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Yang N, Zhang Q, Wang Q, Zhang Y, Li S, Zhao Y, Shi X, Li Q, Xu X. Nsp10-interacting host protein SAP18 restricts PEDV replication in Marc-145 cells via enhancing dephosphorylation of RIG-I. Vet Microbiol 2024; 294:110124. [PMID: 38795403 DOI: 10.1016/j.vetmic.2024.110124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/13/2024] [Accepted: 05/18/2024] [Indexed: 05/27/2024]
Abstract
PEDV, a single-stranded RNA virus, causes significant economic losses in the pig industry. Sin3-associated protein 18 (SAP18) is known for its role in transcriptional inhibition and RNA splicing. However, research on SAP18's involvement in PEDV infection is limited. Here, we identified an interaction between SAP18 and PEDV nonstructural protein 10 (Nsp10) using immunoprecipitation-mass spectrometry (IP-MS) and confirmed it through immunoprecipitation and laser confocal microscopy. Additionally, PEDV Nsp10 reduced SAP18 protein levels and induced its cytoplasmic accumulation. Overexpressing SAP18 suppressed PEDV replication, meanwhile its knockdown via short interfering RNA (siRNA) enhanced replication. SAP18 overexpression boosted IRF3 and NF-κB P65 phosphorylation, nuclear translocation, and IFN-β antiviral response. Furthermore, SAP18 upregulated RIG-I expression and facilitated its dephosphorylation, while SAP18 knockdown had the opposite effect. Finally, SAP18 interacted with phosphatase 1 (PP1) catalytic subunit alpha (PPP1CA), promoting PPP1CA-RIG-I interaction during PEDV infection. These findings highlight SAP18's role in activating the type I interferon pathway and inhibiting viral replication by promoting RIG-I dephosphorylation through its interaction with PPP1CA.
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Affiliation(s)
- Naling Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Qi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Quanqiong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Yanxia Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Shifan Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Yina Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Xiaojie Shi
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Qinfan Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Xingang Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi 712100, China.
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2
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Iyengar SM, Barnsley KK, Vu HY, Bongalonta IJA, Herrod AS, Scott JA, Ondrechen MJ. Identification and characterization of alternative sites and molecular probes for SARS-CoV-2 target proteins. Front Chem 2022; 10:1017394. [PMID: 36385993 PMCID: PMC9659918 DOI: 10.3389/fchem.2022.1017394] [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: 08/12/2022] [Accepted: 10/10/2022] [Indexed: 12/05/2022] Open
Abstract
Three protein targets from SARS-CoV-2, the viral pathogen that causes COVID-19, are studied: the main protease, the 2′-O-RNA methyltransferase, and the nucleocapsid (N) protein. For the main protease, the nucleophilicity of the catalytic cysteine C145 is enabled by coupling to three histidine residues, H163 and H164 and catalytic dyad partner H41. These electrostatic couplings enable significant population of the deprotonated state of C145. For the RNA methyltransferase, the catalytic lysine K6968 that serves as a Brønsted base has significant population of its deprotonated state via strong coupling with K6844 and Y6845. For the main protease, Partial Order Optimum Likelihood (POOL) predicts two clusters of biochemically active residues; one includes the catalytic H41 and C145 and neighboring residues. The other surrounds a second pocket adjacent to the catalytic site and includes S1 residues F140, L141, H163, E166, and H172 and also S2 residue D187. This secondary recognition site could serve as an alternative target for the design of molecular probes. From in silico screening of library compounds, ligands with predicted affinity for the secondary site are reported. For the NSP16-NSP10 complex that comprises the RNA methyltransferase, three different sites are predicted. One is the catalytic core at the conserved K-D-K-E motif that includes catalytic residues D6928, K6968, and E7001 plus K6844. The second site surrounds the catalytic core and consists of Y6845, C6849, I6866, H6867, F6868, V6894, D6895, D6897, I6926, S6927, Y6930, and K6935. The third is located at the heterodimer interface. Ligands predicted to have high affinity for the first or second sites are reported. Three sites are also predicted for the nucleocapsid protein. This work uncovers key interactions that contribute to the function of the three viral proteins and also suggests alternative sites for ligand design.
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3
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Klima M, Khalili Yazdi A, Li F, Chau I, Hajian T, Bolotokova A, Kaniskan HÜ, Han Y, Wang K, Li D, Luo M, Jin J, Boura E, Vedadi M. Crystal structure of
SARS‐CoV
‐2 nsp10–nsp16 in complex with small molecule inhibitors,
SS148
and
WZ16. Protein Sci 2022; 31:e4395. [PMID: 36040262 PMCID: PMC9375521 DOI: 10.1002/pro.4395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/11/2022] [Accepted: 07/12/2022] [Indexed: 01/04/2023]
Abstract
SARS‐CoV‐2 nsp10–nsp16 complex is a 2′‐O‐methyltransferase (MTase) involved in viral RNA capping, enabling the virus to evade the immune system in humans. It has been considered a valuable target in the discovery of antiviral therapeutics, as the RNA cap formation is crucial for viral propagation. Through cross‐screening of the inhibitors that we previously reported for SARS‐CoV‐2 nsp14 MTase activity against nsp10–nsp16 complex, we identified two compounds (SS148 and WZ16) that also inhibited nsp16 MTase activity. To further enable the chemical optimization of these two compounds towards more potent and selective dual nsp14/nsp16 MTase inhibitors, we determined the crystal structure of nsp10–nsp16 in complex with each of SS148 and WZ16. As expected, the structures revealed the binding of both compounds to S‐adenosyl‐L‐methionine (SAM) binding pocket of nsp16. However, our structural data along with the biochemical mechanism of action determination revealed an RNA‐dependent SAM‐competitive pattern of inhibition for WZ16, clearly suggesting that binding of the RNA first may help the binding of some SAM competitive inhibitors. Both compounds also showed some degree of selectivity against human protein MTases, an indication of great potential for chemical optimization towards more potent and selective inhibitors of coronavirus MTases. PDB Code(s): 7R1T and 7R1U
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Affiliation(s)
- Martin Klima
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague 6 Czech Republic
| | | | - Fengling Li
- Structural Genomics Consortium University of Toronto Toronto Ontario Canada
| | - Irene Chau
- Structural Genomics Consortium University of Toronto Toronto Ontario Canada
| | - Taraneh Hajian
- Structural Genomics Consortium University of Toronto Toronto Ontario Canada
| | - Albina Bolotokova
- Structural Genomics Consortium University of Toronto Toronto Ontario Canada
| | - H. Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Yulin Han
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Ke Wang
- Chemical Biology Program Memorial Sloan Kettering Cancer Center New York New York USA
- Department of Pharmacology and Toxicology University of Toronto Toronto Ontario Canada
| | - Deyao Li
- Chemical Biology Program Memorial Sloan Kettering Cancer Center New York New York USA
- Department of Pharmacology and Toxicology University of Toronto Toronto Ontario Canada
| | - Minkui Luo
- Chemical Biology Program Memorial Sloan Kettering Cancer Center New York New York USA
- Department of Pharmacology and Toxicology University of Toronto Toronto Ontario Canada
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague 6 Czech Republic
| | - Masoud Vedadi
- Structural Genomics Consortium University of Toronto Toronto Ontario Canada
- Program of Pharmacology Weill Cornell Medical College of Cornell University New York New York USA
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4
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Zhu L, Liu S, Zhuo Z, Lin Y, Zhang Y, Wang X, Kong L, Wang T. Expression and immunogenicity of nsp10 protein of porcine epidemic diarrhea virus. Res Vet Sci 2022; 144:34-43. [PMID: 35038674 PMCID: PMC8721950 DOI: 10.1016/j.rvsc.2021.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 12/01/2021] [Accepted: 12/28/2021] [Indexed: 12/16/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV), a swine enteropathogenic coronavirus, causes lethal watery diarrhea to the piglets, which poses significant economic losses and public health concerns. The nsp10 protein of PEDV is essential regulatory subunits that are critical for virus replication. Since PEDV nsp10 is a crucial regulator of viral RNA synthesis, it is promising that nsp10 might become anti-virus drugs target or candidate for rapid diagnosis of PEDV infection. In this study, the PEDV nsp10 was inserted into pMAL-c2x-MBP / pET-28a vector, efficiently and stably expressed in E.coli system. Then the purified nsp10 protein was found to mediate potent antibody responses in immunized mice. The antibodies of immunized mice and PEDV infection swine strongly recognized purified nsp10 protein from cell lysates. Furthermore, cytokines test revealed that the expression of IL-2, IL-4, IL-10, TNF-α, IFN-γ were significantly higher than those in control group, indicated that purified nsp10 protein induce the cellular immune response mechanism in mice. Using modified seroneutralization test, we also demonstrated that sera from nsp10-immunized mice inhibited PEDV replication to some extent. These findings suggest that nsp10 has a high immunogenicity. This study may have implications for future development of PEDV detection or anti-virus drugs for swine.
