1
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Marchetti S, Colombo A, Saibene M, Bragato C, La Torretta T, Rizzi C, Gualtieri M, Mantecca P. Shedding light on the cellular mechanisms involved in the combined adverse effects of fine particulate matter and SARS-CoV-2 on human lung cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175979. [PMID: 39233085 DOI: 10.1016/j.scitotenv.2024.175979] [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: 03/15/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Airborne pathogens represent a topic of scientific relevance, especially considering the recent COVID-19 pandemic. Air pollution, and particulate matter (PM) in particular, has been proposed as a possible risk factor for the onset and spread of pathogen-driven respiratory diseases. Regarding SARS-CoV-2 infection, exposure to fine PM (PM2.5, particles with an aerodynamic diameter < 2.5 μm) has been associated with increased incidence of the COVID-19 disease. To provide useful insights into the mechanisms through which PM might be involved in infection, we exposed human lung cells (A549) to PM2.5 and SARS-CoV-2, to evaluate the toxicological properties and the molecular pathways activated when airborne particles are combined with viral particles. Winter PM2.5 was collected in a metropolitan urban area and its physico-chemical composition was analyzed. A549 cells were exposed to SARS-CoV-2 concomitantly or after pre-treatment with PM2.5. Inflammation, oxidative stress and xenobiotic metabolism were the main pathways investigated. Results showed that after 72 h of exposure PM2.5 significantly increased the expression of the angiotensin-converting enzyme 2 (ACE2) receptor, which is one of the keys used by the virus to infect host cells. We also analyzed the endosomal route in the process of internalization, by studying the expression of RAB5 and RAB7. The results show that in cells pre-activated with PM and then exposed to SARS-CoV-2, RAB5 expression is significantly increased. The activation of the inflammatory process was then studied. Our findings show an increase of pro-inflammatory markers (NF-kB and IL-8) in cells pre-activated with PM for 72 h and subsequently exposed to the virus for a further 24 h, further demonstrating that the interaction between PM and SARS-CoV-2 determines the severity of the inflammatory responses in lung epithelial cells. In conclusion, the study provides mechanistic biological evidence of PM contribution to the onset and progression of viral respiratory diseases in exposed populations.
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Affiliation(s)
- Sara Marchetti
- POLARIS Research Centre, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy.
| | - Anita Colombo
- POLARIS Research Centre, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Melissa Saibene
- Platform of Microscopy, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Cinzia Bragato
- POLARIS Research Centre, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Teresa La Torretta
- Laboratory of Atmospheric Pollution, National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, 40129 Bologna, Italy
| | - Cristiana Rizzi
- Department of Earth and Environmental Sciences, University of Milano - Bicocca, Piazza della Scienza, 1, 20126 Milano, Italy
| | - Maurizio Gualtieri
- POLARIS Research Centre, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Paride Mantecca
- POLARIS Research Centre, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
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2
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Saratov GA, Belogurov AA, Kudriaeva AA. Myelin basic protein antagonizes the SARS-CoV-2 protein ORF3a-induced autophagy inhibition. Biochimie 2024; 225:1-9. [PMID: 38703943 DOI: 10.1016/j.biochi.2024.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/06/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024]
Abstract
Inhibition of autophagy is one of the hallmarks of the SARS-CoV-2 infection. Recently it was reported that SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes via interaction with VPS39 thus preventing binding of homotypic fusion and protein sorting (HOPS) complex to RAB7 GTPase. Here we report that myelin basic protein (MBP), a major structural component of the myelin sheath, binds ORF3a and is colocalized with it in mammalian cells. Co-expression of MBP with ORF3a restores autophagy in mammalian cells, inhibited by viral protein. Our data suggest that basic charge of MBP drives suppression of ORF3a-induced autophagy inhibition as its deaminated variants lost ability to bind ORF3a and counteract autophagy blockade. These results together with our recent findings, indicating that MBP interacts with structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3) and Sec1/Munc18-1 family members, may suggest protective role of the MBP in terms of the maintaining of protein traffic and autophagosome-lysosome fusion machinery in oligodendrocytes during SARS-CoV-2 infection. Finally, our data may indicate that deimination of MBP observed in the patients with multiple sclerosis (MS) may contribute to the previously reported worser outcomes of COVID-19 and increase of post-COVID-19 neurologic symptoms in patients with MS.
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Affiliation(s)
- George A Saratov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia; Moscow Institute of Physics and Technology (national Research University), Phystech School of Biological and Medical Physics, 141701, Dolgoprudny, Moscow Region, Russia
| | - Alexey A Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia; Russian University of Medicine, Department of Biological Chemistry, Ministry of Health of Russian Federation, 127473, Moscow, Russia.
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia.
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Rafiyian M, Reiter RJ, Rasooli Manesh SM, Asemi R, Sharifi M, Mohammadi S, Mansournia MA, Asemi Z. Programmed cell death and melatonin: A comprehensive review. Funct Integr Genomics 2024; 24:169. [PMID: 39313718 DOI: 10.1007/s10142-024-01454-4] [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: 08/10/2024] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/25/2024]
Abstract
Melatonin (MLT), a main product of pineal gland, recently has attracted the attention of scientists due to its benefits in various diseases and also regulation of cellular homeostasis. Its receptor scares widely distributed indicating that it influences numerous organs. Programmed cell death (PCD), of which there several types, is a regulated by highly conserved mechanisms and important for development and function of different organs. Enhancement or inhibition of PCDs could be a useful technique for treatment of different diseases and MLT, due to its direct effects on these pathways, is a good candidate for this strategy. Many studies investigated the role of MLT on PCDs in different diseases and in this review, we summarized some of the most significant studies in this field to provide a better insight into the mechanisms of modulation of PCD by MLT modulation.
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Affiliation(s)
- Mahdi Rafiyian
- Student Research Committee, Kashan University of Reiter Sciences, Kashan, Iran
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health. Long School of Medicine, San Antonio, TX, USA.
| | | | - Reza Asemi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehran Sharifi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sotoudeh Mohammadi
- Department of Obstetrics and Gynecology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Mansournia
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Akter S, Islam MJ, Ali MA, Zakaria Tashrif M, Uddin MJ, Ullah MO, Halim MA. Structure and dynamics of whole-sequence homology model of ORF3a protein of SARS-CoV-2: An insight from microsecond molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:6726-6739. [PMID: 37528650 DOI: 10.1080/07391102.2023.2236715] [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: 09/22/2022] [Accepted: 07/08/2023] [Indexed: 08/03/2023]
Abstract
The ORF3a is a large accessory protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which plays an important role in virulence and viral replication; especially in inflammasome activation and apoptosis. However,, the existing cryo-EM structure of SARS-CoV-2 ORF3a is incomplete, . making it challenging to understand its structural and functional features. The aim of this study is to investigate the dynamic behaviors of the full-sequence homology model of ORF3a and compare it with the cryo-EM structure using microsecond molecular dynamics simulations. The previous studies indicated that the unresolved residues of the cryo-EM structure are not only involved in the pathogenesis of the SARS-CoV-2 but also exhibit a significant antigenicity. The dynamics scenario of homology model revealed higher RMSD, Rg, and SASA values with stable pattern when compared to the cryo-EM structure. Moreover, the RMSF analysis demonstrated higher fluctuations at specific positions (1-43, 97-110, 172-180, 219-243) in the model structure, whereas the cryo-EM structure displayed lower overall drift (except 1-43) in comparison to the model structure.Secondary structural features indicated that a significant unfolding in the transmembrane domains and β-strand at positions 166 to 172, affecting the stability and compactness of the cryo-EM structure , whereas the model exhibited noticeable unfolding in transmembrane domains and small-coiled regions in the N-terminal. , The results from molecular docking and steered molecular dynamics investigations showed the model structure had a greater number of non-bonding interactions, leading to enhanced stability when compared to the cryo-EM structure. Consequently, higher forces were necessary for unbinding of the baricitinib and ruxolitinib inhibitors from the model structure.. Our findings can help better understanding of the significance of unresolved residues at the molecular level. Additionally, this information can guide researchers for experimental endeavors aimed at completing the full-sequence structure of the ORF3a.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shaila Akter
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Md Zakaria Tashrif
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Jaish Uddin
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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Geng F, Chen J, Song B, Tang Z, Li X, Zhang S, Yang T, Liu Y, Mo W, Zhang Y, Sun C, Tan L, Tu W, Yu D, Cao J, Zhang S. Chaperone- and PTM-mediated activation of IRF1 tames radiation-induced cell death and the inflammatory response. Cell Mol Immunol 2024; 21:856-872. [PMID: 38849539 PMCID: PMC11291999 DOI: 10.1038/s41423-024-01185-3] [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: 11/07/2023] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
The key role of structural cells in immune modulation has been revealed with the advent of single-cell multiomics, but the underlying mechanism remains poorly understood. Here, we revealed that the transcriptional activation of interferon regulatory factor 1 (IRF1) in response to ionizing radiation, cytotoxic chemicals and SARS-CoV-2 viral infection determines the fate of structural cells and regulates communication between structural and immune cells. Radiation-induced leakage of mtDNA initiates the nuclear translocation of IRF1, enabling it to regulate the transcription of inflammation- and cell death-related genes. Novel posttranslational modification (PTM) sites in the nuclear localization sequence (NLS) of IRF1 were identified. Functional analysis revealed that mutation of the acetylation site and the phosphorylation sites in the NLS blocked the transcriptional activation of IRF1 and reduced cell death in response to ionizing radiation. Mechanistically, reciprocal regulation between the single-stranded DNA sensors SSBP1 and IRF1, which restrains radiation-induced and STING/p300-mediated PTMs of IRF1, was revealed. In addition, genetic deletion or pharmacological inhibition of IRF1 tempered radiation-induced inflammatory cell death, and radiation mitigators also suppressed SARS-CoV-2 NSP-10-mediated activation of IRF1. Thus, we revealed a novel cytoplasm-oriented mechanism of IRF1 activation in structural cells that promotes inflammation and highlighted the potential effectiveness of IRF1 inhibitors against immune disorders.
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Affiliation(s)
- Fenghao Geng
- Laboratory of Radiation Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Department of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jianhui Chen
- Department of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Bin Song
- Laboratory of Radiation Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhicheng Tang
- School of Radiation Medicine and Protection, State Key Laboratory of Radiation Medicine, Soochow University, Suzhou, 215123, China
| | - Xiaoqian Li
- Department of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shuaijun Zhang
- Laboratory of Radiation Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Tingyi Yang
- Department of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yulan Liu
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, 610051, China
| | - Wei Mo
- School of Radiation Medicine and Protection, State Key Laboratory of Radiation Medicine, Soochow University, Suzhou, 215123, China
| | - Yining Zhang
- Department of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Chuntang Sun
- Laboratory of Radiation Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Tan
- Laboratory of Radiation Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenling Tu
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, 610051, China
| | - Daojiang Yu
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, 610051, China
| | - Jianping Cao
- School of Radiation Medicine and Protection, State Key Laboratory of Radiation Medicine, Soochow University, Suzhou, 215123, China
| | - Shuyu Zhang
- Laboratory of Radiation Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
- Department of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, 610051, China.
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, Mianyang, 621099, China.
