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Hassan AM, Zehairy AA, Awatif Abid AJ, Sohrab SS, Esam IA. Cloning and phylogenetic analysis of N protein gene from Rift Valley Fever Virus (RVFV). Bioinformation 2024; 20:91-102. [PMID: 38497067 PMCID: PMC10941780 DOI: 10.6026/973206300200091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Rift Valley Fever (RVF) is a mosquito-borne viral zoonosis caused by RVFV in humans and livestock. Currently, there are no approved vaccines or antiviral therapies available. Additionally, in Saudi Arabia, there is a lack of a routine screening system to monitor RVFV in humans and animals which hinders to design and develop the preventive measures as well as the prediction of future outbreaks and the potential re-emergence of RVFV. Hence, we have performed the cloning, sequencing, and phylogenetic analysis, of nucleocapsid (N) protein gene. The sequence analysis showed high similarities with RVFV isolates reported from humans and animals. The highest similarity (99.5%) was observed with an isolate from Saudi Arabia (KU978775-Human) followed by 99.1% with four RVFV isolates (Human and Bovine) from other locations. A total of 51 nucleotides and 31 amino acid variations were observed throughout the N protein gene sequences. The phylogenetic relationship formed closed clusters with other isolates collected from Saudi Arabia. Thus, we report of the cloning, sequencing, and phylogenetic analysis of the RVFV-N protein gene from Saudi Arabia.
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Affiliation(s)
- Ahmed Mohamed Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arwa Ahmed Zehairy
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Al-Judaibi Awatif Abid
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ibraheem Azhar Esam
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Wang J, Chen D, Wei F, Deng J, Su J, Lin X, Wu S. Generation of Stable Cell Lines Expressing Akabane Virus N Protein and Insight into Its Function in Viral Replication. Pathogens 2023; 12:1058. [PMID: 37624018 PMCID: PMC10459709 DOI: 10.3390/pathogens12081058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/06/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Akabane virus (AKAV) is a world wide epidemic arbovirus belonging to the Bunyavirales order that predominantly infects livestock and causes severe congenital malformations. The nucleocapsid (N) protein of AKAV possesses multiple important functions in the virus life cycle, and it is an ideal choice for AKAV detection. In this study, we successfully constructed two stable BHK-21 cell lines (C8H2 and F7E5) that constitutively express the AKAV N protein using a lentivirus system combined with puromycin selection. RT-PCR analysis confirmed that the AKAV N gene was integrated into the BHK-21 cell genome and consistently transcribed. Indirect immunofluorescence (IFA) and Western blot (WB) assays proved that both C8H2 and F7E5 cells could react with the AKAV N protein mAb specifically, indicating potential applications in AKAV detection. Furthermore, we analyzed the growth kinetics of AKAV in the C8H2 and F7E5 cell lines and observed temporary inhibition of viral replication at 12, 24 and 36 h postinfection (hpi) compared to BHK-21 cells. Subsequent investigations suggested that the reduced viral replication was linked to the down-regulation of the viral mRNAs (Gc and RdRp). In summary, we have established materials for detecting AKAV and gained new insights into the function of the AKAV N protein.
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Affiliation(s)
- Jingjing Wang
- Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (J.W.); (D.C.); (F.W.); (J.D.); (X.L.)
| | - Dongjie Chen
- Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (J.W.); (D.C.); (F.W.); (J.D.); (X.L.)
| | - Fang Wei
- Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (J.W.); (D.C.); (F.W.); (J.D.); (X.L.)
| | - Junhua Deng
- Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (J.W.); (D.C.); (F.W.); (J.D.); (X.L.)
| | - Jia Su
- China Institute of Veterinary Drug Control, Beijing 100081, China;
| | - Xiangmei Lin
- Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (J.W.); (D.C.); (F.W.); (J.D.); (X.L.)
| | - Shaoqiang Wu
- Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (J.W.); (D.C.); (F.W.); (J.D.); (X.L.)
