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Qi H, Yin M, Xiong F, Ren X, Chen K, Qin HB, Wang E, Chen G, Yang L, Liu LD, Zhang H, Cao X, Fraser NW, Luo MH, Zeng WB, Zhou J. ICP22-defined condensates mediate RNAPII deubiquitylation by UL36 and promote HSV-1 transcription. Cell Rep 2024; 43:114792. [PMID: 39383039 DOI: 10.1016/j.celrep.2024.114792] [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: 07/31/2023] [Revised: 07/29/2024] [Accepted: 09/07/2024] [Indexed: 10/11/2024] Open
Abstract
Herpes simplex virus type I (HSV-1) infection leads to RNA polymerase II (RNAPII) degradation and host transcription shutdown. We show that ICP22 defines the virus-induced chaperone-enriched (VICE) domain through liquid-liquid phase separation. Condensate-disrupting point mutations of ICP22 increase ubiquitin modification of RNAPII Ser-2P; reduce its level and occupancy on viral genes; impair viral gene expression, particularly late genes; and severely reduce viral titers. When proteasome activity is blocked, ubiquitinated RNAPII Ser-2P and the viral UL36 begin to accumulate in the ICP22 condensates. The ubiquitin-specific protease (USP) deubiquitinase domain of UL36 interacts with and erases ubiquitin modification from RNAPII Ser-2P, protecting it from degradation in infected cells. A virus carrying a catalytic mutant of the UL36 USP diminishes cellular RNAPII Ser-2P levels, viral transcription, and growth. Thus, ICP22 condensates are processing centers where RNAPII Ser-2P is recruited to be deubiquitinated to ensure viral transcription when host transcription is disrupted following infection.
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Affiliation(s)
- Hansong Qi
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Yunnan 650201, China
| | - Mengqiu Yin
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Yunnan 650201, China
| | - Feng Xiong
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiaoli Ren
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Kangning Chen
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Yunnan 650201, China
| | - Hai-Bin Qin
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Erlin Wang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Guijun Chen
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Liping Yang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Long-Ding Liu
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming 650118, China
| | - Hui Zhang
- Department of Ophthalmology, The First Affiliated Hospital Kunming Medical University, Kunming 650032, China
| | - Xia Cao
- Key Laboratory of Second Affiliated Hospital of Kunming Medical University, Kunming 650000, China
| | - Nigel W Fraser
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Min-Hua Luo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wen-Bo Zeng
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Jumin Zhou
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China.
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2
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Luo J, Yu Y, Wang K, He S, Wang L, Liang F, Chin JW, Tang S. Capturing acyl-enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification. Nat Protoc 2024; 19:2967-2999. [PMID: 38867073 DOI: 10.1038/s41596-024-01006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/29/2024] [Indexed: 06/14/2024]
Abstract
Catalytic mechanism-based, light-activated traps have recently been developed to identify the substrates of cysteine or serine hydrolases. These traps are hydrolase mutants whose catalytic cysteine or serine are replaced with genetically encoded 2,3-diaminopropionic acid (DAP). DAP-containing hydrolases specifically capture the transient thioester- or ester-linked acyl-enzyme intermediates resulting from the first step of the proteolytic reaction as their stable amide analogs. The trapped substrate fragments allow the downstream identification of hydrolase substrates by mass spectrometry and immunoblotting. In this protocol, we provide a detailed step-by-step guide for substrate capture and identification of the peptidase domain of the large tegument protein deneddylase (UL36USP) from human herpesvirus 1, both in mammalian cell lysate and live mammalian cells. Four procedures are included: Procedure 1, DAP-mediated substrate trapping in mammalian cell lysate (~8 d); Procedure 2, DAP-mediated substrate trapping in adherent mammalian cells (~6 d); Procedure 3, DAP-mediated substrate trapping in suspension mammalian cells (~5 d); and Procedure 4, substrate identification and validation (~12-13 d). Basic skills to perform protein expression in bacteria or mammalian cells, affinity enrichment and proteomic analysis are required to implement the protocol. This protocol will be a practical guide for identifying substrates of serine or cysteine hydrolases either in a complex mixture, where genetic manipulation is challenging, or in live cells such as bacteria, yeasts and mammalian cells.
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Affiliation(s)
- Juan Luo
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yao Yu
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ke Wang
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Sizhe He
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Longjie Wang
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fangfang Liang
- Department of Medical Oncology, Guangxi Medical University First Affiliated Hospital, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Shan Tang
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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3
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Döhner K, Serrero MC, Viejo-Borbolla A, Sodeik B. A Hitchhiker's Guide Through the Cell: The World According to the Capsids of Alphaherpesviruses. Annu Rev Virol 2024; 11:215-238. [PMID: 38954634 DOI: 10.1146/annurev-virology-100422-022751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The nucleoplasm, the cytosol, the inside of virions, and again the cytosol comprise the world in which the capsids of alphaherpesviruses encounter viral and host proteins that support or limit them in performing their tasks. Here, we review the fascinating conundrum of how specific protein-protein interactions late in alphaherpesvirus infection orchestrate capsid nuclear assembly, nuclear egress, and cytoplasmic envelopment, but target incoming capsids to the nuclear pores in naive cells to inject the viral genomes into the nucleoplasm for viral transcription and replication. Multiple capsid interactions with viral and host proteins have been characterized using viral mutants and assays that reconstitute key stages of the infection cycle. Keratinocytes, fibroblasts, mucosal epithelial cells, neurons, and immune cells employ cell type-specific intrinsic and cytokine-induced resistance mechanisms to restrict several stages of the viral infection cycle. However, concomitantly, alphaherpesviruses have evolved countermeasures to ensure efficient capsid function during infection.
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Affiliation(s)
- Katinka Döhner
- Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
- RESIST Cluster of Excellence, Hannover Medical School, Hannover, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany;
| | - Manutea Christophe Serrero
- Department of Biomedicine and Center for Immunology of Viral Infections, Aarhus University, Aarhus, Denmark
- RESIST Cluster of Excellence, Hannover Medical School, Hannover, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany;
| | - Abel Viejo-Borbolla
- RESIST Cluster of Excellence, Hannover Medical School, Hannover, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany;
| | - Beate Sodeik
- DZIF German Centre for Infection Research, Partner Site Hannover-Braunschweig, Hannover, Germany
- RESIST Cluster of Excellence, Hannover Medical School, Hannover, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany;
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4
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Yuan F, Gollapudi S, Day KJ, Ashby G, Sangani A, Malady BT, Wang L, Lafer EM, Huibregtse JM, Stachowiak JC. Ubiquitin-driven protein condensation stabilizes clathrin-mediated endocytosis. PNAS NEXUS 2024; 3:pgae342. [PMID: 39253396 PMCID: PMC11382290 DOI: 10.1093/pnasnexus/pgae342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 09/11/2024]
Abstract
Clathrin-mediated endocytosis is an essential cellular pathway that enables signaling and recycling of transmembrane proteins and lipids. During endocytosis, dozens of cytosolic proteins come together at the plasma membrane, assembling into a highly interconnected network that drives endocytic vesicle biogenesis. Recently, multiple groups have reported that early endocytic proteins form flexible condensates, which provide a platform for efficient assembly of endocytic vesicles. Given the importance of this network in the dynamics of endocytosis, how might cells regulate its stability? Many receptors and endocytic proteins are ubiquitylated, while early endocytic proteins such as Eps15 contain ubiquitin-interacting motifs. Therefore, we examined the influence of ubiquitin on the stability of the early endocytic protein network. In vitro, we found that recruitment of small amounts of polyubiquitin dramatically increased the stability of Eps15 condensates, suggesting that ubiquitylation could nucleate endocytic assemblies. In live-cell imaging experiments, a version of Eps15 that lacked the ubiquitin-interacting motif failed to rescue defects in endocytic initiation created by Eps15 knockout. Furthermore, fusion of Eps15 to a deubiquitylase enzyme destabilized nascent endocytic sites within minutes. In both in vitro and live-cell settings, dynamic exchange of Eps15 proteins, a measure of protein network stability, was decreased by Eps15-ubiquitin interactions and increased by loss of ubiquitin. These results collectively suggest that ubiquitylation drives assembly of the flexible protein network responsible for catalyzing endocytic events. More broadly, this work illustrates a biophysical mechanism by which ubiquitylated transmembrane proteins at the plasma membrane could regulate the efficiency of endocytic internalization.
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Affiliation(s)
- Feng Yuan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sadhana Gollapudi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kasey J Day
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Grant Ashby
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Arjun Sangani
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brandon T Malady
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Liping Wang
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Eileen M Lafer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jon M Huibregtse
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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5
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Ferdoush J, Abdul Kadir R, Simay Kaplanoglu S, Osborn M. SARS-CoV-2 and UPS with potentials for therapeutic interventions. Gene 2024; 912:148377. [PMID: 38490508 DOI: 10.1016/j.gene.2024.148377] [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: 01/19/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The Ubiquitin proteasome system (UPS), an essential eukaryotic/host/cellular post-translational modification (PTM), plays a critical role in the regulation of diverse cellular functions including regulation of protein stability, immune signaling, antiviral activity, as well as virus replication. Although UPS regulation of viral proteins may be utilized by the host as a defense mechanism to invade viruses, viruses may have adapted to take advantage of the host UPS. This system can be manipulated by viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to stimulate various steps of the viral replication cycle and facilitate pathogenesis, thereby causing the respiratory disease COVID-19. Many SARS-CoV-2 encoded proteins including open reading frame 3a (ORF3a), ORF6, ORF7a, ORF9b, and ORF10 interact with the host's UPS machinery, influencing host immune signaling and apoptosis. Moreover, SARS-CoV-2 encoded papain-like protease (PLpro) interferes with the host UPS to facilitate viral replication and to evade the host's immune system. These alterations in SARS-CoV-2 infected cells have been revealed by various proteomic studies, suggesting potential targets for clinical treatment. To provide insight into the underlying causes of COVID-19 and suggest possible directions for therapeutic interventions, this paper reviews the intricate relationship between SARS-CoV-2 and UPS. Promising treatment strategies are also investigated in this paper including targeting PLpro with zinc-ejector drugs, as well as targeting viral non-structural protein (nsp12) via heat treatment associated ubiquitin-mediated proteasomal degradation to reduce viral pathogenesis.
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Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Selin Simay Kaplanoglu
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Morgan Osborn
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
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6
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Velez-Brochero M, Behera P, Afreen KS, Odle A, Rajsbaum R. Ubiquitination in viral entry and replication: Mechanisms and implications. Adv Virus Res 2024; 119:1-38. [PMID: 38897707 DOI: 10.1016/bs.aivir.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The ubiquitination process is a reversible posttranslational modification involved in many essential cellular functions, such as innate immunity, cell signaling, trafficking, protein stability, and protein degradation. Viruses can use the ubiquitin system to efficiently enter host cells, replicate and evade host immunity, ultimately enhancing viral pathogenesis. Emerging evidence indicates that enveloped viruses can carry free (unanchored) ubiquitin or covalently ubiquitinated viral structural proteins that can increase the efficiency of viral entry into host cells. Furthermore, viruses continuously evolve and adapt to take advantage of the host ubiquitin machinery, highlighting its importance during virus infection. This review discusses the battle between viruses and hosts, focusing on how viruses hijack the ubiquitination process at different steps of the replication cycle, with a specific emphasis on viral entry. We discuss how ubiquitination of viral proteins may affect tropism and explore emerging therapeutics strategies targeting the ubiquitin system for antiviral drug discovery.
