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Fan J, Xi P, Liu H, Song X, Zhao X, Zhou X, Zou Y, Fu Y, Li L, Jia R, Yin Z. Myricetin inhibits transmissible gastroenteritis virus replication by targeting papain-like protease deubiquitinating enzyme activity. Front Microbiol 2024; 15:1433664. [PMID: 39050632 PMCID: PMC11266173 DOI: 10.3389/fmicb.2024.1433664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Myricetin, a natural flavonoid found in various foods, was investigated for its antiviral effect against transmissible gastroenteritis virus (TGEV). This α-coronavirus causes significant economic losses in the global swine industry. The study focused on the papain-like protease (PLpro), which plays a crucial role in coronavirus immune evasion by mediating deubiquitination. Targeting PLpro could potentially disrupt viral replication and enhance antiviral responses. The results demonstrated that myricetin effectively inhibited TGEV-induced cytopathic effects in a dose-dependent manner, with an EC50 value of 31.19 μM. Myricetin significantly reduced TGEV viral load within 48 h after an 8-h co-incubation period. Further investigations revealed that myricetin at a concentration of 100 μM directly inactivated TGEV and suppressed its intracellular replication stage. Moreover, pretreatment with 100 μM myricetin conferred a protective effect on PK-15 cells against TGEV infection. Myricetin competitively inhibited PLpro with an IC50 value of 6.563 μM. Molecular docking experiments show that myricetin binds to the Cys102 residue of PLpro through conventional hydrogen bonds, Pi-sulfur, and Pi-alkyl interactions. This binding was confirmed through site-directed mutagenesis experiments, indicating myricetin as a potential candidate for preventing and treating TGEV infection.
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Affiliation(s)
- Jiahao Fan
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Pengyuan Xi
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Huimao Liu
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xu Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinghong Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xun Zhou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuanfeng Zou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuping Fu
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lixia Li
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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2
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van Vliet VJE, De Silva A, Mark BL, Kikkert M. Viral deubiquitinating proteases and the promising strategies of their inhibition. Virus Res 2024; 344:199368. [PMID: 38588924 PMCID: PMC11025011 DOI: 10.1016/j.virusres.2024.199368] [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: 11/30/2023] [Revised: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Several viruses are now known to code for deubiquitinating proteases in their genomes. Ubiquitination is an essential post-translational modification of cellular substrates involved in many processes in the cell, including in innate immune signalling. This post-translational modification is regulated by the ubiquitin conjugation machinery, as well as various host deubiquitinating enzymes. The conjugation of ubiquitin chains to several innate immune related factors is often needed to induce downstream signalling, shaping the antiviral response. Viral deubiquitinating proteins, besides often having a primary function in the viral replication cycle by cleaving the viral polyprotein, are also able to cleave ubiquitin chains from such host substrates, in that way exerting a function in innate immune evasion. The presence of viral deubiquitinating enzymes has been firmly established for numerous animal-infecting viruses, such as some well-researched and clinically important nidoviruses, and their presence has now been confirmed in several plant viruses as well. Viral proteases in general have long been highlighted as promising drug targets, with a current focus on small molecule inhibitors. In this review, we will discuss the range of viral deubiquitinating proteases known to date, summarise the various avenues explored to inhibit such proteases and discuss novel strategies and models intended to inhibit and study these specific viral enzymes.
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Affiliation(s)
- Vera J E van Vliet
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands; The Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Anuradha De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands.
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Rivera-Benítez JF, Martínez-Bautista R, González-Martínez R, De la Luz-Armendáriz J, Herrera-Camacho I, Rosas-Murrieta N, Márquez-Valdelamar L, Lara R. Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013-2017). Viruses 2024; 16:309. [PMID: 38400084 PMCID: PMC10891996 DOI: 10.3390/v16020309] [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: 01/15/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The characteristics of the whole PEDV genome that has circulated in Mexico from the first outbreak to the present are unknown. We chose samples obtained from 2013 to 2017 and sequenced them, which enabled us to identify the genetic variation and phylogeny in the virus during the first four years that it circulated in Mexico. A 99% identity was found among the analyzed pandemic strains; however, the 1% difference affected the structure of the S glycoprotein, which is essential for the binding of the virus to the cellular receptor. The S protein induces the most efficacious antibodies; hence, these changes in structure could be implicated in the clinical antecedents of the outbreaks. Antigenic changes could also help PEDV avoid neutralization, even in the presence of previous immunity. The characterization of the complete genome enabled the identification of three circulating strains that have a deletion in ORF1a, which is present in attenuated Asian vaccine strains. The phylogenetic analysis of the complete genome indicates that the first PEDV outbreaks in Mexico were caused by INDEL strains and pandemic strains related to USA strains; however, the possibility of the entry of European strains exists, which may have caused the 2015 and 2016 outbreaks.
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Affiliation(s)
- José Francisco Rivera-Benítez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Mexico City 04010, Mexico
| | | | | | - Jazmín De la Luz-Armendáriz
- Departamento de Medicina y Zootecnia de Rumiantes, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Irma Herrera-Camacho
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico; (I.H.-C.); (N.R.-M.)
| | - Nora Rosas-Murrieta
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico; (I.H.-C.); (N.R.-M.)
| | - Laura Márquez-Valdelamar
- Laboratorio de Secuenciación Genómica de la Biodiversidad y de la Salud, UNAM, Mexico City 04510, Mexico;
| | - Rocio Lara
- Programa de Maestría en Ciencias de la Producción y de la Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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Liu W, Mu G, Jia Y, Yu M, Zhang S, Wang Z, Fang S. The role of IBV PL1pro in virus replication and suppression of host innate immune responses. BMC Vet Res 2023; 19:270. [PMID: 38087313 PMCID: PMC10717896 DOI: 10.1186/s12917-023-03839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Coronavirus papain-like proteases (PLpros) play a crucial role in virus replication and the evasion of the host immune response. Infectious bronchitis virus (IBV) encodes a proteolytically defective remnant of PL1pro and an active PL2pro. However, the function of PL1pro in IBV remains largely unknown. This study aims to explore the effect of PL1pro on virus replication and underlying mechanisms. RESULTS The recombinant viruses rIBV-ΔPL1pro and rIBV-ΔPL1pro-N were obtained using reverse genetic techniques through the deletion of the IBV PL1pro domain and the N-terminal conserved sequence of PL1pro (PL1pro-N). We observed significantly lower replication of rIBV-ΔPL1pro and rIBV-ΔPL1pro-N than wild-type IBV. Further investigation revealed that the lack of PL1pro-N in IBV decreased virus resistance to interferon (IFN) while also inducing host immune response by enhancing the production of IFN-β and activating the downstream STAT1 signaling pathway of IFNs. In addition, the overexpression of PL1pro-N significantly suppressed type I IFN response by down-regulating the expressions of genes in the IFN pathway. CONCLUSIONS Our data demonstrated that IBV PL1pro plays a crucial role in IBV replication and the suppression of host innate immune responses, suggesting that IBV PL1pro could serve as a promising molecular target for antiviral therapy.
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Affiliation(s)
- Weirong Liu
- Yangtze University Health Science Center, Jingzhou, Hubei Province, China
| | - Ge Mu
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, Hubei Province, 434025, China
| | - Yiquan Jia
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, Hubei Province, 434025, China
| | - Mengting Yu
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, Hubei Province, 434025, China
| | - Songbai Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, Hubei Province, China
| | - Zhen Wang
- Yangtze University Health Science Center, Jingzhou, Hubei Province, China
| | - Shouguo Fang
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, Hubei Province, 434025, China.
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Chen Y, Zhang Y, Wang X, Zhou J, Ma L, Li J, Yang L, Ouyang H, Yuan H, Pang D. Transmissible Gastroenteritis Virus: An Update Review and Perspective. Viruses 2023; 15:v15020359. [PMID: 36851573 PMCID: PMC9958687 DOI: 10.3390/v15020359] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 01/29/2023] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is a member of the alphacoronavirus genus, which has caused huge threats and losses to pig husbandry with a 100% mortality in infected piglets. TGEV is observed to be recombining and evolving unstoppably in recent years, with some of these recombinant strains spreading across species, which makes the detection and prevention of TGEV more complex. This paper reviews and discusses the basic biological properties of TGEV, factors affecting virulence, viral receptors, and the latest research advances in TGEV infection-induced apoptosis and autophagy to improve understanding of the current status of TGEV and related research processes. We also highlight a possible risk of TGEV being zoonotic, which could be evidenced by the detection of CCoV-HuPn-2018 in humans.
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Affiliation(s)
- Yiwu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yuanzhu Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Xi Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jian Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Lerong Ma
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jianing Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Lin Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Hongsheng Ouyang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401120, China
| | - Hongming Yuan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
- Correspondence: (H.Y.); (D.P.); Tel.: +86-431-8783-6175 (D.P.)
| | - Daxin Pang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401120, China
- Correspondence: (H.Y.); (D.P.); Tel.: +86-431-8783-6175 (D.P.)
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6
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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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7
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Maiti AK. Identification of G-quadruplex DNA sequences in SARS-CoV2. Immunogenetics 2022; 74:455-463. [PMID: 35303126 PMCID: PMC8931451 DOI: 10.1007/s00251-022-01257-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
G-quadruplex structure or Putative Quadruplex Sequences (PQSs) are abundant in human, microbial, DNA, or RNA viral genomes. These sequences in RNA viral genome play critical roles in integration into human genome as LTR (Long Terminal Repeat), genome replication, chromatin rearrangements, gene regulation, antigen variation (Av), and virulence. Here, we investigated whether the genome of SARS-CoV2, an RNA virus, contained such potential G-quadruplex structures. Using bioinformatic tools, we searched for such sequences and found thirty-seven (forward strand (twenty-five) + reverse strand (Twelve)) QGRSs (Quadruplex forming G-Rich Sequences)/PQSs in SARS-CoV2 genome. These sequences are dispersed mainly in the upstream of SARS-CoV2 genes. We discuss whether existing PQS/QGRS ligands could inhibit the SARS-CoV2 replication and gene transcription as has been observed in other RNA viruses. Further experimental validation would determine the role of these G-quadruplex sequences in SARS-CoV2 genome function to survive in the host cells and identify therapeutic agents to destabilize these PQSs/QGRSs.
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Affiliation(s)
- Amit K Maiti
- Mydnavar, Department of Genetics and Genomics, 2645 Somerset Boulevard, Troy, MI, 48084, USA.
