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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar E, Abu Zeid IM, Bouback TA, Bamagoos A, Aljohny BO, Uversky VN, Redwan EM. Overview of the SARS-CoV-2 nucleocapsid protein. Int J Biol Macromol 2024; 260:129523. [PMID: 38232879 DOI: 10.1016/j.ijbiomac.2024.129523] [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: 06/04/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/19/2024]
Abstract
Since the emergence of SARS-CoV in 2003, researchers worldwide have been toiling away at deciphering this virus's biological intricacies. In line with other known coronaviruses, the nucleocapsid (N) protein is an important structural component of SARS-CoV. As a result, much emphasis has been placed on characterizing this protein. Independent research conducted by a variety of laboratories has clearly demonstrated the primary function of this protein, which is to encapsidate the viral genome. Furthermore, various accounts indicate that this particular protein disrupts diverse intracellular pathways. Such observations imply its vital role in regulating the virus as well. The opening segment of this review will expound upon these distinct characteristics succinctly exhibited by the N protein. Additionally, it has been suggested that the N protein possesses diagnostic and vaccine capabilities when dealing with SARS-CoV. In light of this fact, we will be reviewing some recent headway in the use cases for N protein toward clinical purposes within this article's concluding segments. This forward movement pertains to both developments of COVID-19-oriented therapeutic targets as well as diagnostic measures. The strides made by medical researchers offer encouragement, knowing they are heading toward a brighter future combating global pandemic situations such as these.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab Mattar
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Bassam O Aljohny
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Elrashdy M Redwan
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, 21934 Alexandria, Egypt.
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Terasaki K, Narayanan K, Makino S. Identification of a 1.4-kb-Long Sequence Located in the nsp12 and nsp13 Coding Regions of SARS-CoV-2 Genomic RNA That Mediates Efficient Viral RNA Packaging. J Virol 2023:e0065923. [PMID: 37367225 PMCID: PMC10373556 DOI: 10.1128/jvi.00659-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
The specific packaging of the viral RNA genome into virus particles is an essential step in the replication cycle of coronaviruses (CoVs). Using a single-cycle, replicable severe acute respiratory syndrome CoV-2 (SARS-CoV-2) mutant, we demonstrated the preferential packaging of the SARS-CoV-2 genomic RNA into purified virus particles. Furthermore, based on the sequence of an efficiently packaged defective interfering RNA of SARS-CoV, a closely related CoV, that was generated after serial passages of SARS-CoV in cell culture, we designed a series of replication-competent SARS-CoV-2 minigenome RNAs to identify the specific viral RNA region that is important for SARS-CoV-2 RNA packaging into virus particles. We showed that a 1.4-kb-long sequence, derived from the nsp12 and nsp13 coding regions of the SARS-CoV-2 genomic RNA, is required for the efficient packaging of SARS-CoV-2 minigenome RNA into SARS-CoV-2 particles. In addition, we also showed that the presence of possibly the entire 1.4-kb-long sequence is important for the efficient packaging of SARS-CoV-2 RNA. Our findings highlight the differences between the RNA packaging sequence identified in SARS-CoV-2, a Sarbecovirus, and the packaging signal of mouse hepatitis virus (MHV), an Embecovirus, which is a 95-nt-long sequence located at the nsp15 coding region of MHV genomic RNA. Collectively, our data imply that both the location and the sequence/structural features of the RNA element(s) that drives the selective and efficient packaging of viral genomic RNA are not conserved among the subgenera Embecovirus and Sarbecovirus within the Betacoronavirus genus. IMPORTANCE Elucidating the mechanism of SARS-CoV-2 RNA packaging into virus particles is important for the rational design of antiviral drugs that inhibit this vital step in the replication cycle of CoVs. However, our knowledge about the RNA packaging mechanism in SARS-CoV-2, including the identification of the viral RNA region important for SARS-CoV-2 RNA packaging, is limited, primarily due to the logistical challenges of handing SARS-CoV-2 in biosafety level 3 (BSL3) facilities. Our study, using a single-cycle, replicable SARS-CoV-2 mutant, which can be handled in a BSL2 lab, demonstrated the preferential packaging of full-length SARS-CoV-2 genomic RNA into virus particles and identified a specific 1.4-kb-long RNA region in SARS-CoV-2 genomic RNA that is required for the efficient packaging of SARS-CoV-2 RNA into virus particles. The information generated in our study could be valuable for clarifying the mechanisms of SARS-CoV-2 RNA packaging and for the development of targeted therapeutics against SARS-CoV-2 and other related CoVs.
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Affiliation(s)
- Kaori Terasaki
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Krishna Narayanan
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- UTMB Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- The Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch, Galveston, Texas, USA
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3
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Wang X, Yang Y, Sun Z, Zhou X. Crystal structure of the membrane (M) protein from a bat betacoronavirus. PNAS NEXUS 2023; 2:pgad021. [PMID: 36874273 PMCID: PMC9982069 DOI: 10.1093/pnasnexus/pgad021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/20/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023]
Abstract
The membrane (M) protein is the most abundant structural protein of coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2, and plays a central role in virus assembly through its interaction with various partner proteins. However, mechanistic details about how M protein interacts with others remain elusive due to lack of high-resolution structures. Here, we present the first crystal structure of a betacoronavirus M protein from Pipistrellus bat coronavirus HKU5 (batCOV5-M), which is closely related to MERS-CoV, SARS-CoV, and SARS-CoV-2 M proteins. Furthermore, an interaction analysis indicates that the carboxy-terminus of the batCOV5 nucleocapsid (N) protein mediates its interaction with batCOV5-M. Combined with a computational docking analysis an M-N interaction model is proposed, providing insight into the mechanism of M protein-mediated protein interactions.
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Affiliation(s)
- Xiaodong Wang
- State Key Laboratory of Biotherapy, Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuwei Yang
- State Key Laboratory of Biotherapy, Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ziyi Sun
- State Key Laboratory of Biotherapy, Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaoming Zhou
- State Key Laboratory of Biotherapy, Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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4
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Carlson CR, Adly AN, Bi M, Howard CJ, Frost A, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. J Biol Chem 2022; 298:102560. [PMID: 36202211 PMCID: PMC9529352 DOI: 10.1016/j.jbc.2022.102560] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35 to 40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.
