1
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Taefehshokr N, Lac A, Vrieze AM, Dickson BH, Guo PN, Jung C, Blythe EN, Fink C, Aktar A, Dikeakos JD, Dekaban GA, Heit B. SARS-CoV-2 NSP5 antagonizes MHC II expression by subverting histone deacetylase 2. J Cell Sci 2024; 137:jcs262172. [PMID: 38682259 PMCID: PMC11166459 DOI: 10.1242/jcs.262172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
SARS-CoV-2 interferes with antigen presentation by downregulating major histocompatibility complex (MHC) II on antigen-presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen-presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. CIITA downregulation is independent of the proteolytic activity of NSP5, and rather, NSP5 delivers HDAC2 to the transcription factor IRF3 at an IRF-binding site within the CIITA promoter. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 limits MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.
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Affiliation(s)
- Nima Taefehshokr
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Alex Lac
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Angela M. Vrieze
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Brandon H. Dickson
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Peter N. Guo
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Catherine Jung
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Eoin N. Blythe
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Corby Fink
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Amena Aktar
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Jimmy D. Dikeakos
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Gregory A. Dekaban
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Bryan Heit
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
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2
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Shan X, Li R, Ma X, Qiu G, Xiang Y, Zhang X, Wu D, Wang L, Zhang J, Wang T, Li W, Xiang Y, Song H, Niu D. Epidemiology, pathogenesis, immune evasion mechanism and vaccine development of porcine Deltacoronavirus. Funct Integr Genomics 2024; 24:79. [PMID: 38653845 DOI: 10.1007/s10142-024-01346-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Coronaviruses have been identified as pathogens of gastrointestinal and respiratory diseases in humans and various animal species. In recent years, the global spread of new coronaviruses has had profound influences for global public health and economies worldwide. As highly pathogenic zoonotic viruses, coronaviruses have become the focus of current research. Porcine Deltacoronavirus (PDCoV), an enterovirus belonging to the family of coronaviruses, has emerged on a global scale in the past decade and significantly influenced the swine industry. Moreover, PDCoV infects not only pigs but also other species, including humans, chickens and cattles, exhibiting a broad host tropism. This emphasizes the need for in-depth studies on coronaviruses to mitigate their potential threats. In this review, we provided a comprehensive summary of the current studies on PDCoV. We first reviewed the epidemiological investigations on the global prevalence and distribution of PDCoV. Then, we delved into the studies on the pathogenesis of PDCoV to understand the mechanisms how the virus impacts its hosts. Furthermore, we also presented some exploration studies on the immune evasion mechanisms of the virus to enhance the understanding of host-virus interactions. Despite current limitations in vaccine development for PDCoV, we highlighted the inhibitory effects observed with certain substances, which offers a potential direction for future research endeavors. In conclusion, this review summarized the scientific findings in epidemiology, pathogenesis, immune evasion mechanisms and vaccine development of PDCoV. The ongoing exploration of potential vaccine candidates and the insights gained from inhibitory substances have provided a solid foundation for future vaccine development to prevent and control diseases associated with PDCoV.
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Affiliation(s)
- Xueting Shan
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco- Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, 666 Wusu street, Lin'an District, Hangzhou, 311300, Zhejiang, China
| | - Rui Li
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco- Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, 666 Wusu street, Lin'an District, Hangzhou, 311300, Zhejiang, China
| | - Xiang Ma
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco- Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, 666 Wusu street, Lin'an District, Hangzhou, 311300, Zhejiang, China
- Jinhua Jinfan Feed Co., Ltd, Jinhua, 321000, Zhejiang, China
| | - Guoqiang Qiu
- Deqing County Ecological Forestry Comprehensive Service Center, Deqing, 313200, Zhejiang, China
| | - Yi Xiang
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco- Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, 666 Wusu street, Lin'an District, Hangzhou, 311300, Zhejiang, China
- The Central Hospital of Jinhua City, Jinhua, 321000, Zhejiang, China
| | - Xiaojun Zhang
- Jinhua Academy of Agricultural Sciences, Jinhua, 321000, Zhejiang, China
| | - De Wu
- Postdoctoral Research Station, Jinhua Development Zone, Jinhua, 321000, Zhejiang, China
| | - Lu Wang
- The Agriculture and Rural Affairs Bureau of Jinhua City, Jinhua, 321000, Zhejiang, China
| | - Jianhong Zhang
- The Agriculture and Rural Affairs Bureau of Jinhua City, Jinhua, 321000, Zhejiang, China
| | - Tao Wang
- Nanjing Kgene Genetic Engineering Co., Ltd, Nanjing, 211300, Jiangsu, China
| | - Weifen Li
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yun Xiang
- Jinhua Academy of Agricultural Sciences, Jinhua, 321000, Zhejiang, China.
| | - Houhui Song
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco- Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, 666 Wusu street, Lin'an District, Hangzhou, 311300, Zhejiang, China.
| | - Dong Niu
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco- Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, 666 Wusu street, Lin'an District, Hangzhou, 311300, Zhejiang, China.