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8
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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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9
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Zhou Z, Xu J, Li Z, Lv Y, Wu S, Zhang H, Song Y, Ai Y. Viral deubiquitinases and innate antiviral immune response in livestock and poultry. J Vet Med Sci 2021; 84:102-113. [PMID: 34803084 PMCID: PMC8810313 DOI: 10.1292/jvms.21-0199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Among many of the pathogens, virus is the main cause of diseases in livestock and poultry. A host infected with the virus triggers a series of innate and adaptive immunity. The realization of innate immune responses involves the participation of a series of protein molecules in host cells, including receptors, signal molecules and antiviral molecules. Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular or viral deubiquitinases (DUBs). DUBs have now been identified in diverse viral lineages, and their characterization is providing valuable insights into virus biology and the role of the ubiquitin system in host antiviral mechanisms. In this review, we briefly introduce the mechanisms of ubiquitination and deubiquitination, present antiviral innate immune response and its regulation by ubiquitin, and summarize the prevalence of DUBs encoded by viruses (Arteriviridae, Asfarviridae, Nairoviridae, Coronaviridae, Herpesviridae, and Picornaviridae) infecting domestic animals and poultry. It is found that these DUBs suppress the innate immune responses mainly by affecting the production of type I interferon (IFN), which causes immune evasion of the viruses and promotes their replication. These findings have important reference significance for understanding the virulence and immune evasion mechanisms of the relevant viruses, and thus for the development of more effective prevention and treatment measures.
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Affiliation(s)
- Zhengxuan Zhou
- College of Animal Science, Jilin University.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University
| | - Jiacui Xu
- College of Animal Science, Jilin University.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University
| | - Zhanjun Li
- College of Animal Science, Jilin University.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University
| | - Yan Lv
- College of Animal Science, Jilin University
| | - Shanli Wu
- College of Basic Medical Sciences, Jilin University
| | - Huanmin Zhang
- Avian Disease and Oncology Laboratory, Agriculture Research Service, United States Department of Agriculture
| | - Yu Song
- Key laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education of the People's Republic of China.,Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources
| | - Yongxing Ai
- College of Animal Science, Jilin University.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University
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10
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Abstract
Coronaviral papain-like proteases (PLpros) are essential enzymes that mediate not only the proteolytic processes of viral polyproteins during virus replication, but also the deubiquitination and deISGylation of cellular proteins that attenuate host innate immune responses. Therefore, PLpros are attractive targets for antiviral drug development. Here we report the crystal structure of the papain-like protease 2 (PLP2) of porcine epidemic diarrhea virus (PEDV) in complex with ubiquitin (Ub). The X-ray structural analyses reveal that PEDV PLP2 interacts with Ub substrate mainly through the Ub core region and C-terminal tail. Mutations of Ub-interacting residues resulted in moderately or completely abolished deubiquitinylating function of PEDV PLP2. In addition, our analyses also indicate that the two residues-extended blocking loop 2 at the S4 subsite contributes to the substrate selectivity and binding affinity of PEDV PLP2. Furthermore, the PEDV PLP2 Glu99 residue, conserved in alpha-CoV PLpros, was found to govern the preference of a positively charged P4 residue of peptidyl substrates. Collectively, our data provided structure-based information for substrate binding and selectivity of PEDV PLP2. These findings may help us gain insights into the deubiquitinating and proteolytic functions of PEDV PLP2 from a structural perspective. Importance Current challenges in CoVs include a comprehensive understanding of mechanistic effects of associated enzymes, including the 3C-like and papain-like proteases. We have previously reported that the PEDV PLP2 exhibits a broader substrate preference, superior DUB function, and inferior peptidase activity. However, the structure basis for these functions remains largely unclear. Here, we show the high-resolution X-ray crystal structure of PEDV PLP2 in complex with Ub. Integrated structural and biochemical analyses revealed: (i) three Ub-core interacting residues are essential for DUB function, (ii) two-residue-elongated blocking loop 2 regulates substrate selectivity, and (iii) a conserved glutamate residue governs the substrate specificity of PEDV PLP2. Collectively, our findings provide not only the structural insights to the catalytic mechanism of PEDV PLP2 but also a model for developing antiviral strategies.
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Proulx J, Borgmann K, Park IW. Role of Virally-Encoded Deubiquitinating Enzymes in Regulation of the Virus Life Cycle. Int J Mol Sci 2021; 22:ijms22094438. [PMID: 33922750 PMCID: PMC8123002 DOI: 10.3390/ijms22094438] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 01/21/2023] Open
Abstract
The ubiquitin (Ub) proteasome system (UPS) plays a pivotal role in regulation of numerous cellular processes, including innate and adaptive immune responses that are essential for restriction of the virus life cycle in the infected cells. Deubiquitination by the deubiquitinating enzyme, deubiquitinase (DUB), is a reversible molecular process to remove Ub or Ub chains from the target proteins. Deubiquitination is an integral strategy within the UPS in regulating survival and proliferation of the infecting virus and the virus-invaded cells. Many viruses in the infected cells are reported to encode viral DUB, and these vial DUBs actively disrupt cellular Ub-dependent processes to suppress host antiviral immune response, enhancing virus replication and thus proliferation. This review surveys the types of DUBs encoded by different viruses and their molecular processes for how the infecting viruses take advantage of the DUB system to evade the host immune response and expedite their replication.
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Affiliation(s)
- Jessica Proulx
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.P.); (K.B.)
| | - Kathleen Borgmann
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.P.); (K.B.)
| | - In-Woo Park
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Correspondence: ; Tel.: +1-(817)-735-5115; Fax: +1-(817)-735-2610
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12
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Zhuo LS, Wang MS, Yang JF, Xu HC, Huang W, Shang LQ, Yang GF. Insights into SARS-CoV-2: Medicinal Chemistry Approaches to Combat Its Structural and Functional Biology. Top Curr Chem (Cham) 2021; 379:23. [PMID: 33886017 PMCID: PMC8061463 DOI: 10.1007/s41061-021-00335-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 04/03/2021] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still a pandemic around the world. Currently, specific antiviral drugs to control the epidemic remain deficient. Understanding the details of SARS-CoV-2 structural biology is extremely important for development of antiviral agents that will enable regulation of its life cycle. This review focuses on the structural biology and medicinal chemistry of various key proteins (Spike, ACE2, TMPRSS2, RdRp and Mpro) in the life cycle of SARS-CoV-2, as well as their inhibitors/drug candidates. Representative broad-spectrum antiviral drugs, especially those against the homologous virus SARS-CoV, are summarized with the expectation they will drive the development of effective, broad-spectrum inhibitors against coronaviruses. We are hopeful that this review will be a useful aid for discovery of novel, potent anti-SARS-CoV-2 drugs with excellent therapeutic results in the near future.
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Affiliation(s)
- Lin-Sheng Zhuo
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Ming-Shu Wang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Hong-Chuang Xu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Wei Huang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Lu-Qing Shang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, People's Republic of China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.
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13
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QSAR Modelling of Peptidomimetic Derivatives towards HKU4-CoV 3CLpro Inhibitors against MERS-CoV. CHEMISTRY 2021. [DOI: 10.3390/chemistry3010029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In this paper, we report the relationship between the anti-MERS-CoV activities of the HKU4 derived peptides for some peptidomimetic compounds and various descriptors using the quantitative structure activity relationships (QSAR) methods. The used descriptors were computed using ChemSketch, Marvin Sketch and ChemOffice software. The principal components analysis (PCA) and the multiple linear regression (MLR) methods were used to propose a model with reliable predictive capacity. The original data set of 41 peptidomimetic derivatives was randomly divided into training and test sets of 34 and 7 compounds, respectively. The predictive ability of the best MLR model was assessed by determination coefficient R2 = 0.691, cross-validation parameter Q2cv = 0.528 and the external validation parameter R2test = 0.794.
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14
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Li M, Ye G, Si Y, Shen Z, Liu Z, Shi Y, Xiao S, Fu ZF, Peng G. Structure of the multiple functional domains from coronavirus nonstructural protein 3. Emerg Microbes Infect 2021; 10:66-80. [PMID: 33327866 PMCID: PMC7832007 DOI: 10.1080/22221751.2020.1865840] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coronaviruses (CoVs) are potential pandemic pathogens that can infect a variety of hosts and cause respiratory, enteric, hepatic and neurological diseases. Nonstructural protein 3 (nsp3), an essential component of the replication/transcription complex, is one of the most important antiviral targets. Here, we report the first crystal structure of multiple functional domains from porcine delta-coronavirus (PDCoV) nsp3, including the macro domain (Macro), ubiquitin-like domain 2 (Ubl2) and papain-like protease (PLpro) catalytic domain. In the asymmetric unit, two of the subunits form the head-to-tail homodimer with an interaction interface between Macro and PLpro. However, PDCoV Macro-Ubl2-PLpro mainly exists as a monomer in solution. Then, we conducted fluorescent resonance energy transfer-based protease assays and found that PDCoV PLpro can cleave a peptide by mimicking the cognate nsp2/nsp3 cleavage site in peptide substrates and exhibits deubiquitinating and de-interferon stimulated gene(deISGylating) activities by hydrolysing ubiquitin-7-amino-4-methylcoumarin (Ub-AMC) and ISG15-AMC substrates. Moreover, the deletion of Macro or Macro-Ubl2 decreased the enzyme activity of PLpro, indicating that Macro and Ubl2 play important roles in maintaining the stability of the PLpro domain. Two active sites of PLpro, Cys260 and His398, were determined; unexpectedly, the conserved site Asp412 was not the third active site. Furthermore, the motif "NGYDT" (amino acids 409-413) was important for stabilizing the enzyme activity of PLpro, and the N409A mutant significantly decreased the enzyme activity of PLpro. These results provide novel insights into the replication mechanism of CoV and new clues for future drug design.
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Affiliation(s)
- Mengxia Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Gang Ye
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Yu Si
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Zhou Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuejun Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
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15
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Xu Z, Zhang Y, Cao Y. The Roles of Apoptosis in Swine Response to Viral Infection and Pathogenesis of Swine Enteropathogenic Coronaviruses. Front Vet Sci 2020; 7:572425. [PMID: 33324698 PMCID: PMC7725767 DOI: 10.3389/fvets.2020.572425] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/28/2020] [Indexed: 01/18/2023] Open
Abstract
Apoptosis is a tightly regulated mechanism of cell death that plays important roles in various biological processes including biological evolution, multiple system development, anticancer, and viral infections. Swine enteropathogenic coronaviruses invade and damage villous epithelial cells of the small intestine causing severe diarrhea with high mortality rate in suckling piglets. Transmissible gastroenteritis virus (TGEV), Porcine epidemic diarrhea virus (PEDV), Porcine deltacoronavirus (PDCoV), and Swine acute diarrhea syndrome coronavirus (SADS-CoV) are on the top list of commonly-seen swine coronaviruses with a feature of diarrhea, resulting in significant economic losses to the swine industry worldwide. Apoptosis has been shown to be involved in the pathogenesis process of animal virus infectious diseases. Understanding the roles of apoptosis in host responses against swine enteropathogenic coronaviruses infection contribute to disease prevention and control. Here we summarize the recent findings that focus on the apoptosis during swine coronaviruses infection, in particular, TGEV, PEDV, PDCoV, and SADS-CoV.
