7G cap marks the 5' end of all eukaryotic mRNAs, but there are also capped ends that map downstream within spliced exons. A portion of the mRNA transcriptome undergoes a cyclical process of decapping and recapping, termed cap homeostasis, which impacts the translation and stability of these mRNAs. Blocking cytoplasmic capping results in the appearance of uncapped 5' ends at native cap sites but also near downstream cap sites. If translation initiates at these sites the products would lack the expected N-terminal sequences, raising the possibility of a link between mRNA recapping and proteome complexity. We performed a shotgun proteomics analysis on cells carrying an inducible inhibitor of cytoplasmic capping. A total of 21 875 tryptic peptides corresponding to 3565 proteins were identified in induced and uninduced cells. Of these, only 29 proteins significantly increased, and 28 proteins significantly decreased, when cytoplasmic capping was inhibited, indicating mRNA recapping has little overall impact on protein expression. In addition, overall peptide coverage per protein did not change significantly when cytoplasmic capping was inhibited. Together with previous work, our findings indicate cap homeostasis functions primarily in gating mRNAs between translating and non-translating states, and not as a source of proteome complexity.
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Affiliation(s)
- Bernice A. Agana
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H. Wysocki
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel R. Schoenberg
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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340
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In vitro production of synthetic viral RNAs and their delivery into mammalian cells and the application of viral RNAs in the study of innate interferon responses. Methods 2020; 183:21-29. [PMID: 31682923 DOI: 10.1016/j.ymeth.2019.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 12/24/2022] Open
Abstract
Mammalian cells express different types of RNA molecules that can be classified as protein coding RNAs (mRNA) and non-coding RNAs (ncRNAs) the latter of which have housekeeping and regulatory functions in cells. Cellular RNAs are not recognized by cellular pattern recognition receptors (PRRs) and innate immunity is not activated. RNA viruses encode and express RNA molecules that usually differ from cell-specific RNAs and they include for instance 5'capped and 5'mono- and triphosphorylated RNAs, small viral RNAs and viral RNA-protein complexes called vRNPs. These molecules are recognized by certain members of Toll-like receptor (TLR) and RIG-I-like receptor (RLR) families leading to activation of innate immune responses and the production of antiviral cytokines, such as type I and type III interferons (IFNs). Virus-specific ssRNA and dsRNA molecules that mimic the viral genomic RNAs or their replication intermediates can efficiently be produced by bacteriophage T7 DNA-dependent RNA polymerase and bacteriophage phi6 RNA-dependent RNA polymerase, respectively. These molecules can then be delivered into mammalian cells and the mechanisms of activation of innate immune responses can be studied. In addition, synthetic viral dsRNAs can be processed to small interfering RNAs (siRNAs) by a Dicer enzyme to produce a swarm of antiviral siRNAs. Here we describe the biology of RNAs, their in vitro production and delivery into mammalian cells as well as how these molecules can be used to inhibit virus replication and to study the mechanisms of activation of the innate immune system.
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341
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Reversal of nucleobase methylation by dioxygenases. Nat Chem Biol 2020; 16:1160-1169. [DOI: 10.1038/s41589-020-00675-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
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342
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Cantu F, Cao S, Hernandez C, Dhungel P, Spradlin J, Yang Z. Poxvirus-encoded decapping enzymes promote selective translation of viral mRNAs. PLoS Pathog 2020; 16:e1008926. [PMID: 33031446 PMCID: PMC7575113 DOI: 10.1371/journal.ppat.1008926] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/20/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
Cellular decapping enzymes negatively regulate gene expression by removing the methylguanosine cap at the 5’ end of eukaryotic mRNA, rendering mRNA susceptible to degradation and repressing mRNA translation. Vaccinia virus (VACV), the prototype poxvirus, encodes two decapping enzymes, D9 and D10, that induce the degradation of both cellular and viral mRNAs. Using a genome-wide survey of translation efficiency, we analyzed vaccinia virus mRNAs in cells infected with wild type VACV and mutant VACVs with inactivated decapping enzymes. We found that VACV decapping enzymes are required for selective translation of viral post-replicative mRNAs (transcribed after viral DNA replication) independent of PKR- and RNase L-mediated translation repression. Further molecular characterization demonstrated that VACV decapping enzymes are necessary for efficient translation of mRNA with a 5'-poly(A) leader, which are present in all viral post-replicative mRNAs. Inactivation of D10 alone in VACV significantly impairs poly(A)-leader-mediated translation. Remarkably, D10 stimulates mRNA translation in the absence of VACV infection with a preference for RNA containing a 5’-poly(A) leader. We further revealed that VACV decapping enzymes are needed for 5’-poly(A) leader-mediated cap-independent translation enhancement during infection. Our findings identified a mechanism by which VACV mRNAs are selectively translated through subverting viral decapping enzymes to stimulate 5’-poly(A) leader-mediated translation. Decapping enzymes are encoded in eukaryotic cells and some viruses. Previous studies indicated that decapping enzymes are negative gene expression regulators by accelerating mRNA degradation and repressing translation. Surprisingly however, in this study we found that vaccinia virus (VACV) encoded-decapping enzymes, D9 and D10, are required to promote selective synthesis of viral proteins, although they are known to promote both cellular and viral mRNA degradation. We further showed that the unusual 5'-UTR of VACV mRNA, the 5'-poly(A) leader, confers an advantage to mRNA translation promoted by the decapping enzymes during vaccinia virus infection. Moreover, D9 and D10 are necessary for stimulating poly(A)-leader-mediated cap-independent translation enhancement during VACV infection. In the absence of VACV infection, D10 alone stimulates mRNA translation in a decapping activity-dependent manner, with a preference for mRNA that contains a poly(A) leader. The stimulation of mRNA translation by D10 is unique among decapping enzymes. Therefore, we identified a new mechanism to selectively synthesize VACV proteins through a coordination of viral mRNA 5’-UTR and virus-encoded decapping enzymes.
