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Zeng J, Cao D, Yang S, Jaijyan DK, Liu X, Wu S, Cruz-Cosme R, Tang Q, Zhu H. Insights into the Transcriptome of Human Cytomegalovirus: A Comprehensive Review. Viruses 2023; 15:1703. [PMID: 37632045 PMCID: PMC10458407 DOI: 10.3390/v15081703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a widespread pathogen that poses significant risks to immunocompromised individuals. Its genome spans over 230 kbp and potentially encodes over 200 open-reading frames. The HCMV transcriptome consists of various types of RNAs, including messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), with emerging insights into their biological functions. HCMV mRNAs are involved in crucial viral processes, such as viral replication, transcription, and translation regulation, as well as immune modulation and other effects on host cells. Additionally, four lncRNAs (RNA1.2, RNA2.7, RNA4.9, and RNA5.0) have been identified in HCMV, which play important roles in lytic replication like bypassing acute antiviral responses, promoting cell movement and viral spread, and maintaining HCMV latency. CircRNAs have gained attention for their important and diverse biological functions, including association with different diseases, acting as microRNA sponges, regulating parental gene expression, and serving as translation templates. Remarkably, HCMV encodes miRNAs which play critical roles in silencing human genes and other functions. This review gives an overview of human cytomegalovirus and current research on the HCMV transcriptome during lytic and latent infection.
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Affiliation(s)
- Janine Zeng
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Di Cao
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Shaomin Yang
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Xiaolian Liu
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Songbin Wu
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Ruth Cruz-Cosme
- Department of Microbiology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059, USA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
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Ueda K, Suwanmanee Y. ATP5B Is an Essential Factor for Hepatitis B Virus Entry. Int J Mol Sci 2022; 23:ijms23179570. [PMID: 36076968 PMCID: PMC9455612 DOI: 10.3390/ijms23179570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Elucidation of the factors responsible for hepatitis B virus (HBV) is extremely important in order to understand the viral life cycle and pathogenesis, and thereby explore potential anti-HBV drugs. The recent determination that sodium taurocholate co-transporting peptide (NTCP) is an essential molecule for the HBV entry into cells led to the development of an HBV infection system in vitro using a human hepatocellular carcinoma (HCC) cell line expressing NTCP; however, the precise mechanism of HBV entry is still largely unknown, and thus it may be necessary to elucidate all the molecules involved. Here, we identified ATP5B as another essential factor for HBV entry. ATP5B was expressed on the cell surface of the HCC cell lines and bound with myristoylated but not with non-myristoylated preS1 2-47, which supported the notion that ATP5B is involved in the HBV entry process. Knockdown of ATP5B in NTCP-expressing HepG2 cells, which allowed HBV infection, reduced HBV infectivity with less cccDNA formation. Taken together, these results strongly suggested that ATP5B is an essential factor for HBV entry into the cells.
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ATP1B3 Restricts Hepatitis B Virus Replication Via Reducing the Expression of the Envelope Proteins. Virol Sin 2021; 36:678-691. [PMID: 33534085 PMCID: PMC7856454 DOI: 10.1007/s12250-021-00346-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022] Open
Abstract
Our recent study reported that ATP1B3 inhibits hepatitis B virus (HBV) replication via inducing NF-κB activation. However, ATP1B3 mutants which were defective in NF-κB activation still maintained the moderate degree of suppression on HBV replication, suggesting that another uncharacterized mechanism is also responsible for ATP1B3-mediated HBV suppression. Here, we demonstrated that ATP1B3 reduced the expression of HBV envelope proteins LHBs, MHBs and SHBs, but had no effect on intracellular HBV DNA, RNA levels as well as HBV promoter activities. Further investigation showed that proteasome inhibitor MG132 rescued ATP1B3-mediated envelope proteins degradation, demonstrating that proteasome-dependent pathway is involved in ATP1B3-induced degradation of envelope proteins. Co-IP showed that ATP1B3 interacts with LHBs and MHBs and induces LHBs and MHBs polyubiquitination. Immunofluorescence co-localization analysis confirmed LHBs and MHBs colocalized with ATP1B3 together. Our work provides important information for targeting ATP1B3 as a potential therapeutic molecule for HBV infection.