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3
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Huang H, Lei X, Zhao C, Qin Y, Li Y, Zhang X, Li C, Lan T, Zhao B, Sun W, Lu H, Jin N. Porcine deltacoronavirus nsp5 antagonizes type I interferon signaling by cleaving IFIT3. J Virol 2024; 98:e0168223. [PMID: 38289117 PMCID: PMC10878044 DOI: 10.1128/jvi.01682-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Porcine deltacoronavirus (PDCoV) has caused enormous economic losses to the global pig industry. However, the immune escape mechanism of PDCoV remains to be fully clarified. Transcriptomic analysis revealed a high abundance of interferon (IFN)-induced protein with tetratricopeptide repeats 3 (IFIT3) transcripts after PDCoV infection, which initially implied a correlation between IFIT3 and PDCoV. Further studies showed that PDCoV nsp5 could antagonize the host type I interferon signaling pathway by cleaving IFIT3. We demonstrated that PDCoV nsp5 cleaved porcine IFIT3 (pIFIT3) at Gln-406. Similar cleavage of endogenous IFIT3 has also been observed in PDCoV-infected cells. The pIFIT3-Q406A mutant was resistant to nsp5-mediated cleavage and exhibited a greater ability to inhibit PDCoV infection than wild-type pIFIT3. Furthermore, we found that cleavage of IFIT3 is a common characteristic of nsp5 proteins of human coronaviruses, albeit not alphacoronavirus. This finding suggests that the cleavage of IFIT3 is an important mechanism by which PDCoV nsp5 antagonizes IFN signaling. Our study provides new insights into the mechanisms by which PDCoV antagonizes the host innate immune response.IMPORTANCEPorcine deltacoronavirus (PDCoV) is a potential emerging zoonotic pathogen, and studies on the prevalence and pathogenesis of PDCoV are ongoing. The main protease (nsp5) of PDCoV provides an excellent target for antivirals due to its essential and conserved function in the viral replication cycle. Previous studies have revealed that nsp5 of PDCoV antagonizes type I interferon (IFN) production by targeting the interferon-stimulated genes. Here, we provide the first demonstration that nsp5 of PDCoV antagonizes IFN signaling by cleaving IFIT3, which affects the IFN response after PDCoV infection. Our findings reveal that PDCoV nsp5 is an important interferon antagonist and enhance the understanding of immune evasion by deltacoronaviruses.
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Affiliation(s)
- Haixin Huang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, Shaanxi, China
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Xiaoxiao Lei
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Chenchen Zhao
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Yan Qin
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Yuying Li
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Xinyu Zhang
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Chengkai Li
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Tian Lan
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Baopeng Zhao
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Wenchao Sun
- Institute of Virology, Wenzhou University, Wenzhou, Zhejiang, China
| | - Huijun Lu
- Changchun Institute of Veterinary Medicine, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Ningyi Jin
- College of Veterinary Medicine, Northwest A&F University, Xianyang, Shaanxi, China
- Changchun Institute of Veterinary Medicine, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
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4
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Li Z, Xiao W, Yang Z, Guo J, Zhou J, Xiao S, Fang P, Fang L. Cleavage of HDAC6 to dampen its antiviral activity by nsp5 is a common strategy of swine enteric coronaviruses. J Virol 2024; 98:e0181423. [PMID: 38289103 PMCID: PMC10878235 DOI: 10.1128/jvi.01814-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024] Open
Abstract
HDAC6, a structurally and functionally unique member of the histone deacetylase (HDAC) family, is an important host factor that restricts viral infection. The broad-spectrum antiviral activity of HDAC6 makes it a potent antiviral agent. Previously, we found that HDAC6 functions to antagonize porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus with zoonotic potential. However, the final outcome is typically a productive infection that materializes as cells succumb to viral infection, indicating that the virus has evolved sophisticated mechanisms to combat the antiviral effect of HDAC6. Here, we demonstrate that PDCoV nonstructural protein 5 (nsp5) can cleave HDAC6 at glutamine 519 (Q519), and cleavage of HDAC6 was also detected in the context of PDCoV infection. More importantly, the anti-PDCoV activity of HDAC6 was damaged by nsp5 cleavage. Mechanistically, the cleaved HDAC6 fragments (amino acids 1-519 and 520-1159) lost the ability to degrade PDCoV nsp8 due to their impaired deacetylase activity. Furthermore, nsp5-mediated cleavage impaired the ability of HDAC6 to activate RIG-I-mediated interferon responses. We also tested three other swine enteric coronaviruses (transmissible gastroenteritis virus, porcine epidemic diarrhea virus, and swine acute diarrhea syndrome-coronavirus) and found that all these coronaviruses have adopted similar mechanisms to cleave HDAC6 in both an overexpression system and virus-infected cells, suggesting that cleavage of HDAC6 is a common strategy utilized by swine enteric coronaviruses to antagonize the host's antiviral capacity. Together, these data illustrate how swine enteric coronaviruses antagonize the antiviral function of HDAC6 to maintain their infection, providing new insights to the interaction between virus and host.IMPORTANCEViral infections and host defenses are in constant opposition. Once viruses combat or evade host restriction, productive infection is achieved. HDAC6 is a broad-spectrum antiviral protein that has been demonstrated to inhibit many viruses, including porcine deltacoronavirus (PDCoV). However, whether HDAC6 is reciprocally targeted and disabled by viruses remains unclear. In this study, we used PDCoV as a model and found that HDAC6 is targeted and cleaved by nsp5, a viral 3C-like protease. The cleaved HDAC6 loses its deacetylase activity as well as its ability to degrade viral proteins and activate interferon responses. Furthermore, this cleavage mechanism is shared among other swine enteric coronaviruses. These findings shed light on the intricate interplay between viruses and HDAC6, highlighting the strategies employed by viruses to evade host antiviral defenses.
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Affiliation(s)
- Zhuang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Wenwen Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhixiang Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jiahui Guo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Junwei Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Puxian Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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5
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Melano I, Lo YC, Su WC. Characterization of host substrates of SARS-CoV-2 main protease. Front Microbiol 2023; 14:1251705. [PMID: 37670988 PMCID: PMC10475589 DOI: 10.3389/fmicb.2023.1251705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
The main protease (Mpro) plays a crucial role in coronavirus, as it cleaves viral polyproteins and host cellular proteins to ensure successful replication. In this review, we discuss the preference in the recognition sequence of Mpro based on sequence-based studies and structural information and highlight the recent advances in computational and experimental approaches that have aided in discovering novel Mpro substrates. In addition, we provide an overview of the current understanding of Mpro host substrates and their implications for viral replication and pathogenesis. As Mpro has emerged as a promising target for the development of antiviral drugs, further insight into its substrate specificity may contribute to the design of specific inhibitors.