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6
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Joharinia N, Bonneil É, Grandvaux N, Thibault P, Lippé R. Comprehensive proteomic analysis of HCoV-OC43 virions and virus-modulated extracellular vesicles. J Virol 2024; 98:e0085024. [PMID: 38953378 PMCID: PMC11265355 DOI: 10.1128/jvi.00850-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024] Open
Abstract
Viruses are obligate parasites that depend on the cellular machinery for their propagation. Several viruses also incorporate cellular proteins that facilitate viral spread. Defining these cellular proteins is critical to decipher viral life cycles and delineate novel therapeutic strategies. While numerous studies have explored the importance of host proteins in coronavirus spread, information about their presence in mature virions is limited. In this study, we developed a protocol to highly enrich mature HCoV-OC43 virions and characterize them by proteomics. Recognizing that cells release extracellular vesicles whose content is modulated by viruses, and given our ability to separate virions from these vesicles, we also analyzed their protein content in both uninfected and infected cells. We uncovered 69 unique cellular proteins associated with virions including 31 high-confidence hits. These proteins primarily regulate RNA metabolism, enzymatic activities, vesicular transport, cell adhesion, metabolite interconversion, and translation. We further discovered that the virus had a profound impact on exosome composition, incorporating 47 novel cellular proteins (11 high confidence) and excluding 92 others (61 high confidence) in virus-associated extracellular vesicles compared to uninfected cells. Moreover, a dsiRNA screen revealed that 11 of 18 select targets significantly impacted viral yields, including proteins found in virions or extracellular vesicles. Overall, this study provides new and important insights into the incorporation of numerous host proteins into HCoV-OC43 virions, their biological significance, and the ability of the virus to modulate extracellular vesicles. IMPORTANCE In recent years, coronaviruses have dominated global attention, making it crucial to develop methods to control them and prevent future pandemics. Besides viral proteins, host proteins play a significant role in viral propagation and offer potential therapeutic targets. Targeting host proteins is advantageous because they are less likely to mutate and develop resistance compared to viral proteins, a common issue with many antiviral treatments. In this study, we examined the protein content of the less virulent biosafety level 2 HCoV-OC43 virus as a stand-in for the more virulent SARS-CoV-2. Our findings reveal that several cellular proteins incorporated into the virion regulate viral spread. In addition, we report that the virus extensively modulates the content of extracellular vesicles, enhancing viral dissemination. This underscores the critical interplay between the virus, host proteins, and extracellular vesicles.
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Affiliation(s)
- Negar Joharinia
- Azrieli Research center of the CHU Sainte-Justine, Montreal, Quebec, Canada
- Department of Microbiology, Infectiology and Immunology, University of Montreal, Montreal, Quebec, Canada
| | - Éric Bonneil
- IRIC, University of Montreal, Montreal, Quebec, Canada
| | - Nathalie Grandvaux
- Research center of the CHUM (CRCHUM), Montreal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Pierre Thibault
- IRIC, University of Montreal, Montreal, Quebec, Canada
- Department of Chemistry, University of Montreal, Montreal, Quebec, Canada
| | - Roger Lippé
- Azrieli Research center of the CHU Sainte-Justine, Montreal, Quebec, Canada
- Department of Pathology and Cell biology, University of Montreal, Montreal, Quebec, Canada
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Datta G, Rezagholizadeh N, Hasler WA, Khan N, Chen X. SLC38A9 regulates SARS-CoV-2 viral entry. iScience 2024; 27:110387. [PMID: 39071889 PMCID: PMC11277692 DOI: 10.1016/j.isci.2024.110387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/13/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
SARS-CoV-2 viral entry into host cells depends on the cleavage of spike (S) protein into S1 and S2 proteins. Such proteolytic cleavage by furin results in the exposure of a multibasic motif on S1, which is critical for SARS-CoV-2 viral infection and transmission; however, how such a multibasic motif contributes to the infection of SARS-CoV-2 remains elusive. Here, we demonstrate that the multibasic motif on S1 is critical for its interaction with SLC38A9, an endolysosome-resident arginine sensor. SLC38A9 knockdown prevents S1-induced endolysosome de-acidification and blocks the S protein-mediated entry of pseudo-SARS-CoV-2 in Calu-3, U87MG, Caco-2, and A549 cells. Our findings provide a novel mechanism in regulating SARS-CoV-2 viral entry; S1 present in endolysosome lumen could interact with SLC38A9, which mediates S1-induced endolysosome de-acidification and dysfunction, facilitating the escape of SARS-CoV-2 from endolysosomes and enhancing viral entry.
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Affiliation(s)
- Gaurav Datta
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Neda Rezagholizadeh
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Wendie A. Hasler
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Nabab Khan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Xuesong Chen
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
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8
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Yin X, Pu Y, Yuan S, Pache L, Churas C, Weston S, Riva L, Simons LM, Cisneros WJ, Clausen T, De Jesus PD, Kim HN, Fuentes D, Whitelock J, Esko J, Lord M, Mena I, García-Sastre A, Hultquist JF, Frieman MB, Ideker T, Pratt D, Martin-Sancho L, Chanda SK. Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602835. [PMID: 39026801 PMCID: PMC11257544 DOI: 10.1101/2024.07.10.602835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Defining the subset of cellular factors governing SARS-CoV-2 replication can provide critical insights into viral pathogenesis and identify targets for host-directed antiviral therapies. While a number of genetic screens have previously reported SARS-CoV-2 host dependency factors, these approaches relied on utilizing pooled genome-scale CRISPR libraries, which are biased towards the discovery of host proteins impacting early stages of viral replication. To identify host factors involved throughout the SARS-CoV-2 infectious cycle, we conducted an arrayed genome-scale siRNA screen. Resulting data were integrated with published datasets to reveal pathways supported by orthogonal datasets, including transcriptional regulation, epigenetic modifications, and MAPK signalling. The identified proviral host factors were mapped into the SARS-CoV-2 infectious cycle, including 27 proteins that were determined to impact assembly and release. Additionally, a subset of proteins were tested across other coronaviruses revealing 17 potential pan-coronavirus targets. Further studies illuminated a role for the heparan sulfate proteoglycan perlecan in SARS-CoV-2 viral entry, and found that inhibition of the non-canonical NF-kB pathway through targeting of BIRC2 restricts SARS-CoV-2 replication both in vitro and in vivo. These studies provide critical insight into the landscape of virus-host interactions driving SARS-CoV-2 replication as well as valuable targets for host-directed antivirals.
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Affiliation(s)
- Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Pu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Lars Pache
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Christopher Churas
- Department of Medicine, University of California San Diego, La Jolla, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Laura Riva
- Calibr-Skaggs at Scripps Research Institute, La Jolla, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Departments of Medicine and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - William J. Cisneros
- Division of Infectious Diseases, Departments of Medicine and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Thomas Clausen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, USA
| | - Paul D. De Jesus
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
| | - Ha Na Kim
- Molecular Surface Interaction Laboratory, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Daniel Fuentes
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
| | - John Whitelock
- Molecular Surface Interaction Laboratory, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jeffrey Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, USA
| | - Megan Lord
- Molecular Surface Interaction Laboratory, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ignacio Mena
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA; The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA; The Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Departments of Medicine and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Matthew B. Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, La Jolla, USA
| | - Laura Martin-Sancho
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
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Li Q, Peng G, Liu H, Wang L, Lu R, Li L. Molecular mechanisms of secretory autophagy and its potential role in diseases. Life Sci 2024; 347:122653. [PMID: 38663839 DOI: 10.1016/j.lfs.2024.122653] [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: 03/28/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Autophagy is a cellular degradation system that recycles or degrades damaged organelles, viral particles, and aggregated proteins through the lysosomal pathway. Autophagy plays an indispensable role in cellular homeostasis and communication processes. An interesting aspect is that autophagy also mediates the secretion of cellular contents, a process known as secretory autophagy. Secretory autophagy differs from macroautophagy, which sequesters recruited proteins, organelles, or viral particles into autophagosomes and degrades these sequesters in lysosomes, while the secretory autophagy pathway participates in the extracellular export of cellular contents sequestered by autophagosomes through autophagy and endosomal modulators. Recent evidence reveals that secretory autophagy is pivotal in the occurrence and progression of diseases. In this review, we summarize the molecular mechanisms of secretory autophagy. Furthermore, we review the impact of secretory autophagy on diseases, including cancer, viral infectious diseases, neurodegenerative diseases, and cardiovascular diseases. Considering the pleiotropic actions of secretory autophagy on diseases, studying the mechanism of secretory autophagy may help to understand the relevant pathophysiological processes.
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Affiliation(s)
- Qin Li
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang 421001, Hunan, China
| | - Guolong Peng
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang 421001, Hunan, China
| | - Huimei Liu
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang 421001, Hunan, China
| | - Liwen Wang
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang 421001, Hunan, China
| | - Ruirui Lu
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang 421001, Hunan, China.
| | - Lanfang Li
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang 421001, Hunan, China.
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10
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Rezabakhsh A, Sadaie MR, Ala A, Roosta Y, Habtemariam S, Sahebnasagh A, Khezri MR. STING agonists as promising vaccine adjuvants to boost immunogenicity against SARS-related coronavirus derived infection: possible role of autophagy. Cell Commun Signal 2024; 22:305. [PMID: 38831299 PMCID: PMC11145937 DOI: 10.1186/s12964-024-01680-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/26/2024] [Indexed: 06/05/2024] Open
Abstract
As a major component of innate immunity and a positive regulator of interferons, the Stimulator of interferon gene (STING) has an immunotherapy potential to govern a variety of infectious diseases. Despite the recent advances regarding vaccines against COVID-19, nontoxic novel adjuvants with the potential to enhance vaccine efficacy are urgently desired. In this connection, it has been well-documented that STING agonists are applied to combat COVID-19. This approach is of major significance for boosting immune responses most likely through an autophagy-dependent manner in susceptible individuals against infection induced by severe acute respiratory syndrome Coronavirus (SARS‑CoV‑2). Given that STING agonists exert substantial immunomodulatory impacts under a wide array of pathologic conditions, these agents could be considered novel adjuvants for enhancing immunogenicity against the SARS-related coronavirus. Here, we intend to discuss the recent advances in STING agonists' recruitment to boost innate immune responses upon vaccination against SARS-related coronavirus infections. In light of the primordial role of autophagy modulation, the potential of being an antiviral vaccine adjuvant was also explored.
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Affiliation(s)
- Aysa Rezabakhsh
- Cardiovascular Research Center, Shahid Madani specialized Heart Hospita, Tabriz University of Medical Sciences, University St, Tabriz, 5166615573, Iran.
| | - M Reza Sadaie
- NovoMed Consulting, Biomedical Sciences, Germantown, Maryland, USA
| | - Alireza Ala
- Emergency and Trauma Care Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Roosta
- Hematology, Immune Cell Therapy, and Stem Cells Transplantation Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Solomon Habtemariam
- Pharmacognosy Research and Herbal Analysis Services UK, University of Greenwich, Kent, UK
| | - Adeleh Sahebnasagh
- Clinical Research Center, Department of Internal Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Rafi Khezri
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, 5715799313, Iran.
