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Zhao S, Li F, Li W, Wang M, Wang Y, Zhang Y, Xia P, Chen J. Mass Spectrometry-Based Proteomic Analysis of Potential Host Proteins Interacting with N in PRRSV-Infected PAMs. Int J Mol Sci 2024; 25:7219. [PMID: 39000325 PMCID: PMC11241482 DOI: 10.3390/ijms25137219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
One of the most significant diseases in the swine business, porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory problems in piglets and reproductive failure in sows. The PRRSV nucleocapsid (N) protein is essential for the virus' assembly, replication, and immune evasion. Stages in the viral replication cycle can be impacted by interactions between the PRRSV nucleocapsid protein and the host protein components. Therefore, it is of great significance to explore the interaction between the PRRSV nucleocapsid protein and the host. Nevertheless, no information has been published on the network of interactions between the nucleocapsid protein and the host proteins in primary porcine alveolar macrophages (PAMs). In this study, 349 host proteins interacting with nucleocapsid protein were screened in the PRRSV-infected PAMs through a liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics approach. Bioinformatics analysis, which included gene ontology annotation, Kyoto Encyclopedia of Genes and Genomes database enrichment, and a protein-protein interaction (PPI) network, revealed that the host proteins interacting with PRRSV-N may be involved in protein binding, DNA transcription, metabolism, and innate immune responses. This study confirmed the interaction between the nucleocapsid protein and the natural immune-related proteins. Ultimately, our findings suggest that the nucleocapsid protein plays a pivotal role in facilitating immune evasion during a PRRSV infection. This study contributes to enhancing our understanding of the role played by the nucleocapsid protein in viral pathogenesis and virus-host interaction, thereby offering novel insights for the prevention and control of PRRS as well as the development of vaccines.
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Affiliation(s)
- Shijie Zhao
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Fahao Li
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Wen Li
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Mengxiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Yueshuai Wang
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Yina Zhang
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Pingan Xia
- College of Veterinary Medicine, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China; (S.Z.); (F.L.); (W.L.); (M.W.); (Y.W.); (Y.Z.)
| | - Jing Chen
- College of Life Science, Henan Agricultural University, Longzi Lake 15#, Zhengzhou 450046, China
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Guo J, Li C, Lu H, Wang B, Zhang L, Ding J, Jiao X, Li Q, Zhu S, Wang A, Li Y. Reverse genetics construction and pathogenicity of a novel recombinant NADC30-like PRRSV isolated in China. Front Vet Sci 2024; 11:1434539. [PMID: 38993278 PMCID: PMC11237873 DOI: 10.3389/fvets.2024.1434539] [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: 05/18/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
China has the largest pig herd in the world which accounts for more than 50% of the global pig population. Over the past three decades, the porcine reproductive and respiratory syndrome virus (PRRSV) has caused significant economic loss to the Chinese swine industry. Currently, the prevalent PRRSV strains in the field are extremely complicated, and the NADC30-like strains, NADC34-like strains, and novel recombinant viruses have become a great concern to PRRS control in China. In this study, a novel NADC30-like PRRSV, named GS2022, was isolated from the lung of a dead pig collected from a farm that experienced a PRRS outbreak. The complete genome of GS2022 shares the highest identity with the NADC30 strain and contains a discontinuous deletion of 131 aa in nsp2. Novel deletion and insertion have been identified in ORF7 and 3'UTR. Recombination analysis revealed that the GS2022 is a potential recombinant of NADC30-like and JXA1-like strains. Both inter-lineage and intra-lineage recombination events were predicted to be involved in the generation of the GS2022. An infectious cDNA clone of GS2022 was assembled to generate the isogenic GS2022 (rGS2022). The growth kinetics of rGS2022 were almost identical to those of GS2022. The pathogenicity of the GS2022 and rGS2022 was evaluated using a nursery piglet model. In the infection groups, the piglets exhibited mild clinical symptoms, including short periods of fever and respiratory diseases. Both gross lesions and histopathological lesions were observed in the lungs and lymph nodes of the infected piglets. Therefore, we reported a novel recombinant NADC30-like PRRSV strain with moderate pathogenicity in piglets. These results provide new information on the genomic characteristics and pathogenicity of the NADC30-like PRRSV in China.
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Affiliation(s)
- Jinyao Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Chenxi Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Huipeng Lu
- Jiangsu Agri-animal Husbandry Vocational College, Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Taizhou, China
| | - Bin Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Linjie Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jingjing Ding
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xue Jiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qingyu Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shanyuan Zhu
- Jiangsu Agri-animal Husbandry Vocational College, Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Taizhou, China
| | - Anping Wang
- Jiangsu Agri-animal Husbandry Vocational College, Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Taizhou, China
| | - Yanhua Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
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3
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Liu J, Su G, Duan C, Sun Z, Xiao S, Zhou Y, Fang L. Porcine reproductive and respiratory syndrome virus infection activates ADAM17 to induce inflammatory responses. Vet Microbiol 2024; 292:110066. [PMID: 38555788 DOI: 10.1016/j.vetmic.2024.110066] [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: 01/23/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Porcine reproductive and respiratory syndrome (PRRS), which has posed substantial threats to the swine industry worldwide, is primarily characterized by interstitial pneumonia. A disintegrin and metalloproteinase 17 (ADAM17) is a multifunctional sheddase involved in various inflammatory diseases. Herein, our study showed that PRRS virus (PRRSV) infection elevated ADAM17 activity, as demonstrated in primary porcine alveolar macrophages (PAMs), an immortalized PAM cell line (IPAM cells), and the lung tissues of PRRSV-infected piglets. We found that PRRSV infection promoted ADAM17 translocation from the endoplasmic reticulum to the Golgi by enhancing its interaction with inactive rhomboid protein 2 (iRhom2), a newly identified ADAM17 regulator, which in turn elevated ADAM17 activity. By screening for PRRSV-encoded structural proteins, viral envelope (E) and nucleocapsid (N) proteins were identified as the predominant ADAM17 activators. E and N proteins bind with both ADAM17 and iRhom2 to form ternary protein complexes, ultimately strengthening their interactions. Additionally, we demonstrated, using an ADAM17-knockout cell line, that ADAM17 augmented the shedding of soluble TNF-α, a pivotal inflammatory mediator. We also discovered that ADAM17-mediated cleavage of porcine TNF-α occurred between Arg-78 and Ser-79. By constructing a precision mutant cell line with Arg-78-Glu/Ser-79-Glu substitution mutations in TNF-α, we further revealed that the ADAM17-mediated production of soluble TNF-α contributed to the induction of inflammatory responses by PRRSV and its E and N proteins. Taken together, our results elucidate the mechanism by which PRRSV infection activates the iRhom2/ADAM17/TNF-α axis to enhance inflammatory responses, providing valuable insights into the elucidation of PRRSV pathogenesis.
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Affiliation(s)
- Jiao Liu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Guanning Su
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Chenrui Duan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Zheng Sun
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yanrong Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
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4
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Su CM, Kim J, Tang J, Hung YF, Zuckermann FA, Husmann R, Roady P, Kim J, Lee YM, Yoo D. A clinically attenuated double-mutant of porcine reproductive and respiratory syndrome virus-2 that does not prompt overexpression of proinflammatory cytokines during co-infection with a secondary pathogen. PLoS Pathog 2024; 20:e1012128. [PMID: 38547254 PMCID: PMC11003694 DOI: 10.1371/journal.ppat.1012128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/09/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is known to suppress the type I interferon (IFNs-α/β) response during infection. PRRSV also activates the NF-κB signaling pathway, leading to the production of proinflammatory cytokines during infection. In swine farms, co-infections of PRRSV and other secondary bacterial pathogens are common and exacerbate the production of proinflammatory cytokines, contributing to the porcine respiratory disease complex (PRDC) which is clinically a severe disease. Previous studies identified the non-structural protein 1β (nsp1β) of PRRSV-2 as an IFN antagonist and the nucleocapsid (N) protein as the NF-κB activator. Further studies showed the leucine at position 126 (L126) of nsp1β as the essential residue for IFN suppression and the region spanning the nuclear localization signal (NLS) of N as the NF-κB activation domain. In the present study, we generated a double-mutant PRRSV-2 that contained the L126A mutation in the nsp1β gene and the NLS mutation (ΔNLS) in the N gene using reverse genetics. The immunological phenotype of this mutant PRRSV-2 was examined in porcine alveolar macrophages (PAMs) in vitro and in young pigs in vivo. In PAMs, the double-mutant virus did not suppress IFN-β expression but decreased the NF-κB-dependent inflammatory cytokine productions compared to those for wild-type PRRSV-2. Co-infection of PAMs with the mutant PRRSV-2 and Streptococcus suis (S. suis) also reduced the production of NF-κB-directed inflammatory cytokines. To further examine the cytokine profiles and the disease severity by the mutant virus in natural host animals, 6 groups of pigs, 7 animals per group, were used for co-infection with the mutant PRRSV-2 and S. suis. The double-mutant PRRSV-2 was clinically attenuated, and the expressions of proinflammatory cytokines and chemokines were significantly reduced in pigs after bacterial co-infection. Compared to the wild-type PRRSV-2 and S. suis co-infection control, pigs coinfected with the double-mutant PRRSV-2 exhibited milder clinical signs, lower titers and shorter duration of viremia, and lower expression of proinflammatory cytokines. In conclusion, our study demonstrates that genetic modification of the type I IFN suppression and NF-κB activation functions of PRRSV-2 may allow us to design a novel vaccine candidate to alleviate the clinical severity of PRRS-2 and PRDC during bacterial co-infection.
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Affiliation(s)
- Chia-Ming Su
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jineui Kim
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Junyu Tang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yu Fan Hung
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Federico A. Zuckermann
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Robert Husmann
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Patrick Roady
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jiyoun Kim
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Young-Min Lee
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Dongwan Yoo
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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5
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Huang SH, Chen SC, Wu TY, Chen CY, Yu CH. Programmable modulation of ribosomal frameshifting by mRNA targeting CRISPR-Cas12a system. iScience 2023; 26:108492. [PMID: 38125012 PMCID: PMC10730746 DOI: 10.1016/j.isci.2023.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/13/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Minus 1 programmed ribosomal frameshifting (-1 PRF) is a conserved translational regulation event essential for critical biological processes, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Efficient trans-modulation of the structured RNA element crucial to -1 PRF will endow the therapeutic application. Here, we demonstrate that CRISPR RNA can stimulate efficient -1 PRF. Assembled CRISPR-Cas12a, but not CRISPR-Cas9, complex further enhances -1 PRF efficiency through its higher capacity to stall translating ribosomes. We additionally perform CRISPR-Cas12a targeting to impair the SARS-CoV-2 frameshifting pseudoknot structure via a focused screening. We demonstrate that targeting CRISPR-Cas12a results in more than 70% suppression of -1 PRF in vitro and about 50% suppression in mammalian cells. Our results show the expanded function of the CRISPR-Cas12 system in modulating -1 PRF efficiency through stalling ribosomes and deforming frameshifting stimulatory signals, which could serve as a new strategy for future coronavirus pandemics.