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Min YQ, Huang M, Feng K, Jia Y, Sun X, Ning YJ. A New Cellular Interactome of SARS-CoV-2 Nucleocapsid Protein and Its Biological Implications. Mol Cell Proteomics 2023; 22:100579. [PMID: 37211047 PMCID: PMC10198743 DOI: 10.1016/j.mcpro.2023.100579] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023] Open
Abstract
There is still much to uncover regarding the molecular details of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. As the most abundant protein, coronavirus nucleocapsid (N) protein encapsidates viral RNAs, serving as the structural component of ribonucleoprotein and virion, and participates in transcription, replication, and host regulations. Virus-host interaction might give clues to better understand how the virus affects or is affected by its host during infection and identify promising therapeutic candidates. Considering the critical roles of N, we here established a new cellular interactome of SARS-CoV-2 N by using a high-specific affinity purification (S-pulldown) assay coupled with quantitative mass spectrometry and immunoblotting validations, uncovering many N-interacting host proteins unreported previously. Bioinformatics analysis revealed that these host factors are mainly involved in translation regulations, viral transcription, RNA processes, stress responses, protein folding and modification, and inflammatory/immune signaling pathways, in line with the supposed actions of N in viral infection. Existing pharmacological cellular targets and the directing drugs were then mined, generating a drug-host protein network. Accordingly, we experimentally identified several small-molecule compounds as novel inhibitors against SARS-CoV-2 replication. Furthermore, a newly identified host factor, DDX1, was verified to interact and colocalize with N mainly by binding to the N-terminal domain of the viral protein. Importantly, loss/gain/reconstitution-of-function experiments showed that DDX1 acts as a potent anti-SARS-CoV-2 host factor, inhibiting the viral replication and protein expression. The N-targeting and anti-SARS-CoV-2 abilities of DDX1 are consistently independent of its ATPase/helicase activity. Further mechanism studies revealed that DDX1 impedes multiple activities of N, including the N-N interaction, N oligomerization, and N-viral RNA binding, thus likely inhibiting viral propagation. These data provide new clues to better depiction of the N-cell interactions and SARS-CoV-2 infection and may help inform the development of new therapeutic candidates.
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Affiliation(s)
- Yuan-Qin Min
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Mengzhuo Huang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Kuan Feng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China; State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yajie Jia
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xiulian Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
| | - Yun-Jia Ning
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China; State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Hubei Jiangxia Laboratory, Wuhan, China.
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Alsuwairi FA, Alsaleh AN, Alsanea MS, Al-Qahtani AA, Obeid D, Almaghrabi RS, Alahideb BM, AlAbdulkareem MA, Mutabagani MS, Althawadi SI, Altamimi SA, Alshukairi AN, Alhamlan FS. Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves. Microorganisms 2023; 11:1288. [PMID: 37317262 PMCID: PMC10224071 DOI: 10.3390/microorganisms11051288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 𝜒2 tests and t tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations' associations with clinical outcomes.
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Affiliation(s)
- Feda A. Alsuwairi
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Asma N. Alsaleh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Madain S. Alsanea
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Dalia Obeid
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Public Health Laboratories, Public Health Authority, Riyadh 13351, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Basma M. Alahideb
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maha A. AlAbdulkareem
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maysoon S. Mutabagani
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sahar I. Althawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sara A. Altamimi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Abeer N. Alshukairi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia
| | - Fatimah S. Alhamlan
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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Krashias G, Deeba E, Constantinou A, Hadjiagapiou M, Koptides D, Richter J, Tryfonos C, Bashiardes S, Lambrianides A, Loizidou MA, Hadjisavvas A, Panayiotidis MI, Christodoulou C. Characterization of IgG Antibody Response against SARS-CoV-2 (COVID-19) in the Cypriot Population. Microorganisms 2021; 10:85. [PMID: 35056533 PMCID: PMC8777616 DOI: 10.3390/microorganisms10010085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/16/2021] [Accepted: 12/30/2021] [Indexed: 12/13/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has hit its second year and continues to damage lives and livelihoods across the globe. There continues to be a global effort to present serological data on SARS-CoV-2 antibodies in different individuals. As such, this study aimed to characterize the seroprevalence of SARS-CoV-2 antibodies in the Cypriot population for the first time since the pandemic started. Our results show that a majority of people infected with SARS-CoV-2 developed IgG antibodies against the virus, whether anti-NP, anti-S1RBD, or both, at least 20 days after their infection. Additionally, the percentage of people with at least one antibody against SARS-CoV-2 in the group of volunteers deemed SARS-CoV-2 negative via RT-PCR or who remain untested/undetermined (14.43%) is comparable to other reported percentages worldwide, ranging anywhere from 0.2% to 24%. We postulate that these percentages reflect the underreporting of true infections in the population, and also show the steady increase of herd immunity. Additionally, we showed a significantly marked decrease in anti-NP IgG antibodies in contrast to relatively stable levels of anti-S1RBD IgG antibodies in previously infected individuals across time.
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Affiliation(s)
- George Krashias
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus; (M.H.); (A.L.); (M.A.L.); (A.H.); (M.I.P.); (C.C.)