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Affiliation(s)
- Liting Zhu
- Institute of Pathogenic Microorganism, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Shiguo Liu
- Institute of Pathogenic Microorganism, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zewen Zhuo
- Institute of Pathogenic Microorganism, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yanxi Lin
- Institute of Pathogenic Microorganism, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yanni Zhang
- Jiangxi Province Center for Disease Control and Prevention, Nanchang, Jiangxi, China
| | - Xiaoling Wang
- Institute of Pathogenic Microorganism, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lingbao Kong
- Institute of Pathogenic Microorganism, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ting Wang
- Institute of Pathogenic Microorganism, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
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5
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Bhavaniramya S, Ramar V, Vishnupriya S, Palaniappan R, Sibiya A, Baskaralingam V. Comprehensive analysis of SARS-COV-2 drug targets and pharmacological aspects in treating the COVID-19. Curr Mol Pharmacol 2021; 15:393-417. [PMID: 34382513 DOI: 10.2174/1874467214666210811120635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/27/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
Corona viruses are enveloped, single-stranded RNA (Ribonucleic acid) viruses and they cause pandemic diseases having a devastating effect on both human healthcare and the global economy. To date, six corona viruses have been identified as pathogenic organisms which are significantly responsible for the infection and also cause severe respiratory diseases. Among them, the novel SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) caused a major outbreak of corona virus diseases 2019 (COVID-19). Coronaviridae family members can affects both humans and animals. In human, corona viruses cause severe acute respiratory syndrome with mild to severe outcomes. Several structural and genomics have been investigated, and the genome encodes about 28 proteins most of them with unknown function though it shares remarkable sequence identity with other proteins. There is no potent and licensed vaccine against SARS-CoV-2 and several trials are underway to investigate the possible therapeutic agents against viral infection. However, some of the antiviral drugs that have been investigated against SARS-CoV-2 are under clinical trials. In the current review we comparatively emphasize the emergence and pathogenicity of the SARS-CoV-2 and their infection and discuss the various putative drug targets of both viral and host receptors for developing effective vaccines and therapeutic combinations to overcome the viral outbreak.
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Affiliation(s)
- Sundaresan Bhavaniramya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vanajothi Ramar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024. India
| | - Selvaraju Vishnupriya
- College of Food and Dairy Technology, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600052. India
| | - Ramasamy Palaniappan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education (BIHER), Chennai-600044, Tamilnadu. India
| | - Ashokkumar Sibiya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vaseeharan Baskaralingam
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
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6
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Kubatova N, Qureshi NS, Altincekic N, Abele R, Bains JK, Ceylan B, Ferner J, Fuks C, Hargittay B, Hutchison MT, de Jesus V, Kutz F, Wirtz Martin MA, Meiser N, Linhard V, Pyper DJ, Trucks S, Fürtig B, Hengesbach M, Löhr F, Richter C, Saxena K, Schlundt A, Schwalbe H, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Wöhnert J. 1H, 13C, and 15N backbone chemical shift assignments of coronavirus-2 non-structural protein Nsp10. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:65-71. [PMID: 33159807 PMCID: PMC7648550 DOI: 10.1007/s12104-020-09984-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
The international Covid19-NMR consortium aims at the comprehensive spectroscopic characterization of SARS-CoV-2 RNA elements and proteins and will provide NMR chemical shift assignments of the molecular components of this virus. The SARS-CoV-2 genome encodes approximately 30 different proteins. Four of these proteins are involved in forming the viral envelope or in the packaging of the RNA genome and are therefore called structural proteins. The other proteins fulfill a variety of functions during the viral life cycle and comprise the so-called non-structural proteins (nsps). Here, we report the near-complete NMR resonance assignment for the backbone chemical shifts of the non-structural protein 10 (nsp10). Nsp10 is part of the viral replication-transcription complex (RTC). It aids in synthesizing and modifying the genomic and subgenomic RNAs. Via its interaction with nsp14, it ensures transcriptional fidelity of the RNA-dependent RNA polymerase, and through its stimulation of the methyltransferase activity of nsp16, it aids in synthesizing the RNA cap structures which protect the viral RNAs from being recognized by the innate immune system. Both of these functions can be potentially targeted by drugs. Our data will aid in performing additional NMR-based characterizations, and provide a basis for the identification of possible small molecule ligands interfering with nsp10 exerting its essential role in viral replication.
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Affiliation(s)
- N Kubatova
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - R Abele
- Institute for Biochemistry, Biocentre, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J K Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J Ferner
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - C Fuks
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Hargittay
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M T Hutchison
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - V de Jesus
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - F Kutz
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N Meiser
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - V Linhard
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - D J Pyper
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - S Trucks
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany.
| | - F Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - C Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - K Saxena
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - A Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - H Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany.
| | - S Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - A Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr 10, 64287, Darmstadt, Germany
| | - J Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
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7
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Fang P, Hong Y, Xia S, Zhang J, Ren J, Zhou Y, Fang L, Xiao S. Porcine deltacoronavirus nsp10 antagonizes interferon-β production independently of its zinc finger domains. Virology 2021; 559:46-56. [PMID: 33813212 DOI: 10.1016/j.virol.2021.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 11/18/2022]
Abstract
Porcine deltacoronavirus (PDCoV) is a novel swine enteropathogenic coronavirus that causes serious vomiting and diarrhea in piglets. Previous work demonstrated that PDCoV infection inhibits type I interferon (IFN) production. Here, we found that ectopic expression of PDCoV nsp10 significantly inhibited Sendai virus (SeV)-induced IFN-β production by impairing the phosphorylation and nuclear translocation of two transcription factors, IRF3 and NF-κB p65 subunit. Interestingly, experiments with truncated mutants and site-directed mutagenesis revealed that PDCoV nsp10 mutants with missing or destroyed zinc fingers (ZFs) domains also impeded SeV-induced IFN-β production, suggesting that nsp10 does not require its ZF domains to antagonize IFN-β production. Further work found that co-expression of nsp10 with nsp14 or nsp16, two replicative enzymes, significantly enhanced the inhibitory effects of nsp10 on IFN-β. Taken together, our results demonstrate that PDCoV nsp10 antagonizes IFN via a ZF-independent mechanism and has a synergistic effect with nsp14 and nsp16 on inhibiting IFN-β production.
