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Saçar Demirci MD, Adan A. Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection. PeerJ 2020; 8:e9369. [PMID: 32547891 PMCID: PMC7278893 DOI: 10.7717/peerj.9369] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression found in more than 200 diverse organisms. Although it is still not fully established if RNA viruses could generate miRNAs, there are examples of miRNA like sequences from RNA viruses with regulatory functions. In the case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with viral replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA-based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Overall, 950 hairpin structured sequences were extracted from the virus genome and based on the prediction results, 29 of them could be precursor miRNAs. Targeting analysis showed that 30 viral mature miRNA-like sequences could target 1,367 different human genes. PANTHER gene function analysis results indicated that viral derived miRNA candidates could target various human genes involved in crucial cellular processes including transcription, metabolism, defense system and several signaling pathways such as Wnt and EGFR signalings. Protein class-based grouping of targeted human genes showed that host transcription might be one of the main targets of the virus since 96 genes involved in transcriptional processes were potential targets of predicted viral miRNAs. For instance, basal transcription machinery elements including several components of human mediator complex (MED1, MED9, MED12L, MED19), basal transcription factors such as TAF4, TAF5, TAF7L and site-specific transcription factors such as STAT1 were found to be targeted. In addition, many known human miRNAs appeared to be able to target viral genes involved in viral life cycle such as S, M, N, E proteins and ORF1ab, ORF3a, ORF8, ORF7a and ORF10. Considering the fact that miRNA-based therapies have been paid attention, based on the findings of this study, comprehending mode of actions of miRNAs and their possible roles during SARS-CoV-2 infections could create new opportunities for the development and improvement of new therapeutics.
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Affiliation(s)
| | - Aysun Adan
- Molecular Biology and Genetics, Abdullah Gul University, Kayseri, Turkey
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Huang HH, Chen CS, Wang WH, Hsu SW, Tsai HH, Liu ST, Chang LK. TRIM5α Promotes Ubiquitination of Rta from Epstein-Barr Virus to Attenuate Lytic Progression. Front Microbiol 2017; 7:2129. [PMID: 28105027 PMCID: PMC5214253 DOI: 10.3389/fmicb.2016.02129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/16/2016] [Indexed: 12/04/2022] Open
Abstract
Replication and transcription activator (Rta), a key protein expressed by Epstein–Barr virus (EBV) during the immediate-early stage of the lytic cycle, is responsible for the activation of viral lytic genes. In this study, GST-pulldown and coimmunoprecipitation assays showed that Rta interacts in vitro and in vivo with TRIM5α, a host factor known to be involved in the restriction of retroviral infections. Confocal microscopy results revealed that Rta colocalizes with TRIM5α in the nucleus during lytic progression. The interaction involves 190 amino acids in the N-terminal of Rta and the RING domain in TRIM5α, and it was further found that TRIM5α acts as an E3 ubiquitin ligase to promote Rta ubiquitination. Overexpression of TRIM5α reduced the transactivating capabilities of Rta, while reducing TRIM5α expression enhanced EBV lytic protein expression and DNA replication. Taken together, these results point to a critical role for TRIM5α in attenuating EBV lytic progression through the targeting of Rta for ubiquitination, and suggest that the restrictive capabilities of TRIM5α may go beyond retroviral infections.
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Affiliation(s)
- Hsiang-Hung Huang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University Taipei, Taiwan
| | - Chien-Sin Chen
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University Taipei, Taiwan
| | - Wen-Hung Wang
- Department of Internal Medicine, Kaohsiung Medical University Hospital Kaohsiung, Taiwan
| | - Shih-Wei Hsu
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University Taipei, Taiwan
| | - Hsiao-Han Tsai
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University Taipei, Taiwan
| | - Shih-Tung Liu
- Molecular Genetics Laboratory, Department of Microbiology and Immunology, Chang-Gung University Taoyuan, Taiwan
| | - Li-Kwan Chang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University Taipei, Taiwan
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McKenzie J, Lopez-Giraldez F, Delecluse HJ, Walsh A, El-Guindy A. The Epstein-Barr Virus Immunoevasins BCRF1 and BPLF1 Are Expressed by a Mechanism Independent of the Canonical Late Pre-initiation Complex. PLoS Pathog 2016; 12:e1006008. [PMID: 27855219 PMCID: PMC5113994 DOI: 10.1371/journal.ppat.1006008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/17/2016] [Indexed: 12/26/2022] Open
Abstract