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Affiliation(s)
- Maria Velez-Brochero
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States
| | - Padmanava Behera
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States
| | - Kazi Sabrina Afreen
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States
| | - Abby Odle
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States
| | - Ricardo Rajsbaum
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States.
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7
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Yuan F, Gollapudi S, Day K, Ashby G, Sangani A, Malady B, Wang L, Lafer EM, Huibregtse J, Stachowiak J. Ubiquitin-driven protein condensation initiates clathrin-mediated endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.21.554139. [PMID: 37662320 PMCID: PMC10473642 DOI: 10.1101/2023.08.21.554139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Clathrin-mediated endocytosis is an essential cellular pathway that enables signaling and recycling of transmembrane proteins and lipids. During endocytosis, dozens of cytosolic proteins come together at the plasma membrane, assembling into a highly interconnected network that drives endocytic vesicle biogenesis. Recently, multiple groups have reported that early endocytic proteins form flexible condensates, which provide a platform for efficient assembly of endocytic vesicles. Given the importance of this network in the dynamics of endocytosis, how might cells regulate its stability? Many receptors and endocytic proteins are ubiquitylated, while early endocytic proteins such as Eps15 contain ubiquitin-interacting motifs. Therefore, we examined the influence of ubiquitin on the stability of the early endocytic protein network. In vitro, we found that recruitment of small amounts of polyubiquitin dramatically increased the stability of Eps15 condensates, suggesting that ubiquitylation could nucleate endocytic assemblies. In live cell imaging experiments, a version of Eps15 that lacked the ubiquitin-interacting motif failed to rescue defects in endocytic initiation created by Eps15 knockout. Furthermore, fusion of Eps15 to a deubiquitylase enzyme destabilized nascent endocytic sites within minutes. In both in vitro and live cell settings, dynamic exchange of Eps15 proteins, a hallmark of liquidlike systems, was modulated by Eps15-Ub interactions. These results collectively suggest that ubiquitylation drives assembly of the flexible protein network responsible for catalyzing endocytic events. More broadly, this work illustrates a biophysical mechanism by which ubiquitylated transmembrane proteins at the plasma membrane could regulate the efficiency of endocytic recycling.
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8
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Rocchigiani AM, Bertoldi L, Coradduzza E, Lostia G, Pintus D, Scivoli R, Cancedda MG, Fiori MS, Bechere R, Murtino AP, Pala G, Cardeti G, Macioccu S, Dettori MA, Pintore A, Ligios C, Puggioni G. Whole-Genome Sequencing of Two Canine Herpesvirus 1 (CaHV-1) Isolates and Clinicopathological Outcomes of Infection in French Bulldog Puppies. Viruses 2024; 16:209. [PMID: 38399985 PMCID: PMC10893542 DOI: 10.3390/v16020209] [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: 12/19/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Canine herpesvirus 1 (CaHV-1) infects dogs, causing neonatal death and ocular, neurological, respiratory, and reproductive problems in adults. Although CaHV-1 is widespread in canine populations, only four studies have focused on the CaHV-1 whole genome. In such context, two CaHV-1 strains from both the kidney and spleen of 20-day-old deceased French Bulldog puppies were recently isolated in Sardinia, Italy. The extracted viral DNA underwent whole-genome sequencing using the Illumina MiSeq platform. The Italian CaHV-1 genomes were nearly identical (>99%), shared the same tree branch, and clustered near the ELAL-1 (MW353125) and BTU-1 (KX828242) strains, enlarging the completely separated clade discussed by Lewin et al., in 2020. This study aims to provide new insights on the evolution of the CaHV-1, based on high-resolution whole-genome phylogenetic analysis, and on its clinicopathological characterization during a fatal outbreak in puppies.
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Affiliation(s)
- Angela Maria Rocchigiani
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | | | - Elisabetta Coradduzza
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Giada Lostia
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Davide Pintus
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Rosario Scivoli
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Maria Giovanna Cancedda
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Mariangela Stefania Fiori
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Roberto Bechere
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Anna Pina Murtino
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Giovanni Pala
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Giusy Cardeti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, 00178 Roma, Italy;
| | - Simona Macioccu
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Maria Antonietta Dettori
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Antonio Pintore
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Ciriaco Ligios
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
| | - Giantonella Puggioni
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.M.R.); (G.L.); (D.P.); (R.S.); (M.G.C.); (M.S.F.); (R.B.); (A.P.M.); (G.P.); (S.M.); (M.A.D.); (A.P.); (C.L.); (G.P.)
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9
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Zheng JX, Du TY, Shao GC, Ma ZH, Jiang ZD, Hu W, Suo F, He W, Dong MQ, Du LL. Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers. Nat Commun 2023; 14:8334. [PMID: 38097609 PMCID: PMC10721834 DOI: 10.1038/s41467-023-44151-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. In several fission yeast species, single-gene KMDs belonging to the wtf gene family exert selfish killing by expressing a toxin and an antidote through alternative transcription initiation. Here we investigate how the toxin and antidote products of a wtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs PY motifs (Leu/Pro-Pro-X-Tyr) in its N-terminal cytosolic tail to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
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Affiliation(s)
- Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tong-Yang Du
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhu-Hui Ma
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wen Hu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wanzhong He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
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10
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Moghadasi SA, Moraes SN, Harris RS. Cellular Assays for Dynamic Quantification of Deubiquitinase Activity and Inhibition. J Mol Biol 2023; 435:168316. [PMID: 37858708 DOI: 10.1016/j.jmb.2023.168316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
Deubiquitinases (DUBs) are proteolytic enzymes that catalyze the removal of ubiquitin from protein substrates. The critical role of DUBs in regulating protein ubiquitination makes them attractive drug targets in oncology, neurodegenerative disease, and antiviral development. Biochemical assays for quantifying DUB activity have enabled characterization of substrate preferences and discovery of small molecule inhibitors. However, assessing the efficacy of these inhibitors in cellular contexts to support clinical drug development has been limited by a lack of tractable cell-based assays. To address this gap, we developed a two-color flow cytometry-based assay that allows for sensitive quantification of DUB activity and inhibition in living cells. The utility of this system was demonstrated by quantifying the potency of GRL0617 against the viral DUB SARS-CoV-2 PLpro, identifying potential GRL0617 resistance mutations, and performing structure-function analysis of the vOTU domain from the recently emerged Yezo virus. In addition, the system was optimized for cellular DUBs by modifying a GFP-targeting nanobody to recruit USP7 and USP28 to benchmark a panel of reported inhibitors and assess inhibition kinetics. Together, these results demonstrate the utility of these assays for studying DUB biology in a cellular context with potential to aid in inhibitor discovery and development.
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Affiliation(s)
- Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Sofia N Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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11
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Yue Z, Zhang J, Zhang J, Wang X, Li L, Yu H, Liu B, Li Q, Zhu D, Zou Y. Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus-associated antibiotic resistance genes during composting. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132088. [PMID: 37482039 DOI: 10.1016/j.jhazmat.2023.132088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/15/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
The issue of antibiotic resistance genes (ARGs) pollution in manure has garnered significant attention, with viruses now being recognized as crucial carriers and disseminators of ARGs. However, the virus-associated ARG profiles and potential health risks in composts are still unclear. In this study, the viral communities and associated ARGs in biogas residue and pig faeces composts were profiled by virome analysis. The viral communities were dominated by Caudovirales, and non-thermophilic viruses were inactivated during composting. The diversity and abundance of ARGs were lower in virome than in metagenome, while ARGs' risk was greater in virome than in metagenome. There were six bacterial genera identified as viral hosts at the genomic level, Pseudomonas and Clostridium carried high-risk ARGs. Virus-associated ARGs in viral hosts had a higher risk rank than non-virus-associated ARGs. Composting reduced the diversity, abundance and risk of viral ARGs. The risk of ARGs in biogas residues was significantly lower than that of pig faeces in the initial period of composting, and the two different substracts equally less harmful after composting. These results revealed that viruses play a non-negligible role in spreading ARGs, posing high risk to environmental and human health.
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Affiliation(s)
- Zhengfu Yue
- Key Laboratory of Low-carbon Green Agriculture in Tropical region of China, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Jing Zhang
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Diseases and Pests, Ministry of Education (School of Plant Protection), Hainan University, Haikou 570228, China
| | - Jing Zhang
- Department of Environmental Sciences, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou 571199, China; CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xingxiang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lirong Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Haiyang Yu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Beibei Liu
- Key Laboratory of Low-carbon Green Agriculture in Tropical region of China, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Qinfen Li
- Key Laboratory of Low-carbon Green Agriculture in Tropical region of China, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yukun Zou
- Key Laboratory of Low-carbon Green Agriculture in Tropical region of China, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China.
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12
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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13
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Zhang H, Sandhu PK, Damania B. The Role of RNA Sensors in Regulating Innate Immunity to Gammaherpesviral Infections. Cells 2023; 12:1650. [PMID: 37371120 PMCID: PMC10297173 DOI: 10.3390/cells12121650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) and the Epstein-Barr virus (EBV) are double-stranded DNA oncogenic gammaherpesviruses. These two viruses are associated with multiple human malignancies, including both B and T cell lymphomas, as well as epithelial- and endothelial-derived cancers. KSHV and EBV establish a life-long latent infection in the human host with intermittent periods of lytic replication. Infection with these viruses induce the expression of both viral and host RNA transcripts and activates several RNA sensors including RIG-I-like receptors (RLRs), Toll-like receptors (TLRs), protein kinase R (PKR) and adenosine deaminases acting on RNA (ADAR1). Activation of these RNA sensors induces the innate immune response to antagonize the virus. To counteract this, KSHV and EBV utilize both viral and cellular proteins to block the innate immune pathways and facilitate their own infection. In this review, we summarize how gammaherpesviral infections activate RNA sensors and induce their downstream signaling cascade, as well as how these viruses evade the antiviral signaling pathways to successfully establish latent infection and undergo lytic reactivation.
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14
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Krawczyk E, Kangas C, He B. HSV Replication: Triggering and Repressing STING Functionality. Viruses 2023; 15:226. [PMID: 36680267 PMCID: PMC9864509 DOI: 10.3390/v15010226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Herpes simplex virus (HSV) has persisted within human populations due to its ability to establish both lytic and latent infection. Given this, human hosts have evolved numerous immune responses to protect against HSV infection. Critical in this defense against HSV, the host protein stimulator of interferon genes (STING) functions as a mediator of the antiviral response by inducing interferon (IFN) as well as IFN-stimulated genes. Emerging evidence suggests that during HSV infection, dsDNA derived from either the virus or the host itself ultimately activates STING signaling. While a complex regulatory circuit is in operation, HSV has evolved several mechanisms to neutralize the STING-mediated antiviral response. Within this review, we highlight recent progress involving HSV interactions with the STING pathway, with a focus on how STING influences HSV replication and pathogenesis.