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (E.D.); (A.C.); (D.K.); (J.R.); (C.T.); (S.B.)
| | - Elie Deeba
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (E.D.); (A.C.); (D.K.); (J.R.); (C.T.); (S.B.)
| | - Astero Constantinou
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (E.D.); (A.C.); (D.K.); (J.R.); (C.T.); (S.B.)
| | - Maria Hadjiagapiou
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus; (M.H.); (A.L.); (M.A.L.); (A.H.); (M.I.P.); (C.C.)
- Department of Neuroimmunology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Dana Koptides
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (E.D.); (A.C.); (D.K.); (J.R.); (C.T.); (S.B.)
| | - Jan Richter
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (E.D.); (A.C.); (D.K.); (J.R.); (C.T.); (S.B.)
| | - Christina Tryfonos
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (E.D.); (A.C.); (D.K.); (J.R.); (C.T.); (S.B.)
| | - Stavros Bashiardes
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (E.D.); (A.C.); (D.K.); (J.R.); (C.T.); (S.B.)
| | - Anastasia Lambrianides
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus; (M.H.); (A.L.); (M.A.L.); (A.H.); (M.I.P.); (C.C.)
- Department of Neuroimmunology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Maria A. Loizidou
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus; (M.H.); (A.L.); (M.A.L.); (A.H.); (M.I.P.); (C.C.)
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Andreas Hadjisavvas
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus; (M.H.); (A.L.); (M.A.L.); (A.H.); (M.I.P.); (C.C.)
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Mihalis I. Panayiotidis
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus; (M.H.); (A.L.); (M.A.L.); (A.H.); (M.I.P.); (C.C.)
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Christina Christodoulou
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus; (M.H.); (A.L.); (M.A.L.); (A.H.); (M.I.P.); (C.C.)
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (E.D.); (A.C.); (D.K.); (J.R.); (C.T.); (S.B.)
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Xia J, Tang W, Wang J, Lai D, Xu Q, Huang R, Hu Y, Gong X, Fan J, Shu Q, Xu J. SARS-CoV-2 N Protein Induces Acute Lung Injury in Mice via NF-ĸB Activation. Front Immunol 2021; 12:791753. [PMID: 34950152 PMCID: PMC8688532 DOI: 10.3389/fimmu.2021.791753] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/19/2021] [Indexed: 01/11/2023] Open
Abstract
Background Infection of SARS-CoV-2 may cause acute respiratory syndrome. It has been reported that SARS-CoV-2 nucleocapsid protein (N-protein) presents early in body fluids during infection. The direct involvement of N-protein in lung injury is poorly understood. Methods Recombinant N-protein was pretreated with polymyxin B, a lipopolysaccharide (LPS)-neutralizing agent. C57BL/6, C3H/HeJ (resistant to LPS), and C3H/HeN (control for C3H/HeJ) mice were exposed to N-protein via intratracheal administration to examine acute lung injury. In vitro, bone marrow-derived macrophages (BMDMs) were cultured with N-protein to study phosphorylation of nuclear factor kappa B (NF-ĸB) p65, macrophage polarization, and expression of proinflammatory cytokines. Results N-protein produced acute lung injury in C57BL/6 mice, with elevated protein permeability, total cell count, neutrophil infiltration, and proinflammatory cytokines in the bronchioalveolar lavage. N-protein also induced lung injury in both C3H/HeJ and C3H/HeN mice, indicating that the effect could not be attributed to the LPS contamination. N-protein triggered phosphorylation of NF-ĸB p65 in vitro, which was abolished by both N-protein denaturation and treatment with an antibody for N-protein, demonstrating that the effect is N-protein specific. In addition, N-protein promoted M1 macrophage polarization and the expression of proinflammatory cytokines, which was also blocked by N-protein denaturation and antibody for N-protein. Furthermore, N-protein induced NF-ĸB p65 phosphorylation in the lung, while pyrrolidine dithiocarbamate, an NF-ĸB inhibitor, alleviated the effect of N-protein on acute lung injury. Conclusions SARS-CoV-2 N-protein itself is toxic and induces acute lung injury in mice. Both N-protein and NF-ĸB pathway may be therapeutic targets for treating multi-organ injuries in Coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Jie Xia
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Wenqi Tang
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jiangmei Wang
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Dengming Lai
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Qi Xu
- Hangzhou Medical College of Bioengineering, Hangzhou, China
| | - Ruoqiong Huang
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Yaoqin Hu
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiaojue Gong
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jiajie Fan
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Qiang Shu
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jianguo Xu
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