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Affiliation(s)
- Zhichao Xu
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Yun Zhang
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
- Higher Education Mega Center, School of Life Science, Sun Yat-sen University, Guangzhou, China
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16
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Petushkova AI, Zamyatnin AA. Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations. Pharmaceuticals (Basel) 2020; 13:E277. [PMID: 32998368 PMCID: PMC7601131 DOI: 10.3390/ph13100277] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 12/23/2022] Open
Abstract
Papain-like proteases (PLpro) of coronaviruses (CoVs) support viral reproduction and suppress the immune response of the host, which makes CoV PLpro perspective pharmaceutical targets. Their inhibition could both prevent viral replication and boost the immune system of the host, leading to the speedy recovery of the patient. Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the third CoV outbreak in the last 20 years. Frequent mutations of the viral genome likely lead to the emergence of more CoVs. Inhibitors for CoV PLpro can be broad-spectrum and can diminish present and prevent future CoV outbreaks as PLpro from different CoVs have conservative structures. Several inhibitors have been developed to withstand SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV). This review summarizes the structural features of CoV PLpro, the inhibitors that have been identified over the last 20 years, and the compounds that have the potential to become novel effective therapeutics against CoVs in the near future.
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Affiliation(s)
- Anastasiia I. Petushkova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
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17
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Visser LJ, Aloise C, Swatek KN, Medina GN, Olek KM, Rabouw HH, de Groot RJ, Langereis MA, de los Santos T, Komander D, Skern T, van Kuppeveld FJM. Dissecting distinct proteolytic activities of FMDV Lpro implicates cleavage and degradation of RLR signaling proteins, not its deISGylase/DUB activity, in type I interferon suppression. PLoS Pathog 2020; 16:e1008702. [PMID: 32667958 PMCID: PMC7384677 DOI: 10.1371/journal.ppat.1008702] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 07/27/2020] [Accepted: 06/12/2020] [Indexed: 01/12/2023] Open
Abstract
The type I interferon response is an important innate antiviral pathway. Recognition of viral RNA by RIG-I-like receptors (RLRs) activates a signaling cascade that leads to type I interferon (IFN-α/β) gene transcription. Multiple proteins in this signaling pathway (e.g. RIG-I, MDA5, MAVS, TBK1, IRF3) are regulated by (de)ubiquitination events. Most viruses have evolved mechanisms to counter this antiviral response. The leader protease (Lpro) of foot-and-mouth-disease virus (FMDV) has been recognized to reduce IFN-α/β gene transcription; however, the exact mechanism is unknown. The proteolytic activity of Lpro is vital for releasing itself from the viral polyprotein and for cleaving and degrading specific host cell proteins, such as eIF4G and NF-κB. In addition, Lpro has been demonstrated to have deubiquitination/deISGylation activity. Lpro’s deubiquitination/deISGylation activity and the cleavage/degradation of signaling proteins have both been postulated to be important for reduced IFN-α/β gene transcription. Here, we demonstrate that TBK1, the kinase that phosphorylates and activates the transcription factor IRF3, is cleaved by Lpro in FMDV-infected cells as well as in cells infected with a recombinant EMCV expressing Lpro. In vitro cleavage experiments revealed that Lpro cleaves TBK1 at residues 692–694. We also observed cleavage of MAVS in HeLa cells infected with EMCV-Lpro, but only observed decreasing levels of MAVS in FMDV-infected porcine LFPK αVβ6 cells. We set out to dissect Lpro’s ability to cleave RLR signaling proteins from its deubiquitination/deISGylation activity to determine their relative contributions to the reduction of IFN-α/β gene transcription. The introduction of specific mutations, of which several were based on the recently published structure of Lpro in complex with ISG15, allowed us to identify specific amino acid substitutions that separate the different proteolytic activities of Lpro. Characterization of the effects of these mutations revealed that Lpro’s ability to cleave RLR signaling proteins but not its deubiquitination/deISGylation activity correlates with the reduced IFN-β gene transcription. Outbreaks of the picornavirus foot-and-mouth disease virus (FMDV) have significant consequences for animal health and product safety and place a major economic burden on the global livestock industry. Understanding how this notorious animal pathogen suppresses the antiviral type I interferon (IFN-α/β) response may help to develop countermeasures to control FMDV infections. FMDV suppresses the IFN-α/β response through the activity of its Leader protein (Lpro), a protease that can cleave host cell proteins. Lpro was also shown to have deubiquitinase and deISGylase activity, raising the possibility that Lpro suppresses IFN-α/β by removing ubiquitin and/or ISG15, two posttranslational modifications that can regulate the activation, interactions and localization of (signaling) proteins. Here, we show that TBK1 and MAVS, two signaling proteins that are important for activation of IFN-α/β gene transcription, are cleaved by Lpro. By generating Lpro mutants lacking either of these two activities, we demonstrate that Lpro’s ability to cleave signaling proteins, but not its deubiquitination/deISGylase activity, correlates with suppression of IFN-β gene transcription.
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Affiliation(s)
- Linda J. Visser
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Chiara Aloise
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Kirby N. Swatek
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gisselle N. Medina
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, New York, United States of America
| | - Karin M. Olek
- Department of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Huib H. Rabouw
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Raoul J. de Groot
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Martijn A. Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Teresa de los Santos
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, New York, United States of America
| | - David Komander
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Ubiquitin Signaling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Tim Skern
- Department of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Frank J. M. van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
- * E-mail:
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18
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Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response. Pathogens 2020; 9:pathogens9050367. [PMID: 32403318 PMCID: PMC7281546 DOI: 10.3390/pathogens9050367] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/27/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), a swine enteropathogenic coronavirus (CoV), is the causative agent of porcine epidemic diarrhea (PED). PED causes lethal watery diarrhea in piglets, which has led to substantial economic losses in many countries and is a great threat to the global swine industry. Interferons (IFNs) are major cytokines involved in host innate immune defense, which induce the expression of a broad range of antiviral effectors that help host to control and antagonize viral infections. PEDV infection does not elicit a robust IFN response, and some of the mechanisms used by the virus to counteract the host innate immune response have been unraveled. PEDV evades the host innate immune response by two main strategies including: (1) encoding IFN antagonists to disrupt innate immune pathway, and (2) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs.
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19
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Wang H, He S, Deng W, Zhang Y, Li G, Sun J, Zhao W, Guo Y, Yin Z, Li D, Shang L. Comprehensive Insights into the Catalytic Mechanism of Middle East Respiratory Syndrome 3C-Like Protease and Severe Acute Respiratory Syndrome 3C-Like Protease. ACS Catal 2020; 10:5871-5890. [PMID: 32391184 PMCID: PMC7202269 DOI: 10.1021/acscatal.0c00110] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/28/2020] [Indexed: 12/11/2022]
Abstract
Coronavirus 3C-like protease (3CLPro) is a highly conserved cysteine protease employing a catalytic dyad for its functions. 3CLPro is essential to the viral life cycle and, therefore, is an attractive target for developing antiviral agents. However, the detailed catalytic mechanism of coronavirus 3CLPro remains largely unknown. We took an integrated approach of employing X-ray crystallography, mutational studies, enzyme kinetics study, and inhibitors to gain insights into the mechanism. Such experimental work is supplemented by computational studies, including the prereaction state analysis, the ab initio calculation of the critical catalytic step, and the molecular dynamic simulation of the wild-type and mutant enzymes. Taken together, such studies allowed us to identify a residue pair (Glu-His) and a conserved His as critical for binding; a conserved GSCGS motif as important for the start of catalysis, a partial negative charge cluster (PNCC) formed by Arg-Tyr-Asp as essential for catalysis, and a conserved water molecule mediating the remote interaction between PNCC and catalytic dyad. The data collected and our insights into the detailed mechanism have allowed us to achieve a good understanding of the difference in catalytic efficiency between 3CLPro from SARS and MERS, conduct mutational studies to improve the catalytic activity by 8-fold, optimize existing inhibitors to improve the potency by 4-fold, and identify a potential allosteric site for inhibitor design. All such results reinforce each other to support the overall catalytic mechanism proposed herein.
