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Pattoo TS, Khanday FA. Corelating the molecular structure of BAG3 to its oncogenic role. Cell Biol Int 2024; 48:1080-1096. [PMID: 38924608 DOI: 10.1002/cbin.12199] [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: 03/19/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
BAG3 is a multifaceted protein characterised by having WW domain, PXXP motif and BAG domain. This protein gets upregulated during malignant transformation of cells and has been associated with poorer survival of patients. Procancerous activity of BAG domain of BAG3 is well documented. BAG domain interacts with ATPase domain of Hsp-70 preventing protein delivery to proteasome. This impediment results in enhanced cell survival, proliferation, resistance to apoptosis and chemoresistance. Besides BAG domain other two domains/motifs of BAG3 are under research vigilance to explore its further oncogenic role. This review summarises the role of different structural determinants of BAG3 in elevating oncogenesis. Based on the already existing findings, more interacting partners of BAG3 are anticipated. The anticipated partners of BAG3 can shed a wealth of information into the mechanistic insights of its proproliferative role. Proper insights into the mechanistic details adopted by BAG3 to curtail/elaborate activity of anticipated interacting partners can serve as a potent target for development of therapeutic interventions.
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Affiliation(s)
| | - Firdous A Khanday
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
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2
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Wang L, Song Y, Xu M, Zhang C, Zhang L, Xia L, Wei Z. Proteomics analysis of PK-15 cells infected with porcine parvovirus and the effect of PCBP1 on PPV replication. Microbiol Spectr 2024; 12:e0391423. [PMID: 38742903 DOI: 10.1128/spectrum.03914-23] [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: 11/14/2023] [Accepted: 04/14/2024] [Indexed: 05/16/2024] Open
Abstract
Porcine parvovirus (PPV) is one of the most important pathogens that cause reproductive failure in pigs. However, the pathogenesis of PPV infection remains unclear. Proteomics is a powerful tool to understand the interaction between virus and host cells. In the present study, we analyzed the proteomics of PPV-infected PK-15 cells. A total of 32 and 345 proteins were differentially expressed at the early and replication stages, respectively. Subsequent gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed these differentially expressed proteins were significantly enriched in pathways including toll-like receptor signaling pathway, tumor necrosis factor signaling pathway, and viral carcinogenesis. The expression of poly (rC) binding protein 1 (PCBP1) was observed to decrease after PPV infection. Overexpressed or silenced PCBP1 expression inhibited or promoted PPV infection. Our studies established a foundation for further exploration of the multiplication mechanism of PPV. IMPORTANCE Porcine parvovirus (PPV) is a cause of reproductive failure in the swine industry. Our knowledge of PPV remains limited, and there is no effective treatment for PPV infection. Proteomics of PPV-infected PK-15 cells was conducted to identify differentially expressed proteins at 6 hours post-infection (hpi) and 36 hpi. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that various pathways participate in PPV infection. Poly (rC) binding protein 1 was confirmed to inhibit PPV replication, which provided potential targets for anti-PPV infection. Our findings improve the understanding of PPV infection and pave the way for future research in this area.
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Affiliation(s)
- Linqing Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Molecule Biology Laboratory of Zhengzhou Normal University, Zhengzhou, Henan, China
| | - Yue Song
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Molecule Biology Laboratory of Zhengzhou Normal University, Zhengzhou, Henan, China
| | - Menglong Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan, China
| | - Chi Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Limeng Zhang
- Molecule Biology Laboratory of Zhengzhou Normal University, Zhengzhou, Henan, China
| | - Lu Xia
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan, China
| | - Zhanyong Wei
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan, China
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3
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Merino VF, Yan Y, Ordonez AA, Bullen CK, Lee A, Saeki H, Ray K, Huang T, Jain SK, Pomper MG. Nucleolin mediates SARS-CoV-2 replication and viral-induced apoptosis of host cells. Antiviral Res 2023; 211:105550. [PMID: 36740097 PMCID: PMC9896859 DOI: 10.1016/j.antiviral.2023.105550] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Host-oriented antiviral therapeutics are promising treatment options to combat COVID-19 and its emerging variants. However, relatively little is known about the cellular proteins hijacked by SARS-CoV-2 for its replication. Here we show that SARS-CoV-2 induces expression and cytoplasmic translocation of the nucleolar protein, nucleolin (NCL). NCL interacts with SARS-CoV-2 viral proteins and co-localizes with N-protein in the nucleolus and in stress granules. Knockdown of NCL decreases the stress granule component G3BP1, viral replication and improved survival of infected host cells. NCL mediates viral-induced apoptosis and stress response via p53. SARS-CoV-2 increases NCL expression and nucleolar size and number in lungs of infected hamsters. Inhibition of NCL with the aptamer AS-1411 decreases viral replication and apoptosis of infected cells. These results suggest nucleolin as a suitable target for anti-COVID therapies.
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Affiliation(s)
- Vanessa F Merino
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Yu Yan
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Alvaro A Ordonez
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - C Korin Bullen
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Albert Lee
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harumi Saeki
- Department of Human Pathology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sanjay K Jain
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin G Pomper
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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4
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Feng Z, Pan Y, Liu Y, Zhao J, Peng X, Lu G, Shi W, Zhang D, Cui S. Screening and Analysis of Serum Protein Biomarkers Infected by Coronavirus Disease 2019 (COVID-19). Trop Med Infect Dis 2022; 7:tropicalmed7120397. [PMID: 36548652 PMCID: PMC9788497 DOI: 10.3390/tropicalmed7120397] [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: 09/02/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has spread widely around the world, and in-depth research on COVID-19 is necessary for biomarkers and target drug discovery. This analysis collected serum from six COVID-19-infected patients and six healthy people. The protein changes in the infected and healthy control serum samples were evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and high-performance liquid chromatography (HPLC). The differential protein signature in both groups was retrieved and analyzed by the Kyoto Encyclopedia of Gene and Genomes (KEGG), Gene ontology, COG/KOG, protein-protein interaction, and protein domain interactions tools. We shortlisted 24 differentially expressed proteins between both groups. Ten genes were significantly up-regulated in the infection group, and fourteen genes were significantly down-regulated. The GO and KEGG pathway enrichment analysis suggested that the chromosomal part and chromosome were the most enriched items. The oxytocin signaling pathway was the most enriched item of KEGG analysis. The netrin module (non-TIMP type) was the most enriched protein domain in this study. Functional analysis of S100A9, PIGR, C4B, IL-6R, IGLV3-19, IGLV3-1, and IGLV5-45 revealed that SARS-CoV-2 was closely related to immune response.
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5
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Liang Z, Zhang S, Zou Z, Li J, Wu R, Xia L, Shi G, Cai J, Tang J, Jian J. Functional characterization of BAG3 in orange-spotted grouper (Epinephelus coioides) during viral infection. FISH & SHELLFISH IMMUNOLOGY 2022; 122:465-475. [PMID: 35218970 DOI: 10.1016/j.fsi.2022.02.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/23/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Bcl-2-associated athanogene 3 (BAG3) is a cochaperone protein that interacts with Bcl-2 and mediate cell death. However, little is known about the roles of fish BAG3 during viral infection. In this study, we characterized a BAG3 homolog from orange-spotted grouper (Epinephelus coioides) (EcBAG3) and investigated its roles during viral infection. The EcBAG3 protein encoded 579 amino acids with typical WW, PXXP and BAG domains, which shared high identities with reported fish BAG3. Quantitative real-time PCR (qRT-PCR) analysis revealed that EcBAG3 was highly expressed in brain and heart. And the expression of EcBAG3 was significantly up-regulated after red-spotted grouper nervous necrosis virus (RGNNV) stimulation in vitro. EcBAG3 overexpression could promoted the expression of viral genes (coat protein (CP) and RNA-dependent RNA polymerase (RdRp)), which was enhanced by co-transfection with Hsp70 and Hsp22. Also, EcBAG3 overexpression up-regulated the expression of LC3-Ⅱ and down-regulated the expression of Bax and BNIP3, the IFN- (IRF1, IRF3, IRF7, IFP35, Mx1) or inflammation-related (IL-1β and TNFα) factors, as well as decreased the activities of NF-κB, ISRE and IFN-3. While knockdown of EcBAG3 decreased the transcripts of RGNNV CP gene and RdRp gene. Further studies showed that EcBAG3 knockdown impaired the expression level of autophagy factor LC3-Ⅱ, and promoted the expression level of Bax and BNIP3, inflammatory factors and interferon factors. These data indicate that EcBAG3 can affect viral infection through modulating virus-induced cell death, regulating the expression of IFN- and inflammation-related factors, which will be helpful to further explore the immune response of fish during viral infection.
