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The HSV-1 ubiquitin ligase ICP0: Modifying the cellular proteome to promote infection. Virus Res 2020; 285:198015. [PMID: 32416261 PMCID: PMC7303953 DOI: 10.1016/j.virusres.2020.198015] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 12/16/2022]
Abstract
ICP0 is a viral E3 ubiquitin ligase that promotes HSV-1 infection. ICP0 interacts with multiple component proteins of the ubiquitin pathway. ICP0 disrupts multiple cellular processes activated in response to infection ICP0 remodels the SUMO proteome to counteract host immune defences to infection. ICP0 is an attractive drug target for the development of antiviral HSV-1 therapeutics.
Herpes simplex virus 1 (HSV-1) hijacks ubiquitination machinery to modify the cellular proteome to create an environment permissive for virus replication. HSV-1 encodes its own RING-finger E3 ubiquitin (Ub) ligase, Infected Cell Protein 0 (ICP0), that directly interfaces with component proteins of the Ub pathway to inactivate host immune defences and cellular processes that restrict the progression of HSV-1 infection. Consequently, ICP0 plays a critical role in the infectious cycle of HSV-1 that is required to promote the efficient onset of lytic infection and productive reactivation of viral genomes from latency. This review will describe the current knowledge regarding the biochemical properties and known substrates of ICP0 during HSV-1 infection. We will highlight the gaps in the characterization of ICP0 function and propose future areas of research required to understand fully the biological properties of this important HSV-1 regulatory protein.
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52
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Manska S, Octaviano R, Rossetto CC. 5-Ethynyl-2'-deoxycytidine and 5-ethynyl-2'-deoxyuridine are differentially incorporated in cells infected with HSV-1, HCMV, and KSHV viruses. J Biol Chem 2020; 295:5871-5890. [PMID: 32205447 PMCID: PMC7196651 DOI: 10.1074/jbc.ra119.012378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/18/2020] [Indexed: 11/06/2022] Open
Abstract
Nucleoside analogues are a valuable experimental tool. Incorporation of these molecules into newly synthesized DNA (i.e. pulse-labeling) is used to monitor cell proliferation or to isolate nascent DNA. Some of the most common nucleoside analogues used for pulse-labeling of DNA in cells are the deoxypyrimidine analogues 5-ethynyl-2'-deoxyuridine (EdU) and 5-ethynyl-2'-deoxycytidine (EdC). Click chemistry enables conjugation of an azide molecule tagged with a fluorescent dye or biotin to the alkyne of the analog, which can then be used to detect incorporation of EdU and EdC into DNA. The use of EdC is often recommended because of the potential cytotoxicity associated with EdU during longer incubations. Here, by comparing the relative incorporation efficiencies of EdU and EdC during short 30-min pulses, we demonstrate significantly lower incorporation of EdC than of EdU in noninfected human fibroblast cells or in cells infected with either human cytomegalovirus or Kaposi's sarcoma-associated herpesvirus. Interestingly, cells infected with herpes simplex virus type-1 (HSV-1) incorporated EdC and EdU at similar levels during short pulses. Of note, exogenous expression of HSV-1 thymidine kinase increased the incorporation efficiency of EdC. These results highlight the limitations when using substituted pyrimidine analogues in pulse-labeling and suggest that EdU is the preferable nucleoside analogue for short pulse-labeling experiments, resulting in increased recovery and sensitivity for downstream applications. This is an important discovery that may help to better characterize the biochemical properties of different nucleoside analogues with a given kinase, ultimately leading to significant differences in labeling efficiency of nascent DNA.
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Affiliation(s)
- Salomé Manska
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557
| | - Rionna Octaviano
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557
| | - Cyprian C Rossetto
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557.
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53
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Peters DK, Garcea RL. Murine polyomavirus DNA transitions through spatially distinct nuclear replication subdomains during infection. PLoS Pathog 2020; 16:e1008403. [PMID: 32203554 PMCID: PMC7117779 DOI: 10.1371/journal.ppat.1008403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/02/2020] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
The replication of small DNA viruses requires both host DNA replication and repair factors that are often recruited to subnuclear domains termed viral replication centers (VRCs). Aside from serving as a spatial focus for viral replication, little is known about these dynamic areas in the nucleus. We investigated the organization and function of VRCs during murine polyomavirus (MuPyV) infection using 3D structured illumination microscopy (3D-SIM). We localized MuPyV replication center components, such as the viral large T-antigen (LT) and the cellular replication protein A (RPA), to spatially distinct subdomains within VRCs. We found that viral DNA (vDNA) trafficked sequentially through these subdomains post-synthesis, suggesting their distinct functional roles in vDNA processing. Additionally, we observed disruption of VRC organization and vDNA trafficking during mutant MuPyV infections or inhibition of DNA synthesis. These results reveal a dynamic organization of VRC components that coordinates virus replication.
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Affiliation(s)
- Douglas K. Peters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Robert L. Garcea
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
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54
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RNA Polymerase II Promoter-Proximal Pausing and Release to Elongation Are Key Steps Regulating Herpes Simplex Virus 1 Transcription. J Virol 2020; 94:JVI.02035-19. [PMID: 31826988 DOI: 10.1128/jvi.02035-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) genes are transcribed by cellular RNA polymerase II (Pol II). Expression of viral immediate early (α) genes is followed sequentially by early (β), late (γ1), and true late (γ2) genes. We used precision nuclear run-on with deep sequencing to map and to quantify Pol II on the HSV-1(F) genome with single-nucleotide resolution. Approximately 30% of total Pol II relocated to viral genomes within 3 h postinfection (hpi), when it occupied genes of all temporal classes. At that time, Pol II on α genes accumulated most heavily at promoter-proximal pause (PPP) sites located ∼60 nucleotides downstream of the transcriptional start site, while β genes bore Pol II more evenly across gene bodies. At 6 hpi, Pol II increased on γ1 and γ2 genes while Pol II pausing remained prominent on α genes. At that time, average cytoplasmic mRNA expression from α and β genes decreased, relative to levels at 3 hpi, while γ1 relative expression increased slightly and γ2 expression increased more substantially. Cycloheximide treatment during the first 3 h reduced the amount of Pol II associated with the viral genome and confined most of the remaining Pol II to α gene PPP sites. Inhibition of both cyclin-dependent kinase 9 activity and viral DNA replication reduced Pol II on the viral genome and restricted much of the remaining Pol II to PPP sites.IMPORTANCE These data suggest that viral transcription is regulated not only by Pol II recruitment to viral genes but also by control of elongation into viral gene bodies. We provide a detailed map of Pol II occupancy on the HSV-1 genome that clarifies features of the viral transcriptome, including the first identification of Pol II PPP sites. The data indicate that Pol II is recruited to late genes early in infection. Comparing α and β gene occupancy at PPP sites and gene bodies suggests that Pol II is released more efficiently into the bodies of β genes than α genes at 3 hpi and that repression of α gene expression late in infection is mediated by prolonged promoter-proximal pausing. In addition, DNA replication is required to maintain full Pol II occupancy on viral DNA and to promote elongation on late genes later in infection.