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Affiliation(s)
| | | | - Bin He
- Department of Microbiology and Immunology, College of Medicine, University of Illinois, Chicago, IL 60612, USA
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15
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Erven I, Abraham E, Hermanns T, Baumann U, Hofmann K. A widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins. Nat Commun 2022; 13:7643. [PMID: 36496440 PMCID: PMC9741609 DOI: 10.1038/s41467-022-35244-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Distinct families of eukaryotic deubiquitinases (DUBs) are regulators of ubiquitin signaling. Here, we report on the presence of an additional DUB class broadly distributed in eukaryotes and several bacteria. The only described members of this family are the large tegument proteins of herpesviruses, which are attached to the outside of the viral capsid. By using a bioinformatics screen, we have identified distant homologs of this VTD (Viral tegument-like DUB) family in vertebrate transposons, fungi, insects, nematodes, cnidaria, protists and bacteria. While some VTD activities resemble viral tegument DUBs in that they favor K48-linked ubiquitin chains, other members are highly specific for K6- or K63-linked ubiquitin chains. The crystal structures of K48- and K6-specific members reveal considerable differences in ubiquitin recognition. The VTD family likely evolved from non-DUB proteases and spread through transposons, many of which became 'domesticated', giving rise to the Drosophila male sterile (3)76Ca gene and several nematode genes with male-specific expression.
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Affiliation(s)
- Ilka Erven
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Elena Abraham
- grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, D-50674 Cologne, Germany
| | - Thomas Hermanns
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Ulrich Baumann
- grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, D-50674 Cologne, Germany
| | - Kay Hofmann
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
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16
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Herpesvirus ubiquitin deconjugases. Semin Cell Dev Biol 2022; 132:185-192. [PMID: 34776333 DOI: 10.1016/j.semcdb.2021.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/15/2022]
Abstract
The covalent attachment of ubiquitin and ubiquitin-like polypeptides to cellular and viral proteins regulates numerous processes that enable virus infection, viral genome replication, and the spread of viruses to new hosts. The importance of these protein modifications in the regulation of the life cycle of herpesviruses is underscored by the discovery that all known members of this virus family encode at least one protease that specifically recognizes and disassembles ubiquitin conjugates. The structural and functional characterization of the viral enzymes and the identification of their viral and cellular substrates is providing valuable insights into the biology of viral infection and increasing evidence suggests that the viral deconjugases may also play a role in malignant transformation.
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17
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Mohnke J, Stark I, Fischer M, Fischer PM, Schlosser A, Grothey A, O’Hare P, Sodeik B, Erhard F, Dölken L, Hennig T. pUL36 Deubiquitinase Activity Augments Both the Initiation and the Progression of Lytic Herpes Simplex Virus Infection in IFN-Primed Cells. J Virol 2022; 96:e0096322. [PMID: 36314822 PMCID: PMC9683058 DOI: 10.1128/jvi.00963-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/15/2022] [Indexed: 11/24/2022] Open
Abstract
The evolutionarily conserved, structural HSV-1 tegument protein pUL36 is essential for both virus entry and assembly. While its N-terminal deubiquitinase (DUB) activity is dispensable for infection in cell culture, it is required for efficient virus spread in vivo, as it acts as a potent viral immune evasin. Interferon (IFN) induces the expression of hundreds of antiviral factors, including many ubiquitin modulators, which HSV-1 needs to neutralize to efficiently initiate a productive infection. Herein, we discover two functions of the conserved pUL36 DUB during lytic replication in cell culture in an understudied but equally important scenario of HSV-1 infection in IFN-treated cells. Our data indicate that the pUL36 DUB contributes to overcoming the IFN-mediated suppression of productive infection in both the early and late phases of HSV-1 infection. We show that incoming tegument-derived pUL36 DUB activity contributes to the IFN resistance of HSV-1 in IFN-primed cells to efficiently initiate lytic virus replication. Subsequently, the de novo expressed DUB augmented the efficiency of virus replication and increased the output of infectious virus. Notably, the DUB defect was only apparent when IFN was applied prior to infection. Our data indicate that IFN-induced defense mechanisms exist and that they work to both neutralize infectivity early on and slow the progression of HSV-1 replication in the late stages of infection. Also, our data indicate that pUL36 DUB activity contributes to the disarming of these host responses. IMPORTANCE HSV-1 is a ubiquitous human pathogen that is responsible for common cold sores and may also cause life-threatening disease. pUL36 is an essential, conserved herpesvirus protein with N-terminal deubiquitinating (DUB) activity. The DUB is dispensable for HSV-1 replication in cell culture but represents an important viral immune evasin in vivo. IFN plays a pivotal role in HSV-1 infection and suppresses viral replication both in vitro and in vivo. Here, we show that DUB activity contributes to overcoming IFN-induced cellular resistance in order to more efficiently initiate lytic replication and produce infectious virions. As such, DUB activity in the incoming virions increases their infectivity, while the de novo synthesized DUB augments productive infection. Thus, the HSV-1 DUB antagonizes the activity of IFN-inducible effector proteins to facilitate productive infection at multiple levels. Our findings underscore the importance of using more challenging cell culture systems to fully understand virus protein functions.
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Affiliation(s)
- Jonas Mohnke
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Irmgard Stark
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Mara Fischer
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Patrick M. Fischer
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Arnhild Grothey
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Peter O’Hare
- Department of Virology, Imperial College London, Norfolk Place, London, United Kingdom
| | - Beate Sodeik
- Institut für Virologie, Medizinische Hochschule Hannover, Hannover, Germany
- RESIST Exzellenzcluster, Medizinische Hochschule Hannover, Hannover, Germany
| | - Florian Erhard
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Thomas Hennig
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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18
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Zhao S, Zheng B, Wang L, Cui W, Jiang C, Li Z, Gao W, Zhang W. Deubiquitinase ubiquitin-specific protease 3 (USP3) inhibits HIV-1 replication via promoting APOBEC3G (A3G) expression in both enzyme activity-dependent and -independent manners. Chin Med J (Engl) 2022; 135:2706-2717. [PMID: 36574218 PMCID: PMC9945250 DOI: 10.1097/cm9.0000000000002478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Ubiquitination plays an essential role in many biological processes, including viral infection, and can be reversed by deubiquitinating enzymes (DUBs). Although some studies discovered that DUBs inhibit or enhance viral infection by various mechanisms, there is lack of information on the role of DUBs in virus regulation, which needs to be further investigated. METHODS Immunoblotting, real-time polymerase chain reaction, in vivo / in vitro deubiquitination, protein immunoprecipitation, immunofluorescence, and co-localization biological techniques were employed to examine the effect of ubiquitin-specific protease 3 (USP3) on APOBEC3G (A3G) stability and human immunodeficiency virus (HIV) replication. To analyse the relationship between USP3 and HIV disease progression, we recruited 20 HIV-infected patients to detect the levels of USP3 and A3G in peripheral blood and analysed their correlation with CD4 + T-cell counts. Correlation was estimated by Pearson correlation coefficients (for parametric data). RESULTS The results demonstrated that USP3 specifically inhibits HIV-1 replication in an A3G-dependent manner. Further investigation found that USP3 stabilized 90% to 95% of A3G expression by deubiquitinating Vif-mediated polyubiquitination and blocking its degradation in an enzyme-dependent manner. It also enhances the A3G messenger RNA (mRNA) level by binding to A3G mRNA and stabilizing it in an enzyme-independent manner. Moreover, USP3 expression was positively correlated with A3G expression ( r = 0.5110) and CD4 + T-cell counts ( r = 0.5083) in HIV-1-infected patients. CONCLUSIONS USP3 restricts HIV-1 viral infections by increasing the expression of the antiviral factor A3G. Therefore, USP3 may be an important target for drug development and serve as a novel therapeutic strategy against viral infections.
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Affiliation(s)
- Simin Zhao
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- College of Life Science of Jilin University, Changchun, Jilin 130012, China
| | - Baisong Zheng
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Liuli Wang
- Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Wenzhe Cui
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetics, The Second Hospital of Jilin University, Changchun, Jilin 130041, China
| | - Chunlai Jiang
- College of Life Science of Jilin University, Changchun, Jilin 130012, China
| | - Zhuo Li
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Wenying Gao
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Wenyan Zhang
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin 130021, China
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19
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Date SS, Xu P, Hepowit NL, Diab NS, Best J, Xie B, Du J, Strieter ER, Jackson LP, MacGurn JA, Graham TR. Ubiquitination drives COPI priming and Golgi SNARE localization. eLife 2022; 11:e80911. [PMID: 35904239 PMCID: PMC9374436 DOI: 10.7554/elife.80911] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
Deciphering mechanisms controlling SNARE localization within the Golgi complex is crucial to understanding protein trafficking patterns within the secretory pathway. SNAREs are also thought to prime coatomer protein I (COPI) assembly to ensure incorporation of these essential cargoes into vesicles, but the regulation of these events is poorly understood. Here, we report roles for ubiquitin recognition by COPI in SNARE trafficking and in stabilizing interactions between Arf, COPI, and Golgi SNAREs in Saccharomyces cerevisiae. The ability of COPI to bind ubiquitin, but not the dilysine motif, through its N-terminal WD repeat domain of β'-COP or through an unrelated ubiquitin-binding domain is essential for the proper localization of Golgi SNAREs Bet1 and Gos1. We find that COPI, the ArfGAP Glo3, and multiple Golgi SNAREs are ubiquitinated. Notably, the binding of Arf and COPI to Gos1 is markedly enhanced by ubiquitination of these components. Glo3 is proposed to prime COPI-SNARE interactions; however, Glo3 is not enriched in the ubiquitin-stabilized SNARE-Arf-COPI complex but is instead enriched with COPI complexes that lack SNAREs. These results support a new model for how posttranslational modifications drive COPI priming events crucial for Golgi SNARE localization.