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Affiliation(s)
- Ivonne Melano
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Yan-Chung Lo
- Sinphar Pharmaceutical Co., Ltd., Sinphar Group, Yilan, Taiwan
| | - Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- International Master’s Program of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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6
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Huang HX, Zhao CC, Lei XX, Zhang XY, Li YY, Lan T, Zhao BP, Lu JY, Sun WC, Lu HJ, Jin NY. Swine acute diarrhoea syndrome coronavirus (SADS-CoV) Nsp5 antagonizes type I interferon signaling by cleaving DCP1A. Front Immunol 2023; 14:1196031. [PMID: 37283741 PMCID: PMC10239798 DOI: 10.3389/fimmu.2023.1196031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
Swine acute diarrhoea syndrome coronavirus (SADS-CoV), which is a recently discovered enteric coronavirus, is the major aetiological agent that causes severe clinical diarrhoea and intestinal pathological damage in pigs, and it has caused significant economic losses to the swine industry. Nonstructural protein 5, also called 3C-like protease, cleaves viral polypeptides and host immune-related molecules to facilitate viral replication and immune evasion. Here, we demonstrated that SADS-CoV nsp5 significantly inhibits the Sendai virus (SEV)-induced production of IFN-β and inflammatory cytokines. SADS-CoV nsp5 targets and cleaves mRNA-decapping enzyme 1a (DCP1A) via its protease activity to inhibit the IRF3 and NF-κB signaling pathways in order to decrease IFN-β and inflammatory cytokine production. We found that the histidine 41 and cystine 144 residues of SADS-CoV nsp5 are critical for its cleavage activity. Additionally, a form of DCP1A with a mutation in the glutamine 343 residue is resistant to nsp5-mediated cleavage and has a stronger ability to inhibit SADS-CoV infection than wild-type DCP1A. In conclusion, our findings reveal that SADS-CoV nsp5 is an important interferon antagonist and enhance the understanding of immune evasion by alpha coronaviruses.
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Affiliation(s)
- Hai-xin Huang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Chen-chen Zhao
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Xiao-xiao Lei
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Xin-yu Zhang
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Yu-ying Li
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Tian Lan
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Bao-peng Zhao
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Jing-yi Lu
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Wen-chao Sun
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Hui-jun Lu
- Changchun Institute of Veterinary Medicine, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ning-yi Jin
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Changchun Institute of Veterinary Medicine, Chinese Academy of Agricultural Sciences, Changchun, China
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7
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Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS CENTRAL SCIENCE 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
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Affiliation(s)
- Sizhu
Amelia Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Bashir Khan
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bing Bai
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - James A. Nieman
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
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8
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Avian Metapneumovirus Subgroup C Phosphoprotein Suppresses Type I Interferon Production by Blocking Interferon Regulatory Factor 3 Nuclear Translocation. Microbiol Spectr 2023; 11:e0341322. [PMID: 36537793 PMCID: PMC9927154 DOI: 10.1128/spectrum.03413-22] [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] [Indexed: 02/16/2023] Open
Abstract
Avian metapneumovirus subgroup C (aMPV/C) is an important pathogen that causes upper respiratory symptoms and egg production decline in turkeys and chickens. aMPV/C infection leads to inhibition of the host antiviral immune response. However, our understanding of the molecular mechanisms underlying host immune response antagonized by aMPV/C infection is limited. In this study, we demonstrated that the aMPV/C phosphoprotein (P) inhibits the IFN antiviral signaling pathway triggered by melanoma differentiation gene 5 (MDA5) and reduces interferon β (IFN-β) production and IFN-stimulated genes (ISGs) by targeting IFN regulatory factor 7 (IRF7) but not nuclear factor κB (NF-κB) in DF-1 cells. Moreover, we found that aMPV/C P protein only blocks the nuclear translocation of IRF3 by interacting with IRF3 in HEK-293T cells, instead of affecting IRF3 phosphorylation and inducing IRF3 degradation, which suppresses IRF3 signaling activation and results in a decrease in IFN-β production. Collectively, these results reveal a novel mechanism by which aMPV/C infection disrupts IFN-β production in the host. IMPORTANCE The innate immune response is the first defense line of host cells and organisms against viral infections. When RNA viruses infect cells, viral RNA induces activation of retinoic acid-induced gene I and melanoma differentiation gene 5, which initiates downstream molecules and finally produces type I interferon (IFN-I) to regulate antiviral immune responses. The mechanism for avian metapneumovirus (aMPV) modulating IFN-I production to benefit its replication remains unknown. Here, we demonstrate that phosphoprotein of aMPV subgroup C (aMPV/C) selectively inhibits the nuclear translocation of interferon regulatory 3 (IRF3), instead of affecting the expression and phosphorylation of IRF3, which finally downregulates IFN-I production. This study showed a novel mechanism for aMPV/C infection antagonizing the host IFN response.
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The main protease of SARS-CoV-2 cleaves histone deacetylases and DCP1A, attenuating the immune defense of the interferon-stimulated genes. J Biol Chem 2023; 299:102990. [PMID: 36758802 PMCID: PMC9907797 DOI: 10.1016/j.jbc.2023.102990] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019, constitutes an emerging human pathogen of zoonotic origin. A critical role in protecting the host against invading pathogens is carried out by interferon-stimulated genes (ISGs), the primary effectors of the type I interferon (IFN) response. All coronaviruses studied thus far have to first overcome the inhibitory effects of the IFN/ISG system before establishing efficient viral replication. However, whether SARS-CoV-2 evades IFN antiviral immunity by manipulating ISG activation remains to be elucidated. Here, we show that the SARS-CoV-2 main protease (Mpro) significantly suppresses the expression and transcription of downstream ISGs driven by IFN-stimulated response elements in a dose-dependent manner, and similar negative regulations were observed in two mammalian epithelial cell lines (simian Vero E6 and human A549). Our analysis shows that to inhibit the ISG production, Mpro cleaves histone deacetylases (HDACs) rather than directly targeting IFN signal transducers. Interestingly, Mpro also abolishes the activity of ISG effector mRNA-decapping enzyme 1a (DCP1A) by cleaving it at residue Q343. In addition, Mpro from different genera of coronaviruses has the protease activity to cleave both HDAC2 and DCP1A, even though the alphacoronaviruse Mpro exhibits weaker catalytic activity in cleaving HDAC2. In conclusion, our findings clearly demonstrate that SARS-CoV-2 Mpro constitutes a critical anti-immune effector that modulates the IFN/ISG system at multiple levels, thus providing a novel molecular explanation for viral immune evasion and allowing for new therapeutic approaches against coronavirus disease 2019 infection.