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55
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Hartenian E, Gilbertson S, Federspiel JD, Cristea IM, Glaunsinger BA. RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters. PLoS Pathog 2020; 16:e1008269. [PMID: 32032393 PMCID: PMC7032723 DOI: 10.1371/journal.ppat.1008269] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 02/20/2020] [Accepted: 12/09/2019] [Indexed: 12/11/2022] Open
Abstract
In mammalian cells, widespread acceleration of cytoplasmic mRNA degradation is linked to impaired RNA polymerase II (Pol II) transcription. This mRNA decay-induced transcriptional repression occurs during infection with gammaherpesviruses including Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68), which encode an mRNA endonuclease that initiates widespread RNA decay. Here, we show that MHV68-induced mRNA decay leads to a genome-wide reduction of Pol II occupancy at mammalian promoters. This reduced Pol II occupancy is accompanied by down-regulation of multiple Pol II subunits and TFIIB in the nucleus of infected cells, as revealed by mass spectrometry-based global measurements of protein abundance. Viral genes, despite the fact that they require Pol II for transcription, escape transcriptional repression. Protection is not governed by viral promoter sequences; instead, location on the viral genome is both necessary and sufficient to escape the transcriptional repression effects of mRNA decay. We propose a model in which the ability to escape from transcriptional repression is linked to the localization of viral DNA within replication compartments, providing a means for these viruses to counteract decay-induced transcript loss. While transcription and messenger RNA (mRNA) decay are often considered to be the unlinked beginning and end of gene expression, recent data indicate that alterations to either stage can impact the other. Here we study this connection in the context of lytic gammaherpesvirus infection, which accelerates mRNA degradation through the expression of the viral endonuclease muSOX. We show that RNA polymerase II promoter occupancy is broadly reduced across mammalian promoters in response to infection-induced mRNA decay, and that this phenotype correlates with a reduction in the abundance of several proteins involved in transcription. Notably, gammaherpesviral promoters are resistant to the ensuing transcriptional repression. We show that viral transcriptional escape is conferred by localization of the viral DNA within the protective environment of replication compartments, which are sites of viral genome replication and transcription during infection. Collectively, these findings clarify how mRNA degradation by gammaherpesviruses reshapes the cellular environment and selectively dampens host gene transcription.
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Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
| | - Sarah Gilbertson
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
| | - Joel D. Federspiel
- Department of Molecular Biology, Princeton University, Princeton, United States of America
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, United States of America
| | - Britt A. Glaunsinger
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California Berkeley, CA, United States of America
- * E-mail:
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56
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Brook CE, Boots M, Chandran K, Dobson AP, Drosten C, Graham AL, Grenfell BT, Müller MA, Ng M, Wang LF, van Leeuwen A. Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence. eLife 2020; 9:48401. [PMID: 32011232 PMCID: PMC7064339 DOI: 10.7554/elife.48401] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 02/02/2020] [Indexed: 01/10/2023] Open
Abstract
Bats host virulent zoonotic viruses without experiencing disease. A mechanistic understanding of the impact of bats’ virus hosting capacities, including uniquely constitutive immune pathways, on cellular-scale viral dynamics is needed to elucidate zoonotic emergence. We carried out virus infectivity assays on bat cell lines expressing induced and constitutive immune phenotypes, then developed a theoretical model of our in vitro system, which we fit to empirical data. Best fit models recapitulated expected immune phenotypes for representative cell lines, supporting robust antiviral defenses in bat cells that correlated with higher estimates for within-host viral propagation rates. In general, heightened immune responses limit pathogen-induced cellular morbidity, which can facilitate the establishment of rapidly-propagating persistent infections within-host. Rapidly-transmitting viruses that have evolved with bat immune systems will likely cause enhanced virulence following emergence into secondary hosts with immune systems that diverge from those unique to bats. Bats can carry viruses that are deadly to other mammals without themselves showing serious symptoms. In fact, bats are natural reservoirs for viruses that have some of the highest fatality rates of any viruses that people acquire from wild animals – including rabies, Ebola and the SARS coronavirus. Bats have a suite of antiviral defenses that keep the amount of virus in check. For example, some bats have an antiviral immune response called the interferon pathway perpetually switched on. In most other mammals, having such a hyper-vigilant immune response would cause harmful inflammation. Bats, however, have adapted anti-inflammatory traits that protect them from such harm, include the loss of certain genes that normally promote inflammation. However, no one has previously explored how these unique antiviral defenses of bats impact the viruses themselves. Now, Brook et al. have studied this exact question using bat cells grown in the laboratory. The experiments made use of cells from one bat species – the black flying fox – in which the interferon pathway is always on, and another – the Egyptian fruit bat – in which this pathway is only activated during an infection. The bat cells were infected with three different viruses, and then Brook et al. observed how the interferon pathway helped keep the infections in check, before creating a computer model of this response. The experiments and model helped reveal that the bats’ defenses may have a potential downside for other animals, including humans. In both bat species, the strongest antiviral responses were countered by the virus spreading more quickly from cell to cell. This suggests that bat immune defenses may drive the evolution of faster transmitting viruses, and while bats are well protected from the harmful effects of their own prolific viruses, other creatures like humans are not. The findings may help to explain why bats are often the source for viruses that are deadly in humans. Learning more about bats' antiviral defenses and how they drive virus evolution may help scientists develop better ways to predict, prevent or limit the spread of viruses from bats to humans. More studies are needed in bats to help these efforts. In the meantime, the experiments highlight the importance of warning people to avoid direct contact with wild bats.
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Affiliation(s)
- Cara E Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Andrew P Dobson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States.,Fogarty International Center, National Institutes of Health, Bethesda, United States
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russian Federation
| | - Melinda Ng
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Lin-Fa Wang
- Emerging Infectious Diseases Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Anieke van Leeuwen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States.,Royal Netherlands Institute for Sea Research, Department of Coastal Systems, and Utrecht University, Den Burg, Netherlands
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57
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Replication Compartments of DNA Viruses in the Nucleus: Location, Location, Location. Viruses 2020; 12:v12020151. [PMID: 32013091 PMCID: PMC7077188 DOI: 10.3390/v12020151] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/26/2020] [Accepted: 01/26/2020] [Indexed: 02/08/2023] Open
Abstract
DNA viruses that replicate in the nucleus encompass a range of ubiquitous and clinically important viruses, from acute pathogens to persistent tumor viruses. These viruses must co-opt nuclear processes for the benefit of the virus, whilst evading host processes that would otherwise attenuate viral replication. Accordingly, DNA viruses induce the formation of membraneless assemblies termed viral replication compartments (VRCs). These compartments facilitate the spatial organization of viral processes and regulate virus–host interactions. Here, we review advances in our understanding of VRCs. We cover their initiation and formation, their function as the sites of viral processes, and aspects of their composition and organization. In doing so, we highlight ongoing and emerging areas of research highly pertinent to our understanding of nuclear-replicating DNA viruses.
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58
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Novel replisome-associated proteins at cellular replication forks in EBV-transformed B lymphocytes. PLoS Pathog 2019; 15:e1008228. [PMID: 31841561 PMCID: PMC6936862 DOI: 10.1371/journal.ppat.1008228] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/30/2019] [Accepted: 11/20/2019] [Indexed: 01/08/2023] Open
Abstract
Epstein-Barr virus (EBV) is an oncogenic herpesvirus and WHO class 1 carcinogen that resides in B lymphocytes of nearly all humans. While silent in most, EBV can cause endemic Burkitt lymphoma in children and post-transplant lymphoproliferative disorders/lymphomas in immunocompromised hosts. The pathogenesis of such lymphomas is multifactorial but to a large extent depends on EBV’s ability to aggressively drive cellular DNA replication and B cell proliferation despite cell-intrinsic barriers to replication. One such barrier is oncogenic replication stress which hinders the progression of DNA replication forks. To understand how EBV successfully overcomes replication stress, we examined cellular replication forks in EBV-transformed B cells using iPOND (isolation of Proteins on Nascent DNA)-mass spectrometry and identified several cellular proteins that had not previously been linked to DNA replication. Of eight candidate replisome-associated proteins that we validated at forks in EBV-transformed cells and Burkitt lymphoma-derived cells, three zinc finger proteins (ZFPs) were upregulated early in B cells newly-infected with EBV in culture as well as expressed at high levels in EBV-infected B blasts in the blood of immunocompromised transplant recipients. Expressed highly in S- and G2-phase cells, knockdown of each ZFP resulted in stalling of proliferating cells in the S-phase, cleavage of caspase 3, and cell death. These proteins, newly-identified at replication forks of EBV-transformed and Burkitt lymphoma cells therefore contribute to cell survival and cell cycle progression, and represent novel targets for intervention of EBV-lymphomas while simultaneously offering a window into how the replication machinery may be similarly modified in other cancers. Cancer cells must overcome chronic replication stress, a central barrier to DNA replication. This is true also for cancers caused by Epstein-Barr virus (EBV). To understand how EBV overcomes this barrier to successfully drive cell proliferation, we isolated proteins associated with the cellular replication machinery in EBV-transformed B lymphocytes and identified several cellular proteins that had not previously been linked to DNA replication in cancer or healthy cells. Three of these were zinc finger proteins enriched at the replication machinery in EBV-transformed and EBV-positive Burkitt lymphoma-derived cells, upregulated in newly-infected B cells, and expressed at high levels in infected B cells from transplant recipients. These zinc finger proteins also contributed towards cell proliferation, survival, and cell cycle progression. While these proteins may also contribute to DNA replication in other cancers, they simultaneously represent potential targets in EBV-cancers, some of which are difficult to treat.