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11
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Zhao Y, Xu K, Shu F, Zhang F. Neurotropic virus infection and neurodegenerative diseases: Potential roles of autophagy pathway. CNS Neurosci Ther 2024; 30:e14548. [PMID: 38082503 PMCID: PMC11163195 DOI: 10.1111/cns.14548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 06/11/2024] Open
Abstract
Neurodegenerative diseases (NDs) constitute a group of disorders characterized by the progressive deterioration of nervous system functionality. Currently, the precise etiological factors responsible for NDs remain incompletely elucidated, although it is probable that a combination of aging, genetic predisposition, and environmental stressors participate in this process. Accumulating evidence indicates that viral infections, especially neurotropic viruses, can contribute to the onset and progression of NDs. In this review, emerging evidence supporting the association between viral infection and NDs is summarized, and how the autophagy pathway mediated by viral infection can cause pathological aggregation of cellular proteins associated with various NDs is discussed. Furthermore, autophagy-related genes (ARGs) involved in Herpes simplex virus (HSV-1) infection and NDs are analyzed, and whether these genes could link HSV-1 infection to NDs is discussed. Elucidating the mechanisms underlying NDs is critical for developing targeted therapeutic approaches that prevent the onset and slow the progression of NDs.
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Affiliation(s)
- Yu‐jia Zhao
- Laboratory Animal CentreZunyi Medical UniversityZunyiGuizhouChina
| | - Kai‐fei Xu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education and Key Laboratory of Basic Pharmacology of Guizhou ProvinceZunyi Medical UniversityZunyiGuizhouChina
| | - Fu‐xing Shu
- Bioresource Institute for Healthy UtilizationZunyi Medical UniversityZunyiGuizhouChina
| | - Feng Zhang
- Laboratory Animal CentreZunyi Medical UniversityZunyiGuizhouChina
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education and Key Laboratory of Basic Pharmacology of Guizhou ProvinceZunyi Medical UniversityZunyiGuizhouChina
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12
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Hoenigsperger H, Sivarajan R, Sparrer KM. Differences and similarities between innate immune evasion strategies of human coronaviruses. Curr Opin Microbiol 2024; 79:102466. [PMID: 38555743 DOI: 10.1016/j.mib.2024.102466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/20/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024]
Abstract
So far, seven coronaviruses have emerged in humans. Four recurring endemic coronaviruses cause mild respiratory symptoms. Infections with epidemic Middle East respiratory syndrome-related coronavirus or severe acute respiratory syndrome coronavirus (SARS-CoV)-1 are associated with high mortality rates. SARS-CoV-2 is the causative agent of the coronavirus disease 2019 pandemic. To establish an infection, coronaviruses evade restriction by human innate immune defenses, such as the interferon system, autophagy and the inflammasome. Here, we review similar and distinct innate immune manipulation strategies employed by the seven human coronaviruses. We further discuss the impact on pathogenesis, zoonotic emergence and adaptation. Understanding the nature of the interplay between endemic/epidemic/pandemic coronaviruses and host defenses may help to better assess the pandemic potential of emerging coronaviruses.
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Affiliation(s)
- Helene Hoenigsperger
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rinu Sivarajan
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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13
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Cloherty APM, Rader AG, Patel KS, Eisden TJTHD, van Piggelen S, Schreurs RRCE, Ribeiro CMS. Dengue virus exploits autophagy vesicles and secretory pathways to promote transmission by human dendritic cells. Front Immunol 2024; 15:1260439. [PMID: 38863700 PMCID: PMC11165123 DOI: 10.3389/fimmu.2024.1260439] [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: 07/17/2023] [Accepted: 04/19/2024] [Indexed: 06/13/2024] Open
Abstract
Dengue virus (DENV), transmitted by infected mosquitoes, is a major public health concern, with approximately half the world's population at risk for infection. Recent decades have increasing incidence of dengue-associated disease alongside growing frequency of outbreaks. Although promising progress has been made in anti-DENV immunizations, post-infection treatment remains limited to non-specific supportive treatments. Development of antiviral therapeutics is thus required to limit DENV dissemination in humans and to help control the severity of outbreaks. Dendritic cells (DCs) are amongst the first cells to encounter DENV upon injection into the human skin mucosa, and thereafter promote systemic viral dissemination to additional human target cells. Autophagy is a vesicle trafficking pathway involving the formation of cytosolic autophagosomes, and recent reports have highlighted the extensive manipulation of autophagy by flaviviruses, including DENV, for viral replication. However, the temporal profiling and function of autophagy activity in DENV infection and transmission by human primary DCs remains poorly understood. Herein, we demonstrate that mechanisms of autophagosome formation and extracellular vesicle (EV) release have a pro-viral role in DC-mediated DENV transmission. We show that DENV exploits early-stage canonical autophagy to establish infection in primary human DCs. DENV replication enhanced autophagosome formation in primary human DCs, and intrinsically-heightened autophagosome biogenesis correlated with relatively higher rates of DC susceptibility to DENV. Furthermore, our data suggest that viral replication intermediates co-localize with autophagosomes, while productive DENV infection introduces a block at the late degradative stages of autophagy in infected DCs but not in uninfected bystander cells. Notably, we identify for the first time that approximately one-fourth of DC-derived CD9/CD81/CD63+ EVs co-express canonical autophagy marker LC3, and demonstrate that DC-derived EV populations are an alternative, cell-free mechanism by which DCs promote DENV transmission to additional target sites. Taken together, our study highlights intersections between autophagy and secretory pathways during viral infection, and puts forward autophagosome accumulation and viral RNA-laden EVs as host determinants of DC-mediated DENV infection in humans. Host-directed therapeutics targeting autophagy and exocytosis pathways thus have potential to enhance DC-driven resistance to DENV acquisition and thereby limit viral dissemination by initial human target cells following mosquito-to-human transmission of DENV.
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Affiliation(s)
- Alexandra P. M. Cloherty
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Anusca G. Rader
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
| | - Kharishma S. Patel
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Tracy-Jane T. H. D. Eisden
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Sterre van Piggelen
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Renée R. C. E. Schreurs
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
| | - Carla M. S. Ribeiro
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
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14
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Jassey A, Jackson WT. Viruses and autophagy: bend, but don't break. Nat Rev Microbiol 2024; 22:309-321. [PMID: 38102460 DOI: 10.1038/s41579-023-00995-y] [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] [Accepted: 11/09/2023] [Indexed: 12/17/2023]
Abstract
Autophagy is a constitutive cellular process of degradation required to maintain homeostasis and turn over spent organelles and aggregated proteins. For some viruses, the process can be antiviral, degrading viral proteins or virions themselves. For many other viruses, the induction of the autophagic process provides a benefit and promotes viral replication. In this Review, we survey the roles that the autophagic pathway plays in the replication of viruses. Most viruses that benefit from autophagic induction block autophagic degradation, which is a 'bend, but don't break' strategy initiating but limiting a potentially antiviral response. In almost all cases, it is other effects of the redirected autophagic machinery that benefit these viruses. This rapid mechanism to generate small double-membraned vesicles can be usurped to shape membranes for viral genome replication and virion maturation. However, data suggest that autophagic maintenance of cellular homeostasis is crucial for the initiation of infection, as viruses have evolved to replicate in normal, healthy cells. Inhibition of autophagic degradation is important once infection has initiated. Although true degradative autophagy is probably a negative for most viruses, initiating nondegradative autophagic membranes benefits a wide variety of viruses.
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Affiliation(s)
- Alagie Jassey
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William T Jackson
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA.
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15
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Karim M, Mishra M, Lo CW, Saul S, Cagirici HB, Tran DHN, Agrawal A, Ghita L, Ojha A, East MP, Gammeltoft KA, Sahoo MK, Johnson GL, Das S, Jochmans D, Cohen CA, Gottwein J, Dye J, Neff N, Pinsky BA, Laitinen T, Pantsar T, Poso A, Zanini F, Jonghe SD, Asquith CRM, Einav S. PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589676. [PMID: 38659941 PMCID: PMC11042293 DOI: 10.1101/2024.04.15.589676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In search for broad-spectrum antivirals, we discovered a small molecule inhibitor, RMC-113, that potently suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids. We demonstrated selective dual inhibition of the lipid kinases PIP4K2C and PIKfyve by RMC-113 and target engagement by its clickable analog. Advanced lipidomics revealed alteration of SARS-CoV-2-induced phosphoinositide signature by RMC-113 and linked its antiviral effect with functional PIP4K2C and PIKfyve inhibition. We discovered PIP4K2C's roles in SARS-CoV-2 entry, RNA replication, and assembly/egress, validating it as a druggable antiviral target. Integrating proteomics, single-cell transcriptomics, and functional assays revealed that PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced impairment of autophagic flux. Reversing this autophagic flux impairment is a mechanism of antiviral action of RMC-113. These findings reveal virus-induced autophagy regulation via PIP4K2C, an understudied kinase, and propose dual inhibition of PIP4K2C and PIKfyve as a candidate strategy to combat emerging viruses.
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Affiliation(s)
- Marwah Karim
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Manjari Mishra
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Chieh-Wen Lo
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Sirle Saul
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Halise Busra Cagirici
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Do Hoang Nhu Tran
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Aditi Agrawal
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Luca Ghita
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Amrita Ojha
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karen Anbro Gammeltoft
- Department of Infectious Diseases, University of Copenhagen, Denmark. Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen
- University Hospital-Hvidovre, Hvidovre, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Malaya Kumar Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Soumita Das
- Biomedical & Nutritional Science, Center for Pathogen Research & Training (CPRT), University of Massachusetts-Lowell, USA
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Courtney A Cohen
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Judith Gottwein
- Department of Infectious Diseases, University of Copenhagen, Denmark. Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen
- University Hospital-Hvidovre, Hvidovre, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - John Dye
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Tatu Pantsar
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Fabio Zanini
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | | | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
- Department of Microbiology and Immunology, Stanford University, CA, USA
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16
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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17
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Trépout S, Sgarra ML, Marco S, Ramm G. An introduction to scanning transmission electron microscopy for the study of protozoans. Mol Microbiol 2024; 121:659-670. [PMID: 38140856 DOI: 10.1111/mmi.15213] [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: 08/01/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
Since its inception in the 1930s, transmission electron microscopy (TEM) has been a powerful method to explore the cellular structure of parasites. TEM usually requires samples of <100 nm thick and with protozoans being larger than 1 μm, their study requires resin embedding and ultrathin sectioning. During the past decade, several new methods have been developed to improve, facilitate, and speed up the structural characterisation of biological samples, offering new imaging modalities for the study of protozoans. In particular, scanning transmission electron microscopy (STEM) can be used to observe sample sections as thick as 1 μm thus becoming an alternative to conventional TEM. STEM can also be performed under cryogenic conditions in combination with cryo-electron tomography providing access to the study of thicker samples in their native hydrated states in 3D. This method, called cryo-scanning transmission electron tomography (cryo-STET), was first developed in 2014. This review presents the basic concepts and benefits of STEM methods and provides examples to illustrate the potential for new insights into the structure and ultrastructure of protozoans.