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Affiliation(s)
- Hao Wang
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Drug Discovery Center for Infectious
Disease, Nankai University, 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
| | - Shuai He
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Drug Discovery Center for Infectious
Disease, Nankai University, 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
| | - Weilong Deng
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Drug Discovery Center for Infectious
Disease, Nankai University, 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
| | - Ying Zhang
- Laboratory of Structural Biological
& Ministry of Education and Laboratory of Protein Science, School
of Medicine and Life Sciences, Tsinghua
University, Beijing 100084,
People’s Republic of China
| | - Guobang Li
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Drug Discovery Center for Infectious
Disease, Nankai University, 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
| | - Jixue Sun
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
| | - Wei Zhao
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Drug Discovery Center for Infectious
Disease, Nankai University, 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
| | - Yu Guo
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Drug Discovery Center for Infectious
Disease, Nankai University, 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
| | - Zheng Yin
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Drug Discovery Center for Infectious
Disease, Nankai University, 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Center of Basic Molecular Science,
Department of Chemistry, Tsinghua
University, Beijing 100084,
People’s Republic of China
| | - Dongmei Li
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
| | - Luqing Shang
- State Key Laboratory of Medicinal
Chemical Biology, College of Pharmacy and KLMDASR of Tianjin,
Nankai University, No. 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
- Drug Discovery Center for Infectious
Disease, Nankai University, 38 Tongyan
Road, Haihe Education Park, Tianjin 300350, People’s
Republic of China
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20
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Wang L, Hu W, Fan C. Structural and biochemical characterization of SADS-CoV papain-like protease 2. Protein Sci 2020; 29:1228-1241. [PMID: 32216114 PMCID: PMC7184779 DOI: 10.1002/pro.3857] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 01/12/2023]
Abstract
Swine acute diarrhea syndrome coronavirus (SADS‐CoV) is a novel coronavirus that is involved in severe diarrhea disease in piglets, causing considerable agricultural and economic loss in China. The emergence of this new coronavirus increases the importance of understanding SADS‐CoV as well as antivirals. Coronaviral proteases, including main proteases and papain‐like proteases (PLP), are attractive antiviral targets because of their essential roles in polyprotein processing and thus viral maturation. Here, we describe the biochemical and structural identification of recombinant SADS papain‐like protease 2 (PLP2) domain of nsp3. The SADS‐CoV PLP2 was shown to cleave nsp1 proteins and also peptides mimicking the nsp2|nsp3 cleavage site and also had deubiquitinating and deISGynating activity by in vitro assays. The crystal structure adopts an architecture resembling that of PLPs from other coronaviruses. We characterize both conserved and unique structural features likely directing the interaction of PLP2 with the substrates, including the tentative mapping of active site and other essential residues. These results provide a foundation for understanding the molecular basis of coronaviral PLPs' catalytic mechanism and for the screening and design of therapeutics to combat infection by SADS coronavirus. PDB Code(s): http://firstglance.jmol.org/fg.htm?mol=6L5T;
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Affiliation(s)
- Lu Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesWuhan UniversityWuhanChina
| | - Weihua Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesWuhan UniversityWuhanChina
| | - Chengpeng Fan
- Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesWuhan UniversityWuhanChina
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21
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Wang Y, Sun A, Sun Y, Zhang S, Xia T, Guo T, Hao Z, Sun L, Jiang Y, Qiao X, Cui W, Tang L, Xu Y, Li Y, Wang L. Porcine transmissible gastroenteritis virus inhibits NF-κB activity via nonstructural protein 3 to evade host immune system. Virol J 2019; 16:97. [PMID: 31382996 PMCID: PMC6683377 DOI: 10.1186/s12985-019-1206-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
Background Transmissible gastroenteritis virus (TGEV), a member of the family Coronaviridae, causes lethal watery diarrhea in piglets. Previous studies have revealed that the coronaviruses develop various strategies to evade the host innate immunity through the inhibition of nuclear factor kappa B (NF-κB) signaling pathway. However, the ability of TGEV to inhibit the host innate immune response by modulating the NF-κB signaling pathway is not clear. Methods In this study, a dual luciferase reporter assay was used to confirm the inhibition of NF-κB by TGEV infection and to identify the major viral proteins involved in the inhibition of NF-κB signaling. Real-time quantitative PCR was used to quantify the mRNA expression of inflammatory factors. The deubiquitination of Nsp3 domains and its effect on IκBα and p65 were analyzed by western blotting. The ubiquitination level of IκBα was analyzed by immunoprecipitation. Results In ST and IPEC-J2 cells, TGEV exhibited a dose-dependent inhibition of NF-κB activity. Individual TGEV protein screening revealed the high potential of non-structural protein 3 (Nsp3) to inhibit NF-κB signaling, and leading to the downregulation of the NF-κB-induced cytokine production. We demonstrated that the inhibitory effect of Nsp3 was mainly mediated through the suppression of IκBα degradation as well as the inhibition of p65 phosphorylation and nuclear translocation. Furthermore, the amino acid residues at positions 590–1,215 in Nsp3 were demonstrated to inhibit the degradation of IκBα by inhibiting the IκBα ubiquitination. Conclusion TGEV infection can inhibit the activation of the NF-κB signaling pathway, which is mainly mediated by Nsp3 through the canonical pathway. The amino acid residues at positions 590–1,215 in Nsp3 compose the critical domain that mediates NF-κB inhibition. We speculate that this inhibitory effect is likely to be related to the structure of PLP2 with deubiquitinating enzyme activity of the amino acid residues at positions 590–1,215 in Nsp3. Our study provides a better understanding of the TGEV-mediated innate immune modulation and lays the basis for studies on the pathogenesis of coronavirus.
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Affiliation(s)
- Yanan Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Aoying Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Yu Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Sijia Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Tian Xia
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Tiantian Guo
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Zhenye Hao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Li Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yanping Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Xinyuan Qiao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Wen Cui
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Lijie Tang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Yigang Xu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China
| | - Yijing Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China. .,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China.
| | - Li Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China. .,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, Heilongjiang, China.
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22
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Yuan P, Yang Z, Song H, Wang K, Yang Y, Xie L, Huang S, Liu J, Ran L, Song Z. Three Main Inducers of Alphacoronavirus Infection of Enterocytes: Sialic Acid, Proteases, and Low pH. Intervirology 2018; 61:53-63. [PMID: 30176660 PMCID: PMC7179561 DOI: 10.1159/000492424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 07/19/2018] [Indexed: 12/19/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) are similar coronaviruses, causing diseases characterized by vomiting, diarrhea, and death from severe dehydration in piglets. Thus, they have caused huge losses to the swine-breeding industry worldwide. Nowadays, they are easily transmitted among the continents via vehicles, equipment, and cargo. Both viruses establish an infection in porcine enterocytes in the small intestine, and their spike (S) proteins play a key role in the virus-cell binding process under unfavorable conditions when the intestine with a low pH is filled with a thick layer of mucus and proteases. Sialic acid, proteases, and low pH are three main inducers of coronavirus infection. However, the details of how sialic acid and low pH affect virus binding to the host cell are not determined, and the functions of the proteases are unknown. This review emphasizes the role of three factors in the invasion of TGEV and PEDV into porcine enterocytes and offers more insights into Alphacoronavirus infection in the intestinal environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhenhui Song
- *Zhenhui Song, PhD, Department of Veterinary Medicine, College of Animal Science, Southwest University, Chongqing 402460 (People's Republic of China), E-Mail
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23
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Chu HF, Chen CC, Moses DC, Chen YH, Lin CH, Tsai YC, Chou CY. Porcine epidemic diarrhea virus papain-like protease 2 can be noncompetitively inhibited by 6-thioguanine. Antiviral Res 2018; 158:199-205. [PMID: 30138642 PMCID: PMC7113753 DOI: 10.1016/j.antiviral.2018.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/09/2018] [Accepted: 08/17/2018] [Indexed: 01/25/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) is a coronavirus (CoV) discovered in the 1970s that infects the intestinal tract of pigs, resulting in diarrhea and vomiting. It can cause extreme dehydration and death in neonatal piglets. In Asia, modified live attenuated vaccines have been used to control PEDV infection in recent years. However, a new strain of PEDV that belongs to genogroup 2a appeared in the USA in 2013 and then quickly spread to Canada and Mexico as well as Asian and European countries. Due to the less effective protective immunity provided by the vaccines against this new strain, it has caused considerable agricultural and economic loss worldwide. The emergence of this new strain increases the importance of understanding PEDV as well as strategies for inhibiting it. Coronaviral proteases, including main proteases and papain-like proteases, are ideal antiviral targets because of their essential roles in viral maturation. Here we provide a first description of the expression, purification and structural characteristics of recombinant PEDV papain-like protease 2, moreover present our finding that 6-thioguanine, a chemotherapeutic drug, in contrast to its competitive inhibition on SARS- and MERS-CoV papain-like proteases, is a noncompetitive inhibitor of PEDV papain-like protease 2. PEDV PL2pro exhibits much higher DUB activity than that of other PLpros in spite of their structural similarities. In contrast to its competitive inhibition on SARS- and MERS-CoV PLpros, 6-thioguanine inhibits PEDV PL2pro allosterically. Putative 6-thioguanine binding site is proposed to render the blocking loop less flexible and therefore disfavor catalysis. 6-thioguanine can be a lead compound for anti-coronaviral drug development.
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Affiliation(s)
- Hsu-Feng Chu
- Biomedical Industry Ph.D. Program, National Yang-Ming University, Taipei 112, Taiwan; Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chiao-Che Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - David C Moses
- Department of Chemistry, Tamkang University, Tamsui 251, Taiwan
| | - Yau-Hung Chen
- Department of Chemistry, Tamkang University, Tamsui 251, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Ying-Chieh Tsai
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan; Probiotic Research Center, National Yang-Ming University, Taipei 112, Taiwan
| | - Chi-Yuan Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan.
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24
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Brandão PE. Could human coronavirus OC43 have co-evolved with early humans? Genet Mol Biol 2018; 41:692-698. [PMID: 30004106 PMCID: PMC6136381 DOI: 10.1590/1678-4685-gmb-2017-0192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/05/2018] [Indexed: 12/24/2022] Open
Abstract
This paper reports on an investigation of the role of codon usage evolution on the suggested bovine-to-human spillover of Bovine coronavirus (BCoV), an enteric/respiratory virus of cattle, resulting in the emergence of the exclusively respiratory Human coronavirus OC43 (HCoV-OC43). Analyses based on full genomes of BCoV and HCoV-OC43 and on both human and bovine mRNAs sequences of cholecystokinin (CCK) and surfactant protein 1 A (SFTP1-A), representing the enteric and respiratory tract codon usage, respectively, have shown natural selection leading to optimization or deoptimization of viral codon usage to the human enteric and respiratory tracts depending on the virus genes under consideration. A higher correlation was found for the nucleotide distance at the 3rd nucleotide position of codons and codon usage optimization to the human respiratory tract when BCoV and HCoV-OC43 were compared. An MCC tree based on relative synonymous codon usage (RSCU) data integrating data from both viruses and hosts into a same analysis indicated three putative host/virus contact dates ranging from 1.54E8 to 2.44E5 years ago, suggesting that an ancestor coronavirus might have followed human evolution.
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Affiliation(s)
- Paulo Eduardo Brandão
- Departmento de Medicina Veterinaria Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
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25
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Bailey-Elkin BA, Knaap RCM, Kikkert M, Mark BL. Structure and Function of Viral Deubiquitinating Enzymes. J Mol Biol 2017; 429:3441-3470. [PMID: 28625850 PMCID: PMC7094624 DOI: 10.1016/j.jmb.2017.06.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 01/12/2023]
Abstract
Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes (DUBs), which remove ubiquitin from cellular targets and depolymerize polyubiquitin chains. The importance of protein ubiquitination to host immunity has been underscored by the discovery of viruses that encode proteases with deubiquitinating activity, many of which have been demonstrated to actively corrupt cellular ubiquitin-dependent processes to suppress innate antiviral responses and promote viral replication. DUBs have now been identified in diverse viral lineages, and their characterization is providing valuable insights into virus biology and the role of the ubiquitin system in host antiviral mechanisms. Here, we provide an overview of the structural biology of these fascinating viral enzymes and their role innate immune evasion and viral replication.