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Affiliation(s)
| | - Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Conor J Howard
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Adam Frost
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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5
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Dolan KA, Dutta M, Kern DM, Kotecha A, Voth GA, Brohawn SG. Structure of SARS-CoV-2 M protein in lipid nanodiscs. eLife 2022; 11:e81702. [PMID: 36264056 PMCID: PMC9642992 DOI: 10.7554/elife.81702] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 Å resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity in a simple lipid bilayer and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure.
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Affiliation(s)
- Kimberly A Dolan
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Mandira Dutta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of ChicagoChicagoUnited States
| | - David M Kern
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher ScientificEindhovenNetherlands
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of ChicagoChicagoUnited States
| | - Stephen G Brohawn
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
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6
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Li S, Zandi R. Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding. Viruses 2022; 14:2089. [PMID: 36298645 PMCID: PMC9611094 DOI: 10.3390/v14102089] [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: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022] Open
Abstract
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins: Envelope (E), Membrane (M), Nucleocapsid (N), and Spike (S), which self-assemble along with its RNA into the infectious virus by budding from intracellular lipid membranes. In this paper, we develop a model to explore the mechanisms of RNA condensation by structural proteins, protein oligomerization and cellular membrane-protein interactions that control the budding process and the ultimate virus structure. Using molecular dynamics simulations, we have deciphered how the positively charged N proteins interact and condense the very long genomic RNA resulting in its packaging by a lipid envelope decorated with structural proteins inside a host cell. Furthermore, considering the length of RNA and the size of the virus, we find that the intrinsic curvature of M proteins is essential for virus budding. While most current research has focused on the S protein, which is responsible for viral entry, and it has been motivated by the need to develop efficacious vaccines, the development of resistance through mutations in this crucial protein makes it essential to elucidate the details of the viral life cycle to identify other drug targets for future therapy. Our simulations will provide insight into the viral life cycle through the assembly of viral particles de novo and potentially identify therapeutic targets for future drug development.
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Affiliation(s)
- Siyu Li
- Songshan Lake Materials Laboratory, Dongguan 523808, China
| | - Roya Zandi
- Department of Physics and Astronomy, University of California Riverside, Riverside, CA 92521, USA
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Rafael Ciges-Tomas J, Franco ML, Vilar M. Identification of a guanine-specific pocket in the protein N of SARS-CoV-2. Commun Biol 2022; 5:711. [PMID: 35842466 PMCID: PMC9288159 DOI: 10.1038/s42003-022-03647-8] [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: 01/11/2022] [Accepted: 06/28/2022] [Indexed: 01/14/2023] Open
Abstract
The SARS-CoV-2 nucleocapsid protein (N) is responsible for RNA binding. Here we report the crystal structure of the C-terminal domain (NCTD) in open and closed conformations and in complex with guanine triphosphate, GTP. The crystal structure and biochemical studies reveal a specific interaction between the guanine, a nucleotide enriched in the packaging signals regions of coronaviruses, and a highly conserved tryptophan residue (W330). In addition, EMSA assays with SARS-CoV-2 derived RNA hairpin loops from a putative viral packaging sequence showed the preference interaction of the N-CTD to RNA oligonucleotides containing G and the loss of the specificity in the mutant W330A. Here we propose that this interaction may facilitate the viral assembly process. In summary, we have identified a specific guanine-binding pocket in the N protein that may be used to design viral assembly inhibitors. The molecular basis of GTP binding to the N protein from SARS-CoV-2 is presented, providing a framework for drug design and disruption of the RNA packing function in the N protein.
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Affiliation(s)
- J Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia-CSIC Spanish National Research Council, C/Jaime Roig, 11, 46010, Valencia, Spain. .,Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200, Copenhagen, Denmark.
| | - María Luisa Franco
- Instituto de Biomedicina de Valencia-CSIC Spanish National Research Council, C/Jaime Roig, 11, 46010, Valencia, Spain
| | - Marçal Vilar
- Instituto de Biomedicina de Valencia-CSIC Spanish National Research Council, C/Jaime Roig, 11, 46010, Valencia, Spain.
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Carlson CR, Adly AN, Bi M, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.23.493138. [PMID: 35664996 PMCID: PMC9164447 DOI: 10.1101/2022.05.23.493138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The nucleocapsid (N) protein of coronaviruses is responsible for compaction of the ∼30-kb RNA genome in the ∼100-nm virion. Cryo-electron tomography suggests that each virion contains 35-40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined with viral RNA fragments in vitro, forms cylindrical 15-nm particles similar to the vRNP structures observed within coronavirus virions. These vRNPs form in the presence of stem-loop-containing RNA and depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine (SR) region weakens these interactions and disrupts vRNP assembly. We propose that unmodified N binds stem-loop-rich regions in genomic RNA to form compact vRNP complexes within the nucleocapsid, while phosphorylated N maintains uncompacted viral RNA to promote the protein's transcriptional function.