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Affiliation(s)
- Puxian Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Yingying Hong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Sijin Xia
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Jiansong Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Jie Ren
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Yanrong Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
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8
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Parida PK, Paul D, Chakravorty D. Nature's therapy for COVID-19: Targeting the vital non-structural proteins (NSP) from SARS-CoV-2 with phytochemicals from Indian medicinal plants. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 1:100002. [PMID: 35403083 PMCID: PMC7691168 DOI: 10.1016/j.phyplu.2020.100002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Containing COVID-19 is still a global challenge. It has affected the "normal" world by targeting its economy and health sector. The effect is shifting of focus of research from life threatening diseases like cancer. Thus, we need to develop a medical solution at the earliest. The purpose of this present work was to understand the efficacy of 22 rationally screened phytochemicals from Indian medicinal plants obtained from our previous work, following drug-likeness properties, against 6 non-structural-proteins (NSP) from SARS-CoV-2. METHODS 100 ns molecular dynamics simulations were performed, and relative binding free energies were computed by MM/PBSA. Further, principal component analysis, dynamic cross correlation and hydrogen bond occupancy were analyzed to characterize protein-ligand interactions. Biological pathway enrichment analysis was also carried out to elucidate the therapeutic targets of the phytochemicals in comparison to SARS-CoV-2. RESULTS The potential binding modes and favourable molecular interaction profile of 9 phytochemicals, majorly from Withania somnifera with lowest free binding energies, against the SARS-CoV-2 NSP targets were identified. It was understood that phytochemicals and 2 repurposed drugs with steroidal moieties in their chemical structures formed stable interactions with the NSPs. Additionally, human target pathway analysis for SARS-CoV-2 and phytochemicals showed that cytokine mediated pathway and phosphorylation pathways were with the most significant p-value. CONCLUSIONS To summarize this work, we suggest a global approach of targeting multiple proteins of SARS-CoV-2 with phytochemicals as a natural alternative therapy for COVID-19. We also suggest that these phytochemicals need to be tested experimentally to confirm their efficacy.
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Key Words
- ACPYPE, AnteChamberPYthon Parser interface
- ATP, Adenosine tri phosphate
- Binding energy
- COVID-19, Corona Virus Disease 2019
- DCCM, Dynamic Cross Correlation Matrix
- GO, Gene Ontology enrichment
- H-bond, Hydrogen Bond
- HIV, Human Immuno Deficiency Virus
- India
- JAK-STAT, The Janus kinase (JAK)-signal transducer and activator of transcription (STAT)
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MAPK, Mitogen-activated protein kinase
- MD, Molecular dynamics
- MM/PBSA, Molecular Mechanics/Poisson–Boltzmann (Generalized Born) surface area
- Molecular dynamics simulation
- NSP, Non Structural Proteins
- PCA, Principal Component Analysis
- PME, Particle-Mesh-Ewald summation
- Pathway enrichment
- Phytochemicals
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuations
- RNA, Ribonucleic Acid
- RdRp, RNA-dependent RNA polymerase
- Rg, Radius of gyration (Rg)
- SARS-CoV, Severe acute respiratory syndrome/coronavirus
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- vdW, van der Waal's energy.
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Affiliation(s)
| | - Dipak Paul
- Noor Enzymes Private Limited, 37-B, Darga Road, Kolkata 700 017, India
| | - Debamitra Chakravorty
- Novel Techsciences (OPC) Private Limited, 37-B, Darga Road, 1st Floor, Kolkata 700 017, India
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9
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Cavasotto CN, Lamas MS, Maggini J. Functional and druggability analysis of the SARS-CoV-2 proteome. Eur J Pharmacol 2021; 890:173705. [PMID: 33137330 PMCID: PMC7604074 DOI: 10.1016/j.ejphar.2020.173705] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 02/08/2023]
Abstract
The infectious coronavirus disease (COVID-19) pandemic, caused by the coronavirus SARS-CoV-2, appeared in December 2019 in Wuhan, China, and has spread worldwide. As of today, more than 46 million people have been infected and over 1.2 million fatalities. With the purpose of contributing to the development of effective therapeutics, we performed an in silico determination of binding hot-spots and an assessment of their druggability within the complete SARS-CoV-2 proteome. All structural, non-structural, and accessory proteins have been studied, and whenever experimental structural data of SARS-CoV-2 proteins were not available, homology models were built based on solved SARS-CoV structures. Several potential allosteric or protein-protein interaction druggable sites on different viral targets were identified, knowledge that could be used to expand current drug discovery endeavors beyond the currently explored cysteine proteases and the polymerase complex. It is our hope that this study will support the efforts of the scientific community both in understanding the molecular determinants of this disease and in widening the repertoire of viral targets in the quest for repurposed or novel drugs against COVID-19.
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Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina; Facultad de Ciencias Biomédicas, Facultad de Ingeniería, Universidad Austral, Pilar, Buenos Aires, Argentina; Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina.
| | - Maximiliano Sánchez Lamas
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina; Meton AI, Inc., Wilmington, DE, 19801, USA
| | - Julián Maggini
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina; Technology Transfer Office, Universidad Austral, Pilar, Buenos Aires, Argentina
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10
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Structural and functional insights into non-structural proteins of coronaviruses. Microb Pathog 2020; 150:104641. [PMID: 33242646 PMCID: PMC7682334 DOI: 10.1016/j.micpath.2020.104641] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
Coronaviruses (CoVs) are causing a number of human and animal diseases because of their zoonotic nature such as Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19). These viruses can infect respiratory, gastrointestinal, hepatic and central nervous systems of human, livestock, birds, bat, mouse, and many wild animals. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerging respiratory virus and is causing CoVID-19 with high morbidity and considerable mortality. All CoVs belong to the order Nidovirales, family Coronaviridae, are enveloped positive-sense RNA viruses, characterised by club-like spikes on their surfaces and large RNA genome with a distinctive replication strategy. Coronavirus have the largest RNA genomes (~26–32 kilobases) and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. Non-structural proteins (nsp) 7–16 are cleaved from two large replicase polyproteins and guide the replication and processing of coronavirus RNA. Coronavirus replicase has more or less universal activities, such as RNA polymerase (nsp 12) and helicase (nsp 13), as well as a variety of unusual or even special mRNA capping (nsp 14, nsp 16) and fidelity regulation (nsp 14) domains. Besides that, several smaller subunits (nsp 7– nsp 10) serve as essential cofactors for these enzymes and contribute to the emerging “nsp interactome.” In spite of the significant progress in studying coronaviruses structural and functional properties, there is an urgent need to understand the coronaviruses evolutionary success that will be helpful to develop enhanced control strategies. Therefore, it is crucial to understand the structure, function, and interactions of coronaviruses RNA synthesizing machinery and their replication strategies.
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11
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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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12
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Romano M, Ruggiero A, Squeglia F, Maga G, Berisio R. A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells 2020; 9:E1267. [PMID: 32443810 PMCID: PMC7291026 DOI: 10.3390/cells9051267] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 01/18/2023] Open
Abstract
The current coronavirus disease-2019 (COVID-19) pandemic is due to the novel coronavirus SARS-CoV-2. The scientific community has mounted a strong response by accelerating research and innovation, and has quickly set the foundation for understanding the molecular determinants of the disease for the development of targeted therapeutic interventions. The replication of the viral genome within the infected cells is a key stage of the SARS-CoV-2 life cycle. It is a complex process involving the action of several viral and host proteins in order to perform RNA polymerization, proofreading and final capping. This review provides an update of the structural and functional data on the key actors of the replicatory machinery of SARS-CoV-2, to fill the gaps in the currently available structural data, which is mainly obtained through homology modeling. Moreover, learning from similar viruses, we collect data from the literature to reconstruct the pattern of interactions among the protein actors of the SARS-CoV-2 RNA polymerase machinery. Here, an important role is played by co-factors such as Nsp8 and Nsp10, not only as allosteric activators but also as molecular connectors that hold the entire machinery together to enhance the efficiency of RNA replication.