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Affiliation(s)
- Swapneeta S Date
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Peng Xu
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Nathaniel L Hepowit
- Department of Cell and Developmental Biology, Vanderbilt UniversityNashvilleUnited States
| | - Nicholas S Diab
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Jordan Best
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Boyang Xie
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Jiale Du
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt UniversityNashvilleUnited States
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
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20
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Ismail AM, Saha A, Lee JS, Painter DF, Chen Y, Singh G, Condezo GN, Chodosh J, San Martín C, Rajaiya J. RANBP2 and USP9x regulate nuclear import of adenovirus minor coat protein IIIa. PLoS Pathog 2022; 18:e1010588. [PMID: 35709296 PMCID: PMC9242475 DOI: 10.1371/journal.ppat.1010588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 06/29/2022] [Accepted: 05/11/2022] [Indexed: 11/30/2022] Open
Abstract
As intracellular parasites, viruses exploit cellular proteins at every stage of infection. Adenovirus outbreaks are associated with severe acute respiratory illnesses and conjunctivitis, with no specific antiviral therapy available. An adenoviral vaccine based on human adenovirus species D (HAdV-D) is currently in use for COVID-19. Herein, we investigate host interactions of HAdV-D type 37 (HAdV-D37) protein IIIa (pIIIa), identified by affinity purification and mass spectrometry (AP-MS) screens. We demonstrate that viral pIIIa interacts with ubiquitin-specific protease 9x (USP9x) and Ran-binding protein 2 (RANBP2). USP9x binding did not invoke its signature deubiquitination function but rather deregulated pIIIa-RANBP2 interactions. In USP9x-knockout cells, viral genome replication and viral protein expression increased compared to wild type cells, supporting a host-favored mechanism for USP9x. Conversely, RANBP2-knock down reduced pIIIa transport to the nucleus, viral genome replication, and viral protein expression. Also, RANBP2-siRNA pretreated cells appeared to contain fewer mature viral particles. Transmission electron microscopy of USP9x-siRNA pretreated, virus-infected cells revealed larger than typical paracrystalline viral arrays. RANBP2-siRNA pretreatment led to the accumulation of defective assembly products at an early maturation stage. CRM1 nuclear export blockade by leptomycin B led to the retention of pIIIa within cell nuclei and hindered pIIIa-RANBP2 interactions. In-vitro binding analyses indicated that USP9x and RANBP2 bind to C-terminus of pIIIa amino acids 386–563 and 386–510, respectively. Surface plasmon resonance testing showed direct pIIIa interaction with recombinant USP9x and RANBP2 proteins, without competition. Using an alternative and genetically disparate adenovirus type (HAdV-C5), we show that the demonstrated pIIIa interaction is also important for a severe respiratory pathogen. Together, our results suggest that pIIIa hijacks RANBP2 for nuclear import and subsequent virion assembly. USP9x counteracts this interaction and negatively regulates virion synthesis. This analysis extends the scope of known adenovirus-host interactions and has potential implications in designing new antiviral therapeutics. The compact genomes of viruses must code for proteins with multiple functions, including those that assist with cell entry, replication, and escape from the host immune defenses. Viruses succeed in every stage of this process by hijacking critical cellular proteins for their propagation. Hence, identifying virus-host protein interactions may permit identifying therapeutic applications that restrict viral processes. Human adenovirus structural proteins link together to produce infectious virions. Protein IIIa is required to assemble fully packaged virions, but its interactions with host factors are unknown. Here, we identify novel host protein interactions of pIIIa with cellular RANBP2 and USP9x. We demonstrate that by interacting with cellular RANBP2, viral pIIIa gains entry to the nucleus for subsequent virion assembly and replication. Reduced RANBP2 expression inhibited pIIIa entry into the nucleus, minimized viral replication and viral protein expression, and led to accumulation of defective assembly products in the infected cells. As a defense against viral infection, USP9x reduces the interaction between pIIIa and RANBP2, resulting in decreased viral propagation. We also show that the identified pIIIa-host interactions are crucial in two disparate HAdV types with diverse disease implications.
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Affiliation(s)
- Ashrafali M. Ismail
- Department of Ophthalmology, Viral Pathogenesis Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amrita Saha
- Department of Ophthalmology, Viral Pathogenesis Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ji S. Lee
- Department of Ophthalmology, Viral Pathogenesis Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David F. Painter
- Department of Ophthalmology, Viral Pathogenesis Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yinghua Chen
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gurdeep Singh
- Department of Ophthalmology, Viral Pathogenesis Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gabriela N. Condezo
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Madrid, Spain
| | - James Chodosh
- Department of Ophthalmology, Viral Pathogenesis Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Carmen San Martín
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Madrid, Spain
| | - Jaya Rajaiya
- Department of Ophthalmology, Viral Pathogenesis Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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21
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Zhang Q, Jia Q, Gao W, Zhang W. The Role of Deubiquitinases in Virus Replication and Host Innate Immune Response. Front Microbiol 2022; 13:839624. [PMID: 35283827 PMCID: PMC8908266 DOI: 10.3389/fmicb.2022.839624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
As a critical post-translational modification, ubiquitination is known to affect almost all the cellular processes including immunity, signaling pathways, cell death, cancer development, and viral infection by controlling protein stability. Deubiquitinases (DUBs) cleave ubiquitin from proteins and reverse the process of ubiquitination. Thus, DUBs play an important role in the deubiquitination process and serve as therapeutic targets for various diseases. DUBs are found in eukaryotes, bacteria, and viruses and influence various biological processes. Here, we summarize recent findings on the function of DUBs in modulating viral infection, the mechanism by which viral DUBs regulate host innate immune response, and highlight those DUBs that have recently been discovered as antiviral therapeutic targets.
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Affiliation(s)
- Qinglin Zhang
- College of Life Sciences of Jilin University, Changchun, China
| | - Qizhen Jia
- College of Life Sciences of Jilin University, Changchun, China
| | - Wenying Gao
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Wenyan Zhang
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
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22
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Gong L, Ou X, Hu L, Zhong J, Li J, Deng S, Li B, Pan L, Wang L, Hong X, Luo W, Zeng Q, Zan J, Peng T, Cai M, Li M. The Molecular Mechanism of Herpes Simplex Virus 1 UL31 in Antagonizing the Activity of IFN-β. Microbiol Spectr 2022; 10:e0188321. [PMID: 35196784 PMCID: PMC8865407 DOI: 10.1128/spectrum.01883-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/11/2022] [Indexed: 11/20/2022] Open
Abstract
Virus infection triggers intricate signal cascade reactions to activate the host innate immunity, which leads to the production of type I interferon (IFN-I). Herpes simplex virus 1 (HSV-1), a human-restricted pathogen, is capable of encoding over 80 viral proteins, and several of them are involved in immune evasion to resist the host antiviral response through the IFN-I signaling pathway. Here, we determined that HSV-1 UL31, which is associated with nuclear matrix and is essential for the formation of viral nuclear egress complex, could inhibit retinoic acid-inducible gene I (RIG-I)-like receptor pathway-mediated interferon beta (IFN-β)-luciferase (Luc) and (PRDIII-I)4-Luc (an expression plasmid of IFN-β positive regulatory elements III and I) promoter activation, as well as the mRNA transcription of IFN-β and downstream interferon-stimulated genes (ISGs), such as ISG15, ISG54, ISG56, etc., to promote viral infection. UL31 was shown to restrain IFN-β activation at the interferon regulatory factor 3 (IRF3)/IRF7 level. Mechanically, UL31 was demonstrated to interact with TANK binding kinase 1 (TBK1), inducible IκB kinase (IKKi), and IRF3 to impede the formation of the IKKi-IRF3 complex but not the formation of the IRF7-related complex. UL31 could constrain the dimerization and nuclear translocation of IRF3. Although UL31 was associated with the CREB binding protein (CBP)/p300 coactivators, it could not efficiently hamper the formation of the CBP/p300-IRF3 complex. In addition, UL31 could facilitate the degradation of IKKi and IRF3 by mediating their K48-linked polyubiquitination. Taken together, these results illustrated that UL31 was able to suppress IFN-β activity by inhibiting the activation of IKKi and IRF3, which may contribute to the knowledge of a new immune evasion mechanism during HSV-1 infection. IMPORTANCE The innate immune system is the first line of host defense against the invasion of pathogens. Among its mechanisms, IFN-I is an essential cytokine in the antiviral response, which can help the host eliminate a virus. HSV-1 is a double-stranded DNA virus that can cause herpes and establish a lifelong latent infection, due to its possession of multiple mechanisms to escape host innate immunity. In this study, we illustrate for the first time that the HSV-1-encoded UL31 protein has a negative regulatory effect on IFN-β production by blocking the dimerization and nuclear translocation of IRF3, as well as promoting the K48-linked polyubiquitination and degradation of both IKKi and IRF3. This study may be helpful for fully understanding the pathogenesis of HSV-1.
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Affiliation(s)
- Lan Gong
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaowen Ou
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Hu
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiayi Zhong
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jingjing Li
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- Jinming Yu Academician Workstation of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Shenyu Deng
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bolin Li
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lingxia Pan
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Liding Wang
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xuejun Hong
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenqi Luo
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qiyuan Zeng
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jie Zan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Tao Peng
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Mingsheng Cai
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Meili Li
- State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
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23
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Tang S, Beattie AT, Kafkova L, Petris G, Huguenin-Dezot N, Fiedler M, Freeman M, Chin JW. Mechanism-based traps enable protease and hydrolase substrate discovery. Nature 2022; 602:701-707. [PMID: 35173328 PMCID: PMC8866121 DOI: 10.1038/s41586-022-04414-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/07/2022] [Indexed: 12/28/2022]
Abstract
Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets1. However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond2; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. 3,4). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. 5) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.
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Affiliation(s)
- Shan Tang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Adam T Beattie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Lucie Kafkova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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24
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Zhou Z, Xu J, Li Z, Lv Y, Wu S, Zhang H, Song Y, Ai Y. Viral deubiquitinases and innate antiviral immune response in livestock and poultry. J Vet Med Sci 2021; 84:102-113. [PMID: 34803084 PMCID: PMC8810313 DOI: 10.1292/jvms.21-0199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Among many of the pathogens, virus is the main cause of diseases in livestock and poultry. A host infected with the virus triggers a series of innate and adaptive immunity. The realization of innate immune responses involves the participation of a series of protein molecules in host cells, including receptors, signal molecules and antiviral molecules. Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular or viral deubiquitinases (DUBs). DUBs have now been identified in diverse viral lineages, and their characterization is providing valuable insights into virus biology and the role of the ubiquitin system in host antiviral mechanisms. In this review, we briefly introduce the mechanisms of ubiquitination and deubiquitination, present antiviral innate immune response and its regulation by ubiquitin, and summarize the prevalence of DUBs encoded by viruses (Arteriviridae, Asfarviridae, Nairoviridae, Coronaviridae, Herpesviridae, and Picornaviridae) infecting domestic animals and poultry. It is found that these DUBs suppress the innate immune responses mainly by affecting the production of type I interferon (IFN), which causes immune evasion of the viruses and promotes their replication. These findings have important reference significance for understanding the virulence and immune evasion mechanisms of the relevant viruses, and thus for the development of more effective prevention and treatment measures.