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Affiliation(s)
- Shih-Hong Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | | | - Cheng-Yao Chen
- YD BioLabs, Inc., Hsinchu, Taiwan
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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6
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Huang X, Du Z. Elaborated pseudoknots that stimulate -1 programmed ribosomal frameshifting or stop codon readthrough in RNA viruses. J Biomol Struct Dyn 2023:1-13. [PMID: 38095458 PMCID: PMC11176267 DOI: 10.1080/07391102.2023.2292296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/25/2023] [Indexed: 05/08/2024]
Abstract
Pseudoknots assume various functions including stimulation of -1 programmed ribosomal frameshifting (PRF) or stop codon readthrough (SCR) in RNA viruses. These pseudoknots vary greatly in sizes and structural complexities. Recent biochemical and structural studies confirm the three-stemmed pseudoknots as the -1 PRF stimulators in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses. We reexamined previously reported -1 PRF or SCR stimulating pseudoknots, especially those containing a relatively long connecting loop between the two pseudoknot-forming stems, for their ability to form elaborated structures. Many potential elaborated pseudoknots were identified that contain one or more of the following extra structural elements: stem-loop, embedded pseudoknot, kissing hairpins, and additional loop-loop interactions. The elaborated pseudoknots are found in several different virus families that utilize either the -1 PRF or SCR recoding mechanisms. Model-building studies were performed to not only establish the structural feasibility of the elaborated pseudoknots but also reveal potential additional structural features that cannot be readily inferred from the predicted secondary structures. Some of the structures, such as embedded double pseudoknots and compact loop-loop pseudoknots mediated by the previously established common pseudoknot motif-1 (CPK-1), represent the first of its kind in the literatures. By advancing discovery of new functional RNA structures, we significantly expand the repertoire of known elaborated pseudoknots that could potentially play a role in -1 PRF and SCR regulation. These results contribute to a better understanding of RNA structures in general, facilitating the design of engineering RNA molecules with certain desired functions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiaolan Huang
- School of Computing, Southern Illinois University at Carbondale, IL 62901, USA
| | - Zhihua Du
- School of Chemical and Biomolecular Sciences, Southern Illinois University at Carbondale, IL 62901, USA
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7
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Abstract
Protein synthesis by the ribosome is the final stage of biological information transfer and represents an irreversible commitment to gene expression. Accurate translation of messenger RNA is therefore essential to all life, and spontaneous errors by the translational machinery are highly infrequent (∼1/100,000 codons). Programmed -1 ribosomal frameshifting (-1PRF) is a mechanism in which the elongating ribosome is induced at high frequency to slip backward by one nucleotide at a defined position and to continue translation in the new reading frame. This is exploited as a translational regulation strategy by hundreds of RNA viruses, which rely on -1PRF during genome translation to control the stoichiometry of viral proteins. While early investigations of -1PRF focused on virological and biochemical aspects, the application of X-ray crystallography and cryo-electron microscopy (cryo-EM), and the advent of deep sequencing and single-molecule approaches have revealed unexpected structural diversity and mechanistic complexity. Molecular players from several model systems have now been characterized in detail, both in isolation and, more recently, in the context of the elongating ribosome. Here we provide a summary of recent advances and discuss to what extent a general model for -1PRF remains a useful way of thinking.
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Affiliation(s)
- Chris H Hill
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom;
| | - Ian Brierley
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom;
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8
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Kong C, Li D, Hu Y, Gao P, Zhang Y, Zhou L, Ge X, Guo X, Han J, Yang H. The Genetic Variation of Porcine Reproductive and Respiratory Syndrome Virus Replicase Protein nsp2 Modulates Viral Virulence and Persistence. J Virol 2023; 97:e0168922. [PMID: 36916907 PMCID: PMC10062138 DOI: 10.1128/jvi.01689-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/16/2023] [Indexed: 03/15/2023] Open
Abstract
Fast evolution in the field of the replicase nsp2 represents a most prominent feature of porcine reproductive and respiratory syndrome virus (PRRSV). Here, we determined its biological significance in viral pathogenesis by constructing interlineage chimeric mutants between the Chinese highly pathogenic PRRSV (HP-PRRSV) strain JXwn06 (lineage 8) and the low-virulent NADC30-like strain CHsx1401 (lineage 1). Replacement with nsp2 from JXwn06 was surprisingly lethal to the backbone virus CHsx1401, but combined substitution with the structural protein-coding region (SP) gave rise to viable virus CHsx1401-SPnsp2JX. Meanwhile, a derivative carrying only the SP region (CHsx1401-SPJX) served as a control. Subsequent animal experiments revealed that acquisition of SP alone (CHsx1401-SPJX) did not allow CHsx1401 to gain much virulence, but additional swapping of HP-PRRSV nsp2 (CHsx1401-SPnsp2JX) enabled CHsx1401 to acquire some properties of HP-PRRSV, exemplified by prolonged high fever, microscopic lung hemorrhage, and a significant increase in proinflammatory cytokines in the acute stage. Consistent with this was the transcriptomic analysis of persistently infected secondary lymphoid tissues that revealed a much stronger induction of host cellular immune responses in this group and identified several core immune genes (e.g., TLR4, IL-1β, MPO, etc.) regulated by HP-PRRSV nsp2. Interestingly, immune activation status in the individual groups correlated well with the rate of viremia clearance and viral tissue load reduction. Overall, the above results suggest that the Chinese HP-PRRSV nsp2 is a critical virulence regulator and highlight the importance of nsp2 genetic variation in modulating PRRSV virulence and persistence via immune modulation. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) has been a major threat to the world swine industry. In the field, rapid genetic variations (e.g., deletion, mutation, recombination, etc.) within the nsp2 region present an intriguing conundrum to PRRSV biology and pathogenesis. By making chimeric mutants, here, we show that the Chinese highly pathogenic PRRSV (HP-PRRSV) nsp2 is a virulence factor and a much stronger inducer of host immune responses (e.g., inflammation) than its counterpart, currently epidemic, NADC30-like strains. Differences in the ability to modulate host immunity provide insight into the mechanisms of why NADC30-like strains and their derivatives are rising to be the dominant viruses, whereas the Chinese HP-PRRSV strains gradually give away center stage in the field. Our results have important implications in understanding PRRSV evolution, interlineage recombination, and persistence.
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Affiliation(s)
- Can Kong
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Dan Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yanxin Hu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Peng Gao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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9
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Jiang Y, Gao F, Li L, Zhou Y, Tong W, Yu L, Zhang Y, Zhao K, Zhu H, Liu C, Li G, Tong G. The rPRRSV-E2 strain exhibited a low level of potential risk for virulence reversion. Front Vet Sci 2023; 10:1128863. [PMID: 36960147 PMCID: PMC10027928 DOI: 10.3389/fvets.2023.1128863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/08/2023] [Indexed: 03/09/2023] Open
Abstract
Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Classical Swine Fever Virus (CSFV) are two important pathogens, which cause serious impact on swine industry worldwide. In our previous research, rPRRSV-E2, the recombinant PRRSV expressing CSFV E2 protein, could provide sufficient protection against the lethal challenge of highly pathogenic PRRSV and CSFV, and could maintained genetically stable in vitro. Here, to evaluate the virulence reversion potential risk, rPRRSV-E2 had been continuously passaged in vivo, the stability of E2 expression and virulence of the passage viruses were analyzed. The results showed that no clinical symptoms or pathological changes could be found in the inoculated groups, and there were no significant differences of viraemia among the test groups. Sequencing and IFA analysis showed that the coding gene of exogenous CSFV E2 protein existed in the passaged viruses without any sequence mutations, deletions or insertions, and could expressed steadily. It could be concluded that the foreign CSFV E2 gene in the genome of rPRRSV-E2 could be maintained genetically stable in vivo, and rPRRSV-E2 strain had relatively low level of potential risk for virulence reversion.
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Affiliation(s)
- Yifeng Jiang
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Fei Gao
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Liwei Li
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yanjun Zhou
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Wu Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Lingxue Yu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yujiao Zhang
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Kuan Zhao
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Haojie Zhu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Changlong Liu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Guoxin Li
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
- *Correspondence: Guoxin Li
| | - Guangzhi Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
- Guangzhi Tong
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10
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You X, Lei Y, Zhang P, Xu D, Ahmed Z, Yang Y. Role of transcription factors in porcine reproductive and respiratory syndrome virus infection: A review. Front Microbiol 2022; 13:924004. [PMID: 35928151 PMCID: PMC9344050 DOI: 10.3389/fmicb.2022.924004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is an infectious disease caused by the PRRS virus that leads to reproductive disorders and severe dyspnoea in pigs, which has serious economic impacts. One of the reasons PRRSV cannot be effectively controlled is that it has developed countermeasures against the host immune response, allowing it to survive and replicate for long periods. Transcription Factors acts as a bridge in the interactions between the host and PRRSV. PRRSV can create an environment conducive to PRRSV replication through transcription factors acting on miRNAs, inflammatory factors, and immune cells. Conversely, some transcription factors also inhibit PRRSV proliferation in the host. In this review, we systematically described how PRRSV uses host transcription factors such as SP1, CEBPB, STATs, and AP-1 to escape the host immune system. Determining the role of transcription factors in immune evasion and understanding the pathogenesis of PRRSV will help to develop new treatments for PRRSV.
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Affiliation(s)
- Xiangbin You
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Animal Genetics and Breeding, Luoyang, China
| | - Ying Lei
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Animal Genetics and Breeding, Luoyang, China
| | - Ping Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Dequan Xu
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Pakistan
| | - Youbing Yang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- Luoyang Key Laboratory of Animal Genetics and Breeding, Luoyang, China
- *Correspondence: Youbing Yang
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11
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Abstract
The constrained nature of viral genomes has allowed a translational sleight of hand known as −1 Programmed Ribosomal Frameshifting (−1 PRF) to flourish. Numerous studies have sought to tease apart the mechanisms and implications of −1PRF utilizing a few techniques. The dual-luciferase assay and ribosomal profiling have driven the PRF field to make great advances; however, the use of these assays means that the full impact of the genomic and cellular context on −1 PRF is often lost. Here, we discuss how the Minimal Frameshifting Element (MFE) and its constraints can hide contextual effects on −1 PRF. We review how sequence elements proximal to the traditionally defined MFE, such as the coronavirus attenuator sequence, can affect the observed rates of −1 PRF. Further, the MFE-based approach fully obscured −1 PRF in Barley yellow dwarf virus and would render the exploration of −1 PRF difficult in Porcine reproductive and respiratory syndrome virus, Encephalomyocarditis virus, Theiler’s murine encephalomyelitis virus, and Sindbis virus. Finally, we examine how the cellular context of tRNA abundance, miRNAs, and immune response elements can affect −1 PRF. The use of MFE was instrumental in establishing the basic foundations of PRF; however, it has become clear that the contextual impact on −1 PRF is no longer the exception so much as it is the rule and argues for new approaches to study −1PRF that embrace context. We therefore urge our field to expand the strategies and methods used to explore −1 PRF.