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Bahoussi AN, Wang PH, Shah PT, Bu H, Wu C, Xing L. Evolutionary plasticity of zoonotic porcine Deltacoronavirus (PDCoV): genetic characteristics and geographic distribution. BMC Vet Res 2022; 18:444. [PMID: 36550483 PMCID: PMC9772601 DOI: 10.1186/s12917-022-03554-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence and rapid spread of the acute respiratory syndrome coronavirus-2 have confirmed that animal coronaviruses represent a potential zoonotic source. Porcine deltacoronavirus is a worldwide evolving enteropathogen of swine, detected first in Hong Kong, China, before its global identification. Following the recent detection of PDCoV in humans, we attempted in this report to re-examine the status of PDCoV phylogenetic classification and evolutionary characteristics. A dataset of 166 complete PDCoV genomes was analyzed using the Maximum Likelihood method in IQ-TREE with the best-fitting model GTR + F + I + G4, revealing two major genogroups (GI and GII), with further seven and two sub-genogroups, (GI a-g) and (GII a-b), respectively. PDCoV strains collected in China exhibited the broadest genetic diversity, distributed in all subgenotypes. Thirty-one potential natural recombination events were identified, 19 of which occurred between China strains, and seven involved at least one China strain as a parental sequence. Importantly, we identified a human Haiti PDCoV strain as recombinant, alarming a possible future spillover that could become a critical threat to human health. The similarity and recombination analysis showed that PDCoV spike ORF is highly variable compared to ORFs encoding other structural proteins. Prediction of linear B cell epitopes of the spike glycoprotein and the 3D structural mapping of amino acid variations of two representative strains of GI and GII showed that the receptor-binding domain (RBD) of spike glycoprotein underwent a significant antigenic drift, suggesting its contribution in the genetic diversity and the wider spread of PDCoV.
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Affiliation(s)
- Amina Nawal Bahoussi
- grid.163032.50000 0004 1760 2008Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006 Shanxi province China
| | - Pei-Hua Wang
- grid.163032.50000 0004 1760 2008Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006 Shanxi province China
| | - Pir Tariq Shah
- grid.163032.50000 0004 1760 2008Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006 Shanxi province China
| | - Hongli Bu
- grid.477987.2Department of Laboratory Medicine, The Fourth People’s Hospital of Taiyuan, 231 Xikuang St, Taiyuan, 030053 Shanxi province China
| | - Changxin Wu
- grid.163032.50000 0004 1760 2008Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006 Shanxi province China ,grid.163032.50000 0004 1760 2008Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, 92 Wucheng Road, Taiyuan, 030006 China ,Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, 92 Wucheng Road, Taiyuan, 030006 China ,grid.163032.50000 0004 1760 2008The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006 China
| | - Li Xing
- grid.163032.50000 0004 1760 2008Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006 Shanxi province China ,grid.163032.50000 0004 1760 2008Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, 92 Wucheng Road, Taiyuan, 030006 China ,Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, 92 Wucheng Road, Taiyuan, 030006 China ,grid.163032.50000 0004 1760 2008The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006 China
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11
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Enterovirus 3C Protease Cleaves TRIM7 To Dampen Its Antiviral Activity. J Virol 2022; 96:e0133222. [PMID: 36106874 PMCID: PMC9555159 DOI: 10.1128/jvi.01332-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mammalian TRIM7 is an antiviral protein that inhibits multiple human enteroviruses by degrading the viral 2BC protein. Whether TRIM7 is reciprocally targeted by enteroviruses is not known. Here, we report that the 3C protease (3Cpro) from two enteroviruses, coxsackievirus B3 (CVB3) and poliovirus, targets TRIM7 for cleavage. CVB3 3Cpro cleaves TRIM7 at glutamine 24 (Q24), resulting in a truncated TRIM7 that fails to inhibit CVB3 due to dampened E3 ubiquitin ligase activity. TRIM7 Q24 is highly conserved across mammals, except in marsupials, which instead have a naturally occurring histidine (H24) that is not subject to 3Cpro cleavage. Marsupials also express two isoforms of TRIM7, and the two proteins from koalas have distinct antiviral activities. The longer isoform contains an additional exon due to alternate splice site usage. This additional exon contains a unique 3Cpro cleavage site, suggesting that certain enteroviruses may have evolved to target marsupial TRIM7 even if the canonical Q24 is missing. Combined with computational analyses indicating that TRIM7 is rapidly evolving, our data raise the possibility that TRIM7 may be targeted by enterovirus evasion strategies and that evolution of TRIM7 across mammals may have conferred unique antiviral properties. IMPORTANCE Enteroviruses are significant human pathogens that cause viral myocarditis, pancreatitis, and meningitis. Knowing how the host controls these viruses and how the viruses may evade host restriction is important for understanding fundamental concepts in antiviral immunity and for informing potential therapeutic interventions. In this study, we demonstrate that coxsackievirus B3 uses its virally encoded protease to target the host antiviral protein TRIM7 for cleavage, suggesting a potential mechanism of viral immune evasion. We additionally show that TRIM7 has evolved in certain mammalian lineages to express protein variants with distinct antiviral activities and susceptibilities to viral protease-mediated cleavage.
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12
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Nobori H, Fukao K, Kuroda T, Anan N, Tashima R, Nakashima M, Noda S, Tajiri M, Torii M, Toba S, Uemura K, Sanaki T, Shishido T, Tachibana Y, Kato T. Efficacy of ensitrelvir against SARS-CoV-2 in a delayed-treatment mouse model. J Antimicrob Chemother 2022; 77:2984-2991. [PMID: 35914182 PMCID: PMC9384569 DOI: 10.1093/jac/dkac257] [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: 03/28/2022] [Accepted: 07/06/2022] [Indexed: 11/26/2022] Open
Abstract
Objectives Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the aetiological agent of coronavirus disease 2019 (COVID-19) and a devastating worldwide health concern. Development of safe and effective treatments is not only important for interventions during the current pandemic, but also for providing general treatment options moving forward. We have developed ensitrelvir, an antiviral compound that targets the 3C-like protease of SARS-CoV-2. In this study, a delayed-treatment mouse model was used to clarify the potential in vivo efficacy of ensitrelvir. Methods Female BALB/cAJcl mice of different ages were infected with the SARS-CoV-2 gamma strain (hCoV-19/Japan/TY7-501/2021) or mouse-adapted SARS-CoV-2 MA-P10 and then 24 h post-infection orally administered various doses of ensitrelvir or vehicle. Viral titres and RNA levels in the lungs were quantified using VeroE6/TMPRSS2 cells and RT–qPCR, respectively. Body weight loss, survival, lung weight, cytokine/chemokine production, nucleocapsid protein expression and lung pathology were evaluated to investigate the in vivo efficacy of ensitrelvir. Results Based on infectious viral titres and viral RNA levels in the lungs of infected mice, ensitrelvir reduced viral loads in a dose-dependent manner. The antiviral efficacy correlated with increased survival, reduced body weight loss, reduced pulmonary lesions and suppression of inflammatory cytokine/chemokine levels. Conclusions This was the first evaluation of the in vivo anti-SARS-CoV-2 efficacy of ensitrelvir in a delayed-treatment mouse model. In this model, ensitrelvir demonstrated high antiviral potential and suppressed lung inflammation and lethality caused by SARS-CoV-2 infection. The findings support the continued clinical development of ensitrelvir as an antiviral agent to treat patients with COVID-19.