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Zheng B, Zhang J, Zheng T, Wang H, Li Z, Huan C, Ning S, Wang Y, Zhang W. ATP1B3 cooperates with BST-2 to promote hepatitis B virus restriction. J Med Virol 2019; 92:201-209. [PMID: 31556466 PMCID: PMC7159099 DOI: 10.1002/jmv.25599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022]
Abstract
Increasing evidence indicates ATP1B3, one of the regulatory subunits of Na+ /K+ -ATPase, is involved in numerous viral propagations, such as HIV and EV71. However, the function and mechanism of ATP1B3 on hepatitis B virus (HBV) propagation is unknown. Here, we demonstrated that ATP1B3 overexpression reduced the quantity of hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg) in supernatants of HBV expression plasmids cotransfected HepG2 cells. Correspondingly, small interfering RNA and short hairpin RNA mediated ATP1B3 silencing promoted HBsAg and HBeAg expression in the supernatants of HBV expression plasmids transfected HepG2 cells. Mechanically, we reported that ATP1B3 expression could activate nuclear factor-κB (NF-κB) pathway by inducing the expression, phosphorylation, and nuclear import of P65 for the first time. And NF-κB inhibitor (Bay11) impaired the restraint of ATP1B3 on HBV replication. This counteraction effect of Bay11 proved that ATP1B3-induced NF-κB activation was crucial for HBV restriction. Accordingly, we observed that anti-HBV factors interferon-α (IFN-α) and interleukin-6 (IL-6) production were increased in HepG2 cells after the NF-κB activation. It suggested that ATP1B3 suppressed HBsAg and HBeAg by NF-κB/IFN-α and NF-κB/IL-6 axis. Further experiments proved that ATP1B3 overexpression induced anti-HBV factor BST-2 expression by NF-κB/IFN-α axis in HepG2 cells but not HEK293T cells, and ATP1B3 silencing downregulated BST-2 messenger RNA level in HepG2 cells. As an HBV restriction factor, BST-2 cooperated with ATP1B3 to antagonize HBsAg but not HBeAg in HepG2 cells. Our work identified ATP1B3 as a novel candidate of HBV restrictor with unrevealed mechanism and we highlighted it might serve as a potential therapeutic molecule for HBV infection.
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Affiliation(s)
- Baisong Zheng
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jun Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Tianhang Zheng
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Hong Wang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhaolong Li
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Chen Huan
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Shanshan Ning
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yingchao Wang
- Hepatobiliary Pancreatic Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
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Lu Y, Hou H, Wang F, Qiao L, Wang X, Yu J, Liu W, Sun Z. ATP1B3: a virus-induced host factor against EV71 replication by up-regulating the production of type-I interferons. Virology 2016; 496:28-34. [PMID: 27240146 PMCID: PMC7127048 DOI: 10.1016/j.virol.2016.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/15/2016] [Accepted: 05/17/2016] [Indexed: 12/24/2022]
Abstract
Enterovirus 71 (EV71) infection can cause severe diseases, and is becoming increasingly common in children. In the current study, we carried out yeast two-hybrid assays to screen human proteins that could interact with 3A protein of EV71. Human β3 subunit of Na+/K+-ATPase (ATP1B3) protein was demonstrated to interact with the 3A protein of EV71. Although 3A protein had no effect on the expression of ATP1B3, EV71 infection resulted in elevated expression of ATP1B3 in RD cell line, both on messenger RNA (mRNA) and protein levels. Interestingly, knockdown of ATP1B3 could significantly increase the replication of EV71, whereas overexpression of ATP1B3 significantly suppressed the replication of EV71 in RD cells. Furthermore, we demonstrated that the expression of ATP1B3 could induce the production of type-I interferons. Our study demonstrated that ATP1B3 inhibit EV71 replication by enhancing the production of type-I interferons, which could act as a potential therapeutic target in EV71 infection. Human ATP1B3 protein was demonstrated to interact with EV71 3A protein. We found ATP1B3 can induce the production of type-I IFNs during EV71 infection. ATP1B3 can inhibit EV71 replication by up-regulating the production of type-I interferons.
