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Wu W, Cheng Y, Zhou H, Sun C, Zhang S. The SARS-CoV-2 nucleocapsid protein: its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics. Virol J 2023; 20:6. [PMID: 36627683 PMCID: PMC9831023 DOI: 10.1186/s12985-023-01968-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) continues to take a heavy toll on personal health, healthcare systems, and economies around the globe. Scientists are expending tremendous effort to develop diagnostic technologies for detecting positive infections within the shortest possible time, and vaccines and drugs specifically for the prevention and treatment of COVID-19 disease. At the same time, emerging novel variants have raised serious concerns about vaccine efficacy. The SARS-CoV-2 nucleocapsid (N) protein plays an important role in the coronavirus life cycle, and participates in various vital activities after virus invasion. It has attracted a large amount of attention for vaccine and drug development. Here, we summarize the latest research of the N protein, including its role in the SARS-CoV-2 life cycle, structure and function, and post-translational modifications in addition to its involvement in liquid-liquid phase separation (LLPS) and use as a basis for the development of vaccines and diagnostic techniques.
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Affiliation(s)
- Wenbing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Ying Cheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Hong Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Changzhen Sun
- Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Shujun Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
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102
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Miyake Y, Hara Y, Umeda M, Banerjee I. Influenza A Virus: Cellular Entry. Subcell Biochem 2023; 106:387-401. [PMID: 38159235 DOI: 10.1007/978-3-031-40086-5_14] [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] [Indexed: 01/03/2024]
Abstract
The frequent emergence of pathogenic viruses with pandemic potential has posed a significant threat to human health and economy, despite enormous advances in our understanding of infection mechanisms and devising countermeasures through developing various prophylactic and therapeutic strategies. The recent coronavirus disease (COVID-19) pandemic has re-emphasised the importance of rigorous research on virus infection mechanisms and highlighted the need for our preparedness for potential pandemics. Although viruses cannot self-replicate, they tap into host cell factors and processes for their entry, propagation and dissemination. Upon entering the host cells, viruses ingeniously utilise the innate biological functions of the host cell to replicate themselves and maintain their existence in the hosts. Influenza A virus (IAV), which has a negative-sense, single-stranded RNA as its genome, is no exception. IAVs are enveloped viruses with a lipid bilayer derived from the host cell membrane and have a surface covered with the spike glycoprotein haemagglutinin (HA) and neuraminidase (NA). Viral genome is surrounded by an M1 shell, forming a "capsid" in the virus particle. IAV particles use HA to recognise sialic acids on the cell surface of lung epithelial cells for their attachment. After attachment to the cell surface, IAV particles are endocytosed and sorted into the early endosomes. Subsequently, as the early endosomes mature into late endosomes, the endosomal lumen becomes acidified, and the low pH of the late endosomes induces conformational reaggangements in the HA to initiate fusion between the endosomal and viral membranes. Upon fusion, the viral capsid disintegrates and the viral ribonucleoprotein (vRNP) complexes containing the viral genome are released into the cytosol. The process of viral capsid disintegration is called "uncoating". After successful uncoating, the vRNPs are imported into the nucleus by importin α/β (IMP α/β), where viral replication and transcription take place and the new vRNPs are assembled. Recently, we have biochemically elucidated the molecular mechanisms of the processes of viral capsid uncoating subsequent viral genome dissociation. In this chapter, we present the molecular details of the viral uncoating process.
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Affiliation(s)
- Yasuyuki Miyake
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Institute for Advanced Research (IAR), Nagoya University, Nagoya, Japan.
| | - Yuya Hara
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miki Umeda
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Indranil Banerjee
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali (IISER Mohali), Mohali, India.
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103
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The humoral immune response more than one year after SARS-CoV-2 infection: low detection rate of anti-nucleocapsid antibodies via Euroimmun ELISA. Infection 2023; 51:83-90. [PMID: 35648370 PMCID: PMC9159036 DOI: 10.1007/s15010-022-01830-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/06/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE Antibody assays against SARS-CoV-2 are used in sero-epidemiological studies to estimate the proportion of a population with past infection. IgG antibodies against the spike protein (S-IgG) allow no distinction between infection and vaccination. We evaluated the role of anti-nucleocapsid-IgG (N-IgG) to identify individuals with infection more than one year past infection. METHODS S- and N-IgG were determined using the Euroimmun enzyme-linked immunosorbent assay (ELISA) in two groups: a randomly selected sample from the population of Stuttgart, Germany, and individuals with PCR-proven SARS-CoV-2 infection. Participants were five years or older. Demographics and comorbidities were registered from participants above 17 years. RESULTS Between June 15, 2021 and July 14, 2021, 454 individuals from the random sample participated, as well as 217 individuals with past SARS-CoV-2 infection. Mean time from positive PCR test result to antibody testing was 458.7 days (standard deviation 14.6 days) in the past infection group. In unvaccinated individuals, the seroconversion rate for S-IgG was 25.5% in the random sample and 75% in the past infection group (P = < 0.001). In vaccinated individuals, the mean signal ratios for S-IgG were higher in individuals with prior infection (6.9 vs 11.2; P = < 0.001). N-IgG were only detectable in 17.1% of participants with past infection. Predictors for detectable N-IgG were older age, male sex, fever, wheezing and in-hospital treatment for COVID-19 and cardiovascular comorbidities. CONCLUSION N-IgG is not a reliable marker for SARS-CoV-2 infection after more than one year. In future, other diagnostic tests are needed to identify individuals with past natural infection.
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104
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Brownsword MJ, Locker N. A little less aggregation a little more replication: Viral manipulation of stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1741. [PMID: 35709333 PMCID: PMC10078398 DOI: 10.1002/wrna.1741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
Recent exciting studies have uncovered how membrane-less organelles, also known as biocondensates, are providing cells with rapid response pathways, allowing them to re-organize their cellular contents and adapt to stressful conditions. Their assembly is driven by the phase separation of their RNAs and intrinsically disordered protein components into condensed foci. Among these, stress granules (SGs) are dynamic cytoplasmic biocondensates that form in response to many stresses, including activation of the integrated stress response or viral infections. SGs sit at the crossroads between antiviral signaling and translation because they concentrate signaling proteins and components of the innate immune response, in addition to translation machinery and stalled mRNAs. Consequently, they have been proposed to contribute to antiviral activities, and therefore are targeted by viral countermeasures. Equally, SGs components can be commandeered by viruses for their own efficient replication. Phase separation processes are an important component of the viral life cycle, for example, driving the assembly of replication factories or inclusion bodies. Therefore, in this review, we will outline the recent understanding of this complex interplay and tug of war between viruses, SGs, and their components. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Matthew J. Brownsword
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
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105
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Yun JS, Song H, Kim NH, Cha SY, Hwang KH, Lee JE, Jeong CH, Song SH, Kim S, Cho ES, Kim HS, Yook JI. Glycogen Synthase Kinase-3 Interaction Domain Enhances Phosphorylation of SARS-CoV-2 Nucleocapsid Protein. Mol Cells 2022; 45:911-922. [PMID: 36572560 PMCID: PMC9794558 DOI: 10.14348/molcells.2022.0130] [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: 08/22/2022] [Accepted: 09/16/2022] [Indexed: 12/28/2022] Open
Abstract
A structural protein of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), nucleocapsid (N) protein is phosphorylated by glycogen synthase kinase (GSK)-3 on the serine/arginine (SR) rich motif located in disordered regions. Although phosphorylation by GSK-3β constitutes a critical event for viral replication, the molecular mechanism underlying N phosphorylation is not well understood. In this study, we found the putative alpha-helix L/FxxxL/AxxRL motif known as the GSK-3 interacting domain (GID), found in many endogenous GSK-3β binding proteins, such as Axins, FRATs, WWOX, and GSKIP. Indeed, N interacts with GSK-3β similarly to Axin, and Leu to Glu substitution of the GID abolished the interaction, with loss of N phosphorylation. The N phosphorylation is also required for its structural loading in a virus-like particle (VLP). Compared to other coronaviruses, N of Sarbecovirus lineage including bat RaTG13 harbors a CDK1-primed phosphorylation site and Gly-rich linker for enhanced phosphorylation by GSK-3β. Furthermore, we found that the S202R mutant found in Delta and R203K/G204R mutant found in the Omicron variant allow increased abundance and hyper-phosphorylation of N. Our observations suggest that GID and mutations for increased phosphorylation in N may have contributed to the evolution of variants.
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Affiliation(s)
- Jun Seop Yun
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Hyeeun Song
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Nam Hee Kim
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - So Young Cha
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Kyu Ho Hwang
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Jae Eun Lee
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Cheol-Hee Jeong
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Sang Hyun Song
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Seonghun Kim
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Eunae Sandra Cho
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Hyun Sil Kim
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
| | - Jong In Yook
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul 03722, Korea
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Synthesis of Novel 1,3,4-Oxadiazole-Derived α-Aminophosphonates/ α-Aminophosphonic Acids and Evaluation of Their In Vitro Antiviral Activity against the Avian Coronavirus Infectious Bronchitis Virus. Pharmaceutics 2022; 15:pharmaceutics15010114. [PMID: 36678743 PMCID: PMC9867332 DOI: 10.3390/pharmaceutics15010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/14/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
An efficient and simple approach has been developed for the synthesis of eight dialkyl/aryl[(5-phenyl-1,3,4-oxadiazol-2-ylamino)(aryl)methyl]phosphonates through the Pudovik-type reaction of dialkyl/arylphosphite with imines, obtained from 5-phenyl-1,3,4-oxadiazol-2-amine and aromatic aldehydes, under microwave irradiation. Five of them were hydrolyzed to lead to the corresponding phosphonic acids. Selected synthesized compounds were screened for their in vitro antiviral activity against the avian bronchitis virus (IBV). In the MTT cytotoxicity assay, the dose-response curve showed that all test compounds were safe in the range concentration of 540-1599 µM. The direct contact of novel synthesized compounds with IBV showed that the diethyl[(5-phenyl-1,3,4-oxadiazol-2-ylamino)(4-trifluoromethoxyphenyl)methyl]phosphonate (5f) (at 33 µM) and the [(5-phenyl-1,3,4-oxadiazol-2-ylamino)(4-trifluoromethylphenyl)methyl] phosphonic acid (6a) (at 1.23 µM) strongly inhibited the IBV infectivity, indicating their high virucidal activity. However, virus titers from IBV-infected Vero cells remained unchanged in response to treatment with the lowest non-cytotoxic concentrations of synthesized compounds suggesting their incapacity to inhibit the virus replication inside the host cell. Lack of antiviral activity might presumably be ascribed to their polarity that hampers their diffusion across the lipophilic cytoplasmic membrane. Therefore, the interactions of 5f and 6a were analyzed against the main coronavirus protease, papain-like protease, and nucleocapsid protein by molecular docking methods. Nevertheless, the novel 1,3,4-oxadiazole-based α-aminophosphonic acids and α-amino-phosphonates hold potential for developing new hygienic virucidal products for domestic, chemical, and medical uses.