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Dang M, Song J. CTD of SARS-CoV-2 N protein is a cryptic domain for binding ATP and nucleic acid that interplay in modulating phase separation. Protein Sci 2021; 31:345-356. [PMID: 34734665 PMCID: PMC8661809 DOI: 10.1002/pro.4221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 nucleocapsid (N) protein plays essential roles in many steps of the viral life cycle, thus representing a key drug target. N protein contains the folded N-/C-terminal domains (NTD/CTD) and three intrinsically disordered regions, while its functions including liquid-liquid phase separation (LLPS) depend on the capacity in binding various viral/host-cell RNA/DNA of diverse sequences. Previously NTD was established to bind various RNA/DNA while CTD to dimerize/oligomerize for forming high-order structures. By NMR, here for the first time we decrypt that CTD is not only capable of binding S2m, a specific probe derived from SARS-CoV-2 gRNA but with the affinity even higher than that of NTD. Very unexpectedly, ATP, the universal energy currency for all living cells with high cellular concentrations (2-16 mM), specifically binds CTD with Kd of 1.49 ± 0.28 mM. Strikingly, the ATP-binding residues of NTD/CTD are identical in the SARS-CoV-2 variants while ATP and S2m interplay in binding NTD/CTD, as well as in modulating LLPS critical for the viral life cycle. Results together not only define CTD as a novel binding domain for ATP and nucleic acid, but enforce our previous proposal that ATP has been evolutionarily exploited by SARS-CoV-2 to complete its life cycle in the host cell. Most importantly, the unique ATP-binding pockets on NTD/CTD may offer promising targets for design of specific anti-SARS-CoV-2 molecules to fight the pandemic. Fundamentally, ATP emerges to act at mM as a cellular factor to control the interface between the host cell and virus lacking the ability to generate ATP.
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Affiliation(s)
- Mei Dang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
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8
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Cai T, Yu Z, Wang Z, Liang C, Richard S. Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. J Biol Chem 2021; 297:100821. [PMID: 34029587 PMCID: PMC8141346 DOI: 10.1016/j.jbc.2021.100821] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
Viral proteins are known to be methylated by host protein arginine methyltransferases (PRMTs) necessary for the viral life cycle, but it remains unknown whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins are methylated. Herein, we show that PRMT1 methylates SARS-CoV-2 nucleocapsid (N) protein at residues R95 and R177 within RGG/RG motifs, preferred PRMT target sequences. We confirmed arginine methylation of N protein by immunoblotting viral proteins extracted from SARS-CoV-2 virions isolated from cell culture. Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibited interaction of N protein with the 5'-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging. We also defined the N protein interactome in HEK293 cells, which identified PRMT1 and many of its RGG/RG substrates, including the known interacting protein G3BP1 as well as other components of stress granules (SGs), which are part of the host antiviral response. Methylation of R95 regulated the ability of N protein to suppress the formation of SGs, as R95K substitution or MS023 treatment blocked N-mediated suppression of SGs. Also, the coexpression of methylarginine reader Tudor domain-containing protein 3 quenched N protein-mediated suppression of SGs in a dose-dependent manner. Finally, pretreatment of VeroE6 cells with MS023 significantly reduced SARS-CoV-2 replication. Because type I PRMT inhibitors are already undergoing clinical trials for cancer treatment, inhibiting arginine methylation to target the later stages of the viral life cycle such as viral genome packaging and assembly of virions may represent an additional therapeutic application of these drugs.
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Affiliation(s)
- Ting Cai
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhen Wang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada.
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Malík I, Kovac G, Padrtova T, Hudecova L. Ingavirin might be a promising agent to combat Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2). Ceska Slov Farm 2020; 69:107-111. [PMID: 32972153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Severe Acute Respiratory Coronavirus 2 (SARS--CoV-2) and Coronavirus Disease-19 (COVID-19) pandemic, caused by the virus, have changed the world in just half a year. Lack of effective treatment, coupled with etiology of COVID-19, has resulted in more than 500,000 confirmed deaths at the time of writing, and the global economy is at an unseen unprecedented low level with unknown near- and long-term consequences. Ingavirin has been considered a non-toxic broad-spectrum antiviral with a complex mechanism of action. The molecule was originally designed for the prophylaxis and treatment of flu caused by both Influenza A and B viruses and for the treatment of viral causes of acute respiratory illness. The article hypothesized that the efficiency of given 1H-imidazol-4-yl heterocyclic scaffold-containing compound against SARS-CoV-2 might be connected with its ability to interfere with specific heterogeneous nuclear ribonucleoproteins (A1, for example). These specific cellular RNA-binding proteins showed affinity to Severe Acute Respiratory Coronavirus (SARS-CoV) nucleocapsid (N) protein, which shared high homology with the N protein of SARS-CoV-2 and the fact was expressed by a sequence identity of 90.52%. Impairing of the interactions between nuclear ribonucleoproteins and nucleocapsid (N) protein of SARS-CoV-2 might result in the inhibition of a viral replication cycle. Additional immunomodulating properties of ingavirin could be favorable for induction of adaptive immunity of host cells.