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Affiliation(s)
- Maria Romano
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Giovanni Maga
- Institute of Molecular Genetics, IGM, CNR, 27100 Pavia, Italy;
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
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13
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Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Wiersum G, Kim Y, Jedrzejczak R, Maltseva NI, Endres M, Jaroszewski L, Godzik A, Joachimiak A, Satchell KJF. The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.17.047498. [PMID: 32511376 PMCID: PMC7263505 DOI: 10.1101/2020.04.17.047498] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 is a member of the coronaviridae family and is the etiological agent of the respiratory Coronavirus Disease 2019. The virus has spread rapidly around the world resulting in over two million cases and nearly 150,000 deaths as of April 17, 2020. Since no treatments or vaccines are available to treat COVID-19 and SARS-CoV-2, respiratory complications derived from the infections have overwhelmed healthcare systems around the world. This virus is related to SARS-CoV-1, the virus that caused the 2002-2004 outbreak of Severe Acute Respiratory Syndrome. In January 2020, the Center for Structural Genomics of Infectious Diseases implemented a structural genomics pipeline to solve the structures of proteins essential for coronavirus replication-transcription. Here we show the first structure of the SARS-CoV-2 nsp10-nsp16 2'-O-methyltransferase complex with S-adenosylmethionine at a resolution of 1.80 Å. This heterodimer complex is essential for capping viral mRNA transcripts for efficient translation and to evade immune surveillance.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Nicole L. Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Olga Kiryukhina
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Grant Wiersum
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Natalia I. Maltseva
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Michael Endres
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
| | - Lukasz Jaroszewski
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Biomedical Sciences, University of California, Riverside School of Medicine, Riverside, CA, USA
| | - Adam Godzik
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Biomedical Sciences, University of California, Riverside School of Medicine, Riverside, CA, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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Abstract
Coronaviruses are animal and human pathogens that can cause lethal zoonotic infections like SARS and MERS. They have polycistronic plus-stranded RNA genomes and belong to the order Nidovirales, a diverse group of viruses for which common ancestry was inferred from the common principles underlying their genome organization and expression, and from the conservation of an array of core replicase domains, including key RNA-synthesizing enzymes. Coronavirus genomes (~ 26–32 kilobases) are the largest RNA genomes known to date and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. The primary functions that direct coronavirus RNA synthesis and processing reside in nonstructural protein (nsp) 7 to nsp16, which are cleavage products of two large replicase polyproteins translated from the coronavirus genome. Significant progress has now been made regarding their structural and functional characterization, stimulated by technical advances like improved methods for bioinformatics and structural biology, in vitro enzyme characterization, and site-directed mutagenesis of coronavirus genomes. Coronavirus replicase functions include more or less universal activities of plus-stranded RNA viruses, like an RNA polymerase (nsp12) and helicase (nsp13), but also a number of rare or even unique domains involved in mRNA capping (nsp14, nsp16) and fidelity control (nsp14). Several smaller subunits (nsp7–nsp10) act as crucial cofactors of these enzymes and contribute to the emerging “nsp interactome.” Understanding the structure, function, and interactions of the RNA-synthesizing machinery of coronaviruses will be key to rationalizing their evolutionary success and the development of improved control strategies.
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Affiliation(s)
- E J Snijder
- Leiden University Medical Center, Leiden, The Netherlands.
| | - E Decroly
- Aix-Marseille Université, AFMB UMR 7257, Marseille, France; CNRS, AFMB UMR 7257, Marseille, France
| | - J Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.
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15
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Kaur K, Gupta R, Saraf SA, Saraf SK. Zinc: The Metal of Life. Compr Rev Food Sci Food Saf 2014; 13:358-376. [PMID: 33412710 DOI: 10.1111/1541-4337.12067] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 02/05/2014] [Indexed: 01/15/2023]
Abstract
The importance of zinc was 1st reported for Aspergillus niger. It took over 75 y to realize that zinc is also an essential trace element for rats, and an additional 30 y went by before it was recognized that this was also true for humans. The adult body contains about 2 to 3 g of zinc. Zinc is found in organs, tissues, bones, fluids, and cells. It is essential for many physiological functions and plays a significant role in a number of enzyme actions in the living systems. Bioinformatics estimates report that 10% of the human proteome contains zinc-binding sites. Based on its role in such a plethora of cellular components, zinc has diverse biological functions from enzymatic catalysis to playing a crucial role in cellular neuronal systems. Thus, based on the various published studies and reports, it is pertinent to state that zinc is one of the most important essential trace metals in human nutrition and lifestyle. Its deficiency may severely affect the homeostasis of a biological system. This review compiles the role of zinc in prophylaxis/therapeutics and provides current information about its effect on living beings.
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Affiliation(s)
- Kuljeet Kaur
- Faculty of Pharmacy, Babu Banarasi Das Natl. Inst. of Technology and Management (BBD Univ.), Lucknow, India
| | - Rajiv Gupta
- Faculty of Pharmacy, Babu Banarasi Das Natl. Inst. of Technology and Management (BBD Univ.), Lucknow, India
| | - Shubhini A Saraf
- Dept. of Pharmaceutical Sciences, SB&BT, Babasaheb Bhimrao Ambedkar Univ., Lucknow, India
| | - Shailendra K Saraf
- Faculty of Pharmacy, Babu Banarasi Das Northern India Inst. of Technology, Lucknow, India
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16
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Subissi L, Imbert I, Ferron F, Collet A, Coutard B, Decroly E, Canard B. SARS-CoV ORF1b-encoded nonstructural proteins 12-16: replicative enzymes as antiviral targets. Antiviral Res 2014; 101:122-30. [PMID: 24269475 PMCID: PMC7113864 DOI: 10.1016/j.antiviral.2013.11.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/22/2013] [Accepted: 11/11/2013] [Indexed: 12/17/2022]
Abstract
The SARS (severe acute respiratory syndrome) pandemic caused ten years ago by the SARS-coronavirus (SARS-CoV) has stimulated a number of studies on the molecular biology of coronaviruses. This research has provided significant new insight into many mechanisms used by the coronavirus replication-transcription complex (RTC). The RTC directs and coordinates processes in order to replicate and transcribe the coronavirus genome, a single-stranded, positive-sense RNA of outstanding length (∼27-32kilobases). Here, we review the up-to-date knowledge on SARS-CoV replicative enzymes encoded in the ORF1b, i.e., the main RNA-dependent RNA polymerase (nsp12), the helicase/triphosphatase (nsp13), two unusual ribonucleases (nsp14, nsp15) and RNA-cap methyltransferases (nsp14, nsp16). We also review how these enzymes co-operate with other viral co-factors (nsp7, nsp8, and nsp10) to regulate their activity. These last ten years of research on SARS-CoV have considerably contributed to unravel structural and functional details of one of the most fascinating replication/transcription machineries of the RNA virus world. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses".
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Affiliation(s)
- Lorenzo Subissi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Isabelle Imbert
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - François Ferron
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Axelle Collet
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Bruno Coutard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Etienne Decroly
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Bruno Canard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France.