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Affiliation(s)
- Ben A Bailey-Elkin
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - Robert C M Knaap
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
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26
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Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein. Antiviral Res 2017; 149:58-74. [PMID: 29128390 PMCID: PMC7113668 DOI: 10.1016/j.antiviral.2017.11.001] [Citation(s) in RCA: 423] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/29/2017] [Accepted: 11/02/2017] [Indexed: 12/11/2022]
Abstract
The multi-domain non-structural protein 3 (Nsp3) is the largest protein encoded by the coronavirus (CoV) genome, with an average molecular mass of about 200 kD. Nsp3 is an essential component of the replication/transcription complex. It comprises various domains, the organization of which differs between CoV genera, due to duplication or absence of some domains. However, eight domains of Nsp3 exist in all known CoVs: the ubiquitin-like domain 1 (Ubl1), the Glu-rich acidic domain (also called “hypervariable region”), a macrodomain (also named “X domain”), the ubiquitin-like domain 2 (Ubl2), the papain-like protease 2 (PL2pro), the Nsp3 ectodomain (3Ecto, also called “zinc-finger domain”), as well as the domains Y1 and CoV-Y of unknown functions. In addition, the two transmembrane regions, TM1 and TM2, exist in all CoVs. The three-dimensional structures of domains in the N-terminal two thirds of Nsp3 have been investigated by X-ray crystallography and/or nuclear magnetic resonance (NMR) spectroscopy since the outbreaks of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) in 2003 as well as Middle-East Respiratory Syndrome coronavirus (MERS-CoV) in 2012. In this review, the structures and functions of these domains of Nsp3 are discussed in depth. Nonstructural protein 3 (∼200 kD) is a multifunctional protein comprising up to 16 different domains and regions. Nsp3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins, and participates in polyprotein processing. The papain-like protease of Nsp3 is an established target for new antivirals. Through its de-ADP-ribosylating, de-ubiquitinating, and de-ISGylating activities, Nsp3 counteracts host innate immunity. Structural data are available for the N-terminal two thirds of Nsp3, but domains in the remainder are poorly characterized.
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27
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Hu X, Tian J, Kang H, Guo D, Liu J, Liu D, Jiang Q, Li Z, Qu J, Qu L. Transmissible Gastroenteritis Virus Papain-Like Protease 1 Antagonizes Production of Interferon- β through Its Deubiquitinase Activity. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7089091. [PMID: 29201911 PMCID: PMC5672592 DOI: 10.1155/2017/7089091] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/14/2017] [Accepted: 08/24/2017] [Indexed: 01/12/2023]
Abstract
Coronaviruses (CoVs), such as human coronavirus NL63 (HCoV-NL63), severe acute respiratory syndrome CoV (SARS-CoV), murine hepatitis virus (MHV), porcine epidemic diarrhea virus (PEDV), and Middle East Respiratory Syndrome Coronavirus (MERS-CoV), encode papain-like (PL) proteases that inhibit Sendai virus- (SeV-) induced interferon (IFN-β) production. Recently, the crystal structure of transmissible gastroenteritis virus (TGEV) PL1 has been solved, which was similar to that of SARS-CoV PL2pro, which may antagonize host innate immunity. However, very little is known about whether TGEV PL1 can antagonize host innate immune response. Here, we presented evidence that TGEV PL1 encoded by the replicase gene could suppress the IFN-β expression and inhibit the nuclear translocation of interferon regulatory factor 3 (IRF3). The ability to antagonize IFN-β production was dependent on the intact catalytic activity of PL1. Furthermore, TGEV PL1 exerted deubiquitinase (DUB) activity which strongly inhibited the retinoic acid-induced gene I- (RIG-1-) and stimulator of interferon gene- (STING-) dependent IFN expression. Our data collectively suggest that TGEV PL1 can inhibit the IFN-β expression and interfere with RIG-1- and STING-mediated signaling through a viral DUB activity. Our study has yielded strong evidence for the TGEV PL1 mechanisms that counteract the host innate immunity.
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Affiliation(s)
- Xiaoliang Hu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Jin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Hongtao Kang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Dongchun Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Jiasen Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Dafei Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Qian Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Zhijie Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Juanjuan Qu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Liandong Qu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
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28
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Neuman BW. Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles. Antiviral Res 2016; 135:97-107. [PMID: 27743916 PMCID: PMC7113682 DOI: 10.1016/j.antiviral.2016.10.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/23/2016] [Accepted: 10/12/2016] [Indexed: 12/13/2022]
Abstract
Replication of eukaryotic positive-stranded RNA viruses is usually linked to the presence of membrane-associated replicative organelles. The purpose of this review is to discuss the function of proteins responsible for formation of the coronavirus replicative organelle. This will be done by identifying domains that are conserved across the order Nidovirales, and by summarizing what is known about function and structure at the level of protein domains. Bioinformatics reveals a new domain-level map of coronavirus nsp3-nsp6. Domain-level protein variability is a tool for functional annotation. Ten nsp3 domains are conserved in all known coronaviruses. Review of the role of the nsp5 main protease in RNA synthesis.
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Affiliation(s)
- Benjamin W Neuman
- University of Reading, School of Biological Sciences, RG6 6AH, United Kingdom; College of STEM, Texas A&M University-Texarkana, Texarkana, TX 75503, USA.
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29
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Virulence factors in porcine coronaviruses and vaccine design. Virus Res 2016; 226:142-151. [PMID: 27397100 PMCID: PMC5159199 DOI: 10.1016/j.virusres.2016.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 11/23/2022]
Abstract
Engineered live attenuated vaccines may improve the control porcine CoVs infection. Porcine CoVs affect many host-cell pathways modulating pathogenesis. CoV genes acting as virulence factors should be modified for virus attenuation. To use attenuated CoVs as vaccine candidates several safety guards should be included.
Porcine enteric coronaviruses (CoVs) cause severe disease in the porcine herds worldwide, leading to important economic losses. Despite the knowledge of these viruses since the 1970s, vaccination strategies have not been implemented, leading to continuous re-emergence of novel virulent strains. Live attenuated vaccines historically have been the most efficient. We consider that the new trend is the development of recombinant vaccines by using reverse genetics systems to engineer attenuated viruses, which could be used as effective and safe modified live vaccine candidates. To this end, host cell signaling pathways influencing porcine CoV virulence should be identified. Similarly, the identity of viral proteins involved in the modulation of host cell pathways influencing CoV pathogenesis should be analyzed. With this information, and using reverse genetics systems, it is possible to design viruses with modifications in the viral proteins acting as virulence factors, which may lead to attenuated viruses and, therefore, vaccine candidates. In addition, novel antiviral drugs may be developed once the host cell pathways and the molecular mechanism affecting porcine CoV replication and virulence are known. This review is focused in the host cell responses to enteric porcine CoV infection and the viral proteins involved in pathogenesis.
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30
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Lei J, Hilgenfeld R. Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin. Virol Sin 2016; 31:288-99. [PMID: 27245450 PMCID: PMC7090527 DOI: 10.1007/s12250-016-3742-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022] Open
Abstract
The papain-like protease (PL(pro)) of Middle-East respiratory syndrome coronavirus (MERS-CoV) has proteolytic, deubiquitinating, and deISGylating activities. The latter two are involved in the suppression of the antiviral innate immune response of the host cell. To contribute to an understanding of this process, we present here the X-ray crystal structure of a complex between MERS-CoV PL(pro) and human ubiquitin (Ub) that is devoid of any covalent linkage between the two proteins. Five regions of the PL(pro) bind to two areas of the Ub. The C-terminal five residues of Ub, RLRGG, are similar to the P5-P1 residues of the polyprotein substrates of the PL(pro) and are responsible for the major part of the interaction between the two macromolecules. Through sitedirected mutagenesis, we demonstrate that conserved Asp165 and non-conserved Asp164 are important for the catalytic activities of MERS-CoV PL(pro). The enzyme appears not to be optimized for catalytic efficiency; thus, replacement of Phe269 by Tyr leads to increased peptidolytic and deubiquitinating activities. Ubiquitin binding by MERS-CoV PL(pro) involves remarkable differences compared to the corresponding complex with SARS-CoV PL(pro). The structure and the mutational study help understand common and unique features of the deubiquitinating activity of MERS-CoV PL(pro).
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Affiliation(s)
- Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23562, Lübeck, Germany
- German Center for Infection Research (DZIF), University of Lübeck, 23562, Lübeck, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23562, Lübeck, Germany.
- German Center for Infection Research (DZIF), University of Lübeck, 23562, Lübeck, Germany.
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31
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Chen Y, Savinov SN, Mielech AM, Cao T, Baker SC, Mesecar AD. X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions. J Biol Chem 2015; 290:25293-306. [PMID: 26296883 PMCID: PMC4646180 DOI: 10.1074/jbc.m115.662130] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/06/2022] Open
Abstract
Murine hepatitis virus (MHV) has long served as a model system for the study of coronaviruses. Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus replication. Despite the numerous functional studies on MHV and its nsp3 domain, the structure of only one domain in nsp3, the small ubiquitin-like domain 1 (Ubl1), has been determined. We report here the x-ray structure of three tandemly linked domains of MHV nsp3, including the papain-like protease 2 (PLP2) catalytic domain, the ubiquitin-like domain 2 (Ubl2), and a third domain that we call the DPUP (domain preceding Ubl2 and PLP2) domain. DPUP has close structural similarity to the severe acute respiratory syndrome coronavirus unique domain C (SUD-C), suggesting that this domain may not be unique to the severe acute respiratory syndrome coronavirus. The PLP2 catalytic domain was found to have both deubiquitinating and deISGylating isopeptidase activities in addition to proteolytic activity. A computationally derived model of MHV PLP2 bound to ubiquitin was generated, and the potential interactions between ubiquitin and PLP2 were probed by site-directed mutagenesis. These studies extend substantially our structural knowledge of MHV nsp3, providing a platform for further investigation of the role of nsp3 domains in MHV viral replication.
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Affiliation(s)
| | | | - Anna M Mielech
- the Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois 60153
| | - Thu Cao
- From the Department of Biological Sciences
| | - Susan C Baker
- the Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois 60153
| | - Andrew D Mesecar
- From the Department of Biological Sciences, the Center for Cancer Research, and the Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 and
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32
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V'kovski P, Al-Mulla H, Thiel V, Neuman BW. New insights on the role of paired membrane structures in coronavirus replication. Virus Res 2014; 202:33-40. [PMID: 25550072 PMCID: PMC7114427 DOI: 10.1016/j.virusres.2014.12.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 12/22/2022]
Abstract
Coronavirus replication is tied to formation of double-membrane organelles (DMOs). DMO-making genes are conserved across the Nidovirales. Here, we interpret recent experiments on the role and importance of coronavirus DMOs.