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Affiliation(s)
- Fernando Cantu
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Shuai Cao
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Candy Hernandez
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Pragyesh Dhungel
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Joshua Spradlin
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Zhilong Yang
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
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343
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Xie N, Zhang L, Gao W, Huang C, Huber PE, Zhou X, Li C, Shen G, Zou B. NAD + metabolism: pathophysiologic mechanisms and therapeutic potential. Signal Transduct Target Ther 2020; 5:227. [PMID: 33028824 PMCID: PMC7539288 DOI: 10.1038/s41392-020-00311-7] [Citation(s) in RCA: 372] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) and its metabolites function as critical regulators to maintain physiologic processes, enabling the plastic cells to adapt to environmental changes including nutrient perturbation, genotoxic factors, circadian disorder, infection, inflammation and xenobiotics. These effects are mainly achieved by the driving effect of NAD+ on metabolic pathways as enzyme cofactors transferring hydrogen in oxidation-reduction reactions. Besides, multiple NAD+-dependent enzymes are involved in physiology either by post-synthesis chemical modification of DNA, RNA and proteins, or releasing second messenger cyclic ADP-ribose (cADPR) and NAADP+. Prolonged disequilibrium of NAD+ metabolism disturbs the physiological functions, resulting in diseases including metabolic diseases, cancer, aging and neurodegeneration disorder. In this review, we summarize recent advances in our understanding of the molecular mechanisms of NAD+-regulated physiological responses to stresses, the contribution of NAD+ deficiency to various diseases via manipulating cellular communication networks and the potential new avenues for therapeutic intervention.
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Affiliation(s)
- Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Lu Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Wei Gao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Peter Ernst Huber
- CCU Molecular and Radiation Oncology, German Cancer Research Center; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Xiaobo Zhou
- First Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Changlong Li
- West China School of Basic Medical Sciences & Forensic Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guobo Shen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
| | - Bingwen Zou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
- CCU Molecular and Radiation Oncology, German Cancer Research Center; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.
- Department of Thoracic Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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344
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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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345
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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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346
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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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347
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Li D, Xia L, Zhou Q, Wang L, Chen D, Gao X, Li Y. Label-Free Detection of miRNA Using Surface-Enhanced Raman Spectroscopy. Anal Chem 2020; 92:12769-12773. [DOI: 10.1021/acs.analchem.0c03335] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Dan Li
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang, Guizhou 550025, China
- School of Physics, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang, Guizhou550025, China
| | - Ling Xia
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang, Guizhou 550025, China
| | - Qianjiang Zhou
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang, Guizhou 550025, China
| | | | - Dongmei Chen
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang, Guizhou 550025, China
| | - Xin Gao
- School of Physics, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang, Guizhou550025, China
| | - Yang Li
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang, Guizhou 550025, China
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348
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Zarnack K, Balasubramanian S, Gantier MP, Kunetsky V, Kracht M, Schmitz ML, Sträßer K. Dynamic mRNP Remodeling in Response to Internal and External Stimuli. Biomolecules 2020; 10:biom10091310. [PMID: 32932892 PMCID: PMC7565591 DOI: 10.3390/biom10091310] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Signal transduction and the regulation of gene expression are fundamental processes in every cell. RNA-binding proteins (RBPs) play a key role in the post-transcriptional modulation of gene expression in response to both internal and external stimuli. However, how signaling pathways regulate the assembly of RBPs with mRNAs remains largely unknown. Here, we summarize observations showing that the formation and composition of messenger ribonucleoprotein particles (mRNPs) is dynamically remodeled in space and time by specific signaling cascades and the resulting post-translational modifications. The integration of signaling events with gene expression is key to the rapid adaptation of cells to environmental changes and stress. Only a combined approach analyzing the signal transduction pathways and the changes in post-transcriptional gene expression they cause will unravel the mechanisms coordinating these important cellular processes.
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Affiliation(s)
- Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt a.M., Germany;
| | | | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia;
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Vladislav Kunetsky
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
- Correspondence:
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349
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Interfering with mRNA Methylation by the 2′O-Methyltransferase (NSP16) from SARS-CoV-2 to Tackle the COVID-19 Disease. Catalysts 2020. [DOI: 10.3390/catal10091023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The pandemic associated to Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2) has resulted in a huge number of deaths and infected people. Although several vaccine programmes are currently underway and have reached phase 3, and a few small size drugs repurposed to aid treatment of severe cases of COVID-19 infections, effective therapeutic options for this disease do not currently exist. NSP16 is a S-adenosyl-L-Methionine (SAM) dependent 2′O-Methyltransferase that converts mRNA cap-0 into cap-1 structure to prevent virus detection by cell innate immunity mechanisms. NSP16 methylates the ribose 2′O-position of the first nucleotide of the mRNA only in the presence of an interacting partner, the protein NSP10. This feature suggests that inhibition of the NSP16 may represent a therapeutic window to treat COVID-19. To test this idea, we performed comparative structural analyses of the NSP16 present in human coronaviruses and developed a sinefungin (SFG) similarity-based virtual screening campaign to assess the druggability of the SARS-CoV-2 NSP16 enzyme. Through these studies, we identified the SFG analogue 44601604 as a promising more potent inhibitor of NSP16 to limit viral replication in infected cells, favouring viral clearance.
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350
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
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