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Yi D, An N, Li Q, Liu Q, Shao H, Zhou R, Wang J, Zhang Y, Ma L, Guo F, Li X, Liu Z, Cen S. Interferon-induced MXB protein restricts vimentin-dependent viral infection. Acta Pharm Sin B 2024; 14:2520-2536. [PMID: 38828143 PMCID: PMC11143536 DOI: 10.1016/j.apsb.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/16/2024] [Accepted: 03/14/2024] [Indexed: 06/05/2024] Open
Abstract
Type I interferon (IFN) inhibits a wide spectrum of viruses through stimulating the expression of antiviral proteins. As an IFN-induced protein, myxovirus resistance B (MXB) protein was reported to inhibit multiple highly pathogenic human viruses. It remains to be determined whether MXB employs a common mechanism to restrict different viruses. Here, we find that IFN alters the subcellular localization of hundreds of host proteins, and this IFN effect is partially lost upon MXB depletion. The results of our mechanistic study reveal that MXB recognizes vimentin (VIM) and recruits protein kinase B (AKT) to phosphorylate VIM at amino acid S38, which leads to reorganization of the VIM network and impairment of intracellular trafficking of virus protein complexes, hence causing a restriction of virus infection. These results highlight a new function of MXB in modulating VIM-mediated trafficking, which may lead towards a novel broad-spectrum antiviral strategy to control a large group of viruses that depend on VIM for successful replication.
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Affiliation(s)
- Dongrong Yi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Ni An
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Qian Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Huihan Shao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Rui Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Fei Guo
- Institute of Pathogen Biology, Chinese Academy of Medical Science, Beijing 100730, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Zhenlong Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
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2
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Yin Q, Liu W, Jiang Y, Feng Q, Wang X, Dou H, Liu Z, He F, Fan Y, Jiao B, Jiao B. Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022. BMC Genomics 2024; 25:378. [PMID: 38632523 PMCID: PMC11022347 DOI: 10.1186/s12864-024-10246-w] [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: 12/03/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. METHODS Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. RESULTS All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites. CONCLUSION SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.
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Affiliation(s)
- Qiang Yin
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Wei Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Yajuan Jiang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Qiang Feng
- Department of Laboratory, Rencheng Center for Disease Control and Prevention, Jining, China
| | - Xiaoyu Wang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Huixin Dou
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Zanzan Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Feifei He
- Computer Information Technology, Northern Arizona University, Arizona, USA
| | - Yingying Fan
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
| | - Baihai Jiao
- Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| | - Boyan Jiao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
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3
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Zhao X, Hu Y, Zhao J, Liu Y, Ma X, Chen H, Xing Y. Role of protein Post-translational modifications in enterovirus infection. Front Microbiol 2024; 15:1341599. [PMID: 38596371 PMCID: PMC11002909 DOI: 10.3389/fmicb.2024.1341599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/18/2024] [Indexed: 04/11/2024] Open
Abstract
Enteroviruses (EVs) are the main cause of a number of neurological diseases. Growing evidence has revealed that successful infection with enteroviruses is highly dependent on the host machinery, therefore, host proteins play a pivotal role in viral infections. Both host and viral proteins can undergo post-translational modification (PTM) which can regulate protein activity, stability, solubility and interactions with other proteins; thereby influencing various biological processes, including cell metabolism, metabolic, signaling pathways, cell death, and cancer development. During viral infection, both host and viral proteins regulate the viral life cycle through various PTMs and different mechanisms, including the regulation of host cell entry, viral protein synthesis, genome replication, and the antiviral immune response. Therefore, protein PTMs play important roles in EV infections. Here, we review the role of various host- and virus-associated PTMs during enterovirus infection.
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Affiliation(s)
- Xiaohui Zhao
- Department of Pathogen Biology, School of Medicine, Qinghai University, Qinghai, China
| | - Yibo Hu
- Department of Orthopaedic Trauma, The Affiliated Hospital of Qinghai University, Qinghai, China
| | - Jun Zhao
- Department of Pathogen Biology, School of Medicine, Qinghai University, Qinghai, China
| | - Yan Liu
- Department of Immunology, School of Medicine, Qinghai, China
| | - Xueman Ma
- Department of Traditional Chinese Medicine, School of Medicine, Qinghai University, Qinghai, China
| | - Hongru Chen
- Department of Public Health, School of Medicine, Qinghai University, Qinghai, China
| | - Yonghua Xing
- Department of Genetics, School of Medicine, Qinghai University, Qinghai, China
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4
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Dey S, Mondal A. Unveiling the role of host kinases at different steps of influenza A virus life cycle. J Virol 2024; 98:e0119223. [PMID: 38174932 PMCID: PMC10805039 DOI: 10.1128/jvi.01192-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Abstract
Influenza viruses remain a major public health concern causing contagious respiratory illnesses that result in around 290,000-650,000 global deaths every year. Their ability to constantly evolve through antigenic shifts and drifts leads to the emergence of newer strains and resistance to existing drugs and vaccines. To combat this, there is a critical need for novel antiviral drugs through the introduction of host-targeted therapeutics. Influenza viruses encode only 14 gene products that get extensively modified through phosphorylation by a diverse array of host kinases. Reversible phosphorylation at serine, threonine, or tyrosine residues dynamically regulates the structure, function, and subcellular localization of viral proteins at different stages of their life cycle. In addition, kinases influence a plethora of signaling pathways that also regulate virus propagation by modulating the host cell environment thus establishing a critical virus-host relationship that is indispensable for executing successful infection. This dependence on host kinases opens up exciting possibilities for developing kinase inhibitors as next-generation anti-influenza therapy. To fully capitalize on this potential, extensive mapping of the influenza virus-host kinase interaction network is essential. The key focus of this review is to outline the molecular mechanisms by which host kinases regulate different steps of the influenza A virus life cycle, starting from attachment-entry to assembly-budding. By assessing the contributions of different host kinases and their specific phosphorylation events during the virus life cycle, we aim to develop a holistic overview of the virus-host kinase interaction network that may shed light on potential targets for novel antiviral interventions.
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Affiliation(s)
- Soumik Dey
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Arindam Mondal
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
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Yamada CAO, de Paula Oliveira Santos B, Lemos RP, Batista ACS, da Conceição IMCA, de Paula Sabino A, E Lima LMTDR, de Magalhães MTQ. Applications of Mass Spectrometry in the Characterization, Screening, Diagnosis, and Prognosis of COVID-19. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:33-61. [PMID: 38409415 DOI: 10.1007/978-3-031-50624-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Mass spectrometry (MS) is a powerful analytical technique that plays a central role in modern protein analysis and the study of proteostasis. In the field of advanced molecular technologies, MS-based proteomics has become a cornerstone that is making a significant impact in the post-genomic era and as precision medicine moves from the research laboratory to clinical practice. The global dissemination of COVID-19 has spurred collective efforts to develop effective diagnostics, vaccines, and therapeutic interventions. This chapter highlights how MS seamlessly integrates with established methods such as RT-PCR and ELISA to improve viral identification and disease progression assessment. In particular, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) takes the center stage, unraveling intricate details of SARS-CoV-2 proteins, revealing modifications such as glycosylation, and providing insights critical to formulating therapies and assessing prognosis. However, high-throughput analysis of MALDI data presents challenges in manual interpretation, which has driven the development of programmatic pipelines and specialized packages such as MALDIquant. As we move forward, it becomes clear that integrating proteomic data with various omic findings is an effective strategy to gain a comprehensive understanding of the intricate biology of COVID-19 and ultimately develop targeted therapeutic paradigms.
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Affiliation(s)
- Camila Akemi Oliveira Yamada
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruno de Paula Oliveira Santos
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rafael Pereira Lemos
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Carolina Silva Batista
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Adriano de Paula Sabino
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Clinical and Molecular Hematology - Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mariana T Q de Magalhães
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
- Biochemistry and Immunology Postgraduate Program, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Nie H, Li Q, Pan W. The emerging roles of protein arginine methyltransferases in antiviral innate immune signaling pathways. Front Microbiol 2023; 14:1322929. [PMID: 38116532 PMCID: PMC10728285 DOI: 10.3389/fmicb.2023.1322929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
The Protein Arginine Methyltransferases (PRMTs) family is involved in various biological processes, including gene transcription, pre-mRNA splicing, mRNA translation, and protein stability. Recently, mounting evidence has shown that PRMTs also play critical roles in regulating the host antiviral immune response, either in an enzymatic activity dependent or independent manner. This review aims to provide an overview of the recent findings regarding the function and regulatory mechanisms of PRMTs in the antiviral response. These findings have the potential to aid in the discovery and design of novel therapeutic strategies for viral infections.
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Affiliation(s)
| | | | - Wei Pan
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan, China
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7
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Lin D, Dong X, Xiao X, Xiang Z, Lei X, Wang J. Proteomic and phosphoproteomic analysis of responses to enterovirus A71 infection reveals novel targets for antiviral and viral replication. Antiviral Res 2023; 220:105761. [PMID: 37992763 DOI: 10.1016/j.antiviral.2023.105761] [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: 09/21/2023] [Revised: 11/06/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Hand, foot, and mouth disease (HFMD) is a common infectious disease in infants and children, especially those under five years of age. EV-A71 is a common pathogen that causes HFMD and the primary pathogen leading to severe or fatal HFMD, which is characterized by neurological complications. However, the underlying mechanisms of EV-A71 pathogenesis remain largely unknown. In this report, we used proteomic and phosphorylated proteomic methods to characterize the proteome and phosphoproteome profiles of EV-A71-infected human neuroblastoma SK-N-SH cells. More than 7744 host proteins and 10069 phosphorylation modification sites were successfully quantified. Among them, 974 proteins and 3648 phosphorylation modification sites were regulated significantly during EV-A71 infection. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that EV-A71 altered cell biological processes, including protein synthesis, RNA splicing and metabolism in SK-N-SH cells. Notably, based on the prediction of upregulated kinases during EV-A71 infection, we identified specific kinase inhibitors approved by the FDA, with ceralasertib, bosutinib, flavin mononucleotide, minocycline, pimasertib and acetylcysteine inhibiting EV-A71 infection. Finally, EV-A71 proteins were found to be phosphorylated during infection, with one site (S184 on 3D polymerase) observed to be crucial for viral replication because a S184A mutation knocked out viral replication. The results improve our understanding of the host response to EV-A71 infection of neuroblastoma cells and provide potential targets for developing anti-EV-A71 strategies.