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Affiliation(s)
| | - Armin N. Adly
- Department of Physiology, University of California, San Francisco CA 94143
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - David O. Morgan
- Department of Physiology, University of California, San Francisco CA 94143
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Ren S, Fraser K, Kuo L, Chauhan N, Adrian AT, Zhang F, Linhardt RJ, Kwon PS, Wang X. Designer DNA nanostructures for viral inhibition. Nat Protoc 2022; 17:282-326. [PMID: 35013618 PMCID: PMC8852688 DOI: 10.1038/s41596-021-00641-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/29/2021] [Indexed: 12/26/2022]
Abstract
Emerging viral diseases can substantially threaten national and global public health. Central to our ability to successfully tackle these diseases is the need to quickly detect the causative virus and neutralize it efficiently. Here we present the rational design of DNA nanostructures to inhibit dengue virus infection. The designer DNA nanostructure (DDN) can bind to complementary epitopes on antigens dispersed across the surface of a viral particle. Since these antigens are arranged in a defined geometric pattern that is unique to each virus, the structure of the DDN is designed to mirror the spatial arrangement of antigens on the viral particle, providing very high viral binding avidity. We describe how available structural data can be used to identify unique spatial patterns of antigens on the surface of a viral particle. We then present a procedure for synthesizing DDNs using a combination of in silico design principles, self-assembly, and characterization using gel electrophoresis, atomic force microscopy and surface plasmon resonance spectroscopy. Finally, we evaluate the efficacy of a DDN in inhibiting dengue virus infection via plaque-forming assays. We expect this protocol to take 2-3 d to complete virus antigen pattern identification from existing cryogenic electron microscopy data, ~2 weeks for DDN design, synthesis, and virus binding characterization, and ~2 weeks for DDN cytotoxicity and antiviral efficacy assays.
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Affiliation(s)
- Shaokang Ren
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Keith Fraser
- Department of Biological Science, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Lili Kuo
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Neha Chauhan
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Centre for Pathogen Diagnostics, DREMES at the University of Illinois at Urbana-Champaign and the Zhejiang University-University of Illinois at Urbana-Champaign Institute, Urbana, IL, USA
| | - Addison T Adrian
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Centre for Pathogen Diagnostics, DREMES at the University of Illinois at Urbana-Champaign and the Zhejiang University-University of Illinois at Urbana-Champaign Institute, Urbana, IL, USA
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Robert J Linhardt
- Department of Biological Science, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Paul S Kwon
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Centre for Pathogen Diagnostics, DREMES at the University of Illinois at Urbana-Champaign and the Zhejiang University-University of Illinois at Urbana-Champaign Institute, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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10
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Chen SC, Olsthoorn RCL, Yu CH. Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Virus Evol 2021; 7:veab021. [PMID: 34141447 PMCID: PMC8206606 DOI: 10.1093/ve/veab021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In many single-stranded (ss) RNA viruses, the cis-acting packaging signal that confers selectivity genome packaging usually encompasses short structured RNA repeats. These structural units, termed repetitive structural motifs (RSMs), potentially mediate capsid assembly by specific RNA–protein interactions. However, general knowledge of the conservation and/or the diversity of RSMs in the positive-sense ssRNA coronaviruses (CoVs) is limited. By performing structural phylogenetic analysis, we identified a variety of RSMs in nearly all CoV genomic RNAs, which are exclusively located in the 5′-untranslated regions (UTRs) and/or in the inter-domain regions of poly-protein 1ab coding sequences in a lineage-specific manner. In all alpha- and beta-CoVs, except for Embecovirus spp, two to four copies of 5′-gUUYCGUc-3′ RSMs displaying conserved hexa-loop sequences were generally identified in Stem-loop 5 (SL5) located in the 5′-UTRs of genomic RNAs. In Embecovirus spp., however, two to eight copies of 5′-agc-3′/guAAu RSMs were found in the coding regions of non-structural protein (NSP) 3 and/or NSP15 in open reading frame (ORF) 1ab. In gamma- and delta-CoVs, other types of RSMs were found in several clustered structural elements in 5′-UTRs and/or ORF1ab. The identification of RSM-encompassing structural elements in all CoVs suggests that these RNA elements play fundamental roles in the life cycle of CoVs. In the recently emerged SARS-CoV-2, beta-CoV-specific RSMs are also found in its SL5, displaying two copies of 5′-gUUUCGUc-3′ motifs. However, multiple sequence alignment reveals that the majority of SARS-CoV-2 possesses a variant RSM harboring SL5b C241U, and intriguingly, several variations in the coding sequences of viral proteins, such as Nsp12 P323L, S protein D614G, and N protein R203K-G204R, are concurrently found with such variant RSM. In conclusion, the comprehensive exploration for RSMs reveals phylogenetic insights into the RNA structural elements in CoVs as a whole and provides a new perspective on variations currently found in SARS-CoV-2.
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Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - René C L Olsthoorn
- Department of Supramolecular Biomaterials Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden,The Netherlands
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
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11
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Chauhan A, Avti P, Shekhar N, Prajapat M, Sarma P, Bhattacharyya A, Kumar S, Kaur H, Prakash A, Medhi B. Structural and conformational analysis of SARS CoV 2 N-CTD revealing monomeric and dimeric active sites during the RNA-binding and stabilization: Insights towards potential inhibitors for N-CTD. Comput Biol Med 2021; 134:104495. [PMID: 34022485 PMCID: PMC8123409 DOI: 10.1016/j.compbiomed.2021.104495] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/29/2022]
Abstract
The advent of SARS-CoV-2 has become a universal health issue with no appropriate cure available to date. The coronavirus nucleocapsid (N) protein combines viral genomic RNA into a ribonucleoprotein and protects the viral genome from the host's nucleases. Structurally, the N protein comprises two independent domains: the N-terminal domain (NTD) for RNA-binding and C-terminal domain (CTD) involved in RNA-binding, protein dimerization, and nucleocapsid stabilization. The present study explains the structural aspects associated with the involvement of nucleocapsid C-terminal domain in the subunit assembly that helps the RNA binding and further stabilizing the virus assembly by protecting RNA from the hosts exonucleases degradation. The molecular dynamics (MD) simulations of the N-CTD and RNA complex suggests two active sites (site I: a monomer) and (site II: a dimer) with structural stability (RMSD: ~2 Å), Cα fluctuations (RMSF: ~3 Å) and strong protein-ligand interactions were estimated through the SiteMap module of Schrodinger. Virtual screening of 2456 FDA-approved drugs using structure-based docking identified top two leads distinctively against Site-I (monomer): Ceftaroline fosamil (MM-GBSA = -47.12 kcal/mol) and Cefoperazone (-45.84 kcal/mol); and against Site-II (dimer): Boceprevir, (an antiviral protease inhibitor, -106.78 kcal/mol) and Ceftaroline fosamil (-99.55 kcal/mol). The DCCM and PCA of drugs Ceftaroline fosamil (PC1+PC2 = 71.9%) and Boceprevir (PC1 +PC2 = 61.6%) show significant correlated residue motions which suggests highly induced conformational changes in the N-CTD dimer. Therefore, we propose N-CTD as a druggable target with two active binding sites (monomer and dimer) involved in specific RNA binding and stability. The RNA binding site with Ceftaroline fosamil binding can prevent viral assembly and can act as an antiviral for coronavirus.