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17
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Mao X, Ren XF. Functions of proteins of porcine epidemic diarrhea virus. Shijie Huaren Xiaohua Zazhi 2013; 21:44-53. [DOI: 10.11569/wcjd.v21.i1.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Porcine epidemic diarrhea (PED) is caused by porcine epidemic diarrhea virus (PEDV), which belongs to the order Nidovirales in the family Coronaviridae. Since PED was first discovered in Europe in 1987, it has become a severe infectious disease in Asian countries (including China, Korea, Japan, Philippines and Thailand) and has caused great economic losses in swine industry. Although bivalent vaccine for PEDV and transmissible gastroenteritis virus (TGEV, another porcine coronavirus) can decrease the incidence of both diseases, PED is still increasing annually in China. Unfortunately, there have been few studies on viral proteins and pathogenesis of PEDV. This review aims to provide some functional insights on PEDV viral proteins based on the available information from coronaviruse studies.
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18
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Chen Y, Su C, Ke M, Jin X, Xu L, Zhang Z, Wu A, Sun Y, Yang Z, Tien P, Ahola T, Liang Y, Liu X, Guo D. Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex. PLoS Pathog 2011; 7:e1002294. [PMID: 22022266 PMCID: PMC3192843 DOI: 10.1371/journal.ppat.1002294] [Citation(s) in RCA: 243] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 08/16/2011] [Indexed: 01/10/2023] Open
Abstract
The 5'-cap structure is a distinct feature of eukaryotic mRNAs, and eukaryotic viruses generally modify the 5'-end of viral RNAs to mimic cellular mRNA structure, which is important for RNA stability, protein translation and viral immune escape. SARS coronavirus (SARS-CoV) encodes two S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTase) which sequentially methylate the RNA cap at guanosine-N7 and ribose 2'-O positions, catalyzed by nsp14 N7-MTase and nsp16 2'-O-MTase, respectively. A unique feature for SARS-CoV is that nsp16 requires non-structural protein nsp10 as a stimulatory factor to execute its MTase activity. Here we report the biochemical characterization of SARS-CoV 2'-O-MTase and the crystal structure of nsp16/nsp10 complex bound with methyl donor SAM. We found that SARS-CoV nsp16 MTase methylated m7GpppA-RNA but not m7GpppG-RNA, which is in contrast with nsp14 MTase that functions in a sequence-independent manner. We demonstrated that nsp10 is required for nsp16 to bind both m7GpppA-RNA substrate and SAM cofactor. Structural analysis revealed that nsp16 possesses the canonical scaffold of MTase and associates with nsp10 at 1∶1 ratio. The structure of the nsp16/nsp10 interaction interface shows that nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of nsp16, consistent with the findings in biochemical assays. These results suggest that nsp16/nsp10 interface may represent a better drug target than the viral MTase active site for developing highly specific anti-coronavirus drugs.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Ceyang Su
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Min Ke
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Xu Jin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Lirong Xu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Zhou Zhang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Andong Wu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Ying Sun
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Zhouning Yang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Po Tien
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Tero Ahola
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Yi Liang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Xinqi Liu
- College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Deyin Guo
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, P. R. China
- Institute of Medical Virology, Wuhan University School of Medicine, Wuhan, P. R. China
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19
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Sola I, Mateos-Gomez PA, Almazan F, Zuñiga S, Enjuanes L. RNA-RNA and RNA-protein interactions in coronavirus replication and transcription. RNA Biol 2011; 8:237-48. [PMID: 21378501 PMCID: PMC3230552 DOI: 10.4161/rna.8.2.14991] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/17/2011] [Accepted: 01/19/2011] [Indexed: 02/07/2023] Open
Abstract
Coronavirus (CoV) RNA synthesis includes the replication of the viral genome, and the transcription of sgRNAs by a discontinuous mechanism. Both processes are regulated by RNA sequences such as the 5' and 3' untranslated regions (UTRs), and the transcription regulating sequences (TRSs) of the leader (TRS-L) and those preceding each gene (TRS-Bs). These distant RNA regulatory sequences interact with each other directly and probably through protein-RNA and protein-protein interactions involving viral and cellular proteins. By analogy to other plus-stranded RNA viruses, such as polioviruses, in which translation and replication switch involves a cellular factor (PCBP) and a viral protein (3CD) it is conceivable that in CoVs the switch between replication and transcription is also associated with the binding of proteins that are specifically recruited by the replication or transcription complexes. Complexes between RNA motifs such as TRS-L and the TRS-Bs located along the CoV genome are probably formed previously to the transcription start, and most likely promote template-switch of the nascent minus RNA to the TRS-L region. Many cellular proteins interacting with regulatory CoV RNA sequences are members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family of RNA-binding proteins, involved in mRNA processing and transport, which shuttle between the nucleus and the cytoplasm. In the context of CoV RNA synthesis, these cellular ribonucleoproteins might also participate in RNA-protein complexes to bring into physical proximity TRS-L and distant TRS-B, as proposed for CoV discontinuous transcription. In this review, we summarize RNA-RNA and RNA-protein interactions that represent modest examples of complex quaternary RNA-protein structures required for the fine-tuning of virus replication. Design of chemically defined replication and transcription systems will help to clarify the nature and activity of these structures.
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Affiliation(s)
- Isabel Sola
- Department of Molecular and Cell Biology, CNB, CSIC, Cantoblanco, Madrid, Spain
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20
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Lugari A, Betzi S, Decroly E, Bonnaud E, Hermant A, Guillemot JC, Debarnot C, Borg JP, Bouvet M, Canard B, Morelli X, Lécine P. Molecular mapping of the RNA Cap 2'-O-methyltransferase activation interface between severe acute respiratory syndrome coronavirus nsp10 and nsp16. J Biol Chem 2010; 285:33230-33241. [PMID: 20699222 PMCID: PMC2963367 DOI: 10.1074/jbc.m110.120014] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Several protein-protein interactions within the SARS-CoV proteome have been
identified, one of them being between non-structural proteins nsp10 and nsp16. In
this work, we have mapped key residues on the nsp10 surface involved in this
interaction. Alanine-scanning mutagenesis, bioinformatics, and molecular modeling
were used to identify several “hot spots,” such as Val42,
Met44, Ala71, Lys93, Gly94, and
Tyr96, forming a continuous protein-protein surface of about 830
Å2, bearing very conserved amino acids among coronaviruses.
Because nsp16 carries RNA cap 2′-O-methyltransferase
(2′O-MTase) activity only in the presence of its
interacting partner nsp10 (Bouvet, M., Debarnot, C., Imbert, I., Selisko, B.,
Snijder, E. J., Canard, B., and Decroly, E. (2010) PLoS Pathog. 6,
e1000863), functional consequences of mutations on this surface were evaluated
biochemically. Most changes that disrupted the nsp10-nsp16 interaction without
structural perturbations were shown to abrogate stimulation of nsp16 RNA cap
2′O-MTase activity. More strikingly, the Y96A mutation
abrogates stimulation of nsp16 2′O-MTase activity, whereas
Y96F overstimulates it. Thus, the nsp10-nsp16 interface may represent an attractive
target for antivirals against human and animal pathogenic coronaviruses.