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Affiliation(s)
- Dandan Lin
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China
| | - Xiaojing Dong
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China
| | - Xia Xiao
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China
| | - Zichun Xiang
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China; State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Xiaobo Lei
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China; State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
| | - Jianwei Wang
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China.
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Moens U, Passerini S, Falquet M, Sveinbjørnsson B, Pietropaolo V. Phosphorylation of Human Polyomavirus Large and Small T Antigens: An Ignored Research Field. Viruses 2023; 15:2235. [PMID: 38005912 PMCID: PMC10674619 DOI: 10.3390/v15112235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Protein phosphorylation and dephosphorylation are the most common post-translational modifications mediated by protein kinases and protein phosphatases, respectively. These reversible processes can modulate the function of the target protein, such as its activity, subcellular localization, stability, and interaction with other proteins. Phosphorylation of viral proteins plays an important role in the life cycle of a virus. In this review, we highlight biological implications of the phosphorylation of the monkey polyomavirus SV40 large T and small t antigens, summarize our current knowledge of the phosphorylation of these proteins of human polyomaviruses, and conclude with gaps in the knowledge and a proposal for future research directions.
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Affiliation(s)
- Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway; (M.F.); (B.S.)
| | - Sara Passerini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
| | - Mar Falquet
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway; (M.F.); (B.S.)
| | - Baldur Sveinbjørnsson
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway; (M.F.); (B.S.)
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
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9
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Chen L, Yang J, Hu H, Jiang Y, Feng L, Liu J, Zhong K, Liu P, Ma Y, Chen M, Yang J. Large-scale phosphoproteome analysis in wheat seedling leaves provides evidence for extensive phosphorylation of regulatory proteins during CWMV infection. BMC PLANT BIOLOGY 2023; 23:532. [PMID: 37914991 PMCID: PMC10621099 DOI: 10.1186/s12870-023-04559-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/25/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Chinese wheat mosaic virus (CWMV) often causes severe damage to wheat (Triticum aestivum L.) growth and yield. It is well known that a successful infection in plants depends on a complex interaction between the host plant and the pathogen. Post-translational modification (PTM) of proteins is considered to be one of the main processes that decides the outcome of the plant-pathogen arms race during this interaction. Although numerous studies have investigated PTM in various organisms, there has been no large-scale phosphoproteomic analysis of virus-infected wheat plants. We therefore aimed to investigate the CWMV infection-induced phosphoproteomics changes in wheat by high-resolution liquid chromatography-tandem mass spectroscopy (LC-MS/MS) using affinity-enriched peptides followed by comprehensive bioinformatics analysis. RESULTS Through this study, a total of 4095 phosphorylation sites have been identified in 1968 proteins, and 11.6% of the phosphorylated proteins exhibited significant changes (PSPCs) in their phosphorylation levels upon CWMV infection. The result of Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the PSPCs were associated with photosynthesis, plant-pathogen interactions, and MAPK signaling pathways. The protein-protein interaction (PPI) network analysis result showed that these PSPCs were mainly participated in the regulation of biosynthesis and metabolism, protein kinase activities, and transcription factors. Furthermore, the phosphorylation levels of TaChi1 and TaP5CS, two plant immunity-related enzymes, were significantly changed upon CWMV infection, resulting in a significant decrease in CWMV accumulation in the infected plants. CONCLUSIONS Our results indicate that phosphorylation modification of protein plays a critical role in wheat resistance to CWMV infection. Upon CWMV infection, wheat plants will regulate the levels of extra- and intra-cellular signals and modifications of enzyme activities via protein phosphorylation. This novel information about the strategies used by wheat to resist CWMV infection will help researchers to breed new CWMV-resistant cultivars and to better understand the arms race between wheat and CWMV.
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Affiliation(s)
- Lu Chen
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jin Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Haichao Hu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yaoyao Jiang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lixiao Feng
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jiaqian Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Kaili Zhong
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Peng Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Youzhi Ma
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ming Chen
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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10
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Malvankar S, Singh A, Ravi Kumar YS, Sahu S, Shah M, Murghai Y, Seervi M, Srivastava RK, Verma B. Modulation of various host cellular machinery during COVID-19 infection. Rev Med Virol 2023; 33:e2481. [PMID: 37758688 DOI: 10.1002/rmv.2481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 07/24/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) emerged in December 2019, causing a range of respiratory infections from mild to severe. This resulted in the ongoing global COVID-19 pandemic, which has had a significant impact on public health. The World Health Organization declared COVID-19 as a global pandemic in March 2020. Viruses are intracellular pathogens that rely on the host's machinery to establish a successful infection. They exploit the gene expression machinery of host cells to facilitate their own replication. Gaining a better understanding of gene expression modulation in SARS-CoV2 is crucial for designing and developing effective antiviral strategies. Efforts are currently underway to understand the molecular-level interaction between the host and the pathogen. In this review, we describe how SARS-CoV2 infection modulates gene expression by interfering with cellular processes, including transcription, post-transcription, translation, post-translation, epigenetic modifications as well as processing and degradation pathways. Additionally, we emphasise the therapeutic implications of these findings in the development of new therapies to treat SARS-CoV2 infection.
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Affiliation(s)
- Shivani Malvankar
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Anjali Singh
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Y S Ravi Kumar
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bengaluru, India
| | - Swetangini Sahu
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Megha Shah
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Yamini Murghai
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Mahendra Seervi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Rupesh K Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
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11
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Zheng K, Chen S, Ren Z, Wang Y. Protein arginine methylation in viral infection and antiviral immunity. Int J Biol Sci 2023; 19:5292-5318. [PMID: 37928266 PMCID: PMC10620831 DOI: 10.7150/ijbs.89498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Protein arginine methyltransferase (PRMT)-mediated arginine methylation is an important post-transcriptional modification that regulates various cellular processes including epigenetic gene regulation, genome stability maintenance, RNA metabolism, and stress-responsive signal transduction. The varying substrates and biological functions of arginine methylation in cancer and neurological diseases have been extensively discussed, providing a rationale for targeting PRMTs in clinical applications. An increasing number of studies have demonstrated an interplay between arginine methylation and viral infections. PRMTs have been found to methylate and regulate several host cell proteins and different functional types of viral proteins, such as viral capsids, mRNA exporters, transcription factors, and latency regulators. This modulation affects their activity, subcellular localization, protein-nucleic acid and protein-protein interactions, ultimately impacting their roles in various virus-associated processes. In this review, we discuss the classification, structure, and regulation of PRMTs and their pleiotropic biological functions through the methylation of histones and non-histones. Additionally, we summarize the broad spectrum of PRMT substrates and explore their intricate effects on various viral infection processes and antiviral innate immunity. Thus, comprehending the regulation of arginine methylation provides a critical foundation for understanding the pathogenesis of viral diseases and uncovering opportunities for antiviral therapy.
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Affiliation(s)
- Kai Zheng
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Siyu Chen
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Zhe Ren
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research on Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research on Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
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12
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Hu M, You Y, Li Y, Ma S, Li J, Miao M, Quan Y, Yu W. Deacetylation of ACO2 Is Essential for Inhibiting Bombyx mori Nucleopolyhedrovirus Propagation. Viruses 2023; 15:2084. [PMID: 37896861 PMCID: PMC10612070 DOI: 10.3390/v15102084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is a specific pathogen of Bombyx mori that can significantly impede agricultural development. Accumulating evidence indicates that the viral proliferation in the host requires an ample supply of energy. However, the correlative reports of baculovirus are deficient, especially on the acetylation modification of tricarboxylic acid cycle (TCA cycle) metabolic enzymes. Our recent quantitative analysis of protein acetylome revealed that mitochondrial aconitase (ACO2) could be modified by (de)acetylation at lysine 56 (K56) during the BmNPV infection; however, the underlying mechanism is yet unknown. In order to understand this regulatory mechanism, the modification site K56 was mutated to arginine (Lys56Arg; K56R) to mimic deacetylated lysine. The results showed that mimic deacetylated mitochondrial ACO2 restricted enzymatic activity. Although the ATP production was enhanced after viral infection, K56 deacetylation of ACO2 suppressed BmN cellular ATP levels and mitochondrial membrane potential by affecting citrate synthase and isocitrate dehydrogenase activities compared with wild-type ACO2. Furthermore, the deacetylation of exogenous ACO2 lowered BmNPV replication and generation of progeny viruses. In summary, our study on ACO2 revealed the potential mechanism underlying WT ACO2 promotes the proliferation of BmNPV and K56 deacetylation of ACO2 eliminates this promotional effect, which might provide novel insights for developing antiviral strategies.
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Affiliation(s)
- Miao Hu
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou 310018, China
| | - Yi You
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou 310018, China
| | - Yao Li
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou 310018, China
| | - Shiyi Ma
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou 310018, China
| | - Jiaqi Li
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou 310018, China
| | - Meng Miao
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou 310018, China
| | - Yanping Quan
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou 310018, China
| | - Wei Yu
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou 310018, China
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13
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Zhu Z, You R, Li H, Feng S, Ma H, Tuo C, Meng X, Feng S, Peng Y. Multi-omics data integration reveals the complexity and diversity of host factors associated with influenza virus infection. PeerJ 2023; 11:e16194. [PMID: 37842064 PMCID: PMC10569165 DOI: 10.7717/peerj.16194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Influenza viruses pose a significant and ongoing threat to human health. Many host factors have been identified to be associated with influenza virus infection. However, there is currently a lack of an integrated resource for these host factors. This study integrated human genes and proteins associated with influenza virus infections for 14 subtypes of influenza A viruses, as well as influenza B and C viruses, and built a database named H2Flu to store and organize these genes or proteins. The database includes 28,639 differentially expressed genes (DEGs), 1,850 differentially expressed proteins, and 442 proteins with differential posttranslational modifications after influenza virus infection, as well as 3,040 human proteins that interact with influenza virus proteins and 57 human susceptibility genes. Further analysis showed that the dynamic response of human cells to virus infection, cell type and strain specificity contribute significantly to the diversity of DEGs. Additionally, large heterogeneity was also observed in protein-protein interactions between humans and different types or subtypes of influenza viruses. Overall, the study deepens our understanding of the diversity and complexity of interactions between influenza viruses and humans, and provides a valuable resource for further studies on such interactions.