The replication of coronaviruses, as in other positive-strand RNA viruses, is closely tied to the formation of membrane-bound replicative organelles inside infected cells. The proteins responsible for rearranging cellular membranes to form the organelles are conserved not just among the Coronaviridae family members, but across the order Nidovirales. Taken together, these observations suggest that the coronavirus replicative organelle plays an important role in viral replication, perhaps facilitating the production or protection of viral RNA. However, the exact nature of this role, and the specific contexts under which it is important have not been fully elucidated. Here, we collect and interpret the recent experimental evidence about the role and importance of membrane-bound organelles in coronavirus replication.
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Affiliation(s)
- Philip V'kovski
- Federal Institute of Virology and Immunology, Mittelhäusern, Bern, Switzerland; Graduate School for Biomedical Sciences, University of Bern, Switzerland
| | - Hawaa Al-Mulla
- School of Biological Sciences, University of Reading, Reading, Berkshire, United Kingdom; University of Baghdad, College of Science, Baghdad, Iraq
| | - Volker Thiel
- Federal Institute of Virology and Immunology, Mittelhäusern, Bern, Switzerland; Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Benjamin W Neuman
- School of Biological Sciences, University of Reading, Reading, Berkshire, United Kingdom.
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Bailey-Elkin BA, Knaap RCM, Johnson GG, Dalebout TJ, Ninaber DK, van Kasteren PB, Bredenbeek PJ, Snijder EJ, Kikkert M, Mark BL. Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression. J Biol Chem 2014; 289:34667-82. [PMID: 25320088 PMCID: PMC4263872 DOI: 10.1074/jbc.m114.609644] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human
pathogen that was first isolated in 2012. MERS-CoV replication depends in part
on a virus-encoded papain-like protease (PLpro) that cleaves the
viral replicase polyproteins at three sites releasing non-structural protein 1
(nsp1), nsp2, and nsp3. In addition to this replicative function, MERS-CoV
PLpro was recently shown to be a deubiquitinating enzyme (DUB)
and to possess deISGylating activity, as previously reported for other
coronaviral PLpro domains, including that of severe acute respiratory
syndrome coronavirus. These activities have been suggested to suppress host
antiviral responses during infection. To understand the molecular basis for
ubiquitin (Ub) recognition and deconjugation by MERS-CoV PLpro, we
determined its crystal structure in complex with Ub. Guided by this structure,
mutations were introduced into PLpro to specifically disrupt Ub
binding without affecting viral polyprotein cleavage, as determined using an in
trans nsp3↓4 cleavage assay. Having developed a
strategy to selectively disable PLpro DUB activity, we were able to
specifically examine the effects of this activity on the innate immune response.
Whereas the wild-type PLpro domain was found to suppress
IFN-β promoter activation, PLpro variants specifically
lacking DUB activity were no longer able to do so. These findings directly
implicate the DUB function of PLpro, and not its proteolytic activity
per se, in the inhibition of IFN-β promoter
activity. The ability to decouple the DUB activity of PLpro from its
role in viral polyprotein processing now provides an approach to further dissect
the role(s) of PLpro as a viral DUB during MERS-CoV infection.
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Affiliation(s)
- Ben A Bailey-Elkin
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - Robert C M Knaap
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Garrett G Johnson
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - Tim J Dalebout
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dennis K Ninaber
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Puck B van Kasteren
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Peter J Bredenbeek
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Eric J Snijder
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marjolein Kikkert
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian L Mark
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
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Han M, Yoo D. Modulation of innate immune signaling by nonstructural protein 1 (nsp1) in the family Arteriviridae. Virus Res 2014; 194:100-9. [PMID: 25262851 PMCID: PMC7114407 DOI: 10.1016/j.virusres.2014.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/16/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Abstract
Arteriviruses infect immune cells and may cause persistence in infected hosts. Inefficient induction of pro-inflammatory cytokines and type I IFNs are observed during infection of this group of viruses, suggesting that they may have evolved to escape the host immune surveillance for efficient survival. Recent studies have identified viral proteins regulating the innate immune signaling, and among these, nsp1 (nonstructural protein 1) is the most potent IFN antagonist. For porcine reproductive and respiratory syndrome virus (PRRSV), individual subunits (nsp1α and nsp1β) of nsp1 suppress type I IFN production. In particular, PRRSV-nsp1α degrades CREB (cyclic AMP responsive element binding)-binding protein (CBP), a key component of the IFN enhanceosome, whereas PRRSV-nsp1β degrades karyopherin-α1 which is known to mediate the nuclear import of ISGF3 (interferon-stimulated gene factor 3). All individual subunits of nsp1 of PRRSV, equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), and simian hemorrhagic fever virus (SHFV) appear to contain IFN suppressive activities. As with PRRSV-nsp1α, CBP degradation is evident by LDV-nsp1α and partly by SHFV-nsp1γ. This review summarizes the biogenesis and the role of individual subunits of nsp1 of arteriviruses for innate immune modulation.
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Affiliation(s)
- Mingyuan Han
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Dongwan Yoo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA.
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Lei J, Mesters JR, Drosten C, Anemüller S, Ma Q, Hilgenfeld R. Crystal structure of the papain-like protease of MERS coronavirus reveals unusual, potentially druggable active-site features. Antiviral Res 2014; 109:72-82. [PMID: 24992731 PMCID: PMC7113875 DOI: 10.1016/j.antiviral.2014.06.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/14/2014] [Accepted: 06/18/2014] [Indexed: 01/17/2023]
Abstract
The 3D structure of the MERS-CoV papain-like protease (PLpro) has been determined. The enzyme has a deficient oxyanion hole and unique S3 as well as S5 subsites. In-vitro kinetics of the MERS-CoV PLpro are slower than for the SARS-CoV enzyme. Restoring the oxyanion hole through mutagenesis enhances the enzyme kinetics. The unique features of the enzyme will allow design of MERS-specific antivirals.
The Middle-East Respiratory Syndrome coronavirus (MERS-CoV) causes severe acute pneumonia and renal failure. The MERS-CoV papain-like protease (PLpro) is a potential target for the development of antiviral drugs. To facilitate these efforts, we determined the three-dimensional structure of the enzyme by X-ray crystallography. The molecule consists of a ubiquitin-like domain and a catalytic core domain. The catalytic domain displays an extended right-hand fold with a zinc ribbon and embraces a solvent-exposed substrate-binding region. The overall structure of the MERS-CoV PLpro is similar to that of the corresponding SARS-CoV enzyme, but the architecture of the oxyanion hole and of the S3 as well as the S5 specificity sites differ from the latter. These differences are the likely reason for reduced in vitro peptide hydrolysis and deubiquitinating activities of the MERS-CoV PLpro, compared to the homologous enzyme from the SARS coronavirus. Introduction of a side-chain capable of oxyanion stabilization through the Leu106Trp mutation greatly enhances the in vitro catalytic activity of the MERS-CoV PLpro. The unique features observed in the crystal structure of the MERS-CoV PLpro should allow the design of antivirals that would not interfere with host ubiquitin-specific proteases.
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Affiliation(s)
- Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center for Infection Research (DZIF), Germany
| | - Jeroen R Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center for Infection Research (DZIF), Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical School, 53127 Bonn, Germany; German Center for Infection Research (DZIF), Germany
| | - Stefan Anemüller
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center for Infection Research (DZIF), Germany
| | - Qingjun Ma
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center for Infection Research (DZIF), Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center for Infection Research (DZIF), Germany.
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Lin MH, Chuang SJ, Chen CC, Cheng SC, Cheng KW, Lin CH, Sun CY, Chou CY. Structural and functional characterization of MERS coronavirus papain-like protease. J Biomed Sci 2014; 21:54. [PMID: 24898546 PMCID: PMC4051379 DOI: 10.1186/1423-0127-21-54] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/19/2014] [Indexed: 12/11/2022] Open
Abstract
Backgrounds A new highly pathogenic human coronavirus (CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), has emerged in Jeddah and Saudi Arabia and quickly spread to some European countries since September 2012. Until 15 May 2014, it has infected at least 572 people with a fatality rate of about 30% globally. Studies to understand the virus and to develop antiviral drugs or therapy are necessary and urgent. In the present study, MERS-CoV papain-like protease (PLpro) is expressed, and its structural and functional consequences are elucidated. Results Circular dichroism and Tyr/Trp fluorescence analyses indicated that the secondary and tertiary structure of MERS-CoV PLpro is well organized and folded. Analytical ultracentrifugation analyses demonstrated that MERS-CoV PLpro is a monomer in solution. The steady-state kinetic and deubiquitination activity assays indicated that MERS-CoV PLpro exhibits potent deubiquitination activity but lower proteolytic activity, compared with SARS-CoV PLpro. A natural mutation, Leu105, is the major reason for this difference. Conclusions Overall, MERS-CoV PLpro bound by an endogenous metal ion shows a folded structure and potent proteolytic and deubiquitination activity. These findings provide important insights into the structural and functional properties of coronaviral PLpro family, which is applicable to develop strategies inhibiting PLpro against highly pathogenic coronaviruses.
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Affiliation(s)
| | | | | | | | | | | | - Chiao-Yin Sun
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan.
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Bailey-Elkin BA, van Kasteren PB, Snijder EJ, Kikkert M, Mark BL. Viral OTU deubiquitinases: a structural and functional comparison. PLoS Pathog 2014; 10:e1003894. [PMID: 24676359 PMCID: PMC3968130 DOI: 10.1371/journal.ppat.1003894] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent studies have revealed that proteases encoded by three very diverse RNA virus groups share structural similarity with enzymes of the Ovarian Tumor (OTU) superfamily of deubiquitinases (DUBs). The publication of the latest of these reports in quick succession prevented proper recognition and discussion of the shared features of these viral enzymes. Here we provide a brief structural and functional comparison of these virus-encoded OTU DUBs. Interestingly, although their shared structural features and substrate specificity tentatively place them within the same protease superfamily, they also show interesting differences that trigger speculation as to their origins.
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Affiliation(s)
| | - Puck B. van Kasteren
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
- * E-mail: (MK); (BLM)
| | - Brian L. Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
- * E-mail: (MK); (BLM)
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38
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Mielech AM, Chen Y, Mesecar AD, Baker SC. Nidovirus papain-like proteases: multifunctional enzymes with protease, deubiquitinating and deISGylating activities. Virus Res 2014; 194:184-90. [PMID: 24512893 PMCID: PMC4125544 DOI: 10.1016/j.virusres.2014.01.025] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/23/2014] [Accepted: 01/29/2014] [Indexed: 12/14/2022]
Abstract
Coronaviruses and arteriviruses encode papain-like protease domains that process the replicase polyprotein and are required for viral replication. Many viral papain-like proteases are multifunctional and have protease, deubiquitinating and deISGylating activity. Structural and enzymatic studies revealed the multifunctional nature of coronavirus and arterivirus papain-like proteases. Viral DUB and deISGylating activity is proposed to modulate the innate immune response. An arterivirus papain-like protease has been shown to modulate the innate immune response to viral infection.