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Affiliation(s)
- Zhengxuan Zhou
- College of Animal Science, Jilin University.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University
| | - Jiacui Xu
- College of Animal Science, Jilin University.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University
| | - Zhanjun Li
- College of Animal Science, Jilin University.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University
| | - Yan Lv
- College of Animal Science, Jilin University
| | - Shanli Wu
- College of Basic Medical Sciences, Jilin University
| | - Huanmin Zhang
- Avian Disease and Oncology Laboratory, Agriculture Research Service, United States Department of Agriculture
| | - Yu Song
- Key laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education of the People's Republic of China.,Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources
| | - Yongxing Ai
- College of Animal Science, Jilin University.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University
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25
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Human Cytomegalovirus UL48 Deubiquitinase Primarily Targets Innermost Tegument Proteins pp150 and Itself To Regulate Their Stability and Protects Virions from Inclusion of Ubiquitin Conjugates. J Virol 2021; 95:e0099121. [PMID: 34549978 DOI: 10.1128/jvi.00991-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viral deubiquitinases (DUBs) regulate cellular innate immunity to benefit viral replication. In human cytomegalovirus (HCMV), the UL48-encoded DUB regulates innate immune responses, including NF-κB signaling. Although UL48 DUB is known to regulate its stability via auto-deubiquitination, its impact on other viral proteins is not well understood. In this study, we investigated the role of UL48 DUB in regulating the ubiquitination of viral proteins by comparing the levels of ubiquitinated viral peptides in cells infected with wild-type virus and DUB active-site mutants using mass spectrometry. We found that ubiquitinated peptides were increased in DUB mutant virus infection for 90% of viral proteins, with the innermost tegument proteins pp150 (encoded by UL32) and pUL48 itself being most significantly affected. The highly deubiquitinated lysine residues of pUL48 were mapped within its N-terminal DUB domain and the nuclear localization signal. Among them, the arginine substitution of lysine 2 (K2R) increased pUL48 stability and enhanced viral growth at low multiplicity of infection, indicating that K2 auto-deubiquitination has a role in regulating pUL48 stability. pUL48 also interacted with pp150 and increased pp150 expression by downregulating its ubiquitination. Furthermore, we found that, unlike the wild-type virus, mutant viruses expressing the UL48 protein with the DUB domain deleted or DUB active site mutated contain higher levels of ubiquitin conjugates, including the ubiquitinated forms of pp150, in their virions. Collectively, our results demonstrate that UL48 DUB mainly acts on the innermost tegument proteins pp150 and pUL48 itself during HCMV infection and may play a role in protecting virions from the inclusion of ubiquitin conjugates. IMPORTANCE Herpesviruses encode highly conserved tegument proteins that contain deubiquitinase (DUB) activity. Although the role of viral DUBs in the regulation of host innate immune responses has been established, their roles in the stability and function of viral proteins are not well understood. In this study, we performed a comparative analysis of the levels of ubiquitinated viral peptides between wild-type and DUB-inactive HCMV infections and demonstrated that the innermost tegument proteins pp150 and pUL48 (DUB itself) are major targets of viral DUB. We also show that ubiquitinated viral proteins are effectively incorporated into the virions of DUB mutant viruses but not the wild-type virus. Our study demonstrates that viral DUBs may play important roles in promoting the stability of viral proteins and inhibiting the inclusion of ubiquitin conjugates into virions.
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26
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Precursors of Viral Proteases as Distinct Drug Targets. Viruses 2021; 13:v13101981. [PMID: 34696411 PMCID: PMC8537868 DOI: 10.3390/v13101981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Viral proteases are indispensable for successful virion maturation, thus making them a prominent drug target. Their enzyme activity is tightly spatiotemporally regulated by expression in the precursor form with little or no activity, followed by activation via autoprocessing. These cleavage events are frequently triggered upon transportation to a specific compartment inside the host cell. Typically, precursor oligomerization or the presence of a co-factor is needed for activation. A detailed understanding of these mechanisms will allow ligands with non-canonical mechanisms of action to be designed, which would specifically modulate the initial irreversible steps of viral protease autoactivation. Binding sites exclusive to the precursor, including binding sites beyond the protease domain, can be exploited. Both inhibition and up-regulation of the proteolytic activity of viral proteases can be detrimental for the virus. All these possibilities are discussed using examples of medically relevant viruses including herpesviruses, adenoviruses, retroviruses, picornaviruses, caliciviruses, togaviruses, flaviviruses, and coronaviruses.
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27
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The Epstein-Barr virus deubiquitinating enzyme BPLF1 regulates the activity of topoisomerase II during productive infection. PLoS Pathog 2021; 17:e1009954. [PMID: 34543352 PMCID: PMC8483405 DOI: 10.1371/journal.ppat.1009954] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/30/2021] [Accepted: 09/11/2021] [Indexed: 12/12/2022] Open
Abstract
Topoisomerases are essential for the replication of herpesviruses but the mechanisms by which the viruses hijack the cellular enzymes are largely unknown. We found that topoisomerase-II (TOP2) is a substrate of the Epstein-Barr virus (EBV) ubiquitin deconjugase BPLF1. BPLF1 co-immunoprecipitated and deubiquitinated TOP2, and stabilized SUMOylated TOP2 trapped in cleavage complexes (TOP2ccs), which halted the DNA damage response to TOP2-induced double strand DNA breaks and promoted cell survival. Induction of the productive virus cycle in epithelial and lymphoid cell lines carrying recombinant EBV encoding the active enzyme was accompanied by TOP2 deubiquitination, accumulation of TOP2ccs and resistance to Etoposide toxicity. The protective effect of BPLF1 was dependent on the expression of tyrosyl-DNA phosphodiesterase 2 (TDP2) that releases DNA-trapped TOP2 and promotes error-free DNA repair. These findings highlight a previously unrecognized function of BPLF1 in supporting a non-proteolytic pathway for TOP2ccs debulking that favors cell survival and virus production. The N-terminal domains of the herpesvirus large tegument proteins encode a conserved cysteine protease with ubiquitin- and NEDD8-specific deconjugase activity. Members of the viral enzyme family regulate different aspects of the virus life cycle including virus replication, the assembly of infectious virus particles and the host innate anti-viral response. However, only few substrates have been validated under physiological conditions of expression and very little is known on the mechanisms by which the enzymes contribute to the reprograming of cellular functions that are required for efficient infection and virus production. Cellular type I and type II topoisomerases (TOP1 and TOP2) resolve topological problems that arise during DNA replication and transcription and are therefore essential for herpesvirus replication. We report that the Epstein-Barr virus (EBV) ubiquitin deconjugase BPLF1 selectively regulates the activity of TOP2 in cells treated with the TOP2 poison Etoposide and during productive infection. Using transiently transfected and stable cell lines that express catalytically active or inactive BPLF1, we found that BPLF1 interacts with both TOP2α and TOP2β in co-immunoprecipitation and in vitro pull-down assays and the active enzyme stabilizes TOP2 trapped in TOP2ccs, promoting a shift towards TOP2 SUMOylation. This hinders the activation of DNA-damage responses and reduces the toxicity of Etoposide. The physiological relevance of this finding was validated using pairs of EBV carrying HEK-293T cells and EBV immortalized lymphoblastoid cell lines (LCLs) expressing the wild type or catalytic mutant enzyme. Using knockout LCLs we found that the capacity of BPLF1 to rescue of Etoposide toxicity is dependent on the expression of tyrosyl-DNA phosphodiesterase 2 (TDP2) that releases DNA-trapped TOP2 and promotes error-free DNA repair.
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28
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Inhibition of selective autophagy by members of the herpesvirus ubiquitin-deconjugase family. Biochem J 2021; 478:2297-2308. [PMID: 34143865 PMCID: PMC8238521 DOI: 10.1042/bcj20210225] [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: 03/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022]
Abstract
Autophagy is an important component of the innate immune response that restricts infection by different types of pathogens. Viruses have developed multiple strategies to avoid autophagy to complete their replication cycle and promote spreading to new hosts. Here, we report that the ubiquitin deconjugases encoded in the N-terminal domain of the large tegument proteins of Epstein–Barr virus (EBV), Kaposi Sarcoma herpesvirus (KSHV) and human cytomegalovirus (HCMV), but not herpes simplex virus-1 (HSV-1), regulate selective autophagy by inhibiting the activity of the autophagy receptor SQSTM1/p62. We found that all the homologs bind to and deubiquitinate SQSTM1/p62 but with variable efficiency, which correlates with their capacity to prevent the colocalization of light chain 3 (LC3) with SQSTM1/p62 aggregates and promote the accumulation of a model autophagy substrate. The findings highlight important differences in the strategies by which herpesviruses interfere with selective autophagy.
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29
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Proulx J, Borgmann K, Park IW. Role of Virally-Encoded Deubiquitinating Enzymes in Regulation of the Virus Life Cycle. Int J Mol Sci 2021; 22:ijms22094438. [PMID: 33922750 PMCID: PMC8123002 DOI: 10.3390/ijms22094438] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 01/21/2023] Open
Abstract
The ubiquitin (Ub) proteasome system (UPS) plays a pivotal role in regulation of numerous cellular processes, including innate and adaptive immune responses that are essential for restriction of the virus life cycle in the infected cells. Deubiquitination by the deubiquitinating enzyme, deubiquitinase (DUB), is a reversible molecular process to remove Ub or Ub chains from the target proteins. Deubiquitination is an integral strategy within the UPS in regulating survival and proliferation of the infecting virus and the virus-invaded cells. Many viruses in the infected cells are reported to encode viral DUB, and these vial DUBs actively disrupt cellular Ub-dependent processes to suppress host antiviral immune response, enhancing virus replication and thus proliferation. This review surveys the types of DUBs encoded by different viruses and their molecular processes for how the infecting viruses take advantage of the DUB system to evade the host immune response and expedite their replication.
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Affiliation(s)
- Jessica Proulx
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.P.); (K.B.)
| | - Kathleen Borgmann
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.P.); (K.B.)
| | - In-Woo Park
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Correspondence: ; Tel.: +1-(817)-735-5115; Fax: +1-(817)-735-2610
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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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Krabill AD, Chen H, Hussain S, Hewitt CS, Imhoff RD, Muli CS, Das C, Galardy PJ, Wendt MK, Flaherty DP. Optimization and Anti-Cancer Properties of Fluoromethylketones as Covalent Inhibitors for Ubiquitin C-Terminal Hydrolase L1. Molecules 2021; 26:1227. [PMID: 33668938 PMCID: PMC7956625 DOI: 10.3390/molecules26051227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
The deubiquitinating enzyme (DUB) UCHL1 is implicated in various disease states including neurodegenerative disease and cancer. However, there is a lack of quality probe molecules to gain a better understanding on UCHL1 biology. To this end a study was carried out to fully characterize and optimize the irreversible covalent UCHL1 inhibitor VAEFMK. Structure-activity relationship studies identified modifications to improve activity versus the target and a full cellular characterization was carried out for the first time with this scaffold. The studies produced a new inhibitor, 34, with an IC50 value of 7.7 µM against UCHL1 and no observable activity versus the closest related DUB UCHL3. The molecule was also capable of selectively inhibiting UCHL1 in cells and did not demonstrate any discernible off-target toxicity. Finally, the molecule was used for initial probe studies to assess the role of UCHL1 role in proliferation of myeloma cells and migration behavior in small cell lung cancer cells making 34 a new tool to be used in the biological evaluation of UCHL1.
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Affiliation(s)
- Aaron D. Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Hao Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Sajjad Hussain
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA; (S.H.); (P.J.G.)