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Affiliation(s)
- Haruaki Nobori
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Keita Fukao
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Takayuki Kuroda
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Naomi Anan
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Ryoichi Tashima
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Masaaki Nakashima
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Sayuri Noda
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Minako Tajiri
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Mikinori Torii
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shinsuke Toba
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.,Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan
| | - Kentaro Uemura
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.,Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan.,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6 Kita-ku, Sapporo, Hokkaido 060-0812, Japan
| | - Takao Sanaki
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Takao Shishido
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Yuki Tachibana
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Teruhisa Kato
- Pharmaceutical Research Division, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
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Chen H, Zhu Z, Qiu Y, Ge X, Zheng H, Peng Y. Prediction of coronavirus 3C-like protease cleavage sites using machine-learning algorithms. Virol Sin 2022; 37:437-444. [PMID: 35513273 PMCID: PMC9060714 DOI: 10.1016/j.virs.2022.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/02/2022] [Indexed: 12/05/2022] Open
Abstract
The coronavirus 3C-like (3CL) protease, a cysteine protease, plays an important role in viral infection and immune escape. However, there is still a lack of effective tools for determining the cleavage sites of the 3CL protease. This study systematically investigated the diversity of the cleavage sites of the coronavirus 3CL protease on the viral polyprotein, and found that the cleavage motif were highly conserved for viruses in the genera of Alphacoronavirus, Betacoronavirus and Gammacoronavirus. Strong residue preferences were observed at the neighboring positions of the cleavage sites. A random forest (RF) model was built to predict the cleavage sites of the coronavirus 3CL protease based on the representation of residues in cleavage motifs by amino acid indexes, and the model achieved an AUC of 0.96 in cross-validations. The RF model was further tested on an independent test dataset which were composed of cleavage sites on 99 proteins from multiple coronavirus hosts. It achieved an AUC of 0.95 and predicted correctly 80% of the cleavage sites. Then, 1,352 human proteins were predicted to be cleaved by the 3CL protease by the RF model. These proteins were enriched in several GO terms related to the cytoskeleton, such as the microtubule, actin and tubulin. Finally, a webserver named 3CLP was built to predict the cleavage sites of the coronavirus 3CL protease based on the RF model. Overall, the study provides an effective tool for identifying cleavage sites of the 3CL protease and provides insights into the molecular mechanism underlying the pathogenicity of coronaviruses. A view of the diversity of the cleavage sites by the coronavirus 3CL protease. An accurate RF model for predicting the cleavage of coronavirus 3CL protease. A web-server named 3CLP for predicting the cleavage of coronavirus 3CL protease. The 3CLP is available at http://www.computationalbiology.cn/3CLPHost/home.html. 1352 human proteins were predicted to be cleaved by the coronavirus 3CL protease.
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Affiliation(s)
- Huiting Chen
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Zhaozhong Zhu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Ye Qiu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Xingyi Ge
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Heping Zheng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
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14
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SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. J Virol 2022; 96:e0003722. [PMID: 35389264 PMCID: PMC9044939 DOI: 10.1128/jvi.00037-22] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose an enormous threat to economic activity and public health worldwide. Previous studies have shown that the nonstructural protein 5 (nsp5, also called 3C-like protease) of alpha- and deltacoronaviruses cleaves Q231 of the NF-κB essential modulator (NEMO), a key kinase in the RIG-I-like receptor pathway, to inhibit type I interferon (IFN) production. In this study, we found that both SARS-CoV-2 nsp5 and SARS-CoV nsp5 cleaved NEMO at multiple sites (E152, Q205, and Q231). Notably, SARS-CoV-2 nsp5 exhibited a stronger ability to cleave NEMO than SARS-CoV nsp5. Sequence and structural alignments suggested that an S/A polymorphism at position 46 of nsp5 in SARS-CoV versus SARS-CoV-2 may be responsible for this difference. Mutagenesis experiments showed that SARS-CoV-2 nsp5 (S46A) exhibited poorer cleavage of NEMO than SARS-CoV-2 nsp5 wild type (WT), while SARS-CoV nsp5 (A46S) showed enhanced NEMO cleavage compared with the WT protein. Purified recombinant SARS-CoV-2 nsp5 WT and SARS-CoV nsp5 (A46S) proteins exhibited higher hydrolysis efficiencies than SARS-CoV-2 nsp5 (S46A) and SARS-CoV nsp5 WT proteins in vitro. Furthermore, SARS-CoV-2 nsp5 exhibited stronger inhibition of Sendai virus (SEV)-induced interferon beta (IFN-β) production than SARS-CoV-2 nsp5 (S46A), while introduction of the A46S substitution in SARS-CoV nsp5 enhanced suppression of SEV-induced IFN-β production. Taken together, these data show that S46 is associated with the catalytic activity and IFN antagonism by SARS-CoV-2 nsp5. IMPORTANCE The nsp5-encoded 3C-like protease is the main coronavirus protease, playing a vital role in viral replication and immune evasion by cleaving viral polyproteins and host immune-related molecules. We showed that both SARS-CoV-2 nsp5 and SARS-CoV nsp5 cleave the NEMO at multiple sites (E152, Q205, and Q231). This specificity differs from NEMO cleavage by alpha- and deltacoronaviruses, demonstrating the distinct substrate recognition of SARS-CoV-2 and SARS-CoV nsp5. Compared with SARS-CoV nsp5, SARS-CoV-2 nsp5 encodes S instead of A at position 46. This substitution is associated with stronger catalytic activity, enhanced cleavage of NEMO, and increased interferon antagonism of SARS-CoV-2 nsp5. These data provide new insights into the pathogenesis and transmission of SARS-CoV-2.