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59
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Chromatin dynamics and the transcriptional competence of HSV-1 genomes during lytic infections. PLoS Pathog 2019; 15:e1008076. [PMID: 31725813 PMCID: PMC6855408 DOI: 10.1371/journal.ppat.1008076] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/11/2019] [Indexed: 12/20/2022] Open
Abstract
During latent infections with herpes simplex virus 1 (HSV-1), viral transcription is restricted and the genomes are mostly maintained in silenced chromatin, whereas in lytically infected cells all viral genes are transcribed and the genomes are dynamically chromatinized. Histones in the viral chromatin bear markers of silenced chromatin at early times in lytic infection or of active transcription at later times. The virion protein VP16 activates transcription of the immediate-early (IE) genes by recruiting transcription activators and chromatin remodelers to their promoters. Two IE proteins, ICP0 and ICP4 which modulate chromatin epigenetics, then activate transcription of early and late genes. Although chromatin is involved in the mechanism of activation of HSV- transcription, its precise role is not entirely understood. In the cellular genome, chromatin dynamics often modulate transcription competence whereas promoter-specific transcription factors determine transcription activity. Here, biophysical fractionation of serially digested HSV-1 chromatin followed by short-read deep sequencing indicates that nuclear HSV-1 DNA has different biophysical properties than protein-free or encapsidated HSV-1 DNA. The entire HSV-1 genomes in infected cells were equally accessible. The accessibility of transcribed or non-transcribed genes under any given condition did not differ, and each gene was entirely sampled in both the most and least accessible chromatin. However, HSV-1 genomes fractionated differently under conditions of generalized or restricted transcription. Approximately 1/3 of the HSV-1 DNA including fully sampled genes resolved to the most accessible chromatin when HSV-1 transcription was active, but such enrichment was reduced to only 3% under conditions of restricted HSV-1 transcription. Short sequences of restricted accessibility separated genes with different transcription levels. Chromatin dynamics thus provide a first level of regulation on HSV-1 transcription, dictating the transcriptional competency of the genomes during lytic infections, whereas the transcription of individual genes is then most likely activated by specific transcription factors. Moreover, genes transcribed to different levels are separated by short sequences with limited accessibility. Although chromatin epigenetics modulate transcription of the nuclear replicating DNA viruses, and play major roles in the process of establishment of, and reactivation from, latency, the specific mechanisms of this modulation are not totally clear. Chromatin often regulates the transcriptional competency of cellular genes, rather than the actual level of transcription of individual genes. Here, we show that chromatin dynamics regulate the transcription competency of entire herpes simplex virus 1 (HSV-1) genomes, rather than the actual transcription level of individual genes. Moreover, CTCF/ insulator containing sequences flanking the immediate-early gene loci are more inaccessible when these genes are highly transcribed in a context of little transcription from the rest of the genome than when no gene was highly transcribed or all genes were. We postulate that chromatin dynamics modulate the transcriptional competency of the HSV-1 genome. Genes in genomes rendered transcriptionally inactive by chromatin dynamics cannot be transcribed, whereas transcription of individual genes, or of group of genes, is regulated separately in the transcriptionally competent genomes.
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60
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Dremel SE, DeLuca NA. Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off. eLife 2019; 8:e51109. [PMID: 31638576 PMCID: PMC6805162 DOI: 10.7554/elife.51109] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022] Open
Abstract
Herpes simplex virus-1 (HSV-1) replicates within the nucleus coopting the host's RNA Polymerase II (Pol II) machinery for production of viral mRNAs culminating in host transcriptional shut off. The mechanism behind this rapid reprogramming of the host transcriptional environment is largely unknown. We identified ICP4 as responsible for preferential recruitment of the Pol II machinery to the viral genome. ICP4 is a viral nucleoprotein which binds double-stranded DNA. We determined ICP4 discriminately binds the viral genome due to the absence of cellular nucleosomes and high density of cognate binding sites. We posit that ICP4's ability to recruit not just Pol II, but also more limiting essential components, such as TBP and Mediator, create a competitive transcriptional environment. These distinguishing characteristics ultimately result in a rapid and efficient reprogramming of the host's transcriptional machinery, which does not occur in the absence of ICP4.
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Affiliation(s)
- Sarah E Dremel
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghUnited States
| | - Neal A DeLuca
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghUnited States
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61
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Tomer E, Cohen EM, Drayman N, Afriat A, Weitzman MD, Zaritsky A, Kobiler O. Coalescing replication compartments provide the opportunity for recombination between coinfecting herpesviruses. FASEB J 2019; 33:9388-9403. [PMID: 31107607 PMCID: PMC6662979 DOI: 10.1096/fj.201900032r] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/23/2019] [Indexed: 12/15/2022]
Abstract
Homologous recombination (HR) is considered a major driving force of evolution because it generates and expands genetic diversity. Evidence of HR between coinfecting herpesvirus DNA genomes can be found frequently both in vitro and in clinical isolates. Each herpes simplex virus type 1 (HSV-1) replication compartment (RC) derives from a single incoming genome and maintains a specific territory within the nucleus. This raises intriguing questions about where and when coinfecting viral genomes interact. To study the spatiotemporal requirements for intergenomic recombination, we developed an assay with dual-color FISH that enables detection of HR between different pairs of coinfecting HSV-1 genomes. Our results revealed that HR increases intermingling of RCs derived from different genomes. Furthermore, inhibition of RC movement reduces the rate of HR events among coinfecting viruses. Finally, we observed correlation between nuclear size and the number of RCs per nucleus. Our findings suggest that both viral replication and recombination are subject to nuclear spatial constraints. Other DNA viruses and cellular DNA are likely to encounter similar restrictions.-Tomer, E., Cohen, E. M., Drayman, N., Afriat, A., Weitzman, M. D., Zaritsky, A., Kobiler, O. Coalescing replication compartments provide the opportunity for recombination between coinfecting herpesviruses.
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Affiliation(s)
- Enosh Tomer
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Efrat M. Cohen
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Drayman
- Institute for Genomics and Systems Biology and Institute for Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Amichay Afriat
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matthew D. Weitzman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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62
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Kobiler O, Weitzman MD. Herpes simplex virus replication compartments: From naked release to recombining together. PLoS Pathog 2019; 15:e1007714. [PMID: 31158262 PMCID: PMC6546242 DOI: 10.1371/journal.ppat.1007714] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Oren Kobiler
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| | - Matthew D. Weitzman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
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63
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Drayman N, Patel P, Vistain L, Tay S. HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations. eLife 2019; 8:e46339. [PMID: 31090537 PMCID: PMC6570482 DOI: 10.7554/elife.46339] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/11/2019] [Indexed: 12/12/2022] Open
Abstract
Viral infection is usually studied at the population level by averaging over millions of cells. However, infection at the single-cell level is highly heterogeneous, with most infected cells giving rise to no or few viral progeny while some cells produce thousands. Analysis of Herpes Simplex virus 1 (HSV-1) infection by population-averaged measurements has taught us a lot about the course of viral infection, but has also produced contradictory results, such as the concurrent activation and inhibition of type I interferon signaling during infection. Here, we combine live-cell imaging and single-cell RNA sequencing to characterize viral and host transcriptional heterogeneity during HSV-1 infection of primary human cells. We find extreme variability in the level of viral gene expression among individually infected cells and show that these cells cluster into transcriptionally distinct sub-populations. We find that anti-viral signaling is initiated in a rare group of abortively infected cells, while highly infected cells undergo cellular reprogramming to an embryonic-like transcriptional state. This reprogramming involves the recruitment of β-catenin to the host nucleus and viral replication compartments, and is required for late viral gene expression and progeny production. These findings uncover the transcriptional differences in cells with variable infection outcomes and shed new light on the manipulation of host pathways by HSV-1.