Subversion of host immune surveillance is a crucial step in viral pathogenesis. Epstein-Barr virus (EBV) encodes two immune evasion gene products, BCRF1 (viral IL-10) and BPLF1 (deubiquitinase/deneddylase); both proteins suppress antiviral immune responses during primary infection. The BCRF1 and BPLF1 genes are expressed during the late phase of the lytic cycle, an essential but poorly understood phase of viral gene expression. Several late gene regulators recently identified in beta and gamma herpesviruses form a viral pre-initiation complex for transcription. Whether each of these late gene regulators is necessary for transcription of all late genes is not known. Here, studying viral gene expression in the absence and presence of siRNAs to individual components of the viral pre-initiation complex, we identified two distinct groups of late genes. One group includes late genes encoding the two immunoevasins, BCRF1 and BPLF1, and is transcribed independently of the viral pre-initiation complex. The second group primarily encodes viral structural proteins and is dependent on the viral pre-initiation complex. The protein kinase BGLF4 is the only known late gene regulator necessary for expression of both groups of late genes. ChIP-seq analysis showed that the transcription activator Rta associates with the promoters of eight late genes including genes encoding the viral immunoevasins. Our results demonstrate that late genes encoding immunomodulatory proteins are transcribed by a mechanism distinct from late genes encoding viral structural proteins. Understanding the mechanisms that specifically regulate expression of the late immunomodulatory proteins could aid the development of antiviral drugs that impair immune evasion by the oncogenic EB virus. Late proteins are expressed during the productive cycle of Epstein-Barr virus (EBV) after the onset of viral DNA replication. Many late proteins serve structural functions; they form the capsid shell around the viral genome or mediate attachment and fusion of the virus to the host cell. EBV also encodes two late proteins that suppress the immune system during primary infection. The current model suggests that transcription of all late genes is regulated by a common mechanism involving seven late gene regulators. Here, we demonstrate that late genes encoding two viral immune suppressants are transcribed by a mechanism different from that regulating late genes encoding structural proteins. Abolishing expression of the late immunomodulators without disrupting expression of the antigenic viral structural proteins could serve as an approach to block EBV de novo infection and its associated malignancies.
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Affiliation(s)
- Jessica McKenzie
- Department of Pediatrics Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Francesc Lopez-Giraldez
- Yale Center for Genome Analysis (YCGA), Yale University, West Haven, Connecticut, United States of America
| | - Henri-Jacques Delecluse
- Department of Tumor Virology, German Cancer Research Center, Im Neuenheimer Feld, Heidelberg, Germany
| | - Ann Walsh
- Department of Pediatrics Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ayman El-Guindy
- Department of Pediatrics Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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Li H, Liu S, Hu J, Luo X, Li N, M Bode A, Cao Y. Epstein-Barr virus lytic reactivation regulation and its pathogenic role in carcinogenesis. Int J Biol Sci 2016; 12:1309-1318. [PMID: 27877083 PMCID: PMC5118777 DOI: 10.7150/ijbs.16564] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/20/2016] [Indexed: 12/27/2022] Open
Abstract
Epstein-Barr virus (EBV) has been associated with several types of human cancers. In the host, EBV can establish two alternative modes of life cycle, known as latent or lytic and the switch from latency to the lytic cycle is known as EBV reactivation. Although EBV in cancer cells is found mostly in latency, a small number of lytically-infected cells promote carcinogenesis through the release of growth factors and oncogenic cytokines. This review focuses on the mechanisms by which EBV reactivation is controlled by cellular and viral factors, and discusses how EBV lytic infection contributes to human malignancies.
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Affiliation(s)
- Hongde Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, China; Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha 410078, China
| | - Sufang Liu
- Division of Hematology, Institute of Molecular Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jianmin Hu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, China; Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha 410078, China
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, China; Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha 410078, China
| | - Namei Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, China; Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha 410078, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Ya Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, China; Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha 410078, China
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Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PLoS Comput Biol 2016; 12:e1005074. [PMID: 27632082 PMCID: PMC5025164 DOI: 10.1371/journal.pcbi.1005074] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/22/2016] [Indexed: 02/05/2023] Open
Abstract
Viruses require host cellular factors for successful replication. A comprehensive systems-level investigation of the virus-host interactome is critical for understanding the roles of host factors with the end goal of discovering new druggable antiviral targets. Gene-trap insertional mutagenesis is a high-throughput forward genetics approach to randomly disrupt (trap) host genes and discover host genes that are essential for viral replication, but not for host cell survival. In this study, we used libraries of randomly mutagenized cells to discover cellular genes that are essential for the replication of 10 distinct cytotoxic mammalian viruses, 1 gram-negative bacterium, and 5 toxins. We herein reported 712 candidate cellular genes, characterizing distinct topological network and evolutionary signatures, and occupying central hubs in the human interactome. Cell cycle phase-specific network analysis showed that host cell cycle programs played critical roles during viral replication (e.g. MYC and TAF4 regulating G0/1 phase). Moreover, the viral perturbation of host cellular networks reflected disease etiology in that host genes (e.g. CTCF, RHOA, and CDKN1B) identified were frequently essential and significantly associated with Mendelian and orphan diseases, or somatic mutations in cancer. Computational