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15
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Yan Q, Liu X, Sun Y, Zeng W, Li Y, Zhao F, Wu K, Fan S, Zhao M, Chen J, Yi L. Swine Enteric Coronavirus: Diverse Pathogen–Host Interactions. Int J Mol Sci 2022; 23:ijms23073953. [PMID: 35409315 PMCID: PMC8999375 DOI: 10.3390/ijms23073953] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/23/2022] Open
Abstract
Swine enteric coronavirus (SeCoV) causes acute gastroenteritis and high mortality in newborn piglets. Since the last century, porcine transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) have swept farms all over the world and caused substantial economic losses. In recent years, porcine delta coronavirus (PDCoV) and swine acute diarrhea syndrome coronavirus (SADS-CoV) have been emerging SeCoVs. Some of them even spread across species, which made the epidemic situation of SeCoV more complex and changeable. Recent studies have begun to reveal the complex SeCoV–host interaction mechanism in detail. This review summarizes the current advances in autophagy, apoptosis, and innate immunity induced by SeCoV infection. These complex interactions may be directly involved in viral replication or the alteration of some signal pathways.
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Affiliation(s)
- Quanhui Yan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Xiaodi Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yawei Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Weijun Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Feifan Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Correspondence: (J.C.); (L.Y.); Tel.: +86-20-8528-8017 (J.C. & L.Y.)
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.Y.); (X.L.); (Y.S.); (W.Z.); (Y.L.); (F.Z.); (K.W.); (S.F.); (M.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Correspondence: (J.C.); (L.Y.); Tel.: +86-20-8528-8017 (J.C. & L.Y.)
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Zhao Y, Chen R, Xiao D, Zhang L, Song D, Wen Y, Wu R, Zhao Q, Du S, Wen X, Cao S, Huang X. A Comparative Transcriptomic Analysis Reveals That HSP90AB1 Is Involved in the Immune and Inflammatory Responses to Porcine Deltacoronavirus Infection. Int J Mol Sci 2022; 23:ijms23063280. [PMID: 35328701 PMCID: PMC8953809 DOI: 10.3390/ijms23063280] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
PDCoV is an emerging enteropathogenic coronavirus that mainly causes acute diarrhea in piglets, seriously affecting pig breeding industries worldwide. To date, the molecular mechanisms of PDCoV-induced immune and inflammatory responses or host responses in LLC-PK cells in vitro are not well understood. HSP90 plays important roles in various viral infections. In this study, HSP90AB1 knockout cells (HSP90AB1KO) were constructed and a comparative transcriptomic analysis between PDCoV-infected HSP90AB1WT and HSP90AB1KO cells was conducted using RNA sequencing to explore the effect of HSP90AB1 on PDCoV infection. A total of 1295 and 3746 differentially expressed genes (DEGs) were identified in PDCoV-infected HSP90AB1WT and HSP90AB1KO cells, respectively. Moreover, most of the significantly enriched pathways were related to immune and inflammatory response-associated pathways upon PDCoV infection. The DEGs enriched in NF-κB pathways were specifically detected in HSP90AB1WT cells, and NF-κB inhibitors JSH-23, SC75741 and QNZ treatment reduced PDCoV infection. Further research revealed most cytokines associated with immune and inflammatory responses were upregulated during PDCoV infection. Knockout of HSP90AB1 altered the upregulated levels of some cytokines. Taken together, our findings provide new insights into the host response to PDCoV infection from the transcriptome perspective, which will contribute to illustrating the molecular basis of the interaction between PDCoV and HSP90AB1.
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Affiliation(s)
- Yujia Zhao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Rui Chen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Dai Xiao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Luwen Zhang
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Daili Song
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Yiping Wen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Rui Wu
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Qin Zhao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Senyan Du
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Xintian Wen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
| | - Sanjie Cao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
- Sichuan Science-Observation Experimental Station for Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu 611130, China
- National Animal Experiments Teaching Demonstration Center, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaobo Huang
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (R.C.); (D.X.); (L.Z.); (D.S.); (Y.W.); (R.W.); (Q.Z.); (S.D.); (X.W.); (S.C.)
- Sichuan Science-Observation Experimental Station for Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu 611130, China
- National Animal Experiments Teaching Demonstration Center, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: ; Tel.: +86-180-4845-1618
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17
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Porcine Deltacoronavirus (PDCoV) Entry into PK-15 Cells by Caveolae-Mediated Endocytosis. Viruses 2022; 14:v14030496. [PMID: 35336903 PMCID: PMC8950576 DOI: 10.3390/v14030496] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 01/07/2023] Open
Abstract
(1) Background: Porcine deltacoronavirus (PDCoV) is a newly emerged enteric virus affecting pig breeding industries worldwide, and its pathogenic mechanism remains unclear. (2) Methods: In this study, we preliminarily identified the endocytic pathway of PDCoV in PK-15 cells, using six chemical inhibitors (targeting clathrin-mediated endocytosis, caveolae-mediated endocytosis, macropinocytosis pathway and endosomal acidification), overexpression of dominant-negative (DN) mutants to treat PK-15 cells and proteins knockdown. (3) Results: The results revealed that PDCoV entry was not affected after treatment with chlorpromazine (CPZ), 5-(N-ethyl-N-isopropyl) amiloride (EIPA)or ammonium chloride (NH4Cl), indicating that the entry of PDCoV into PK-15 cells were clathrin-, micropinocytosis-, PH-independent endocytosis. Conversely, PDCoV infection was sensitive to nystatin, dynasore and methyl-β-cyclodextrin (MβCD) with reduced PDCoV internalization, indicating that entry of PDCoV into PK-15 cells was caveolae-mediated endocytosis that required dynamin and cholesterol; indirect immunofluorescence and shRNA interference further validated these results. (4) Conclusions: In conclusion, PDCoV entry into PK-15 cells depends on caveolae-mediated endocytosis, which requires cholesterol and dynamin. Our finding is the first initial identification of the endocytic pathway of PDCoV in PK-15 cells, providing a theoretical basis for an in-depth understanding of the pathogenic mechanism of PDCoV and the design of new antiviral targets.