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Affiliation(s)
- Nir Drayman
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Parthiv Patel
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Luke Vistain
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Savaş Tay
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
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64
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McSwiggen DT, Hansen AS, Teves SS, Marie-Nelly H, Hao Y, Heckert AB, Umemoto KK, Dugast-Darzacq C, Tjian R, Darzacq X. Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. eLife 2019; 8:e47098. [PMID: 31038454 PMCID: PMC6522219 DOI: 10.7554/elife.47098] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
RNA Polymerase II (Pol II) and transcription factors form concentrated hubs in cells via multivalent protein-protein interactions, often mediated by proteins with intrinsically disordered regions. During Herpes Simplex Virus infection, viral replication compartments (RCs) efficiently enrich host Pol II into membraneless domains, reminiscent of liquid-liquid phase separation. Despite sharing several properties with phase-separated condensates, we show that RCs operate via a distinct mechanism wherein unrestricted nonspecific protein-DNA interactions efficiently outcompete host chromatin, profoundly influencing the way DNA-binding proteins explore RCs. We find that the viral genome remains largely nucleosome-free, and this increase in accessibility allows Pol II and other DNA-binding proteins to repeatedly visit nearby DNA binding sites. This anisotropic behavior creates local accumulations of protein factors despite their unrestricted diffusion across RC boundaries. Our results reveal underappreciated consequences of nonspecific DNA binding in shaping gene activity, and suggest additional roles for chromatin in modulating nuclear function and organization.
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Affiliation(s)
- David Trombley McSwiggen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Anders S Hansen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Sheila S Teves
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Department of Biochemistry and Molecular BiologyUniversity of British ColumbiaVancouverCanada
| | - Hervé Marie-Nelly
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Yvonne Hao
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Alec Basil Heckert
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Kayla K Umemoto
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
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65
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D'Aiuto L, Bloom DC, Naciri JN, Smith A, Edwards TG, McClain L, Callio JA, Jessup M, Wood J, Chowdari K, Demers M, Abrahamson EE, Ikonomovic MD, Viggiano L, De Zio R, Watkins S, Kinchington PR, Nimgaonkar VL. Modeling Herpes Simplex Virus 1 Infections in Human Central Nervous System Neuronal Cells Using Two- and Three-Dimensional Cultures Derived from Induced Pluripotent Stem Cells. J Virol 2019; 93:e00111-19. [PMID: 30787148 PMCID: PMC6475775 DOI: 10.1128/jvi.00111-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/05/2019] [Indexed: 12/12/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) establishes latency in both peripheral nerve ganglia and the central nervous system (CNS). The outcomes of acute and latent infections in these different anatomic sites appear to be distinct. It is becoming clear that many of the existing culture models using animal primary neurons to investigate HSV-1 infection of the CNS are limited and not ideal, and most do not recapitulate features of CNS neurons. Human induced pluripotent stem cells (hiPSCs) and neurons derived from them are documented as tools to study aspects of neuropathogenesis, but few have focused on modeling infections of the CNS. Here, we characterize functional two-dimensional (2D) CNS-like neuron cultures and three-dimensional (3D) brain organoids made from hiPSCs to model HSV-1-human-CNS interactions. Our results show that (i) hiPSC-derived CNS neurons are permissive for HSV-1 infection; (ii) a quiescent state exhibiting key landmarks of HSV-1 latency described in animal models can be established in hiPSC-derived CNS neurons; (iii) the complex laminar structure of the organoids can be efficiently infected with HSV, with virus being transported from the periphery to the central layers of the organoid; and (iv) the organoids support reactivation of HSV-1, albeit less efficiently than 2D cultures. Collectively, our results indicate that hiPSC-derived neuronal platforms, especially 3D organoids, offer an extraordinary opportunity for modeling the interaction of HSV-1 with the complex cellular and architectural structure of the human CNS.IMPORTANCE This study employed human induced pluripotent stem cells (hiPSCs) to model acute and latent HSV-1 infections in two-dimensional (2D) and three-dimensional (3D) CNS neuronal cultures. We successfully established acute HSV-1 infections and infections showing features of latency. HSV-1 infection of the 3D organoids was able to spread from the outer surface of the organoid and was transported to the interior lamina, providing a model to study HSV-1 trafficking through complex neuronal tissue structures. HSV-1 could be reactivated in both culture systems; though, in contrast to 2D cultures, it appeared to be more difficult to reactivate HSV-1 in 3D cultures, potentially paralleling the low efficiency of HSV-1 reactivation in the CNS of animal models. The reactivation events were accompanied by dramatic neuronal morphological changes and cell-cell fusion. Together, our results provide substantive evidence of the suitability of hiPSC-based neuronal platforms to model HSV-1-CNS interactions in a human context.
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Affiliation(s)
- Leonardo D'Aiuto
- Department of Psychiatry, University of Pittsburgh School of Medicine Western Psychiatric Institute and Clinic, Pittsburgh, Pennsylvania, USA
| | - David C Bloom
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jennifer N Naciri
- Department of Psychiatry, University of Pittsburgh School of Medicine Western Psychiatric Institute and Clinic, Pittsburgh, Pennsylvania, USA
| | - Adam Smith
- Department of Psychiatry, University of Pittsburgh School of Medicine Western Psychiatric Institute and Clinic, Pittsburgh, Pennsylvania, USA
| | - Terri G Edwards
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Lora McClain
- Magee-Women's Research Institute, Pittsburgh, Pennsylvania, USA
| | - Jason A Callio
- Department of Pathology, Division of Neuropathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Morgan Jessup
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joel Wood
- Department of Psychiatry, University of Pittsburgh School of Medicine Western Psychiatric Institute and Clinic, Pittsburgh, Pennsylvania, USA
| | - Kodavali Chowdari
- Department of Psychiatry, University of Pittsburgh School of Medicine Western Psychiatric Institute and Clinic, Pittsburgh, Pennsylvania, USA
| | - Matthew Demers
- Department of Psychiatry, University of Pittsburgh School of Medicine Western Psychiatric Institute and Clinic, Pittsburgh, Pennsylvania, USA
| | - Eric E Abrahamson
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Milos D Ikonomovic
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Luigi Viggiano
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Roberta De Zio
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Bari, Italy
| | - Simon Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Paul R Kinchington
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vishwajit L Nimgaonkar
- Department of Psychiatry, University of Pittsburgh School of Medicine Western Psychiatric Institute and Clinic, Pittsburgh, Pennsylvania, USA
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66
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A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention. J Virol 2019; 93:JVI.02143-18. [PMID: 30814291 DOI: 10.1128/jvi.02143-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/07/2019] [Indexed: 12/14/2022] Open
Abstract
Chromatin-based modifications of herpesviral genomes play a crucial role in dictating the outcome of infection. Consistent with this, host cell multiprotein complexes, such as polycomb repressive complexes (PRCs), were proposed to act as epigenetic regulators of herpesviral latency. In particular, PRC2 has recently been shown to contribute to the silencing of human cytomegalovirus (HCMV) genomes. Here, we identify a novel proviral role of PRC1 and PRC2, the two main polycomb repressive complexes, during productive HCMV infection. Western blot analyses revealed strong HCMV-mediated upregulation of RING finger protein 1B (RING1B) and B lymphoma Moloney murine leukemia virus insertion region 1 homolog (BMI1) as well as of enhancer of zeste homolog 2 (EZH2), suppressor of zeste 12 (SUZ12), and embryonic ectoderm development (EED), which constitute the core components of PRC1 and PRC2, respectively. Furthermore, we observed a relocalization of PRC components to viral replication compartments, whereas histone modifications conferred by the respective PRCs were specifically excluded from these sites. Depletion of individual PRC1/PRC2 proteins by RNA interference resulted in a significant reduction of newly synthesized viral genomes and, in consequence, a decreased release of viral particles. Furthermore, accelerated native isolation of protein on nascent DNA (aniPOND) revealed a physical association of EZH2 and BMI1 with nascent HCMV DNA, suggesting a direct contribution of PRC proteins to viral DNA replication. Strikingly, substances solely inhibiting the enzymatic activity of PRC1/2 did not exert antiviral effects, while drugs affecting the abundance of PRC core components strongly compromised HCMV genome synthesis and particle release. Taken together, our data reveal an enzymatically independent, noncanonical function of both PRC1 and PRC2 during HCMV DNA replication, which may serve as a novel cellular target for antiviral therapy.IMPORTANCE Polycomb group (PcG) proteins are primarily known as transcriptional repressors that modify chromatin and contribute to the establishment and maintenance of cell fates. Furthermore, emerging evidence indicates that overexpression of PcG proteins in various types of cancers contributes to the dysregulation of cellular proliferation. Consequently, several inhibitors targeting PcG proteins are presently undergoing preclinical and clinical evaluation. Here, we show that infection with human cytomegalovirus also induces a strong upregulation of several PcG proteins. Our data suggest that viral DNA replication depends on a noncanonical function of polycomb repressor complexes which is independent of the so-far-described enzymatic activities of individual PcG factors. Importantly, we observe that a subclass of inhibitory drugs that affect the abundance of PcG proteins strongly interferes with viral replication. This principle may serve as a novel promising target for antiviral treatment.