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Affiliation(s)
- Zhaozhong Zhu
- College of Biology, Hunan University, Changsha, China
- School of Public Health, University of South China, Hengyang, China
| | - Ruina You
- College of Biology, Hunan University, Changsha, China
| | - Huiru Li
- College of Biology, Hunan University, Changsha, China
| | - Shuidong Feng
- School of Public Health, University of South China, Hengyang, China
| | - Huan Ma
- College of Biology, Hunan University, Changsha, China
| | - Chaohao Tuo
- College of Biology, Hunan University, Changsha, China
| | | | - Song Feng
- Xiangya Hospital, Central South University, Changsha, China
| | - Yousong Peng
- College of Biology, Hunan University, Changsha, China
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14
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Li R, Chen F, Li S, Yuan L, Zhao L, Tian S, Chen B. Comparative acetylomic analysis reveals differentially acetylated proteins regulating fungal metabolism in hypovirus-infected chestnut blight fungus. MOLECULAR PLANT PATHOLOGY 2023; 24:1126-1138. [PMID: 37278715 PMCID: PMC10423328 DOI: 10.1111/mpp.13358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/19/2023] [Accepted: 05/16/2023] [Indexed: 06/07/2023]
Abstract
Cryphonectria parasitica, the chestnut blight fungus, and hypoviruses are excellent models for examining fungal pathogenesis and virus-host interactions. Increasing evidence suggests that lysine acetylation plays a regulatory role in cell processes and signalling. To understand protein regulation in C. parasitica by hypoviruses at the level of posttranslational modification, a label-free comparative acetylome analysis was performed in the fungus with or without Cryphonectria hypovirus 1 (CHV1) infection. Using enrichment of acetyl-peptides with a specific anti-acetyl-lysine antibody, followed by high accuracy liquid chromatography-tandem mass spectrometry analysis, 638 lysine acetylation sites were identified on 616 peptides, corresponding to 325 unique proteins. Further analysis revealed that 80 of 325 proteins were differentially acetylated between C. parasitica strain EP155 and EP155/CHV1-EP713, with 43 and 37 characterized as up- and down-regulated, respectively. Moreover, 75 and 65 distinct acetylated proteins were found in EP155 and EP155/CHV1-EP713, respectively. Bioinformatics analysis revealed that the differentially acetylated proteins were involved in various biological processes and were particularly enriched in metabolic processes. Differences in acetylation in C. parasitica citrate synthase, a key enzyme in the tricarboxylic acid cycle, were further validated by immunoprecipitation and western blotting. Site-specific mutagenesis and biochemical studies demonstrated that the acetylation of lysine-55 plays a vital role in the regulation of the enzymatic activity of C. parasitica citrate synthase in vitro and in vivo. These findings provide a valuable resource for the functional analysis of lysine acetylation in C. parasitica, as well as improving our understanding of fungal protein regulation by hypoviruses from a protein acetylation perspective.
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Affiliation(s)
- Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Fengyue Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Shuangcai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Luying Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Lijiu Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Shigen Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Life Science and TechnologyGuangxi UniversityNanningChina
- Guangxi Key Laboratory of Sugarcane Biology, College of AgricultureGuangxi UniversityNanningChina
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15
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Leal CS, Carvalho CAM. In Silico Physicochemical Characterization of Fusion Proteins from Emerging Amazonian Arboviruses. Life (Basel) 2023; 13:1687. [PMID: 37629544 PMCID: PMC10455688 DOI: 10.3390/life13081687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Mayaro (MAYV), Saint Louis encephalitis (SLEV), and Oropouche (OROV) viruses are neglected members of the three main families of arboviruses with medical relevance that circulate in the Amazon region as etiological agents of outbreaks of febrile illnesses in humans. As enveloped viruses, MAYV, SLEV, and OROV largely depend on their class II fusion proteins (E1, E, and Gc, respectively) for entry into the host cell. Since many aspects of the structural biology of such proteins remain unclear, the present study aimed at physicochemically characterizing them by an in silico approach. The complete amino acid sequences of MAYV E1, SLEV E, and OROV Gc proteins derived by conceptual translation from annotated coding regions in the reference sequence genome of the respective viruses were obtained from the NCBI Protein database in the FASTA format and then submitted to the ClustalO, Protcalc, Pepstats, Predator, Proscan, PCprof, Phyre2, and 3Drefine web servers for the determination of sequence identities, the estimation of residual properties, the prediction of secondary structures, the identification of potential post-translational modifications, the recognition of antigenic propensities, and the modeling/refinement of three-dimensional structures. Sequence identities were 20.44%, 18.82%, and 13.70% between MAYV/SLEV, SLEV/OROV, and MAYV/OROV fusion proteins, respectively. As for the residual properties, MAYV E1 and SLEV E proteins showed a predominance of the non-polar profile (56% and 55% of the residues, respectively), whereas the OROV Gc protein showed a predominance of the polar profile (52% of the residues). Regarding predicted secondary structures, MAYV E1 and SLEV E proteins showed fewer alpha-helices (16.51% and 15.17%, respectively) than beta-sheets (21.79% and 25.15%, respectively), while the opposite was observed in the OROV Gc protein (20.39% alpha-helices and 12.14% beta-sheets). Regarding post-translational modifications, MAYV E1, SLEV E, and OROV Gc proteins showed greater relative potential for protein kinase C phosphorylation, N-myristoylation, and casein kinase II phosphorylation, respectively. Finally, antigenic propensities were higher in the N-terminus half than in the C-terminus half of these three proteins, whose three-dimensional structures revealed three distinctive domains. In conclusion, MAYV E1 and SLEV E proteins were found to share more physicochemical characteristics with each other than the OROV Gc protein, although they are all grouped under the same class of viral fusion proteins.
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Affiliation(s)
| | - Carlos Alberto M. Carvalho
- Graduate Program in Parasite Biology in the Amazon, Center for Biological and Health Sciences, University of Pará State, Belém 66095-662, PA, Brazil;
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16
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Wang YW, Zuo JC, Chen C, Li XH. Post-translational modifications and immune responses in liver cancer. Front Immunol 2023; 14:1230465. [PMID: 37609076 PMCID: PMC10441662 DOI: 10.3389/fimmu.2023.1230465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/26/2023] [Indexed: 08/24/2023] Open
Abstract
Post-translational modification (PTM) refers to the covalent attachment of functional groups to protein substrates, resulting in structural and functional changes. PTMs not only regulate the development and progression of liver cancer, but also play a crucial role in the immune response against cancer. Cancer immunity encompasses the combined efforts of innate and adaptive immune surveillance against tumor antigens, tumor cells, and tumorigenic microenvironments. Increasing evidence suggests that immunotherapies, which harness the immune system's potential to combat cancer, can effectively improve cancer patient prognosis and prolong the survival. This review presents a comprehensive summary of the current understanding of key PTMs such as phosphorylation, ubiquitination, SUMOylation, and glycosylation in the context of immune cancer surveillance against liver cancer. Additionally, it highlights potential targets associated with these modifications to enhance the response to immunotherapies in the treatment of liver cancer.
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Affiliation(s)
| | | | - Chong Chen
- Academy of Medical Engineering and Translational Medicine, Medical College of Tianjin University, Tianjin, China
| | - Xiao-Hong Li
- Academy of Medical Engineering and Translational Medicine, Medical College of Tianjin University, Tianjin, China
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17
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Luo J, Cao J, Chen C, Xie H. Emerging role of RNA acetylation modification ac4C in diseases: Current advances and future challenges. Biochem Pharmacol 2023; 213:115628. [PMID: 37247745 DOI: 10.1016/j.bcp.2023.115628] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
The oldest known highly conserved modification of RNA, N4-acetylcytidine, is widely distributed from archaea to eukaryotes and acts as a posttranscriptional chemical modification of RNA, contributing to the correct reading of specific nucleotide sequences during translation, stabilising mRNA and improving transcription efficiency. Yeast Kre33 and human NAT10, the only known authors of ac4C, modify tRNA with the help of the Tan1/THUMPD1 adapter to stabilise its structure. Currently, the mRNA for N4-acetylcytidine (ac4C), catalysed by NAT10 (N-acetyltransferase 10), has been implicated in a variety of human diseases, particularly cancer. This article reviews advances in the study of ac4C modification of RNA and the ac4C-related gene NAT10 in normal physiological cell development, cancer, premature disease and viral infection and discusses its therapeutic promise and future research challenges.
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Affiliation(s)
- Jie Luo
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jingsong Cao
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Institute of Clinical Medicine, University of South China, Hengyang 421001, China
| | - Cong Chen
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Haitao Xie
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
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18
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Zhang B, Cai T, He H, Huang X, Chen G, Lai Y, Luo Y, Huang S, Luo J, Guo X. TRIM21 Promotes Rabies Virus Production by Degrading IRF7 through Ubiquitination. Int J Mol Sci 2023; 24:10892. [PMID: 37446070 PMCID: PMC10341556 DOI: 10.3390/ijms241310892] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Rabies, a highly fatal zoonotic disease, is a significant global public health threat. Currently, the pathogenic mechanism of rabies has not been fully elucidated, and no effective treatment for rabies is available. Increasing evidence shows that the tripartite-motif protein (TRIM) family of proteins participates in the host's regulation of viral replication. Studies have demonstrated the upregulated expression of tripartite-motif protein 21 (TRIM21) in the brain tissue of mice infected with the rabies virus. Related studies have shown that TRIM21 knockdown inhibits RABV replication, while overexpression of TRIM21 exerted the opposite effect. Knockdown of interferon-alpha and interferon-beta modulates the inhibition of RABV replication caused by TRIM21 knockdown and promotes the replication of the virus. Furthermore, our previous study revealed that TRIM21 regulates the secretion of type I interferon during RABV infection by targeting interferon regulatory factor 7 (IRF7). IRF7 knockdown reduced the inhibition of RABV replication caused by the knockdown of TRIM21 and promoted viral replication. TRIM21 regulates RABV replication via the IRF7-IFN axis. Our study identified TRIM21 as a novel host factor required by RABV for replication. Thus, TRIM21 is a potential target for rabies treatment or management.