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12
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Li W, Li M, Zhang H, Li C, Xu H, Gong B, Fu J, Guo Z, Peng J, Zhou G, Tian Z, Wang Q. A Novel Immunochromatographic Strip Based on Latex Microspheres for the Rapid Detection of North American-Type Porcine Reproductive and Respiratory Syndrome Virus. Front Microbiol 2022; 13:882112. [PMID: 35572691 PMCID: PMC9100670 DOI: 10.3389/fmicb.2022.882112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
A latex microsphere-based immunochromatographic strip (ICS) test was successfully developed for the rapid and sensitive detection of porcine reproductive and respiratory syndrome virus (PRRSV). The PRRSV N protein-specific monoclonal antibody (mAb) 1H4 labeled with latex microspheres was dispensed on a conjugate pad for use as the detector. The same mAb and goat anti-mouse antibody were blotted on a nitrocellulose membrane to generate test and control lines, respectively. The limit of virus detection was approximately 5 × 102.0 median tissue culture infectious dose (TCID50)/ml, and the limit of N protein detection was approximately 15 ng/ml. Other common porcine viruses were tested to evaluate the specificity of the ICS, and positive results were observed for only North American-type PRRSV. A comparison of the strip with a standard diagnostic test (reverse transcriptase polymerase chain reaction, RT-PCR) was also performed, and the results showed that the ICS test exhibited relatively high specificity and sensitivity (90.32 and 73.91%, respectively) and relatively high positive predictive value (PPV) and negative predictive value (NPV; 85 and 82.35%, respectively). These results suggest that the ICS test can be used to rapidly and accurately detect PRRSV and can be suitable for diagnostic applications in the field.
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Affiliation(s)
- Wansheng Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Minhua Li
- Beijing IDEXX Yuanheng Laboratories, Co., Ltd., Beijing, China
| | - Hongliang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chao Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hu Xu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Bangjun Gong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jun Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhenyang Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinmei Peng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guohui Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhijun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Qian Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- *Correspondence: Qian Wang,
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13
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Cook GM, Brown K, Shang P, Li Y, Soday L, Dinan AM, Tumescheit C, Mockett APA, Fang Y, Firth AE, Brierley I. Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression. eLife 2022; 11:e75668. [PMID: 35226596 PMCID: PMC9000960 DOI: 10.7554/elife.75668] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/26/2022] [Indexed: 11/13/2022] Open
Abstract
The arterivirus porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the swine industry worldwide. Here we apply ribosome profiling (RiboSeq) and parallel RNA sequencing (RNASeq) to characterise the transcriptome and translatome of both species of PRRSV and to analyse the host response to infection. We calculated programmed ribosomal frameshift (PRF) efficiency at both sites on the viral genome. This revealed the nsp2 PRF site as the second known example where temporally regulated frameshifting occurs, with increasing -2 PRF efficiency likely facilitated by accumulation of the PRF-stimulatory viral protein, nsp1β. Surprisingly, we find that PRF efficiency at the canonical ORF1ab frameshift site also increases over time, in contradiction of the common assumption that RNA structure-directed frameshift sites operate at a fixed efficiency. This has potential implications for the numerous other viruses with canonical PRF sites. Furthermore, we discovered several highly translated additional viral ORFs, the translation of which may be facilitated by multiple novel viral transcripts. For example, we found a highly expressed 125-codon ORF overlapping nsp12, which is likely translated from novel subgenomic RNA transcripts that overlap the 3' end of ORF1b. Similar transcripts were discovered for both PRRSV-1 and PRRSV-2, suggesting a potential conserved mechanism for temporally regulating expression of the 3'-proximal region of ORF1b. We also identified a highly translated, short upstream ORF in the 5' UTR, the presence of which is highly conserved amongst PRRSV-2 isolates. These findings reveal hidden complexity in the gene expression programmes of these important nidoviruses.
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Affiliation(s)
- Georgia M Cook
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Katherine Brown
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Pengcheng Shang
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Yanhua Li
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Lior Soday
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Adam M Dinan
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | | | - Ying Fang
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Andrew E Firth
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Ian Brierley
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
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14
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Riegger RJ, Caliskan N. Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting. Front Mol Biosci 2022; 9:842261. [PMID: 35281266 PMCID: PMC8915115 DOI: 10.3389/fmolb.2022.842261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/26/2022] [Indexed: 01/08/2023] Open
Abstract
Translation facilitates the transfer of the genetic information stored in the genome via messenger RNAs to a functional protein and is therefore one of the most fundamental cellular processes. Programmed ribosomal frameshifting is a ubiquitous alternative translation event that is extensively used by viruses to regulate gene expression from overlapping open reading frames in a controlled manner. Recent technical advances in the translation field enabled the identification of precise mechanisms as to how and when ribosomes change the reading frame on mRNAs containing cis-acting signals. Several studies began also to illustrate that trans-acting RNA modulators can adjust the timing and efficiency of frameshifting illuminating that frameshifting can be a dynamically regulated process in cells. Here, we intend to summarize these new findings and emphasize how it fits in our current understanding of PRF mechanisms as previously described.
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Affiliation(s)
- Ricarda J. Riegger
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Graduate School of Life Sciences (GSLS), University of Würzburg, Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
- *Correspondence: Neva Caliskan,
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15
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Insights from structural studies of the Cardiovirus 2A protein. Biosci Rep 2022; 42:230648. [PMID: 35022657 PMCID: PMC8777194 DOI: 10.1042/bsr20210406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
Cardioviruses are single-stranded RNA viruses of the family Picornaviridae. In addition to being the first example of internal ribosome entry site (IRES) utilization, cardioviruses also employ a series of alternative translation strategies, such as Stop-Go translation and programmed ribosome frameshifting. Here, we focus on cardiovirus 2A protein, which is not only a primary virulence factor, but also exerts crucial regulatory functions during translation, including activation of viral ribosome frameshifting and inhibition of host cap-dependent translation. Only recently, biochemical and structural studies have allowed us to close the gaps in our knowledge of how cardiovirus 2A is able to act in diverse translation-related processes as a novel RNA-binding protein. This review will summarize these findings, which ultimately may lead to the discovery of other RNA-mediated gene expression strategies across a broad range of RNA viruses.
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16
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Ke W, Zhou Y, Lai Y, Long S, Fang L, Xiao S. Porcine reproductive and respiratory syndrome virus nsp4 positively regulates cellular cholesterol to inhibit type I interferon production. Redox Biol 2021; 49:102207. [PMID: 34911669 PMCID: PMC8758914 DOI: 10.1016/j.redox.2021.102207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/26/2021] [Accepted: 12/07/2021] [Indexed: 02/07/2023] Open
Abstract
Cellular cholesterol plays an important role in the life cycles of enveloped viruses. Previous studies by our group and other groups have demonstrated that the depletion of cellular cholesterol by methyl-β-cyclodextrin (MβCD) reduces the proliferation of porcine reproductive and respiratory syndrome virus (PRRSV), a porcine Arterivirus that has been devastating the swine industry worldwide for over two decades. However, how PRRSV infection regulates cholesterol synthesis is not fully understood. In this study, we showed that PRRSV infection upregulated the activity of protein phosphatase 2 (PP2A), which subsequently activated 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), the rate-limiting enzyme in the cholesterol synthesis pathway, to increase the levels of cellular cholesterol. By screening the PRRSV-encoded proteins, we showed that nsp4 dominated the upregulation of cellular cholesterol, independently of the 3C-like protease activity of nsp4. A mutation analysis showed that domain I (amino acids 1–80) of PRRSV nsp4 interacted with PR65 alpha (PR65α), the structural subunit, and PP2Ac, the catalytic subunit, of PP2A. Importantly, domain I of nsp4 inhibited Sendai virus-induced interferon β production, and this inhibitory effect was eliminated by Lovastatin, an HMGCR inhibitor, indicating that the upregulation of cellular cholesterol by nsp4 is a strategy used by PRRSV to suppress the antiviral innate immunity of its host. Collectively, we here demonstrated the mechanism by which PRRSV regulates cellular cholesterol synthesis and reported a novel strategy by which PRRSV evades its host's antiviral innate immune response. PRRSV nsp4 up-regulates cellular cholesterol via the PP2A-HMGCR pathway. Nsp4 domain I (amino acids 1–80) interacts with A and C subunits of PP2A. Nsp4 domain I inhibits IFN-I production by upregulating cellular cholesterol. The HMGCR inhibitor Lovastatin inhibits PRRSV proliferation.
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Affiliation(s)
- Wenting Ke
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Yanrong Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Yinan Lai
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Siwen Long
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.
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17
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Hill CH, Cook GM, Napthine S, Kibe A, Brown K, Caliskan N, Firth AE, Graham SC, Brierley I. Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus. Nucleic Acids Res 2021; 49:11938-11958. [PMID: 34751406 PMCID: PMC8599813 DOI: 10.1093/nar/gkab969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022] Open
Abstract
The 2A protein of Theiler's murine encephalomyelitis virus (TMEV) acts as a switch to stimulate programmed -1 ribosomal frameshifting (PRF) during infection. Here, we present the X-ray crystal structure of TMEV 2A and define how it recognises the stimulatory RNA element. We demonstrate a critical role for bases upstream of the originally predicted stem-loop, providing evidence for a pseudoknot-like conformation and suggesting that the recognition of this pseudoknot by beta-shell proteins is a conserved feature in cardioviruses. Through examination of PRF in TMEV-infected cells by ribosome profiling, we identify a series of ribosomal pauses around the site of PRF induced by the 2A-pseudoknot complex. Careful normalisation of ribosomal profiling data with a 2A knockout virus facilitated the identification, through disome analysis, of ribosome stacking at the TMEV frameshifting signal. These experiments provide unparalleled detail of the molecular mechanisms underpinning Theilovirus protein-stimulated frameshifting.
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Affiliation(s)
- Chris H Hill
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Georgia M Cook
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Sawsan Napthine
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Katherine Brown
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
- Medical Faculty, Julius-Maximilians University Würzburg, 97074 Würzburg, Germany
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Stephen C Graham
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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18
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Zhu Z, Yuan L, Hu D, Lian Z, Yao X, Liu P, Li X. Isolation and genomic characterization of a Chinese NADC34-like PRRSV isolated from Jiangsu province. Transbound Emerg Dis 2021; 69:e1015-e1027. [PMID: 34786872 DOI: 10.1111/tbed.14392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 11/30/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important causative agents to swine industry, which has been epidemic more than 30 years. The emergence and recombination of new virus strains bring great challenges to the prevention and control of PRRSV. In the present study, we reported and characterized a novel PRRSV strain, designated as JS2021NADC34, which was for the first time isolated from clinical samples in Jiangsu province, China. Phylogenetic analysis demonstrated that JS2021NADC34 belonging to sublineage 1.5 of PRRSV-2 and was highly related to NADC34-like strains. Genetically, JS2021NADC34 strain had a continuous 100 aa depletion in NSP2, as compared to VR-2332 strain, which was consistent with most reported NADC34-like strains. Moreover, there were several amino acid substitutions occurred in the antigenic regions of GP2-GP5. Similar to other reported NADC34-like PRRSV in China, JS2021NADC34 had no recombination with other domestic strains, which indicates this sublineage of PRRSV may be directly transported from the United States and have not undergone extensive mutation and recombination with local strains yet.