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67
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McFarlane S, Orr A, Roberts APE, Conn KL, Iliev V, Loney C, da Silva Filipe A, Smollett K, Gu Q, Robertson N, Adams PD, Rai TS, Boutell C. The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PLoS Pathog 2019; 15:e1007667. [PMID: 30901352 PMCID: PMC6472835 DOI: 10.1371/journal.ppat.1007667] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/18/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
Host innate immune defences play a critical role in restricting the intracellular propagation and pathogenesis of invading viral pathogens. Here we show that the histone H3.3 chaperone HIRA (histone cell cycle regulator) associates with promyelocytic leukaemia nuclear bodies (PML-NBs) to stimulate the induction of innate immune defences against herpes simplex virus 1 (HSV-1) infection. Following the activation of innate immune signalling, HIRA localized at PML-NBs in a Janus-Associated Kinase (JAK), Cyclin Dependent Kinase (CDK), and Sp100-dependent manner. RNA-seq analysis revealed that HIRA promoted the transcriptional upregulation of a broad repertoire of host genes that regulate innate immunity to HSV-1 infection, including those involved in MHC-I antigen presentation, cytokine signalling, and interferon stimulated gene (ISG) expression. ChIP-seq analysis revealed that PML, the principle scaffolding protein of PML-NBs, was required for the enrichment of HIRA onto ISGs, identifying a role for PML in the HIRA-dependent regulation of innate immunity to virus infection. Our data identifies independent roles for HIRA in the intrinsic silencing of viral gene expression and the induction of innate immune defences to restrict the initiation and propagation of HSV-1 infection, respectively. These intracellular host defences are antagonized by the HSV-1 ubiquitin ligase ICP0, which disrupts the stable recruitment of HIRA to infecting viral genomes and PML-NBs at spatiotemporally distinct phases of infection. Our study highlights the importance of histone chaperones to regulate multiple phases of intracellular immunity to virus infection, findings that are likely to be highly pertinent in the cellular restriction of many clinically important viral pathogens. Host innate immune defences play critical roles in the cellular restriction of invading viral pathogens and the stimulation of adaptive immune responses. A key component in the regulation of this arm of host immunity is the rapid induction of cytokine signalling and the expression of interferon stimulated gene products (ISGs), which confer a refractory antiviral state to limit virus propagation and pathogenesis. While the signal transduction cascades that activate innate immune defences are well established, little is known about the cellular host factors that expedite the expression of this broad repertoire of antiviral host genes in response to pathogen invasion. Here we show that HIRA, a histone H3.3 chaperone, associates with PML-NBs to stimulate the induction of innate immune defences in response to HSV-1 infection. Our study highlights the importance of histone chaperones in the coordinated regulation of multiple phases of host immunity in response to pathogen invasion and identifies a key role for HIRA in the induction of innate immunity to virus infection.
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Affiliation(s)
- Steven McFarlane
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Anne Orr
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Ashley P. E. Roberts
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Kristen L. Conn
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatoon, CA
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, CA
| | - Victor Iliev
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Neil Robertson
- Beatson Institute for Cancer Research, Glasgow, Scotland, United Kingdom
| | - Peter D. Adams
- Beatson Institute for Cancer Research, Glasgow, Scotland, United Kingdom
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, United States of America
| | - Taranjit Singh Rai
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry, United Kingdom
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
- * E-mail:
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68
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Müller TG, Sakin V, Müller B. A Spotlight on Viruses-Application of Click Chemistry to Visualize Virus-Cell Interactions. Molecules 2019; 24:molecules24030481. [PMID: 30700005 PMCID: PMC6385038 DOI: 10.3390/molecules24030481] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 01/03/2023] Open
Abstract
The replication of a virus within its host cell involves numerous interactions between viral and cellular factors, which have to be tightly controlled in space and time. The intricate interplay between viral exploitation of cellular pathways and the intrinsic host defense mechanisms is difficult to unravel by traditional bulk approaches. In recent years, novel fluorescence microscopy techniques and single virus tracking have transformed the investigation of dynamic virus-host interactions. A prerequisite for the application of these imaging-based methods is the attachment of a fluorescent label to the structure of interest. However, their small size, limited coding capacity and multifunctional proteins render viruses particularly challenging targets for fluorescent labeling approaches. Click chemistry in conjunction with genetic code expansion provides virologists with a novel toolbox for site-specific, minimally invasive labeling of virion components, whose potential has just recently begun to be exploited. Here, we summarize recent achievements, current developments and future challenges for the labeling of viral nucleic acids, proteins, glycoproteins or lipids using click chemistry in order to study dynamic processes in virus-cell interactions.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Volkan Sakin
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
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Mahdaviani SA, Rezaei N. Pulmonary Manifestations of Predominantly Antibody Deficiencies. PULMONARY MANIFESTATIONS OF PRIMARY IMMUNODEFICIENCY DISEASES 2019. [PMCID: PMC7123456 DOI: 10.1007/978-3-030-00880-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Predominantly antibody deficiencies (PADs) are the most frequent forms of primary immunodeficiency diseases (PIDs). Commonly accompanied with complications involving several body systems, immunoglobulin substitution therapy along with prophylactic antibiotics remained the cornerstone of treatment for PADs and related complications. Patients with respiratory complications should be prescribed an appropriate therapy as soon as possible and have to be adhering to more and longer medical therapies. Recent studies identified a gap for screening protocols to monitor respiratory manifestations in patients with PADs. In the present chapter, the pulmonary manifestations of different PADs for each have been discussed. The chapter is mainly focused on X-linked agammaglobulinemia, common variable immunodeficiency, activated PI3K-δ syndrome, LRBA deficiency, CD19 complex deficiencies, CD20 deficiency, other monogenic defects associated with hypogammaglobulinemia, immunoglobulin class switch recombination deficiencies affecting B-cells, transient hypogammaglobulinemia of infancy, and selective IgA deficiency.
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Affiliation(s)
- Seyed Alireza Mahdaviani
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies Children’s Medical Center, Tehran University of Medical Sciences (TUMS), Tehran, Iran
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Sierecki E. The Mediator complex and the role of protein-protein interactions in the gene regulation machinery. Semin Cell Dev Biol 2018; 99:20-30. [PMID: 30278226 DOI: 10.1016/j.semcdb.2018.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
At the core of gene regulation, a complex network of dynamic interactions between proteins, DNA and RNA has to be integrated in order to generate a binary biological output. Large protein complexes, called adaptors, transfer information from the transcription factors to the transcription machinery [1,2]. Here we focus on Mediator, one of the largest adaptor proteins in humans [3]. Assembled from 30 different subunits, this system provides extraordinary illustrations for the various roles played by protein-protein interactions. Recruitment of new subunits during evolution is an adaptive mechanism to the growing complexity of the organism. Integration of information happens at multiple scales, with allosteric effects at the level of individual subunits resulting in large conformational changes. Mediator is also rich in disordered regions that increase the potential for interactions by presenting a malleable surface to its environment. Potentially, 3000 transcription factors can interact with Mediator and so understanding the molecular mechanisms that support the processing of this overload of information is one of the great challenges in molecular biology.