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Affiliation(s)
- Zhenyu Liang
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), 524002, PR China
| | - Shuping Zhang
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), 524002, PR China
| | - Zihong Zou
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), 524002, PR China
| | - Jinze Li
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), 524002, PR China
| | - Rimin Wu
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), 524002, PR China
| | - Liqun Xia
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China
| | - Gang Shi
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China
| | - Jia Cai
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), 524002, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China; Guangxi Key Lab for Marine Natural Products and Combinational Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Centre, Guangxi Academy of Sciences, Nanning, 530007, PR China.
| | - Jufen Tang
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China
| | - Jichang Jian
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, PR China; Guangdong Key Laboratory of Control for Diseases of Aquatic Economic Animals, Zhanjiang, 524088, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), 524002, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
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6
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Lin H, Koren SA, Cvetojevic G, Girardi P, Johnson GV. The role of BAG3 in health and disease: A "Magic BAG of Tricks". J Cell Biochem 2022; 123:4-21. [PMID: 33987872 PMCID: PMC8590707 DOI: 10.1002/jcb.29952] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/25/2021] [Indexed: 01/03/2023]
Abstract
The multi-domain structure of Bcl-2-associated athanogene 3 (BAG3) facilitates its interaction with many different proteins that participate in regulating a variety of biological pathways. After revisiting the BAG3 literature published over the past ten years with Citespace software, we classified the BAG3 research into several clusters, including cancer, cardiomyopathy, neurodegeneration, and viral propagation. We then highlighted recent key findings in each cluster. To gain greater insight into the roles of BAG3, we analyzed five different published mass spectrometry data sets of proteins that co-immunoprecipitate with BAG3. These data gave us insight into universal, as well as cell-type-specific BAG3 interactors in cancer cells, cardiomyocytes, and neurons. Finally, we mapped variable BAG3 SNPs and also mutation data from previous publications to further explore the link between the domains and function of BAG3. We believe this review will provide a better understanding of BAG3 and direct future studies towards understanding BAG3 function in physiological and pathological conditions.
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Affiliation(s)
- Heng Lin
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Shon A. Koren
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Gregor Cvetojevic
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Peter Girardi
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Gail V.W. Johnson
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
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7
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Karim L, Kosmider B, Bahmed K. Mitochondrial ribosomal stress in lung diseases. Am J Physiol Lung Cell Mol Physiol 2021; 322:L507-L517. [PMID: 34873929 DOI: 10.1152/ajplung.00078.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mitochondria are involved in a variety of critical cellular functions, and their impairment drives cell injury. The mitochondrial ribosome (mitoribosome) is responsible for the protein synthesis of mitochondrial DNA encoded genes. These proteins are involved in oxidative phosphorylation, respiration, and ATP production required in the cell. Mitoribosome components originate from both mitochondrial and nuclear genomes. Their dysfunction can be caused by impaired mitochondrial protein synthesis or mitoribosome misassembly, leading to a decline in mitochondrial translation. This decrease can trigger mitochondrial ribosomal stress and contribute to pulmonary cell injury, death, and diseases. This review focuses on the contribution of the impaired mitoribosome structural components and function to respiratory disease pathophysiology. We present recent findings in the fields of lung cancer, chronic obstructive pulmonary disease, interstitial lung disease, and asthma. We also include reports on the mitoribosome dysfunction in pulmonary hypertension, high altitude pulmonary edema, bacterial and viral infections. Studies of the mitoribosome alterations in respiratory diseases can lead to novel therapeutic targets.
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Affiliation(s)
- Loukmane Karim
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
| | - Beata Kosmider
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Biomedical Education and Data Science, Temple University, Philadelphia, PA, United States
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, United States
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Gerassimovich YA, Miladinovski-Bangall SJ, Bridges KM, Boateng L, Ball LE, Valafar H, Nag A. Proximity-dependent biotinylation detects associations between SARS coronavirus nonstructural protein 1 and stress granule-associated proteins. J Biol Chem 2021; 297:101399. [PMID: 34774526 PMCID: PMC8580555 DOI: 10.1016/j.jbc.2021.101399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
The nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus 2 is a critical viral protein that suppresses host gene expression by blocking the assembly of the ribosome on host mRNAs. To understand the mechanism of inhibition of host gene expression, we sought to identify cellular proteins that interact with nsp1. Using proximity-dependent biotinylation followed by proteomic analyses of biotinylated proteins, here we captured multiple dynamic interactions of nsp1 with host cell proteins. In addition to ribosomal proteins, we identified several pre-mRNA processing proteins that interact with nsp1, including splicing factors and transcription termination proteins, as well as exosome, and stress granule (SG)-associated proteins. We found that the interactions with transcription termination factors are primarily governed by the C-terminal region of nsp1 and are disrupted by the mutation of amino acids K164 and H165 that are essential for its host shutoff function. We further show that nsp1 interacts with Ras GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and colocalizes with G3BP1 in SGs under sodium arsenite-induced stress. Finally, we observe that the presence of nsp1 disrupts the maturation of SGs over a long period. Isolation of SG core at different times shows a gradual loss of G3BP1 in the presence of nsp1.
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Affiliation(s)
- Yevgeniy A Gerassimovich
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA
| | | | - Kaitlin M Bridges
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA
| | - Linkel Boateng
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, USA
| | - Lauren E Ball
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Homayoun Valafar
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, USA
| | - Anita Nag
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA.
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Aging whole blood transcriptome reveals candidate genes for SARS-CoV-2-related vascular and immune alterations. J Mol Med (Berl) 2021; 100:285-301. [PMID: 34741638 PMCID: PMC8571664 DOI: 10.1007/s00109-021-02161-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 10/08/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022]
Abstract
Abstract The risk of severe COVID-19 increases with age as older patients are at highest risk. Thus, there is an urgent need to identify how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interacts with blood components during aging. We investigated the whole blood transcriptome from the Genotype-Tissue Expression (GTEx) database to explore differentially expressed genes (DEGs) translated into proteins interacting with viral proteins during aging. From 22 DEGs in aged blood, FASLG, CTSW, CTSE, VCAM1, and BAG3 were associated with immune response, inflammation, cell component and adhesion, and platelet activation/aggregation. Males and females older than 50 years old overexpress FASLG, possibly inducing a hyperinflammatory cascade. The expression of cathepsins (CTSW and CTSE) and the anti-apoptotic co-chaperone molecule BAG3 also increased throughout aging in both genders. By exploring single-cell RNA-sequencing data from peripheral blood of SARS-CoV-2-infected patients, we found FASLG and CTSW expressed in natural killer cells and CD8 + T lymphocytes, whereas BAG3 was expressed mainly in CD4 + T cells, naive T cells, and CD14 + monocytes. In addition, T cell exhaustion was associated with increased expression of CCL4L2 and DUSP4 over blood aging. LAG3, PDCD1, TIGIT, VCAM1, HLA-DRA, and TOX also increased in individuals aged 60–69 years old; conversely, the RGS2 gene decreased with aging. We further identified a distinct gene expression profile associated with type I interferon signaling following blood aging. These results revealed changes in blood molecules potentially related to SARS-CoV-2 infection throughout aging, emphasizing them as therapeutic candidates for aggressive clinical manifestation of COVID-19. Key messages • Prediction of host-viral interactions in the whole blood transcriptome during aging. • Expression levels of FASLG, CTSW, CTSE, VCAM1, and BAG3 increase in aged blood. • Blood interactome reveals targets involved with immune response, inflammation, and blood clots. • SARS-CoV-2-infected patients with high viral load showed FASLG overexpression. • Gene expression profile associated with T cell exhaustion and type I interferon signaling were affected with blood aging. Supplementary Information The online version contains supplementary material available at 10.1007/s00109-021-02161-4.
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10
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Basu S, Naha A, Veeraraghavan B, Ramaiah S, Anbarasu A. In silico structure evaluation of BAG3 and elucidating its association with bacterial infections through protein-protein and host-pathogen interaction analysis. J Cell Biochem 2021; 123:115-127. [PMID: 33998043 DOI: 10.1002/jcb.29953] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/11/2021] [Accepted: 05/03/2021] [Indexed: 01/30/2023]
Abstract
BAG3, a co-chaperone protein with a Bcl-2-associated athanogene (BAG) domain, has diverse functionalities in protein-folding, apoptosis, inflammation, and cell cycle regulatory cross-talks. It has been well characterised in cardiac diseases, cancers, and viral pathogenesis. The multiple roles of BAG3 are attributed to its functional regions like BAG, Tryptophan-rich (WW), isoleucine-proline-valine-rich (IPV), and proline-rich (PXXP) domains. However, to study its structural impact on various functions, the experimental 3D structure of BAG3 protein was not available. Hence, the structure was predicted through in silico modelling and validated through computational tools and molecular dynamics simulation studies. To the best of our knowledge, the role of BAG3 in bacterial infections is not explicitly reported. We attempted to study them through an in-silico protein-protein interaction network and host-pathogen interaction analysis. From structure-function relationships, it was identified that the WW and PXXP domains were associated with cellular cytoskeleton rearrangement and adhesion-mediated response, which might be involved in BAG3-related intracellular bacterial proliferation. From functional enrichment analysis, Gene Ontology terms and topological matrices, 18 host proteins and 29 pathogen proteins were identified in the BAG3 interactome pertaining to Legionellosis, Tuberculosis, Salmonellosis, Shigellosis, and Pertussis through differential phosphorylation events associated with serine metabolism. Furthermore, it was evident that direct (MAPK8, MAPK14) and associated (MAPK1, HSPD1, NFKBIA, TLR2, RHOA) interactors of BAG3 could be considered as therapeutic markers to curb down intracellular bacterial propagation in humans.