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107
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Morse M, Sefcikova J, Rouzina I, Beuning PJ, Williams M. Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates. Nucleic Acids Res 2022; 51:290-303. [PMID: 36533523 PMCID: PMC9841419 DOI: 10.1093/nar/gkac1179] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein performs several functions including binding, compacting, and packaging the ∼30 kb viral genome into the viral particle. N protein consists of two ordered domains, with the N terminal domain (NTD) primarily associated with RNA binding and the C terminal domain (CTD) primarily associated with dimerization/oligomerization, and three intrinsically disordered regions, an N-arm, a C-tail, and a linker that connects the NTD and CTD. We utilize an optical tweezers system to isolate a long single-stranded nucleic acid substrate to measure directly the binding and packaging function of N protein at a single molecule level in real time. We find that N protein binds the nucleic acid substrate with high affinity before oligomerizing and forming a highly compact structure. By comparing the activities of truncated protein variants missing the NTD, CTD, and/or linker, we attribute specific steps in this process to the structural domains of N protein, with the NTD driving initial binding to the substrate and ensuring high localized protein density that triggers interprotein interactions mediated by the CTD, which forms a compact and stable protein-nucleic acid complex suitable for packaging into the virion.
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Affiliation(s)
- Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Mark C Williams
- To whom correspondence should be addressed. Tel: +1 617 373 5705;
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108
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Shapira T, Vimalanathan S, Rens C, Pichler V, Peña-Díaz S, Jordana G, Rees W, Winkler DFH, Sarai I, Steiner T, Jean F, Pelech S, Av-Gay Y. Inhibition of glycogen synthase kinase-3-beta (GSK3β) blocks nucleocapsid phosphorylation and SARS-CoV-2 replication. MOLECULAR BIOMEDICINE 2022; 3:43. [PMID: 36508083 PMCID: PMC9742639 DOI: 10.1186/s43556-022-00111-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/19/2022] [Indexed: 12/14/2022] Open
Abstract
GSK3β has been proposed to have an essential role in Coronaviridae infections. Screening of a targeted library of GSK3β inhibitors against both SARS-CoV-2 and HCoV-229E to identify broad-spectrum anti-Coronaviridae inhibitors resulted in the identification of a high proportion of active compounds with low toxicity to host cells. A selected lead compound, T-1686568, showed low micromolar, dose-dependent activity against SARS-CoV-2 and HCoV-229E. T-1686568 showed efficacy in viral-infected cultured cells and primary 2D organoids. T-1686568 also inhibited SARS-CoV-2 variants of concern Delta and Omicron. Importantly, while inhibition by T-1686568 resulted in the overall reduction of viral load and protein translation, GSK3β inhibition resulted in cellular accumulation of the nucleocapsid protein relative to the spike protein. Following identification of potential phosphorylation sites of Coronaviridae nucleocapsid, protein kinase substrate profiling assays combined with Western blotting analysis of nine host kinases showed that the SARS-CoV-2 nucleocapsid could be phosphorylated by GSK3β and PKCa. GSK3β phosphorylated SARS-CoV-2 nucleocapsid on the S180/S184, S190/S194 and T198 phospho-sites, following previous priming in the adjacent S188, T198 and S206, respectively. Such inhibition presents a compelling target for broad-spectrum anti-Coronaviridae compound development, and underlies the mechanism of action of GSK3β host-directed therapy against this class of obligate intracellular pathogens.
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Affiliation(s)
- Tirosh Shapira
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada ,grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Selvarani Vimalanathan
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Celine Rens
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Virginia Pichler
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Sandra Peña-Díaz
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Grace Jordana
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - William Rees
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Dirk F. H. Winkler
- grid.292479.3Kinexus Bioinformatics Corporation, Suite 1 – 8755 Ash Street, Vancouver, BC V6P 6T3 Canada
| | - Iqbal Sarai
- grid.292479.3Kinexus Bioinformatics Corporation, Suite 1 – 8755 Ash Street, Vancouver, BC V6P 6T3 Canada
| | - Theodore Steiner
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - François Jean
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Steven Pelech
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada ,grid.292479.3Kinexus Bioinformatics Corporation, Suite 1 – 8755 Ash Street, Vancouver, BC V6P 6T3 Canada
| | - Yossef Av-Gay
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada ,grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
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109
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Chen YM, Wei JL, Qin RS, Hou JP, Zang GC, Zhang GY, Chen TT. Folic acid: a potential inhibitor against SARS-CoV-2 nucleocapsid protein. PHARMACEUTICAL BIOLOGY 2022; 60:862-878. [PMID: 35594385 PMCID: PMC9132477 DOI: 10.1080/13880209.2022.2063341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 02/03/2022] [Accepted: 04/01/2022] [Indexed: 06/01/2023]
Abstract
CONTEXT Coronavirus disease 2019 is a global pandemic. Studies suggest that folic acid has antiviral effects. Molecular docking shown that folic acid can act on SARS-CoV-2 Nucleocapsid Phosphoprotein (SARS-CoV-2 N). OBJECTIVE To identify novel molecular therapeutic targets for SARS-CoV-2. MATERIALS AND METHODS Traditional Chinese medicine targets and virus-related genes were identified with network pharmacology and big data analysis. Folic acid was singled out by molecular docking, and its potential target SARS-CoV-2 N was identified. Inhibition of SARS-CoV-2 N of folic acid was verified at the cellular level. RESULTS In total, 8355 drug targets were potentially involved in the inhibition of SARS-CoV-2. 113 hub genes were screened by further association analysis between targets and virus-related genes. The hub genes related compounds were analysed and folic acid was screened as a potential new drug. Moreover, molecular docking showed folic acid could target on SARS-CoV-2 N which inhibits host RNA interference (RNAi). Therefore, this study was based on RNAi to verify whether folic acid antagonises SARS-CoV-2 N. Cell-based experiments shown that RNAi decreased mCherry expression by 81.7% (p < 0.001). This effect was decreased by 8.0% in the presence of SARS-CoV-2 N, indicating that SARS-CoV-2 N inhibits RNAi. With increasing of folic acid concentration, mCherry expression decreased, indicating that folic acid antagonises the regulatory effect of SARS-CoV-2 N on host RNAi. DISCUSSION AND CONCLUSIONS Folic acid may be an antagonist of SARS-CoV-2 N, but its effect on viruses unclear. In future, the mechanisms of action of folic acid against SARS-CoV-2 N should be studied.
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Affiliation(s)
- Yu-meng Chen
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
| | - Jin-lai Wei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Rui-si Qin
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
| | - Jin-ping Hou
- General Surgery of Neonatal Surgery, Liangjiang District, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Guang-chao Zang
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
| | - Guang-yuan Zhang
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
- Pathogen Biology and Immunology Laboratory, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
| | - Ting-ting Chen
- Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
- Pathogen Biology and Immunology Laboratory, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, PR China
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Vesely CH, Reardon PN, Yu Z, Barbar E, Mehl RA, Cooley RB. Accessing isotopically labeled proteins containing genetically encoded phosphoserine for NMR with optimized expression conditions. J Biol Chem 2022; 298:102613. [PMID: 36265582 PMCID: PMC9678770 DOI: 10.1016/j.jbc.2022.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Phosphoserine (pSer) sites are primarily located within disordered protein regions, making it difficult to experimentally ascertain their effects on protein structure and function. Therefore, the production of 15N- (and 13C)-labeled proteins with site-specifically encoded pSer for NMR studies is essential to uncover molecular mechanisms of protein regulation by phosphorylation. While genetic code expansion technologies for the translational installation of pSer in Escherichia coli are well established and offer a powerful strategy to produce site-specifically phosphorylated proteins, methodologies to adapt them to minimal or isotope-enriched media have not been described. This shortcoming exists because pSer genetic code expansion expression hosts require the genomic ΔserB mutation, which increases pSer bioavailability but also imposes serine auxotrophy, preventing growth in minimal media used for isotopic labeling of recombinant proteins. Here, by testing different media supplements, we restored normal BL21(DE3) ΔserB growth in labeling media but subsequently observed an increase of phosphatase activity and mis-incorporation not typically seen in standard rich media. After rounds of optimization and adaption of a high-density culture protocol, we were able to obtain ≥10 mg/L homogenously labeled, phosphorylated superfolder GFP. To demonstrate the utility of this method, we also produced the intrinsically disordered serine/arginine-rich region of the SARS-CoV-2 Nucleocapsid protein labeled with 15N and pSer at the key site S188 and observed the resulting peak shift due to phosphorylation by 2D and 3D heteronuclear single quantum correlation analyses. We propose this cost-effective methodology will pave the way for more routine access to pSer-enriched proteins for 2D and 3D NMR analyses.
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Affiliation(s)
- Cat Hoang Vesely
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA; Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Patrick N Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon, USA
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Ryan A Mehl
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA; Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Richard B Cooley
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA; Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA.