Coronaviruses and arteriviruses, members of the order Nidovirales, are positive strand RNA viruses that encode large replicase polyproteins that are processed by viral proteases to generate the nonstructural proteins which mediate viral RNA synthesis. The viral papain-like proteases (PLPs) are critical for processing the amino-terminal end of the replicase and are attractive targets for antiviral therapies. With the analysis of the papain-like protease of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), came the realization of the multifunctional nature of these enzymes. Structural and enzymatic studies revealed that SARS-CoV PLpro can act as both a protease to cleave peptide bonds and also as a deubiquitinating (DUB) enzyme to cleave the isopeptide bonds found in polyubiquitin chains. Furthermore, viral DUBs can also remove the protective effect of conjugated ubiquitin-like molecules such as interferon stimulated gene 15 (ISG15). Extension of these studies to other coronaviruses and arteriviruses led to the realization that viral protease/DUB activity is conserved in many family members. Overexpression studies revealed that viral protease/DUB activity can modulate or block activation of the innate immune response pathway. Importantly, mutations that alter DUB activity but not viral protease activity have been identified and arteriviruses expressing DUB mutants stimulated higher levels of acute inflammatory cytokines after infection. Further understanding of the multifunctional nature of the Nidovirus PLP/DUBs may facilitate vaccine development. Here, we review studies describing the PLPs’ enzymatic activity and their role in virus pathogenesis.
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Affiliation(s)
- Anna M Mielech
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL 60153, United States
| | - Yafang Chen
- Department of Biological Sciences, Purdue University, Hockmeyer Hall of Structural Biology, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, United States
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, Hockmeyer Hall of Structural Biology, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, United States
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL 60153, United States.
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Neuman BW, Chamberlain P, Bowden F, Joseph J. Atlas of coronavirus replicase structure. Virus Res 2013; 194:49-66. [PMID: 24355834 PMCID: PMC7114488 DOI: 10.1016/j.virusres.2013.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022]
Abstract
Complete and up to date coverage of replicase protein structures for SARS-CoV. Discusses SARS-CoV structure in the context of other coronavirus structures. Summarizes data from a variety of structural methods to illuminate protein function. Uses models and predictions to fill gaps in the SARS-CoV structure. Discusses the high percentage of novel protein folds among SARS-CoV proteins.
The international response to SARS-CoV has produced an outstanding number of protein structures in a very short time. This review summarizes the findings of functional and structural studies including those derived from cryoelectron microscopy, small angle X-ray scattering, NMR spectroscopy, and X-ray crystallography, and incorporates bioinformatics predictions where no structural data is available. Structures that shed light on the function and biological roles of the proteins in viral replication and pathogenesis are highlighted. The high percentage of novel protein folds identified among SARS-CoV proteins is discussed.
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Affiliation(s)
| | | | - Fern Bowden
- School of Biological Sciences, University of Reading, Reading, UK
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Wu WM, Wu HC, Xu QQ, Nie J. Predictive significance of serum levels of gastrointestinal hormones and cytokines for disease progression in patients with rotavirus diarrhea. Shijie Huaren Xiaohua Zazhi 2013; 21:3296-3300. [DOI: 10.11569/wcjd.v21.i30.3296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To assess the early predictive value of serum levels of gastrointestinal hormones and cytokines in patients with rotavirus diarrhea.
METHODS: Serum levels of 5-serotonin, vasoactive intestinal peptide (VIP), gastrin (GAS), motilin (MOT) and cytokines (endothelin, IL-10) were determined by enzyme-linked immunosorbent assay (ELISA) in 65 children with severe, moderate or mild rotavirus infection during acute or convalescent phase and 60 normal healthy children.
RESULTS: Serum levels of 5-serotonin, VIP, GAS, MOT, and endothelin were significantly higher and that of IL-10 was significantly lower in children with rotavirus infection during the acute phase than in normal control controls (all P < 0.05). Serum levels of 5-HT, VIP, MOT, and endothelin were significantly higher in patients with severe rotavirus infection than in those with moderate or mild rotavirus infection (all P < 0.05). Serum levels of GAS and IL-10 showed no significant difference between patients with moderate rotavirus infection and those with mild disease (P > 0.05). Serum levels of 5-serotonin, VIP, endothelin and IL-10 were significantly higher in patients with acute phase rotavirus infection having diarrhea >3 d than in those having diarrhea <3 d (all P < 0.05), while GAS and MOT levels were not statistically significant between the two groups (both P > 0.05).
CONCLUSION: Pathophysiological changes in rotavirus diarrhea may be associated with the changes in serum levels of gastrointestinal hormones and cytokines. The relevant gastrointestinal hormones and cytokines may be used to predict rotavirus disease progression.
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Hilgenfeld R, Peiris M. From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses. Antiviral Res 2013; 100:286-95. [PMID: 24012996 PMCID: PMC7113673 DOI: 10.1016/j.antiviral.2013.08.015] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 08/18/2013] [Indexed: 12/13/2022]
Abstract
We review the outbreak of severe acute respiratory syndrome (SARS) in 2002–2003 and antiviral treatment of patients. We review efforts towards the rational design of anti-SARS therapeutics. We present a comprehensive list of all available 3-dimensional structures of coronavirus proteins. We discuss the emerging MERS coronavirus and review the few antivirals available for treatment. We critically discuss which lessons have been learned from SARS and which are yet to be learned.
This article introduces a series of invited papers in Antiviral Research marking the 10th anniversary of the outbreak of severe acute respiratory syndrome (SARS), caused by a novel coronavirus that emerged in southern China in late 2002. Until that time, coronaviruses had not been recognized as agents causing severe disease in humans, hence, the emergence of the SARS-CoV came as a complete surprise. Research during the past ten years has revealed the existence of a diverse pool of coronaviruses circulating among various bat species and other animals, suggesting that further introductions of highly pathogenic coronaviruses into the human population are not merely probable, but inevitable. The recent emergence of another coronavirus causing severe disease, Middle East respiratory syndrome (MERS), in humans, has made it clear that coronaviruses pose a major threat to human health, and that more research is urgently needed to elucidate their replication mechanisms, identify potential drug targets, and develop effective countermeasures. In this series, experts in many different aspects of coronavirus replication and disease will provide authoritative, up-to-date reviews of the following topics: – clinical management and infection control of SARS; – reservoir hosts of coronaviruses; – receptor recognition and cross-species transmission of SARS-CoV; – SARS-CoV evasion of innate immune responses; – structures and functions of individual coronaviral proteins; – anti-coronavirus drug discovery and development; and – the public health legacy of the SARS outbreak. Each article will be identified in the last line of its abstract as belonging to the series “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”
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Affiliation(s)
- Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center for Infection Research (DZIF), University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.
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Lombardi C, Ayach M, Beaurepaire L, Chenon M, Andreani J, Guerois R, Jupin I, Bressanelli S. A compact viral processing proteinase/ubiquitin hydrolase from the OTU family. PLoS Pathog 2013; 9:e1003560. [PMID: 23966860 PMCID: PMC3744425 DOI: 10.1371/journal.ppat.1003560] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 07/02/2013] [Indexed: 01/06/2023] Open
Abstract
Turnip yellow mosaic virus (TYMV) - a member of the alphavirus-like supergroup of viruses - serves as a model system for positive-stranded RNA virus membrane-bound replication. TYMV encodes a precursor replication polyprotein that is processed by the endoproteolytic activity of its internal cysteine proteinase domain (PRO). We recently reported that PRO is actually a multifunctional enzyme with a specific ubiquitin hydrolase (DUB) activity that contributes to viral infectivity. Here, we report the crystal structure of the 150-residue PRO. Strikingly, PRO displays no homology to other processing proteinases from positive-stranded RNA viruses, including that of alphaviruses. Instead, the closest structural homologs of PRO are DUBs from the Ovarian tumor (OTU) family. In the crystal, one molecule's C-terminus inserts into the catalytic cleft of the next, providing a view of the N-terminal product complex in replication polyprotein processing. This allows us to locate the specificity determinants of PRO for its proteinase substrates. In addition to the catalytic cleft, at the exit of which the active site is unusually pared down and solvent-exposed, a key element in molecular recognition by PRO is a lobe N-terminal to the catalytic domain. Docking models and the activities of PRO and PRO mutants in a deubiquitylating assay suggest that this N-terminal lobe is also likely involved in PRO's DUB function. Our data thus establish that DUBs can evolve to specifically hydrolyze both iso- and endopeptide bonds with different sequences. This is achieved by the use of multiple specificity determinants, as recognition of substrate patches distant from the cleavage sites allows a relaxed specificity of PRO at the sites themselves. Our results thus shed light on how such a compact protein achieves a diversity of key functions in viral genome replication and host-pathogen interaction. Positive-stranded RNA viruses are ultimate parasites. In order to replicate their genome, they first need to invade a host cell and, with usually very limited viral genetic material, subvert the host's molecular machinery. Turnip yellow mosaic virus (TYMV) is an excellent model system for studying positive-stranded RNA virus replication. As for many such viruses, TYMV genome replication is dependent on the activity of a viral proteinase (PRO) to properly process the virus' replication molecules. We have recently established that PRO is a multifunctional enzyme and is also used by TYMV to subvert a key host defense against pathogens. We report here the atomic structure of PRO as well as new functional data on PRO's interaction with the host. Our data shed light on how PRO can perform such multiple activities despite its small size, providing TYMV with a Swiss army knife in its ongoing fight with a vastly more complex host.