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Affiliation(s)
- Emma Sierecki
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, Faculty of Medecine, The University of New South Wales, Sydney, Australia.
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71
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Ibáñez FJ, Farías MA, Gonzalez-Troncoso MP, Corrales N, Duarte LF, Retamal-Díaz A, González PA. Experimental Dissection of the Lytic Replication Cycles of Herpes Simplex Viruses in vitro. Front Microbiol 2018; 9:2406. [PMID: 30386309 PMCID: PMC6198116 DOI: 10.3389/fmicb.2018.02406] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/20/2018] [Indexed: 12/16/2022] Open
Abstract
Herpes simplex viruses type 1 and type 2 (HSV-1 and HSV-2) produce lifelong infections and are highly prevalent in the human population. Both viruses elicit numerous clinical manifestations and produce mild-to-severe diseases that affect the skin, eyes, and brain, among others. Despite the existence of numerous antivirals against HSV, such as acyclovir and acyclovir-related analogs, virus variants that are resistant to these compounds can be isolated from immunosuppressed individuals. For such isolates, second-line drugs can be used, yet they frequently produce adverse side effects. Furthermore, topical antivirals for treating cutaneous HSV infections usually display poor to moderate efficacy. Hence, better or novel anti-HSV antivirals are needed and details on their mechanisms of action would be insightful for improving their efficacy and identifying specific molecular targets. Here, we review and dissect the lytic replication cycles of herpes simplex viruses, discussing key steps involved in cell infection and the processes that yield new virions. Additionally, we review and discuss rapid, easy-to-perform and simple experimental approaches for studying key steps involved in HSV replication to facilitate the identification of the mechanisms of action of anti-HSV compounds.
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Affiliation(s)
- Francisco J Ibáñez
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mónica A Farías
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maria P Gonzalez-Troncoso
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicolás Corrales
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luisa F Duarte
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Angello Retamal-Díaz
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A González
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Abstract
Viral DNA genomes have limited coding capacity and therefore harness cellular factors to facilitate replication of their genomes and generate progeny virions. Studies of viruses and how they interact with cellular processes have historically provided seminal insights into basic biology and disease mechanisms. The replicative life cycles of many DNA viruses have been shown to engage components of the host DNA damage and repair machinery. Viruses have evolved numerous strategies to navigate the cellular DNA damage response. By hijacking and manipulating cellular replication and repair processes, DNA viruses can selectively harness or abrogate distinct components of the cellular machinery to complete their life cycles. Here, we highlight consequences for viral replication and host genome integrity during the dynamic interactions between virus and host.
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Affiliation(s)
- Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104;
| | - Amélie Fradet-Turcotte
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Faculty of Medicine, Université Laval, Québec G1V 0A6, Canada;
- CHU de Québec Research Center-Université Laval (L'Hôtel-Dieu de Québec), Cancer Research Center, Québec G1R 2J6, Canada
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73
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Temporal Viral Genome-Protein Interactions Define Distinct Stages of Productive Herpesviral Infection. mBio 2018; 9:mBio.01182-18. [PMID: 30018111 PMCID: PMC6050965 DOI: 10.1128/mbio.01182-18] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Herpesviruses utilize multiple mechanisms to redirect host proteins for use in viral processes and to avoid recognition and repression by the host. To investigate dynamic interactions between herpes simplex virus type 1 (HSV-1) DNA and viral and host proteins throughout infection, we developed an approach to identify proteins that associate with the infecting viral genome from nuclear entry through packaging. To accomplish this, virus stocks were prepared in the presence of ethynyl-modified nucleotides to enable covalent tagging of viral genomes after infection for analysis of viral genome-protein interactions by imaging or affinity purification. Affinity purification was combined with stable isotope labeling of amino acids in cell culture (SILAC) mass spectrometry to enable the distinction between proteins that were brought into the cell by the virus or expressed within the infected cell before or during infection. We found that input viral DNA progressed within 6 h through four temporal stages where the genomes sequentially (i) interacted with intrinsic antiviral and DNA damage response proteins, (ii) underwent a robust transcriptional switch mediated largely by ICP4, (iii) engaged in replication, repair, and continued transcription, and then (iv) transitioned to a more transcriptionally inert state engaging de novo-synthesized viral structural components while maintaining interactions with replication proteins. Using a combination of genetic, imaging, and proteomic approaches, we provide a new and temporally compressed view of the HSV-1 life cycle based on input genome-proteome dynamics. Herpesviruses are highly prevalent and ubiquitous human pathogens. Studies of herpesviruses and other viruses have previously been limited by the ability to directly study events that occur on the viral DNA throughout infection. We present a new powerful approach, which allows for the temporal investigation of viral genome-protein interactions at all phases of infection. This work has integrated many results from previous studies with the discovery of novel factors potentially involved in viral infection that may represent new antiviral targets. In addition, the study provides a new view of the HSV-1 life cycle based on genome-proteome dynamics.
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Abstract
Viral DNA genomes have limited coding capacity and therefore harness cellular factors to facilitate replication of their genomes and generate progeny virions. Studies of viruses and how they interact with cellular processes have historically provided seminal insights into basic biology and disease mechanisms. The replicative life cycles of many DNA viruses have been shown to engage components of the host DNA damage and repair machinery. Viruses have evolved numerous strategies to navigate the cellular DNA damage response. By hijacking and manipulating cellular replication and repair processes, DNA viruses can selectively harness or abrogate distinct components of the cellular machinery to complete their life cycles. Here, we highlight consequences for viral replication and host genome integrity during the dynamic interactions between virus and host.
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Affiliation(s)
- Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104;
| | - Amélie Fradet-Turcotte
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Faculty of Medicine, Université Laval, Québec G1V 0A6, Canada; .,CHU de Québec Research Center-Université Laval (L'Hôtel-Dieu de Québec), Cancer Research Center, Québec G1R 2J6, Canada
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75
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Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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Herpes Simplex Virus 1 Dramatically Alters Loading and Positioning of RNA Polymerase II on Host Genes Early in Infection. J Virol 2018; 92:JVI.02184-17. [PMID: 29437966 DOI: 10.1128/jvi.02184-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/19/2018] [Indexed: 12/11/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) transcription is mediated by cellular RNA polymerase II (Pol II). Recent studies investigating how Pol II transcription of host genes is altered after HSV-1 are conflicting. Chromatin immunoprecipitation sequencing (ChIP-seq) studies suggest that Pol II is almost completely removed from host genes at 4 h postinfection (hpi), while 4-thiouridine (4SU) labeling experiments show that host transcription termination is extended at 7 hpi, implying that a significant amount of Pol II remains associated with host genes in infected cells. To address this discrepancy, we used precision nuclear run-on analysis (PRO-seq) to determine the location of Pol II to single-base-pair resolution in combination with quantitative reverse transcription-PCR (qRT-PCR) analysis at 3 hpi. HSV-1 decreased Pol II on approximately two-thirds of cellular genes but increased Pol II on others. For more than 85% of genes for which transcriptional termination could be statistically assessed, Pol II was displaced to positions downstream of the normal termination zone, suggesting extensive termination defects. Pol II amounts at the promoter, promoter-proximal pause site, and gene body were also modulated in a gene-specific manner. qRT-PCR of selected RNAs showed that HSV-1-induced extension of the termination zone strongly correlated with decreased RNA and mRNA accumulation. However, HSV-1-induced increases of Pol II occupancy on genes without termination zone extension correlated with increased cytoplasmic mRNA. Functional grouping of genes with increased Pol II occupancy suggested an upregulation of exosome secretion and downregulation of apoptosis, both of which are potentially beneficial to virus production.IMPORTANCE This study provides a map of RNA polymerase II location on host genes after infection with HSV-1 with greater detail than previous ChIP-seq studies and rectifies discrepancies between ChIP-seq data and 4SU labeling experiments with HSV-1. The data show the effects that a given change in RNA Pol II location on host genes has on the abundance of different RNA types, including nuclear, polyadenylated mRNA and cytoplasmic, polyadenylated mRNA. It gives a clearer understanding of how HSV-1 augments host transcription of some genes to provide an environment favorable to HSV-1 replication.