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18
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Coronaviruses Nsp5 Antagonizes Porcine Gasdermin D-Mediated Pyroptosis by Cleaving Pore-Forming p30 Fragment. mBio 2022; 13:e0273921. [PMID: 35012343 PMCID: PMC8749417 DOI: 10.1128/mbio.02739-21] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coronaviruses (CoVs) are a family of RNA viruses that typically cause respiratory, enteric, and hepatic diseases in animals and humans. Here, we use porcine epidemic diarrhea virus (PEDV) as a model of CoVs to illustrate the reciprocal regulation between CoV infection and pyroptosis. For the first time, we elucidate the molecular mechanism of porcine gasdermin D (pGSDMD)-mediated pyroptosis and demonstrate that amino acids R238, T239, and F240 within pGSDMD-p30 are critical for pyroptosis. Furthermore, 3C-like protease Nsp5 from SARS-CoV-2, MERS-CoV, PDCoV, and PEDV can cleave pGSDMD at the Q193-G194 junction to produce two fragments unable to trigger pyroptosis. The two cleaved fragments could not inhibit PEDV replication. In addition, Nsp5 from SARS-CoV-2 and MERS-CoV also cleave human GSDMD (hGSDMD). Therefore, we provide clear evidence that PEDV may utilize the Nsp5-GSDMD pathway to inhibit pyroptosis and, thus, facilitate viral replication during the initial period, suggesting an important strategy for the coronaviruses to sustain their infection. IMPORTANCE Recently, GSDMD has been reported as a key executioner for pyroptosis. This study first demonstrates the molecular mechanism of pGSDMD-mediated pyroptosis and that the pGSDMD-mediated pyroptosis protects host cells against PEDV infection. Notably, PEDV employs its Nsp5 to directly cleave pGSDMD in favor of its replication. We found that Nsp5 proteins from other coronaviruses, such as porcine deltacoronavirus, severe acute respiratory syndrome coronavirus 2, and Middle East respiratory syndrome coronavirus, also had the protease activity to cleave human and porcine GSDMD. Thus, we provide clear evidence that the coronaviruses might utilize Nsp5 to inhibit the host pyroptotic cell death and facilitate their replication during the initial period, an important strategy for their sustaining infection. We suppose that GSDMD is an appealing target for the design of anticoronavirus therapies.
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19
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Burgess HM, Vink EI, Mohr I. Minding the message: tactics controlling RNA decay, modification, and translation in virus-infected cells. Genes Dev 2022; 36:108-132. [PMID: 35193946 PMCID: PMC8887129 DOI: 10.1101/gad.349276.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
With their categorical requirement for host ribosomes to translate mRNA, viruses provide a wealth of genetically tractable models to investigate how gene expression is remodeled post-transcriptionally by infection-triggered biological stress. By co-opting and subverting cellular pathways that control mRNA decay, modification, and translation, the global landscape of post-transcriptional processes is swiftly reshaped by virus-encoded factors. Concurrent host cell-intrinsic countermeasures likewise conscript post-transcriptional strategies to mobilize critical innate immune defenses. Here we review strategies and mechanisms that control mRNA decay, modification, and translation in animal virus-infected cells. Besides settling infection outcomes, post-transcriptional gene regulation in virus-infected cells epitomizes fundamental physiological stress responses in health and disease.
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Affiliation(s)
- Hannah M Burgess
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Elizabeth I Vink
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA.,Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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20
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Qu H, Wen Y, Hu J, Xiao D, Li S, Zhang L, Liao Y, Chen R, Zhao Y, Wen Y, Wu R, Zhao Q, Du S, Yan Q, Wen X, Cao S, Huang X. Study of the inhibitory effect of STAT1 on PDCoV infection. Vet Microbiol 2022; 266:109333. [PMID: 35033844 DOI: 10.1016/j.vetmic.2022.109333] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/24/2021] [Accepted: 01/02/2022] [Indexed: 11/27/2022]
Abstract
Porcine deltacoronavirus (PDCoV) is an enteropathogen found in many pig producing countries. It can cause acute diarrhea, vomiting, dehydration, and death in newborn piglets, seriously affecting the development of pig breeding industries. To date, our knowledge of the pathogenesis of PDCoV and its interactions with host cell factors remains incomplete. Using Co-IP coupled with LC/MS-MS, we identified 67 proteins that potentially interact with PDCoV in LLC-PK1 cells; five of the identified proteins were chosen for further evaluation (IMMT, STAT1, XPO5, PIK3AP1, and TMPRSS11E). Five LLC-PK1 cell lines, each with one of the genes of interest knocked down, were constructed using CRISPR/cas9. In these knockdown cells lines, only STAT1KD resulted in a significantly greater virus yield. Knockdown of the remaining four genes resulted, to varying degrees, in a lower virus yield that wild-type LLC-PK1 cells. The absence of STAT1 did not significantly affect the attachment of PDCoV to cells, but did result in increased viral internalization. Additionally, PDCoV infection stimulated expression of interferon stimulated genes (ISGs) downstream of STAT1 (IFIT1, IFIT2, RADS2, ISG15, MX1, and OAS1) while knockdown of STAT1 resulted in a greater than 80 % decrease in the expression of all six ISGs. Our findings show that STAT1 interacts with PDCoV, and plays a negative regulatory role in PDCoV infection.
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Affiliation(s)
- Huan Qu
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yimin Wen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jingfei Hu
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Dai Xiao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Shiqian Li
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Luwen Zhang
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yijie Liao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Rui Chen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yujia Zhao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yiping Wen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Rui Wu
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Qin Zhao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Senyan Du
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Qigui Yan
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Xintian Wen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Sanjie Cao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China; Sichuan Science-observation Experiment Station of Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, 611130, China; National Animal Experiments Teaching Demonstration Center, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Xiaobo Huang
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China; Sichuan Science-observation Experiment Station of Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, 611130, China; National Animal Experiments Teaching Demonstration Center, Sichuan Agricultural University, Chengdu, 611130, China.