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Affiliation(s)
- Sylvain Trépout
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Monash, Victoria, Australia
| | | | - Sergio Marco
- Vaccine CMC Development & Supply, Sanofi, Neuville sur Saône, France
| | - Georg Ramm
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Monash, Victoria, Australia
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18
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Ke PY. Molecular Mechanism of Autophagosome-Lysosome Fusion in Mammalian Cells. Cells 2024; 13:500. [PMID: 38534345 DOI: 10.3390/cells13060500] [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: 02/09/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
In eukaryotes, targeting intracellular components for lysosomal degradation by autophagy represents a catabolic process that evolutionarily regulates cellular homeostasis. The successful completion of autophagy initiates the engulfment of cytoplasmic materials within double-membrane autophagosomes and subsequent delivery to autolysosomes for degradation by acidic proteases. The formation of autolysosomes relies on the precise fusion of autophagosomes with lysosomes. In recent decades, numerous studies have provided insights into the molecular regulation of autophagosome-lysosome fusion. In this review, an overview of the molecules that function in the fusion of autophagosomes with lysosomes is provided. Moreover, the molecular mechanism underlying how these functional molecules regulate autophagosome-lysosome fusion is summarized.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
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19
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Walia K, Sharma A, Paul S, Chouhan P, Kumar G, Ringe R, Sharma M, Tuli A. SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle. Nat Commun 2024; 15:2053. [PMID: 38448435 PMCID: PMC10918171 DOI: 10.1038/s41467-024-46417-2] [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: 06/12/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, uses the host endolysosomal system for entry, replication, and egress. Previous studies have shown that the SARS-CoV-2 virulence factor ORF3a interacts with the lysosomal tethering factor HOPS complex and blocks HOPS-mediated late endosome and autophagosome fusion with lysosomes. Here, we report that SARS-CoV-2 infection leads to hyperactivation of the late endosomal and lysosomal small GTP-binding protein Rab7, which is dependent on ORF3a expression. We also observed Rab7 hyperactivation in naturally occurring ORF3a variants encoded by distinct SARS-CoV-2 variants. We found that ORF3a, in complex with Vps39, sequesters the Rab7 GAP TBC1D5 and displaces Rab7 from this complex. Thus, ORF3a disrupts the GTP hydrolysis cycle of Rab7, which is beneficial for viral production, whereas the Rab7 GDP-locked mutant strongly reduces viral replication. Hyperactivation of Rab7 in ORF3a-expressing cells impaired CI-M6PR retrieval from late endosomes to the trans-Golgi network, disrupting the biosynthetic transport of newly synthesized hydrolases to lysosomes. Furthermore, the tethering of the Rab7- and Arl8b-positive compartments was strikingly reduced upon ORF3a expression. As SARS-CoV-2 egress requires Arl8b, these findings suggest that ORF3a-mediated hyperactivation of Rab7 serves a multitude of functions, including blocking endolysosome formation, interrupting the transport of lysosomal hydrolases, and promoting viral egress.
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Affiliation(s)
- Kshitiz Walia
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Abhishek Sharma
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Sankalita Paul
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Priya Chouhan
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Kumar
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Rajesh Ringe
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Amit Tuli
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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20
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Luo H, Yan J, Gong R, Zhang D, Zhou X, Wang X. Identification of biomarkers and pathways for the SARS-CoV-2 infections in obstructive sleep apnea patients based on machine learning and proteomic analysis. BMC Pulm Med 2024; 24:112. [PMID: 38443855 PMCID: PMC10913609 DOI: 10.1186/s12890-024-02921-1] [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: 10/12/2023] [Accepted: 02/22/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND The prevalence of obstructive sleep apnea (OSA) was found to be higher in individuals following COVID-19 infection. However, the intricate mechanisms that underscore this concomitance remain partially elucidated. The aim of this study was to delve deeper into the molecular mechanisms that underpin this comorbidity. METHODS We acquired gene expression profiles for COVID-19 (GSE157103) and OSA (GSE75097) from the Gene Expression Omnibus (GEO) database. Upon identifying shared feature genes between OSA and COVID-19 utilizing LASSO, Random forest and Support vector machines algorithms, we advanced to functional annotation, analysis of protein-protein interaction networks, module construction, and identification of pivotal genes. Furthermore, we established regulatory networks encompassing transcription factor (TF)-gene and TF-miRNA interactions, and searched for promising drug targets. Subsequently, the expression levels of pivotal genes were validated through proteomics data from COVID-19 cases. RESULTS Fourteen feature genes shared between OSA and COVID-19 were selected for further investigation. Through functional annotation, it was indicated that metabolic pathways play a role in the pathogenesis of both disorders. Subsequently, employing the cytoHubba plugin, ten hub genes were recognized, namely TP53, CCND1, MDM2, RB1, HIF1A, EP300, STAT3, CDK2, HSP90AA1, and PPARG. The finding of proteomics unveiled a substantial augmentation in the expression level of HSP90AA1 in COVID-19 patient samples, especially in severe conditions. CONCLUSIONS Our investigation illuminate a mutual pathogenic mechanism that underlies both OSA and COVID-19, which may provide novel perspectives for future investigations into the underlying mechanisms.
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Affiliation(s)
- Hong Luo
- Department of Tuberculosis and Respiratory, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jisong Yan
- Department of Tuberculosis and Respiratory, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Gong
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Dingyu Zhang
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Center for Translational Medicine, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
| | - Xia Zhou
- Department of Tuberculosis and Respiratory, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Hubei Clinical Research Center for Infectious Diseases, Wuhan, China.
- Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China.
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, China.
| | - Xianguang Wang
- Department of Tuberculosis and Respiratory, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Hubei Clinical Research Center for Infectious Diseases, Wuhan, China.
- Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China.
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jinyintan Hospital, Chinese Academy of Sciences, Wuhan, China.
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21
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Yeo SK, Haas M, Manupati K, Hao M, Yang F, Chen S, Guan JL. AZI2 mediates TBK1 activation at unresolved selective autophagy cargo receptor complexes with implications for CD8 T-cell infiltration in breast cancer. Autophagy 2024; 20:525-540. [PMID: 37733921 PMCID: PMC10936636 DOI: 10.1080/15548627.2023.2259775] [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] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Most breast cancers do not respond to immune checkpoint inhibitors and there is an urgent need to identify novel sensitization strategies. Herein, we uncovered that activation of the TBK-IFN pathway that is mediated by the TBK1 adapter protein AZI2 is a potent strategy for this purpose. Our initial observations showed that RB1CC1 depletion leads to accumulation of AZI2, in puncta along with selective macroautophagy/autophagy cargo receptors, which are both required for TBK1 activation. Specifically, disrupting the selective autophagy function of RB1CC1 was sufficient to sustain AZI2 puncta accumulation and TBK1 activation. AZI2 then mediates downstream activation of DDX3X, increasing its interaction with IRF3 for transcription of pro-inflammatory chemokines. Consequently, we performed a screen to identify inhibitors that can induce the AZI2-TBK1 pathway, and this revealed Lys05 as a pharmacological agent that induced pro-inflammatory chemokine expression and CD8+ T cell infiltration into tumors. Overall, we have identified a distinct AZI2-TBK1-IFN signaling pathway that is responsive to selective autophagy blockade and can be activated to make breast cancers more immunogenic.Abbreviations: AZI2/NAP1: 5-azacytidine induced 2; CALCOCO2: calcium binding and coiled-coil domain 2; DDX3X: DEAD-box helicase 3 X-linked; FCCP: carbonyl cyanide p-triflouromethoxyphenylhydrazone; a protonophore that depolarizes the mitochondrial inner membrane; ICI: immune checkpoint inhibitor; IFN: interferon; NBR1: NBR1 autophagy cargo receptor; OPTN: optineurin; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SQSTM1/p62: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1.
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Affiliation(s)
- Syn Kok Yeo
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael Haas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kanakaraju Manupati
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Mingang Hao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Fuchun Yang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Song Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Translational Research Institute, Henan Provincial People’s Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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22
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Liu LK, Jian JT, Jing SS, Gao RL, Chi XD, Tian G, Liu HP. The crustacean DNA virus tegument protein VP26 binds to SNAP29 to inhibit SNARE complex assembly and autophagic degradation. J Virol 2024; 98:e0140823. [PMID: 38189252 PMCID: PMC10878264 DOI: 10.1128/jvi.01408-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Autophagy generally functions as a cellular surveillance mechanism to combat invading viruses, but viruses have evolved various strategies to block autophagic degradation and even subvert it to promote viral propagation. White spot syndrome virus (WSSV) is the most highly pathogenic crustacean virus, but little is currently known about whether crustacean viruses such as WSSV can subvert autophagic degradation for escape. Here, we show that even though WSSV proliferation triggers the accumulation of autophagosomes, autophagic degradation is blocked in the crustacean species red claw crayfish. Interestingly, the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex including CqSNAP29, CqVAMP7, and the novel autophagosome SNARE protein CqSyx12 is required for autophagic flux to restrict WSSV replication, as revealed by gene silencing experiments. Simultaneously, the expressed WSSV tegument protein VP26, which likely localizes on autophagic membrane mediated by its transmembrane region, binds the Qb-SNARE domain of CqSNAP29 to competitively inhibit the binding of CqSyx12-Qa-SNARE with CqSNAP29-Qb-SNARE; this in turn disrupts the assembly of the CqSyx12-SNAP29-VAMP7 SNARE complex, which is indispensable for the proposed fusion of autophagosomes and lysosomes. Consequently, the autophagic degradation of WSSV is likely suppressed by the expressed VP26 protein in vivo in crayfish, thus probably protecting WSSV components from degradation via the autophagosome-lysosome pathway, resulting in evasion by WSSV. Collectively, these findings highlight how a DNA virus can subvert autophagic degradation by impairing the assembly of the SNARE complex to achieve evasion, paving the way for understanding host-DNA virus interactions from an evolutionary point of view, from crustaceans to mammals.IMPORTANCEWhite spot syndrome virus (WSSV) is one of the largest animal DNA viruses in terms of its genome size and has caused huge economic losses in the farming of crustaceans such as shrimp and crayfish. Detailed knowledge of WSSV-host interactions is still lacking, particularly regarding viral escape from host immune clearance. Intriguingly, we found that the presence of WSSV-VP26 might inhibit the autophagic degradation of WSSV in vivo in the crustacean species red claw crayfish. Importantly, this study is the first to show that viral protein VP26 functions as a core factor to benefit WSSV escape by disrupting the assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, which is necessary for the proposed fusion of autophagosomes with lysosomes for subsequent degradation. These findings highlight a novel mechanism of DNA virus evasion by blocking SNARE complex assembly and identify viral VP26 as a key candidate for anti-WSSV targeting.
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Affiliation(s)
- Ling-Ke Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiu-Ting Jian
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shan-Shan Jing
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Rui-Lin Gao
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiao-Dong Chi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Geng Tian
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Hai-Peng Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, China
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23
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Ma L, Han T, Zhan YA. Mechanism and role of mitophagy in the development of severe infection. Cell Death Discov 2024; 10:88. [PMID: 38374038 PMCID: PMC10876966 DOI: 10.1038/s41420-024-01844-4] [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: 10/23/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
Mitochondria produce adenosine triphosphate and potentially contribute to proinflammatory responses and cell death. Mitophagy, as a conservative phenomenon, scavenges waste mitochondria and their components in the cell. Recent studies suggest that severe infections develop alongside mitochondrial dysfunction and mitophagy abnormalities. Restoring mitophagy protects against excessive inflammation and multiple organ failure in sepsis. Here, we review the normal mitophagy process, its interaction with invading microorganisms and the immune system, and summarize the mechanism of mitophagy dysfunction during severe infection. We highlight critical role of normal mitophagy in preventing severe infection.