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111
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Calder LJ, Calcraft T, Hussain S, Harvey R, Rosenthal PB. Electron cryotomography of SARS-CoV-2 virions reveals cylinder-shaped particles with a double layer RNP assembly. Commun Biol 2022; 5:1210. [PMID: 36357779 PMCID: PMC9648435 DOI: 10.1038/s42003-022-04183-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
SARS-CoV-2 is a lipid-enveloped Betacoronavirus and cause of the Covid-19 pandemic. To study the three-dimensional architecture of the virus, we perform electron cryotomography (cryo-ET) on SARS-Cov-2 virions and three variants revealing particles of regular cylindrical morphology. The ribonucleoprotein particles packaging the genome in the virion interior form a dense, double layer assembly with a cylindrical shape related to the overall particle morphology. This organisation suggests structural interactions important to virus assembly.
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Affiliation(s)
- Lesley J. Calder
- grid.451388.30000 0004 1795 1830Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Thomas Calcraft
- grid.451388.30000 0004 1795 1830Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Saira Hussain
- grid.451388.30000 0004 1795 1830Worldwide Influenza Centre, The Francis Crick Institute, NW1 1AT London, UK ,grid.451388.30000 0004 1795 1830RNA Virus Replication Laboratory, The Francis Crick Institute, NW1 1AT London, UK
| | - Ruth Harvey
- grid.451388.30000 0004 1795 1830Worldwide Influenza Centre, The Francis Crick Institute, NW1 1AT London, UK
| | - Peter B. Rosenthal
- grid.451388.30000 0004 1795 1830Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
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112
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Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor. Sci Rep 2022; 12:18500. [PMID: 36323732 PMCID: PMC9628480 DOI: 10.1038/s41598-022-22576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/17/2022] [Indexed: 01/06/2023] Open
Abstract
The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal. Several phenolic compounds, including L-chicoric acid (CA), were identified as high-affinity N-protein ligands. The binding of CA to the N protein was confirmed by isothermal titration calorimetry, 1H-STD and 15N-HSQC NMR, and by the crystal structure of CA bound to the N protein C-terminal domain (CTD), further revealing a new modulatory site in the SARS-CoV-2 N protein. Moreover, CA reduced SARS-CoV-2 replication in cell cultures. These data thus open venues for the development of new antivirals targeting the N protein, an essential and yet underexplored coronavirus target.
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113
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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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114
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Yaron TM, Heaton BE, Levy TM, Johnson JL, Jordan TX, Cohen BM, Kerelsky A, Lin TY, Liberatore KM, Bulaon DK, Van Nest SJ, Koundouros N, Kastenhuber ER, Mercadante MN, Shobana-Ganesh K, He L, Schwartz RE, Chen S, Weinstein H, Elemento O, Piskounova E, Nilsson-Payant BE, Lee G, Trimarco JD, Burke KN, Hamele CE, Chaparian RR, Harding AT, Tata A, Zhu X, Tata PR, Smith CM, Possemato AP, Tkachev SL, Hornbeck PV, Beausoleil SA, Anand SK, Aguet F, Getz G, Davidson AD, Heesom K, Kavanagh-Williamson M, Matthews DA, tenOever BR, Cantley LC, Blenis J, Heaton NS. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication. Sci Signal 2022; 15:eabm0808. [PMID: 36282911 PMCID: PMC9830954 DOI: 10.1126/scisignal.abm0808] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccinated or who experience breakthrough infections. Understanding the common host factors necessary for the life cycles of coronaviruses may reveal conserved therapeutic targets. Here, we used the known substrate specificities of mammalian protein kinases to deconvolute the sequence of phosphorylation events mediated by three host protein kinase families (SRPK, GSK-3, and CK1) that coordinately phosphorylate a cluster of serine and threonine residues in the viral N protein, which is required for viral replication. We also showed that loss or inhibition of SRPK1/2, which we propose initiates the N protein phosphorylation cascade, compromised the viral replication cycle. Because these phosphorylation sites are highly conserved across coronaviruses, inhibitors of these protein kinases not only may have therapeutic potential against COVID-19 but also may be broadly useful against coronavirus-mediated diseases.
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Affiliation(s)
- Tomer M. Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- Tri-Institutional PhD Program in Computational Biology & Medicine, Weill Cornell Medicine/Memorial Sloan Kettering Cancer Center/The Rockefeller University, New York, NY 10021, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Jared L. Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tristan X. Jordan
- New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Benjamin M. Cohen
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexander Kerelsky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ting-Yu Lin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Weill Cornell Graduate School of Medical Sciences, Cell and Developmental Biology Program, New York, NY 10065, USA
| | - Katarina M. Liberatore
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Danielle K. Bulaon
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Samantha J. Van Nest
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nikos Koundouros
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Edward R. Kastenhuber
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Marisa N. Mercadante
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kripa Shobana-Ganesh
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Weill Cornell Graduate School of Medical Sciences, Cell and Developmental Biology Program, New York, NY 10065, USA
| | - Long He
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Robert E. Schwartz
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Harel Weinstein
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Elena Piskounova
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Gina Lee
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Irvine, CA 92868, USA
| | - Joseph D. Trimarco
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kaitlyn N. Burke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cait E. Hamele
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ryan R. Chaparian
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alfred T. Harding
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Clare M. Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | | | | | | | - François Aguet
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Kate Heesom
- Proteomics Facility, University of Bristol, Bristol, BS8 1TD, UK
| | | | - David A. Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | | | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
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115
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Rapid Reversible Osmoregulation of Cytoplasmic Biomolecular Condensates of Human Interferon-α-Induced Antiviral MxA GTPase. Int J Mol Sci 2022; 23:ijms232112739. [PMID: 36361529 PMCID: PMC9655878 DOI: 10.3390/ijms232112739] [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: 09/28/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 01/24/2023] Open
Abstract
We previously discovered that exogenously expressed GFP-tagged cytoplasmic human myxovirus resistance protein (MxA), a major antiviral effector of Type I and III interferons (IFNs) against several RNA- and DNA-containing viruses, existed in the cytoplasm in phase-separated membraneless biomolecular condensates of varying sizes and shapes with osmotically regulated disassembly and reassembly. In this study we investigated whether cytoplasmic IFN-α-induced endogenous human MxA structures were also biomolecular condensates, displayed hypotonic osmoregulation and the mechanisms involved. Both IFN-α-induced endogenous MxA and exogenously expressed GFP-MxA formed cytoplasmic condensates in A549 lung and Huh7 hepatoma cells which rapidly disassembled within 1-2 min when cells were exposed to 1,6-hexanediol or to hypotonic buffer (~40-50 mOsm). Both reassembled into new structures within 1-2 min of shifting cells to isotonic culture medium (~330 mOsm). Strikingly, MxA condensates in cells continuously exposed to culture medium of moderate hypotonicity (in the range one-fourth, one-third or one-half isotonicity; range 90-175 mOsm) first rapidly disassembled within 1-3 min, and then, in most cells, spontaneously reassembled 7-15 min later into new structures. This spontaneous reassembly was inhibited by 2-deoxyglucose (thus, was ATP-dependent) and by dynasore (thus, required membrane internalization). Indeed, condensate reassembly was preceded by crowding of the cytosolic space by large vacuole-like dilations (VLDs) derived from internalized plasma membrane. Remarkably, the antiviral activity of GFP-MxA against vesicular stomatitis virus survived hypoosmolar disassembly and subsequent reassembly. The data highlight the exquisite osmosensitivity of MxA condensates, and the preservation of antiviral activity in the face of hypotonic stress.
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116
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Amahong K, Zhang W, Zhou Y, Zhang S, Yin J, Li F, Xu H, Yan T, Yue Z, Liu Y, Hou T, Qiu Y, Tao L, Han L, Zhu F. CovInter: interaction data between coronavirus RNAs and host proteins. Nucleic Acids Res 2022; 51:D546-D556. [PMID: 36200814 PMCID: PMC9825556 DOI: 10.1093/nar/gkac834] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/07/2022] [Accepted: 09/16/2022] [Indexed: 01/29/2023] Open
Abstract
Coronavirus has brought about three massive outbreaks in the past two decades. Each step of its life cycle invariably depends on the interactions among virus and host molecules. The interaction between virus RNA and host protein (IVRHP) is unique compared to other virus-host molecular interactions and represents not only an attempt by viruses to promote their translation/replication, but also the host's endeavor to combat viral pathogenicity. In other words, there is an urgent need to develop a database for providing such IVRHP data. In this study, a new database was therefore constructed to describe the interactions between coronavirus RNAs and host proteins (CovInter). This database is unique in (a) unambiguously characterizing the interactions between virus RNA and host protein, (b) comprehensively providing experimentally validated biological function for hundreds of host proteins key in viral infection and (c) systematically quantifying the differential expression patterns (before and after infection) of these key proteins. Given the devastating and persistent threat of coronaviruses, CovInter is highly expected to fill the gap in the whole process of the 'molecular arms race' between viruses and their hosts, which will then aid in the discovery of new antiviral therapies. It's now free and publicly accessible at: https://idrblab.org/covinter/.
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Affiliation(s)
| | | | | | - Song Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Hongquan Xu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Tianci Yan
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Zixuan Yue
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuhong Liu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Lin Tao
- Correspondence may also be addressed to Lin Tao.
| | - Lianyi Han
- Correspondence may also be addressed to Lianyi Han.
| | - Feng Zhu
- To whom correspondence should be addressed. Tel: +86 189 8946 6518; Fax: +86 571 8820 8444;
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117
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Laine L, Skön M, Väisänen E, Julkunen I, Österlund P. SARS-CoV-2 variants Alpha, Beta, Delta and Omicron show a slower host cell interferon response compared to an early pandemic variant. Front Immunol 2022; 13:1016108. [PMID: 36248817 PMCID: PMC9561549 DOI: 10.3389/fimmu.2022.1016108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/15/2022] [Indexed: 11/15/2022] Open
Abstract
Since the start of the pandemic at the end of 2019, arising mutations in SARS-CoV-2 have improved its transmission and ability to circumvent the immunity induced by vaccination and previous COVID-19 infection. Studies on the effects of SARS-CoV-2 genomic mutations on replication and innate immunity will give us valuable insight into the evolution of the virus which can aid in further development of vaccines and new treatment modalities. Here we systematically analyzed the kinetics of virus replication, innate immune activation, and host cell antiviral response patterns in Alpha, Beta, Delta, Kappa, Omicron and two early pandemic SARS-CoV-2 variant-infected human lung epithelial Calu-3 cells. We observed overall comparable replication patterns for these variants with modest variations. Particularly, the sublineages of Omicron BA.1, BA.2 and a recombinant sublineage, XJ, all showed attenuated replication in Calu-3 cells compared to Alpha and Delta. Furthermore, there was relatively weak activation of primary innate immune signaling pathways, however, all variants produced enough interferons to induce the activation of STAT2 and production of interferon stimulated genes (ISGs). While interferon mRNA expression and STAT2 activation correlated with cellular viral RNA levels, ISG production did not. Although clear cut effects of specific SARS-CoV-2 genomic mutations could not be concluded, the variants of concern, including Omicron, showed a lower replication efficiency and a slower interferon response compared to an early pandemic variant in the study.