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Affiliation(s)
- Boyue Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Ting Cai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Hongling He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Xuezhe Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Guie Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Yanqin Lai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Yongwen Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130-3932, USA;
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA 71130-3932, USA
| | - Jun Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
| | - Xiaofeng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (B.Z.); (T.C.); (H.H.); (X.H.); (G.C.); (Y.L.); (Y.L.)
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19
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Allgoewer K, Wu S, Choi H, Vogel C. Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection. Mol Omics 2023; 19:308-320. [PMID: 36810580 PMCID: PMC10175154 DOI: 10.1039/d2mo00258b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Zika virus (ZIKV) and dengue virus (DENV) are two closely related flaviviruses with similar symptoms. However, due to the implications of ZIKV infections for pregnancy outcomes, understanding differences in their molecular impact on the host is of high interest. Viral infections change the host proteome, including post-translational modifications. As modifications are diverse and of low abundance, they typically require additional sample processing which is not feasible for large cohort studies. Therefore, we tested the potential of next-generation proteomics data in its ability to prioritize specific modifications for later analysis. We re-mined published mass spectra from 122 serum samples from ZIKV and DENV patients for the presence of phosphorylated, methylated, oxidized, glycosylated/glycated, sulfated, and carboxylated peptides. We identified 246 modified peptides with significantly differential abundance in ZIKV and DENV patients. Amongst these, methionine-oxidized peptides from apolipoproteins and glycosylated peptides from immunoglobulin proteins were more abundant in ZIKV patient serum and generate hypotheses on the potential roles of the modification in the infection. The results demonstrate how data-independent acquisition techniques can help prioritize future analyses of peptide modifications.
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Affiliation(s)
- Kristina Allgoewer
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York, NY, USA.
- Humboldt University, Department of Biology, Berlin, Germany
| | - Shaohuan Wu
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York, NY, USA.
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University, Singapore, Singapore
| | - Christine Vogel
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York, NY, USA.
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20
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Liang T, Li G, Lu Y, Hu M, Ma X. The Involvement of Ubiquitination and SUMOylation in Retroviruses Infection and Latency. Viruses 2023; 15:v15040985. [PMID: 37112965 PMCID: PMC10144533 DOI: 10.3390/v15040985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Retroviruses, especially the pathogenic human immunodeficiency virus type 1 (HIV-1), have severely threatened human health for decades. Retroviruses can form stable latent reservoirs via retroviral DNA integration into the host genome, and then be temporarily transcriptional silencing in infected cells, which makes retroviral infection incurable. Although many cellular restriction factors interfere with various steps of the life cycle of retroviruses and the formation of viral latency, viruses can utilize viral proteins or hijack cellular factors to evade intracellular immunity. Many post-translational modifications play key roles in the cross-talking between the cellular and viral proteins, which has greatly determined the fate of retroviral infection. Here, we reviewed recent advances in the regulation of ubiquitination and SUMOylation in the infection and latency of retroviruses, focusing on both host defense- and virus counterattack-related ubiquitination and SUMOylation system. We also summarized the development of ubiquitination- and SUMOylation-targeted anti-retroviral drugs and discussed their therapeutic potential. Manipulating ubiquitination or SUMOylation pathways by targeted drugs could be a promising strategy to achieve a "sterilizing cure" or "functional cure" of retroviral infection.
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Affiliation(s)
- Taizhen Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Guojie Li
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Yunfei Lu
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Meilin Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Xiancai Ma
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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21
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Cheng CC, Ke GM, Chu PY, Ke LY. Elucidating the Implications of Norovirus N- and O-Glycosylation, O-GlcNAcylation, and Phosphorylation. Viruses 2023; 15:v15030798. [PMID: 36992506 PMCID: PMC10054809 DOI: 10.3390/v15030798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Norovirus is the most common cause of foodborne gastroenteritis, affecting millions of people worldwide annually. Among the ten genotypes (GI-GX) of norovirus, only GI, GII, GIV, GVIII, and GIX infect humans. Some genotypes reportedly exhibit post-translational modifications (PTMs), including N- and O-glycosylation, O-GlcNAcylation, and phosphorylation, in their viral antigens. PTMs have been linked to increased viral genome replication, viral particle release, and virulence. Owing to breakthroughs in mass spectrometry (MS) technologies, more PTMs have been discovered in recent years and have contributed significantly to preventing and treating infectious diseases. However, the mechanisms by which PTMs act on noroviruses remain poorly understood. In this section, we outline the current knowledge of the three common types of PTM and investigate their impact on norovirus pathogenesis. Moreover, we summarize the strategies and techniques for the identification of PTMs.
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Affiliation(s)
- Chia-Chi Cheng
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Guan-Ming Ke
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
| | - Pei-Yu Chu
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Liang-Yin Ke
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
- Center for Lipid Biosciences, Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807378, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
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22
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Deubiquitinating Enzyme Inhibitors Block Chikungunya Virus Replication. Viruses 2023; 15:v15020481. [PMID: 36851696 PMCID: PMC9966916 DOI: 10.3390/v15020481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Ubiquitination and deubiquitination processes are widely involved in modulating the function, activity, localization, and stability of multiple cellular proteins regulating almost every aspect of cellular function. Several virus families have been shown to exploit the cellular ubiquitin-conjugating system to achieve a productive infection: enter the cell, promote genome replication, or assemble and release viral progeny. In this study, we analyzed the role of deubiquitinating enzymes (DUBs) during chikungunya virus (CHIKV) infection. HEK293T, Vero-E6, and Huh-7 cells were treated with two DUB inhibitors (PR619 or WP1130). Then, infected cells were evaluated by flow cytometry, and viral progeny was quantified using the plaque assay method. The changes in viral proteins and viral RNA were analyzed using Western blotting and RT-qPCR, respectively. Results indicate that treatment with DUB inhibitors impairs CHIKV replication due to significant protein and viral RNA synthesis deregulation. Therefore, DUB activity may be a pharmacological target for blocking CHIKV infection.
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Saito K, Shimasaki K, Fukasawa M, Suzuki R, Okemoto-Nakamura Y, Katoh K, Takasaki T, Hanada K. Establishment of Vero cell lines persistently harboring a yellow fever virus 17D subgenomic replicon. Virus Res 2022; 322:198935. [PMID: 36152929 DOI: 10.1016/j.virusres.2022.198935] [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: 04/18/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 12/24/2022]
Abstract
Yellow fever virus (YFV), a member of the genus Flavivirus, family Flaviviridae, is the etiological agent for an acute viral hemorrhagic disease, yellow fever. Although effective live attenuated vaccines based on the strain YFV 17D are currently available, no specific antiviral drug is available, and the disease remains a major public health concern. Hence, the discovery and development of antiviral drugs should lead to great benefits in controlling the disease. To provide a screening platform for antiviral agents targeting YFV RNA translation/replication, we have established and characterized two Vero cell lines that persistently harbor a subgenomic replicon derived from YFV 17D-204 (referred to as replicon cells). The replicon carries YFV nucleotides (1 - 176 and 2382-10,862) and a green fluorescent protein (GFP)-Zeocin resistance fusion gene as a selection marker and indicator of persistent replication. Immunofluorescence analysis revealed that both replicon cells and YFV 17D-infected cells showed similar distribution patterns of viral NS4B protein and replication intermediate, double-stranded RNA. Sequencing analysis of persistent replicons from the two replicon cell lines suggested that their nucleotide sequences did not vary greatly following multiple passages. We examined the effect of five agents, the antiviral cytokines interferon-β and -γ, the nucleoside analog ribavirin, the squalene synthase inhibitor zaragozic acid A, and the antibiotic rifapentine, a recently reported entry and replication inhibitor against YFV, on the persistent replication in the two replicon cell lines. These agents were selected because they inhibited both production of YFV 17D and transient replication of a luciferase-expressing replicon in Vero cells, without greatly affecting cell viability. We found that each of the agents decreased GFP fluorescence in the replicon cells, albeit to varying degrees. The agents other than rifapentine also showed a decrease in viral RNA levels in the replicon cells comparable to that seen for GFP fluorescence. These results indicate that persistent replication is susceptible to each of these five agents, although their mechanisms of action may differ. Taken together, these results provide evidence that translation/replication of the replicon in the replicon cells mimics that of the viral genome upon YFV 17D infection, indicating that the replicon cell lines can serve as a useful tool for high-throughput antiviral drug screening.
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Affiliation(s)
- Kyoko Saito
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.
| | - Kentaro Shimasaki
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Masayoshi Fukasawa
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo, Japan
| | - Yuko Okemoto-Nakamura
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kaoru Katoh
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba-shi, Ibaragi, Japan; AIRC, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, Chigasaki-shi, Kanagawa, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan; Department of Quality Assurance, Radiation Safety, and Information System, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
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Liu J, Rui K, Peng N, Luo H, Zhu B, Zuo X, Lu L, Chen J, Tian J. The cGAS-STING pathway: Post-translational modifications and functional implications in diseases. Cytokine Growth Factor Rev 2022; 68:69-80. [PMID: 36151014 DOI: 10.1016/j.cytogfr.2022.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 01/30/2023]
Abstract
Recent studies have illustrated the functional significance of DNA recognition in the activation of innate immune responses among a variety of diseases. The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway has been found to be modulated by post-translational modifications and can regulate the immune response via type I IFNs. Accumulating evidence indicates a pivotal role of cGAS-STING signaling, being protective or pathogenic, in the development of diseases. Thus, a comprehensive understanding of the post-translational modifications of cGAS-STING pathway and their role in disease development will provide insights in predicting individual disease outcomes and developing appropriate therapies. In this review, we will discuss the regulation of the cGAS-STING pathway and its implications in disease pathologies, as well as pharmacologic strategies to target the cGAS-STING pathway for therapeutic intervention.