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Affiliation(s)
- Adrien Lugari
- From the CNRS and Aix-Marseille Universités, IMR Laboratory (UPR 3243), Institut de Microbiologie de la Méditérannée, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Stephane Betzi
- From the CNRS and Aix-Marseille Universités, IMR Laboratory (UPR 3243), Institut de Microbiologie de la Méditérannée, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Emmanuel Bonnaud
- INSERM, UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France; Institut Paoli-Calmettes, Marseille F-13009, France; Université Méditerranée, Marseille F-13007, France
| | - Aurélie Hermant
- INSERM, UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France; Institut Paoli-Calmettes, Marseille F-13009, France; Université Méditerranée, Marseille F-13007, France
| | - Jean-Claude Guillemot
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Claire Debarnot
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Jean-Paul Borg
- INSERM, UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France; Institut Paoli-Calmettes, Marseille F-13009, France; Université Méditerranée, Marseille F-13007, France
| | - Mickaël Bouvet
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
| | - Xavier Morelli
- From the CNRS and Aix-Marseille Universités, IMR Laboratory (UPR 3243), Institut de Microbiologie de la Méditérannée, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
| | - Patrick Lécine
- INSERM, UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille F-13009, France; Institut Paoli-Calmettes, Marseille F-13009, France; Université Méditerranée, Marseille F-13007, France.
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Abstract
Coronaviruses induce in infected cells the formation of double-membrane vesicles (DMVs) in which the replication-transcription complexes (RTCs) are anchored. To study the dynamics of these coronavirus replicative structures, we generated recombinant murine hepatitis coronaviruses that express tagged versions of the nonstructural protein nsp2. We demonstrated by using immunofluorescence assays and electron microscopy that this protein is recruited to the DMV-anchored RTCs, for which its C terminus is essential. Live-cell imaging of infected cells demonstrated that small nsp2-positive structures move through the cytoplasm in a microtubule-dependent manner. In contrast, large fluorescent structures are rather immobile. Microtubule-mediated transport of DMVs, however, is not required for efficient replication. Biochemical analyses indicated that the nsp2 protein is associated with the cytoplasmic side of the DMVs. Yet, no recovery of fluorescence was observed when (part of) the nsp2-positive foci were bleached. This result was confirmed by the observation that preexisting RTCs did not exchange fluorescence after fusion of cells expressing either a green or a red fluorescent nsp2. Apparently, nsp2, once recruited to the RTCs, is not exchanged with nsp2 present in the cytoplasm or at other DMVs. Our data show a remarkable resemblance to results obtained recently by others with hepatitis C virus. The observations point to intriguing and as yet unrecognized similarities between the RTC dynamics of different plus-strand RNA viruses.
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Piotrowski Y, Hansen G, Boomaars-van der Zanden AL, Snijder EJ, Gorbalenya AE, Hilgenfeld R. Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property. Protein Sci 2009; 18:6-16. [PMID: 19177346 PMCID: PMC2708038 DOI: 10.1002/pro.15] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The polyproteins of coronaviruses are cleaved by viral proteases into at least 15 nonstructural proteins (Nsps). Consisting of five domains, Nsp3 is the largest of these (180-210 kDa). Among these domains, the so-called X-domain is believed to act as ADP-ribose-1''-phosphate phosphatase or to bind poly(ADP-ribose). However, here we show that the X-domain of Infectious Bronchitis Virus (strain Beaudette), a Group-3 coronavirus, fails to bind ADP-ribose. This is explained on the basis of the crystal structure of the protein, determined at two different pH values. For comparison, we also describe the crystal structure of the homologous X-domain from Human Coronavirus 229E, a Group-1 coronavirus, which does bind ADP-ribose.
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Affiliation(s)
- Yvonne Piotrowski
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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23
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Gustin KM, Guan BJ, Dziduszko A, Brian DA. Bovine coronavirus nonstructural protein 1 (p28) is an RNA binding protein that binds terminal genomic cis-replication elements. J Virol 2009; 83:6087-97. [PMID: 19357173 PMCID: PMC2687364 DOI: 10.1128/jvi.00160-09] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 03/29/2009] [Indexed: 01/08/2023] Open
Abstract
Nonstructural protein 1 (nsp1), a 28-kDa protein in the bovine coronavirus (BCoV) and closely related mouse hepatitis coronavirus, is the first protein cleaved from the open reading frame 1 (ORF 1) polyprotein product of genome translation. Recently, a 30-nucleotide (nt) cis-replication stem-loop VI (SLVI) has been mapped at nt 101 to 130 within a 288-nt 5'-terminal segment of the 738-nt nsp1 cistron in a BCoV defective interfering (DI) RNA. Since a similar nsp1 coding region appears in all characterized groups 1 and 2 coronavirus DI RNAs and must be translated in cis for BCoV DI RNA replication, we hypothesized that nsp1 might regulate ORF 1 expression by binding this intra-nsp1 cistronic element. Here, we (i) establish by mutation analysis that the 72-nt intracistronic SLV immediately upstream of SLVI is also a DI RNA cis-replication signal, (ii) show by gel shift and UV-cross-linking analyses that cellular proteins of approximately 60 and 100 kDa, but not viral proteins, bind SLV and SLVI, (SLV-VI) and (iii) demonstrate by gel shift analysis that nsp1 purified from Escherichia coli does not bind SLV-VI but does bind three 5' untranslated region (UTR)- and one 3' UTR-located cis-replication SLs. Notably, nsp1 specifically binds SLIII and its flanking sequences in the 5' UTR with approximately 2.5 muM affinity. Additionally, under conditions enabling expression of nsp1 from DI RNA-encoded subgenomic mRNA, DI RNA levels were greatly reduced, but there was only a slight transient reduction in viral RNA levels. These results together indicate that nsp1 is an RNA-binding protein that may function to regulate viral genome translation or replication but not by binding SLV-VI within its own coding region.
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Affiliation(s)
- Kortney M Gustin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996-0845, USA
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24
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Topology and membrane anchoring of the coronavirus replication complex: not all hydrophobic domains of nsp3 and nsp6 are membrane spanning. J Virol 2008; 82:12392-405. [PMID: 18842706 DOI: 10.1128/jvi.01219-08] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coronaviruses express two very large replicase polyproteins, the 16 autoproteolytic cleavage products of which collectively form the membrane-anchored replication complexes. How these structures are assembled is still largely unknown, but it is likely that the membrane-spanning members of these nonstructural proteins (nsps) are responsible for the induction of the double-membrane vesicles and for anchoring the replication complexes to these membranes. For 3 of the 16 coronavirus nsps-nsp3, nsp4, and nsp6-multiple transmembrane domains are predicted. Previously we showed that, consistent with predictions, nsp4 occurs in membranes with both of its termini exposed in the cytoplasm (M. Oostra et al., J. Virol. 81:12323-12336, 2007). Strikingly, however, for both nsp3 and nsp6, predictions based on a multiple alignment of 27 coronavirus genome sequences indicate an uneven number of transmembrane domains. As a consequence, the proteinase domains present in nsp3 and nsp5 would be separated from their target sequences by the lipid bilayer. To look into this incongruity, we studied the membrane disposition of nsp3 and nsp6 of the severe acute respiratory syndrome coronavirus and murine hepatitis virus by analyzing tagged forms of the proteins expressed in cultured cells. Contrary to the predictions, in both viruses, both proteins had their amino terminus, as well as their carboxy terminus, exposed in the cytoplasm. We established that two of the three hydrophobic domains in nsp3 and six of the seven in nsp6 are membrane spanning. Subsequently, we verified that in nsp4, all four hydrophobic domains span the lipid bilayer. The occurrence of conserved non-membrane-spanning hydrophobic domains in nsp3 and nsp6 suggests an important function for these domains in coronavirus replication.