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Affiliation(s)
- Arushi Chauhan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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12
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Tan Y, Schneider T, Shukla PK, Chandrasekharan MB, Aravind L, Zhang D. Unification and extensive diversification of M/Orf3-related ion channel proteins in coronaviruses and other nidoviruses. Virus Evol 2021; 7:veab014. [PMID: 33692906 PMCID: PMC7928690 DOI: 10.1093/ve/veab014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The coronavirus, Severe Acute Respiratory Syndrome (SARS)-CoV-2, responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, has emphasized the need for a better understanding of the evolution of virus-host interactions. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) implicated in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. We present computational evidence that these viral families might utilize specific conserved polar residues to constitute an aqueous pore within the membrane-spanning region. We reconstruct an evolutionary history of these families and objectively establish the common origin of the M proteins of CoVs and Toroviruses. We also show that the divergent ORF3 clade (ORF3a/ORF3b/ORF3c/ORF5 families) represents a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a hypothesis for their role in virion assembly of CoVs, ToroVs, and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly and membrane budding. We show that M and ORF3 are under different evolutionary pressures; in contrast to the slow evolution of M as core structural component, the ORF3 clade is under selection for diversification, which suggests it might act at the interface with host molecules and/or immune attack.
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Affiliation(s)
- Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO 63103, USA
| | - Theresa Schneider
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO 63103, USA
| | - Prakash K Shukla
- Department of Radiation Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO 63103, USA
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13
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Ou Z, Ouzounis C, Wang D, Sun W, Li J, Chen W, Marlière P, Danchin A. A Path toward SARS-CoV-2 Attenuation: Metabolic Pressure on CTP Synthesis Rules the Virus Evolution. Genome Biol Evol 2020; 12:2467-2485. [PMID: 33125064 PMCID: PMC7665462 DOI: 10.1093/gbe/evaa229] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
In the context of the COVID-19 pandemic, we describe here the singular metabolic background that constrains enveloped RNA viruses to evolve toward likely attenuation in the long term, possibly after a step of increased pathogenicity. Cytidine triphosphate (CTP) is at the crossroad of the processes allowing SARS-CoV-2 to multiply, because CTP is in demand for four essential metabolic steps. It is a building block of the virus genome, it is required for synthesis of the cytosine-based liponucleotide precursors of the viral envelope, it is a critical building block of the host transfer RNAs synthesis and it is required for synthesis of dolichol-phosphate, a precursor of viral protein glycosylation. The CCA 3'-end of all the transfer RNAs required to translate the RNA genome and further transcripts into the proteins used to build active virus copies is not coded in the human genome. It must be synthesized de novo from CTP and ATP. Furthermore, intermediary metabolism is built on compulsory steps of synthesis and salvage of cytosine-based metabolites via uridine triphosphate that keep limiting CTP availability. As a consequence, accidental replication errors tend to replace cytosine by uracil in the genome, unless recombination events allow the sequence to return to its ancestral sequences. We document some of the consequences of this situation in the function of viral proteins. This unique metabolic setup allowed us to highlight and provide a raison d'être to viperin, an enzyme of innate antiviral immunity, which synthesizes 3'-deoxy-3',4'-didehydro-CTP as an extremely efficient antiviral nucleotide.
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Affiliation(s)
- Zhihua Ou
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Christos Ouzounis
- Biological Computation and Process Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessalonica, Greece
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Wanying Sun
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Weijun Chen
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China.,BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, Paris, France
| | - Antoine Danchin
- Kodikos Labs, Institut Cochin, Paris, France.,School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, Pokfulam, Hong Kong
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14
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Perdikari TM, Murthy AC, Ryan VH, Watters S, Naik MT, Fawzi NL. SARS-CoV-2 nucleocapsid protein phase-separates with RNA and with human hnRNPs. EMBO J 2020; 39:e106478. [PMID: 33200826 PMCID: PMC7737613 DOI: 10.15252/embj.2020106478] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Tightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and assemble within viral factories, dynamic compartments formed within the host cells associated with human stress granules. Here, we test the possibility that the multivalent RNA-binding nucleocapsid protein (N) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) condenses with RNA via liquid-liquid phase separation (LLPS) and that N protein can be recruited in phase-separated forms of human RNA-binding proteins associated with SG formation. Robust LLPS with RNA requires two intrinsically disordered regions (IDRs), the N-terminal IDR and central-linker IDR, as well as the folded C-terminal oligomerization domain, while the folded N-terminal domain and the C-terminal IDR are not required. N protein phase separation is induced by addition of non-specific RNA. In addition, N partitions in vitro into phase-separated forms of full-length human hnRNPs (TDP-43, FUS, hnRNPA2) and their low-complexity domains (LCs). These results provide a potential mechanism for the role of N in SARS-CoV-2 viral genome packing and in host-protein co-opting necessary for viral replication and infectivity.