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Affiliation(s)
- Zhenbang Zhu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Lili Yuan
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Danhe Hu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhengmin Lian
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiaohui Yao
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Panrao Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiangdong Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
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19
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Rajkhowa TK, Thanga L, Hauhnar L, Zodinpui D, Subbiah M. Molecular detection and characterization of highly pathogenic porcine reproductive and respiratory syndrome virus from a natural outbreak in wild pigs, Mizoram, India. Transbound Emerg Dis 2021; 69:e288-e298. [PMID: 34406700 DOI: 10.1111/tbed.14296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 03/28/2021] [Accepted: 08/17/2021] [Indexed: 11/29/2022]
Abstract
This study reports for the first time a natural outbreak of highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRS) caused by HP-PRRS virus (HP-PRRSV) in wild pigs characterized by sudden onset of depression, anorexia, respiratory distress, and high fever. The disease has caused severe haemorrhagic pneumonia, haemorrhagic lymphadenitis, enlarged spleen with areas of infarction, and petechial haemorrhages on the myocardium and on the surface of kidneys. HP-PRRSV was detected in representative tissue samples by reverse transcription-PCR, and the field strain was isolated in the MA104 cell line. The phylogenetic analyses based on the whole genome sequences and nucleotide sequences of open reading frame 5 (ORF5) gene showed close grouping with the subtype IV of lineage 8/8.7 of PRRSV II, which represents the HP-PRRSV strains that predominate in the pig population of China since 2010. The amino acid sequence analysis of the ORF5 gene revealed the replacement of leucine (L) at position 39 to isoleucine (I) in the primary neutralizing epitope. Among the four potential N glycosylation sites, the N34 was mutated and found to be restricted to only three N glycosylation sites. The present findings have indicated that HP-PRRSV can cause fatal outbreaks and may emerge as a major threat to the wild pig population.
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Affiliation(s)
- Tridib Kumar Rajkhowa
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Aizawl, Mizoram, India
| | - Lalnun Thanga
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Aizawl, Mizoram, India
| | - Lalthapui Hauhnar
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Aizawl, Mizoram, India
| | - Doris Zodinpui
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Aizawl, Mizoram, India
| | - Madhuri Subbiah
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
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20
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Atkins JF, O’Connor KM, Bhatt PR, Loughran G. From Recoding to Peptides for MHC Class I Immune Display: Enriching Viral Expression, Virus Vulnerability and Virus Evasion. Viruses 2021; 13:1251. [PMID: 34199077 PMCID: PMC8310308 DOI: 10.3390/v13071251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 01/02/2023] Open
Abstract
Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.
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Affiliation(s)
- John F. Atkins
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Kate M. O’Connor
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Pramod R. Bhatt
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Gary Loughran
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
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21
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Napthine S, Hill CH, Nugent HCM, Brierley I. Modulation of Viral Programmed Ribosomal Frameshifting and Stop Codon Readthrough by the Host Restriction Factor Shiftless. Viruses 2021; 13:v13071230. [PMID: 34202160 PMCID: PMC8310280 DOI: 10.3390/v13071230] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 12/18/2022] Open
Abstract
The product of the interferon-stimulated gene C19orf66, Shiftless (SHFL), restricts human immunodeficiency virus replication through downregulation of the efficiency of the viral gag/pol frameshifting signal. In this study, we demonstrate that bacterially expressed, purified SHFL can decrease the efficiency of programmed ribosomal frameshifting in vitro at a variety of sites, including the RNA pseudoknot-dependent signals of the coronaviruses IBV, SARS-CoV and SARS-CoV-2, and the protein-dependent stimulators of the cardioviruses EMCV and TMEV. SHFL also reduced the efficiency of stop-codon readthrough at the murine leukemia virus gag/pol signal. Using size-exclusion chromatography, we confirm the binding of the purified protein to mammalian ribosomes in vitro. Finally, through electrophoretic mobility shift assays and mutational analysis, we show that expressed SHFL has strong RNA binding activity that is necessary for full activity in the inhibition of frameshifting, but shows no clear specificity for stimulatory RNA structures.
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Affiliation(s)
| | | | | | - Ian Brierley
- Correspondence: ; Tel.: +44-12-2333-6914; Fax: +44-12-2333-6926
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22
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Wen X, Ge X, Zhou L, Zhang Y, Guo X, Yang H. PRRSV Promotes MARC-145 Cells Entry Into S Phase of the Cell Cycle to Facilitate Viral Replication via Degradation of p21 by nsp11. Front Vet Sci 2021; 8:642095. [PMID: 33869322 PMCID: PMC8044838 DOI: 10.3389/fvets.2021.642095] [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: 12/15/2020] [Accepted: 03/03/2021] [Indexed: 12/21/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) remains one of the most economically significant pathogens that seriously affect the global swine industry. Despite sustained efforts, the factors that affect PRRSV replication in host cells are far from being fully elucidated and thus warrants further investigation. In this study, we first demonstrated that PRRSV infection can cause downregulation of endogenous p21 protein in MARC-145 cells in a virus dose-dependent manner. Next, we analyzed the effect of p21 knockdown by RNA interference on cell cycle progression using flow cytometric analysis, and found that knockdown of p21 promotes MARC-145 cells entry into S phase of the cell cycle. Interestingly, we further discovered PRRSV infection is also able to promote MARC-145 cells entry into the S phase. Subsequently, we synchronized MARC-145 cells into G0/G1, S and G2/M phases, respectively, and then determined PRRSV replication in these cells. Results here show that the MARC-145 cells synchronized into the S phase exhibited the highest viral titer among the cells synchronized to different phases. Additionally, to reliably analyze the potential role of endogenous p21 protein in PRRSV replication, we constructed a p21 gene-knockout MARC-145 cell line (p21-/-) using CRISPR/Cas9 technology and evaluated its capability to support PRRSV replication. Our results indicate that knockout of p21 is conducive to PRRSV replication in MARC-145 cells. Furthermore, through construction of a series of eukaryotic plasmids expressing each of individual PRRSV proteins combined with cell transfection, we demonstrated that the nonstructural protein 11 (nsp11) of PRRSV mediates p21 degradation, which was further confirmed by generating a stable MARC-145 cell line constitutively expressing nsp11 using a lentivirus system. Notably, we further demonstrated that the endoribonuclease activity rather than the deubiquitinating activity of nsp11 is essential for p21 degradation via mutagenic analysis. Finally, we demonstrated that nsp11 mediates p21 degradation via a ubiquitin-independent proteasomal degradation manner. Altogether, our study not only uncovers a new pathogenesis of PRRSV, but also provides new insights into development of novel antiviral strategies.
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Affiliation(s)
- Xuexia Wen
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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23
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A swine arterivirus deubiquitinase stabilizes two major envelope proteins and promotes production of viral progeny. PLoS Pathog 2021; 17:e1009403. [PMID: 33735221 PMCID: PMC7971519 DOI: 10.1371/journal.ppat.1009403] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/17/2021] [Indexed: 11/23/2022] Open
Abstract
Arteriviruses are enveloped positive-strand RNA viruses that assemble and egress using the host cell’s exocytic pathway. In previous studies, we demonstrated that most arteriviruses use a unique -2 ribosomal frameshifting mechanism to produce a C-terminally modified variant of their nonstructural protein 2 (nsp2). Like full-length nsp2, the N-terminal domain of this frameshift product, nsp2TF, contains a papain-like protease (PLP2) that has deubiquitinating (DUB) activity, in addition to its role in proteolytic processing of replicase polyproteins. In cells infected with porcine reproductive and respiratory syndrome virus (PRRSV), nsp2TF localizes to compartments of the exocytic pathway, specifically endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and Golgi complex. Here, we show that nsp2TF interacts with the two major viral envelope proteins, the GP5 glycoprotein and membrane (M) protein, which drive the key process of arterivirus assembly and budding. The PRRSV GP5 and M proteins were found to be poly-ubiquitinated, both in an expression system and in cells infected with an nsp2TF-deficient mutant virus. In contrast, ubiquitinated GP5 and M proteins did not accumulate in cells infected with the wild-type, nsp2TF-expressing virus. Further analysis implicated the DUB activity of the nsp2TF PLP2 domain in deconjugation of ubiquitin from GP5/M proteins, thus antagonizing proteasomal degradation of these key viral structural proteins. Our findings suggest that nsp2TF is targeted to the exocytic pathway to reduce proteasome-driven turnover of GP5/M proteins, thus promoting the formation of GP5-M dimers that are critical for arterivirus assembly. Arteriviruses are a rapidly expanding family of positive-stranded RNA viruses, which includes economically important veterinary pathogens like equine arteritis virus (EAV) and two species of porcine reproductive and respiratory syndrome virus (PRRSV-1 and PRRSV-2). In our previous studies, we uncovered an unprecedented arterivirus gene expression mechanism: a highly efficient -2 programmed ribosomal frameshift (PRF) that is controlled by an interaction of viral protein nsp1ß with specific RNA sequences and host poly(C) binding proteins. It is used by PRRSVs, and most other arteriviruses, to efficiently produce a previously unknown nonstructural protein variant, nsp2TF. In this study, we demonstrate that PRRSV nsp2TF interacts with the two major arteriviral envelope proteins, GP5 and M, whose heterodimerization in the secretory pathway is a key step in envelope protein trafficking and virus assembly. Our findings suggest that nsp2TF promotes arterivirus assembly by antagonizing the ubiquitination-dependent proteasomal degradation of GP5 and M proteins. This mechanism is based on the DUB activity of the PLP2 protease domain located within the N-terminal region of nsp2TF. To our knowledge, this is the first study to demonstrate that viruses can express a DUB that functions specifically to counteract the ubiquitination and degradation of key viral structural proteins.
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24
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Yin B, Qi S, Sha W, Qin H, Liu L, Yun J, Zhu J, Li G, Sun D. Molecular Characterization of the Nsp2 and ORF5 (ORF5a) Genes of PRRSV Strains in Nine Provinces of China During 2016-2018. Front Vet Sci 2021; 8:605832. [PMID: 33748205 PMCID: PMC7969665 DOI: 10.3389/fvets.2021.605832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) causes a highly contagious disease and brings huge economic losses to commercial pork production worldwide. PRRSV causes severe reproductive failure in sows and respiratory distress in piglets. To trace the evolution of PRRSV in pigs with respiratory diseases in some regions of China, 112 samples were collected from nine provinces in China during 2016–2018. All samples were detected by RT-PCR and analyzed by the Nsp2/ORF5 (ORF5a)-genes-phylogeny. Sequence analysis and recombination analysis were conducted on the Nsp2/ORF5 (ORF5a) genes of the identified strain in the study. The RT-PCR result shown that the positive rate of PRRSV was 50.89% (57/112). Phylogenetic analysis showed that the identified PRRSV strains were all NA genotype and belonged to lineage 1, 3, and 8. The Nsp2 gene of identified PRRSV strains exhibited nucleotide homologies of 53.0 ~ 99.8%, and amino acid homologies of 46.8 ~ 99.7%. The ORF5 gene of identified PRRSV strains exhibited nucleotide homologies of 82.4 ~ 100%, and amino acid homologies of 79.6 ~ 100%. Sequence analysis revealed that a discontinuous 30-amino-acid deletion (positions 481 and 533–561) and a 131-amino-acid discontinuity deletion (positions 323–433, 481, and 533–551) in Nsp2 of PPRSV isolates; all identified strains in this study may be wild strains, and most identified strains may be highly virulent strains. Sequence analysis of ORF5 and ORF5a revealed that the mutation sites of GP5 were mainly concentrated in the signal peptide and epitopes region, while the mutation sites of ORF5a were mainly concentrated in the transmembrane and the intramembrane region. The recombination analysis indicated that there may be multiple recombination regions in identified strains, and the recombination pattern was more complex. This study showed that the prevalent PRRSV strain in some regions of China was still HP-PRRSV, while NADC30 strain also occupied a certain proportion; different types of PRRSV strains showed different patterns and variation in China. This study suggested that the monitoring of PRRSV prevalence and genetic variation should be further strengthened.