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA
| | - Chad S. Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Ryan D. Imhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Christine S. Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Chittaranjan Das
- Department of Chemistry, College of Science, 560 Oval Dr., West Lafayette, IN 47907, USA;
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
| | - Paul J. Galardy
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA; (S.H.); (P.J.G.)
| | - Michael K. Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Ln., West Lafayette, IN 47907, USA
| | - Daniel P. Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Ln., West Lafayette, IN 47907, USA
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32
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Why Cells and Viruses Cannot Survive without an ESCRT. Cells 2021; 10:cells10030483. [PMID: 33668191 PMCID: PMC7995964 DOI: 10.3390/cells10030483] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 12/15/2022] Open
Abstract
Intracellular organelles enwrapped in membranes along with a complex network of vesicles trafficking in, out and inside the cellular environment are one of the main features of eukaryotic cells. Given their central role in cell life, compartmentalization and mechanisms allowing their maintenance despite continuous crosstalk among different organelles have been deeply investigated over the past years. Here, we review the multiple functions exerted by the endosomal sorting complex required for transport (ESCRT) machinery in driving membrane remodeling and fission, as well as in repairing physiological and pathological membrane damages. In this way, ESCRT machinery enables different fundamental cellular processes, such as cell cytokinesis, biogenesis of organelles and vesicles, maintenance of nuclear–cytoplasmic compartmentalization, endolysosomal activity. Furthermore, we discuss some examples of how viruses, as obligate intracellular parasites, have evolved to hijack the ESCRT machinery or part of it to execute/optimize their replication cycle/infection. A special emphasis is given to the herpes simplex virus type 1 (HSV-1) interaction with the ESCRT proteins, considering the peculiarities of this interplay and the need for HSV-1 to cross both the nuclear-cytoplasmic and the cytoplasmic-extracellular environment compartmentalization to egress from infected cells.
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33
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Abdallah AE, Alesawy MS, Eissa SI, El-Fakharany EM, Kalaba MH, Sharaf MH, Abo Shama NM, Mahmoud SH, Mostafa A, Al-Karmalawy AA, Elkady H. Design and synthesis of new 4-(2-nitrophenoxy)benzamide derivatives as potential antiviral agents: molecular modeling and in vitro antiviral screening. NEW J CHEM 2021. [DOI: 10.1039/d1nj02710g] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Novel benzamide derivatives as anti adenovirus, HSV-1, coxsackievirus, and SARS-CoV-2: in vitro and in silico study.
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Affiliation(s)
- Abdallah E. Abdallah
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Mohamed S. Alesawy
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Sally I. Eissa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11884, Egypt
- Faculty of Pharmacy Al-Maareffa University for Science and Technology, Riyadh, Kingdom of Saudi Arabia
| | - Esmail M. El-Fakharany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Egypt
| | - Mohamed H. Kalaba
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Egypt
| | - Mohamed H. Sharaf
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Egypt
| | - Noura M. Abo Shama
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
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34
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Zhu H, Zheng C. The Race between Host Antiviral Innate Immunity and the Immune Evasion Strategies of Herpes Simplex Virus 1. Microbiol Mol Biol Rev 2020; 84:e00099-20. [PMID: 32998978 PMCID: PMC7528619 DOI: 10.1128/mmbr.00099-20] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) is very successful in establishing acute and latent infections in humans by counteracting host antiviral innate immune responses. HSV-1 has evolved various strategies to evade host antiviral innate immunity and some cellular survival-associated pathways. Since there is still no vaccine available for HSV-1, a continuous update of information regarding the interaction between HSV-1 infection and the host antiviral innate immunity will provide novel insights to develop new therapeutic strategies for HSV-1 infection and its associated diseases. Here, we update recent studies about how HSV-1 evades the host antiviral innate immunity, specifically how HSV-1 proteins directly or indirectly target the adaptors in the antiviral innate immunity signaling pathways to downregulate the signal transduction. Additionally, some classical intracellular stress responses, which also play important roles in defense of viral invasion, will be discussed here. With a comprehensive review of evasion mechanisms of antiviral innate immunity by HSV-1, we will be able to develop potential new targets for therapies and a possible vaccine against HSV-1 infections.
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Affiliation(s)
- Huifang Zhu
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Neonatal/Pediatric Intensive Care Unit, Children's Medical Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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35
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Schneider SM, Lee BH, Nicola AV. Viral entry and the ubiquitin-proteasome system. Cell Microbiol 2020; 23:e13276. [PMID: 33037857 DOI: 10.1111/cmi.13276] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023]
Abstract
Viruses confiscate cellular components of the ubiquitin-proteasome system (UPS) to facilitate many aspects of the infectious cycle. The 26S proteasome is an ATP-dependent, multisubunit proteolytic machine present in all eukaryotic cells. The proteasome executes the controlled degradation of functional proteins, as well as the hydrolysis of aberrantly folded polypeptides. There is growing evidence for the role of the UPS in viral entry. The UPS assists in several steps of the initiation of infection, including endosomal escape of the entering virion, intracellular transport of incoming nucleocapsids and uncoating of the viral genome. Inhibitors of proteasome activity, including MG132, epoxomicin, lactacystin and bortezomib have been integral to developments in this area. Here, we review the mechanistic details of UPS involvement in the entry process of viruses from a multitude of families. The possibility of proteasome inhibitors as therapeutic antiviral agents is highlighted.
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Affiliation(s)
- Seth M Schneider
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA.,School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Becky H Lee
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Anthony V Nicola
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA.,School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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36
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Nielsen CP, Jernigan KK, Diggins NL, Webb DJ, MacGurn JA. USP9X Deubiquitylates DVL2 to Regulate WNT Pathway Specification. Cell Rep 2020; 28:1074-1089.e5. [PMID: 31340145 PMCID: PMC6884140 DOI: 10.1016/j.celrep.2019.06.083] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 05/22/2019] [Accepted: 06/24/2019] [Indexed: 01/12/2023] Open
Abstract
The WNT signaling network is comprised of multiple receptors that relay various input signals via distinct transduction pathways to execute multiple complex and context-specific output processes. Integrity of the WNT signaling network relies on proper specification between canonical and noncanonical pathways, which presents a regulatory challenge given that several signal transducing elements are shared between pathways. Here, we report that USP9X, a deubiquitylase, and WWP1, an E3 ubiquitin ligase, regulate a ubiquitin rheostat on DVL2, a WNT signaling protein. Our findings indicate that USP9X-mediated deubiquitylation of DVL2 is required for canonical WNT activation, while increased DVL2 ubiquitylation is associated with localization to actin-rich projections and activation of the planar cell polarity (PCP) pathway. We propose that a WWP1-USP9X axis regulates a ubiquitin rheostat on DVL2 that specifies its participation in either canonical WNT or WNT-PCP pathways. These findings have important implications for therapeutic targeting of USP9X in human cancer. DVL2 is a signal transducing protein that participates in canonical and noncanonical WNT signaling relays. Here, Nielsen et al. report that the deubiquitylase USP9X and the E3 ubiquitin ligase WWP1 operate on DVL2 to establish a ubiquitin rheostat that contributes to WNT pathway specification in human breast cancer cells.
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Affiliation(s)
- Casey P Nielsen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kristin K Jernigan
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Nicole L Diggins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37240, USA
| | - Donna J Webb
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37240, USA
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA.
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37
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Masucci MG. Viral Ubiquitin and Ubiquitin-Like Deconjugases-Swiss Army Knives for Infection. Biomolecules 2020; 10:E1137. [PMID: 32752270 PMCID: PMC7464072 DOI: 10.3390/biom10081137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/16/2022] Open
Abstract
Posttranslational modifications of cellular proteins by covalent conjugation of ubiquitin and ubiquitin-like polypeptides regulate numerous cellular processes that are captured by viruses to promote infection, replication, and spreading. The importance of these protein modifications for the viral life cycle is underscored by the discovery that many viruses encode deconjugases that reverse their functions. The structural and functional characterization of these viral enzymes and the identification of their viral and cellular substrates is providing valuable insights into the biology of viral infections and the host's antiviral defense. Given the growing body of evidence demonstrating their key contribution to pathogenesis, the viral deconjugases are now recognized as attractive targets for the design of novel antiviral therapeutics.
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Affiliation(s)
- Maria Grazia Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, S-17177 Stockholm, Sweden
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38
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Bodda C, Reinert LS, Fruhwürth S, Richardo T, Sun C, Zhang BC, Kalamvoki M, Pohlmann A, Mogensen TH, Bergström P, Agholme L, O’Hare P, Sodeik B, Gyrd-Hansen M, Zetterberg H, Paludan SR. HSV1 VP1-2 deubiquitinates STING to block type I interferon expression and promote brain infection. J Exp Med 2020; 217:151747. [PMID: 32383759 PMCID: PMC7336311 DOI: 10.1084/jem.20191422] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/13/2020] [Accepted: 03/04/2020] [Indexed: 12/18/2022] Open
Abstract
Herpes simplex virus (HSV) is the main cause of viral encephalitis in the Western world, and the type I interferon (IFN) system is important for antiviral control in the brain. Here, we have compared Ifnb induction in mixed murine brain cell cultures by a panel of HSV1 mutants, each devoid of one mechanism to counteract the IFN-stimulating cGAS-STING pathway. We found that a mutant lacking the deubiquitinase (DUB) activity of the VP1-2 protein induced particularly strong expression of Ifnb and IFN-stimulated genes. HSV1 ΔDUB also induced elevated IFN expression in murine and human microglia and exhibited reduced viral replication in the brain. This was associated with increased ubiquitination of STING and elevated phosphorylation of STING, TBK1, and IRF3. VP1-2 associated directly with STING, leading to its deubiquitination. Recruitment of VP1-2 to STING was dependent on K150 of STING, which was ubiquitinated by TRIM32. Thus, the DUB activity of HSV1 VP1-2 is a major viral immune-evasion mechanism in the brain.
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Affiliation(s)
- Chiranjeevi Bodda
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Line S. Reinert
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Stefanie Fruhwürth
- Department of Rheumatology and Inflammation Research, Institute of Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Timmy Richardo
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility, Hannover Medical School, Hannover, Germany
| | - Chenglong Sun
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Bao-cun Zhang
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Maria Kalamvoki
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, KS
| | - Anja Pohlmann
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility, Hannover Medical School, Hannover, Germany
| | - Trine H. Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Petra Bergström
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lotta Agholme
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Peter O’Hare
- Section of Virology, Department of Medicine, Imperial College, St Mary's Medical School, London, UK
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility, Hannover Medical School, Hannover, Germany
| | - Mads Gyrd-Hansen
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- UK Dementia Research Institute at University College London, London, UK
- Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK
| | - Søren R. Paludan
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Rheumatology and Inflammation Research, Institute of Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Correspondence to Søren R. Paludan:
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39
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Gu H, Jan Fada B. Specificity in Ubiquitination Triggered by Virus Infection. Int J Mol Sci 2020; 21:E4088. [PMID: 32521668 PMCID: PMC7313089 DOI: 10.3390/ijms21114088] [Citation(s) in RCA: 28] [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: 05/07/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
Ubiquitination is a prominent posttranslational modification, in which the ubiquitin moiety is covalently attached to a target protein to influence protein stability, interaction partner and biological function. All seven lysine residues of ubiquitin, along with the N-terminal methionine, can each serve as a substrate for further ubiquitination, which effectuates a diverse combination of mono- or poly-ubiquitinated proteins with linear or branched ubiquitin chains. The intricately composed ubiquitin codes are then recognized by a large variety of ubiquitin binding domain (UBD)-containing proteins to participate in the regulation of various pathways to modulate the cell behavior. Viruses, as obligate parasites, involve many aspects of the cell pathways to overcome host defenses and subjugate cellular machineries. In the virus-host interactions, both the virus and the host tap into the rich source of versatile ubiquitination code in order to compete, combat, and co-evolve. Here, we review the recent literature to discuss the role of ubiquitin system as the infection progresses in virus life cycle and the importance of ubiquitin specificity in the regulation of virus-host relation.