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Affiliation(s)
| | - Anastasia C Murthy
- Molecular BiologyCell Biology & Biochemistry Graduate ProgramBrown UniversityProvidenceRIUSA
| | - Veronica H Ryan
- Neuroscience Graduate ProgramBrown UniversityProvidenceRIUSA
| | - Scott Watters
- Department of Molecular Pharmacology, Physiology, and BiotechnologyBrown UniversityProvidenceRIUSA
| | - Mandar T Naik
- Department of Molecular Pharmacology, Physiology, and BiotechnologyBrown UniversityProvidenceRIUSA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and BiotechnologyBrown UniversityProvidenceRIUSA
- Robert J. and Nancy D. Carney Institute for Brain ScienceBrown UniversityProvidenceRIUSA
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15
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Tan Y, Schneider T, Shukla PK, Chandrasekharan MB, Aravind L, Zhang D. Unification of the M/ORF3-related proteins points to a diversified role for ion conductance in pathogenesis of coronaviruses and other nidoviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.10.377366. [PMID: 33200132 PMCID: PMC7668736 DOI: 10.1101/2020.11.10.377366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The new coronavirus, SARS-CoV-2, responsible for the COVID-19 pandemic has emphasized the need for a better understanding of the evolution of virus-host conflicts. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) and involved in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. By sequence analysis and structural modeling, we show that these viral families utilize specific conserved polar residues to constitute an ion-conducting pore in the membrane. We reconstruct the evolutionary history of these families, objectively establish the common origin of the M proteins of CoVs and Toroviruses. We show that the divergent ORF3a/ORF3b/ORF5 families represent a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a model for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly, membrane fusion and budding. We show that the M and ORF3 are under differential evolutionary pressures; in contrast to the slow evolution of M as core structural component, the CoV-ORF3 clade is under selection for diversification, which indicates it is likely at the interface with host molecules and/or immune attack. IMPORTANCE Coronaviruses (CoVs) have become a major threat to human welfare as the causative agents of several severe infectious diseases, namely Severe Acute Respiratory Syndrome (SARS), Middle Eastern Respiratory Syndrome (MERS), and the recently emerging human coronavirus disease 2019 (COVID-19). The rapid spread, severity of these diseases, as well as the potential re-emergence of other CoV-associated diseases have imposed a strong need for a thorough understanding of function and evolution of these CoVs. By utilizing robust domain-centric computational strategies, we have established homologous relationships between many divergent families of CoV proteins, including SARS-CoV/SARS-CoV-2 ORF3a, MERS-CoV ORF5, proteins from both beta-CoVs (ORF3c) and alpha-CoVs (ORF3b), the typical CoV Matrix proteins, and many distant homologs from other nidoviruses. We present evidence that they are active ion channel proteins, and the Cov-specific ORF3 clade proteins are under selection for rapid diversification, suggesting they might have been involved in interfering host molecules and/or immune attack.
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16
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Nikolakaki E, Giannakouros T. SR/RS Motifs as Critical Determinants of Coronavirus Life Cycle. Front Mol Biosci 2020; 7:219. [PMID: 32974389 PMCID: PMC7471607 DOI: 10.3389/fmolb.2020.00219] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/04/2020] [Indexed: 01/24/2023] Open
Abstract
SR/RS domains are found in almost all eukaryotic genomes from C. elegans to human. These domains are thought to mediate interactions between proteins but also between proteins and RNA in complex networks associated with mRNA splicing, chromatin structure, transcription, cell cycle and cell structure. A precise and tight regulation of their function is achieved through phosphorylation of a number of serine residues within the SR/RS motifs by the Serine-Arginine protein kinases (SRPKs) that lead to delicate structural alterations. Given that coronavirus N proteins also contain SR/RS domains, we formulate the hypothesis that the viruses exploit the properties of these motifs to promote unpacking of viral RNA and virion assembly.
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Affiliation(s)
- Eleni Nikolakaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University, Thessaloniki, Greece
| | - Thomas Giannakouros
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University, Thessaloniki, Greece
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17
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Wolff G, Limpens RWAL, Zevenhoven-Dobbe JC, Laugks U, Zheng S, de Jong AWM, Koning RI, Agard DA, Grünewald K, Koster AJ, Snijder EJ, Bárcena M. A molecular pore spans the double membrane of the coronavirus replication organelle. Science 2020; 369:1395-1398. [PMID: 32763915 PMCID: PMC7665310 DOI: 10.1126/science.abd3629] [Citation(s) in RCA: 314] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
Coronaviruses transform host cell membranes into peculiar double-membrane vesicles that have long been thought to accommodate viral genome replication. However, because these compartments appeared to be completely sealed, it has remained unknown how the newly made viral RNA could be exported to the cytosol for translation and packaging into new virions. Wolff et al. used cryo–electron microscopy to identify a molecular pore that spans the double membrane (see the Perspective by Unchwaniwala and Ahlquist). Six copies of a large coronavirus transmembrane protein formed the core of this structure, which may constitute a viral RNA export channel and provide a target for future antiviral interventions. Science, this issue p. 1395; see also p. 1306 Coronavirus genome replication is associated with virus-induced cytosolic double-membrane vesicles, which may provide a tailored microenvironment for viral RNA synthesis in the infected cell. However, it is unclear how newly synthesized genomes and messenger RNAs can travel from these sealed replication compartments to the cytosol to ensure their translation and the assembly of progeny virions. In this study, we used cellular cryo–electron microscopy to visualize a molecular pore complex that spans both membranes of the double-membrane vesicle and would allow export of RNA to the cytosol. A hexameric assembly of a large viral transmembrane protein was found to form the core of the crown-shaped complex. This coronavirus-specific structure likely plays a key role in coronavirus replication and thus constitutes a potential drug target.
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Affiliation(s)
- Georg Wolff
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - Ronald W A L Limpens
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - Jessika C Zevenhoven-Dobbe
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Ulrike Laugks
- Department of Structural Cell Biology of Viruses, Centre for Structural Systems Biology, Heinrich Pette Institute, Leibnitz Institute of Experimental Virology, 22607 Hamburg, Germany
| | - Shawn Zheng
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Anja W M de Jong
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - Roman I Koning
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kay Grünewald
- Department of Structural Cell Biology of Viruses, Centre for Structural Systems Biology, Heinrich Pette Institute, Leibnitz Institute of Experimental Virology, 22607 Hamburg, Germany.,Department of Chemistry, MIN Faculty, Universität Hamburg, 20146 Hamburg, Germany
| | - Abraham J Koster
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands.