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Affiliation(s)
- Lixiu Ma
- Department of Respiratory and Critical Care Medicine, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Tianyu Han
- Jiangxi Institute of Respiratory Disease, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yi-An Zhan
- Department of Respiratory and Critical Care Medicine, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
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24
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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25
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Song MS, Lee DK, Lee CY, Park SC, Yang J. Host Subcellular Organelles: Targets of Viral Manipulation. Int J Mol Sci 2024; 25:1638. [PMID: 38338917 PMCID: PMC10855258 DOI: 10.3390/ijms25031638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Viruses have evolved sophisticated mechanisms to manipulate host cell processes and utilize intracellular organelles to facilitate their replication. These complex interactions between viruses and cellular organelles allow them to hijack the cellular machinery and impair homeostasis. Moreover, viral infection alters the cell membrane's structure and composition and induces vesicle formation to facilitate intracellular trafficking of viral components. However, the research focus has predominantly been on the immune response elicited by viruses, often overlooking the significant alterations that viruses induce in cellular organelles. Gaining a deeper understanding of these virus-induced cellular changes is crucial for elucidating the full life cycle of viruses and developing potent antiviral therapies. Exploring virus-induced cellular changes could substantially improve our understanding of viral infection mechanisms.
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Affiliation(s)
- Min Seok Song
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Dong-Kun Lee
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Sang-Cheol Park
- Artificial Intelligence and Robotics Laboratory, Myongji Hospital, Goyang 10475, Republic of Korea
| | - Jinsung Yang
- Department of Biochemistry and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
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26
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Zhang J, Cruz-Cosme R, Zhang C, Liu D, Tang Q, Zhao RY. Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation. mBio 2024; 15:e0303023. [PMID: 38078754 PMCID: PMC10790703 DOI: 10.1128/mbio.03030-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has tragically claimed millions of lives through coronavirus disease 2019 (COVID-19), and there remains a critical gap in our understanding of the precise molecular mechanisms responsible for the associated fatality. One key viral factor of interest is the SARS-CoV-2 ORF3a protein, which has been identified as a potent inducer of host cellular proinflammatory responses capable of triggering the catastrophic cytokine storm, a primary contributor to COVID-19-related deaths. Moreover, ORF3a, much like the spike protein, exhibits a propensity for frequent mutations, with certain variants linked to the severity of COVID-19. Our previous research unveiled two distinct types of ORF3a mutant proteins, categorized by their subcellular localizations, setting the stage for a comparative investigation into the functional and mechanistic disparities between these two types of ORF3a variants. Given the clinical significance and functional implications of the natural ORF3a mutations, the findings of this study promise to provide invaluable insights into the potential roles undertaken by these mutant ORF3a proteins in the pathogenesis of COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ruth Cruz-Cosme
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Chenyu Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dongxiao Liu
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
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27
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Anand A, Long C, Chandran K. NYC metropolitan wastewater reveals links between SARS-CoV-2 amino acid mutations and disease outcomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:167971. [PMID: 37914132 DOI: 10.1016/j.scitotenv.2023.167971] [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: 02/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Since late 2020, diverse SARS-CoV-2 variants with enhanced infectivity and transmissibility have emerged. In contrast to the focus on amino acid mutations in the spike protein, mutations in non-spike proteins and their associated impacts remain relatively understudied. New York City metropolitan wastewater revealed over 60 % of the most frequently occurring amino acid mutations in regions outside the spike protein. Strikingly, ~50 % of the mutations detected herein remain uncharacterized for functional impacts. Our results suggest that there are several understudied mutations within non-spike proteins N, ORF1a, ORF1b, ORF9b, and ORF9c, that could increase transmissibility, and infectivity among human populations. We also demonstrate significant correlations of P314L, D614G, T95I, G50E, G50R, G204R, R203K, G662S, P10S, and P13L with documented mortality rates, hospitalization rates, and percent positivity suggesting that amino acid mutations are likely to be indicators of COVID-19 infection outcomes.
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Affiliation(s)
- Archana Anand
- Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, United States of America
| | - Chenghua Long
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th Street, New York, NY 10027, United States of America
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th Street, New York, NY 10027, United States of America.
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28
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Zhang J, Hom K, Zhang C, Nasr M, Gerzanich V, Zhang Y, Tang Q, Xue F, Simard JM, Zhao RY. SARS-CoV-2 ORF3a Protein as a Therapeutic Target against COVID-19 and Long-Term Post-Infection Effects. Pathogens 2024; 13:75. [PMID: 38251382 PMCID: PMC10819734 DOI: 10.3390/pathogens13010075] [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: 12/19/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has posed unparalleled challenges due to its rapid transmission, ability to mutate, high mortality and morbidity, and enduring health complications. Vaccines have exhibited effectiveness, but their efficacy diminishes over time while new variants continue to emerge. Antiviral medications offer a viable alternative, but their success has been inconsistent. Therefore, there remains an ongoing need to identify innovative antiviral drugs for treating COVID-19 and its post-infection complications. The ORF3a (open reading frame 3a) protein found in SARS-CoV-2, represents a promising target for antiviral treatment due to its multifaceted role in viral pathogenesis, cytokine storms, disease severity, and mortality. ORF3a contributes significantly to viral pathogenesis by facilitating viral assembly and release, essential processes in the viral life cycle, while also suppressing the body's antiviral responses, thus aiding viral replication. ORF3a also has been implicated in triggering excessive inflammation, characterized by NF-κB-mediated cytokine production, ultimately leading to apoptotic cell death and tissue damage in the lungs, kidneys, and the central nervous system. Additionally, ORF3a triggers the activation of the NLRP3 inflammasome, inciting a cytokine storm, which is a major contributor to the severity of the disease and subsequent mortality. As with the spike protein, ORF3a also undergoes mutations, and certain mutant variants correlate with heightened disease severity in COVID-19. These mutations may influence viral replication and host cellular inflammatory responses. While establishing a direct link between ORF3a and mortality is difficult, its involvement in promoting inflammation and exacerbating disease severity likely contributes to higher mortality rates in severe COVID-19 cases. This review offers a comprehensive and detailed exploration of ORF3a's potential as an innovative antiviral drug target. Additionally, we outline potential strategies for discovering and developing ORF3a inhibitor drugs to counteract its harmful effects, alleviate tissue damage, and reduce the severity of COVID-19 and its lingering complications.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (J.Z.); (C.Z.)
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA; (K.H.); (F.X.)
| | - Chenyu Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (J.Z.); (C.Z.)
| | - Mohamed Nasr
- Drug Development and Clinical Sciences Branch, Division of AIDS, NIAID, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Volodymyr Gerzanich
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (V.G.); (J.M.S.)
| | - Yanjin Zhang
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA;
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC 20059, USA;
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA; (K.H.); (F.X.)
| | - J. Marc Simard
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (V.G.); (J.M.S.)
- Research & Development Service, VA Maryland Health Care System, Baltimore, MD 21201, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (J.Z.); (C.Z.)
- Research & Development Service, VA Maryland Health Care System, Baltimore, MD 21201, USA
- Department of Microbiology-Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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29
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Gavilán E, Medina-Guzman R, Bahatyrevich-Kharitonik B, Ruano D. Protein Quality Control Systems and ER Stress as Key Players in SARS-CoV-2-Induced Neurodegeneration. Cells 2024; 13:123. [PMID: 38247815 PMCID: PMC10814689 DOI: 10.3390/cells13020123] [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: 11/29/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic has brought to the forefront the intricate relationship between SARS-CoV-2 and its impact on neurological complications, including potential links to neurodegenerative processes, characterized by a dysfunction of the protein quality control systems and ER stress. This review article explores the role of protein quality control systems, such as the Unfolded Protein Response (UPR), the Endoplasmic Reticulum-Associated Degradation (ERAD), the Ubiquitin-Proteasome System (UPS), autophagy and the molecular chaperones, in SARS-CoV-2 infection. Our hypothesis suggests that SARS-CoV-2 produces ER stress and exploits the protein quality control systems, leading to a disruption in proteostasis that cannot be solved by the host cell. This disruption culminates in cell death and may represent a link between SARS-CoV-2 and neurodegeneration.
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Affiliation(s)
- Elena Gavilán
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Rafael Medina-Guzman
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
| | - Bazhena Bahatyrevich-Kharitonik
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Diego Ruano
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
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30
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Chen B, Guo G, Wang G, Zhu Q, Wang L, Shi W, Wang S, Chen Y, Chi X, Wen F, Maarouf M, Huang S, Yang Z, Chen JL. ATG7/GAPLINC/IRF3 axis plays a critical role in regulating pathogenesis of influenza A virus. PLoS Pathog 2024; 20:e1011958. [PMID: 38227600 PMCID: PMC10817227 DOI: 10.1371/journal.ppat.1011958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/26/2024] [Accepted: 01/08/2024] [Indexed: 01/18/2024] Open
Abstract
Autophagy-related protein 7 (ATG7) is an essential autophagy effector enzyme. Although it is well known that autophagy plays crucial roles in the infections with various viruses including influenza A virus (IAV), function and underlying mechanism of ATG7 in infection and pathogenesis of IAV remain poorly understood. Here, in vitro studies showed that ATG7 had profound effects on replication of IAV. Depletion of ATG7 markedly attenuated the replication of IAV, whereas overexpression of ATG7 facilitated the viral replication. ATG7 conditional knockout mice were further employed and exhibited significantly resistant to viral infections, as evidenced by a lower degree of tissue injury, slower body weight loss, and better survival, than the wild type animals challenged with either IAV (RNA virus) or pseudorabies virus (DNA virus). Interestingly, we found that ATG7 promoted the replication of IAV in autophagy-dependent and -independent manners, as inhibition of autophagy failed to completely block the upregulation of IAV replication by ATG7. To determine the autophagy-independent mechanism, transcriptome analysis was utilized and demonstrated that ATG7 restrained the production of interferons (IFNs). Loss of ATG7 obviously enhanced the expression of type I and III IFNs in ATG7-depleted cells and mice, whereas overexpression of ATG7 impaired the interferon response to IAV infection. Consistently, our experiments demonstrated that ATG7 significantly suppressed IRF3 activation during the IAV infection. Furthermore, we identified long noncoding RNA (lncRNA) GAPLINC as a critical regulator involved in the promotion of IAV replication by ATG7. Importantly, both inactivation of IRF3 and inhibition of IFN response caused by ATG7 were mediated through control over GAPLINC expression, suggesting that GAPLINC contributes to the suppression of antiviral immunity by ATG7. Together, these results uncover an autophagy-independent mechanism by which ATG7 suppresses host innate immunity and establish a critical role for ATG7/GAPLINC/IRF3 axis in regulating IAV infection and pathogenesis.