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Affiliation(s)
- Haidong Gu
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA;
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40
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The HSV-1 ubiquitin ligase ICP0: Modifying the cellular proteome to promote infection. Virus Res 2020; 285:198015. [PMID: 32416261 PMCID: PMC7303953 DOI: 10.1016/j.virusres.2020.198015] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 12/16/2022]
Abstract
ICP0 is a viral E3 ubiquitin ligase that promotes HSV-1 infection. ICP0 interacts with multiple component proteins of the ubiquitin pathway. ICP0 disrupts multiple cellular processes activated in response to infection ICP0 remodels the SUMO proteome to counteract host immune defences to infection. ICP0 is an attractive drug target for the development of antiviral HSV-1 therapeutics.
Herpes simplex virus 1 (HSV-1) hijacks ubiquitination machinery to modify the cellular proteome to create an environment permissive for virus replication. HSV-1 encodes its own RING-finger E3 ubiquitin (Ub) ligase, Infected Cell Protein 0 (ICP0), that directly interfaces with component proteins of the Ub pathway to inactivate host immune defences and cellular processes that restrict the progression of HSV-1 infection. Consequently, ICP0 plays a critical role in the infectious cycle of HSV-1 that is required to promote the efficient onset of lytic infection and productive reactivation of viral genomes from latency. This review will describe the current knowledge regarding the biochemical properties and known substrates of ICP0 during HSV-1 infection. We will highlight the gaps in the characterization of ICP0 function and propose future areas of research required to understand fully the biological properties of this important HSV-1 regulatory protein.
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Lin J, Ai Y, Zhou H, Lv Y, Wang M, Xu J, Yu C, Zhang H, Wang M. UL36 Encoded by Marek's Disease Virus Exhibits Linkage-Specific Deubiquitinase Activity. Int J Mol Sci 2020; 21:E1783. [PMID: 32150874 PMCID: PMC7084888 DOI: 10.3390/ijms21051783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/19/2022] Open
Abstract
(1) Background: Deubiquitinase (DUB) regulates various important cellular processes via reversing the protein ubiquitination. The N-terminal fragment of a giant tegument protein, UL36, encoded by the Marek's disease (MD) virus (MDV), encompasses a putative DUB (UL36-DUB) and shares no homology with any known DUBs. The N-terminus 75 kDa fragment of UL36 exists in MD T lymphoma cells at a high level and participates in MDV pathogenicity. (2) Methods: To characterize deubiquitinating activity and substrate specificity of UL36-DUB, the UL36 N-terminal fragments, UL36(323), UL36(480), and mutants were prepared using the Bac-to-Bac system. The deubiquitinating activity and substrate specificity of these recombinant UL36-DUBs were analyzed using various ubiquitin (Ub) or ubiquitin-like (UbL) substrates and activity-based deubiquitinating enzyme probes. (3) Results: The results indicated that wild type UL36-DUBs show a different hydrolysis ability against varied types of ubiquitin chains. These wild type UL36-DUBs presented the highest activity to K11, K48, and K63 linkage Ub chains, weak activity to K6, K29, and K33 Ub chains, and no activity to K27 linkage Ub chain. UL36 has higher cleavage efficiency for K48 and K63 poly-ubiquitin than linear ubiquitin chain (M1-Ub4), but no activity on various ubiquitin-like modifiers. The mutation of C98 and H234 residues eliminated the deubiquitinating activity of UL36-DUB. D232A mutation impacted, but did not eliminated UL36(480) activity. The Ub-Br probe can bind to wild type UL36-DUB and mutants UL36(480)H234A and UL36(480)D232A, but not C98 mutants. These in vitro results suggested that the C98 and H234 are essential catalytic residues of UL36-DUB. UL36-DUB exhibited a strict substrate specificity. Inhibition assay revealed that UL36-DUB exhibits resistance to the Roche protease inhibitor cocktail and serine protease inhibitor, but not to the Solarbio protease inhibitor cocktail. (4) Conclusions: UL36-DUB exhibited a strict substrate preference, and the protocol developed in the current study for obtaining active UL36-DUB protein should promote the high-throughput screening of UL36 inhibitors and the study on the function of MDV-encoded UL36.
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Affiliation(s)
- Junyan Lin
- College of Animal Science, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China; (J.L.); (Y.A.); (H.Z.); (Y.L.); (M.W.); (J.X.)
| | - Yongxing Ai
- College of Animal Science, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China; (J.L.); (Y.A.); (H.Z.); (Y.L.); (M.W.); (J.X.)
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China
| | - Hongda Zhou
- College of Animal Science, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China; (J.L.); (Y.A.); (H.Z.); (Y.L.); (M.W.); (J.X.)
| | - Yan Lv
- College of Animal Science, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China; (J.L.); (Y.A.); (H.Z.); (Y.L.); (M.W.); (J.X.)
| | - Menghan Wang
- College of Animal Science, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China; (J.L.); (Y.A.); (H.Z.); (Y.L.); (M.W.); (J.X.)
| | - Jiacui Xu
- College of Animal Science, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China; (J.L.); (Y.A.); (H.Z.); (Y.L.); (M.W.); (J.X.)
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China
| | - Cong Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Avenue, Changchun 130022, Jilin, China;
| | - Huanmin Zhang
- Avian Disease and Oncology Laboratory, Agriculture Research Service, United States Department of Agriculture, 4279 East Mount Hope Road East Lansing, MI 48823, USA
| | - Mengyun Wang
- College of Animal Science, Jilin University, 5333 Xi An Road, Changchun 130062, Jilin, China; (J.L.); (Y.A.); (H.Z.); (Y.L.); (M.W.); (J.X.)
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Mukhtar MU, Iqbal N, Yang J, Niu Q, Zhao S, Li Z, Zhao Y, Rashid M, Chen Z, Guan G, Liu Z, Yin H. Identification and evaluation of UL36 protein from Dermacentor silvarum salivary gland and its interaction with Anaplasma ovis VirB10. Parasit Vectors 2020; 13:105. [PMID: 32103780 PMCID: PMC7045605 DOI: 10.1186/s13071-020-3975-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anaplasma ovis is a gram-negative, tick-borne obligate intraerythrocytic pathogen, which causes ovine anaplasmosis in small ruminants worldwide. VirB10 of A. ovis is an integral component of the Type IV Secretion System (T4SS). The T4SS is used by bacteria to transfer DNA and/or proteins undeviatingly into the host cell to increase their virulence. To more thoroughly understand the interaction between A. ovis and Dermacentor silvarum, a vector containing the virb10 gene of A. ovis was used as a bait plasmid to screen interacting proteins from the cDNA library of the D. silvarum salivary gland using the yeast two-hybrid system. METHODS The cDNA of the D. silvarum salivary gland was cloned into the pGADT7-SmaI vector (prey plasmid) to construct the yeast two-hybrid cDNA library. The virb10 gene was cloned into the pGBKT7 vector to generate a bait plasmid. Any gene auto-activation or toxicity effects in the yeast strain Y2HGold were excluded. The screening was performed by combining the bait and prey plasmids in yeast strains to identify positive preys. The positive preys were then sequenced, and the obtained sequences were subjected to further analyses using Gene Ontology, UniProt, SMART, and STRING. Additionally, the interaction between the bait and the prey was evaluated using the glutathione S-transferase (GST) pull-down assay. RESULTS A total of two clones were obtained from the cDNA library using the yeast two-hybrid system, and the sequence analysis showed that both clones encoded the same large tegument protein, UL36. Furthermore, the proteins GST-UL36 and His-VirB10 were successfully expressed in vitro and the interaction between the two proteins was successfully demonstrated by the GST pull-down assay. CONCLUSIONS To our knowledge, this study is the first to screen for D. silvarum salivary gland proteins that interact with A. ovis VirB10. The resulting candidate, UL36, is a multi-functional protein. Further investigations into the functionality of UL36 should be carried out, which might help in identifying novel prevention and treatment strategies for A. ovis infection. The present study provides a base for exploring and further understanding the interactions between A. ovis and D. silvarum.
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Affiliation(s)
- Muhammad Uzair Mukhtar
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Naveed Iqbal
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Jifei Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Qingli Niu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Shuaiyang Zhao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Zhi Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Yaru Zhao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Muhammad Rashid
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Ze Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Zhijie Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China.
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, People's Republic of China.
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Gupta S, Ylä-Anttila P, Sandalova T, Achour A, Masucci MG. Interaction With 14-3-3 Correlates With Inactivation of the RIG-I Signalosome by Herpesvirus Ubiquitin Deconjugases. Front Immunol 2020; 11:437. [PMID: 32226432 PMCID: PMC7080818 DOI: 10.3389/fimmu.2020.00437] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/25/2020] [Indexed: 12/23/2022] Open
Abstract
The hijacking of cellular function through expression of proteins that interfere with the activity of cellular enzymes and regulatory complexes is a common strategy used by viruses to remodel the cell environment in favor of their own replication and spread. Here we report that the ubiquitin deconjugases encoded in the N-terminal domain of the large tegument proteins of Epstein-Barr virus (EBV), Kaposi Sarcoma herpesvirus (KSHV) and human cytomegalovirus (HCMV), but not herpes simplex virus-1 (HSV-1), target an early step of the IFN signaling cascade that involves the formation of a trimolecular complex with the ubiquitin ligase TRIM25 and the 14-3-3 molecular scaffold. Different from other homologs, the HSV-1 encoded enzyme fails to interact with 14-3-3, which correlates with failure to promote the autoubiquitination and sequestration of TRIM25 in cytoplasmic aggregates, and inability to block the activation and nuclear translocation of the IRF3 transcription factor. These findings highlight a key role for 14-3-3 molecular scaffolds in the regulation of innate immune response to herpesvirus infections and points to a possible target for the development of a new type of antivirals with applications in a broad spectrum of human diseases.