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Affiliation(s)
- Soumya Basu
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Aniket Naha
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College & Hospital, Vellore, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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11
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V'kovski P, Kratzel A, Steiner S, Stalder H, Thiel V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 2021; 19:155-170. [PMID: 33116300 PMCID: PMC7592455 DOI: 10.1038/s41579-020-00468-6] [Citation(s) in RCA: 1686] [Impact Index Per Article: 562.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 pandemic and its unprecedented global societal and economic disruptive impact has marked the third zoonotic introduction of a highly pathogenic coronavirus into the human population. Although the previous coronavirus SARS-CoV and MERS-CoV epidemics raised awareness of the need for clinically available therapeutic or preventive interventions, to date, no treatments with proven efficacy are available. The development of effective intervention strategies relies on the knowledge of molecular and cellular mechanisms of coronavirus infections, which highlights the significance of studying virus-host interactions at the molecular level to identify targets for antiviral intervention and to elucidate critical viral and host determinants that are decisive for the development of severe disease. In this Review, we summarize the first discoveries that shape our current understanding of SARS-CoV-2 infection throughout the intracellular viral life cycle and relate that to our knowledge of coronavirus biology. The elucidation of similarities and differences between SARS-CoV-2 and other coronaviruses will support future preparedness and strategies to combat coronavirus infections.
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Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), 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
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), 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
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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12
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Abstract
In the following continuation article, the author will expand on how the mechanisms discussed in Part One capitalise on host characteristics to produce the organ specific damage seen in severe coronavirus disease (COVID-19), with specific reference to pulmonary and cardiac manifestations. Pneumonia is the primary manifestation of COVID-19; presentation varies from a mild, self-limiting pneumonitis to a fulminant and progressive respiratory failure. Features of disease severity tend to directly correlate with patient age, with elderly populations faring poorest. Advancing age parallels an increasingly pro-oxidative pulmonary milieu, a consequence of increasing host expression of phospholipase A2 Group IID. Virally induced expression of NADPH oxidase intensifies this pro-oxidant environment. The virus avails of the host response by exploiting caveolin-1 to assist in disabling host defenses and adopting a glycolytic metabolic pathway to self-replicate.
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13
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Sperk M, van Domselaar R, Rodriguez JE, Mikaeloff F, Sá Vinhas B, Saccon E, Sönnerborg A, Singh K, Gupta S, Végvári Á, Neogi U. Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses. J Proteome Res 2020; 19:4259-4274. [PMID: 33095583 PMCID: PMC7640957 DOI: 10.1021/acs.jproteome.0c00380] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Indexed: 12/21/2022]
Abstract
Emerging and re-emerging infectious diseases due to RNA viruses cause major negative consequences for the quality of life, public health, and overall economic development. Most of the RNA viruses causing illnesses in humans are of zoonotic origin. Zoonotic viruses can directly be transferred from animals to humans through adaptation, followed by human-to-human transmission, such as in human immunodeficiency virus (HIV), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and, more recently, SARS coronavirus 2 (SARS-CoV-2), or they can be transferred through insects or vectors, as in the case of Crimean-Congo hemorrhagic fever virus (CCHFV), Zika virus (ZIKV), and dengue virus (DENV). At the present, there are no vaccines or antiviral compounds against most of these viruses. Because proteins possess a vast array of functions in all known biological systems, proteomics-based strategies can provide important insights into the investigation of disease pathogenesis and the identification of promising antiviral drug targets during an epidemic or pandemic. Mass spectrometry technology has provided the capacity required for the precise identification and the sensitive and high-throughput analysis of proteins on a large scale and has contributed greatly to unravelling key protein-protein interactions, discovering signaling networks, and understanding disease mechanisms. In this Review, we present an account of quantitative proteomics and its application in some prominent recent examples of emerging and re-emerging RNA virus diseases like HIV-1, CCHFV, ZIKV, and DENV, with more detail with respect to coronaviruses (MERS-CoV and SARS-CoV) as well as the recent SARS-CoV-2 pandemic.
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Affiliation(s)
- Maike Sperk
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Robert van Domselaar
- Division
of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Jimmy Esneider Rodriguez
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 14152 Sweden
| | - Flora Mikaeloff
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Beatriz Sá Vinhas
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Elisa Saccon
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Anders Sönnerborg
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
- Division
of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Kamal Singh
- Department
of Molecular Microbiology and Immunology and the Bond Life Science
Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Soham Gupta
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Ákos Végvári
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 14152 Sweden
| | - Ujjwal Neogi
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
- Department
of Molecular Microbiology and Immunology and the Bond Life Science
Center, University of Missouri, Columbia, Missouri 65211, United States
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14
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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15
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Lyu C, Li WD, Wang SW, Peng JM, Yang YB, Tian ZJ, Cai XH. Host BAG3 Is Degraded by Pseudorabies Virus pUL56 C-Terminal 181L- 185L and Plays a Negative Regulation Role during Viral Lytic Infection. Int J Mol Sci 2020; 21:ijms21093148. [PMID: 32365661 PMCID: PMC7247713 DOI: 10.3390/ijms21093148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/23/2020] [Accepted: 04/23/2020] [Indexed: 11/16/2022] Open
Abstract
Bcl2-associated athanogene (BAG) 3, which is a chaperone-mediated selective autophagy protein, plays a pivotal role in modulating the life cycle of a wide variety of viruses. Both positive and negative modulations of viruses by BAG3 were reported. However, the effects of BAG3 on pseudorabies virus (PRV) remain unknown. To investigate whether BAG3 could modulate the PRV life cycle during a lytic infection, we first identified PRV protein UL56 (pUL56) as a novel BAG3 interactor by co-immunoprecipitation and co-localization analyses. The overexpression of pUL56 induced a significant degradation of BAG3 at protein level via the lysosome pathway. The C-terminal mutations of 181L/A, 185L/A, or 181L/A-185L/A in pUL56 resulted in a deficiency in pUL56-induced BAG3 degradation. In addition, the pUL56 C-terminal mutants that lost Golgi retention abrogated pUL56-induced BAG3 degradation, which indicates a Golgi retention-dependent manner. Strikingly, BAG3 was not observed to be degraded in either wild-type or UL56-deleted PRV infected cells as compared to mock infected ones, whereas the additional two adjacent BAG3 cleaved products were found in the infected cells in a species-specific manner. Overexpression of BAG3 significantly suppressed PRV proliferation, while knockdown of BAG3 resulted in increased viral yields in HEK293T cells. Thus, these data indicated a negative regulation role of BAG3 during PRV lytic infection. Collectively, our findings revealed a novel molecular mechanism on host protein degradation induced by PRV pUL56. Moreover, we identified BAG3 as a host restricted protein during PRV lytic infection in cells.
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16
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Gomez GN, Abrar F, Dodhia MP, Gonzalez FG, Nag A. SARS coronavirus protein nsp1 disrupts localization of Nup93 from the nuclear pore complex. Biochem Cell Biol 2019; 97:758-766. [PMID: 30943371 DOI: 10.1139/bcb-2018-0394] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus nonstructural protein 1 (nsp1) is a key factor in virus-induced down-regulation of host gene expression. In infected cells, nsp1 engages in a multipronged mechanism to inhibit host gene expression by binding to the 40S ribosome to block the assembly of translationally competent ribosome, and then inducing endonucleolytic cleavage and the degradation of host mRNAs. Here, we report a previously undetected mechanism by which nsp1 exploits the nuclear pore complex and disrupts the nuclear-cytoplasmic transport of biomolecules. We identified members of the nuclear pore complex from the nsp1-associated protein assembly and found that the expression of nsp1 in HEK cells disrupts Nup93 localization around the nuclear envelope without triggering proteolytic degradation, while the nuclear lamina remains unperturbed. Consistent with its role in host shutoff, nsp1 alters the nuclear-cytoplasmic distribution of an RNA binding protein, nucleolin. Our results suggest that nsp1, alone, can regulate multiple steps of gene expression including nuclear-cytoplasmic transport.
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Affiliation(s)
- Garret N Gomez
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Fareeha Abrar
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Maya P Dodhia
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Fabiola G Gonzalez
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | - Anita Nag
- Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
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17
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Abstract
Coronaviruses are pathogens with a serious impact on human and animal health. They mostly cause enteric or respiratory disease, which can be severe and life threatening, e.g., in the case of the zoonotic coronaviruses causing severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) in humans. Despite the economic and societal impact of such coronavirus infections, and the likelihood of future outbreaks of additional pathogenic coronaviruses, our options to prevent or treat coronavirus infections remain very limited. This highlights the importance of advancing our knowledge on the replication of these viruses and their interactions with the host. Compared to other +RNA viruses, coronaviruses have an exceptionally large genome and employ a complex genome expression strategy. Next to a role in basic virus replication or virus assembly, many of the coronavirus proteins expressed in the infected cell contribute to the coronavirus-host interplay. For example, by interacting with the host cell to create an optimal environment for coronavirus replication, by altering host gene expression or by counteracting the host’s antiviral defenses. These coronavirus–host interactions are key to viral pathogenesis and will ultimately determine the outcome of infection. Due to the complexity of the coronavirus proteome and replication cycle, our knowledge of host factors involved in coronavirus replication is still in an early stage compared to what is known for some other +RNA viruses. This review summarizes our current understanding of coronavirus–host interactions at the level of the infected cell, with special attention for the assembly and function of the viral RNA-synthesising machinery and the evasion of cellular innate immune responses.