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Affiliation(s)
- Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- *Correspondence: Larissa Laine,
| | - Marika Skön
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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118
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Wu C, Holehouse AS, Leung DW, Amarasinghe GK, Dutch RE. Liquid Phase Partitioning in Virus Replication: Observations and Opportunities. Annu Rev Virol 2022; 9:285-306. [PMID: 35709511 PMCID: PMC11331907 DOI: 10.1146/annurev-virology-093020-013659] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses frequently carry out replication in specialized compartments within cells. The effect of these structures on virus replication is poorly understood. Recent research supports phase separation as a foundational principle for organization of cellular components with the potential to influence viral replication. In this review, phase separation is described in the context of formation of viral replication centers, with an emphasis on the nonsegmented negative-strand RNA viruses. Consideration is given to the interplay between phase separation and the critical processes of viral transcription and genome replication, and the role of these regions in pathogen-host interactions is discussed. Finally, critical questions that must be addressed to fully understand how phase separation influences viral replication and the viral life cycle are presented, along with information about new approaches that could be used to make important breakthroughs in this emerging field.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Science and Engineering Living Systems, Washington University, St. Louis, Missouri, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA;
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119
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Mohler K, Moen J, Rogulina S, Rinehart J. Cell type-independent profiling of interactions between intracellular pathogens and the human phosphoproteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509702. [PMID: 36203552 PMCID: PMC9536036 DOI: 10.1101/2022.09.27.509702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Interactions between proteins from intracellular pathogens and host proteins in an infected cell are often mediated by post-translational modifications encoded in the host proteome. Identifying protein modifications, such as phosphorylation, that dictate these interactions remains a defining challenge in unraveling the molecular mechanisms of pathogenesis. We have developed a platform in engineered bacteria that displays over 110,000 phosphorylated human proteins coupled to a fluorescent reporter system capable of identifying the host-pathogen interactome of phosphoproteins (H-PIP). This resource broadly enables cell-type independent interrogation and discovery of proteins from intracellular pathogens capable of binding phosphorylated human proteins. As an example of the H-PIP platform, we generated a unique, high-resolution SARS-CoV-2 interaction network which expanded our knowledge of viral protein function and identified understudied areas of host pathology.
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120
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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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Schiavina M, Pontoriero L, Tagliaferro G, Pierattelli R, Felli IC. The Role of Disordered Regions in Orchestrating the Properties of Multidomain Proteins: The SARS-CoV-2 Nucleocapsid Protein and Its Interaction with Enoxaparin. Biomolecules 2022; 12:1302. [PMID: 36139141 PMCID: PMC9496478 DOI: 10.3390/biom12091302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Novel and efficient strategies need to be developed to interfere with the SARS-CoV-2 virus. One of the most promising pharmaceutical targets is the nucleocapsid protein (N), responsible for genomic RNA packaging. N is composed of two folded domains and three intrinsically disordered regions (IDRs). The globular RNA binding domain (NTD) and the tethered IDRs are rich in positively charged residues. The study of the interaction of N with polyanions can thus help to elucidate one of the key driving forces responsible for its function, i.e., electrostatics. Heparin, one of the most negatively charged natural polyanions, has been used to contrast serious cases of COVID-19 infection, and we decided to study its interaction with N at the molecular level. We focused on the NTR construct, which comprises the NTD and two flanking IDRs, and on the NTD construct in isolation. We characterized this interaction using different nuclear magnetic resonance approaches and isothermal titration calorimetry. With these tools, we were able to identify an extended surface of NTD involved in the interaction. Moreover, we assessed the importance of the IDRs in increasing the affinity for heparin, highlighting how different tracts of these flexible regions modulate the interaction.
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Affiliation(s)
| | | | | | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Isabella C. Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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122
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Fan S, Sun W, Fan L, Wu N, Sun W, Ma H, Chen S, Li Z, Li Y, Zhang J, Yan J. The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity. Comput Struct Biotechnol J 2022; 20:5040-5044. [PMID: 36097552 PMCID: PMC9454191 DOI: 10.1016/j.csbj.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022] Open
Abstract
The binding of SARS-CoV-2 nucleocapsid (N) protein to both the 5'- and 3'-ends of genomic RNA has different implications arising from its binding to the central region during virion assembly. However, the mechanism underlying selective binding remains unknown. Herein, we performed the high-throughput RNA-SELEX (HTR-SELEX) to determine the RNA-binding specificity of the N proteins of various SARS-CoV-2 variants as well as other β-coronaviruses and showed that N proteins could bind two unrelated sequences, both of which were highly conserved across all variants and species. Interestingly, both sequences are virtually absent from the human transcriptome; however, they exhibit a highly enriched, mutually complementary distribution in the coronavirus genome, highlighting their varied functions in genome packaging. Our results provide mechanistic insights into viral genome packaging, thereby increasing the feasibility of developing drugs with broad-spectrum anti-coronavirus activity by targeting RNA binding by N proteins.
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Affiliation(s)
- Shaorong Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
| | - Wenju Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
| | - Ligang Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
- Department of Precision Diagnostic and Therapeutic Technology, The City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China
| | - Nan Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
| | - Wei Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
| | - Haiqian Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
| | - Siyuan Chen
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region
| | - Zitong Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region
| | - Yu Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region
| | - Jilin Zhang
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
| | - Jian Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
- Department of Precision Diagnostic and Therapeutic Technology, The City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China
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123
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Zachrdla M, Savastano A, Ibáñez de Opakua A, Cima‐Omori M, Zweckstetter M. Contributions of the N-terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA-induced phase separation. Protein Sci 2022; 31:e4409. [PMID: 36040256 PMCID: PMC9387207 DOI: 10.1002/pro.4409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein is an essential structural component of mature virions, encapsulating the genomic RNA and modulating RNA transcription and replication. Several of its activities might be associated with the protein's ability to undergo liquid-liquid phase separation. NSARS-CoV-2 contains an intrinsically disordered region at its N-terminus (NTE) that can be phosphorylated and is affected by mutations found in human COVID-19 infections, including in the Omicron variant of concern. Here, we show that NTE deletion decreases the range of RNA concentrations that can induce phase separation of NSARS-CoV-2 . In addition, deletion of the prion-like NTE allows NSARS-CoV-2 droplets to retain their liquid-like nature during incubation. We further demonstrate that RNA-binding engages multiple parts of the NTE and changes NTE's structural properties. The results form the foundation to characterize the impact of N-terminal mutations and post-translational modifications on the molecular properties of the SARS-CoV-2 nucleocapsid protein. STATEMENT: The nucleocapsid protein of SARS-CoV-2 plays an important role in both genome packaging and viral replication upon host infection. Replication has been associated with RNA-induced liquid-liquid phase separation of the nucleocapsid protein. We present insights into the role of the N-terminal part of the nucleocapsid protein in the protein's RNA-mediated liquid-liquid phase separation.
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Affiliation(s)
- Milan Zachrdla
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Adriana Savastano
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Alain Ibáñez de Opakua
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Maria‐Sol Cima‐Omori
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Markus Zweckstetter
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
- NMR‐based Structural BiologyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
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124
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Ahmad A, Uversky VN, Khan RH. Aberrant liquid-liquid phase separation and amyloid aggregation of proteins related to neurodegenerative diseases. Int J Biol Macromol 2022; 220:703-720. [PMID: 35998851 DOI: 10.1016/j.ijbiomac.2022.08.132] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/05/2022]
Abstract
Recent evidence has shown that the processes of liquid-liquid phase separation (LLPS) or liquid-liquid phase transitions (LLPTs) are a crucial and prevalent phenomenon that underlies the biogenesis of numerous membrane-less organelles (MLOs) and biomolecular condensates within the cells. Findings show that processes associated with LLPS play an essential role in physiology and disease. In this review, we discuss the physical and biomolecular factors that contribute to the development of LLPS, the associated functions, as well as their consequences for cell physiology and neurological disorders. Additionally, the finding of mis-regulated proteins, which have long been linked to aggregates in neuropathology, are also known to induce LLPS/LLPTs, prompting a lot of interest in understanding the connection between aberrant phase separation and disorder conditions. Moreover, the methods used in recent and ongoing studies in this field are also explored, as is the possibility that these findings will encourage new lines of inquiry into the molecular causes of neurodegenerative diseases.
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Affiliation(s)
- Azeem Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P. 202002, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russia.
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P. 202002, India.