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Affiliation(s)
- Jun Liu
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Ke Rui
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
| | - Na Peng
- Department of Rheumatology, the Second People's Hospital, China Three Gorges University, Yichang, China
| | - Hui Luo
- Department of Rheumatology and immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Zhu
- Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaoxia Zuo
- Department of Rheumatology and immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Liwei Lu
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong; Chongqing International Institute for Immunology, China
| | - Jixiang Chen
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
| | - Jie Tian
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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Molecular Mechanism and Role of Japanese Encephalitis Virus Infection in Central Nervous System-Mediated Diseases. Viruses 2022; 14:v14122686. [PMID: 36560690 PMCID: PMC9781168 DOI: 10.3390/v14122686] [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: 09/22/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The Japanese encephalitis virus (JEV) is the most common cause of neurodegenerative disease in Southeast Asia and the Western Pacific region; approximately 1.15 billion people are at risk, and thousands suffer from permanent neurological disorders across Asian countries, with 10-15 thousand people dying each year. JEV crosses the blood-brain barrier (BBB) and forms a complex with receptors on the surface of neurons. GRP78, Src, TLR7, caveolin-1, and dopamine receptor D2 are involved in JEV binding and entry into the neurons, and these receptors also play a role in carcinogenic activity in cells. JEV binds to GRP78, a member of the HSP70 overexpressed on malignant cells to enter neurons, indicating a higher chance of JEV infection in cancer patients. However, JEV enters human brain microvascular endothelial cells via an endocytic pathway mediated by caveolae and the ezrin protein and also targets dopamine-rich areas for infection of the midbrain via altering dopamine levels. In addition, JEV complexed with CLEC5A receptor of macrophage cells is involved in the breakdown of the BBB and central nervous system (CNS) inflammation. CLEC5A-mediated infection is also responsible for the influx of cytokines into the CNS. In this review, we discuss the neuronal and macrophage surface receptors involved in neuronal death.
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Gomes F, Alfson K, Junqueira M. Editorial: The application of OMICS technologies to interrogate host-virus interactions. Front Cell Infect Microbiol 2022; 12:1050012. [DOI: 10.3389/fcimb.2022.1050012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/21/2022] [Indexed: 11/16/2022] Open
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Minor structural changes, major functional impacts: posttranslational modifications and drug targets. Arch Pharm Res 2022; 45:693-703. [PMID: 36251238 DOI: 10.1007/s12272-022-01409-y] [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: 10/16/2021] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
Abstract
Posttranslational modifications (PTMs) are essential mechanisms that provide chemical diversity to proteins. The additional functional and structural elements can be introduced to exceed the primary amino acid composition. PTMs impact key biological and physiological processes including cell signaling, metabolism, protein degradation and influences interactions with other macromolecules. However, characterization of the structural and functional signatures of modified proteins has been historically limited. Since defects in PTMs are linked to numerous disorders and diseases, PTMs and their modifying enzymes are considered as potential drug targets. This has fueled new initiatives to determine how PTMs affect protein structure and function. In this review, I summarize some of the major, well-studied protein PTMs and related drug targets. Since PTMs are widely used for therapeutic targets or disease markers, highlighting structural changes after PTM provides new frontiers in understanding the detailed mechanism and related drug developments.
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28
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Adams C, Boonen K, Laukens K, Bittremieux W. Open Modification Searching of SARS-CoV-2-Human Protein Interaction Data Reveals Novel Viral Modification Sites. Mol Cell Proteomics 2022; 21:100425. [PMID: 36241021 PMCID: PMC9554009 DOI: 10.1016/j.mcpro.2022.100425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/18/2022] [Accepted: 10/09/2022] [Indexed: 01/18/2023] Open
Abstract
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus 2019 disease, has led to an ongoing global pandemic since 2019. Mass spectrometry can be used to understand the molecular mechanisms of viral infection by SARS-CoV-2, for example, by determining virus-host protein-protein interactions through which SARS-CoV-2 hijacks its human hosts during infection, and to study the role of post-translational modifications. We have reanalyzed public affinity purification-mass spectrometry data using open modification searching to investigate the presence of post-translational modifications in the context of the SARS-CoV-2 virus-host protein-protein interaction network. Based on an over twofold increase in identified spectra, our detected protein interactions show a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. In addition, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. A detailed analysis of relevant modifications, including phosphorylation, ubiquitination, and S-nitrosylation, provides important hypotheses about the functional role of these modifications during viral infection by SARS-CoV-2.
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Affiliation(s)
- Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium,Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium,Sustainable Health Department, Flemish Institute for Technological Research (VITO), Antwerp, Belgium
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,For correspondence: Wout Bittremieux
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29
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Zhang H, Huang J, Song Y, Liu X, Qian M, Huang P, Li Y, Zhao L, Wang H. Regulation of innate immune responses by rabies virus. Animal Model Exp Med 2022; 5:418-429. [PMID: 36138548 DOI: 10.1002/ame2.12273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/31/2022] [Indexed: 11/10/2022] Open
Abstract
Rabies virus (RABV) is an infectious and neurotropic pathogen that causes rabies and infects humans and almost all warm-blooded animals, posing a great threat to people and public safety. It is well known that innate immunity is the critical first line of host defense against viral infection. It monitors the invading pathogens by recognizing the pathogen-associated molecular patterns and danger-associated molecular patterns through pattern-recognition receptors, leading to the production of type I interferons (IFNα/β), inflammatory cytokines, and chemokines, or the activation of autophagy or apoptosis to inhibit virus replication. In the case of RABV, the innate immune response is usually triggered when the skin or muscle is bitten or scratched. However, RABV has evolved many ways to escape or even hijack innate immune response to complete its own replication and eventually invades the central nervous system (CNS). Once RABV reaches the CNS, it cannot be wiped out by the immune system or any drugs. Therefore, a better understanding of the interplay between RABV and innate immunity is necessary to develop effective strategies to combat its infection. Here, we review the innate immune responses induced by RABV and illustrate the antagonism mechanisms of RABV to provide new insights for the control of rabies.
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Affiliation(s)
- Haili Zhang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jingbo Huang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yumeng Song
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xingqi Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Meichen Qian
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pei Huang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yuanyuan Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Hualei Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
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Vann KR, Acharya A, Jang SM, Lachance C, Zandian M, Holt TA, Smith AL, Pandey K, Durden DL, El-Gamal D, Côté J, Byrareddy SN, Kutateladze TG. Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection. Structure 2022; 30:1224-1232.e5. [PMID: 35716662 PMCID: PMC9212912 DOI: 10.1016/j.str.2022.05.020] [Citation(s) in RCA: 14] [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: 03/05/2022] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 10/26/2022]
Abstract
Emerging new variants of SARS-CoV-2 and inevitable acquired drug resistance call for the continued search of new pharmacological targets to fight the potentially fatal infection. Here, we describe the mechanisms by which the E protein of SARS-CoV-2 hijacks the human transcriptional regulator BRD4. We found that SARS-CoV-2 E is acetylated in vivo and co-immunoprecipitates with BRD4 in human cells. Bromodomains (BDs) of BRD4 bind to the C-terminus of the E protein, acetylated by human acetyltransferase p300, whereas the ET domain of BRD4 recognizes the unmodified motif of the E protein. Inhibitors of BRD4 BDs, JQ1 or OTX015, decrease SARS-CoV-2 infectivity in lung bronchial epithelial cells, indicating that the acetyllysine binding function of BDs is necessary for the virus fitness and that BRD4 represents a potential anti-COVID-19 target. Our findings provide insight into molecular mechanisms that contribute to SARS-CoV-2 pathogenesis and shed light on a new strategy to block SARS-CoV-2 infection.
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Affiliation(s)
- Kendra R Vann
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Québec City, QC G1R 3S3, Canada
| | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Québec City, QC G1R 3S3, Canada
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Tina A Holt
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Audrey L Smith
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Donald L Durden
- Division of Hematology and Oncology, Department of Pediatrics, Moores Cancer Center, University of California San Diego, La Jolla, CA 92130, USA
| | - Dalia El-Gamal
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Québec City, QC G1R 3S3, Canada.
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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Sandalova T, Sala BM, Achour A. Structural aspects of chemical modifications in the MHC-restricted immunopeptidome; Implications for immune recognition. Front Chem 2022; 10:861609. [PMID: 36017166 PMCID: PMC9395651 DOI: 10.3389/fchem.2022.861609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022] Open
Abstract
Significant advances in mass-spectroscopy (MS) have made it possible to investigate the cellular immunopeptidome, a large collection of MHC-associated epitopes presented on the surface of healthy, stressed and infected cells. These approaches have hitherto allowed the unambiguous identification of large cohorts of epitope sequences that are restricted to specific MHC class I and II molecules, enhancing our understanding of the quantities, qualities and origins of these peptide populations. Most importantly these analyses provide essential information about the immunopeptidome in responses to pathogens, autoimmunity and cancer, and will hopefully allow for future tailored individual therapies. Protein post-translational modifications (PTM) play a key role in cellular functions, and are essential for both maintaining cellular homeostasis and increasing the diversity of the proteome. A significant proportion of proteins is post-translationally modified, and thus a deeper understanding of the importance of PTM epitopes in immunopeptidomes is essential for a thorough and stringent understanding of these peptide populations. The aim of the present review is to provide a structural insight into the impact of PTM peptides on stability of MHC/peptide complexes, and how these may alter/modulate immune responses.