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18
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Liang J, Sagum CA, Bedford MT, Sidhu SS, Sudol M, Han Z, Harty RN. Chaperone-Mediated Autophagy Protein BAG3 Negatively Regulates Ebola and Marburg VP40-Mediated Egress. PLoS Pathog 2017; 13:e1006132. [PMID: 28076420 PMCID: PMC5226679 DOI: 10.1371/journal.ppat.1006132] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/15/2016] [Indexed: 12/18/2022] Open
Abstract
Ebola (EBOV) and Marburg (MARV) viruses are members of the Filoviridae family which cause outbreaks of hemorrhagic fever. The filovirus VP40 matrix protein is essential for virus assembly and budding, and its PPxY L-domain motif interacts with WW-domains of specific host proteins, such as Nedd4 and ITCH, to facilitate the late stage of virus-cell separation. To identify additional WW-domain-bearing host proteins that interact with VP40, we used an EBOV PPxY-containing peptide to screen an array of 115 mammalian WW-domain-bearing proteins. Using this unbiased approach, we identified BCL2 Associated Athanogene 3 (BAG3), a member of the BAG family of molecular chaperone proteins, as a specific VP40 PPxY interactor. Here, we demonstrate that the WW-domain of BAG3 interacts with the PPxY motif of both EBOV and MARV VP40 and, unexpectedly, inhibits budding of both eVP40 and mVP40 virus-like particles (VLPs), as well as infectious VSV-EBOV recombinants. BAG3 is a stress induced protein that regulates cellular protein homeostasis and cell survival through chaperone-mediated autophagy (CMA). Interestingly, our results show that BAG3 alters the intracellular localization of VP40 by sequestering VP40 away from the plasma membrane. As BAG3 is the first WW-domain interactor identified that negatively regulates budding of VP40 VLPs and infectious virus, we propose that the chaperone-mediated autophagy function of BAG3 represents a specific host defense strategy to counteract the function of VP40 in promoting efficient egress and spread of virus particles.
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Affiliation(s)
- Jingjing Liang
- Department of Pathobiology, School Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
| | - Cari A. Sagum
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, University of Texas Smithville, Smithville, TX, United States of America
| | - Mark T. Bedford
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, University of Texas Smithville, Smithville, TX, United States of America
| | - Sachdev S. Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marius Sudol
- Department of Physiology, National University of Singapore, Mechanobiology Institute and Institute for Molecular and Cell Biology (IMCB, A*STAR), Republic of Singapore
| | - Ziying Han
- Department of Pathobiology, School Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Ronald N. Harty
- Department of Pathobiology, School Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- * E-mail:
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19
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Oxford KL, Wendler JP, McDermott JE, White III RA, Powell JD, Jacobs JM, Adkins JN, Waters KM. The landscape of viral proteomics and its potential to impact human health. Expert Rev Proteomics 2016; 13:579-91. [DOI: 10.1080/14789450.2016.1184091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Tanaka Y, Amano A, Morisaki M, Sato Y, Sasaki T. Cellular peptidyl-prolyl cis/trans isomerase Pin1 facilitates replication of feline coronavirus. Antiviral Res 2015; 126:1-7. [PMID: 26675666 PMCID: PMC7113879 DOI: 10.1016/j.antiviral.2015.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/18/2015] [Accepted: 11/29/2015] [Indexed: 01/23/2023]
Abstract
Although feline coronavirus (FCoV) causes feline infectious peritonitis (FIP), which is a fatal infectious disease, there are no effective therapeutic medicines or vaccines. Previously, in vitro studies have shown that cyclosporin (CsA) and FK506 inhibit virus replication in diverse coronaviruses. CsA and FK506 are targets of clinically relevant immunosuppressive drugs and bind to cellular cyclophilins (Cyps) or FK506 binding proteins (FKBPs), respectively. Both Cyp and FKBP have peptidyl-prolyl cis-trans isomerase (PPIase) activity. However, protein interacting with NIMA (Pin1), a member of the parvulin subfamily of PPIases that differs from Cyps and FKBPs, is essential for various signaling pathways. Here we demonstrated that genetic silencing or knockout of Pin1 resulted in decreased FCoV replication in vitro. Dipentamethylene thiuram monosulfide, a specific inhibitor of Pin1, inhibited FCoV replication. These data indicate that Pin1 modulates FCoV propagation. Pin1 facilitates FCoV replication in vitro. RNA interference experiments for Pin1 reduced FCoV replication and viral protein expression. The Pin1 inhibitor DTM results in the reduction of FCoV replication and protein expression. Knockout of the Pin1 gene inhibits FCoV replication and protein expression.
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Affiliation(s)
- Yoshikazu Tanaka
- Department of Veterinary Hygiene, Veterinary School, Nippon Veterinary and Life Science University, 1-7-1 Kyounan, Musashino, Tokyo 180-8602, Japan.
| | - Arisa Amano
- Department of Veterinary Hygiene, Veterinary School, Nippon Veterinary and Life Science University, 1-7-1 Kyounan, Musashino, Tokyo 180-8602, Japan
| | - Masateru Morisaki
- Department of Veterinary Hygiene, Veterinary School, Nippon Veterinary and Life Science University, 1-7-1 Kyounan, Musashino, Tokyo 180-8602, Japan
| | - Yuka Sato
- Department of Microbiology and Immunology, Division of Molecular Virology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takashi Sasaki
- Department of Bacteriology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan
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21
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Reid CR, Airo AM, Hobman TC. The Virus-Host Interplay: Biogenesis of +RNA Replication Complexes. Viruses 2015; 7:4385-413. [PMID: 26287230 PMCID: PMC4576186 DOI: 10.3390/v7082825] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/21/2015] [Accepted: 07/24/2015] [Indexed: 12/22/2022] Open
Abstract
Positive-strand RNA (+RNA) viruses are an important group of human and animal pathogens that have significant global health and economic impacts. Notable members include West Nile virus, Dengue virus, Chikungunya, Severe acute respiratory syndrome (SARS) Coronavirus and enteroviruses of the Picornaviridae family.Unfortunately, prophylactic and therapeutic treatments against these pathogens are limited. +RNA viruses have limited coding capacity and thus rely extensively on host factors for successful infection and propagation. A common feature among these viruses is their ability to dramatically modify cellular membranes to serve as platforms for genome replication and assembly of new virions. These viral replication complexes (VRCs) serve two main functions: To increase replication efficiency by concentrating critical factors and to protect the viral genome from host anti-viral systems. This review summarizes current knowledge of critical host factors recruited to or demonstrated to be involved in the biogenesis and stabilization of +RNA virus VRCs.
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Affiliation(s)
- Colleen R Reid
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada.
| | - Adriana M Airo
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada.
| | - Tom C Hobman
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada.
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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Almazán F, Sola I, Zuñiga S, Marquez-Jurado S, Morales L, Becares M, Enjuanes L. Reprint of: Coronavirus reverse genetic systems: infectious clones and replicons. Virus Res 2014; 194:67-75. [PMID: 25261606 PMCID: PMC7114485 DOI: 10.1016/j.virusres.2014.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last 13 years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV).
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Affiliation(s)
- Fernando Almazán
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Silvia Marquez-Jurado
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Lucia Morales
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Martina Becares
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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Almazán F, Sola I, Zuñiga S, Marquez-Jurado S, Morales L, Becares M, Enjuanes L. Coronavirus reverse genetic systems: infectious clones and replicons. Virus Res 2014; 189:262-70. [PMID: 24930446 PMCID: PMC4727449 DOI: 10.1016/j.virusres.2014.05.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 01/09/2023]
Abstract
Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last 13 years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV).
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Affiliation(s)
- Fernando Almazán
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Silvia Marquez-Jurado
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Lucia Morales
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Martina Becares
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, C/ Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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Cotugno R, Basile A, Romano E, Gallotta D, Belisario MA. BAG3 down-modulation sensitizes HPV18(+) HeLa cells to PEITC-induced apoptosis and restores p53. Cancer Lett 2014; 354:263-71. [PMID: 25175321 PMCID: PMC7116956 DOI: 10.1016/j.canlet.2014.08.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/28/2014] [Accepted: 08/18/2014] [Indexed: 12/19/2022]
Abstract
BAG3 down-modulation by siRNA technology restored p53. Reduced BAG3 expression sensitized HeLa but not C33A (HPV-negative) cells to PEITC. Reduced BAG3 expression was associated with a decrease of E6 viral protein levels.