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Affiliation(s)
- Baishuang Yin
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Shanshan Qi
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wanli Sha
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Hongyu Qin
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Liming Liu
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Jinyan Yun
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Jinhai Zhu
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guojiang Li
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Dongbo Sun
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China.,Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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25
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Patel A, Treffers EE, Meier M, Patel TR, Stetefeld J, Snijder EJ, Mark BL. Molecular characterization of the RNA-protein complex directing -2/-1 programmed ribosomal frameshifting during arterivirus replicase expression. J Biol Chem 2020; 295:17904-17921. [PMID: 33127640 PMCID: PMC7939443 DOI: 10.1074/jbc.ra120.016105] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a mechanism used by arteriviruses like porcine reproductive and respiratory syndrome virus (PRRSV) to generate multiple proteins from overlapping reading frames within its RNA genome. PRRSV employs -1 PRF directed by RNA secondary and tertiary structures within its viral genome (canonical PRF), as well as a noncanonical -1 and -2 PRF that are stimulated by the interactions of PRRSV nonstructural protein 1β (nsp1β) and host protein poly(C)-binding protein (PCBP) 1 or 2 with the viral genome. Together, nsp1β and one of the PCBPs act as transactivators that bind a C-rich motif near the shift site to stimulate -1 and -2 PRF, thereby enabling the ribosome to generate two frameshift products that are implicated in viral immune evasion. How nsp1β and PCBP associate with the viral RNA genome remains unclear. Here, we describe the purification of the nsp1β:PCBP2:viral RNA complex on a scale sufficient for structural analysis using small-angle X-ray scattering and stochiometric analysis by analytical ultracentrifugation. The proteins associate with the RNA C-rich motif as a 1:1:1 complex. The monomeric form of nsp1β within the complex differs from previously reported homodimer identified by X-ray crystallography. Functional analysis of the complex via mutational analysis combined with RNA-binding assays and cell-based frameshifting reporter assays reveal a number of key residues within nsp1β and PCBP2 that are involved in complex formation and function. Our results suggest that nsp1β and PCBP2 both interact directly with viral RNA during formation of the complex to coordinate this unusual PRF mechanism.
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Affiliation(s)
- Ankoor Patel
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Emmely E Treffers
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
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26
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Hufsky F, Beerenwinkel N, Meyer IM, Roux S, Cook GM, Kinsella CM, Lamkiewicz K, Marquet M, Nieuwenhuijse DF, Olendraite I, Paraskevopoulou S, Young F, Dijkman R, Ibrahim B, Kelly J, Le Mercier P, Marz M, Ramette A, Thiel V. The International Virus Bioinformatics Meeting 2020. Viruses 2020; 12:E1398. [PMID: 33291220 PMCID: PMC7762161 DOI: 10.3390/v12121398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Niko Beerenwinkel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA;
| | - Georgia May Cook
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Cormac M. Kinsella
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Kevin Lamkiewicz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Mike Marquet
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- CaSe Group, Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, 07743 Jena, Germany
| | - David F. Nieuwenhuijse
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Viroscience Department, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Ingrida Olendraite
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Francesca Young
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK;
| | - Ronald Dijkman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
| | - Bashar Ibrahim
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Centre for Applied Mathematics and Bioinformatics, Hawally 32093, Kuwait
- Department of Mathematics and Natural Sciences Gulf University for Science and Technology, Hawally 32093, Kuwait
| | - Jenna Kelly
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
| | - Philippe Le Mercier
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1205 Geneva, Switzerland
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alban Ramette
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
| | - Volker Thiel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
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27
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Whole-Genome Sequencing of Porcine Reproductive and Respiratory Syndrome Virus from Field Clinical Samples Improves the Genomic Surveillance of the Virus. J Clin Microbiol 2020; 58:JCM.00097-20. [PMID: 32817228 DOI: 10.1128/jcm.00097-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/04/2020] [Indexed: 11/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economic concern worldwide. There are currently large data sets available about the ORF5 gene of the virus, with thousands of sequences available, but little data are currently available on the full-length genome of PRRSV. We hypothesized that whole-genome sequencing (WGS) of the PRRSV genome would allow better epidemiological monitoring than ORF5 gene sequencing. PRRSV PCR-positive serum, oral fluid, and tissue clinical samples submitted to the diagnostic laboratory for routine surveillance or diagnosis of PRRSV infection in Québec, Canada, swine herds were used. The PRRSV reverse transcription-quantitative PCR Cq values of the processed samples varied between 11.5 and 34.34. PRRSV strain genomes were isolated using a poly (A)-tail method and were sequenced with a MiSeq Illumina sequencer. Ninety-two full-length PRRSV genomes were obtained from 88 clinical samples out of 132 tested samples, resulting in a PRRSV WGS success rate of 66.67%. Three important deletions in ORF1a were found in most wild-type (i.e., not vaccine-like) strains. The importance of these deletions remains undetermined. Two different full-length PRRSV genomes were found in four different samples (three serum samples and one pool of tissues), suggesting a 4.55% PRRSV strain coinfection prevalence in swine. Moreover, six PRRSV whole genomes (6.52% of PRRSV strains) were found to cluster differently than they did under the ORF5 classification method. Overall, WGS of PRRSV enables better strain classification and/or interpretation of results in 9.10% of clinical samples than ORF5 sequencing, as well as allowing interesting research avenues.
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Penn WD, Harrington HR, Schlebach JP, Mukhopadhyay S. Regulators of Viral Frameshifting: More Than RNA Influences Translation Events. Annu Rev Virol 2020; 7:219-238. [PMID: 32600156 DOI: 10.1146/annurev-virology-012120-101548] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Programmed ribosomal frameshifting (PRF) is a conserved translational recoding mechanism found in all branches of life and viruses. In bacteria, archaea, and eukaryotes PRF is used to downregulate protein production by inducing a premature termination of translation, which triggers messenger RNA (mRNA) decay. In viruses, PRF is used to drive the production of a new protein while downregulating the production of another protein, thus maintaining a stoichiometry optimal for productive infection. Traditionally, PRF motifs have been defined by the characteristics of two cis elements: a slippery heptanucleotide sequence followed by an RNA pseudoknot or stem-loop within the mRNA. Recently, additional cis and new trans elements have been identified that regulate PRF in both host and viral translation. These additional factors suggest PRF is an evolutionarily conserved process whose function and regulation we are just beginning to understand.
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Affiliation(s)
- Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Haley R Harrington
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Rodnina MV, Korniy N, Klimova M, Karki P, Peng BZ, Senyushkina T, Belardinelli R, Maracci C, Wohlgemuth I, Samatova E, Peske F. Translational recoding: canonical translation mechanisms reinterpreted. Nucleic Acids Res 2020; 48:1056-1067. [PMID: 31511883 PMCID: PMC7026636 DOI: 10.1093/nar/gkz783] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/21/2019] [Accepted: 08/30/2019] [Indexed: 01/15/2023] Open
Abstract
During canonical translation, the ribosome moves along an mRNA from the start to the stop codon in exact steps of one codon at a time. The collinearity of the mRNA and the protein sequence is essential for the quality of the cellular proteome. Spontaneous errors in decoding or translocation are rare and result in a deficient protein. However, dedicated recoding signals in the mRNA can reprogram the ribosome to read the message in alternative ways. This review summarizes the recent advances in understanding the mechanisms of three types of recoding events: stop-codon readthrough, –1 ribosome frameshifting and translational bypassing. Recoding events provide insights into alternative modes of ribosome dynamics that are potentially applicable to other non-canonical modes of prokaryotic and eukaryotic translation.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Mariia Klimova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Bee-Zen Peng
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Tamara Senyushkina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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Hyper-phosphorylation of nsp2-related proteins of porcine reproductive and respiratory syndrome virus. Virology 2020; 543:63-75. [PMID: 32174300 PMCID: PMC7112050 DOI: 10.1016/j.virol.2020.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/31/2020] [Accepted: 01/31/2020] [Indexed: 01/07/2023]
Abstract
Viruses exploit phosphorylation of both viral and host proteins to support viral replication. In this study, we demonstrate that porcine reproductive and respiratory syndrome virus replicase nsp2, and two nsp2-related −2/−1 frameshifting products, nsp2TF and nsp2N, are hyper-phosphorylated. By mapping phosphorylation sites, we subdivide an extended, previously uncharacterized region, located between the papain-like protease-2 (PLP2) domain and frameshifting site, into three distinct domains. These domains include two large hypervariable regions (HVR) with putative intrinsically disordered structures, separated by a conserved and partly structured interval domain that we defined as the inter-HVR conserved domain (IHCD). Abolishing phosphorylation of the inter-species conserved residue serine918, which is located within the IHCD region, abrogates accumulation of viral genomic and subgenomic RNAs and recombinant virus production. Our study reveals the biological significance of phosphorylation events in nsp2-related proteins, emphasizes pleiotropic functions of nsp2-related proteins in the viral life cycle, and presents potential links to pathogenesis.
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Abstract
Viruses must co-opt the cellular translation machinery to produce progeny virions. Eukaryotic viruses have evolved a variety of ways to manipulate the cellular translation apparatus, in many cases using elegant RNA-centred strategies. Viral RNAs can alter or control every phase of protein synthesis and have diverse targets, mechanisms and structures. In addition, as cells attempt to limit infection by downregulating translation, some of these viral RNAs enable the virus to overcome this response or even take advantage of it to promote viral translation over cellular translation. In this Review, we present important examples of viral RNA-based strategies to exploit the cellular translation machinery. We describe what is understood of the structures and mechanisms of diverse viral RNA elements that alter or regulate translation, the advantages that are conferred to the virus and some of the major unknowns that provide motivation for further exploration. Eukaryotic viruses have evolved a variety of ways to manipulate the cellular translation apparatus. In this Review, Jaafar and Kieft present important examples of viral RNA-based strategies to exploit the cellular translation machinery.
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Affiliation(s)
- Zane A Jaafar
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO, USA.