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Affiliation(s)
- Charlotte Lombardi
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Maya Ayach
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Lionel Beaurepaire
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
| | - Mélanie Chenon
- Laboratoire de Virologie Moléculaire, CNRS - Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592, Paris, France
| | - Jessica Andreani
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
| | - Raphaël Guerois
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes (SB2SM), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Gif sur Yvette, France
| | - Isabelle Jupin
- Laboratoire de Virologie Moléculaire, CNRS - Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592, Paris, France
- * E-mail: (IJ); (SB)
| | - Stéphane Bressanelli
- The Laboratoire de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France
- * E-mail: (IJ); (SB)
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Identification of cellular proteome using two-dimensional difference gel electrophoresis in ST cells infected with transmissible gastroenteritis coronavirus. Proteome Sci 2013; 11:31. [PMID: 23855489 PMCID: PMC3734006 DOI: 10.1186/1477-5956-11-31] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 06/23/2013] [Indexed: 01/05/2023] Open
Abstract
Background Transmissible gastroenteritis coronavirus (TGEV) is an enteropathogenic coronavirus that causes diarrhea in pigs, which is correlated with high morbidity and mortality in suckling piglets. Information remains limited about the comparative protein expression of host cells in response to TGEV infection. In this study, cellular protein response to TGEV infection in swine testes (ST) cells was analyzed, using the proteomic method of two-dimensional difference gel electrophoresis (2D DIGE) coupled with MALDI-TOF-TOF/MS identification. Results 33 differentially expressed protein spots, of which 23 were up-regulated and 10 were down-regulated were identified. All the protein spots were successfully identified. The identified proteins were involved in the regulation of essential processes such as cellular structure and integrity, RNA processing, protein biosynthesis and modification, vesicle transport, signal transduction, and the mitochondrial pathway. Western blot analysis was used to validate the changes of alpha tubulin, keratin 19, and prohibitin during TGEV infection. Conclusions To our knowledge, we have performed the first analysis of the proteomic changes in host cell during TGEV infection. 17 altered cellular proteins that differentially expressed in TGEV infection were identified. The present study provides protein-related information that should be useful for understanding the host cell response to TGEV infection and the underlying mechanism of TGEV replication and pathogenicity.
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Xing Y, Chen J, Tu J, Zhang B, Chen X, Shi H, Baker SC, Feng L, Chen Z. The papain-like protease of porcine epidemic diarrhea virus negatively regulates type I interferon pathway by acting as a viral deubiquitinase. J Gen Virol 2013; 94:1554-1567. [PMID: 23596270 DOI: 10.1099/vir.0.051169-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is the cause of an economically important swine disease. Previous studies suggested that PEDV does not elicit a robust IFN response, but the mechanism(s) used to evade or block this innate immune response was not known. In this study, we found that PEDV infection blocked synthetic dsRNA-induced IFN-β production by interfering with the activation of interferon regulatory factor 3 (IRF3). We identified PEDV replicase encoded papain-like protease 2 (PLP2) as an IFN antagonist that depends on catalytic activity for its function. We show that levels of ubiquitinated proteins are reduced during PEDV infection and that PEDV PLP2 has deubiquitinase (DUB) activity that recognizes and processes both K-48 and K-63 linked polyubiquitin chains. Furthermore, we found that PEDV PLP2 strongly inhibits RIG-I- and STING-activated IFN expression and that PEDV PLP2 can be co-immunoprecipitated with and deubiquitinates RIG-I and STING, the key components of the signalling pathway for IFN expression. These results show that PEDV infection suppresses production of IFN-β and provides evidence indicating that the PEDV papain-like protease 2 acts as a viral DUB to interfere with the RIG-I- and STING-mediated signalling pathway.
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Affiliation(s)
- Yaling Xing
- Beijing Institute of Radiation Medicine, Beijing 100850, China
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Harbin 150001, China
| | - Jianfei Chen
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Harbin 150001, China
| | - Jian Tu
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Bailing Zhang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaojuan Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hongyan Shi
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Harbin 150001, China
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University of Chicago Stritch School of Medicine, Maywood, Illinois, USA
| | - Li Feng
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Harbin 150001, China
| | - Zhongbin Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, China
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Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells. Proc Natl Acad Sci U S A 2013; 110:E838-47. [PMID: 23401522 DOI: 10.1073/pnas.1218464110] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Protein ubiquitination regulates important innate immune responses. The discovery of viruses encoding deubiquitinating enzymes (DUBs) suggests they remove ubiquitin to evade ubiquitin-dependent antiviral responses; however, this has never been conclusively demonstrated in virus-infected cells. Arteriviruses are economically important positive-stranded RNA viruses that encode an ovarian tumor (OTU) domain DUB known as papain-like protease 2 (PLP2). This enzyme is essential for arterivirus replication by cleaving a site within the viral replicase polyproteins and also removes ubiquitin from cellular proteins. To dissect this dual specificity, which relies on a single catalytic site, we determined the crystal structure of equine arteritis virus PLP2 in complex with ubiquitin (1.45 Å). PLP2 binds ubiquitin using a zinc finger that is uniquely integrated into an exceptionally compact OTU-domain fold that represents a new subclass of zinc-dependent OTU DUBs. Notably, the ubiquitin-binding surface is distant from the catalytic site, which allowed us to mutate this surface to significantly reduce DUB activity without affecting polyprotein cleavage. Viruses harboring such mutations exhibited WT replication kinetics, confirming that PLP2-mediated polyprotein cleavage was intact, but the loss of DUB activity strikingly enhanced innate immune signaling. Compared with WT virus infection, IFN-β mRNA levels in equine cells infected with PLP2 mutants were increased by nearly an order of magnitude. Our findings not only establish PLP2 DUB activity as a critical factor in arteriviral innate immune evasion, but the selective inactivation of DUB activity also opens unique possibilities for developing improved live attenuated vaccines against arteriviruses and other viruses encoding similar dual-specificity proteases.
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Mao X, Ren XF. Functions of proteins of porcine epidemic diarrhea virus. Shijie Huaren Xiaohua Zazhi 2013; 21:44-53. [DOI: 10.11569/wcjd.v21.i1.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Porcine epidemic diarrhea (PED) is caused by porcine epidemic diarrhea virus (PEDV), which belongs to the order Nidovirales in the family Coronaviridae. Since PED was first discovered in Europe in 1987, it has become a severe infectious disease in Asian countries (including China, Korea, Japan, Philippines and Thailand) and has caused great economic losses in swine industry. Although bivalent vaccine for PEDV and transmissible gastroenteritis virus (TGEV, another porcine coronavirus) can decrease the incidence of both diseases, PED is still increasing annually in China. Unfortunately, there have been few studies on viral proteins and pathogenesis of PEDV. This review aims to provide some functional insights on PEDV viral proteins based on the available information from coronaviruse studies.
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Recent progress in studies of arterivirus- and coronavirus-host interactions. Viruses 2012; 4:980-1010. [PMID: 22816036 PMCID: PMC3397358 DOI: 10.3390/v4060980] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 05/30/2012] [Accepted: 06/14/2012] [Indexed: 12/15/2022] Open
Abstract
Animal coronaviruses, such as infectious bronchitis virus (IBV), and arteriviruses, such as porcine reproductive and respiratory syndrome virus (PRRSV), are able to manifest highly contagious infections in their specific native hosts, thereby arising in critical economic damage to animal industries. This review discusses recent progress in studies of virus-host interactions during animal and human coronavirus and arterivirus infections, with emphasis on IBV-host cell interactions. These interactions may be directly involved in viral replication or lead to the alteration of certain signaling pathways, such as cell stress response and innate immunity, to facilitate viral replication and pathogenesis.
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Smoum R, Rubinstein A, Dembitsky VM, Srebnik M. Boron containing compounds as protease inhibitors. Chem Rev 2012; 112:4156-220. [PMID: 22519511 DOI: 10.1021/cr608202m] [Citation(s) in RCA: 300] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Reem Smoum
- The School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel.
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Chou YW, Cheng SC, Lai HY, Chou CY. Differential domain structure stability of the severe acute respiratory syndrome coronavirus papain-like protease. Arch Biochem Biophys 2012; 520:74-80. [PMID: 22391227 PMCID: PMC7094420 DOI: 10.1016/j.abb.2012.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 02/21/2012] [Accepted: 02/22/2012] [Indexed: 12/13/2022]
Abstract
Papain-like protease (PLpro) from severe acute respiratory syndrome (SARS) coronavirus is one of the two proteases involved in the proteolytic processing of the virion polyproteins. In addition, PLpro shows significant in vitro deubiquitinating and de-ISGylating activities. All these findings demonstrated the multifunctional nature of the PLpro. Here we report the sensitivity of PLpro to denaturant urea. An increase in urea concentration induced a reversible biphasic unfolding of the enzyme. Differently, the unfolding of the catalytic triad region located within the palm and thumb domains followed a monophasic unfolding curve. Further observations suggest that the zinc-binding domain may start to unfold during the first transition. An 80% lost of its enzymatic activity at a urea concentration lower than 1 M showed a close correlation with unfolding of the zinc-binding domain. The enzyme was also characterized in terms of hydrophobicity and size-and-shape distribution. We have demonstrated that PLpro displayed differential domain structure stability and molten globule state in its folding. These studies will not only assist in our understanding of the folding of this viral enzyme, but also that of other deubiquitinating enzymes with a similar scaffold.
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Affiliation(s)
- Ya-Wen Chou
- Department of Life Sciences, National Yang-Ming University, Taipei, Taiwan
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Arterivirus and nairovirus ovarian tumor domain-containing Deubiquitinases target activated RIG-I to control innate immune signaling. J Virol 2011; 86:773-85. [PMID: 22072774 DOI: 10.1128/jvi.06277-11] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The innate immune response constitutes the first line of defense against viral infection and is extensively regulated through ubiquitination. The removal of ubiquitin from innate immunity signaling factors by deubiquitinating enzymes (DUBs) therefore provides a potential opportunity for viruses to evade this host defense system. It was previously found that specific proteases encoded by the unrelated arteri- and nairoviruses resemble the ovarian tumor domain-containing (OTU) family of DUBs. In arteriviruses, this domain has been characterized before as a papain-like protease (PLP2) that is also involved in replicase polyprotein processing. In nairoviruses, the DUB resides in the polymerase protein but is not essential for RNA replication. Using both in vitro and cell-based assays, we now show that PLP2 DUB activity is conserved in all members of the arterivirus family and that both arteri- and nairovirus DUBs inhibit RIG-I-mediated innate immune signaling when overexpressed. The potential relevance of RIG-I-like receptor (RLR) signaling for the innate immune response against arterivirus infection is supported by our finding that in mouse embryonic fibroblasts, the production of beta interferon primarily depends on the recognition of arterivirus RNA by the pattern-recognition receptor MDA5. Interestingly, we also found that both arteri- and nairovirus DUBs inhibit RIG-I ubiquitination upon overexpression, suggesting that both MDA5 and RIG-I have a role in countering infection by arteriviruses. Taken together, our results support the hypothesis that arteri- and nairoviruses employ their deubiquitinating potential to inactivate cellular proteins involved in RLR-mediated innate immune signaling, as exemplified by the deubiquitination of RIG-I.
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