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Affiliation(s)
- Biao Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Guijie Guo
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Guoqing Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Qianwen Zhu
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Lulu Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Wenhao Shi
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Song Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Xiaojuan Chi
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Faxin Wen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Mohamed Maarouf
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Zhou Yang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Ji-Long Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
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Zhai H, Wang T, Liu D, Pan L, Sun Y, Qiu HJ. Autophagy as a dual-faced host response to viral infections. Front Cell Infect Microbiol 2023; 13:1289170. [PMID: 38125906 PMCID: PMC10731275 DOI: 10.3389/fcimb.2023.1289170] [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: 09/05/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Autophagy selectively degrades viral particles or cellular components, either facilitating or inhibiting viral replication. Conversely, most viruses have evolved strategies to escape or exploit autophagy. Moreover, autophagy collaborates with the pattern recognition receptor signaling, influencing the expression of adaptor molecules involved in the innate immune response and regulating the expression of interferons (IFNs). The intricate relationship between autophagy and IFNs plays a critical role in the host cell defense against microbial invasion. Therefore, it is important to summarize the interactions between viral infections, autophagy, and the host defense mechanisms against viruses. This review specifically focuses on the interactions between autophagy and IFN pathways during viral infections, providing a comprehensive summary of the molecular mechanisms utilized or evaded by different viruses.
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Affiliation(s)
| | | | | | | | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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32
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Knupp J, Pletan ML, Arvan P, Tsai B. Autophagy of the ER: the secretome finds the lysosome. FEBS J 2023; 290:5656-5673. [PMID: 37920925 PMCID: PMC11044768 DOI: 10.1111/febs.16986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Lysosomal degradation of the endoplasmic reticulum (ER) and its components through the autophagy pathway has emerged as a major regulator of ER proteostasis. Commonly referred to as ER-phagy and ER-to-lysosome-associated degradation (ERLAD), how the ER is targeted to the lysosome has been recently clarified by a growing number of studies. Here, we summarize the discoveries of the molecular components required for lysosomal degradation of the ER and their proposed mechanisms of action. Additionally, we discuss how cells employ these machineries to create the different routes of ER-lysosome-associated degradation. Further, we review the role of ER-phagy in viral infection pathways, as well as the implication of ER-phagy in human disease. In sum, we provide a comprehensive overview of the current field of ER-phagy.
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Affiliation(s)
- Jeffrey Knupp
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Madison L Pletan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
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33
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Cesar-Silva D, Pereira-Dutra FS, Giannini ALM, Maya-Monteiro CM, de Almeida CJG. Lipid compartments and lipid metabolism as therapeutic targets against coronavirus. Front Immunol 2023; 14:1268854. [PMID: 38106410 PMCID: PMC10722172 DOI: 10.3389/fimmu.2023.1268854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/24/2023] [Indexed: 12/19/2023] Open
Abstract
Lipids perform a series of cellular functions, establishing cell and organelles' boundaries, organizing signaling platforms, and creating compartments where specific reactions occur. Moreover, lipids store energy and act as secondary messengers whose distribution is tightly regulated. Disruption of lipid metabolism is associated with many diseases, including those caused by viruses. In this scenario, lipids can favor virus replication and are not solely used as pathogens' energy source. In contrast, cells can counteract viruses using lipids as weapons. In this review, we discuss the available data on how coronaviruses profit from cellular lipid compartments and why targeting lipid metabolism may be a powerful strategy to fight these cellular parasites. We also provide a formidable collection of data on the pharmacological approaches targeting lipid metabolism to impair and treat coronavirus infection.
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Affiliation(s)
- Daniella Cesar-Silva
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Filipe S. Pereira-Dutra
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Lucia Moraes Giannini
- Laboratory of Functional Genomics and Signal Transduction, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarissa M. Maya-Monteiro
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratory of Endocrinology and Department of Endocrinology and Metabolism, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Cecília Jacques G. de Almeida
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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34
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Busscher BM, Befekadu HB, Liu Z, Xiao TS. SARS-CoV-2 ORF3a-Mediated NF-κB Activation Is Not Dependent on TRAF-Binding Sequence. Viruses 2023; 15:2229. [PMID: 38005906 PMCID: PMC10675646 DOI: 10.3390/v15112229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/31/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus Disease 2019 (COVID-19). Excessive inflammation is a hallmark of severe COVID-19, and several proteins encoded in the SARS-CoV-2 genome are capable of stimulating inflammatory pathways. Among these, the accessory protein open reading frame 3a (ORF3a) has been implicated in COVID-19 pathology. Here we investigated the roles of ORF3a in binding to TNF receptor-associated factor (TRAF) proteins and inducing nuclear factor kappa B (NF-κB) activation. X-ray crystallography and a fluorescence polarization assay revealed low-affinity binding between an ORF3a N-terminal peptide and TRAFs, and a dual-luciferase assay demonstrated NF-κB activation by ORF3a. Nonetheless, mutation of the N-terminal TRAF-binding sequence PIQAS in ORF3a did not significantly diminish NF-κB activation in our assay. Our results thus suggest that the SARS-CoV-2 protein may activate NF-κB through alternative mechanisms.
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Affiliation(s)
- Brianna M. Busscher
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.M.B.); (Z.L.)
| | - Henock B. Befekadu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Zhonghua Liu
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.M.B.); (Z.L.)
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Tsan Sam Xiao
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.M.B.); (Z.L.)
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35
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Huang ZX, Zhou ST, Wang J, Yang ZB, Wang Z. Remdesivir inhibits Porcine epidemic diarrhea virus infection in vitro. Heliyon 2023; 9:e21468. [PMID: 38027806 PMCID: PMC10663732 DOI: 10.1016/j.heliyon.2023.e21468] [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: 07/02/2023] [Revised: 10/09/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023] Open
Abstract
Porcine Epidemic Diarrhea Virus (PEDV) is a highly contagious and pathogenic virus that causes symptoms such as diarrhea, vomiting, weight loss, and even death in piglets. Due to its high transmission rate, PEDV has resulted in significant global losses. Although some vaccines have been developed and utilized to prevent PEDV, their effectiveness is limited due to the virus's mutations. Therefore, it is imperative to investigate new strategies to combat PEDV. Remdesivir, a classic antiviral drug for coronaviruses, has been proven in our experiment to effectively suppress PEDV replication in Vero and LLC-PK1 cells. Additionally, the cell experiment demonstrated its direct inhibition of PEDV RNA-dependent RNA polymerase (RdRp) enzyme activity. Molecular docking simulations were employed to predict the binding site of remdesivir and PEDV RdRp. Moreover, we observed that remdesivir does not impact the production of inflammatory factors and exhibits antagonistic effects with exogenous nucleosides. Furthermore, we conducted RNA-Seq analysis to investigate the global changes in transcriptome of infected cells treated with remdesivir. Overall, our findings indicate that remdesivir holds promise as a potential candidate for the treatment of PEDV infection.
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Affiliation(s)
- Zi-Xin Huang
- Shanghai Collaborative Innovation Center of Agri-Seeds / School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Ting Zhou
- Shanghai Collaborative Innovation Center of Agri-Seeds / School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yang ling, Xianyang 712100, China
| | - Zhi-Biao Yang
- Shanghai Collaborative Innovation Center of Agri-Seeds / School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhe Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds / School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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36
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Li S, Li X, Liang H, Yu K, Zhai J, Xue M, Luo Z, Zheng C, Zhang H. SARS-CoV-2 ORF7a blocked autophagy flux by intervening in the fusion between autophagosome and lysosome to promote viral infection and pathogenesis. J Med Virol 2023; 95:e29200. [PMID: 37916857 DOI: 10.1002/jmv.29200] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
The coronavirus disease 2019 (COVID-19) continues to pose a major threat to public health worldwide. Although many studies have clarified the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection process, the underlying mechanisms of viral invasion and immune evasion were still unclear. This study focused on SARS-CoV-2 ORF7a (open reading frame-7a), one of the essential open reading frames (ORFs) in infection and pathogenesis. First, by analyzing its physical and chemical characteristics, SARS-CoV-2 ORF7a is an unstable hydrophobic transmembrane protein. Then, the ORF7a transmembrane domain three-dimensional crystal structure model was predicted and verified. SARS-CoV-2 ORF7a localized in the endoplasmic reticulum and participated in the autophagy-lysosome pathway via interacting with p62. In addition, we elucidated the underlying molecular mechanisms by which ORF7a intercepted autophagic flux, promoted double membrane vesicle formation, and evaded host autophagy-lysosome degradation and antiviral innate immunity. This study demonstrated that ORF7a could be a therapeutic target, and Glecaprevir may be a potential drug against SARS-CoV-2 by targeting ORF7a. A comprehensive understanding of ORF7a's functions may contribute to developing novel therapies and clinical drugs against COVID-19.
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Affiliation(s)
- Shun Li
- Department of Spine Surgery, People's Hospital of Longhua, Affiliated Hospital of Southern Medical University, Shenzhen, China
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Xiaobo Li
- Department of Respiratory, Chengdu Seventh People's Hospital (Affiliated Cancer Hospital of Chengdu Medical College), Chengdu, Sichuan, China
| | - Haowei Liang
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
| | - Kuike Yu
- Department of Spine Surgery, People's Hospital of Longhua, Affiliated Hospital of Southern Medical University, Shenzhen, China
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhuojing Luo
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology & Infection Diseases, University of Calgary, Calgary, Canada
| | - Hao Zhang
- Department of Spine Surgery, People's Hospital of Longhua, Affiliated Hospital of Southern Medical University, Shenzhen, China
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Daniels A, Fletcher S, Kerr HEM, Kratzel A, Pinto RM, Kriplani N, Craig N, Hastie CJ, Davies P, Digard P, Thiel V, Tait-Burkard C. One for all-human kidney Caki-1 cells are highly susceptible to infection with corona- and other respiratory viruses. J Virol 2023; 97:e0055523. [PMID: 37668370 PMCID: PMC10537734 DOI: 10.1128/jvi.00555-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/05/2023] [Indexed: 09/06/2023] Open
Abstract
In vitro investigations of host-virus interactions are reliant on suitable cell and tissue culture models. Results are only as good as the model they are generated in. However, choosing cell models for in vitro work often depends on availability and previous use alone. Despite the vast increase in coronavirus research over the past few years, scientists are still heavily reliant on: non-human, highly heterogeneous or not fully differentiated, or naturally unsusceptible cells requiring overexpression of receptors and other accessory factors. Complex primary or stem cell models are highly representative of human tissues but are expensive and time-consuming to develop and maintain with limited suitability for high-throughput experiments.Using tissue-specific expression patterns, we identified human kidney cells as an ideal target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and broader coronavirus infection. We show the use of the well-characterized human kidney cell line Caki-1 for infection with three human coronaviruses (hCoVs): Betacoronaviruses SARS-CoV-2 and Middle Eastern respiratory syndrome coronavirus and Alphacoronavirus hCoV 229E. Caki-1 cells show equal or superior susceptibility to all three coronaviruses when compared to other commonly used cell lines for the cultivation of the respective virus. Antibody staining against SARS-CoV-2 N protein shows comparable replication rates. A panel of 26 custom antibodies shows the location of SARS-CoV-2 proteins during replication using immunocytochemistry. In addition, Caki-1 cells were found to be susceptible to two other human respiratory viruses, influenza A virus and respiratory syncytial virus, making them an ideal model for cross-comparison for a broad range of respiratory viruses. IMPORTANCE Cell lines remain the backbone of virus research, but results are only as good as their originating model. Despite increased research into human coronaviruses following the COVID-19 pandemic, researchers continue to rely on suboptimal cell line models of: non-human origin, incomplete differentiation, or lacking active interferon responses. We identified the human kidney Caki-1 cell line as a potential target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This cell line could be shown to be infectable with a wide range of coronaviruses including common cold virus hCoV-229E, epidemic virus MERS-CoV, and SARS-CoV-2 as well as other important respiratory viruses influenza A virus and respiratory syncytial virus. We could show the localization of 26 SARS-CoV-2 proteins in Caki-1 cells during natural replication and the cells are competent of forming a cellular immune response. Together, this makes Caki-1 cells a unique tool for cross-virus comparison in one cell line.