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32
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The nsp2 Hypervariable Region of Porcine Reproductive and Respiratory Syndrome Virus Strain JXwn06 Is Associated with Viral Cellular Tropism to Primary Porcine Alveolar Macrophages. J Virol 2019; 93:JVI.01436-19. [PMID: 31554681 DOI: 10.1128/jvi.01436-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/18/2019] [Indexed: 11/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) poses a major threat to global pork production and has been notorious for its rapid genetic evolution in the field. The nonstructural protein 2 (nsp2) replicase protein represents the fastest evolving region of PRRSV, but the underlying biological significance has remained poorly understood. By deletion mutagenesis, we discovered that the nsp2 hypervariable region plays an important role in controlling the balance of genomic mRNA and a subset of subgenomic mRNAs. More significantly, we revealed an unexpected link of the nsp2 hypervariable region to viral tropism. Specifically, a mutant of the Chinese highly pathogenic PRRSV strain JXwn06 carrying a deletion spanning nsp2 amino acids 323 to 521 (nsp2Δ323-521) in its hypervariable region was found to lose infectivity in primary porcine alveolar macrophages (PAMs), although it could replicate relatively efficiently in the supporting cell line MARC-145. Consequently, this mutant failed to establish an infection in piglets. Further dissection of the viral life cycle revealed that the mutant had a defect (or defects) lying in the steps between virus penetration and negative-stranded RNA synthesis. Taken together, our results reveal novel functions of nsp2 in the PRRSV life cycle and provide important insights into the mechanisms of PRRSV RNA synthesis and cellular tropism.IMPORTANCE The PRRSV nsp2 replicase protein undergoes rapid and broad genetic variations in its middle region in the field, but the underlying significance has remained enigmatic. Here, we demonstrate that the nsp2 hypervariable region not only plays an important regulatory role in maintaining the balance of different viral mRNA species but also regulates PRRSV tropism to primary PAMs. Our results reveal novel functions for PRRSV nsp2 and have important implications for understanding the mechanisms of PRRSV RNA synthesis and cellular tropism.
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Nonstructural Protein 11 of Porcine Reproductive and Respiratory Syndrome Virus Induces STAT2 Degradation To Inhibit Interferon Signaling. J Virol 2019; 93:JVI.01352-19. [PMID: 31462568 DOI: 10.1128/jvi.01352-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/25/2019] [Indexed: 12/31/2022] Open
Abstract
Interferons (IFNs) play a crucial role in host antiviral response by activating the JAK/STAT (Janus kinase/signal transducer and activator of transcription) signaling pathway to induce the expression of myriad genes. STAT2 is a key player in the IFN-activated JAK/STAT signaling. Porcine reproductive and respiratory syndrome virus (PRRSV) is an important viral pathogen, causing huge losses to the swine industry. PRRSV infection elicits a meager protective immune response in pigs. The objective of this study was to investigate the effect of PRRSV on STAT2 signaling. Here, we demonstrated that PRRSV downregulated STAT2 to inhibit IFN-activated signaling. PRRSV strains of both PRRSV-1 and PRRSV-2 species reduced the STAT2 protein level, whereas the STAT2 transcript level had minimal change. PRRSV reduced the STAT2 level in a dose-dependent manner and shortened STAT2 half-life significantly from approximately 30 to 5 h. PRRSV-induced STAT2 degradation could be restored by treatment with the proteasome inhibitor MG132 and lactacystin. In addition, PRRSV nonstructural protein 11 (nsp11) was identified to interact with and reduce STAT2. The N-terminal domain (NTD) of nsp11 was responsible for STAT2 degradation and interacted with STAT2 NTD and the coiled-coil domain. Mutagenesis analysis showed that the amino acid residue K59 of nsp11 was indispensable for inducing STAT2 reduction. Mutant PRRSV with the K59A mutation generated by reverse genetics almost lost the ability to reduce STAT2. Together, these results demonstrate that PRRSV nsp11 antagonizes IFN signaling via mediating STAT2 degradation and provide further insights into the PRRSV interference of the innate immunity.IMPORTANCE PRRSV infection elicits a meager protective immune response in pigs. One of the possible reasons is that PRRSV antagonizes interferon induction and its downstream signaling. Interferons are key components in the innate immunity and play crucial roles against viral infection and in the activation of adaptive immune response via JAK/STAT signaling. STAT2 is indispensable in the JAK/STAT signaling since it is also involved in activation of antiviral activity in the absence of STAT1. Here, we discovered that PRRSV nsp11 downregulates STAT2. Interestingly, the N-terminal domain of nsp11 is responsible for inducing STAT2 degradation and directly interacts with STAT2 N-terminal domain. We also identified a crucial amino acid residue K59 in nsp11 since a mutation of it led to loss of the ability to downregulate STAT2. A mutant PRRSV with mutation of K59 had minimal effect on STAT2 reduction. Our data provide further insights into PRRSV interference with interferon signaling.
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Napthine S, Bell S, Hill CH, Brierley I, Firth AE. Characterization of the stimulators of protein-directed ribosomal frameshifting in Theiler's murine encephalomyelitis virus. Nucleic Acids Res 2019; 47:8207-8223. [PMID: 31180502 PMCID: PMC6735917 DOI: 10.1093/nar/gkz503] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/24/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023] Open
Abstract
Many viruses utilize programmed -1 ribosomal frameshifting (-1 PRF) to express additional proteins or to produce frameshift and non-frameshift protein products at a fixed stoichiometric ratio. PRF is also utilized in the expression of a small number of cellular genes. Frameshifting is typically stimulated by signals contained within the mRNA: a 'slippery' sequence and a 3'-adjacent RNA structure. Recently, we showed that -1 PRF in encephalomyocarditis virus (EMCV) is trans-activated by the viral 2A protein, leading to a temporal change in PRF efficiency from 0% to 70% during virus infection. Here we analyzed PRF in the related Theiler's murine encephalomyelitis virus (TMEV). We show that 2A is also required for PRF in TMEV and can stimulate PRF to levels as high as 58% in rabbit reticulocyte cell-free translations and 81% during virus infection. We also show that TMEV 2A trans-activates PRF on the EMCV signal but not vice versa. We present an extensive mutational analysis of the frameshift stimulators (mRNA signals and 2A protein) analysing activity in in vitro translation, electrophoretic mobility shift and in vitro ribosome pausing assays. We also investigate the PRF mRNA signal with RNA structure probing. Our results substantially extend previous characterization of protein-stimulated PRF.
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Affiliation(s)
- Sawsan Napthine
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Susanne Bell
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Chris H Hill
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Ian Brierley
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Andrew E Firth
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
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35
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Li Y, Firth AE, Brierley I, Cai Y, Napthine S, Wang T, Yan X, Kuhn JH, Fang Y. Programmed -2/-1 Ribosomal Frameshifting in Simarteriviruses: an Evolutionarily Conserved Mechanism. J Virol 2019; 93:e00370-19. [PMID: 31167906 PMCID: PMC6675879 DOI: 10.1128/jvi.00370-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023] Open
Abstract
The -2/-1 programmed ribosomal frameshifting (-2/-1 PRF) mechanism in porcine reproductive and respiratory syndrome virus (PRRSV) leads to the translation of two additional viral proteins, nonstructural protein 2TF (nsp2TF) and nsp2N. This -2/-1 PRF mechanism is transactivated by a viral protein, nsp1β, and cellular poly(rC) binding proteins (PCBPs). Critical elements for -2/-1 PRF, including a slippery sequence and a downstream C-rich motif, were also identified in 11 simarteriviruses. However, the slippery sequences (XXXUCUCU instead of XXXUUUUU) in seven simarteriviruses can only facilitate -2 PRF to generate nsp2TF. The nsp1β of simian hemorrhagic fever virus (SHFV) was identified as a key factor that transactivates both -2 and -1 PRF, and the universally conserved Tyr111 and Arg114 in nsp1β are essential for this activity. In vitro translation experiments demonstrated the involvement of PCBPs in simarterivirus -2/-1 PRF. Using SHFV reverse genetics, we confirmed critical roles of nsp1β, slippery sequence, and C-rich motif in -2/-1 PRF in SHFV-infected cells. Attenuated virus growth ability was observed in SHFV mutants with impaired expression of nsp2TF and nsp2N. Comparative genomic sequence analysis showed that key elements of -2/-1 PRF are highly conserved in all known arteriviruses except equine arteritis virus (EAV) and wobbly possum disease virus (WPDV). Furthermore, -2/-1 PRF with SHFV PRF signal RNA can be stimulated by heterotypic nsp1βs of all non-EAV arteriviruses tested. Taken together, these data suggest that -2/-1 PRF is an evolutionarily conserved mechanism employed in non-EAV/-WPDV arteriviruses for the expression of additional viral proteins that are important for viral replication.IMPORTANCE Simarteriviruses are a group of arteriviruses infecting nonhuman primates, and a number of new species have been established in recent years. Although these arteriviruses are widely distributed among African nonhuman primates of different species, and some of them cause lethal hemorrhagic fever disease, this group of viruses has been undercharacterized. Since wild nonhuman primates are historically important sources or reservoirs of human pathogens, there is concern that simarteriviruses may be preemergent zoonotic pathogens. Thus, molecular characterization of simarteriviruses is becoming a priority in arterivirology. In this study, we demonstrated that an evolutionarily conserved ribosomal frameshifting mechanism is used by simarteriviruses and other distantly related arteriviruses for the expression of additional viral proteins. This mechanism is unprecedented in eukaryotic systems. Given the crucial role of ribosome function in all living systems, the potential impact of the in-depth characterization of this novel mechanism reaches beyond the field of virology.
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Affiliation(s)
- Yanhua Li
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Yingyun Cai
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Sawsan Napthine
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Tao Wang
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
- Yangzhou University, Yangzhou, People's Republic of China
| | - Xingyu Yan
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Ying Fang
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
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36
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Wei C, Dai A, Fan J, Li Y, Chen A, Zhou X, Luo M, Yang X, Liu J. Efficacy of Type 2 PRRSV vaccine against challenge with the Chinese lineage 1 (NADC30-like) PRRSVs in pigs. Sci Rep 2019; 9:10781. [PMID: 31346199 PMCID: PMC6658503 DOI: 10.1038/s41598-019-47239-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 07/03/2019] [Indexed: 11/09/2022] Open
Abstract
The objective of the present study was to determine the cross-protection of Ingelvac PRRS MLV against challenge with the new lineage 1 PRRSV emerged in China in pigs. Two lineage 1 PRRSV strains (FJZ03 and FJWQ16 originated from recombination event between NADC30 and JXA1-like strain). We found that pigs vaccinated with the vaccine were protected against challenge with the FJZ03 as shown by fewer days of clinical fever, reduced lung pathology scores, lower PRRS virus load in the blood and developed broadly neutralizing antibodies with high titers to FJZ03. In contrast, vaccine provided limited protection against challenge with FJWQ16 with higher fever, lower antibody titers, lower neutralizing antibodies and higher viral loads in blood. These results demonstrate PRRSV-MLV provides incomplete protection against new lineage 1 PRRSVs.
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Affiliation(s)
- Chunhua Wei
- College of Life Sciences of Longyan University, Longyan, 364012, Fujian, China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China
| | - Ailing Dai
- College of Life Sciences of Longyan University, Longyan, 364012, Fujian, China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China
| | - Jialin Fan
- College of Life Sciences of Longyan University, Longyan, 364012, Fujian, China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China
| | - Yan Li
- College of Life Sciences of Longyan University, Longyan, 364012, Fujian, China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China
| | - Anni Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xia Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Manlin Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiaoyan Yang
- College of Life Sciences of Longyan University, Longyan, 364012, Fujian, China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China
| | - Jiankui Liu
- College of Life Sciences of Longyan University, Longyan, 364012, Fujian, China. .,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China. .,College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Abstract
Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Replication of HCoV is regulated by a diversity of host factors and induces drastic alterations in cellular structure and physiology. Activation of critical signaling pathways during HCoV infection modulates the induction of antiviral immune response and contributes to the pathogenesis of HCoV. Recent studies have begun to reveal some fundamental aspects of the intricate HCoV-host interaction in mechanistic detail. In this review, we summarize the current knowledge of host factors co-opted and signaling pathways activated during HCoV infection, with an emphasis on HCoV-infection-induced stress response, autophagy, apoptosis, and innate immunity. The cross talk among these pathways, as well as the modulatory strategies utilized by HCoV, is also discussed.