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Lee SH, Baek YH, Kim YH, Choi YK, Song MS, Ahn JY. One-Pot Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) for Detecting MERS-CoV. Front Microbiol 2017; 7:2166. [PMID: 28119682 PMCID: PMC5220095 DOI: 10.3389/fmicb.2016.02166] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/23/2016] [Indexed: 01/09/2023] Open
Abstract
Due to the limitation of rapid development of specific antiviral drug or vaccine for novel emerging viruses, an accurate and rapid diagnosis is a key to manage the virus spread. We developed an efficient and rapid method with high specificity for the Middle East Respiratory Syndrome coronavirus (MERS-CoV), based on one-pot reverse transcription loop-mediated isothermal amplification (one-pot RT-LAMP). A set of six LAMP primers [F3, B3, FIP, BIP, LF (Loop-F), and LB (Loop-B)] were designed using the sequence of nucleocapsid (N) gene with optimized RT-LAMP enzyme conditions: 100 U M-MLV RTase and 4 U Bst polymerase, implying that the reaction was able to detect four infectious viral genome copies of MERS-CoV within a 60 min reaction time period. Significantly, EvaGreen dye has better signal read-out properties in one-pot RT-LAMP reaction and is more compatible with DNA polymerase than SYBR green I. Isothermally amplified specific N genes were further evaluated using field-deployable microchamber devices, leading to the specific identification of as few as 0.4 infectious viral genome copies, with no cross-reaction to the other acute respiratory disease viruses, including influenza type A (H1N1 and H3N2), type B, human coronavirus 229E, and human metapneumovirus. This sensitive, specific and feasible method provides a large-scale technical support in emergencies, and is also applied as a sample-to-detection module in Point of Care Testing devices.
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Affiliation(s)
- Se Hee Lee
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
| | - Yun Hee Baek
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
| | - Young-Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Min-Suk Song
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
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Roh C, Jo SK. Quantitative and sensitive detection of SARS coronavirus nucleocapsid protein using quantum dots-conjugated RNA aptamer on chip. J Chem Technol Biotechnol 2011; 86:1475-1479. [PMID: 32336860 PMCID: PMC7167159 DOI: 10.1002/jctb.2721] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 07/14/2011] [Accepted: 07/24/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND: Globally, severe acute respiratory syndrome coronavirus (SARS-CoV) is a newly emerging virus that causes SARS with high mortality rate in infected people. The nucleocapsid (N) protein of the severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) is an important antigen for the early diagnosis of SARS and the detection of diseases. Here, a new quantum dots (QDs)-conjugated RNA aptamer with high sensitivity and rapidity is proposed for the detection of SARS-CoV N protein using an on chip system. RESULTS: A QDs-conjugated RNA aptamer can specifically hybridize on the immobilized SARS-CoV N protein on the surface of a glass chip. Detection is based on the optical signal variation of a QDs-supported RNA aptamer interacting on an immobilized protein chip. Using an optical QDs-based RNA aptamer chip, SARS N protein was detected at concentrations as low as 0.1 pg mL-1. CONCLUSIONS: It was demonstrated that the QDs-conjugated RNA aptamer could interact on a designed chip specifically and sensitively. This device could form a QDs-conjugated biosensor prototype chip for SARS-CoV N protein diagnosis. The proposed visual SARS-CoV N protein detection technique may avoid the limitations of other reported methods because of its high sensitivity, good specificity, ease of use, and the ability to perform one-spot monitoring. Copyright © 2011 Society of Chemical Industry.
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Affiliation(s)
- Changhyun Roh
- Radiation Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 1266, Sinjeong‐dong, Jeongeup, Jeonbuk 580‐185, Republic of Korea
| | - Sung Kee Jo
- Radiation Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 1266, Sinjeong‐dong, Jeongeup, Jeonbuk 580‐185, Republic of Korea
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