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Alandijany T, Roberts APE, Conn KL, Loney C, McFarlane S, Orr A, Boutell C. Distinct temporal roles for the promyelocytic leukaemia (PML) protein in the sequential regulation of intracellular host immunity to HSV-1 infection. PLoS Pathog 2018; 14:e1006769. [PMID: 29309427 PMCID: PMC5757968 DOI: 10.1371/journal.ppat.1006769] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/24/2017] [Indexed: 12/22/2022] Open
Abstract
Detection of viral nucleic acids plays a critical role in the induction of intracellular host immune defences. However, the temporal recruitment of immune regulators to infecting viral genomes remains poorly defined due to the technical difficulties associated with low genome copy-number detection. Here we utilize 5-Ethynyl-2'-deoxyuridine (EdU) labelling of herpes simplex virus 1 (HSV-1) DNA in combination with click chemistry to examine the sequential recruitment of host immune regulators to infecting viral genomes under low multiplicity of infection conditions. Following viral genome entry into the nucleus, PML-nuclear bodies (PML-NBs) rapidly entrapped viral DNA (vDNA) leading to a block in viral replication in the absence of the viral PML-NB antagonist ICP0. This pre-existing intrinsic host defence to infection occurred independently of the vDNA pathogen sensor IFI16 (Interferon Gamma Inducible Protein 16) and the induction of interferon stimulated gene (ISG) expression, demonstrating that vDNA entry into the nucleus alone is not sufficient to induce a robust innate immune response. Saturation of this pre-existing intrinsic host defence during HSV-1 ICP0-null mutant infection led to the stable recruitment of PML and IFI16 into vDNA complexes associated with ICP4, and led to the induction of ISG expression. This induced innate immune response occurred in a PML-, IFI16-, and Janus-Associated Kinase (JAK)-dependent manner and was restricted by phosphonoacetic acid, demonstrating that vDNA polymerase activity is required for the robust induction of ISG expression during HSV-1 infection. Our data identifies dual roles for PML in the sequential regulation of intrinsic and innate immunity to HSV-1 infection that are dependent on viral genome delivery to the nucleus and the onset of vDNA replication, respectively. These intracellular host defences are counteracted by ICP0, which targets PML for degradation from the outset of nuclear infection to promote vDNA release from PML-NBs and the onset of HSV-1 lytic replication.
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MESH Headings
- Cell Line
- Cell Line, Transformed
- Cells, Cultured
- Click Chemistry
- Gene Deletion
- Gene Expression Regulation, Viral/drug effects
- Herpes Simplex/drug therapy
- Herpes Simplex/metabolism
- Herpes Simplex/pathology
- Herpes Simplex/virology
- Herpesvirus 1, Human/growth & development
- Herpesvirus 1, Human/physiology
- Host-Pathogen Interactions/drug effects
- Humans
- Immunity, Innate/drug effects
- Inclusion Bodies, Viral/drug effects
- Inclusion Bodies, Viral/metabolism
- Inclusion Bodies, Viral/pathology
- Inclusion Bodies, Viral/virology
- Kinetics
- Lysogeny/drug effects
- Mutation
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphoproteins/antagonists & inhibitors
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Promyelocytic Leukemia Protein/antagonists & inhibitors
- Promyelocytic Leukemia Protein/genetics
- Promyelocytic Leukemia Protein/metabolism
- RNA Interference
- Reverse Transcriptase Inhibitors/pharmacology
- Ubiquitin-Protein Ligases/genetics
- Ubiquitin-Protein Ligases/metabolism
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Internalization/drug effects
- Virus Replication/drug effects
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Affiliation(s)
- Thamir Alandijany
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ashley P. E. Roberts
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Kristen L. Conn
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Steven McFarlane
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Anne Orr
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus, Glasgow, Scotland, United Kingdom
- * E-mail:
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78
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Döhner K, Ramos-Nascimento A, Bialy D, Anderson F, Hickford-Martinez A, Rother F, Koithan T, Rudolph K, Buch A, Prank U, Binz A, Hügel S, Lebbink RJ, Hoeben RC, Hartmann E, Bader M, Bauerfeind R, Sodeik B. Importin α1 is required for nuclear import of herpes simplex virus proteins and capsid assembly in fibroblasts and neurons. PLoS Pathog 2018; 14:e1006823. [PMID: 29304174 PMCID: PMC5773220 DOI: 10.1371/journal.ppat.1006823] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/18/2018] [Accepted: 12/16/2017] [Indexed: 01/28/2023] Open
Abstract
Herpesviruses are large DNA viruses which depend on many nuclear functions, and therefore on host transport factors to ensure specific nuclear import of viral and host components. While some import cargoes bind directly to certain transport factors, most recruit importin β1 via importin α. We identified importin α1 in a small targeted siRNA screen to be important for herpes simplex virus (HSV-1) gene expression. Production of infectious virions was delayed in the absence of importin α1, but not in cells lacking importin α3 or importin α4. While nuclear targeting of the incoming capsids, of the HSV-1 transcription activator VP16, and of the viral genomes were not affected, the nuclear import of the HSV-1 proteins ICP4 and ICP0, required for efficient viral transcription, and of ICP8 and pUL42, necessary for DNA replication, were reduced. Furthermore, quantitative electron microscopy showed that fibroblasts lacking importin α1 contained overall fewer nuclear capsids, but an increased proportion of mature nuclear capsids indicating that capsid formation and capsid egress into the cytoplasm were impaired. In neurons, importin α1 was also not required for nuclear targeting of incoming capsids, but for nuclear import of ICP4 and for the formation of nuclear capsid assembly compartments. Our data suggest that importin α1 is specifically required for the nuclear localization of several important HSV1 proteins, capsid assembly, and capsid egress into the cytoplasm, and may become rate limiting in situ upon infection at low multiplicity or in terminally differentiated cells such as neurons. Nuclear pore complexes are highly selective gateways that penetrate the nuclear envelope for bidirectional trafficking between the cytoplasm and the nucleoplasm. Viral and host cargoes have to engage specific transport factors to achieve active nuclear import and export. Like many human and animal DNA viruses, herpesviruses are critically dependent on many functions of the host cell nucleus. Alphaherpesviruses such as herpes simplex virus (HSV) cause many diseases upon productive infection in epithelial cells, fibroblasts and neurons. Here, we asked which nuclear transport factors of the host cells help HSV-1 to translocate viral components into the nucleus for viral gene expression, nuclear capsid assembly, capsid egress into the cytoplasm, and production of infectious virions. Our data show that HSV-1 requires the nuclear import factor importin α1 for efficient replication and virus assembly in fibroblasts and in mature neurons. To our knowledge this is the first time that a specific importin α isoform is shown to be required for herpesvirus infection. Our study fosters our understanding on how the different but highly homologous importin α isoforms could fulfill specific functions in vivo which are only understood for a very limited number of host and viral cargos.