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125
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Roden C, Dai Y, Giannetti C, Seim I, Lee M, Sealfon R, McLaughlin G, Boerneke M, Iserman C, Wey S, Ekena J, Troyanskaya O, Weeks K, You L, Chilkoti A, Gladfelter A. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res 2022; 50:8168-8192. [PMID: 35871289 PMCID: PMC9371935 DOI: 10.1093/nar/gkac596] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 12/11/2022] Open
Abstract
Nucleocapsid protein (N-protein) is required for multiple steps in betacoronaviruses replication. SARS-CoV-2-N-protein condenses with specific viral RNAs at particular temperatures making it a powerful model for deciphering RNA sequence specificity in condensates. We identify two separate and distinct double-stranded, RNA motifs (dsRNA stickers) that promote N-protein condensation. These dsRNA stickers are separately recognized by N-protein's two RNA binding domains (RBDs). RBD1 prefers structured RNA with sequences like the transcription-regulatory sequence (TRS). RBD2 prefers long stretches of dsRNA, independent of sequence. Thus, the two N-protein RBDs interact with distinct dsRNA stickers, and these interactions impart specific droplet physical properties that could support varied viral functions. Specifically, we find that addition of dsRNA lowers the condensation temperature dependent on RBD2 interactions and tunes translational repression. In contrast RBD1 sites are sequences critical for sub-genomic (sg) RNA generation and promote gRNA compression. The density of RBD1 binding motifs in proximity to TRS-L/B sequences is associated with levels of sub-genomic RNA generation. The switch to packaging is likely mediated by RBD1 interactions which generate particles that recapitulate the packaging unit of the virion. Thus, SARS-CoV-2 can achieve biochemical complexity, performing multiple functions in the same cytoplasm, with minimal protein components based on utilizing multiple distinct RNA motifs that control N-protein interactions.
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Affiliation(s)
- Christine A Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Catherine A Giannetti
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Ian Seim
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Rachel Sealfon
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Grace A McLaughlin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark A Boerneke
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Christiane Iserman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel A Wey
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Joanne L Ekena
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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126
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Li Y, Lu S, Gu J, Xia W, Zhang S, Zhang S, Wang Y, Zhang C, Sun Y, Lei J, Liu C, Su Z, Yang J, Peng X, Li D. SARS-CoV-2 impairs the disassembly of stress granules and promotes ALS-associated amyloid aggregation. Protein Cell 2022; 13:602-614. [PMID: 35384603 PMCID: PMC8983322 DOI: 10.1007/s13238-022-00905-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023] Open
Abstract
The nucleocapsid (N) protein of SARS-CoV-2 has been reported to have a high ability of liquid-liquid phase separation, which enables its incorporation into stress granules (SGs) of host cells. However, whether SG invasion by N protein occurs in the scenario of SARS-CoV-2 infection is unknow, neither do we know its consequence. Here, we used SARS-CoV-2 to infect mammalian cells and observed the incorporation of N protein into SGs, which resulted in markedly impaired self-disassembly but stimulated cell cellular clearance of SGs. NMR experiments further showed that N protein binds to the SG-related amyloid proteins via non-specific transient interactions, which not only expedites the phase transition of these proteins to aberrant amyloid aggregation in vitro, but also promotes the aggregation of FUS with ALS-associated P525L mutation in cells. In addition, we found that ACE2 is not necessary for the infection of SARS-CoV-2 to mammalian cells. Our work indicates that SARS-CoV-2 infection can impair the disassembly of host SGs and promote the aggregation of SG-related amyloid proteins, which may lead to an increased risk of neurodegeneration.
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Affiliation(s)
- Yichen Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shuaiyao Lu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Jinge Gu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wencheng Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shenqing Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yan Wang
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chong Zhang
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunpeng Sun
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Lei
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoming Su
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Juntao Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
| | - Xiaozhong Peng
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China.
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China.
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127
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Kleer M, Mulloy RP, Robinson CA, Evseev D, Bui-Marinos MP, Castle EL, Banerjee A, Mubareka S, Mossman K, Corcoran JA. Human coronaviruses disassemble processing bodies. PLoS Pathog 2022; 18:e1010724. [PMID: 35998203 PMCID: PMC9439236 DOI: 10.1371/journal.ppat.1010724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 09/02/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
A dysregulated proinflammatory cytokine response is characteristic of severe coronavirus infections caused by SARS-CoV-2, yet our understanding of the underlying mechanism responsible for this imbalanced immune response remains incomplete. Processing bodies (PBs) are cytoplasmic membraneless ribonucleoprotein granules that control innate immune responses by mediating the constitutive decay or suppression of mRNA transcripts, including many that encode proinflammatory cytokines. PB formation promotes turnover or suppression of cytokine RNAs, whereas PB disassembly corresponds with the increased stability and/or translation of these cytokine RNAs. Many viruses cause PB disassembly, an event that can be viewed as a switch that rapidly relieves cytokine RNA repression and permits the infected cell to respond to viral infection. Prior to this submission, no information was known about how human coronaviruses (CoVs) impacted PBs. Here, we show SARS-CoV-2 and the common cold CoVs, OC43 and 229E, induced PB loss. We screened a SARS-CoV-2 gene library and identified that expression of the viral nucleocapsid (N) protein from SARS-CoV-2 was sufficient to mediate PB disassembly. RNA fluorescent in situ hybridization revealed that transcripts encoding TNF and IL-6 localized to PBs in control cells. PB loss correlated with the increased cytoplasmic localization of these transcripts in SARS-CoV-2 N protein-expressing cells. Ectopic expression of the N proteins from five other human coronaviruses (OC43, MERS, 229E, NL63 and SARS-CoV) did not cause significant PB disassembly, suggesting that this feature is unique to SARS-CoV-2 N protein. These data suggest that SARS-CoV-2-mediated PB disassembly contributes to the dysregulation of proinflammatory cytokine production observed during severe SARS-CoV-2 infection.
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Affiliation(s)
- Mariel Kleer
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Rory P. Mulloy
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Carolyn-Ann Robinson
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Danyel Evseev
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Maxwell P. Bui-Marinos
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Elizabeth L. Castle
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan; Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, Saskatchewan, Canada
- Department of Biology, University of Waterloo; Waterloo, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Karen Mossman
- Department of Medicine, Master University, Hamilton, Ontario, Canada
- Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer A. Corcoran
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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128
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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129
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Zhang B, Xie Y, Lan Z, Li D, Tian J, Zhang Q, Tian H, Yang J, Zhou X, Qiu S, Lu K, Liu Y. SARS-CoV-2 Nucleocapsid Protein Has DNA-Melting and Strand-Annealing Activities With Different Properties From SARS-CoV-2 Nsp13. Front Microbiol 2022; 13:851202. [PMID: 35935242 PMCID: PMC9354549 DOI: 10.3389/fmicb.2022.851202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the world and has had a devastating impact on health and economy. The biochemical characterization of SARS-CoV-2 proteins is important for drug design and development. In this study, we discovered that the SARS-CoV-2 nucleocapsid protein can melt double-stranded DNA (dsDNA) in the 5′-3′ direction, similar to SARS-CoV-2 nonstructural protein 13. However, the unwinding activity of SARS-CoV-2 nucleocapsid protein was found to be more than 22 times weaker than that of SARS-CoV-2 nonstructural protein 13, and the melting process was independent of nucleoside triphosphates and Mg2+. Interestingly, at low concentrations, the SARS-CoV-2 nucleocapsid protein exhibited a stronger annealing activity than SARS-CoV-2 nonstructural protein 13; however, at high concentrations, it promoted the melting of dsDNA. These findings have deepened our understanding of the SARS-CoV-2 nucleocapsid protein and will help provide novel insights into antiviral drug development.
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Affiliation(s)
- Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- Bo Zhang,
| | - Yan Xie
- School of Public Health, Zunyi Medical University, Zunyi, China
| | - Zhaoling Lan
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Dayu Li
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Junjie Tian
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Qintao Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Hongji Tian
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Jiali Yang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Xinnan Zhou
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Keyu Lu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- Keyu Lu,
| | - Yang Liu
- School of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Yang Liu,
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130
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Saville JW, Berezuk AM, Srivastava SS, Subramaniam S. Three-Dimensional Visualization of Viral Structure, Entry, and Replication Underlying the Spread of SARS-CoV-2. Chem Rev 2022; 122:14066-14084. [PMID: 35863749 PMCID: PMC9344915 DOI: 10.1021/acs.chemrev.1c01062] [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] [Indexed: 11/23/2022]
Abstract
![]()
The global spread
of SARS-CoV-2 has proceeded at an unprecedented
rate. Remarkably, characterization of the virus using modern tools
in structural biology has also progressed at exceptional speed. Advances
in electron-based imaging techniques, combined with decades of foundational
studies on related viruses, have enabled the research community to
rapidly investigate structural aspects of the novel coronavirus from
the level of individual viral proteins to imaging the whole virus
in a native context. Here, we provide a detailed review of the structural
biology and pathobiology of SARS-CoV-2 as it relates to all facets
of the viral life cycle, including cell entry, replication, and three-dimensional
(3D) packaging based on insights obtained from X-ray crystallography,
cryo-electron tomography, and single-particle cryo-electron microscopy.
The structural comparison between SARS-CoV-2 and the related earlier
viruses SARS-CoV and MERS-CoV is a common thread throughout this review.
We conclude by highlighting some of the outstanding unanswered structural
questions and underscore areas that are under rapid current development
such as the design of effective therapeutics that block viral infection.
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Affiliation(s)
- James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Shanti S Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3.,Gandeeva Therapeutics Inc., Vancouver, British Columbia, Canada, V5C 6N5
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131
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Wu L, Pan T, Zhou M, Chen T, Wu S, Lv X, Liu J, Yu F, Guan Y, Liu B, Zhang W, Deng X, Chen Q, Liang A, Lin Y, Wang L, Tang X, Cai W, Li L, He X, Zhang H, Ma X. CBX4 contributes to HIV-1 latency by forming phase-separated nuclear bodies and SUMOylating EZH2. EMBO Rep 2022; 23:e53855. [PMID: 35642598 PMCID: PMC9253744 DOI: 10.15252/embr.202153855] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 04/17/2022] [Accepted: 05/18/2022] [Indexed: 09/13/2023] Open
Abstract
The retrovirus HIV-1 integrates into the host genome and establishes a latent viral reservoir that escapes immune surveillance. Molecular mechanisms of HIV-1 latency have been studied extensively to achieve a cure for the acquired immunodeficiency syndrome (AIDS). Latency-reversing agents (LRAs) have been developed to reactivate and eliminate the latent reservoir by the immune system. To develop more promising LRAs, it is essential to evaluate new therapeutic targets. Here, we find that CBX4, a component of the Polycomb Repressive Complex 1 (PRC1), contributes to HIV-1 latency in seven latency models and primary CD4+ T cells. CBX4 forms nuclear bodies with liquid-liquid phase separation (LLPS) properties on the HIV-1 long terminal repeat (LTR) and recruits EZH2, the catalytic subunit of PRC2. CBX4 SUMOylates EZH2 utilizing its SUMO E3 ligase activity, thereby enhancing the H3K27 methyltransferase activity of EZH2. Our results indicate that CBX4 acts as a bridge between the repressor complexes PRC1 and PRC2 that act synergistically to maintain HIV-1 latency. Dissolution of phase-separated CBX4 bodies could be a potential intervention to reactivate latent HIV-1.