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25
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Ponnusamy R, Moll R, Weimar T, Mesters JR, Hilgenfeld R. Variable oligomerization modes in coronavirus non-structural protein 9. J Mol Biol 2008; 383:1081-96. [PMID: 18694760 PMCID: PMC7094590 DOI: 10.1016/j.jmb.2008.07.071] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2008] [Revised: 07/17/2008] [Accepted: 07/24/2008] [Indexed: 12/24/2022]
Abstract
Non-structural protein 9 (Nsp9) of coronaviruses is believed to bind single-stranded RNA in the viral replication complex. The crystal structure of Nsp9 of human coronavirus (HCoV) 229E reveals a novel disulfide-linked homodimer, which is very different from the previously reported Nsp9 dimer of SARS coronavirus. In contrast, the structure of the Cys69Ala mutant of HCoV-229E Nsp9 shows the same dimer organization as the SARS-CoV protein. In the crystal, the wild-type HCoV-229E protein forms a trimer of dimers, whereas the mutant and SARS-CoV Nsp9 are organized in rod-like polymers. Chemical cross-linking suggests similar modes of aggregation in solution. In zone-interference gel electrophoresis assays and surface plasmon resonance experiments, the HCoV-229E wild-type protein is found to bind oligonucleotides with relatively high affinity, whereas binding by the Cys69Ala and Cys69Ser mutants is observed only for the longest oligonucleotides. The corresponding mutations in SARS-CoV Nsp9 do not hamper nucleic acid binding. From the crystal structures, a model for single-stranded RNA binding by Nsp9 is deduced. We propose that both forms of the Nsp9 dimer are biologically relevant; the occurrence of the disulfide-bonded form may be correlated with oxidative stress induced in the host cell by the viral infection.
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Affiliation(s)
- Rajesh Ponnusamy
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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26
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Cao J, Wu CC, Lin TL. Complete nucleotide sequence of polyprotein gene 1 and genome organization of turkey coronavirus. Virus Res 2008; 136:43-9. [PMID: 18514348 PMCID: PMC7114415 DOI: 10.1016/j.virusres.2008.04.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Revised: 04/12/2008] [Accepted: 04/18/2008] [Indexed: 11/30/2022]
Abstract
The complete nucleotide sequence of polyprotein gene 1 and the assembled full-length genome sequence are presented for turkey coronavirus (TCoV) isolates 540 and ATCC. The TCoV polyprotein gene encoded two open reading frames (ORFs), which are translated into two products, pp1a and pp1ab, the latter being produced via −1 frameshift translation. TCoV polyprotein pp1a and pp1ab were predicted to be processed to 15 non-structure proteins (nsp2–nsp16), with nsp1 missing. ClustalW analysis revealed 88.99% identity and 96.99% similarity for pp1ab between TCoV and avian infectious bronchitis virus (IBV) at the amino acid level. The whole genome consists of 27,749 nucleotides for 540 and 27,816 nucleotides for ATCC, excluding the poly(A) tail. A total of 13 ORFs were predicted for TCoV. Five subgenomic RNAs were detected from ATCC-infected turkey small intestines by Northern blotting. The whole genome sequence had 86.9% identity between TCoV and IBV, supporting that TCoV is a group 3 coronavirus.
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Affiliation(s)
- Jianzhong Cao
- Department of Comparative Pathobiology, 406 South University Street, Purdue University, West Lafayette, IN 47907, USA.
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27
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Imbert I, Snijder EJ, Dimitrova M, Guillemot JC, Lécine P, Canard B. The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein. Virus Res 2008; 133:136-48. [PMID: 18255185 PMCID: PMC7114086 DOI: 10.1016/j.virusres.2007.11.017] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 11/12/2007] [Accepted: 11/21/2007] [Indexed: 12/14/2022]
Abstract
Many genetic and mechanistic features distinguish the coronavirus replication machinery from that encoded by most other RNA viruses. The coronavirus replication/transcription complex is an assembly of viral and, most probably, cellular proteins that mediate the synthesis of both the unusually large (approximately 30 kb) RNA genome and an extensive set of subgenomic mRNAs. The viral components of the complex are encoded by the giant replicase gene, which is expressed in the form of two polyproteins (pp1a and pp1ab) that are processed into 16 cleavage products (nonstructural proteins 1-16). Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. We demonstrate the existence of a complex network of interactions involving all 16 nonstructural proteins. Our results both confirmed previously described associations and identified novel heterodimerizations. The interaction map thus provides a sum of the interactions that may occur at some point during coronavirus RNA synthesis and provides a framework for future research.
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Affiliation(s)
- Isabelle Imbert
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, LUMC P4-26, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Maria Dimitrova
- INSERM U748, Institut de Virologie, 3 rue Koeberlé, 67000 Strasbourg, France
| | - Jean-Claude Guillemot
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Patrick Lécine
- Inserm, U599, Centre de Recherches en Cancérologie de Marseille, Marseille F-13009, France
- Institut Paoli-Calmettes, Marseille F-13009, France
- Univ Méditerranée, F-13007 Marseille, France
| | - Bruno Canard
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
- Corresponding author. Tel.: +33 491 82 86 44; fax: +33 491 82 86 46.
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28
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Care S, Bignon C, Pelissier MC, Blanc E, Canard B, Coutard B. The translation of recombinant proteins in E. coli can be improved by in silico generating and screening random libraries of a -70/+96 mRNA region with respect to the translation initiation codon. Nucleic Acids Res 2007; 36:e6. [PMID: 18084029 PMCID: PMC2248745 DOI: 10.1093/nar/gkm1097] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recombinant protein translation in Escherichia coli may be limited by stable (i.e. low free energy) secondary structures in the mRNA translation initiation region. To circumvent this issue, we have set-up a computer tool called ‘ExEnSo’ (Expression Enhancer Software) that generates a random library of 8192 sequences, calculates the free energy of secondary structures of each sequence in the −70/+96 region (base 1 is the translation initiation codon), and then selects the sequence having the highest free energy. The software uses this ‘optimized’ sequence to create a 5′ primer that can be used in PCR experiments to amplify the coding sequence of interest prior to sub-cloning into a prokaryotic expression vector. In this article, we report how ExEnSo was set-up and the results obtained with nine coding sequences with low expression levels in E. coli. The free energy of the −70/+96 region of all these coding sequences was increased compared to the non-optimized sequences. Moreover, the protein expression of eight out of nine of these coding sequences was increased in E. coli, indicating a good correlation between in silico and in vivo results. ExEnSo is available as a free online tool.
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Affiliation(s)
- S Care
- AFMB UMR6098 CNRS/Université Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
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29
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Deming DJ, Graham RL, Denison MR, Baric RS. Processing of open reading frame 1a replicase proteins nsp7 to nsp10 in murine hepatitis virus strain A59 replication. J Virol 2007; 81:10280-91. [PMID: 17634238 PMCID: PMC2045455 DOI: 10.1128/jvi.00017-07] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Coronaviruses express open reading frame 1a (ORF1a) and ORF1b polyproteins from which 16 nonstructural proteins (nsp) are derived. The highly conserved region at the carboxy terminus of ORF1a is processed by the nsp5 proteinase (Mpro) into mature products, including nsp7, nsp8, nsp9, and nsp10, proteins with predicted or identified activities involved in RNA synthesis. Although continuous translation and proteolytic processing of ORF1ab by Mpro is required for replication, it is unknown whether specific cleavage events within the polyprotein are dispensable. We determined the requirement for the nsp7 to nsp10 proteins and their processing during murine hepatitis virus (MHV) replication. Through use of an MHV reverse genetics system, in-frame deletions of the coding sequences for nsp7 to nsp10, or ablation of their flanking Mpro cleavage sites, were made and the effects upon replication were determined. Viable viruses were characterized by analysis of Mpro processing, RNA transcription, and growth fitness. Deletion of any of the regions encoding nsp7 to nsp10 was lethal. Disruption of the cleavage sites was lethal with the exception of that of the nsp9-nsp10 site, which resulted in a mutant virus with attenuated replication. Passage of the attenuated nsp9-nsp10 cleavage mutant increased fitness to near-wild-type kinetics without reversion to a virus capable of processing nsp9-nsp10. We also confirmed the presence of a second cleavage site between nsp7 and nsp8. In order to determine whether a distinct function could be attributed to preprocessed forms of the polyprotein, including nsp7 to nsp10, the genes encoding nsp7 and nsp8 were rearranged. The mutant virus was not viable, suggesting that the uncleaved protein may be essential for replication or proteolytic processing.