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Affiliation(s)
- Alison Daniels
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- Infection Medicine, University of Edinburgh, Little France Crescent, United Kingdom
| | - Sarah Fletcher
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Holly E. M. Kerr
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rute Maria Pinto
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nisha Kriplani
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nicky Craig
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - C. James Hastie
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Davies
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Digard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christine Tait-Burkard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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Chen L, Yang L, Li Y, Liu T, Yang B, Liu L, Wu R. Autophagy and Inflammation: Regulatory Roles in Viral Infections. Biomolecules 2023; 13:1454. [PMID: 37892135 PMCID: PMC10604974 DOI: 10.3390/biom13101454] [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: 08/25/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Autophagy is a highly conserved intracellular degradation pathway in eukaryotic organisms, playing an adaptive role in various pathophysiological processes throughout evolution. Inflammation is the immune system's response to external stimuli and tissue damage. However, persistent inflammatory reactions can lead to a range of inflammatory diseases and cancers. The interaction between autophagy and inflammation is particularly evident during viral infections. As a crucial regulator of inflammation, autophagy can either promote or inhibit the occurrence of inflammatory responses. In turn, inflammation can establish negative feedback loops by modulating autophagy to suppress excessive inflammatory reactions. This interaction is pivotal in the pathogenesis of viral diseases. Therefore, elucidating the regulatory roles of autophagy and inflammation in viral infections will significantly enhance our understanding of the mechanisms underlying related diseases. Furthermore, it will provide new insights and theoretical foundations for disease prevention, treatment, and drug development.
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Affiliation(s)
- Li Chen
- School of Medicine, Jiamusi University, Jiamusi 154007, China; (L.C.); (Y.L.); (T.L.); (B.Y.)
| | - Limin Yang
- School of Medicine, Dalian University, Dalian 116622, China;
| | - Yingyu Li
- School of Medicine, Jiamusi University, Jiamusi 154007, China; (L.C.); (Y.L.); (T.L.); (B.Y.)
| | - Tianrun Liu
- School of Medicine, Jiamusi University, Jiamusi 154007, China; (L.C.); (Y.L.); (T.L.); (B.Y.)
| | - Bolun Yang
- School of Medicine, Jiamusi University, Jiamusi 154007, China; (L.C.); (Y.L.); (T.L.); (B.Y.)
| | - Lei Liu
- School of Medicine, Jiamusi University, Jiamusi 154007, China; (L.C.); (Y.L.); (T.L.); (B.Y.)
| | - Rui Wu
- School of Medicine, Jiamusi University, Jiamusi 154007, China; (L.C.); (Y.L.); (T.L.); (B.Y.)
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39
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Justo Arevalo S, Castillo-Chávez A, Uribe Calampa CS, Zapata Sifuentes D, Huallpa CJ, Landa Bianchi G, Garavito-Salini Casas R, Quiñones Aguilar M, Pineda Chavarría R. What do we know about the function of SARS-CoV-2 proteins? Front Immunol 2023; 14:1249607. [PMID: 37790934 PMCID: PMC10544941 DOI: 10.3389/fimmu.2023.1249607] [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: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
The COVID-19 pandemic has highlighted the importance in the understanding of the biology of SARS-CoV-2. After more than two years since the first report of COVID-19, it remains crucial to continue studying how SARS-CoV-2 proteins interact with the host metabolism to cause COVID-19. In this review, we summarize the findings regarding the functions of the 16 non-structural, 6 accessory and 4 structural SARS-CoV-2 proteins. We place less emphasis on the spike protein, which has been the subject of several recent reviews. Furthermore, comprehensive reviews about COVID-19 therapeutic have been also published. Therefore, we do not delve into details on these topics; instead we direct the readers to those other reviews. To avoid confusions with what we know about proteins from other coronaviruses, we exclusively report findings that have been experimentally confirmed in SARS-CoV-2. We have identified host mechanisms that appear to be the primary targets of SARS-CoV-2 proteins, including gene expression and immune response pathways such as ribosome translation, JAK/STAT, RIG-1/MDA5 and NF-kβ pathways. Additionally, we emphasize the multiple functions exhibited by SARS-CoV-2 proteins, along with the limited information available for some of these proteins. Our aim with this review is to assist researchers and contribute to the ongoing comprehension of SARS-CoV-2's pathogenesis.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Daniela Zapata Sifuentes
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - César J. Huallpa
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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Roe K. Eight influenza virus cellular manipulations which can boost concurrent SARS-CoV-2 infections to severe outcomes. Hum Cell 2023; 36:1581-1592. [PMID: 37306884 DOI: 10.1007/s13577-023-00923-5] [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: 02/22/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023]
Abstract
Viral pathogens in the lungs can cause severe outcomes, including acute lung injury and acute respiratory distress syndrome. Dangerous respiratory pathogens include some influenza A and B viruses, and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Unfortunately, concurrent infections of influenza virus and SARS-CoV-2 increase severe outcome probabilities. Influenza viruses have eight cellular manipulations which can assist concurrent SARS-CoV-2 viral infections. The eight cellular manipulations include: (1) viral protein binding with cellular sensors to block antiviral transcription factors and cytokine expressions, (2) viral protein binding with cell proteins to impair cellular pre-messenger ribonucleic acid splicing, (3) increased ribonucleic acid virus replication through the phosphatidylinositol 3-kinase/Akt (protein kinase B) pathway, (4) regulatory ribonucleic acids to manipulate cellular sensors and pathways to suppress antiviral defenses, (5) exosomes to transmit influenza virus to uninfected cells to weaken cellular defenses before SARS-CoV-2 infection, (6) increased cellular cholesterol and lipids to improve virion synthesis stability, quality and virion infectivity, (7) increased cellular autophagy, benefiting influenza virus and SARS-CoV-2 replications and (8) adrenal gland stimulation to produce glucocorticoids, which suppress immune cells, including reduced synthesis of cytokines, chemokines and adhesion molecules. Concurrent infections by one of the influenza viruses and SARS-CoV-2 will increase the probability of severe outcomes, and with sufficient synergy potentially enable the recurrence of tragic pandemics.
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the causative agent of the recent COVID-19 pandemic, continues representing one of the main health concerns worldwide. Autophagy, in addition to its role in cellular homeostasis and metabolism, plays an important part for the host antiviral immunity. However, viruses including SARS-CoV-2 have evolved diverse mechanisms to not only overcome autophagy's antiviral pressure but also manipulate its machinery in order to enhance viral replication and propagation. Here, we discuss our current knowledge on the impact that autophagy exerts on SARS-CoV-2 replication, as well as the different counteracting measures that this virus has developed to manipulate autophagy's complex machinery. Some of the elements regarding this interplay may become future therapeutic targets in the fight against SARS-CoV-2.
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Affiliation(s)
- Hao Zhou
- Department of Microbiology and Immunology, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhiqiang Hu
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd, Dezhou, China
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Lee YB, Jung M, Kim J, Charles A, Christ W, Kang J, Kang MG, Kwak C, Klingström J, Smed-Sörensen A, Kim JS, Mun JY, Rhee HW. Super-resolution proximity labeling reveals anti-viral protein network and its structural changes against SARS-CoV-2 viral proteins. Cell Rep 2023; 42:112835. [PMID: 37478010 DOI: 10.1016/j.celrep.2023.112835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in human cells by interacting with host factors following infection. To understand the virus and host interactome proximity, we introduce a super-resolution proximity labeling (SR-PL) method with a "plug-and-playable" PL enzyme, TurboID-GBP (GFP-binding nanobody protein), and we apply it for interactome mapping of SARS-CoV-2 ORF3a and membrane protein (M), which generates highly perturbed endoplasmic reticulum (ER) structures. Through SR-PL analysis of the biotinylated interactome, 224 and 272 peptides are robustly identified as ORF3a and M interactomes, respectively. Within the ORF3a interactome, RNF5 co-localizes with ORF3a and generates ubiquitin modifications of ORF3a that can be involved in protein degradation. We also observe that the SARS-CoV-2 infection rate is efficiently reduced by the overexpression of RNF5 in host cells. The interactome data obtained using the SR-PL method are presented at https://sarscov2.spatiomics.org. We hope that our method will contribute to revealing virus-host interactions of other viruses in an efficient manner.
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Affiliation(s)
- Yun-Bin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jeesoo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea
| | - Afandi Charles
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Wanda Christ
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Jiwoong Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jonas Klingström
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden; Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea.
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Emslander Q, Krey K, Hamad S, Maidl S, Oubraham L, Hesse J, Henrici A, Austen K, Mergner J, Grass V, Pichlmair A. MDM2 Influences ACE2 Stability and SARS-CoV-2 Uptake. Viruses 2023; 15:1763. [PMID: 37632105 PMCID: PMC10459000 DOI: 10.3390/v15081763] [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: 06/02/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the central entry receptor for SARS-CoV-2. However, surprisingly little is known about the effects of host regulators on ACE2 localization, expression, and the associated influence on SARS-CoV-2 infection. Here we identify that ACE2 expression levels are regulated by the E3 ligase MDM2 and that MDM2 levels indirectly influence infection with SARS-CoV-2. Genetic depletion of MDM2 elevated ACE2 expression levels, which strongly promoted infection with all SARS-CoV-2 isolates tested. SARS-CoV-2 spike-pseudotyped viruses and the uptake of non-replication-competent virus-like particles showed that MDM2 affects the viral uptake process. MDM2 ubiquitinates Lysine 788 of ACE2 to induce proteasomal degradation, and degradation of this residue led to higher ACE2 expression levels and superior virus particle uptake. Our study illustrates that cellular regulators of ACE2 stability, such as MDM2, play an important role in defining the infection capabilities of SARS-CoV-2.
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Affiliation(s)
- Quirin Emslander
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Karsten Krey
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Sabri Hamad
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Susanne Maidl
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Lila Oubraham
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Joshua Hesse
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Alexander Henrici
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Katharina Austen
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Julia Mergner
- BayBioMS@MRI—Bavarian Center for Biomolecular Mass Spectrometry at Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
- German Centre for Infection Research (DZIF), Partner site Munich, 81675 Munich, Germany
- Center of Immunology of Viral Infection (CiViA), Aarhus University, 8000 Aarhus, Denmark
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Jiao S, Miranda P, Li Y, Maric D, Holmgren M. Some aspects of the life of SARS-CoV-2 ORF3a protein in mammalian cells. Heliyon 2023; 9:e18754. [PMID: 37609425 PMCID: PMC10440475 DOI: 10.1016/j.heliyon.2023.e18754] [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: 01/24/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023] Open
Abstract
The accessory protein ORF3a, from SARS-CoV-2, plays a critical role in viral infection and pathogenesis. Here, we characterized ORF3a assembly, ion channel activity, subcellular localization, and interactome. At the plasma membrane, ORF3a exists mostly as monomers and dimers, which do not alter the native cell membrane conductance, suggesting that ORF3a does not function as a viroporin at the cell surface. As a membrane protein, ORF3a is synthesized at the ER and sorted via a canonical route. ORF3a overexpression induced an approximately 25% increase in cell death. By developing an APEX2-based proximity labeling assay, we uncovered proteins proximal to ORF3a, suggesting that ORF3a recruits some host proteins to weaken the cell. In addition, it exposed a set of mitochondria related proteins that triggered mitochondrial fission. Overall, this work can be an important instrument in understanding the role of ORF3a in the virus pathogenicity and searching for potential therapeutic treatments for COVID-19.