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Affiliation(s)
- To Sing Fung
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control and Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China;
| | - Ding Xiang Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control and Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China;
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38
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Abstract
Innovation follows discovery. If the 20th century was a golden age of discovery in the biomolecular biosciences, the current century may be remembered by the explosion of beneficial devices and therapies conceived by the bioengineers of the era. Much as the development of solid-state electronic components made possible the information revolution, the rational combining of millions of basic molecular control modules will enable the development of highly sophisticated biomachines that will make today's smartphones appear rudimentary. The molecular toolbox is already well-stocked, particularly in our ability to manipulate DNA, control transcription, generate functionally novel hybrid proteins, and expand the genetic code to include unnatural amino acids. This review focuses on how RNA-based regulatory modules that direct alternative readings of the genetic code can be employed as basic circuit components to expand our ability to control gene expression.
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Affiliation(s)
- Jonathan D Dinman
- From the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
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39
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Stern-Ginossar N, Thompson SR, Mathews MB, Mohr I. Translational Control in Virus-Infected Cells. Cold Spring Harb Perspect Biol 2019; 11:a033001. [PMID: 29891561 PMCID: PMC6396331 DOI: 10.1101/cshperspect.a033001] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As obligate intracellular parasites, virus reproduction requires host cell functions. Despite variations in genome size and configuration, nucleic acid composition, and their repertoire of encoded functions, all viruses remain unconditionally dependent on the protein synthesis machinery resident within their cellular hosts to translate viral messenger RNAs (mRNAs). A complex signaling network responsive to physiological stress, including infection, regulates host translation factors and ribosome availability. Furthermore, access to the translation apparatus is patrolled by powerful host immune defenses programmed to restrict viral invaders. Here, we review the tactics and mechanisms used by viruses to appropriate control over host ribosomes, subvert host defenses, and dominate the infected cell translational landscape. These not only define aspects of infection biology paramount for virus reproduction, but continue to drive fundamental discoveries into how cellular protein synthesis is controlled in health and disease.
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Affiliation(s)
- Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sunnie R Thompson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey 07103
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016
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40
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A Nanobody Targeting Viral Nonstructural Protein 9 Inhibits Porcine Reproductive and Respiratory Syndrome Virus Replication. J Virol 2019; 93:JVI.01888-18. [PMID: 30463975 DOI: 10.1128/jvi.01888-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/13/2018] [Indexed: 11/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is of great concern to the swine industry due to pandemic outbreaks of the disease, current ineffective vaccinations, and a lack of efficient antiviral strategies. In our previous study, a PRRSV Nsp9-specific nanobody, Nb6, was successfully isolated, and the intracellularly expressed Nb6 could dramatically inhibit PRRSV replication in MARC-145 cells. However, despite its small size, the application of Nb6 protein in infected cells is greatly limited, as the protein itself cannot enter the cells physically. In this study, a trans-activating transduction (TAT) peptide was fused with Nb6 to promote protein entry into cells. TAT-Nb6 was expressed as an inclusion body in Escherichia coli, and indirect enzyme-linked immunosorbent assays and pulldown assays showed that E. coli-expressed TAT-Nb6 maintained the binding ability to E. coli-expressed or PRRSV-encoded Nsp9. We demonstrated that TAT delivered Nb6 into MARC-145 cells and porcine alveolar macrophages (PAMs) in a dose- and time-dependent manner, and TAT-Nb6 efficiently inhibited the replication of several PRRSV genotype 2 strains as well as a genotype 1 strain. Using a yeast two-hybrid assay, Nb6 recognition sites were identified in the C-terminal part of Nsp9 and spanned two discontinuous regions (Nsp9aa454-551 and Nsp9aa599-646). Taken together, these results suggest that TAT-Nb6 can be developed as an antiviral drug for the inhibition of PRRSV replication and controlling PRRS disease.IMPORTANCE The pandemic outbreak of PRRS, which is caused by PRRSV, has greatly affected the swine industry. We still lack an efficient vaccine, and it is an immense challenge to control its infection. An intracellularly expressed Nsp9-specific nanobody, Nb6, has been shown to be able to inhibit PRRSV replication in MARC-145 cells. However, its application is limited, because Nb6 cannot physically enter cells. Here, we demonstrated that the cell-penetrating peptide TAT could deliver Nb6 into cultured cells. In addition, TAT-Nb6 fusion protein could suppress the replication of various PRRSV strains in MARC-145 cells and PAMs. These findings may provide a new approach for drug development to control PRRS.
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41
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Mapping the Nonstructural Protein Interaction Network of Porcine Reproductive and Respiratory Syndrome Virus. J Virol 2018; 92:JVI.01112-18. [PMID: 30282705 DOI: 10.1128/jvi.01112-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/25/2018] [Indexed: 12/13/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a positive-stranded RNA virus belonging to the family Arteriviridae Synthesis of the viral RNA is directed by replication/transcription complexes (RTC) that are mainly composed of a network of PRRSV nonstructural proteins (nsps) and likely cellular proteins. Here, we mapped the interaction network among PRRSV nsps by using yeast two-hybrid screening in conjunction with coimmunoprecipitation (co-IP) and cotransfection assays. We identified a total of 24 novel interactions and found that the interactions were centered on open reading frame 1b (ORF1b)-encoded nsps that were mainly connected by the transmembrane proteins nsp2, nsp3, and nsp5. Interestingly, the interactions of the core enzymes nsp9 and nsp10 with transmembrane proteins did not occur in a straightforward manner, as they worked in the co-IP assay but were poorly capable of finding each other within intact mammalian cells. Further proof that they can interact within cells required the engineering of N-terminal truncations of both nsp9 and nsp10. However, despite the poor colocalization relationship in cotransfected cells, both nsp9 and nsp10 came together with membrane proteins (e.g., nsp2) at the viral replication and transcription complexes (RTC) in PRRSV-infected cells. Thus, our results indicate the existence of a complex interaction network among PRRSV nsps and raise the possibility that the recruitment of key replicase proteins to membrane-associated nsps may involve some regulatory mechanisms during infection.IMPORTANCE Synthesis of PRRSV RNAs within host cells depends on the efficient and correct assembly of RTC that takes places on modified intracellular membranes. As an important step toward dissecting this poorly understood event, we investigated the interaction network among PRRSV nsps. Our studies established a comprehensive interaction map for PRRSV nsps and revealed important players within the network. The results also highlight the likely existence of a regulated recruitment of the PRRSV core enzymes nsp9 and nsp10 to viral membrane nsps during PRRSV RTC assembly.
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Wang J, Zhou J, Yang Q, Grayhack EJ. Multi-protein bridging factor 1(Mbf1), Rps3 and Asc1 prevent stalled ribosomes from frameshifting. eLife 2018; 7:39637. [PMID: 30465652 PMCID: PMC6301793 DOI: 10.7554/elife.39637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022] Open
Abstract
Reading frame maintenance is critical for accurate translation. We show that the conserved eukaryotic/archaeal protein Mbf1 acts with ribosomal proteins Rps3/uS3 and eukaryotic Asc1/RACK1 to prevent frameshifting at inhibitory CGA-CGA codon pairs in the yeast Saccharomyces cerevisiae. Mutations in RPS3 that allow frameshifting implicate eukaryotic conserved residues near the mRNA entry site. Mbf1 and Rps3 cooperate to maintain the reading frame of stalled ribosomes, while Asc1 also mediates distinct events that result in recruitment of the ribosome quality control complex and mRNA decay. Frameshifting occurs through a +1 shift with a CGA codon in the P site and involves competition between codons entering the A site, implying that the wobble interaction of the P site codon destabilizes translation elongation. Thus, eukaryotes have evolved unique mechanisms involving both a universally conserved ribosome component and two eukaryotic-specific proteins to maintain the reading frame at ribosome stalls. Proteins perform all the chemical reactions needed to keep a cell alive; thus, it is essential to assemble them correctly. They are made by molecular machines called ribosomes, which follow a sequence of instructions written in genetic code in molecules known as mRNAs. Ribosomes essentially read the genetic code three letters at a time; each triplet either codes for the insertion of one of 20 building blocks into the emerging protein, or serves as a signal to stop the process. It is critical that, after reading one triplet, the ribosome moves precisely three letters to read the next triplet. If, for example, the ribosome shifted just two letters instead of three – a phenomenon known as “frameshifting” – it would completely change the building blocks that were used to make the protein. This could lead to atypical or aberrant proteins that either do not work or are even toxic to the cell. For a variety of reasons, ribosomes will often stall before they have finished building a protein. When this happens, the ribosome is more likely to frameshift. Cells commonly respond to stalled ribosomes by recruiting other molecules that work as quality control systems, some of which can disassemble the ribosome and break down the mRNA. In budding yeast, one part of the ribosome – named Asc1 – plays a key role in recruiting these quality control systems and in mRNA breakdown. If this component is removed, stalled ribosomes frameshift more frequently and, as a result, aberrant proteins accumulate in the cell. Since the Asc1 recruiter protein sits on the outside of the ribosome, it seemed likely that it might act through other factors to stop the ribosome from frameshifting when it stalls. However, it was unknown if such factors exist, what they are, or how they might work. Now, Wang et al. have identified two additional yeast proteins, named Mbf1 and Rps3, which cooperate to stop the ribosome from frameshifting after it stalls. Rps3, like Asc1, is a component of the ribosome, while Mbf1 is not. It appears that Rps3 likely stops frameshifting via an interaction with the incoming mRNA, because a region of Rps3 near the mRNA entry site to the ribosome is important for its activity. Further experiments then showed that the known Asc1-mediated breakdown of mRNAs did not depend on Mbf1 and Rps3, but also assists in stopping frameshifting. Thus, frameshifting of stalled ribosomes is prevented via two distinct ways: one that directly involves Mbf1 and Rps3 and one that is promoted by Asc1, which reduces the amounts of mRNAs on which ribosomes frameshift. These newly identified factors may provide insights into the precisely controlled protein-production machinery in the cell and into roles of the quality control systems. An improved understanding of mechanisms that prevent frameshifting could eventually lead to better treatments for some human diseases that result when these processes go awry, which include certain neurological conditions.