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Affiliation(s)
- Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Benedetta Maria Sala
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- *Correspondence: Adnane Achour,
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32
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Gómez-Bañuelos E, Konig MF, Andrade F. Microbial pathways to subvert host immunity generate citrullinated neoantigens targeted in rheumatoid arthritis. Curr Opin Struct Biol 2022; 75:102423. [PMID: 35834948 PMCID: PMC9668488 DOI: 10.1016/j.sbi.2022.102423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 11/03/2022]
Abstract
The specific association between antibodies to citrullinated proteins and rheumatoid arthritis (RA) has centered interest on understanding why citrullinated proteins become immunogenic in this disease, which is believed to inform the origins of autoimmunity in RA. Since citrullination is a physiologic post-translational modification (PTM), one theory is that conditions promoting abnormal citrullination are initiators of self-reactive immune responses to citrullinated proteins in RA. Foremost candidates that dysregulate the normal balance of citrullination are microbial agents, which can exploit citrullination as an effector mechanism to subvert host antimicrobial activities and maximize their progeny. Here, we will use the host-pathogen interface as a unifying model to link microbe-induced citrullination and the loss of immunological tolerance to citrullinated antigens in RA.
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Affiliation(s)
- Eduardo Gómez-Bañuelos
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. https://twitter.com/@Eduardo95668787
| | - Maximilian F Konig
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. https://twitter.com/@MaxKonigMD
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Abstract
The cytokine storm (CS) in hyperinflammation is characterized by high levels of cytokines, extreme activation of innate as well as adaptive immune cells and initiation of apoptosis. High levels of apoptotic cells overwhelm the proper recognition and removal system of these cells. Phosphatidylserine on the apoptotic cell surface, which normally provides a recognition signal for removal, becomes a target for hemostatic proteins and secretory phospholipase A2. The dysregulation of these normal pathways in hemostasis and the inflammasome result in a prothrombotic state, cellular death, and end-organ damage. In this review, we provide the argument that this imbalance in recognition and removal is a common denominator regardless of the inflammatory trigger. The complex reaction of the immune defense system in hyperinflammation leads to self-inflicted damage. This common endpoint may provide additional options to monitor the progression of the inflammatory syndrome, predict severity, and may add to possible treatment strategies.
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Bell EW, Schwartz JH, Freddolino PL, Zhang Y. PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. J Mol Biol 2022; 434:167530. [PMID: 35662463 PMCID: PMC8897833 DOI: 10.1016/j.jmb.2022.167530] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/17/2022] [Accepted: 03/03/2022] [Indexed: 01/31/2023]
Abstract
Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, but few leverage both the sensitivity of structural information and the wide availability of sequence data. We present PEPPI, a pipeline which integrates structural similarity, sequence similarity, functional association data, and machine learning-based classification through a naïve Bayesian classifier model to accurately predict protein-protein interactions at a proteomic scale. Through benchmarking against a set of 798 ground truth interactions and an equal number of non-interactions, we have found that PEPPI attains 4.5% higher AUROC than the best of other state-of-the-art methods. As a proteomic-scale application, PEPPI was applied to model the interactions which occur between SARS-CoV-2 and human host cells during coronavirus infection, where 403 high-confidence interactions were identified with predictions covering 73% of a gold standard dataset from PSICQUIC and demonstrating significant complementarity with the most recent high-throughput experiments. PEPPI is available both as a webserver and in a standalone version and should be a powerful and generally applicable tool for computational screening of protein-protein interactions.
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Affiliation(s)
- Eric W Bell
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jacob H Schwartz
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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35
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Neddylation of Enterovirus 71 VP2 Protein Reduces Its Stability and Restricts Viral Replication. J Virol 2022; 96:e0059822. [PMID: 35510863 DOI: 10.1128/jvi.00598-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Posttranslational modifications (PTMs) of viral proteins play critical roles in virus infection. The role of neddylation in enterovirus 71 (EV71) replication remains poorly defined. Here, we showed that the structural protein VP2 of EV71 can be modified by neural precursor cell-expressed developmentally downregulated protein 8 (NEDD8) in an E3 ligase X-linked inhibitor of apoptosis protein (XIAP)-dependent manner. Mutagenesis and biochemical analyses mapped the neddylation site at lysine 69 (K69) of VP2 and demonstrated that neddylation reduced the stability of VP2. In agreement with the essential role of VP2 in viral replication, studies with EV71 reporter viruses with wild-type VP2 (enhanced green fluorescent protein [EGFP]-EV71) and a K69R mutant VP2 (EGFP-EV71-VP2 K69R) showed that abolishment of VP2 neddylation increased EV71 replication. In support of this finding, overexpression of NEDD8 significantly inhibited the replication of wild-type EV71 and EGFP-EV71, but not EGFP-EV71-VP2 K69R, whereas pharmacologic inhibition of neddylation with the NEDD8-activating enzyme inhibitor MLN4924 promoted the replication of EV71 in biologically relevant cell types. Our results thus support the notion that EV71 replication can be negatively regulated by host cellular and pathobiological cues through neddylation of VP2 protein. IMPORTANCE Neddylation is a ubiquitin-like posttranslational modification by conjugation of neural precursor cell-expressed developmentally downregulated protein 8 (NEDD8) to specific proteins for regulation of their metabolism and biological activities. In this study, we demonstrated for the first time that EV71 VP2 protein is neddylated at K69 residue to promote viral protein degradation and consequentially suppress multiplication of the virus. Our findings advance knowledge related to the roles of VP2 in EV71 virulence and the neddylation pathway in the host restriction of EV71 infection.
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Tayal S, Bhatia V, Mehrotra T, Bhatnagar S. ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. Amino Acids 2022; 54:923-934. [PMID: 35487995 PMCID: PMC9054641 DOI: 10.1007/s00726-022-03163-3] [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: 11/23/2021] [Accepted: 04/09/2022] [Indexed: 11/26/2022]
Abstract
Molecular mimicry of host proteins by pathogens constitutes a strategy to hijack the host pathways. At present, there is no dedicated resource for mimicked domains and motifs in the host-pathogen interactome. In this work, the experimental host-pathogen (HP) and host-host (HH) protein-protein interactions (PPIs) were collated. The domains and motifs of these proteins were annotated using CD Search and ScanProsite, respectively. Host and pathogen proteins with a shared host interactor and similar domain/motif constitute a mimicry pair exhibiting global structural similarity (domain mimicry pair; DMP) or local sequence motif similarity (motif mimicry pair; MMP). Mimicry pairs are likely to be co-expressed and co-localized. 1,97,607 DMPs and 32,67,568 MMPs were identified in 49,265 experimental HP-PPIs and organized in a web-based resource, ImitateDB ( http://imitatedb.sblab-nsit.net ) that can be easily queried. The results are externally integrated using hyperlinked domain PSSM ID, motif ID, protein ID and PubMed ID. Kinase, UL36, Smc and DEXDc were frequent DMP domains whereas protein kinase C phosphorylation, casein kinase 2 phosphorylation, glycosylation and myristoylation sites were frequent MMP motifs. Novel DMP domains SANT, Tudor, PhoX and MMP motif microbody C-terminal targeting signal, cornichon signature and lipocalin signature were proposed. ImitateDB is a novel resource for identifying mimicry in interacting host and pathogen proteins.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078, India
| | - Venugopal Bhatia
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India
| | - Tanya Mehrotra
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078, India.
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India.
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Park ES, Dezhbord M, Lee AR, Kim KH. The Roles of Ubiquitination in Pathogenesis of Influenza Virus Infection. Int J Mol Sci 2022; 23:ijms23094593. [PMID: 35562987 PMCID: PMC9105177 DOI: 10.3390/ijms23094593] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 01/14/2023] Open
Abstract
The ubiquitin system denotes a potent post-translational modification machinery that is capable of activation or deactivation of target proteins through reversible linkage of a single ubiquitin or ubiquitin chains. Ubiquitination regulates major cellular functions such as protein degradation, trafficking and signaling pathways, innate immune response, antiviral defense, and virus replication. The RNA sensor RIG-I ubiquitination is specifically induced by influenza A virus (IAV) to activate type I IFN production. Influenza virus modulates the activity of major antiviral proteins in the host cell to complete its full life cycle. Its structural and non-structural proteins, matrix proteins and the polymerase complex can regulate host immunity and antiviral response. The polymerase PB1-F2 of mutated 1918 IAV, adapts a novel IFN antagonist function by sending the DDX3 into proteasomal degradation. Ultimately the fate of virus is determined by the outcome of interplay between viral components and host antiviral proteins and ubiquitination has a central role in the encounter of virus and its host cell.
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Affiliation(s)
- Eun-Sook Park
- Institute of Biomedical Science and Technology, School of Medicine, Konkuk University, Seoul 05029, Korea;
| | - Mehrangiz Dezhbord
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
| | - Ah Ram Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
| | - Kyun-Hwan Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
- Correspondence: ; Tel.: +82-31-299-6126
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SGK1, a Serine/Threonine Kinase, Inhibits Prototype Foamy Virus Replication. Microbiol Spectr 2022; 10:e0199521. [PMID: 35438526 PMCID: PMC9241813 DOI: 10.1128/spectrum.01995-21] [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: 11/23/2022] Open
Abstract
Foamy viruses (FVs) are complex retroviruses belonging to the Spumaretrovirinae subfamily of the Retroviridae family. In contrast to human immunodeficiency virus (HIV), another member of the Retroviridae family, FVs are nonpathogenic in their natural hosts or in experimentally infected animals. Prototype foamy virus (PFV) is the only foamy virus that can infect humans through cross-species transmission and does not show any pathogenicity after infection. Consequently, PFV is considered a safe and efficient gene transfer vector. Understanding the host proteins involved in the replication of PFV and the mechanism of interaction between the host and the virus might lead to studies to improve the efficiency of gene transfer. To date, only a few host factors have been identified that affect PFV replication. In the present study, we report that PFV infection enhances the promoter activity of SGK1 (encoding serum/glucocorticoid regulated kinase 1) via the Tas protein signaling pathway, and then upregulates the mRNA and protein levels of SGK1. Overexpression of SGK1 reduced PFV replication, whereas its depletion using small interfering RNA increased PFV replication. SGK1 inhibits PFV replication by impairing the function of the PFV Tas activation domain in a kinase-independent manner and reducing the stability of the Gag protein in a kinase-dependent manner. In addition, both human and bovine SGK1 proteins inhibit the replication of bovine foamy virus (BFV) and PFV. These findings not only improved our understanding of the function of SGK1 and its relationship with foamy viruses, but also contributed to determining the antiviral mechanism of the host. IMPORTANCE Foamy viruses can integrate into the host chromosome and are nonpathogenic in natural hosts or in experimentally infected animals. Therefore, foamy viruses are considered to be safe and efficient gene transfer vectors. Persistent infection of foamy viruses is partly caused by the restrictive effect of host factors on the virus. However, only a few cellular proteins are known to influence the replication of foamy viruses. In this study, we report that SGK1 inhibits the replication of prototype foamy virus by affecting the function of the transcription activator, Tas, and reducing the stability of the structural protein, Gag. These results will increase our understanding of the interaction between the virus and host factors, deepening our perception of host antiviral defenses and the function of SGK1, and could improve the gene transfer efficiency of foamy viruses.