BAG3 is a multi-functional component of tumor cell pro-survival machinery, and its biological functions have been largely associated to proteasome system. Here, we show that BAG3 down-modulation resulted in reduced cell viability and enhanced PEITC-induced apoptosis largely more extensively in HeLa (HPV18+) rather than in C33A (HPV−) cervical carcinoma cell lines. Moreover, we demonstrate that BAG3 suppression led to a decrease of viral E6 oncoprotein and a concomitant recovery of p53 tumor suppressor, the best recognized target of E6 for proteasome degradation. E6 and p53 expression were modulated at protein level, since their respective mRNAs were unaffected. Taken together our findings reveal a novel role for BAG3 as host protein contributing to HPV18 E6-activated pro-survival strategies, and suggest a possible relevance of its expression levels in drug/radiotherapy-resistance of HPV18-bearing cervical carcinomas.
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Affiliation(s)
- Roberta Cotugno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II n.132, Fisciano, 84084, Salerno, Italy
| | - Anna Basile
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II n.132, Fisciano, 84084, Salerno, Italy
| | - Elena Romano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II n.132, Fisciano, 84084, Salerno, Italy
| | - Dario Gallotta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II n.132, Fisciano, 84084, Salerno, Italy
| | - Maria Antonietta Belisario
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II n.132, Fisciano, 84084, Salerno, Italy.
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Chen Y, Yang LN, Cheng L, Tu S, Guo SJ, Le HY, Xiong Q, Mo R, Li CY, Jeong JS, Jiang L, Blackshaw S, Bi LJ, Zhu H, Tao SC, Ge F. Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. Mol Cell Proteomics 2013; 12:2804-19. [PMID: 23824909 DOI: 10.1074/mcp.m112.025882] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bcl2-associated athanogene 3 (BAG3), a member of the BAG family of co-chaperones, plays a critical role in regulating apoptosis, development, cell motility, autophagy, and tumor metastasis and in mediating cell adaptive responses to stressful stimuli. BAG3 carries a BAG domain, a WW domain, and a proline-rich repeat (PXXP), all of which mediate binding to different partners. To elucidate BAG3's interaction network at the molecular level, we employed quantitative immunoprecipitation combined with knockdown and human proteome microarrays to comprehensively profile the BAG3 interactome in humans. We identified a total of 382 BAG3-interacting proteins with diverse functions, including transferase activity, nucleic acid binding, transcription factors, proteases, and chaperones, suggesting that BAG3 is a critical regulator of diverse cellular functions. In addition, we characterized interactions between BAG3 and some of its newly identified partners in greater detail. In particular, bioinformatic analysis revealed that the BAG3 interactome is strongly enriched in proteins functioning within the proteasome-ubiquitination process and that compose the proteasome complex itself, suggesting that a critical biological function of BAG3 is associated with the proteasome. Functional studies demonstrated that BAG3 indeed interacts with the proteasome and modulates its activity, sustaining cell survival and underlying resistance to therapy through the down-modulation of apoptosis. Taken as a whole, this study expands our knowledge of the BAG3 interactome, provides a valuable resource for understanding how BAG3 affects different cellular functions, and demonstrates that biologically relevant data can be harvested using this kind of integrated approach.
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Affiliation(s)
- Ying Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
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Arpaci T, Ugurluer G, Akbas T, Arpaci RB, Serin M. Imaging of the skeletal muscle metastases. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2013. [PMID: 23280019 PMCID: PMC7163697 DOI: 10.1002/ddr.21049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Copyright 2011 Wiley-Liss, Inc., A Wiley CompanyThis article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency. Omics technologies include genomics, transcriptomics, proteomics, metabolomics, and immunomics. These technologies have been used in vaccine research, which can be summarized using the term “vaccinomics.” These omics technologies combined with advanced bioinformatics analysis form the core of “systems vaccinology.” Omics technologies provide powerful methods in vaccine target identification. The genomics‐based reverse vaccinology starts with predicting vaccine protein candidates through in silico bioinformatics analysis of genome sequences. The VIOLIN Vaxign vaccine design program (http://www.violinet.org/vaxign) is the first web‐based vaccine target prediction software based on the reverse vaccinology strategy. Systematic transcriptomics and proteomics analyses facilitate rational vaccine target identification by detesting genome‐wide gene expression profiles. Immunomics is the study of the set of antigens recognized by host immune systems and has also been used for efficient vaccine target prediction. With the large amount of omics data available, it is necessary to integrate various vaccine data using ontologies, including the Gene Ontology (GO) and Vaccine Ontology (VO), for more efficient vaccine target prediction and assessment. All these omics technologies combined with advanced bioinformatics analysis methods for a systems biology‐based vaccine target prediction strategy. This article reviews the various omics technologies and how they can be used in vaccine target identification.
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Affiliation(s)
- T Arpaci
- Department of Radiology, Acibadem Adana Hospital, Adana, Turkey.
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Zhang LK, Chai F, Li HY, Xiao G, Guo L. Identification of host proteins involved in Japanese encephalitis virus infection by quantitative proteomics analysis. J Proteome Res 2013; 12:2666-78. [PMID: 23647205 DOI: 10.1021/pr400011k] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Japanese encephalitis virus (JEV) enters host cells via receptor-mediated endocytosis and replicates in the cytoplasm of infected cells. To study virus-host cell interactions, we performed a SILAC-based quantitative proteomics study of JEV-infected HeLa cells using a subcellular fractionation strategy. We identified 158 host proteins as differentially regulated by JEV (defined as exhibiting a greater than 1.5-fold change in protein abundance upon JEV infection). The mass spectrometry quantitation data for selected proteins were validated by Western blot and immunofluorescence confocal microscopy. Bioinformatics analyses were used to generate JEV-regulated host response networks consisting of regulated proteins, which included 35 proteins that were newly added based on the results of this study. The JEV infection-induced host response was found to be coordinated primarily through the immune response process, the ubiquitin-proteasome system (UPS), the intracellular membrane system, and lipid metabolism-related proteins. Protein functional studies of selected host proteins using RNA interference-based techniques were carried out in HeLa cells infected with an attenuated or a highly virulent strain of JEV. We demonstrated that the knockdown of interferon-induced transmembrane protein 3 (IFITM3), Ran-binding protein 2 (RANBP2), sterile alpha motif domain-containing protein 9 (SAMD9) and vesicle-associated membrane protein 8 (VAMP8) significantly increased JEV replication. The results presented here not only promote a better understanding of the host response to JEV infection but also highlight multiple potential targets for the development of antiviral agents.
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Affiliation(s)
- Lei-Ke Zhang
- State Key Laboratory of Virology, Wuhan University, Wuhan, China
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28
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Cellular chaperonin CCTγ contributes to rabies virus replication during infection. J Virol 2013; 87:7608-21. [PMID: 23637400 DOI: 10.1128/jvi.03186-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Rabies, as the oldest known infectious disease, remains a serious threat to public health worldwide. The eukaryotic cytosolic chaperonin TRiC/CCT complex facilitates the folding of proteins through ATP hydrolysis. Here, we investigated the expression, cellular localization, and function of neuronal CCTγ during neurotropic rabies virus (RABV) infection using mouse N2a cells as a model. Following RABV infection, 24 altered proteins were identified by using two-dimensional electrophoresis and mass spectrometry, including 20 upregulated proteins and 4 downregulated proteins. In mouse N2a cells infected with RABV or cotransfected with RABV genes encoding nucleoprotein (N) and phosphoprotein (P), confocal microscopy demonstrated that upregulated cellular CCTγ was colocalized with viral proteins N and P, which formed a hollow cricoid inclusion within the region around the nucleus. These inclusions, which correspond to Negri bodies (NBs), did not form in mouse N2a cells only expressing the viral protein N or P. Knockdown of CCTγ by lentivirus-mediated RNA interference led to significant inhibition of RABV replication. These results demonstrate that the complex consisting of viral proteins N and P recruits CCTγ to NBs and identify the chaperonin CCTγ as a host factor that facilitates intracellular RABV replication. This work illustrates how viruses can utilize cellular chaperonins and compartmentalization for their own benefit.
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Global secretome characterization of herpes simplex virus 1-infected human primary macrophages. J Virol 2012; 86:12770-8. [PMID: 22973042 DOI: 10.1128/jvi.01545-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) is a common pathogen infecting the majority of people worldwide at some stage in their lives. The early host response to viral infection is initiated by the cells of the innate immune response, including macrophages. Here, we have characterized the secretome of HSV-1-infected human primary macrophages using high-throughput quantitative proteomics. We identified and quantified 516 distinct human proteins with high confidence from the macrophage secretome upon HSV-1 infection, and the secretion of 411 proteins was >2-fold increased upon beta interferon (IFN-β) priming and/or HSV-1 infection. Bioinformatics analysis of the secretome data revealed that most of the secreted proteins were intracellular, and almost 80% of the proteins whose secretion increased more than 2-fold were known exosomal proteins. This strongly suggests that nonclassical, vesicle-mediated protein secretion is activated in IFN-β-primed and HSV-1-infected macrophages. Proteins related to immune and inflammatory responses, interferon-induced proteins, and endogenous danger signal proteins were efficiently secreted upon IFN-β priming and HSV-1 infection. The secreted IFN-induced proteins include interferon-induced tetratricopeptide protein 2 (IFIT2), IFIT3, signal transducer and activator of transcription 1 (STAT1), and myxovirus resistance protein A (MxA), implicating that these proteins also have important extracellular antiviral functions. Proinflammatory cytokine interleukin-1β was not released by HSV-1-infected macrophages, demonstrating that HSV-1 can antagonize inflammasome function. In conclusion, our results provide a global view of the secretome of HSV-1-infected macrophages, revealing host factors possibly having a role in antiviral defense.