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18
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Asghari A, Naseri M, Safari H, Saboory E, Parsamanesh N. The Novel Insight of SARS-CoV-2 Molecular Biology and Pathogenesis and Therapeutic Options. DNA Cell Biol 2020; 39:1741-1753. [PMID: 32716648 DOI: 10.1089/dna.2020.5703] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
On December 31, 2019, a novel coronavirus, being the third highly infective CoV and named as coronavirus disease 2019 (COVID-19) in the city of Wuhan, was announced by the World Health Organization. COVID-19 has a 2% mortality rate, is known as the third extremely infective CoV infection, and has a mortality rate less than MERS-CoV and SARS-CoV. The CoV family comprises a chief number of positive single-stranded ss (+) RNA viruses that are recognized in mammals. The 2019-nCoV patients showed that the angiotensin-converting enzyme II (ACE2) was the same for SARS-CoV. Structural proteins have an essential role in virus released and budding to various host cells. Notably, evidence indicated human-to-human transmission, along with several exported patients of virus infection worldwide. Nowadays, no licensed antivirals drugs or vaccines for being utilized against these coronavirus infections are recognized. There is an urgent requirement for an extensive research of CoV infections to disclose the route of extension, pathogenesis, and diagnosis and then to recognize the therapeutic targets to facilitate disease control and surveillance. In this article, we present an overview of the common biological criteria of CoVs and explain pathogenesis with a focus on the therapeutic approach to suggest potential goals for treating and monitoring this emerging zoonotic disease.
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Affiliation(s)
- Arghavan Asghari
- Student Research Committee and Birjand University of Medical Sciences, Birjand, Iran
| | - Mohsen Naseri
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hamidreza Safari
- Department of Immunology, Torbat Jam Faculty of Medical Sciences, Torbat Jam, Iran
| | - Ehsan Saboory
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
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19
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Bhowmik D, Nandi R, Jagadeesan R, Kumar N, Prakash A, Kumar D. Identification of potential inhibitors against SARS-CoV-2 by targeting proteins responsible for envelope formation and virion assembly using docking based virtual screening, and pharmacokinetics approaches. INFECTION GENETICS AND EVOLUTION 2020; 84:104451. [PMID: 32640381 PMCID: PMC7335633 DOI: 10.1016/j.meegid.2020.104451] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
WHO has declared the outbreak of COVID-19 as a public health emergency of international concern. The ever-growing new cases have called for an urgent emergency for specific anti-COVID-19 drugs. Three structural proteins (Membrane, Envelope and Nucleocapsid protein) play an essential role in the assembly and formation of the infectious virion particles. Thus, the present study was designed to identify potential drug candidates from the unique collection of 548 anti-viral compounds (natural and synthetic anti-viral), which target SARS-CoV-2 structural proteins. High-end molecular docking analysis was performed to characterize the binding affinity of the selected drugs-the ligand, with the SARS-CoV-2 structural proteins, while high-level Simulation studies analyzed the stability of drug-protein interactions. The present study identified rutin, a bioflavonoid and the antibiotic, doxycycline, as the most potent inhibitor of SARS-CoV-2 envelope protein. Caffeic acid and ferulic acid were found to inhibit SARS-CoV-2 membrane protein while the anti-viral agent's simeprevir and grazoprevir showed a high binding affinity for nucleocapsid protein. All these compounds not only showed excellent pharmacokinetic properties, absorption, metabolism, minimal toxicity and bioavailability but were also remain stabilized at the active site of proteins during the MD simulation. Thus, the identified lead compounds may act as potential molecules for the development of effective drugs against SARS-CoV-2 by inhibiting the envelope formation, virion assembly and viral pathogenesis.
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Affiliation(s)
- Deep Bhowmik
- Department of Microbiology, Assam University, Silchar 788011, Assam, India
| | - Rajat Nandi
- Department of Microbiology, Assam University, Silchar 788011, Assam, India
| | - Rahul Jagadeesan
- CAS in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai 600025, India
| | - Niranjan Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon 122413, India
| | - Diwakar Kumar
- Department of Microbiology, Assam University, Silchar 788011, Assam, India.
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20
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Llanes A, Restrepo CM, Caballero Z, Rajeev S, Kennedy MA, Lleonart R. Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 Pandemic. Int J Mol Sci 2020; 21:E4546. [PMID: 32604724 PMCID: PMC7352669 DOI: 10.3390/ijms21124546] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/22/2022] Open
Abstract
In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of coronaviruses in the aftermath of the 2002-2003 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-2020 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2. We focus on shared genomic features of the betacoronaviruses and the application of genomic information to phylogenetic analysis, molecular epidemiology and the design of diagnostic systems, potential drugs and vaccine candidates.
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Affiliation(s)
- Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; (A.L.); (C.M.R.); (Z.C.)
| | - Carlos M. Restrepo
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; (A.L.); (C.M.R.); (Z.C.)
| | - Zuleima Caballero
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; (A.L.); (C.M.R.); (Z.C.)
| | - Sreekumari Rajeev
- College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Melissa A. Kennedy
- College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA;
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; (A.L.); (C.M.R.); (Z.C.)
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21
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Perdikari TM, Murthy AC, Ryan VH, Watters S, Naik MT, Fawzi NL. SARS-CoV-2 nucleocapsid protein undergoes liquid-liquid phase separation stimulated by RNA and partitions into phases of human ribonucleoproteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.09.141101. [PMID: 32577653 PMCID: PMC7302208 DOI: 10.1101/2020.06.09.141101] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and may assemble within viral factories, dynamic compartments formed within the host cells. Here, we examine the possibility that the multivalent RNA-binding nucleocapsid protein (N) from the severe acute respiratory syndrome coronavirus (SARS-CoV-2) compacts RNA via protein-RNA liquid-liquid phase separation (LLPS) and that N interactions with host RNA-binding proteins are mediated by phase separation. To this end, we created a construct expressing recombinant N fused to a N-terminal maltose binding protein tag which helps keep the oligomeric N soluble for purification. Using in vitro phase separation assays, we find that N is assembly-prone and phase separates avidly. Phase separation is modulated by addition of RNA and changes in pH and is disfavored at high concentrations of salt. Furthermore, N enters into in vitro phase separated condensates of full-length human hnRNPs (TDP-43, FUS, and hnRNPA2) and their low complexity domains (LCs). However, N partitioning into the LC of FUS, but not TDP-43 or hnRNPA2, requires cleavage of the solubilizing MBP fusion. Hence, LLPS may be an essential mechanism used for SARS-CoV-2 and other RNA viral genome packing and host protein co-opting, functions necessary for viral replication and hence infectivity.