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Affiliation(s)
- Jiyu Wang
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York.,Center for RNA Biology, University of Rochester, Rochester, New York
| | - Jie Zhou
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York
| | - Qidi Yang
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York
| | - Elizabeth J Grayhack
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York.,Center for RNA Biology, University of Rochester, Rochester, New York
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Double-stranded viral RNA persists in vitro and in vivo during prolonged infection of porcine reproductive and respiratory syndrome virus. Virology 2018; 524:78-89. [DOI: 10.1016/j.virol.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022]
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RAJKHOWA TK, VANLALRUATI C, SINGH YD, RAVINDRAN R, ARYA RS. Genetic variation of highly pathogenic Indian porcine reproductive and respiratory syndrome viruses after introduction in 2013. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i10.84071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
To study its possible link to pathogenicity, the genomic variation in full ORF5 and ORF7 genes, and their encoded proteins in 26 field HP-PRRSV isolates from three major HP-PRRS outbreaks occurred in India, since 2013 was analysed. Sequence analysis and phylogenetic tree revealed involvement of genetically different strain in each outbreak of India rather persistence of a single strain. Analysis and comparison of N protein amino acid sequences of HP-PRRSV with VR2332 revealed consistent mutation at position 15D to N or K and 46 K to R in all the HP-PRRSV. GP5 protein showed consistent mutations at 29 positions from that of VR2332. The potential Nglycosylation sites in GP5 was found variable from 4–5 with one additional N-glycan moiety around the neutralizing epitope B. However, the ‘decoy’ epitope A was found highly conserved in all the HP-PRRSV.
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Chung CJ, Cha SH, Grimm AL, Ajithdoss D, Rzepka J, Chung G, Yu J, Davis WC, Ho CS. Pigs that recover from porcine reproduction and respiratory syndrome virus infection develop cytotoxic CD4+CD8+ and CD4+CD8- T-cells that kill virus infected cells. PLoS One 2018; 13:e0203482. [PMID: 30188946 PMCID: PMC6126854 DOI: 10.1371/journal.pone.0203482] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/21/2018] [Indexed: 11/24/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) infection is difficult to control because the virus undergoes antigenic variation during infection and also modulates the protective host immune response. Although current vaccines do not provide full protection, they have provided insight into the mechanisms of protection. Live PRRSV vaccines induce partial protection before the appearance of neutralizing antibody, suggesting cell-mediated immunity or other mechanisms may be involved. Herein, we demonstrate recovery from infection is associated with development of cytotoxic T-lymphocytes (CTL) that can kill PRRSV-infected target cells. Initial experiments showed survival of PRRSV-infected monocyte derived macrophage (MDM) targets is reduced when overlaid with peripheral blood mononuclear cells (PBMC) from gilts that had recovered from PRRSV infection. Further studies with PBMC depleted of either CD4+ or CD8+ T-cells and positively selected subpopulations of CD4+ and CD8+ T-cells showed that both CD4+ and CD8+ T-cells were involved in killing. Examination of killing at different time points revealed killing was biphasic and mediated by CTL of different phenotypes. CD4+CD8+high were associated with killing target cells infected for 3–6 hours. CD4+CD8- CTL were associated with killing at 16–24 hours. Thus, all the anti-PRRSV CTL activity in pigs was attributed to two phenotypes of CD4+ cells which is different from the anti-viral CD4-CD8+ CTL phenotype found in most other animals. These findings will be useful for evaluating CTL responses induced by current and future vaccines, guiding to a novel direction for future vaccine development.
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Affiliation(s)
- Chungwon J. Chung
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
- VMRD Inc., Pullman, Washington, United States of America
- * E-mail: (CJC); (SHC)
| | - Sang-Ho Cha
- Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
- * E-mail: (CJC); (SHC)
| | | | - Dharani Ajithdoss
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Joanna Rzepka
- VMRD Inc., Pullman, Washington, United States of America
| | - Grace Chung
- VMRD Inc., Pullman, Washington, United States of America
| | - Jieun Yu
- Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - William C. Davis
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Chak-Sum Ho
- Gift of life Michigan, Ann Arbor, Michigan, United States of America
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Dever TE, Dinman JD, Green R. Translation Elongation and Recoding in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a032649. [PMID: 29610120 DOI: 10.1101/cshperspect.a032649] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this review, we highlight the current understanding of translation elongation and recoding in eukaryotes. In addition to providing an overview of the process, recent advances in our understanding of the role of the factor eIF5A in both translation elongation and termination are discussed. We also highlight mechanisms of translation recoding with a focus on ribosomal frameshifting during elongation. We see that the balance between the basic steps in elongation and the less common recoding events is determined by the kinetics of the different processes as well as by specific sequence determinants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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Vanmechelen B, Vergote V, Laenen L, Koundouno FR, Bore JA, Wada J, Kuhn JH, Carroll MW, Maes P. Expanding the Arterivirus Host Spectrum: Olivier's Shrew Virus 1, A Novel Arterivirus Discovered in African Giant Shrews. Sci Rep 2018; 8:11171. [PMID: 30042503 PMCID: PMC6057926 DOI: 10.1038/s41598-018-29560-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022] Open
Abstract
The family Arteriviridae harbors a rapidly expanding group of viruses known to infect a divergent group of mammals, including horses, pigs, possums, primates, and rodents. Hosts infected with arteriviruses present with a wide variety of (sub) clinical symptoms, depending on the virus causing the infection and the host being infected. In this study, we determined the complete genome sequences of three variants of a previously unknown virus found in Olivier's shrews (Crocidura olivieri guineensis) sampled in Guinea. On the nucleotide level, the three genomes of this new virus, named Olivier's shrew virus 1 (OSV-1), are 88-89% similar. The genome organization of OSV-1 is characteristic of all known arteriviruses, yet phylogenetic analysis groups OSV-1 separately from all currently established arterivirus lineages. Therefore, we postulate that OSV-1 represents a member of a novel arterivirus genus. The virus described here represents the first discovery of an arterivirus in members of the order Eulipotyphla, thereby greatly expanding the known host spectrum of arteriviruses.
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Affiliation(s)
- Bert Vanmechelen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49-Box 1040, BE3000, Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49-Box 1040, BE3000, Leuven, Belgium
| | - Lies Laenen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49-Box 1040, BE3000, Leuven, Belgium
| | | | | | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, Maryland, 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, Maryland, 21702, USA
| | - Miles W Carroll
- Research & Development Institute, National Infections Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Piet Maes
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49-Box 1040, BE3000, Leuven, Belgium.
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Identification of the RNA Pseudoknot within the 3' End of the Porcine Reproductive and Respiratory Syndrome Virus Genome as a Pathogen-Associated Molecular Pattern To Activate Antiviral Signaling via RIG-I and Toll-Like Receptor 3. J Virol 2018; 92:JVI.00097-18. [PMID: 29618647 DOI: 10.1128/jvi.00097-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/28/2018] [Indexed: 12/24/2022] Open
Abstract
Once infected by viruses, cells can detect pathogen-associated molecular patterns (PAMPs) on viral nucleic acid by host pattern recognition receptors (PRRs) to initiate the antiviral response. Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of porcine reproductive and respiratory syndrome (PRRS), characterized by reproductive failure in sows and respiratory diseases in pigs of different ages. To date, the sensing mechanism of PRRSV has not been elucidated. Here, we reported that the pseudoknot region residing in the 3' untranslated regions (UTR) of the PRRSV genome, which has been proposed to regulate RNA synthesis and virus replication, was sensed as nonself by retinoic acid-inducible gene I (RIG-I) and Toll-like receptor 3 (TLR3) and strongly induced type I interferons (IFNs) and interferon-stimulated genes (ISGs) in porcine alveolar macrophages (PAMs). The interaction between the two stem-loops inside the pseudoknot structure was sufficient for IFN induction, since disruption of the pseudoknot interaction powerfully dampened the IFN induction. Furthermore, transfection of the 3' UTR pseudoknot transcripts in PAMs inhibited PRRSV replication in vitro Importantly, the predicted similar structures of other arterivirus members, including equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), and simian hemorrhagic fever virus (SHFV), also displayed strong IFN induction activities. Together, in this work we identified an innate recognition mechanism by which the PRRSV 3' UTR pseudoknot region served as PAMPs of arteriviruses and activated innate immune signaling to produce IFNs that inhibit virus replication. All of these results provide novel insights into innate immune recognition during virus infection.IMPORTANCE PRRS is the most common viral disease in the pork industry. It is caused by PRRSV, a positive single-stranded RNA virus, whose infection often leads to persistent infection. To date, it is not yet clear how PRRSV is recognized by the host and what is the exact mechanism of IFN induction. Here, we investigated the nature of PAMPs on PRRSV and the associated PRRs. We found that the 3' UTR pseudoknot region of PRRSV, which has been proposed to regulate viral RNA synthesis, could act as PAMPs recognized by RIG-I and TLR3 to induce type I IFN production to suppress PRRSV infection. This report is the first detailed description of pattern recognition for PRRSV, which is important in understanding the antiviral response of arteriviruses, especially PRRSV, and extends our knowledge on virus recognition.
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Karyopherin Alpha 6 Is Required for Replication of Porcine Reproductive and Respiratory Syndrome Virus and Zika Virus. J Virol 2018; 92:JVI.00072-18. [PMID: 29444946 DOI: 10.1128/jvi.00072-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/09/2018] [Indexed: 12/16/2022] Open
Abstract
Movement of macromolecules between the cytoplasm and the nucleus occurs through the nuclear pore complex (NPC). Karyopherins comprise a family of soluble transport factors facilitating the nucleocytoplasmic translocation of proteins through the NPC. In this study, we found that karyopherin α6 (KPNA6; also known as importin α7) was required for the optimal replication of porcine reproductive and respiratory syndrome virus (PRRSV) and Zika virus (ZIKV), which are positive-sense, single-stranded RNA viruses replicating in the cytoplasm. The KPNA6 protein level in virus-infected cells was much higher than that in mock-infected controls, whereas the KPNA6 transcript remains stable. Viral infection blocked the ubiquitin-proteasomal degradation of KPNA6, which led to an extension of the KPNA6 half-life and the elevation of the KPNA6 level in comparison to mock-infected cells. PRRSV nsp12 protein induced KPNA6 stabilization. KPNA6 silencing was detrimental to the replication of PRRSV, and KPNA6 knockout impaired ZIKV replication. Moreover, KPNA6 knockout blocked the nuclear translocation of PRRSV nsp1β but had a minimal effect on two other PRRSV proteins with nuclear localization. Exogenous restitution of KPNA6 expression in the KPNA6-knockout cells results in restoration of the nuclear translocation of PRRSV nsp1β and the replication of ZIKV. These results indicate that KPNA6 is an important cellular factor for the replication of PRRSV and ZIKV.IMPORTANCE Positive-sense, single-stranded RNA (+ssRNA) viruses replicate in the cytoplasm of infected cells. The roles of transport factors in the nucleocytoplasmic trafficking system for the replication of +ssRNA viruses are not known. In this study, we discovered that PRRSV and ZIKV viruses needed karyopherin α6 (KPNA6), one of the transport factors, to enhance the virus replication. Our data showed that viral infection induced an elevation of the KPNA6 protein level due to an extension of the KPNA6 half-life via viral interference of the ubiquitin-proteasomal degradation of KPNA6. Notably, KPNA6 silencing or knockout dramatically reduced the replication of PRRSV and ZIKV. PRRSV nsp1β depended on KPNA6 to translocate into the nucleus. In addition, exogenous restitution of KPNA6 expression in KPNA6-knockout cells led to the restoration of nsp1β nuclear translocation and ZIKV replication. These results reveal a new aspect in the virus-cell interaction and may facilitate the development of novel antiviral therapeutics.
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Intercellular transfer of mitochondria rescues virus-induced cell death but facilitates cell-to-cell spreading of porcine reproductive and respiratory syndrome virus. Virology 2018; 517:122-134. [DOI: 10.1016/j.virol.2017.12.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 11/21/2022]
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