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Shvets D, Vinogradova S. Occurrence and Genetic Characterization of Grapevine Pinot Gris Virus in Russia. PLANTS (BASEL, SWITZERLAND) 2022; 11:1061. [PMID: 35448789 PMCID: PMC9028157 DOI: 10.3390/plants11081061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Grapevine Pinot gris virus (GPGV) is a widespread grapevine pathogen associated with symptoms of leaf mottling and deformation. In order to study the distribution and genetic diversity of GPGV in Russia, we tested 1347 grapevine samples from 3 regions of Russia-the Krasnodar Krai, Stavropol Krai, and Republic of Crimea-using duplex real-time RT-PCR. GPGV was detected in 993 grapevines, both symptomatic and asymptomatic. In 119 isolates, we sequenced complete movement protein (MP) and coat protein (CP) genes of the GPGV genome. The percentage of identity of the obtained nucleotide MP/CP sequences with the closest isolates from the GenBank was 97.75-99.56%. A phylogenetic analysis showed that these Russian GPGV isolates are mainly grouped with previously described representative asymptomatic isolates. New post-translational modifications of the MP and CP at the positions of polymorphisms in the genomes of Russian isolates were predicted. The present work is the first study on the distribution and genetic diversity of GPGV in Russia.
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Zapata-Cardona MI, Flórez-Álvarez L, Zapata-Builes W, Guerra-Sandoval AL, Guerra-Almonacid CM, Hincapié-García J, Rugeles MT, Hernandez JC. Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Front Microbiol 2022; 13:721103. [PMID: 35369500 PMCID: PMC8972052 DOI: 10.3389/fmicb.2022.721103] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
This article evaluated the in vitro antiviral effect of atorvastatin (ATV) against SARS-CoV-2 and identified the interaction affinity between this compound and two SARS-CoV-2 proteins. The antiviral activity of atorvastatin against this virus was evaluated by three different treatment strategies [(i) pre-post treatment, (ii) pre-infection treatment, and (iii) post-infection treatment] using Vero E6 and Caco-2 cells. The interaction of atorvastatin with RdRp (RNA-dependent RNA polymerase) and 3CL protease (3-chymotrypsin-like protease) was evaluated by molecular docking. The CC50s (half-maximal cytotoxic concentrations) obtained for ATV were 50.3 and 64.5 μM in Vero E6 and Caco-2, respectively. This compound showed antiviral activity against SARS-CoV-2 D614G strain in Vero E6 with median effective concentrations (EC50s) of 15.4, 12.1, and 11.1 μM by pre-post, pre-infection, and post-infection treatments, respectively. ATV also inhibited Delta and Mu variants by pre-post treatment (EC50s of 16.8 and 21.1 μM, respectively). In addition, ATV showed an antiviral effect against the D614G strain independent of the cell line (EC50 of 7.4 μM in Caco-2). The interaction of atorvastatin with SARS-CoV-2 RdRp and 3CL protease yielded a binding affinity of -6.7 kcal/mol and -7.5 kcal/mol, respectively. Our study demonstrated the in vitro antiviral activity of atorvastatin against the ancestral SARS-CoV-2 D614G strain and two emerging variants (Delta and Mu), with an independent effect of the cell line. A favorable binding affinity between ATV and viral proteins by bioinformatics methods was found. Due to the extensive clinical experience of atorvastatin use, it could prove valuable in the treatment of COVID-19.
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Affiliation(s)
- María I. Zapata-Cardona
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
| | | | | | - Jaime Hincapié-García
- Grupo de investigación, Promoción y prevención farmacéutica, Facultad de ciencias farmacéuticas y alimentarias, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María T. Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Juan C. Hernandez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
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Thongboonkerd V, Chaiyarit S. Gel-Based and Gel-Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins. Curr Protoc 2022; 2:e390. [PMID: 35275445 DOI: 10.1002/cpz1.390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitochondrion is a key intracellular organelle regulating metabolic processes, oxidative stress, energy production, calcium homeostasis, and cell survival. Protein phosphorylation plays an important role in regulating mitochondrial functions and cellular signaling pathways. Dysregulation of protein phosphorylation status can cause protein malfunction and abnormal signal transduction, leading to organ dysfunction and disease. Investigating the mitochondrial phosphoproteins is therefore crucial to better understand the molecular and pathogenic mechanisms of many metabolic disorders. Conventional analyses of phosphoproteins, for instance, via western blotting, can be done only for proteins for which specific antibodies to their phosphorylated forms are available. Moreover, such an approach is not suitable for large-scale study of phosphoproteins. Currently, proteomics represents an important tool for large-scale analysis of proteins and their post-translational modifications, including phosphorylation. Here, we provide step-by-step protocols for the proteomics analysis of mitochondrial phosphoproteins (the phosphoproteome), using renal tubular cells as an example. These protocols include methods to effectively isolate mitochondria and to validate the efficacy of mitochondrial enrichment as well as its purity. We also provide detailed protocols for performing both gel-based and gel-free phosphoproteome analyses. The gel-based analysis involves two-dimensional gel electrophoresis and phosphoprotein-specific staining, followed by protein identification via mass spectrometry, whereas the gel-free approach is based on in-solution mass spectrometric identification of specific phosphorylation sites and residues. In all, these approaches allow large-scale analyses of mitochondrial phosphoproteins that can be applied to other cells and tissues of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Mitochondrial isolation/purification from renal tubular cells Support Protocol: Validation of enrichment efficacy and purity of mitochondrial isolation Basic Protocol 2: Gel-based phosphoproteome analysis Basic Protocol 3: Gel-free phosphoproteome analysis.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Tang X, Liu T, Li X, Sheng X, Xing J, Chi H, Zhan W. Protein phosphorylation in hemocytes of Fenneropenaeus chinensis in response to white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2022; 122:106-114. [PMID: 35092807 DOI: 10.1016/j.fsi.2022.01.038] [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: 11/08/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Protein phosphorylation and dephosphorylation are the most common and important regulatory mechanisms in signal transduction, which play a vital role in immune defense response. Our previous study has found the level of tyrosine phosphorylation was significantly changed in the hemocytes of Fenneropenaeus chinensis upon white spot syndrome virus (WSSV) infection. In order to explore the relationship between protein phosphorylation and WSSV infection, the quantitative phosphoproteomics was employed to identify differential phosphorylated proteins in hemocytes of F. chinensis before and after WSSV infection, and elucidate the role of key differential phosphorylated proteins in WSSV infection process. The results showed that a total of 147 differential phosphorylated proteins were identified in the hemocytes, including 64 phosphorylated proteins and 83 dephosphorylated proteins, which were mostly enriched in pyruvate metabolism, TCA cycle, glycolysis, and ribosomal biosynthesis. Functional analysis of differential phosphorylated proteins showed that they were involved in cell apoptosis, cell phagocytosis, cell metabolism and antiviral infection. A total of 236 differential phosphorylation sites were found, including 91 modified sites in the phosphorylation proteins and 145 modified sites in the dephosphorylation proteins. Motif analysis showed that these phosphorylation sites could activate mitogen-activated protein kinase, P70 S6 kinase and other kinases in hemocytes. Moveover, the phosphorylation levels of eukaryotic protein initiation factor 4E binding proteins and histone H3 were further determined by ELISA and Western blotting, which both exhibited a significant increase post WSSV infection and reach their peak levels at 6 and 12 h, respectively. Moreover, we found that lactate, a metabolite closely related to pyruvate metabolism, TCA cycle and glycolysis, was significantly increased in the hemocytes after WSSV infection. This study revealed the protein phosphorylation response in hemocytes of F. chinensis to WSSV infection, which help to clarify the response characteristics and virus resistance mechanism of hemocytes in F. chinensis, and also facilitate further understanding of the interaction between WSSV and shrimp hemocytes.
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Affiliation(s)
- Xiaoqian Tang
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ting Liu
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China
| | - Xiaoai Li
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China
| | - Xiuzhen Sheng
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China
| | - Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Heng Chi
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Wenbin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants. Life (Basel) 2022; 12:life12020324. [PMID: 35207610 PMCID: PMC8874572 DOI: 10.3390/life12020324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.
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Li Y, Zhang Y, Pan T, Zhou P, Zhou W, Gao Y, Zheng S, Xu J. Shedding light on the hidden human proteome expands immunopeptidome in cancer. Brief Bioinform 2022; 23:6533503. [PMID: 35189633 DOI: 10.1093/bib/bbac034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 01/04/2023] Open
Abstract
Unrestrained cellular growth and immune escape of a tumor are associated with the incidental errors of the genome and transcriptome. Advances in next-generation sequencing have identified thousands of genomic and transcriptomic aberrations that generate variant peptides that assemble the hidden proteome, further expanding the immunopeptidome. Emerging next-generation sequencing technologies and a number of computational methods estimated the abundance of immune infiltration from bulk transcriptome have advanced our understanding of tumor microenvironments. Here, we will characterize several major types of tumor-specific antigens arising from single-nucleotide variants, insertions and deletions, gene fusion, alternative splicing, RNA editing and non-coding RNAs. Finally, we summarize the current state-of-the-art computational and experimental approaches or resources and provide an integrative pipeline for the identification of candidate tumor antigens. Together, the systematic investigation of the hidden proteome in cancer will help facilitate the development of effective and durable immunotherapy targets for cancer.