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Affiliation(s)
| | - Anastasia C Murthy
- Molecular Biology, Cell Biology & Biochemistry Graduate Program, Brown University, Providence, RI, USA
| | - Veronica H Ryan
- Neuroscience Graduate Program, Brown University, Providence, RI, USA
| | - Scott Watters
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
| | - Mandar T Naik
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
- Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
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22
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Danchin A, Marlière P. Cytosine drives evolution of SARS-CoV-2. Environ Microbiol 2020; 22:1977-1985. [PMID: 32291894 PMCID: PMC7262064 DOI: 10.1111/1462-2920.15025] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Antoine Danchin
- Kodikos Labs, 24 rue Jean Baldassini, 69007 Lyon/Institut Cochin, 75013 Paris, France
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 81 rue Réaumur, 75002, Paris, France
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23
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Abstract
RNA viruses carry out selective packaging of their genomes in a variety of ways, many involving a genomic packaging signal. The first coronavirus packaging signal was discovered nearly thirty years ago, but how it functions remains incompletely understood. This review addresses the current state of knowledge of coronavirus genome packaging, which has mainly been studied in two prototype species, mouse hepatitis virus and transmissible gastroenteritis virus. Despite the progress that has been made in the mapping and characterization of some packaging signals, there is conflicting evidence as to whether the viral nucleocapsid protein or the membrane protein plays the primary role in packaging signal recognition. The different models for the mechanism of genomic RNA packaging that have been prompted by these competing views are described. Also discussed is the recent exciting discovery that selective coronavirus genome packaging is critical for in vivo evasion of the host innate immune response. Selective incorporation of the coronavirus genome into virions is mediated by a cis-acting RNA packaging signal. Packaging signals vary across different coronavirus genera and lineages. Different lines of evidence attribute packaging signal recognition to either the nucleocapsid or the membrane protein. Selective coronavirus genome packaging plays a role in evasion of host innate immunity.
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Affiliation(s)
- Paul S Masters
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, United States.
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24
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Chen J, Fang P, Wang M, Peng Q, Ren J, Wang D, Peng G, Fang L, Xiao S, Ding Z. Porcine deltacoronavirus nucleocapsid protein antagonizes IFN-β production by impairing dsRNA and PACT binding to RIG-I. Virus Genes 2019; 55:520-531. [PMID: 31129785 PMCID: PMC7088841 DOI: 10.1007/s11262-019-01673-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/17/2019] [Indexed: 12/24/2022]
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that causes watery diarrhea, vomiting and mortality in newborn piglets. Previous studies have suggested that PDCoV infection antagonizes RIG-I-like receptor (RLR)-mediated IFN-β production to evade host innate immune defense, and PDCoV-encoded nonstructural protein nsp5 and accessory protein NS6 are associated with this process. However, whether the structural protein(s) of PDCoV also antagonize IFN-β production remains unclear. In this study, we found that PDCoV nucleocapsid (N) protein, the most abundant viral structural protein, suppressed Sendai virus (SEV)-induced IFN-β production and transcription factor IRF3 activation, but did not block IFN-β production induced by overexpressing RIG-I/MDA5. Furthermore, study revealed that PDCoV N protein interacted with RIG-I and MDA5 in an in vitro overexpression system and evident interactions between N protein and RIG-I could be detected in the context of PDCoV infection, which interfered with the binding of dsRNA and protein activator of protein kinase R (PACT) to RIG-I. Together, our results demonstrate that PDCoV N protein is an IFN antagonist and utilizes diverse strategies to attenuate RIG-I recognition and activation.
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Affiliation(s)
- Jun Chen
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - 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
| | - Mohan Wang
- 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
| | - Qi Peng
- 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
| | - Dang Wang
- 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
| | - Guiqing Peng
- 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
| | - Zhen Ding
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Zhimin Street, Qingshan Lake, Nanchang, 330045, China.
- 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.
- Jiangxi Provincial Key Laboratory for Animal Science and Technology, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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25
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Naskalska A, Dabrowska A, Nowak P, Szczepanski A, Jasik K, Milewska A, Ochman M, Zeglen S, Rajfur Z, Pyrc K. Novel coronavirus-like particles targeting cells lining the respiratory tract. PLoS One 2018; 13:e0203489. [PMID: 30183777 PMCID: PMC6124810 DOI: 10.1371/journal.pone.0203489] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/21/2018] [Indexed: 12/13/2022] Open
Abstract
Virus like particles (VLPs) produced by the expression of viral structural proteins can serve as versatile nanovectors or potential vaccine candidates. In this study we describe for the first time the generation of HCoV-NL63 VLPs using baculovirus system. Major structural proteins of HCoV-NL63 have been expressed in tagged or native form, and their assembly to form VLPs was evaluated. Additionally, a novel procedure for chromatography purification of HCoV-NL63 VLPs was developed. Interestingly, we show that these nanoparticles may deliver cargo and selectively transduce cells expressing the ACE2 protein such as ciliated cells of the respiratory tract. Production of a specific delivery vector is a major challenge for research concerning targeting molecules. The obtained results show that HCoV-NL63 VLPs may be efficiently produced, purified, modified and serve as a delivery platform. This study constitutes an important basis for further development of a promising viral vector displaying narrow tissue tropism.