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Affiliation(s)
- Song Jiao
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Pablo Miranda
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Miguel Holmgren
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
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45
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Henke W, Kalamvoki M, Stephens EB. The Role of the Tyrosine-Based Sorting Signals of the ORF3a Protein of SARS-CoV-2 on Intracellular Trafficking, Autophagy, and Apoptosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550379. [PMID: 37547007 PMCID: PMC10402054 DOI: 10.1101/2023.07.24.550379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The open reading frame 3a (ORF3a) is an accessory transmembrane protein that is important to the pathogenicity of SARS-CoV-2. The cytoplasmic domain of ORF3a has three canonical tyrosine-based sorting signals (YxxΦ; where x is any amino acid and Φ is a hydrophobic amino acid with a bulky -R group). They have been implicated in the trafficking of membrane proteins to the cell plasma membrane and to intracellular organelles. Previous studies have indicated that mutation of the 160YSNV163 motif abrogated plasma membrane expression and inhibited ORF3a-induced apoptosis. However, two additional canonical tyrosine-based sorting motifs (211YYQL213, 233YNKI236) exist in the cytoplasmic domain of ORF3a that have not been assessed. We removed all three potential tyrosine-based motifs and systematically restored them to assess the importance of each motif or combination of motifs that restored efficient trafficking to the cell surface and lysosomes. Our results indicate that the YxxΦ motif at position 160 was insufficient for the trafficking of ORF3a to the cell surface. Our studies also showed that ORF3a proteins with an intact YxxΦ at position 211 or at 160 and 211 were most important. We found that ORF3a cell surface expression correlated with the co-localization of ORF3a with LAMP-1 near the cell surface. These results suggest that YxxΦ motifs within the cytoplasmic domain may act cooperatively in ORF3a transport to the plasma membrane and endocytosis to lysosomes. Further, our results indicate that certain tyrosine mutants failed to activate caspase 3 and did not correlate with autophagy functions associated with this protein.
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Affiliation(s)
- Wyatt Henke
- Department of Microbiology, Molecular Genetics, and Immunology, 2000 Hixon Hall, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
| | - Maria Kalamvoki
- Department of Microbiology, Molecular Genetics, and Immunology, 2000 Hixon Hall, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
| | - Edward B Stephens
- Department of Microbiology, Molecular Genetics, and Immunology, 2000 Hixon Hall, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
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46
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Liu H, Li Q, Li L. SARS-CoV-2 ORF7a protein blocks virusclearance by regulating autophagy. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1334-1336. [PMID: 37408373 PMCID: PMC10448037 DOI: 10.3724/abbs.2023123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/14/2023] [Indexed: 07/07/2023] Open
Affiliation(s)
- Huimei Liu
- />Institute of Pharmacy and PharmacologyHunan Provincial Key Laboratoryof Tumor Microenvironment Responsive Drug ResearchHunan Province Cooperative Innovation Centerfor Molecular Target New Drug StudyHengyang Medical SchoolUniversity of South ChinaHengyang421001China
| | - Qin Li
- />Institute of Pharmacy and PharmacologyHunan Provincial Key Laboratoryof Tumor Microenvironment Responsive Drug ResearchHunan Province Cooperative Innovation Centerfor Molecular Target New Drug StudyHengyang Medical SchoolUniversity of South ChinaHengyang421001China
| | - Lanfang Li
- />Institute of Pharmacy and PharmacologyHunan Provincial Key Laboratoryof Tumor Microenvironment Responsive Drug ResearchHunan Province Cooperative Innovation Centerfor Molecular Target New Drug StudyHengyang Medical SchoolUniversity of South ChinaHengyang421001China
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47
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Wu N, Zheng C, Xu J, Ma S, Jia H, Yan M, An F, Zhou Y, Qi J, Bian H. Race between virus and inflammasomes: inhibition or escape, intervention and therapy. Front Cell Infect Microbiol 2023; 13:1173505. [PMID: 37465759 PMCID: PMC10351387 DOI: 10.3389/fcimb.2023.1173505] [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: 02/24/2023] [Accepted: 05/17/2023] [Indexed: 07/20/2023] Open
Abstract
The inflammasome is a multiprotein complex that further regulates cell pyroptosis and inflammation by activating caspase-1. The assembly and activation of inflammasome are associated with a variety of diseases. Accumulative studies have shown that inflammasome is a key modulator of the host's defense response to viral infection. Indeed, it has been established that activation of inflammasome occurs during viral infection. At the same time, the host has evolved a variety of corresponding mechanisms to inhibit unnecessary inflammasome activation. Therefore, here, we review and summarize the latest research progress on the interaction between inflammosomes and viruses, highlight the assembly and activation of inflammosome in related cells after viral infection, as well as the corresponding molecular regulatory mechanisms, and elucidate the effects of this activation on virus immune escape and host innate and adaptive immune defenses. Finally, we also discuss the potential therapeutic strategies to prevent and/or ameliorate viral infection-related diseases via targeting inflammasomes and its products.
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Affiliation(s)
- Nijin Wu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Chunzhi Zheng
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jiarui Xu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Shujun Ma
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huimin Jia
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Meizhu Yan
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Fuxiang An
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yi Zhou
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Jianni Qi
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Hongjun Bian
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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48
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Qu Y, Wang W, Xiao MZX, Zheng Y, Liang Q. The interplay between lipid droplets and virus infection. J Med Virol 2023; 95:e28967. [PMID: 37496184 DOI: 10.1002/jmv.28967] [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: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023]
Abstract
As an intracellular parasite, the virus usurps cellular machinery and modulates cellular metabolism pathways to replicate itself in cells. Lipid droplets (LDs) are universally conserved energy storage organelles that not only play vital roles in maintaining lipid homeostasis but are also involved in viral replication. Increasing evidence has demonstrated that viruses take advantage of cellular lipid metabolism by targeting the biogenesis, hydrolysis, and lipophagy of LD during viral infection. In this review, we summarize the current knowledge about the modulation of cellular LD by different viruses, with a special emphasis on the Hepatitis C virus, Dengue virus, and SARS-CoV-2.
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Affiliation(s)
- Yafei Qu
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weili Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Maggie Z X Xiao
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yuejuan Zheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai University of Traditional Medicine, Shanghai, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Medicine, Shanghai, China
| | - Qiming Liang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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49
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Shariq M, Malik AA, Sheikh JA, Hasnain SE, Ehtesham NZ. Regulation of autophagy by SARS-CoV-2: The multifunctional contributions of ORF3a. J Med Virol 2023; 95:e28959. [PMID: 37485696 DOI: 10.1002/jmv.28959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-1 (SARS-CoV-2) regulates autophagic flux by blocking the fusion of autophagosomes with lysosomes, causing the accumulation of membranous vesicles for replication. Multiple SARS-CoV-2 proteins regulate autophagy with significant roles attributed to ORF3a. Mechanistically, open reading frame 3a (ORF3a) forms a complex with UV radiation resistance associated, regulating the functions of the PIK3C3-1 and PIK3C3-2 lipid kinase complexes, thereby modulating autophagosome biogenesis. ORF3a sequesters VPS39 onto the late endosome/lysosome, inhibiting assembly of the soluble NSF attachement protein REceptor (SNARE) complex and preventing autolysosome formation. ORF3a promotes the interaction between BECN1 and HMGB1, inducing the assembly of PIK3CA kinases into the ER (endoplasmic reticulum) and activating reticulophagy, proinflammatory responses, and ER stress. ORF3a recruits BORCS6 and ARL8B to lysosomes, initiating the anterograde transport of the virus to the plasma membrane. ORF3a also activates the SNARE complex (STX4-SNAP23-VAMP7), inducing fusion of lysosomes with the plasma membrane for viral egress. These mechanistic details can provide multiple targets for inhibiting SARS-CoV-2 by developing host- or host-pathogen interface-based therapeutics.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signalling Laboratory, ICMR-National Institute of Pathology, New Delhi, India
| | - Asrar A Malik
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Javaid A Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Seyed E Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Nasreen Z Ehtesham
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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50
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Keramidas P, Papachristou E, Papi RM, Mantsou A, Choli-Papadopoulou T. Inhibition of PERK Kinase, an Orchestrator of the Unfolded Protein Response (UPR), Significantly Reduces Apoptosis and Inflammation of Lung Epithelial Cells Triggered by SARS-CoV-2 ORF3a Protein. Biomedicines 2023; 11:1585. [PMID: 37371681 DOI: 10.3390/biomedicines11061585] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 ORF3a accessory protein was found to be involved in virus release, immunomodulation and exhibited a pro-apoptotic character. In order to unravel a potential ORF3a-induced apoptotic and inflammatory death mechanism, lung epithelial cells (A549) were transfected with in vitro synthesized ORF3a mRNA. The protein's dynamic involvement as "stress factor" for the endoplasmic reticulum, causing the activation of PERK kinase and other UPR-involved proteins and therefore the upregulation of their signaling pathway executioners (ATF6, XBP-1s, PERK, phospho eIF2a, ATF4, CHOP, GADD34), has been clearly demonstrated. Furthermore, the overexpression of BAX and BH3-only pro-apoptotic protein PUMA, the upregulation of Bcl-2 family genes (BAX, BAK, BID, BAD), the reduced expression of Bcl-2 in mRNA and protein levels, and lastly, the cleavage of PARP-1 and caspase family members (caspase-3,-8 and -9) indicate that ORF3a displays its apoptotic character through the mitochondrial pathway of apoptosis. Moreover, the upregulation of NFκB, phosphorylation of p65 and IκΒα and the elevated expression of pro-inflammatory cytokines (IL-1b, IL-6, IL-8 and IL-18) in transfected cells with ORF3a mRNA indicate that this protein causes the inflammatory response through NFκB activation and therefore triggers lung injury. An intriguing finding of our study is that upon treatment of the ORF3a-transfected cells with GSK2606414, a selective PERK inhibitor, both complications (apoptosis and inflammatory response) were neutralized, and cell survival was favored, whereas treatment of transfected cells with z-VAD (a pan-caspase inhibitor) despite inhibiting cell death, could not ameliorate the inflammatory response of transfected A549 cells. Given the above, we point out that PERK kinase is a "master tactician" and its activation constitutes the main stimulus for the emergence of ORF3a apoptotic and inflammatory nature and therefore could serve as potential target for developing novel therapeutic approaches against COVID-19.
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Affiliation(s)
- Panagiotis Keramidas
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Eleni Papachristou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Rigini M Papi
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Aglaia Mantsou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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