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Affiliation(s)
- Yongsheng Li
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tao Pan
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Ping Zhou
- Department of Radiotherapy, the First Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yueying Gao
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Shaojiang Zheng
- Key Laboratory of Emergency and Trauma of Ministry of Education, Tumor Institute of the First Affiliated Hospital, Hainan Medical University, Haikou, 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Klein RS. Encephalitic Arboviruses of Africa: Emergence, Clinical Presentation and Neuropathogenesis. Front Immunol 2022; 12:769942. [PMID: 35003087 PMCID: PMC8733932 DOI: 10.3389/fimmu.2021.769942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
Many mosquito-borne viruses (arboviruses) are endemic in Africa, contributing to systemic and neurological infections in various geographical locations on the continent. While most arboviral infections do not lead to neuroinvasive diseases of the central nervous system, neurologic diseases caused by arboviruses include flaccid paralysis, meningitis, encephalitis, myelitis, encephalomyelitis, neuritis, and post-infectious autoimmune or memory disorders. Here we review endemic members of the Flaviviridae and Togaviridae families that cause neurologic infections, their neuropathogenesis and host neuroimmunological responses in Africa. We also discuss the potential for neuroimmune responses to aide in the development of new diagnostics and therapeutics, and current knowledge gaps to be addressed by arbovirus research.
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Affiliation(s)
- Robyn S Klein
- Center for Neuroimmunology & Neuroinfectious Diseases, Departments of Medicine, Neuroscience, and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, United States
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Cosar B, Karagulleoglu ZY, Unal S, Ince AT, Uncuoglu DB, Tuncer G, Kilinc BR, Ozkan YE, Ozkoc HC, Demir IN, Eker A, Karagoz F, Simsek SY, Yasar B, Pala M, Demir A, Atak IN, Mendi AH, Bengi VU, Cengiz Seval G, Gunes Altuntas E, Kilic P, Demir-Dora D. SARS-CoV-2 Mutations and their Viral Variants. Cytokine Growth Factor Rev 2022; 63:10-22. [PMID: 34580015 PMCID: PMC8252702 DOI: 10.1016/j.cytogfr.2021.06.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022]
Abstract
Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occur spontaneously during replication. Thousands of mutations have accumulated and continue to since the emergence of the virus. As novel mutations continue appearing at the scene, naturally, new variants are increasingly observed. Since the first occurrence of the SARS-CoV-2 infection, a wide variety of drug compounds affecting the binding sites of the virus have begun to be studied. As the drug and vaccine trials are continuing, it is of utmost importance to take into consideration the SARS-CoV-2 mutations and their respective frequencies since these data could lead the way to multi-drug combinations. The lack of effective therapeutic and preventive strategies against human coronaviruses (hCoVs) necessitates research that is of interest to the clinical applications. The reason why the mutations in glycoprotein S lead to vaccine escape is related to the location of the mutation and the affinity of the protein. At the same time, it can be said that variations should occur in areas such as the receptor-binding domain (RBD), and vaccines and antiviral drugs should be formulated by targeting more than one viral protein. In this review, a literature survey in the scope of the increasing SARS-CoV-2 mutations and the viral variations is conducted. In the light of current knowledge, the various disguises of the mutant SARS-CoV-2 forms and their apparent differences from the original strain are examined as they could possibly aid in finding the most appropriate therapeutic approaches.
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Affiliation(s)
- Begum Cosar
- Başkent University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, Ankara, Turkey
| | - Zeynep Yagmur Karagulleoglu
- Yıldız Technical University, Faculty of Arts and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Sinan Unal
- Yıldız Technical University, Faculty of Arts and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | | | - Dilruba Beyza Uncuoglu
- Ankara University, Graduate School of Natural and Applied Sciences, Department of Biology, Ankara, Turkey
| | - Gizem Tuncer
- Hacettepe University, Graduate School of Science and Engineering, General Biology Program, Ankara, Turkey; HücreCELL Biotechnology Development and Commerce, Inc., Ankara, Turkey
| | - Bugrahan Regaip Kilinc
- Kastamonu University, School of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey; Kastamonu University, School of Engineering and Architecture, Department of Biomedical Engineering, Kastamonu, Turkey
| | - Yunus Emre Ozkan
- Gebze Technical University, Faculty of Science, Department of Molecular Biology and Genetics, Kocaeli, Turkey
| | - Hikmet Ceyda Ozkoc
- Akdeniz University, Faculty of Medicine, Department of Medical Pharmacology, Antalya, Turkey
| | | | - Ali Eker
- Akdeniz University, Faculty of Medicine, Antalya, Turkey
| | | | | | - Bunyamin Yasar
- Alanya Alaaddin Keykubat University, Department of Molecular Medicine, Antalya, Turkey
| | - Mehmetcan Pala
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, Sivas, Turkey
| | - Aysegul Demir
- Üsküdar University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Irem Naz Atak
- Ankara University, Faculty of Science, Department of Biology, Ankara, Turkey
| | - Aysegul Hanife Mendi
- Gazi University, Faculty of Dentistry, Department of Basic Sciences, Division of Medical Microbiology, Ankara, Turkey
| | - Vahdi Umut Bengi
- Gülhane Training and Research Hospital, Faculty of Dentistry, Department of Periodontology, Ankara, Turkey
| | - Guldane Cengiz Seval
- Ankara University, School of Medicine Department of Hematology, Cebeci, Ankara, Turkey
| | | | - Pelin Kilic
- HücreCELL Biotechnology Development and Commerce, Inc., Ankara, Turkey; Ankara University, Stem Cell Institute, Ankara, Turkey.
| | - Devrim Demir-Dora
- Akdeniz University, Faculty of Medicine, Department of Medical Pharmacology, Antalya, Turkey; Akdeniz University, Health Sciences Institute, Department of Gene and Cell Therapy, Antalya, Turkey; Akdeniz University, Health Sciences Institute, Department of Medical Biotechnology, Antalya, Turkey.
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RNA-Binding Proteins as Regulators of Internal Initiation of Viral mRNA Translation. Viruses 2022; 14:v14020188. [PMID: 35215780 PMCID: PMC8879377 DOI: 10.3390/v14020188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Viruses are obligate intracellular parasites that depend on the host’s protein synthesis machinery for translating their mRNAs. The viral mRNA (vRNA) competes with the host mRNA to recruit the translational machinery, including ribosomes, tRNAs, and the limited eukaryotic translation initiation factor (eIFs) pool. Many viruses utilize non-canonical strategies such as targeting host eIFs and RNA elements known as internal ribosome entry sites (IRESs) to reprogram cellular gene expression, ensuring preferential translation of vRNAs. In this review, we discuss vRNA IRES-mediated translation initiation, highlighting the role of RNA-binding proteins (RBPs), other than the canonical translation initiation factors, in regulating their activity.
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Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems 2021; 6:e0038821. [PMID: 34519533 PMCID: PMC8547474 DOI: 10.1128/msystems.00388-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.
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Affiliation(s)
- Merve Cakir
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
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49
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Hu QX, Wang HY, Jiang L, Wang CY, Ju LG, Zhu Y, Zhong B, Wu M, Wang Z, Li LY. Histone demethylase LSD1 promotes RIG-I poly-ubiquitination and anti-viral gene expression. PLoS Pathog 2021; 17:e1009918. [PMID: 34529741 PMCID: PMC8445485 DOI: 10.1371/journal.ppat.1009918] [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: 04/26/2021] [Accepted: 08/26/2021] [Indexed: 11/19/2022] Open
Abstract
Under RNA virus infection, retinoic acid-inducible gene I (RIG-I) in host cells recognizes viral RNA and activates the expression of type I IFN. To investigate the roles of protein methyltransferases and demethylases in RIG-I antiviral signaling pathway, we screened all the known related enzymes with a siRNA library and identified LSD1 as a positive regulator for RIG-I signaling. Exogenous expression of LSD1 enhances RIG-I signaling activated by virus stimulation, whereas its deficiency restricts it. LSD1 interacts with RIG-I, promotes its K63-linked polyubiquitination and interaction with VISA/MAVS. Interestingly, LSD1 exerts its function in antiviral response not dependent on its demethylase activity but through enhancing the interaction between RIG-I with E3 ligases, especially TRIM25. Furthermore, we provide in vivo evidence that LSD1 increases antiviral gene expression and inhibits viral replication. Taken together, our findings demonstrate that LSD1 is a positive regulator of signaling pathway triggered by RNA-virus through mediating RIG-I polyubiquitination. RIG-I signaling pathway is critical for human cells to defend from RNA virus infection, such as SARS-CoV-2, influenza virus, and Vesicular Stomatitis Virus (VSV). LSD1 is a histone demethylase regulating transcription. The current study reveals a novel function of LSD1 in regulating the activation of RIG-I signaling pathway. LSD1 interacts with RIG-I and promotes RIG-I poly-ubiquitination independent of its demethylase activity. LSD1 facilitates the interaction between RIG-I and its ubiquitin E3 ligase TRIM25, which is crucial for recruitment of downstream proteins. The mice with LSD1 deficiency are susceptible to virus infection and have lower survival rate. Taken together, our findings demonstrate a novel molecular mechanism for regulating the anti-viral RIG-I signaling pathway.
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Affiliation(s)
- Qi-Xin Hu
- Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Hui-Yi Wang
- Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Lu Jiang
- Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Chen-Yu Wang
- Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Lin-Gao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yuan Zhu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Bo Zhong
- Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Department of Immunology, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
- * E-mail: (MW); (ZW); (L-YL)
| | - Zhen Wang
- Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
- * E-mail: (MW); (ZW); (L-YL)
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
- * E-mail: (MW); (ZW); (L-YL)
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50
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Inhibition of the Neddylation Pathway Suppresses Enterovirus Replication. Virol Sin 2021; 36:1664-1667. [PMID: 34351571 DOI: 10.1007/s12250-021-00427-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/26/2021] [Indexed: 01/04/2023] Open
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