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Affiliation(s)
- Damon J Deming
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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30
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Donaldson EF, Sims AC, Graham RL, Denison MR, Baric RS. Murine hepatitis virus replicase protein nsp10 is a critical regulator of viral RNA synthesis. J Virol 2007; 81:6356-68. [PMID: 17392363 PMCID: PMC1900072 DOI: 10.1128/jvi.02805-06] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Coronavirus replication requires proteolytic processing of the large polyprotein encoded by ORF1a/ab into putative functional intermediates and eventually approximately 15 mature proteins. The C-terminal ORF1a protein nsp10 colocalizes with viral replication complexes, but its role in transcription/replication is not well defined. To investigate the role of nsp10 in coronavirus transcription/replication, alanine replacements were engineered into a murine hepatitis virus (MHV) infectious clone in place of conserved residues in predicted functional domains or charged amino acid pairs/triplets, and rescued viruses were analyzed for mutant phenotypes. Of the 16 engineered clones, 5 viable viruses were rescued, 3 mutant viruses generated no cytopathic effect but were competent to synthesize viral subgenomic RNAs, and 8 were not viable. All viable mutants showed reductions in growth kinetics and overall viral RNA synthesis, implicating nsp10 as being a cofactor in positive- or negative-strand synthesis. Viable mutant nsp10-E2 was compromised in its ability to process the nascent polyprotein, as processing intermediates were detected in cells infected with this virus that were not detectable in wild-type infections. Mapping the mutations onto the crystal structure of severe acute respiratory syndrome virus nsp10 identified a central core resistant to mutation. Mutations targeting residues in or near either zinc-binding finger generated nonviable phenotypes, demonstrating that both domains are essential to nsp10 function and MHV replication. All mutations resulting in viable phenotypes mapped to loops outside the central core and were characterized by a global decrease in RNA synthesis. These results demonstrate that nsp10 is a critical regulator of coronavirus RNA synthesis and may play an important role in polyprotein processing.
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Affiliation(s)
- Eric F Donaldson
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
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31
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Ziebuhr J, Schelle B, Karl N, Minskaia E, Bayer S, Siddell SG, Gorbalenya AE, Thiel V. Human coronavirus 229E papain-like proteases have overlapping specificities but distinct functions in viral replication. J Virol 2007; 81:3922-32. [PMID: 17251282 PMCID: PMC1866161 DOI: 10.1128/jvi.02091-06] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Expression of the exceptionally large RNA genomes of CoVs involves multiple regulatory mechanisms, including extensive proteolytic processing of the large replicase polyproteins, pp1a and pp1ab, by two types of cysteine proteases: the chymotrypsin-like main protease and papain-like accessory proteases (PLpros). Here, we characterized the proteolytic processing of the human coronavirus 229E (HCoV-229E) amino-proximal pp1a/pp1ab region by two paralogous PLpro activities. Reverse-genetics data revealed that replacement of the PL2pro active-site cysteine was lethal. By contrast, the PL1pro activity proved to be dispensable for HCoV-229E virus replication, although reversion of the PL1pro active-site substitution to the wild-type sequence after several passages in cell culture indicated that there was selection pressure to restore the PL1pro activity. Further experiments showed that both PL1pro and PL2pro were able to cleave the nsp1-nsp2 cleavage site, with PL2pro cleaving the site less efficiently. The PL1pro-negative mutant genotype could be stably maintained in cell culture when the nsp1-nsp2 site was replaced by a short autoproteolytic sequence, suggesting that the major driving force for the observed reversion of the PL1pro mutation was the requirement for efficient nsp1-nsp2 cleavage. The data suggest that the two HCoV-229E PLpro paralogs have overlapping substrate specificities but different functions in viral replication. Within the tightly controlled interplay of the two protease activities, PL2pro plays a universal and essential proteolytic role that appears to be assisted by the PL1pro paralog at specific sites. Functional and evolutionary implications of the differential amino-terminal polyprotein-processing pathways among the main CoV lineages are discussed.
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Affiliation(s)
- John Ziebuhr
- Centre for Cancer Research and Cell Biology, School of Biomedical Sciences, The Queen's University of Belfast, UK, and Kantonal Hospital St. Gallen, Research Department, 9007 St. Gallen, Switzerland
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Mesters JR, Tan J, Hilgenfeld R. Viral enzymes. Curr Opin Struct Biol 2006; 16:776-86. [PMID: 17085042 PMCID: PMC7127120 DOI: 10.1016/j.sbi.2006.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 10/16/2006] [Accepted: 10/24/2006] [Indexed: 01/09/2023]
Abstract
Viral genomes show unequalled diversity, ranging from single-stranded DNA to double-stranded RNA. Moreover, viruses can quickly adapt to the host's immune response and drug treatment. Although they tend to make optimal use of the host cell's reservoir of proteins, viruses need to carry some enzymatic functions with them, as they may not be available or accessible in the infected cell. Recently, progress has been made in our structural understanding of viral enzymes involved in all stages of the viral life cycle, which includes entry, hijack, replication and exit stages.
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Affiliation(s)
- Jeroen R Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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Matthes N, Mesters JR, Coutard B, Canard B, Snijder EJ, Moll R, Hilgenfeld R. The non-structural protein Nsp10 of mouse hepatitis virus binds zinc ions and nucleic acids. FEBS Lett 2006; 580:4143-9. [PMID: 16828088 PMCID: PMC7094219 DOI: 10.1016/j.febslet.2006.06.061] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 06/06/2006] [Accepted: 06/15/2006] [Indexed: 11/22/2022]
Abstract
The non‐structural protein Nsp10 of coronaviruses is a small cleavage product of the viral replicase polyprotein that has been implicated in RNA synthesis. Nsp10 of mouse hepatitis virus (MHV) displays an apparent molecular mass of 13–16 kDa in reducing SDS–PAGE and analytical gel filtration, while dynamic light scattering suggests the existence of oligomeric forms. Atomic absorption spectroscopy reveals two metal ions per Nsp10 monomer, with a preference for Zn2+ over Fe2+/3+ and Co2+. These are probably bound by two Zn‐finger‐like motifs. Moreover, MHV Nsp10 interacts with tRNA, single‐stranded RNA, double‐stranded DNA and, to a lesser extent, single‐stranded DNA as shown by gel‐shift experiments. The Kd for tRNA is 2.1 ± 0.2 μM.
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Affiliation(s)
- Nele Matthes
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538 Lubeck, Germany
| | - Jeroen R. Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538 Lubeck, Germany
| | - Bruno Coutard
- AFMB UMR6098 CNRS/Université Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Bruno Canard
- AFMB UMR6098 CNRS/Université Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Ralf Moll
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538 Lubeck, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538 Lubeck, Germany
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