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The interactome of the human respiratory syncytial virus NS1 protein highlights multiple effects on host cell biology. J Virol 2012; 86:7777-89. [PMID: 22593156 DOI: 10.1128/jvi.00460-12] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Viral proteins can have multiple effects on host cell biology. Human respiratory syncytial virus (HRSV) nonstructural protein 1 (NS1) is a good example of this. During the virus life cycle, NS1 can act as an antagonist of host type I and III interferon production and signaling, inhibit apoptosis, suppress dendritic cell maturation, control protein stability, and regulate transcription of host cell mRNAs, among other functions. It is likely that NS1 performs these different roles through interactions with multiple host cell proteins. To investigate this and identify cellular proteins that could interact with NS1, we used quantitative proteomics in combination with green fluorescent protein (GFP)-trap immunoprecipitation and bioinformatic analysis. This analysis identified 221 proteins that were potentially part of complexes that could interact with NS1, with many of these associated with transcriptional regulation as part of the mediator complex, cell cycle regulation, and other functions previously assigned to NS1. Specific immunoprecipitation using the GFP trap was used to confirm the ability of selected cellular proteins to interact individually with NS1. Infection of A549 cells with recombinant viruses deficient in the expression of NS1 and overexpression analysis both demonstrated that NS1 was necessary and sufficient for the enrichment of cells in the G(1) phase of the cell cycle.
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Cao Z, Han Z, Shao Y, Liu X, Sun J, Yu D, Kong X, Liu S. Proteomics analysis of differentially expressed proteins in chicken trachea and kidney after infection with the highly virulent and attenuated coronavirus infectious bronchitis virus in vivo. Proteome Sci 2012; 10:24. [PMID: 22463732 PMCID: PMC3342233 DOI: 10.1186/1477-5956-10-24] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/31/2012] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Infectious bronchitis virus (IBV) is first to be discovered coronavirus which is probably endemic in all regions with intensive impact on poultry production. In this study, we used two-dimensional gel electrophoresis (2-DE) and two-dimensional fluorescence difference gel electrophoresis (2-DIGE), coupled with matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS), to explore the global proteome profiles of trachea and kidney tissues from chicken at different stages infected in vivo with the highly virulent ck/CH/LDL/97I P5 strain of infectious bronchitis virus (IBV) and the embryo-passaged, attenuated ck/CH/LDL/97I P115 strain. RESULTS Fifty-eight differentially expressed proteins were identified. Results demonstrated that some proteins which had functions in cytoskeleton organization, anti-oxidative stress, and stress response, showed different change patterns in abundance from chicken infected with the highly virulent ck/CH/LDL/97I P5 strain and those given the embryo-passaged, attenuated P115 stain. In addition, the dynamic transcriptional alterations of 12 selected proteins were analyzed by the real-time RT-PCR, and western blot analysis confirmed the change in abundance of heat shock proteins (HSP) beta-1, annexin A2, and annexin A5. CONCLUSIONS The proteomic alterations described here may suggest that these changes to protein expression correlate with IBV virus' virulence in chicken, hence provides valuable insights into the interactions of IBV with its host and may also assist with investigations of the pathogenesis of IBV and other coronavirus infections.
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Affiliation(s)
- Zhongzan Cao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China.
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Carbajo-Lozoya J, Müller MA, Kallies S, Thiel V, Drosten C, von Brunn A. Replication of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E is inhibited by the drug FK506. Virus Res 2012; 165:112-7. [PMID: 22349148 PMCID: PMC7114512 DOI: 10.1016/j.virusres.2012.02.002] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 01/31/2012] [Accepted: 02/03/2012] [Indexed: 02/07/2023]
Abstract
Recent research has shown that Coronavirus (CoV) replication depends on active immunophilin pathways. Here we demonstrate that the drug FK506 (Tacrolimus) inhibited strongly the growth of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E at low, non-cytotoxic concentrations in cell culture. As shown by plaque titration, qPCR, Luciferase- and green fluorescent protein (GFP) reporter gene expression, replication was diminished by several orders of magnitude. Knockdown of the cellular FK506-binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth.
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Affiliation(s)
- Javier Carbajo-Lozoya
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstrasse 9a, 80336 München, Germany
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DeDiego ML, Nieto-Torres JL, Jiménez-Guardeño JM, Regla-Nava JA, Alvarez E, Oliveros JC, Zhao J, Fett C, Perlman S, Enjuanes L. Severe acute respiratory syndrome coronavirus envelope protein regulates cell stress response and apoptosis. PLoS Pathog 2011; 7:e1002315. [PMID: 22028656 PMCID: PMC3197621 DOI: 10.1371/journal.ppat.1002315] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 08/29/2011] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome virus (SARS-CoV) that lacks the envelope (E) gene (rSARS-CoV-ΔE) is attenuated in vivo. To identify factors that contribute to rSARS-CoV-ΔE attenuation, gene expression in cells infected by SARS-CoV with or without E gene was compared. Twenty-five stress response genes were preferentially upregulated during infection in the absence of the E gene. In addition, genes involved in signal transduction, transcription, cell metabolism, immunoregulation, inflammation, apoptosis and cell cycle and differentiation were differentially regulated in cells infected with rSARS-CoV with or without the E gene. Administration of E protein in trans reduced the stress response in cells infected with rSARS-CoV-ΔE or with respiratory syncytial virus, or treated with drugs, such as tunicamycin and thapsigargin that elicit cell stress by different mechanisms. In addition, SARS-CoV E protein down-regulated the signaling pathway inositol-requiring enzyme 1 (IRE-1) of the unfolded protein response, but not the PKR-like ER kinase (PERK) or activating transcription factor 6 (ATF-6) pathways, and reduced cell apoptosis. Overall, the activation of the IRE-1 pathway was not able to restore cell homeostasis, and apoptosis was induced probably as a measure to protect the host by limiting virus production and dissemination. The expression of proinflammatory cytokines was reduced in rSARS-CoV-ΔE-infected cells compared to rSARS-CoV-infected cells, suggesting that the increase in stress responses and the reduction of inflammation in the absence of the E gene contributed to the attenuation of rSARS-CoV-ΔE. To identify potential mechanisms mediating the in vivo attenuation of SARS-CoV lacking the E gene (rSARS-CoV-ΔE), the effect of the presence of the E gene on host gene expression was studied. In rSARS-CoV-ΔE-infected cells, the expression of at least 25 stress response genes was preferentially upregulated, compared to cells infected with rSARS-CoV. E protein supplied in trans reversed the increase in stress response genes observed in cells infected with rSARS-CoV-ΔE or with respiratory syncytial virus, and by treatment with drugs causing stress by different mechanisms. Furthermore, in the presence of the E protein a subset (IRE-1 pathway), but not two others (PERK and ATF-6), of the unfolded protein response was also reduced. Nevertheless, the activation of the unfolded protein response to control cell homeostasis was not sufficient to alleviate cell stress, and an increase in cell apoptosis in cells infected with the virus lacking E protein was observed. This apoptotic response was probably induced to protect the host by limiting virus production and dissemination. In cells infected with rSARS-CoV-ΔE, genes associated with the proinflammatory pathway were down-regulated compared to cells infected with virus expressing E protein, supporting the idea that a reduction in inflammation was also relevant in the attenuation of the virus deletion mutant.
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Affiliation(s)
- Marta L DeDiego
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
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Zheng J, Sugrue RJ, Tang K. Mass spectrometry based proteomic studies on viruses and hosts--a review. Anal Chim Acta 2011; 702:149-59. [PMID: 21839192 PMCID: PMC7094357 DOI: 10.1016/j.aca.2011.06.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 02/07/2023]
Abstract
In terms of proteomic research in the 21st century, the realm of virology is still regarded as an enormous challenge mainly brought by three aspects, namely, studying on the complex proteome of the virus with unexpected variations, developing more accurate analytical techniques as well as understanding viral pathogenesis and virus-host interaction dynamics. Progresses in these areas will be helpful to vaccine design and antiviral drugs discovery. Mass spectrometry based proteomics have shown exceptional display of capabilities, not only precisely identifying viral and cellular proteins that are functionally, structurally, and dynamically changed upon virus infection, but also enabling us to detect important pathway proteins. In addition, many isolation and purification techniques and quantitative strategies in conjunction with MS can significantly improve the sensitivity of mass spectrometry for detecting low-abundant proteins, replenishing the stock of virus proteome and enlarging the protein-protein interaction maps. Nevertheless, only a small proportion of the infectious viruses in both of animal and plant have been studied using this approach. As more virus and host genomes are being sequenced, MS-based proteomics is becoming an indispensable tool for virology. In this paper, we provide a brief review of the current technologies and their applications in studying selected viruses and hosts.