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Affiliation(s)
- Yanfang Lu
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hongyan Hou
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Feng Wang
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Long Qiao
- Cancer Biology Research Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiong Wang
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Yu
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weiyong Liu
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Ziyong Sun
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, Wang ECY, Aicheler R, Murrell I, Wilkinson GWG, Lehner PJ, Gygi SP. Quantitative temporal viromics: an approach to investigate host-pathogen interaction. Cell 2014; 157:1460-1472. [PMID: 24906157 PMCID: PMC4048463 DOI: 10.1016/j.cell.2014.04.028] [Citation(s) in RCA: 316] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/18/2014] [Accepted: 04/03/2014] [Indexed: 12/11/2022]
Abstract
A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model. PaperClip
>8,000 proteins quantified over eight time points, including 1,200 cell-surface proteins Temporal profiles of 139/171 canonical HCMV proteins and 14 noncanonical HCMV ORFs Multiple families of cell-surface receptors selectively modulated by HCMV Multiple signaling pathways modulated during HCMV infection
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Affiliation(s)
- Michael P Weekes
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.
| | - Peter Tomasec
- School of Medicine, Cardiff University, Tenovus Building, Heath Park, Cardiff CF14 4XX, UK
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Ceri A Fielding
- School of Medicine, Cardiff University, Tenovus Building, Heath Park, Cardiff CF14 4XX, UK
| | - David Nusinow
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Richard J Stanton
- School of Medicine, Cardiff University, Tenovus Building, Heath Park, Cardiff CF14 4XX, UK
| | - Eddie C Y Wang
- School of Medicine, Cardiff University, Tenovus Building, Heath Park, Cardiff CF14 4XX, UK
| | - Rebecca Aicheler
- School of Medicine, Cardiff University, Tenovus Building, Heath Park, Cardiff CF14 4XX, UK
| | - Isa Murrell
- School of Medicine, Cardiff University, Tenovus Building, Heath Park, Cardiff CF14 4XX, UK
| | - Gavin W G Wilkinson
- School of Medicine, Cardiff University, Tenovus Building, Heath Park, Cardiff CF14 4XX, UK
| | - Paul J Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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Hu C, Chen J, Ye L, Chen R, Zhang L, Xue X. Codon usage bias in human cytomegalovirus and its biological implication. Gene 2014; 545:5-14. [PMID: 24814188 DOI: 10.1016/j.gene.2014.05.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 05/02/2014] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
Abstract
Human cytomegalovirus (HCMV) infection, a worldwide contagion, causes a serious disorder in infected individuals. Analysis of codon usage can reveal much molecular information about this virus. The effective number of codon (ENC) values, relative synonymous codon usage (RSCU) values, codon adaptation index (CAI), and nucleotide contents was investigated in approximately 160 coding sequences (CDS) among 17 human cytomegalovirus genomes using the software CodonW. Linear regression analysis and logistic regression were performed to explore the preliminary data. The results showed that, overall, HCMV genomes had low codon usage bias (mean ENC=47.619). However, the ENC of individual CDS varied widely and was distributed unevenly between host-related genes and viral-self-function genes (P=0.002, odds ratio (OR)=3.194), as did the GC content (P=0.016, OR=2.178). The ENC values correlated with CAI, GC content, and the nucleotide composing at the 3rd codon position (GC3s) (P<0.001). There was a significant variation in the codon preference that depended on the RSCU data. The predicted ENC curve suggested that mutational pressure, rather than natural selection, was one of the main factors that determined the codon usage bias in HCMV. Among 123 genes with known function, the genes related to viral self-replication and viral-host interaction showed different ENC and CAI values, and GC and GC3s contents. In conclusion, the detailed codon usage bias theoretically revealed information concerning HCMV evolution and could be a valuable additional parameter for HCMV gene function research.
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Affiliation(s)
- Changyuan Hu
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China
| | - Jing Chen
- Department of Rheumatism and Immunology, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China
| | - Lulu Ye
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China
| | - Renpin Chen
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China
| | - Lifang Zhang
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China.
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