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Affiliation(s)
- Soham Gupta
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Soham Gupta
| | - Päivi Ylä-Anttila
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tatyana Sandalova
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Adnane Achour
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Maria G. Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Maria G. Masucci
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Diwaker D, Wilson DW. Microtubule-Dependent Trafficking of Alphaherpesviruses in the Nervous System: The Ins and Outs. Viruses 2019; 11:v11121165. [PMID: 31861082 PMCID: PMC6950448 DOI: 10.3390/v11121165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/12/2022] Open
Abstract
The Alphaherpesvirinae include the neurotropic pathogens herpes simplex virus and varicella zoster virus of humans and pseudorabies virus of swine. These viruses establish lifelong latency in the nuclei of peripheral ganglia, but utilize the peripheral tissues those neurons innervate for productive replication, spread, and transmission. Delivery of virions from replicative pools to the sites of latency requires microtubule-directed retrograde axonal transport from the nerve terminus to the cell body of the sensory neuron. As a corollary, during reactivation newly assembled virions must travel along axonal microtubules in the anterograde direction to return to the nerve terminus and infect peripheral tissues, completing the cycle. Neurotropic alphaherpesviruses can therefore exploit neuronal microtubules and motors for long distance axonal transport, and alternate between periods of sustained plus end- and minus end-directed motion at different stages of their infectious cycle. This review summarizes our current understanding of the molecular details by which this is achieved.
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Affiliation(s)
- Drishya Diwaker
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA;
| | - Duncan W. Wilson
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA;
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
- Correspondence: ; Tel.: +1-(718)-430-2305
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Stults AM, Smith GA. The Herpes Simplex Virus 1 Deamidase Enhances Propagation but Is Dispensable for Retrograde Axonal Transport into the Nervous System. J Virol 2019; 93:e01172-19. [PMID: 31462572 PMCID: PMC6819922 DOI: 10.1128/jvi.01172-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
Upon replication in mucosal epithelia and transmission to nerve endings, capsids of herpes simplex virus 1 (HSV-1) travel retrogradely within axons to peripheral ganglia, where life-long latent infections are established. A capsid-bound tegument protein, pUL37, is an essential effector of retrograde axonal transport and also houses a deamidase activity that antagonizes innate immune signaling. In this report, we examined whether the deamidase of HSV-1 pUL37 contributes to the neuroinvasive retrograde axonal transport mechanism. We conclude that neuroinvasion is enhanced by the deamidase, but the critical contribution of pUL37 to retrograde axonal transport functions independently of this activity.IMPORTANCE Herpes simplex virus 1 invades the nervous system by entering nerve endings and sustaining long-distance retrograde axonal transport to reach neuronal nuclei in ganglia of the peripheral nervous system. The incoming viral particle carries a deamidase activity on its surface that antagonizes antiviral responses. We examined the contribution of the deamidase to the hallmark neuroinvasive property of this virus.
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Affiliation(s)
- Austin M Stults
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Gregory A Smith
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Carriere J, Rao Y, Liu Q, Lin X, Zhao J, Feng P. Post-translational Control of Innate Immune Signaling Pathways by Herpesviruses. Front Microbiol 2019; 10:2647. [PMID: 31798565 PMCID: PMC6868034 DOI: 10.3389/fmicb.2019.02647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/30/2019] [Indexed: 12/21/2022] Open
Abstract
Herpesviruses constitute a large family of disease-causing DNA viruses. Each herpesvirus strain is capable of infecting particular organisms with a specific cell tropism. Upon infection, pattern recognition receptors (PRRs) recognize conserved viral features to trigger signaling cascades that culminate in the production of interferons and pro-inflammatory cytokines. To invoke a proper immune response while avoiding collateral tissue damage, signaling proteins involved in these cascades are tightly regulated by post-translational modifications (PTMs). Herpesviruses have developed strategies to subvert innate immune signaling pathways in order to ensure efficient viral replication and achieve persistent infection. The ability of these viruses to control the proteins involved in these signaling cascades post-translationally, either directly via virus-encoded enzymes or indirectly through the deregulation of cellular enzymes, has been widely reported. This ability provides herpesviruses with a powerful tool to shut off or restrict host antiviral and inflammatory responses. In this review, we highlight recent findings on the herpesvirus-mediated post-translational control along PRR-mediated signaling pathways.
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Affiliation(s)
| | | | | | | | | | - Pinghui Feng
- Section of Infection and Immunity, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, United States
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Karpiyevich M, Adjalley S, Mol M, Ascher DB, Mason B, van der Heden van Noort GJ, Laman H, Ovaa H, Lee MCS, Artavanis-Tsakonas K. Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathog 2019; 15:e1008086. [PMID: 31658303 PMCID: PMC6837540 DOI: 10.1371/journal.ppat.1008086] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/07/2019] [Accepted: 09/16/2019] [Indexed: 11/19/2022] Open
Abstract
Plasmodium parasites are the causative agents of malaria, a disease with wide public health repercussions. Increasing drug resistance and the absence of a vaccine make finding new chemotherapeutic strategies imperative. Components of the ubiquitin and ubiquitin-like pathways have garnered increased attention as novel targets given their necessity to parasite survival. Understanding how these pathways are regulated in Plasmodium and identifying differences to the host is paramount to selectively interfering with parasites. Here, we focus on Nedd8 modification in Plasmodium falciparum, given its central role to cell division and DNA repair, processes critical to Plasmodium parasites given their unusual cell cycle and requirement for refined repair mechanisms. By applying a functional chemical approach, we show that deNeddylation is controlled by a different set of enzymes in the parasite versus the human host. We elucidate the molecular determinants of the unusual dual ubiquitin/Nedd8 recognition by the essential PfUCH37 enzyme and, through parasite transgenics and drug assays, determine that only its ubiquitin activity is critical to parasite survival. Our experiments reveal interesting evolutionary differences in how neddylation is controlled in higher versus lower eukaryotes, and highlight the Nedd8 pathway as worthy of further exploration for therapeutic targeting in antimalarial drug design. Ubiquitin and ubiquitin-like post-translational modifications are evolutionarily conserved and involved in fundamental cellular processes essential to all eukaryotes. As such, enzymatic components of these pathways present attractive targets for therapeutic intervention for both chronic and communicable diseases. Nedd8 modification of cullin ubiquitin E3 ligases is critical to the viability of eukaryotic organisms and mediates cell cycle progression and DNA damage repair. Given the complex lifecycle and unusual replication mechanisms of the malaria parasite, one would expect neddylation to be of central importance to its survival, yet little is known about this pathway in Plasmodium. Here we present our findings on how Nedd8 removal is controlled in Plasmodium falciparum and how this pathway differs to that of its human host.
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Affiliation(s)
- Maryia Karpiyevich
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Sophie Adjalley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Marco Mol
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - David B. Ascher
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Melbourne, Melbourne, Australia
| | - Bethany Mason
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Heike Laman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marcus C. S. Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
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Characterizing the PRRSV nsp2 Deubiquitinase Reveals Dispensability of Cis-Activity for Replication and a Link of nsp2 to Inflammation Induction. Viruses 2019; 11:v11100896. [PMID: 31561412 PMCID: PMC6832237 DOI: 10.3390/v11100896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/14/2019] [Accepted: 09/19/2019] [Indexed: 12/11/2022] Open
Abstract
The papain-like cysteine protease 2 (PLP2) within the N-terminus of the porcine reproductive and respiratory syndrome virus (PRRSV) nsp2 replicase protein specifies a deubiquitinating enzyme (DUB), but its biochemical properties and the role in infection have remained poorly defined. By using in vitro assays, we found that the purified PLP2 could efficiently cleave K63 and K48 linked polyubiquitin chains Ub3-7 in vitro although displaying a differential activity in converting the respective ubiquitin dimers to monomer. The subsequent mutagenesis analyses revealed that the requirement for PLP2 DUB activity surprisingly resembled that for cis-cleavage activity, as several mutations (e.g., D91R, D85R, etc.) that largely ablated the DUB function also blocked the cis- but not trans-proteolytic cleavage of nsp2/3 polyprotein. Moreover, the analyses identified key mutations that could differentiate DUB from PLP2 cis- and trans-cleavage activities. Further reverse genetics analyses revealed the following findings: (i) mutations that largely blocked the DUB activity were all lethal to the virus, (ii) a point mutation T88G that selectively blocked the cis-cleavage activity of PLP2 did not affect viral viability in cell culture, and (iii) an E90Q mutation that did not affect either of the PLP2 activities led to rescue of WT-like virus but displayed significantly reduced ability to induce TNF-α production. Our findings support the possibility that the PLP2 DUB activity, but not cis-cleavage activity, is essential for PRRSV replication. The data also establish a strong link of nsp2 to pro-inflammatory cytokine induction during infection that operates in a manner independent of PLP2 DUB activity.
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Abstract
The Herpesviridae are structurally complex DNA viruses whose capsids undergo primary envelopment at the inner nuclear membrane and secondary envelopment at organelles in the cytoplasm. In both locations, there is evidence that envelope formation and scission involve the participation of multiple viral proteins and also the cellular ESCRT apparatus. It nevertheless appears that the best-understood viral strategies for ESCRT recruitment, those adopted by the retroviruses and many other families of enveloped RNA viruses, are not utilized by the Herpesviridae, at least during envelopment in the cytoplasm. Thus, although a large number of herpesvirus proteins have been assigned roles in envelopment, there is a dearth of candidates for the acquisition of the ESCRT complex and the control of envelope scission. This review summarizes our current understanding of ESCRT association by enveloped viruses, examines what is known of herpesvirus ESCRT utilization in the nucleus and cytoplasm, and identifies candidate cellular and viral proteins that could link enveloping herpesviruses to cellular ESCRT components.
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50
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Koenigsberg AL, Heldwein EE. The dynamic nature of the conserved tegument protein UL37 of herpesviruses. J Biol Chem 2018; 293:15827-15839. [PMID: 30166339 PMCID: PMC6187633 DOI: 10.1074/jbc.ra118.004481] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/26/2018] [Indexed: 12/26/2022] Open
Abstract
In all herpesviruses, the space between the capsid shell and the lipid envelope is occupied by the unique tegument layer composed of proteins that, in addition to structural roles, play many other roles in the viral replication. UL37 is a highly conserved tegument protein that has activities ranging from virion morphogenesis to directional capsid trafficking to manipulation of the host innate immune response and binds multiple partners. The N-terminal half of UL37 (UL37N) has a compact bean-shaped α-helical structure that contains a surface region essential for neuroinvasion. However, no biochemical or structural information is currently available for the C-terminal half of UL37 (UL37C) that mediates most of its interactions with multiple binding partners. Here, we show that the C-terminal half of UL37 from pseudorabies virus UL37C is a conformationally flexible monomer composed of an elongated folded core and an unstructured C-terminal tail. This elongated structure, along with that of its binding partner UL36, explains the nature of filamentous tegument structures bridging the capsid and the envelope. We propose that the dynamic nature of UL37 underlies its ability to perform diverse roles during viral replication.
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Affiliation(s)
- Andrea L Koenigsberg
- From the Department of Molecular Biology and Microbiology and Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts 02111
| | - Ekaterina E Heldwein
- From the Department of Molecular Biology and Microbiology and Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts 02111
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