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Affiliation(s)
- Liyang Wu
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Ting Pan
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenChina
| | - Mo Zhou
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Tao Chen
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Shiyu Wu
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Xi Lv
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Jun Liu
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Fei Yu
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Yuanjun Guan
- Core Laboratory Platform for Medical ScienceZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Bingfeng Liu
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Wanying Zhang
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Xiaohui Deng
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenChina
| | - Qianyu Chen
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Anqi Liang
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Yingtong Lin
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | | | - Xiaoping Tang
- Department of Infectious DiseasesGuangzhou 8 People's HospitalGuangzhouChina
| | - Weiping Cai
- Department of Infectious DiseasesGuangzhou 8 People's HospitalGuangzhouChina
| | - Linghua Li
- Department of Infectious DiseasesGuangzhou 8 People's HospitalGuangzhouChina
| | - Xin He
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Hui Zhang
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Guangzhou LaboratoryGuangzhou International Bio‐IslandGuangzhouChina
| | - Xiancai Ma
- Institute of Human VirologyKey Laboratory of Tropical Disease Control of Ministry EducationGuangdong Engineering Research Center for Antimicrobial Agent and ImmunotechnologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
- Guangzhou LaboratoryGuangzhou International Bio‐IslandGuangzhouChina
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132
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Hao M, Wang D, Xia Q, Kan S, Chang L, Liu H, Yang Z, Liu W. Pathogenic Mechanism and Multi-omics Analysis of Oral Manifestations in COVID-19. Front Immunol 2022; 13:879792. [PMID: 35860279 PMCID: PMC9290522 DOI: 10.3389/fimmu.2022.879792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a respiratory infectious disease that seriously threatens human life. The clinical manifestations of severe COVID-19 include acute respiratory distress syndrome and multiple organ failure. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19, spreads through contaminated droplets. SARS-CoV-2 particles have been detected in the saliva of COVID-19 patients, implying that the virus can infect and damage the oral cavity. The oral manifestations of COVID-19 include xerostomia and gustatory dysfunction. Numerous studies showed that the four structural proteins of SARS-CoV-2 are its potential pathogenic factors, especially the S protein, which binds to human ACE2 receptors facilitating the entry of the virus into the host cells. Usually, upon entry into the host cell, a pathogen triggers the host’s immune response. However, a mount of multi-omics and immunological analyses revealed that COVID-19 is caused by immune dysregulation. A decrease in the number and phenotypes of immune cells, IFN-1 production and excessive release of certain cytokines have also been reported. In conclusion, this review summarizes the oral manifestations of COVID-19 and multi-omics analysis of SARS-CoV-2 infection.
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Affiliation(s)
- Ming Hao
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Qianyun Xia
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Shaoning Kan
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Lu Chang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Huimin Liu
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Zhijing Yang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Weiwei Liu
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun, China
- *Correspondence: Weiwei Liu,
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133
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Pontoriero L, Schiavina M, Korn SM, Schlundt A, Pierattelli R, Felli IC. NMR Reveals Specific Tracts within the Intrinsically Disordered Regions of the SARS-CoV-2 Nucleocapsid Protein Involved in RNA Encountering. Biomolecules 2022; 12:biom12070929. [PMID: 35883485 PMCID: PMC9312987 DOI: 10.3390/biom12070929] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is crucial for the highly organized packaging and transcription of the genomic RNA. Studying atomic details of the role of its intrinsically disordered regions (IDRs) in RNA recognition is challenging due to the absence of structure and to the repetitive nature of their primary sequence. IDRs are known to act in concert with the folded domains of N and here we use NMR spectroscopy to identify the priming events of N interacting with a regulatory SARS-CoV-2 RNA element. 13C-detected NMR experiments, acquired simultaneously to 1H detected ones, provide information on the two IDRs flanking the N-terminal RNA binding domain (NTD) within the N-terminal region of the protein (NTR, 1–248). We identify specific tracts of the IDRs that most rapidly sense and engage with RNA, and thus provide an atom-resolved picture of the interplay between the folded and disordered regions of N during RNA interaction.
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Affiliation(s)
- Letizia Pontoriero
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
| | - Marco Schiavina
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
| | - Sophie M. Korn
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany;
| | - Andreas Schlundt
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany;
- Correspondence: (A.S.); (R.P.); (I.C.F.)
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
- Correspondence: (A.S.); (R.P.); (I.C.F.)
| | - Isabella C. Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
- Correspondence: (A.S.); (R.P.); (I.C.F.)
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134
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Structural basis for SARS-CoV-2 nucleocapsid (N) protein recognition by 14-3-3 proteins. J Struct Biol 2022; 214:107879. [PMID: 35781025 PMCID: PMC9245327 DOI: 10.1016/j.jsb.2022.107879] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/22/2022]
Abstract
14-3-3 proteins are important dimeric scaffolds that regulate the function of hundreds of proteins in a phosphorylation-dependent manner. The SARS-CoV-2 nucleocapsid (N) protein forms a complex with human 14-3-3 proteins upon phosphorylation, which has also been described for other coronaviruses. Here, we report a high-resolution crystal structure of 14-3-3 bound to an N phosphopeptide bearing the phosphoserine 197 in the middle. The structure revealed two copies of the N phosphopeptide bound, each in the central binding groove of each 14-3-3 monomer. A complex network of hydrogen bonds and water bridges between the peptide and 14-3-3 was observed explaining the high affinity of the N protein for 14-3-3 proteins.
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135
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Boggs KB, Edmonds K, Cifuentes-Munoz N, El Najjar F, Ossandón C, Roe M, Wu C, Moncman CL, Creamer TP, Amarasinghe GK, Leung DW, Dutch RE. Human Metapneumovirus Phosphoprotein Independently Drives Phase Separation and Recruits Nucleoprotein to Liquid-Like Bodies. mBio 2022; 13:e0109922. [PMID: 35536005 PMCID: PMC9239117 DOI: 10.1128/mbio.01099-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Human metapneumovirus (HMPV) inclusion bodies (IBs) are dynamic structures required for efficient viral replication and transcription. The minimum components needed to form IB-like structures in cells are the nucleoprotein (N) and the tetrameric phosphoprotein (P). HMPV P binds to the following two versions of the N protein in infected cells: N-terminal P residues interact with monomeric N (N0) to maintain a pool of protein to encapsidate new RNA and C-terminal P residues interact with oligomeric, RNA-bound N (N-RNA). Recent work on other negative-strand viruses has suggested that IBs are, at least in part, liquid-like phase-separated membraneless organelles. Here, HMPV IBs in infected or transfected cells were shown to possess liquid organelle properties, such as fusion and fission. Recombinant versions of HMPV N and P proteins were purified to analyze the interactions required to drive phase separation in vitro. Purified HMPV P was shown to form liquid droplets in isolation. This observation is distinct from other viral systems that also form IBs. Partial removal of nucleic acid from purified P altered phase-separation dynamics, suggesting that nucleic acid interactions play a role in IB formation. HMPV P also recruits monomeric N (N0-P) and N-RNA to droplets in vitro. These findings suggest that HMPV P may also act as a scaffold protein to mediate multivalent interactions with monomeric and oligomeric N, as well as RNA, to promote phase separation of IBs. Together, these findings highlight an additional layer of regulation in HMPV replication by the viral P and N proteins. IMPORTANCE Human metapneumovirus (HMPV) is a leading cause of respiratory disease among children, immunocompromised individuals, and the elderly. Currently, no vaccines or antivirals are available for the treatment of HMPV infections. Cytoplasmic inclusion bodies (IBs), where HMPV replication and transcription occur, represent a promising target for the development of novel antivirals. The HMPV nucleoprotein (N) and phosphoprotein (P) are the minimal components needed for IB formation in eukaryotic cells. However, interactions that regulate the formation of these dynamic structures are poorly understood. Here, we showed that HMPV IBs possess the properties of liquid organelles and that purified HMPV P phase separates independently in vitro. Our work suggests that HMPV P phase-separation dynamics are altered by nucleic acid. We provide strong evidence that, unlike results reported from other viral systems, HMPV P alone can serve as a scaffold for multivalent interactions with monomeric (N0) and oligomeric (N-RNA) HMPV N for IB formation.
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Affiliation(s)
- Kerri Beth Boggs
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Kearstin Edmonds
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Nicolas Cifuentes-Munoz
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Farah El Najjar
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Conny Ossandón
- Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - McKenna Roe
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carole L. Moncman
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Trevor P. Creamer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daisy W. Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
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136
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Mechanisms of host type I interferon response modulation by the nucleocapsid proteins of alpha- and betacoronaviruses. Arch Virol 2022; 167:1925-1930. [PMID: 35763067 PMCID: PMC9244355 DOI: 10.1007/s00705-022-05513-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022]
Abstract
Coronaviruses can have a devastating impact on the health of humans and animals. Porcine epidemic diarrhea virus (PEDV) causes extremely high fatality rates in neonatal piglets, whereas severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic in humans. As a critical component of the host antiviral innate immune response, type I interferon production and signaling play a very important role, especially in the initial phase of the antiviral responses. Coronaviruses have evolved multiple ways to counteract type I interferon responses. Although the primary functions of the nucleocapsid protein are to facilitate viral RNA replication and package viral genomic RNA into virions, recent studies have shown that the nucleocapsid protein is also involved in virus-host interactions. The aim of this review is to summarize our current understanding of how the nucleocapsid proteins of PEDV and SARS-CoV-2 modulate type I interferon responses. This knowledge will be useful for developing strategies to combat coronavirus infections.