drug repositioning framework via incorporating drug-gene signatures from the Connectivity Map into the virus-host interactome identified 110 putative druggable antiviral targets and prioritized several existing drugs (e.g. ajmaline) that may be potential for antiviral indication (e.g. anti-Ebola). In summary, this work provides a powerful methodology with a tight integration of gene-trap insertional mutagenesis testing and systems biology to identify new antiviral targets and drugs for the development of broadly acting and targeted clinical antiviral therapeutics. Infectious diseases result in millions of deaths and cost billions of dollars annually. Hence, there is urgency for developing more innovative and effective antiviral therapeutics. In this study, we used libraries of randomly mutagenized cells to discover cellular genes that are essential for the replication of 10 distinct cytotoxic mammalian viruses. We herein reported over 700 candidate cellular genes, over 20% of which were independently selected by multiple viruses in one or more cell types. Using systems biology-based analysis, we found that host genes associated with viral replication tended to occupy central hubs in the human protein interactome and to be ancient genes with low evolutionary rates, compared to non-virus-associated genes. Cell cycle phase-specific sub-network analysis showed that host cell cycle program played important roles during viral replication by regulating specific cell cycle phases. Moreover, we presented novel evidences to suggest that host genes supporting viral replication were frequently implicated in Mendelian and orphan diseases, or played critical roles in cancer. Importantly, we found approximately 110 new putative druggable antiviral targets by merging genome-wide gene-trap insertional mutagenesis, drug-gene network, and bioinformatics data. Furthermore, we have demonstrated the use of a computable representation of genetic testing to effectively identify new potential antiviral indications for existing drugs. In summary, this study presents new and important methodologies for developing broadly active antiviral therapeutics.
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Herbert KM, Nag A. A Tale of Two RNAs during Viral Infection: How Viruses Antagonize mRNAs and Small Non-Coding RNAs in The Host Cell. Viruses 2016; 8:E154. [PMID: 27271653 PMCID: PMC4926174 DOI: 10.3390/v8060154] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/12/2016] [Accepted: 05/20/2016] [Indexed: 02/06/2023] Open
Abstract
Viral infection initiates an array of changes in host gene expression. Many viruses dampen host protein expression and attempt to evade the host anti-viral defense machinery. Host gene expression is suppressed at several stages of host messenger RNA (mRNA) formation including selective degradation of translationally competent messenger RNAs. Besides mRNAs, host cells also express a variety of noncoding RNAs, including small RNAs, that may also be subject to inhibition upon viral infection. In this review we focused on different ways viruses antagonize coding and noncoding RNAs in the host cell to its advantage.
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Affiliation(s)
- Kristina M Herbert
- Department of Experimental Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California 22860, Mexico.
| | - Anita Nag
- Department of Chemistry, Florida A&M University, Tallahassee, FL 32307, USA.
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Yang YC, Feng TH, Chen TY, Huang HH, Hung CC, Liu ST, Chang LK. RanBPM regulates Zta-mediated transcriptional activity in Epstein–Barr virus. J Gen Virol 2015; 96:2336-2348. [DOI: 10.1099/vir.0.000157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Ya-Chun Yang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Tzu-Hui Feng
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Tse-Yao Chen
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Hsiang-Hung Huang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Chen-Chia Hung
- Molecular Genetics Laboratory, Department of Microbiology and Immunology, Chang-Gung University, Taoyuan, 333, Taiwan, ROC
| | - Shih-Tung Liu
- Molecular Genetics Laboratory, Department of Microbiology and Immunology, Chang-Gung University, Taoyuan, 333, Taiwan, ROC
| | - Li-Kwan Chang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan, ROC
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MCAF1 and Rta-activated BZLF1 transcription in Epstein-Barr virus. PLoS One 2014; 9:e90698. [PMID: 24598729 PMCID: PMC3944714 DOI: 10.1371/journal.pone.0090698] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 02/03/2014] [Indexed: 01/25/2023] Open
Abstract
Epstein-Barr virus (EBV) expresses two transcription factors, Rta and Zta, which are involved in the transcriptional activation of EBV lytic genes. This study sought to elucidate the mechanism by which Rta activates transcription of the Zta-encoding gene, BZLF1, through the ZII element in the gene promoter. In a DNA affinity precipitation assay, ATF2 was found to associate with an Rta-interacting protein, MCAF1, at the ZII element. The interaction between Rta, MCAF1, and ATF2 at the same site in the ZII region was further verified in vivo by chromatin immunoprecipitation assay. The complex appears to be crucial for the activation of BZLF1 transcription, as the overexpression of two ATF2-dominant negative mutants, or the introduction of MCAF1 siRNA into 293T cells, were both found to substantially reduce Rta-mediated transcription levels of BZLF1. Moreover, this study also found that the Rta-MCAF1-ATF2 complex binds to a typical AP-1 binding sequence on the promoter of BMRF2, a key viral gene for EBV infection. Mutation of this sequence decreased Rta-mediated promoter activity significantly. Taken together, these results indicate a critical role for MCAF1 in AP-1-dependent Rta activation of BZLF1 transcription.
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