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Affiliation(s)
- Jie Zheng
- Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Richard J. Sugrue
- Division of Molecular and Cell Biology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kai Tang
- Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Uetrecht C, Heck AJR. Modern biomolecular mass spectrometry and its role in studying virus structure, dynamics, and assembly. Angew Chem Int Ed Engl 2011; 50:8248-62. [PMID: 21793131 PMCID: PMC7159578 DOI: 10.1002/anie.201008120] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 01/04/2023]
Abstract
Over a century since its development, the analytical technique of mass spectrometry is blooming more than ever, and applied in nearly all aspects of the natural and life sciences. In the last two decades mass spectrometry has also become amenable to the analysis of proteins and even intact protein complexes, and thus begun to make a significant impact in the field of structural biology. In this Review, we describe the emerging role of mass spectrometry, with its different technical facets, in structural biology, focusing especially on structural virology. We describe how mass spectrometry has evolved into a tool that can provide unique structural and functional information about viral-protein and protein-complex structure, conformation, assembly, and topology, extending to the direct analysis of intact virus capsids of several million Dalton in mass. Mass spectrometry is now used to address important questions in virology ranging from how viruses assemble to how they interact with their host.
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Affiliation(s)
- Charlotte Uetrecht
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
- Netherlands Proteomics Centre (The Netherlands)
- Present address: Molecular Biophysics, Uppsala University, Uppsala (Sweden)
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
- Netherlands Proteomics Centre (The Netherlands)
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Uetrecht C, Heck AJR. Moderne biomolekulare Massenspektrometrie und ihre Bedeutung für die Erforschung der Struktur, der Dynamik und des Aufbaus von Viren. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008120] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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de Wilde AH, Zevenhoven-Dobbe JC, van der Meer Y, Thiel V, Narayanan K, Makino S, Snijder EJ, van Hemert MJ. Cyclosporin A inhibits the replication of diverse coronaviruses. J Gen Virol 2011; 92:2542-2548. [PMID: 21752960 DOI: 10.1099/vir.0.034983-0] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Low micromolar, non-cytotoxic concentrations of cyclosporin A (CsA) strongly affected the replication of severe acute respiratory syndrome coronavirus (SARS-CoV), human coronavirus 229E and mouse hepatitis virus in cell culture, as was evident from the strong inhibition of GFP reporter gene expression and a reduction of up to 4 logs in progeny titres. Upon high-multiplicity infection, CsA treatment rendered SARS-CoV RNA and protein synthesis almost undetectable, suggesting an early block in replication. siRNA-mediated knockdown of the expression of the prominent CsA targets cyclophilin A and B did not affect SARS-CoV replication, suggesting either that these specific cyclophilin family members are dispensable or that the reduced expression levels suffice to support replication.
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Affiliation(s)
- Adriaan H de Wilde
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Jessika C Zevenhoven-Dobbe
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Yvonne van der Meer
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Volker Thiel
- Vetsuisse Faculty, University of Zürich, Zürich, Switzerland.,Institute of Immunobiology, Kantonal Hospital St Gallen, St Gallen, Switzerland
| | - Krishna Narayanan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Shinji Makino
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Martijn J van Hemert
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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Zhou S, Liu R, Zhao X, Huang C, Wei Y. Viral proteomics: the emerging cutting-edge of virus research. SCIENCE CHINA-LIFE SCIENCES 2011; 54:502-12. [PMID: 21706410 PMCID: PMC7089374 DOI: 10.1007/s11427-011-4177-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 12/03/2010] [Indexed: 11/21/2022]
Abstract
Viruses replicate and proliferate in host cells while continuously adjusting to and modulating the host environment. They encode a wide spectrum of multifunctional proteins, which interplay with and modify proteins in host cells. Viral genomes were chronologically the first to be sequenced. However, the corresponding viral proteomes, the alterations of host proteomes upon viral infection, and the dynamic nature of proteins, such as post-translational modifications, enzymatic cleavage, and activation or destruction by proteolysis, remain largely unknown. Emerging high-throughput techniques, in particular quantitative or semi-quantitative mass spectrometry-based proteomics analysis of viral and cellular proteomes, have been applied to define viruses and their interactions with their hosts. Here, we review the major areas of viral proteomics, including virion proteomics, structural proteomics, viral protein interactomics, and changes to the host cell proteome upon viral infection.
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Affiliation(s)
- ShengTao Zhou
- Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, China
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Bagnoli F, Baudner B, Mishra RPN, Bartolini E, Fiaschi L, Mariotti P, Nardi-Dei V, Boucher P, Rappuoli R. Designing the next generation of vaccines for global public health. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:545-66. [PMID: 21682594 DOI: 10.1089/omi.2010.0127] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Vaccine research and development are experiencing a renaissance of interest from the global scientific community. There are four major reasons for this: (1) the lack of efficacious treatment for many devastating infections; (2) the emergence of multidrug resistant bacteria; (3) the need for improving the safety of the more traditional licensed vaccines; and finally, (4) the great promise for innovative vaccine design and research with convergence of omics sciences, such as genomics, proteomics, immunomics, and vaccinology. Our first project based on omics was initiated in 2000 and was termed reverse vaccinology. At that time, antigen identification was mainly based on bioinformatic analysis of a singular genome. Since then, omics-guided approaches have been applied to its full potential in several proof-of-concept studies in the industry, with the first reverse vaccinology-derived vaccine now in late stage clinical trials and several vaccines developed by omics in preclinical studies. In the meantime, vaccine discovery and development has been further improved with the support of proteomics, functional genomics, comparative genomics, structural biology, and most recently vaccinomics. We illustrate in this review how omics biotechnologies and integrative biology are expected to accelerate the identification of vaccine candidates against difficult pathogens for which traditional vaccine development has thus far been failing, and how research will provide safer vaccines and improved formulations for immunocompromised patients in the near future. Finally, we present a discussion to situate omics-guided rational vaccine design in the broader context of global public health and how it can benefit citizens in both developed and developing countries.
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Abstract
Bcl2-associated athanogene 3 (BAG3) protein is a member of BAG family of co-chaperones that interacts with the ATPase domain of the heat shock protein (Hsp) 70 through BAG domain (110–124 amino acids). BAG3 is the only member of the family to be induced by stressful stimuli, mainly through the activity of heat shock factor 1 on bag3 gene promoter. In addition to the BAG domain, BAG3 contains also a WW domain and a proline-rich (PXXP) repeat, that mediate binding to partners different from Hsp70. These multifaceted interactions underlie BAG3 ability to modulate major biological processes, that is, apoptosis, development, cytoskeleton organization and autophagy, thereby mediating cell adaptive responses to stressful stimuli. In normal cells, BAG3 is constitutively present in a very few cell types, including cardiomyocytes and skeletal muscle cells, in which the protein appears to contribute to cell resistance to mechanical stress. A growing body of evidence indicate that BAG3 is instead expressed in several tumor types. In different tumor contexts, BAG3 protein was reported to sustain cell survival, resistance to therapy, and/or motility and metastatization. In some tumor types, down-modulation of BAG3 levels was shown, as a proof-of-principle, to inhibit neoplastic cell growth in animal models. This review attempts to outline the emerging mechanisms that can underlie some of the biological activities of the protein, focusing on implications in tumor progression.
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Sola I, Mateos-Gomez PA, Almazan F, Zuñiga S, Enjuanes L. RNA-RNA and RNA-protein interactions in coronavirus replication and transcription. RNA Biol 2011; 8:237-48. [PMID: 21378501 PMCID: PMC3230552 DOI: 10.4161/rna.8.2.14991] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/17/2011] [Accepted: 01/19/2011] [Indexed: 02/07/2023] Open
Abstract
Coronavirus (CoV) RNA synthesis includes the replication of the viral genome, and the transcription of sgRNAs by a discontinuous mechanism. Both processes are regulated by RNA sequences such as the 5' and 3' untranslated regions (UTRs), and the transcription regulating sequences (TRSs) of the leader (TRS-L) and those preceding each gene (TRS-Bs). These distant RNA regulatory sequences interact with each other directly and probably through protein-RNA and protein-protein interactions involving viral and cellular proteins. By analogy to other plus-stranded RNA viruses, such as polioviruses, in which translation and replication switch involves a cellular factor (PCBP) and a viral protein (3CD) it is conceivable that in CoVs the switch between replication and transcription is also associated with the binding of proteins that are specifically recruited by the replication or transcription complexes. Complexes between RNA motifs such as TRS-L and the TRS-Bs located along the CoV genome are probably formed previously to the transcription start, and most likely promote template-switch of the nascent minus RNA to the TRS-L region. Many cellular proteins interacting with regulatory CoV RNA sequences are members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family of RNA-binding proteins, involved in mRNA processing and transport, which shuttle between the nucleus and the cytoplasm. In the context of CoV RNA synthesis, these cellular ribonucleoproteins might also participate in RNA-protein complexes to bring into physical proximity TRS-L and distant TRS-B, as proposed for CoV discontinuous transcription. In this review, we summarize RNA-RNA and RNA-protein interactions that represent modest examples of complex quaternary RNA-protein structures required for the fine-tuning of virus replication. Design of chemically defined replication and transcription systems will help to clarify the nature and activity of these structures.