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137
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Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther 2022; 7:202. [PMID: 35764603 PMCID: PMC9240077 DOI: 10.1038/s41392-022-01039-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lan-Yi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Guangdong-Hong Kong Joint Laboratory for RNA Medicine, 510060, Guangzhou, China.
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138
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Dang M, Song J. A review of the effects of ATP and hydroxychloroquine on the phase separation of the SARS-CoV-2 nucleocapsid protein. Biophys Rev 2022; 14:709-715. [PMID: 35756710 PMCID: PMC9214679 DOI: 10.1007/s12551-022-00957-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 05/05/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is the coronavirus causing the ongoing pandemic with > 460 millions of infections and > 6 millions of deaths. SARS-CoV-2 nucleocapsid (N) is the only structural protein which plays essential roles in almost all key steps of the viral life cycle with its diverse functions depending on liquid-liquid phase separation (LLPS) driven by interacting with various nucleic acids. The 419-residue N protein is highly conserved in all variants including delta and omicron, and composed of both folded N-/C-terminal domains (NTD/CTD) as well as three long intrinsically disordered regions (IDRs). Recent results have suggested that its CTD and IDRs are also cryptic nucleic acid-binding domains. In this context, any small molecules capable of interfering in its interaction with nucleic acids are anticipated to modulate its LLPS and associated functions. Indeed, ATP, the energy currency existing at very high concentrations (2-12 mM) in all living cells but absent in viruses, modulates LLPS of N protein, and consequently appears to be evolutionarily hijacked by SARS-CoV-2 to promote its life cycle. Hydroxychloroquine (HCQ) has been also shown to specifically bind NTD and CTD to inhibit their interactions with nucleic acids, as well as to disrupt LLPS. Particularly, the unique structure of the HCQ-CTD complex offers a promising strategy for further design of anti-SARS-CoV-2 drugs with better affinity and specificity. The finding may indicate that LLPS is indeed druggable by small molecules, thus opening up a promising direction for drug discovery/design by targeting LLPS in general.
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Affiliation(s)
- Mei Dang
- Department of Biological Sciences, Faculty of Science, National University of Singapore; 10 Kent Ridge Crescent, Singapore, 119260 Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore; 10 Kent Ridge Crescent, Singapore, 119260 Singapore
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139
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Johnson BA, Zhou Y, Lokugamage KG, Vu MN, Bopp N, Crocquet-Valdes PA, Kalveram B, Schindewolf C, Liu Y, Scharton D, Plante JA, Xie X, Aguilar P, Weaver SC, Shi PY, Walker DH, Routh AL, Plante KS, Menachery VD. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. PLoS Pathog 2022; 18:e1010627. [PMID: 35728038 PMCID: PMC9275689 DOI: 10.1371/journal.ppat.1010627] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/12/2022] [Accepted: 05/30/2022] [Indexed: 12/27/2022] Open
Abstract
While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203-205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral 'RG' motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2's continued adaptation to human infection.
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Affiliation(s)
- Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kumari G. Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle N. Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nathen Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Birte Kalveram
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Patricia Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Drug Discovery, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Andrew L. Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kenneth S. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
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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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141
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Characterization of RNA content in individual phase-separated coacervate microdroplets. Nat Commun 2022; 13:2626. [PMID: 35551426 PMCID: PMC9098875 DOI: 10.1038/s41467-022-30158-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/05/2022] [Indexed: 11/08/2022] Open
Abstract
Condensates formed by complex coacervation are hypothesized to have played a crucial part during the origin-of-life. In living cells, condensation organizes biomolecules into a wide range of membraneless compartments. Although RNA is a key component of biological condensates and the central component of the RNA world hypothesis, little is known about what determines RNA accumulation in condensates and to which extend single condensates differ in their RNA composition. To address this, we developed an approach to read the RNA content from single synthetic and protein-based condensates using high-throughput sequencing. We find that certain RNAs efficiently accumulate in condensates. These RNAs are strongly enriched in sequence motifs which show high sequence similarity to short interspersed elements (SINEs). We observe similar results for protein-derived condensates, demonstrating applicability across different in vitro reconstituted membraneless organelles. Thus, our results provide a new inroad to explore the RNA content of phase-separated droplets at single condensate resolution.
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142
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Cell cycle-specific phase separation regulated by protein charge blockiness. Nat Cell Biol 2022; 24:625-632. [PMID: 35513709 PMCID: PMC9106583 DOI: 10.1038/s41556-022-00903-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/17/2022] [Indexed: 12/16/2022]
Abstract
Dynamic morphological changes of intracellular organelles are often regulated by protein phosphorylation or dephosphorylation1–6. Phosphorylation modulates stereospecific interactions among structured proteins, but how it controls molecular interactions among unstructured proteins and regulates their macroscopic behaviours remains unknown. Here we determined the cell cycle-specific behaviour of Ki-67, which localizes to the nucleoli during interphase and relocates to the chromosome periphery during mitosis. Mitotic hyperphosphorylation of disordered repeat domains of Ki-67 generates alternating charge blocks in these domains and increases their propensity for liquid–liquid phase separation (LLPS). A phosphomimetic sequence and the sequences with enhanced charge blockiness underwent strong LLPS in vitro and induced chromosome periphery formation in vivo. Conversely, mitotic hyperphosphorylation of NPM1 diminished a charge block and suppressed LLPS, resulting in nucleolar dissolution. Cell cycle-specific phase separation can be modulated via phosphorylation by enhancing or reducing the charge blockiness of disordered regions, rather than by attaching phosphate groups to specific sites. Yamazaki et al. show that cell cycle-regulated changes in hyperphosphorylation of Ki-67 and NPM1 modulate alternating charge blocks in these proteins, which defines their propensity for liquid–liquid phase separation at chromatin.
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143
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Fitzgerald K, Chen Y, Lei X, Jiang Z, Humphries F, Mustone N, Ramos I, Mutetwa T, Fernandez-Sesma A. CNBP restricts SARS-CoV2 by regulating IFN and disrupting RNA-protein condensates. RESEARCH SQUARE 2022:rs.3.rs-1576788. [PMID: 35547851 PMCID: PMC9094105 DOI: 10.21203/rs.3.rs-1576788/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades antiviral immunity through the expression of viral proteins that block detection, signaling, interferon (IFN) induction, and IFN-stimulated gene (ISG) expression1, 2. Weak induction of type I IFNs is associated with a hyperinflammatory response in patients that develop severe COVID-193, 4, 5. Here we uncover a role for cellular nucleic acid-binding protein (CNBP) in restricting SARS-CoV-2. Typically, CNBP resides in the cytosol and, in response to RNA sensing pathways, undergoes phosphorylation, nuclear translocation, and IFNβ enhancer DNA binding to turn on IFNβ gene transcription. In SARS-CoV-2-infected cells CNBP coordinates IFNβ gene transcription. In addition, CNBP binds SARS-CoV-2 viral RNA directly. CNBP competes with the nucleocapsid (N) protein and prevents viral RNA and nucleocapsid protein from undergoing liquid-liquid phase separation (LLPS) forming condensates critical for viral replication. Consequently, cells and animals lacking CNBP have higher viral loads and CNBP-deficient mice succumb rapidly to infection. Altogether, these findings identify CNBP as a key antiviral factor for SARS-CoV-2, functioning both as a regulator of antiviral IFN gene expression and a cell intrinsic restriction factor that disrupts LLPS to limit viral replication and spread.
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Affiliation(s)
| | | | - Xuqiu Lei
- University of Massachusetts Medical School
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144
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Ribeiro-Filho HV, Jara GE, Batista FAH, Schleder GR, Costa Tonoli CC, Soprano AS, Guimarães SL, Borges AC, Cassago A, Bajgelman MC, Marques RE, Trivella DBB, Franchini KG, Figueira ACM, Benedetti CE, Lopes-de-Oliveira PS. Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding. PLoS Comput Biol 2022; 18:e1010121. [PMID: 35551296 PMCID: PMC9129039 DOI: 10.1371/journal.pcbi.1010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/24/2022] [Accepted: 04/19/2022] [Indexed: 12/23/2022] Open
Abstract
The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we show that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that is consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein. The nucleocapsid (N) protein of the SARS-CoV-2 virus plays an essential role in virus particle assembly as it specifically binds to and wraps the virus genomic RNA into a well-organized structure known as the ribonucleoprotein. Understanding how the N protein wraps around the virus RNA is critical for the development of strategies to inhibit virus assembly within host cells. One of the limitations regarding the molecular structure of the ribonucleoprotein, however, is that the N protein has several unstructured and mobile regions that preclude the resolution of its full atomic structure. Moreover, the N protein can form higher-order oligomers, both in the presence and absence of RNA. Here we employed computational methods, supported by experimental data, to simulate the N protein structural dynamics in the absence and presence of RNA. Our data suggest that the N protein forms structurally dynamic dimers in the absence of RNA, with its structured N- and C-terminal domains oriented in extended conformations. In the presence of RNA, however, the N protein assumes a more compact conformation. Our model for the oligomeric structure of the N protein bound to RNA helps to understand how N protein dimers interact to each other to form the ribonucleoprotein.