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Affiliation(s)
- Antonina Naskalska
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- * E-mail: (AN); (KP)
| | - Agnieszka Dabrowska
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Paulina Nowak
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur Szczepanski
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Jasik
- Department of Skin Structural Studies, Medical University of Silesia in Katowice, School of Pharmacy with the Division of Laboratory Medicine, Sosnowiec, Poland
| | - Aleksandra Milewska
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marek Ochman
- Department of Cardiac Surgery and Transplantology, Silesian Center for Heart Diseases, Zabrze, Poland
| | - Slawomir Zeglen
- Department of Cardiac Surgery and Transplantology, Silesian Center for Heart Diseases, Zabrze, Poland
| | - Zenon Rajfur
- Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Sciences, Jagiellonian University, Krakow, Poland
| | - Krzysztof Pyrc
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- * E-mail: (AN); (KP)
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26
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Hsin WC, Chang CH, Chang CY, Peng WH, Chien CL, Chang MF, Chang SC. Nucleocapsid protein-dependent assembly of the RNA packaging signal of Middle East respiratory syndrome coronavirus. J Biomed Sci 2018; 25:47. [PMID: 29793506 PMCID: PMC5966903 DOI: 10.1186/s12929-018-0449-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/15/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Middle East respiratory syndrome coronavirus (MERS-CoV) consists of a positive-sense, single-stranded RNA genome and four structural proteins: the spike, envelope, membrane, and nucleocapsid protein. The assembly of the viral genome into virus particles involves viral structural proteins and is believed to be mediated through recognition of specific sequences and RNA structures of the viral genome. METHODS AND RESULTS A culture system for the production of MERS coronavirus-like particles (MERS VLPs) was determined and established by electron microscopy and the detection of coexpressed viral structural proteins. Using the VLP system, a 258-nucleotide RNA fragment, which spans nucleotides 19,712 to 19,969 of the MERS-CoV genome (designated PS258(19712-19969)ME), was identified to function as a packaging signal. Assembly of the RNA packaging signal into MERS VLPs is dependent on the viral nucleocapsid protein. In addition, a 45-nucleotide stable stem-loop substructure of the PS258(19712-19969)ME interacted with both the N-terminal domain and the C-terminal domain of the viral nucleocapsid protein. Furthermore, a functional SARS-CoV RNA packaging signal failed to assemble into the MERS VLPs, which indicated virus-specific assembly of the RNA genome. CONCLUSIONS A MERS-oV RNA packaging signal was identified by the detection of GFP expression following an incubation of MERS VLPs carrying the heterologous mRNA GFP-PS258(19712-19969)ME with virus permissive Huh7 cells. The MERS VLP system could help us in understanding virus infection and morphogenesis.
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Affiliation(s)
- Wei-Chen Hsin
- Institute of Microbiology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Chan-Hua Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Chi-You Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Wei-Hao Peng
- Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Chung-Liang Chien
- Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan
| | - Ming-Fu Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan.
| | - Shin C Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, No. 1, Jen-Ai Road, First Section, Taipei, 100, Taiwan.
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27
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Abstract
Selective packaging is a mechanism used by multiple virus families to specifically incorporate genomic RNA (gRNA) into virions and exclude other types of RNA. Lineage A betacoronaviruses incorporate a 95-bp stem-loop structure, the packaging signal (PS), into the nsp15 locus of ORF1b that is both necessary and sufficient for the packaging of RNAs. However, unlike other viral PSs, where mutations generally resulted in viral replication defects, mutation of the coronavirus (CoV) PS results in large increases in subgenomic RNA packaging with minimal effects on gRNA packaging in vitro and on viral titers. Here, we show that selective packaging is also required for viral evasion of the innate immune response and optimal pathogenicity. We engineered two distinct PS mutants in two different strains of murine hepatitis virus (MHV) that packaged increased levels of subgenomic RNAs, negative-sense genomic RNA, and even cellular RNAs. All PS mutant viruses replicated normally in vitro but caused dramatically reduced lethality and weight loss in vivo. PS mutant virus infection of bone marrow-derived macrophages resulted in increased interferon (IFN) production, indicating that the innate immune system limited the replication and/or pathogenesis of PS mutant viruses in vivo. PS mutant viruses remained attenuated in MAVS−/− and Toll-like receptor 7-knockout (TLR7−/−) mice, two well-known RNA sensors for CoVs, but virulence was restored in interferon alpha/beta receptor-knockout (IFNAR−/−) mice or in MAVS−/− mice treated with IFNAR-blocking antibodies. Together, these data indicate that coronaviruses promote virulence by utilizing selective packaging to avoid innate immune detection. Coronaviruses (CoVs) produce many types of RNA molecules during their replication cycle, including both positive- and negative-sense genomic and subgenomic RNAs. Despite this, coronaviruses selectively package only positive-sense genomic RNA into their virions. Why CoVs selectively package their genomic RNA is not clear, as disruption of the packaging signal in MHV, which leads to loss of selective packaging, does not affect genomic RNA packaging or virus replication in cultured cells. This contrasts with other viruses, where disruption of selective packaging generally leads to altered replication. Here, we demonstrate that in the absence of selective packaging, the virulence of MHV was significantly reduced. Importantly, virulence was restored in the absence of interferon signaling, indicating that selective packaging is a mechanism used by CoVs to escape innate immune detection.
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28
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Coronavirus nucleocapsid proteins assemble constitutively in high molecular oligomers. Sci Rep 2017; 7:5740. [PMID: 28720894 PMCID: PMC5515880 DOI: 10.1038/s41598-017-06062-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/07/2017] [Indexed: 01/19/2023] Open
Abstract
Coronaviruses (CoV) are enveloped viruses and rely on their nucleocapsid N protein to incorporate the positive-stranded genomic RNA into the virions. CoV N proteins form oligomers but the mechanism and relevance underlying their multimerization remain to be fully understood. Using in vitro pull-down experiments and density glycerol gradients, we found that at least 3 regions distributed over its entire length mediate the self-interaction of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) N protein. The fact that these regions can bind reciprocally between themselves provides a possible molecular basis for N protein oligomerization. Interestingly, cytoplasmic N molecules of MHV-infected cells constitutively assemble into oligomers through a process that does not require binding to genomic RNA. Based on our data, we propose a model where constitutive N protein oligomerization allows the optimal loading of the genomic viral RNA into a ribonucleoprotein complex via the presentation of multiple viral RNA binding motifs.
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