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Affiliation(s)
- Isabel Sola
- Department of Molecular and Cell Biology, CNB, CSIC, Cantoblanco, Madrid, Spain
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Ge F, Bi LJ, Tao SC, Xu XD, Zhang ZP, Kitazato K, Zhang XE. Proteomic analysis of multiple myeloma: Current status and future perspectives. Proteomics Clin Appl 2011; 5:30-7. [DOI: 10.1002/prca.201000044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Gout E, Gutkowska M, Takayama S, Reed JC, Chroboczek J. Co-chaperone BAG3 and adenovirus penton base protein partnership. J Cell Biochem 2011; 111:699-708. [PMID: 20607728 PMCID: PMC7166384 DOI: 10.1002/jcb.22756] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The BAG family of Hsp70/Hsc70 co‐chaperones is characterised by the presence of a conserved BAG domain at the carboxyl‐terminus. BAG3 protein is the only member of this family containing also the N‐terminally located WW domain. We describe here the identification of adenovirus (Ad) penton base protein as the first BAG3 partner recognising BAG3 WW domain. Ad penton base is the viral capsid constituent responsible for virus internalisation. It contains in the N‐terminal part two conserved PPxY motifs, known ligands of WW domains. In cells producing Ad penton base protein, cytoplasmic endogenous BAG3 interacts with it and co‐migrates to the nucleus. Preincubation of BAG3 with Ad base protein results in only slight modulation of BAG3 co‐chaperone activity, suggesting that this interaction is not related to the classical BAG3 co‐chaperone function. However, depletion of BAG3 impairs the cell entry of the virus and viral progeny production in Ad‐infected cells, suggesting that the interaction between virus penton base protein and cellular co‐chaperone BAG3 positively influences virus life cycle. These results thus demonstrate a novel host–pathogen interaction, which contributes to the successful infectious life cycle of adenoviruses. In addition, these data enrich our knowledge about the multifunctionality of the BAG3 co‐chaperone. J. Cell. Biochem. 111: 699–708, 2010. © 2010 Wiley‐Liss, Inc.
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Affiliation(s)
- E Gout
- Institut de Biologie Structurale, 41 rue Jules Horowitz, CEA, CNRS, Université Joseph Fourier, 38027 Grenoble, France
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Vogels MW, van Balkom BWM, Kaloyanova DV, Batenburg JJ, Heck AJ, Helms JB, Rottier PJM, de Haan CAM. Identification of host factors involved in coronavirus replication by quantitative proteomics analysis. Proteomics 2010; 11:64-80. [PMID: 21182195 PMCID: PMC7167679 DOI: 10.1002/pmic.201000309] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 09/15/2010] [Accepted: 09/27/2010] [Indexed: 12/24/2022]
Abstract
In this study, we applied a quantitative proteomic approach, based on SILAC, to investigate the interactions of coronaviruses with the secretory pathway of the host cell, with the aim to identify host factors involved in coronavirus replication. Comparison of the protein profiles of Golgi‐enriched fractions of cells that were either mock infected or infected with mouse hepatitis virus revealed the significant depletion or enrichment of 116 proteins. Although ribosomal/nucleic acid binding proteins were enriched in the Golgi‐fractions of mouse hepatitis virus‐infected cells, proteins annotated to localize to several organelles of the secretory pathway were overrepresented among the proteins that were depleted from these fractions upon infection. We hypothesized that proteins, of which the abundance or distribution is affected by infection, are likely to be involved in the virus life cycle. Indeed, depletion of a small subset of the affected proteins by using small interfering RNAs identified several host factors involved in coronavirus infection. Transfection of small interfering RNAs targeting either C11orf59 or Golgi apparatus glycoprotein 1 resulted in increased virus replication, whereas depletion of vesicle‐trafficking protein vesicle‐trafficking protein sec22b enhanced the release of infectious progeny virus. Overexpression of these proteins, on the other hand, had a negative effect on virus replication. Overall, our study shows that the SILAC approach is a suitable tool to study host–pathogen interactions and to identify host proteins involved in virus replication.
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Affiliation(s)
- Mijke W Vogels
- Department of Biochemistry and Cell Biology, Biochemistry Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Ge F, Zhang L, Tao SC, Kitazato K, Zhang ZP, Zhang XE, Bi LJ. Quantitative Proteomic Analysis of Tumor Reversion in Multiple Myeloma Cells. J Proteome Res 2010; 10:845-55. [DOI: 10.1021/pr100992e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Feng Ge
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Division of Research, Singapore Health Research Facilities, Singapore 169611, Republic of Singapore, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China, Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki City, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of
| | - Liang Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Division of Research, Singapore Health Research Facilities, Singapore 169611, Republic of Singapore, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China, Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki City, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of
| | - Sheng-Ce Tao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Division of Research, Singapore Health Research Facilities, Singapore 169611, Republic of Singapore, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China, Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki City, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of
| | - Kaio Kitazato
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Division of Research, Singapore Health Research Facilities, Singapore 169611, Republic of Singapore, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China, Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki City, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of
| | - Zhi-Ping Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Division of Research, Singapore Health Research Facilities, Singapore 169611, Republic of Singapore, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China, Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki City, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of
| | - Xian-En Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Division of Research, Singapore Health Research Facilities, Singapore 169611, Republic of Singapore, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China, Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki City, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of
| | - Li-Jun Bi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Division of Research, Singapore Health Research Facilities, Singapore 169611, Republic of Singapore, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China, Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki City, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of
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Ge F, Li WL, Bi LJ, Tao SC, Zhang ZP, Zhang XE. Identification of novel 14-3-3ζ interacting proteins by quantitative immunoprecipitation combined with knockdown (QUICK). J Proteome Res 2010; 9:5848-58. [PMID: 20879785 DOI: 10.1021/pr100616g] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The family of 14-3-3 proteins has emerged as critical regulators of diverse cellular responses under both physiological and pathological conditions. To gain insight into the molecular action of 14-3-3ζ in multiple myeloma (MM), we performed a systematic proteomic analysis of 14-3-3ζ-associated proteins. This analysis, recently developed by Matthias Mann, termed quantitative immunoprecipitation combined with knockdown (QUICK), integrates RNAi, SILAC, immunoprecipitation, and quantitative MS technologies. Quantitative mass spectrometry analysis allowed us to distinguish 14-3-3ζ-interacting proteins from background proteins, resulting in the identification of 292 proteins in total with 95 novel interactions. Three 14-3-3ζ-interacting proteins-BAX, HSP70, and BAG3-were further confirmed by reciprocal coimmunoprecipitations and colocalization analysis. Our results therefore not only uncover a large number of novel 14-3-3ζ-associated proteins that possess a variety of cellular functions, but also provide new research directions for the study of the functions of 14-3-3ζ. This study also demonstrated that QUICK is a useful approach to detect specific protein-protein interactions with very high confidence and may have a wide range of applications in the investigation of protein complex interaction networks.
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Affiliation(s)
- Feng Ge
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.
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Ge F, Xiao CL, Bi LJ, Tao SC, Xiong S, Yin XF, Li LP, Lu CH, Jia HT, He QY. Quantitative phosphoproteomics of proteasome inhibition in multiple myeloma cells. PLoS One 2010; 5. [PMID: 20927383 PMCID: PMC2947515 DOI: 10.1371/journal.pone.0013095] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 09/06/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The proteasome inhibitor bortezomib represents an important advance in the treatment of multiple myeloma (MM). Bortezomib inhibits the activity of the 26S proteasome and induces cell death in a variety of tumor cells; however, the mechanism of cytotoxicity is not well understood. METHODOLOGY/PRINCIPAL FINDINGS We investigated the differential phosphoproteome upon proteasome inhibition by using stable isotope labeling by amino acids in cell culture (SILAC) in combination with phosphoprotein enrichment and LC-MS/MS analysis. In total 233 phosphoproteins were identified and 72 phosphoproteins showed a 1.5-fold or greater change upon bortezomib treatment. The phosphoproteins with expression alterations encompass all major protein classes, including a large number of nucleic acid binding proteins. Site-specific phosphopeptide quantitation revealed that Ser38 phosphorylation on stathmin increased upon bortezomib treatment, suggesting new mechanisms associated to bortezomib-induced apoptosis in MM cells. Further studies demonstrated that stathmin phosphorylation profile was modified in response to bortezomib treatment and the regulation of stathmin by phosphorylation at specific Ser/Thr residues participated in the cellular response induced by bortezomib. CONCLUSIONS/SIGNIFICANCE Our systematic profiling of phosphorylation changes in response to bortezomib treatment not only advanced the global mechanistic understanding of the action of bortezomib on myeloma cells but also identified previously uncharacterized signaling proteins in myeloma cells.
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Affiliation(s)
- Feng Ge
- Institute of Life and Health Engineering and National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chuan-Le Xiao
- Institute of Life and Health Engineering and National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
| | - Li-Jun Bi
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Sheng Xiong
- Institute of Life and Health Engineering and National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
| | - Xin-Feng Yin
- Institute of Life and Health Engineering and National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
| | - Li-Ping Li
- Institute of Life and Health Engineering and National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
| | - Chun-Hua Lu
- Institute of Life and Health Engineering and National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
| | - Hai-Tao Jia
- Institute of Life and Health Engineering and National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Institute of Life and Health Engineering and National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
- * E-mail:
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