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Affiliation(s)
- Helder Veras Ribeiro-Filho
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Gabriel Ernesto Jara
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Gabriel Ravanhani Schleder
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Adriana Santos Soprano
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Samuel Leite Guimarães
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Antonio Carlos Borges
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Alexandre Cassago
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marcio Chaim Bajgelman
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- * E-mail: (CEB); (PSLO)
| | - Paulo Sergio Lopes-de-Oliveira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- * E-mail: (CEB); (PSLO)
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145
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Lithium salts as a treatment for COVID-19: Pre-clinical outcomes. Biomed Pharmacother 2022; 149:112872. [PMID: 35364381 PMCID: PMC8947939 DOI: 10.1016/j.biopha.2022.112872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Identifying effective drugs for Coronavirus disease 2019 (COVID-19) is urgently needed. An efficient approach is to evaluate whether existing approved drugs have anti-SARS-CoV-2 effects. The antiviral properties of lithium salts have been studied for many years. Their anti-inflammatory and immune-potentiating effects result from the inhibition of glycogen synthase kinase-3. AIMS To obtain pre-clinical evidence on the safety and therapeutic effects of lithium salts in the treatment of COVID-19. RESULTS Six different concentrations of lithium, ranging 2-12 mmol/L, were evaluated. Lithium inhibited the replication of SARS-CoV-2 virus in a dose-dependent manner with an IC50 value of 4 mmol/L. Lithium-treated wells showed a significantly higher percentage of monolayer conservation than viral control, particularly at concentrations higher than 6 mmol/L, verified through microscopic observation, the neutral red assay, and the determination of N protein in the supernatants of treated wells. Hamsters treated with lithium showed less intense disease with fewer signs. No lithium-related mortality or overt signs of toxicity were observed during the experiment. A trend of decreasing viral load in nasopharyngeal swabs and lungs was observed in treated hamsters compared to controls. CONCLUSIONS These results provide pre-clinical evidence of the antiviral and immunotherapeutic effects of lithium against SARS-CoV-2, which supports an advance to clinical trials on COVID-19's patients.
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Zhao H, Nguyen A, Wu D, Li Y, Hassan SA, Chen J, Shroff H, Piszczek G, Schuck P. Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. PNAS NEXUS 2022; 1:pgac049. [PMID: 35783502 PMCID: PMC9235412 DOI: 10.1093/pnasnexus/pgac049] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 02/06/2023]
Abstract
Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by three to four different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced coassembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergio A Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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Zhou H, Ni WJ, Huang W, Wang Z, Cai M, Sun YC. Advances in Pathogenesis, Progression, Potential Targets and Targeted Therapeutic Strategies in SARS-CoV-2-Induced COVID-19. Front Immunol 2022; 13:834942. [PMID: 35450063 PMCID: PMC9016159 DOI: 10.3389/fimmu.2022.834942] [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: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
As the new year of 2020 approaches, an acute respiratory disease quietly caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as coronavirus disease 2019 (COVID-19) was reported in Wuhan, China. Subsequently, COVID-19 broke out on a global scale and formed a global public health emergency. To date, the destruction that has lasted for more than two years has not stopped and has caused the virus to continuously evolve new mutant strains. SARS-CoV-2 infection has been shown to cause multiple complications and lead to severe disability and death, which has dealt a heavy blow to global development, not only in the medical field but also in social security, economic development, global cooperation and communication. To date, studies on the epidemiology, pathogenic mechanism and pathological characteristics of SARS-CoV-2-induced COVID-19, as well as target confirmation, drug screening, and clinical intervention have achieved remarkable effects. With the continuous efforts of the WHO, governments of various countries, and scientific research and medical personnel, the public's awareness of COVID-19 is gradually deepening, a variety of prevention methods and detection methods have been implemented, and multiple vaccines and drugs have been developed and urgently marketed. However, these do not appear to have completely stopped the pandemic and ravages of this virus. Meanwhile, research on SARS-CoV-2-induced COVID-19 has also seen some twists and controversies, such as potential drugs and the role of vaccines. In view of the fact that research on SARS-CoV-2 and COVID-19 has been extensive and in depth, this review will systematically update the current understanding of the epidemiology, transmission mechanism, pathological features, potential targets, promising drugs and ongoing clinical trials, which will provide important references and new directions for SARS-CoV-2 and COVID-19 research.
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Affiliation(s)
- Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei-Jian Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Huang
- The Third People’s Hospital of Hefei, The Third Clinical College of Anhui Medical University, Hefei, China
| | - Zhen Wang
- Anhui Provincial Children’s Hospital, Children’s Hospital of Fudan University-Anhui Campus, Hefei, China
| | - Ming Cai
- Department of Pharmacy, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yan-Cai Sun
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Caruso IP, Dos Santos Almeida V, do Amaral MJ, de Andrade GC, de Araújo GR, de Araújo TS, de Azevedo JM, Barbosa GM, Bartkevihi L, Bezerra PR, Dos Santos Cabral KM, de Lourenço IO, Malizia-Motta CLF, de Luna Marques A, Mebus-Antunes NC, Neves-Martins TC, de Sá JM, Sanches K, Santana-Silva MC, Vasconcelos AA, da Silva Almeida M, de Amorim GC, Anobom CD, Da Poian AT, Gomes-Neto F, Pinheiro AS, Almeida FCL. Insights into the specificity for the interaction of the promiscuous SARS-CoV-2 nucleocapsid protein N-terminal domain with deoxyribonucleic acids. Int J Biol Macromol 2022; 203:466-480. [PMID: 35077748 PMCID: PMC8783401 DOI: 10.1016/j.ijbiomac.2022.01.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 nucleocapsid protein (N) is a multifunctional promiscuous nucleic acid-binding protein, which plays a major role in nucleocapsid assembly and discontinuous RNA transcription, facilitating the template switch of transcriptional regulatory sequences (TRS). Here, we dissect the structural features of the N protein N-terminal domain (N-NTD) and N-NTD plus the SR-rich motif (N-NTD-SR) upon binding to single and double-stranded TRS DNA, as well as their activities for dsTRS melting and TRS-induced liquid-liquid phase separation (LLPS). Our study gives insights on the specificity for N-NTD(-SR) interaction with TRS. We observed an approximation of the triple-thymidine (TTT) motif of the TRS to β-sheet II, giving rise to an orientation difference of ~25° between dsTRS and non-specific sequence (dsNS). It led to a local unfavorable energetic contribution that might trigger the melting activity. The thermodynamic parameters of binding of ssTRSs and dsTRS suggested that the duplex dissociation of the dsTRS in the binding cleft is entropically favorable. We showed a preference for TRS in the formation of liquid condensates when compared to NS. Moreover, our results on DNA binding may serve as a starting point for the design of inhibitors, including aptamers, against N, a possible therapeutic target essential for the virus infectivity.
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Affiliation(s)
- Icaro Putinhon Caruso
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil.
| | - Vitor Dos Santos Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Mariana Juliani do Amaral
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Guilherme Caldas de Andrade
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Gabriela Rocha de Araújo
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Talita Stelling de Araújo
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Jéssica Moreira de Azevedo
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Glauce Moreno Barbosa
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Leonardo Bartkevihi
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Peter Reis Bezerra
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Katia Maria Dos Santos Cabral
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Isabella Otênio de Lourenço
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Clara L F Malizia-Motta
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Aline de Luna Marques
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Nathane Cunha Mebus-Antunes
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Thais Cristtina Neves-Martins
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Jéssica Maróstica de Sá
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Karoline Sanches
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Marcos Caique Santana-Silva
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Ariana Azevedo Vasconcelos
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Marcius da Silva Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Protein Advanced Biochemistry (PAB), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Gisele Cardoso de Amorim
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Cristiane Dinis Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Andrea T Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Center of Nuclear Magnetic Resonance (CNRMN), CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Rio BioNMR Network, Rio de Janeiro, Brazil.
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149
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Johnson BA, Zhou Y, Lokugamage KG, Vu MN, Bopp N, Crocquet-Valdes PA, Kalveram B, Schindewolf C, Liu Y, Scharton D, Plante JA, Xie X, Aguilar P, Weaver SC, Shi PY, Walker DH, Routh AL, Plante KS, Menachery VD. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.10.14.464390. [PMID: 34671771 PMCID: PMC8528077 DOI: 10.1101/2021.10.14.464390] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203-205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo . Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral 'RG' motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2's continued adaptation to human infection. AUTHOR SUMMARY Since its emergence, SARS-CoV-2 has continued to adapt for human infection resulting in the emergence of variants with unique genetic profiles. Most studies of genetic variation have focused on spike, the target of currently available vaccines, leaving the importance of variation elsewhere understudied. Here, we characterize a highly variable motif at residues 203-205 in nucleocapsid. Recreating the prominent nucleocapsid R203K+G204R mutation in an early pandemic background, we show that this mutation is alone sufficient to enhance SARS-CoV-2 replication and pathogenesis. We also link augmentation of SARS-CoV-2 infection by the R203K+G204R mutation to its modulation of nucleocapsid phosphorylation. Finally, we characterize an analogous alanine double substitution at positions 203-204. This mutant was found to mimic R203K+G204R, suggesting augmentation of infection occurs by disrupting the ancestral sequence. Together, our findings illustrate that mutations outside of spike are key components of SARS-CoV-2's adaptation to human infection.
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Affiliation(s)
- Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Kumari G. Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Michelle N. Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Nathen Bopp
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | | | - Birte Kalveram
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Patricia Aguilar
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch; Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch; Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch; Galveston, Texas, United States of America
- Institute for Drug Discovery, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Andrew L. Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Kenneth S. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch; Galveston, Texas, United States of America
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150
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Cascarina SM, Ross ED. Phase separation by the SARS-CoV-2 nucleocapsid protein: Consensus and open questions. J Biol Chem 2022; 298:101677. [PMID: 35131265 PMCID: PMC8813722 DOI: 10.1016/j.jbc.2022.101677] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 01/09/2023] Open
Abstract
In response to the recent SARS-CoV-2 pandemic, a number of labs across the world have reallocated their time and resources to better our understanding of the virus. For some viruses, including SARS-CoV-2, viral proteins can undergo phase separation: a biophysical process often related to the partitioning of protein and RNA into membraneless organelles in vivo. In this review, we discuss emerging observations of phase separation by the SARS-CoV-2 nucleocapsid (N) protein-an essential viral protein required for viral replication-and the possible in vivo functions that have been proposed for N-protein phase separation, including viral replication, viral genomic RNA packaging, and modulation of host-cell response to infection. Additionally, since a relatively large number of studies examining SARS-CoV-2 N-protein phase separation have been published in a short span of time, we take advantage of this situation to compare results from similar experiments across studies. Our evaluation highlights potential strengths and pitfalls of drawing conclusions from a single set of experiments, as well as the value of publishing overlapping scientific observations performed simultaneously by multiple labs.
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Affiliation(s)
- Sean M Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Eric D Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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