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21
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Kasuga Y, Zhu B, Jang KJ, Yoo JS. Innate immune sensing of coronavirus and viral evasion strategies. Exp Mol Med 2021; 53:723-736. [PMID: 33953325 PMCID: PMC8099713 DOI: 10.1038/s12276-021-00602-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
The innate immune system is the first line of the host defense program against pathogens and harmful substances. Antiviral innate immune responses can be triggered by multiple cellular receptors sensing viral components. The activated innate immune system produces interferons (IFNs) and cytokines that perform antiviral functions to eliminate invading viruses. Coronaviruses are single-stranded, positive-sense RNA viruses that have a broad range of animal hosts. Coronaviruses have evolved multiple means to evade host antiviral immune responses. Successful immune evasion by coronaviruses may enable the viruses to adapt to multiple species of host organisms. Coronavirus transmission from zoonotic hosts to humans has caused serious illnesses, such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease-2019 (COVID-19), resulting in global health and economic crises. In this review, we summarize the current knowledge of the mechanisms underlying host sensing of and innate immune responses against coronavirus invasion, as well as host immune evasion strategies of coronaviruses. Understanding how the innate immune system senses coronaviruses and how coronaviruses can escape detection could provide novel approaches to tackle infections. Coronaviruses, including SARS-CoV-2, constantly evolve to manipulate, obstruct and evade host immune responses. A team led by Ji-Seung Yoo, Hokkaido University, Sapporo, Japan, reviewed understanding of innate immune responses to coronaviruses and viral evasion strategies. Two major receptor families recognise RNA viruses upon infection, but how they respond to SARS-CoV-2 is unclear. One receptor, TLR7, plays a critical role in sensing coronavirus infections, and mutations in the TLR7 gene are associated with severe illness and mortality in young Covid-19 patients. Activating host TLR pathways may prove a useful therapeutic approach. Further in-depth investigations are needed into specific coronavirus proteins and viral mechanisms that suppress host immunity.
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Affiliation(s)
- Yusuke Kasuga
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Baohui Zhu
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Kyoung-Jin Jang
- Department of Pathology, School of Medicine, Institute of Biomedical Science and Technology, Konkuk University, Chungju, 27478, Republic of Korea.
| | - Ji-Seung Yoo
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan.
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22
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Fung SY, Siu KL, Lin H, Yeung ML, Jin DY. SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Int J Biol Sci 2021; 17:1547-1554. [PMID: 33907518 PMCID: PMC8071772 DOI: 10.7150/ijbs.59943] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Suppression of type I interferon (IFN) response is one pathological outcome of the infection of highly pathogenic human coronaviruses. To effect this, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 encode multiple IFN antagonists. In this study, we reported on the IFN antagonism of SARS-CoV-2 main protease NSP5. NSP5 proteins of both SARS-CoV and SARS-CoV-2 counteracted Sendai virus-induced IFN production. NSP5 variants G15S and K90R commonly seen in circulating strains of SARS-CoV-2 retained the IFN-antagonizing property. The suppressive effect of NSP5 on IFN-β gene transcription induced by RIG-I, MAVS, TBK1 and IKKϵ suggested that NSP5 likely acts at a step downstream of IRF3 phosphorylation in the cytoplasm. NSP5 did not influence steady-state expression or phosphorylation of IRF3, suggesting that IRF3, regardless of its phosphorylation state, might not be the substrate of NSP5 protease. However, nuclear translocation of phosphorylated IRF3 was severely compromised in NSP5-expressing cells. Taken together, our work revealed a new mechanism by which NSP5 proteins encoded by SARS-CoV and SARS-CoV-2 antagonize IFN production by retaining phosphorylated IRF3 in the cytoplasm. Our findings have implications in rational design and development of antiviral agents against SARS-CoV-2.
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Affiliation(s)
- Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Huayue Lin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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23
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Moustaqil M, Ollivier E, Chiu HP, Van Tol S, Rudolffi-Soto P, Stevens C, Bhumkar A, Hunter DJB, Freiberg AN, Jacques D, Lee B, Sierecki E, Gambin Y. SARS-CoV-2 proteases PLpro and 3CLpro cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species. Emerg Microbes Infect 2021; 10:178-195. [PMID: 33372854 PMCID: PMC7850364 DOI: 10.1080/22221751.2020.1870414] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The genome of SARS-CoV-2 encodes two viral proteases (NSP3/papain-like protease and NSP5/3C-like protease) that are responsible for cleaving viral polyproteins during replication. Here, we discovered new functions of the NSP3 and NSP5 proteases of SARS-CoV-2, demonstrating that they could directly cleave proteins involved in the host innate immune response. We identified 3 proteins that were specifically and selectively cleaved by NSP3 or NSP5: IRF-3, and NLRP12 and TAB1, respectively. Direct cleavage of IRF3 by NSP3 could explain the blunted Type-I IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of cytokines and inflammatory response observed in COVID-19 patients. We demonstrate that in the mouse NLRP12 protein, one of the recognition site is not cleaved in our in-vitro assay. We pushed this comparative alignment of IRF-3 and NLRP12 homologs and show that the lack or presence of cognate cleavage motifs in IRF-3 and NLRP12 could contribute to the presentation of disease in cats and tigers, for example. Our findings provide an explanatory framework for indepth studies into the pathophysiology of COVID-19.
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Affiliation(s)
- Mehdi Moustaqil
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, Australia
| | - Emma Ollivier
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, Australia
| | - Hsin-Ping Chiu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah Van Tol
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - Paulina Rudolffi-Soto
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, Australia
| | - Christian Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Akshay Bhumkar
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, Australia
| | - Dominic J B Hunter
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, Australia.,Institute for Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Alexander N Freiberg
- Department of Pathology, Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - David Jacques
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, Australia
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma Sierecki
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, Australia
| | - Yann Gambin
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, Australia
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