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Affiliation(s)
- Katinka Döhner
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | | | - Dagmara Bialy
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Fenja Anderson
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | | | - Franziska Rother
- Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
- Institute for Biology, University of Lübeck, Lübeck, Germany
| | - Thalea Koithan
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Kathrin Rudolph
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Anna Buch
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Ute Prank
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Anne Binz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Stefanie Hügel
- Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
- Institute for Biology, University of Lübeck, Lübeck, Germany
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob C. Hoeben
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Enno Hartmann
- Institute for Biology, University of Lübeck, Lübeck, Germany
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
- Institute for Biology, University of Lübeck, Lübeck, Germany
| | - Rudolf Bauerfeind
- Research Core Unit Laser Microscopy, Hannover Medical School, Hannover, Germany
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, Hannover, Germany
- * E-mail:
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79
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Sekine E, Schmidt N, Gaboriau D, O’Hare P. Spatiotemporal dynamics of HSV genome nuclear entry and compaction state transitions using bioorthogonal chemistry and super-resolution microscopy. PLoS Pathog 2017; 13:e1006721. [PMID: 29121649 PMCID: PMC5697887 DOI: 10.1371/journal.ppat.1006721] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/21/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
We investigated the spatiotemporal dynamics of HSV genome transport during the initiation of infection using viruses containing bioorthogonal traceable precursors incorporated into their genomes (HSVEdC). In vitro assays revealed a structural alteration in the capsid induced upon HSVEdC binding to solid supports that allowed coupling to external capture agents and demonstrated that the vast majority of individual virions contained bioorthogonally-tagged genomes. Using HSVEdC in vivo we reveal novel aspects of the kinetics, localisation, mechanistic entry requirements and morphological transitions of infecting genomes. Uncoating and nuclear import was observed within 30 min, with genomes in a defined compaction state (ca. 3-fold volume increase from capsids). Free cytosolic uncoated genomes were infrequent (7-10% of the total uncoated genomes), likely a consequence of subpopulations of cells receiving high particle numbers. Uncoated nuclear genomes underwent temporal transitions in condensation state and while ICP4 efficiently associated with condensed foci of initial infecting genomes, this relationship switched away from residual longer lived condensed foci to increasingly decondensed genomes as infection progressed. Inhibition of transcription had no effect on nuclear entry but in the absence of transcription, genomes persisted as tightly condensed foci. Ongoing transcription, in the absence of protein synthesis, revealed a distinct spatial clustering of genomes, which we have termed genome congregation, not seen with non-transcribing genomes. Genomes expanded to more decondensed forms in the absence of DNA replication indicating additional transitional steps. During full progression of infection, genomes decondensed further, with a diffuse low intensity signal dissipated within replication compartments, but frequently with tight foci remaining peripherally, representing unreplicated genomes or condensed parental strands of replicated DNA. Uncoating and nuclear entry was independent of proteasome function and resistant to inhibitors of nuclear export. Together with additional data our results reveal new insight into the spatiotemporal dynamics of HSV genome uncoating, transport and organisation.
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Affiliation(s)
- Eiki Sekine
- Section of Virology, Department of Medicine, Imperial College, St Mary’s Medical School, London, United Kingdom
| | - Nora Schmidt
- Section of Virology, Department of Medicine, Imperial College, St Mary’s Medical School, London, United Kingdom
| | - David Gaboriau
- Department of Medicine, Facility for Imaging by Light Microscopy, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Peter O’Hare
- Section of Virology, Department of Medicine, Imperial College, St Mary’s Medical School, London, United Kingdom
- * E-mail:
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80
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Ralph M, Bednarchik M, Tomer E, Rafael D, Zargarian S, Gerlic M, Kobiler O. Promoting Simultaneous Onset of Viral Gene Expression Among Cells Infected with Herpes Simplex Virus-1. Front Microbiol 2017; 8:2152. [PMID: 29163436 PMCID: PMC5671993 DOI: 10.3389/fmicb.2017.02152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/20/2017] [Indexed: 11/30/2022] Open
Abstract
Synchronous viral infection facilitates the study of viral gene expression, viral host interactions, and viral replication processes. However, the protocols for achieving synchronous infections were hardly ever tested in proper temporal resolution at the single-cell level. We set up a fluorescence-based, time lapse microscopy assay to study sources of variability in the timing of gene expression during herpes simplex virus-1 (HSV-1) infection. We found that with the common protocol, the onset of gene expression within different cells can vary by more than 3 h. We showed that simultaneous viral genome entry to the nucleus can be achieved with a derivative of the previously characterized temperature sensitive mutant tsB7, however, this did not improve gene expression synchrony. We found that elevating the temperature in which the infection is done and increasing the multiplicity of infection (MOI) significantly promoted simultaneous onset of viral gene expression among infected cells. Further, elevated temperature result in a decrease in the coefficient of variation (a standardized measure of dispersion) of viral replication compartments (RCs) sizes among cells as well as a slight increment of viral late gene expression synchrony. We conclude that simultaneous viral gene expression can be improved by simple modifications to the infection process and may reduce the effect of single-cell variability on population-based assays.
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Affiliation(s)
| | | | | | | | | | | | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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81
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Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD. Identifying Host Factors Associated with DNA Replicated During Virus Infection. Mol Cell Proteomics 2017; 16:2079-2097. [PMID: 28972080 DOI: 10.1074/mcp.m117.067116] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/14/2017] [Indexed: 01/22/2023] Open
Abstract
Viral DNA genomes replicating in cells encounter a myriad of host factors that facilitate or hinder viral replication. Viral proteins expressed early during infection modulate host factors interacting with viral genomes, recruiting proteins to promote viral replication, and limiting access to antiviral repressors. Although some host factors manipulated by viruses have been identified, we have limited knowledge of pathways exploited during infection and how these differ between viruses. To identify cellular processes manipulated during viral replication, we defined proteomes associated with viral genomes during infection with adenovirus, herpes simplex virus and vaccinia virus. We compared enrichment of host factors between virus proteomes and confirmed association with viral genomes and replication compartments. Using adenovirus as an illustrative example, we uncovered host factors deactivated by early viral proteins, and identified a subgroup of nucleolar proteins that aid virus replication. Our data sets provide valuable resources of virus-host interactions that affect proteins on viral genomes.
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Affiliation(s)
- Emigdio D Reyes
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katarzyna Kulej
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Neha J Pancholi
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,¶Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lisa N Akhtar
- ‖Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daphne C Avgousti
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Eui Tae Kim
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daniel K Bricker
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lynn A Spruce
- **Protein and Proteomics Core, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sarah A Koniski
- §Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Steven H Seeholzer
- **Protein and Proteomics Core, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stuart N Isaacs
- ‡‡Division of Infectious Diseases, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Benjamin A Garcia
- §§Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Matthew D Weitzman
- From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; .,§Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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82
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Identification of Vaccinia Virus Replisome and Transcriptome Proteins by Isolation of Proteins on Nascent DNA Coupled with Mass Spectrometry. J Virol 2017; 91:JVI.01015-17. [PMID: 28747503 DOI: 10.1128/jvi.01015-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/19/2017] [Indexed: 12/22/2022] Open
Abstract
Poxviruses replicate within the cytoplasm and encode proteins for DNA and mRNA synthesis. To investigate poxvirus replication and transcription from a new perspective, we incorporated 5-ethynyl-2'-deoxyuridine (EdU) into nascent DNA in cells infected with vaccinia virus (VACV). The EdU-labeled DNA was conjugated to fluor- or biotin-azide and visualized by confocal, superresolution, and transmission electron microscopy. Nuclear labeling decreased dramatically after infection, accompanied by intense labeling of cytoplasmic foci. The nascent DNA colocalized with the VACV single-stranded DNA binding protein I3 in multiple puncta throughout the interior of factories, which were surrounded by endoplasmic reticulum. Complexes containing EdU-biotin-labeled DNA cross-linked to proteins were captured on streptavidin beads. After elution and proteolysis, the peptides were analyzed by mass spectrometry to identify proteins associated with nascent DNA. The known viral replication proteins, a telomere binding protein, and a protein kinase were associated with nascent DNA, as were the DNA-dependent RNA polymerase and intermediate- and late-stage transcription initiation and elongation factors, plus the capping and methylating enzymes. These results suggested that the replicating pool of DNA is transcribed and that few if any additional viral proteins directly engaged in replication and transcription remain to be discovered. Among the host proteins identified by mass spectrometry, topoisomerases IIα and IIβ and PCNA were noteworthy. The association of the topoisomerases with nascent DNA was dependent on expression of the viral DNA ligase, in accord with previous proteomic studies. Further investigations are needed to determine possible roles for PCNA and other host proteins detected.IMPORTANCE Poxviruses, unlike many well-characterized animal DNA viruses, replicate entirely within the cytoplasm of animal cells, raising questions regarding the relative roles of viral and host proteins. We adapted newly developed procedures for click chemistry and iPOND (Isolation of proteins on nascent DNA) to investigate vaccinia virus (VACV), the prototype poxvirus. Nuclear DNA synthesis ceased almost immediately following VACV infection, followed swiftly by the synthesis of viral DNA within discrete cytoplasmic foci. All viral proteins known from genetic and proteomic studies to be required for poxvirus DNA replication were identified in the complexes containing nascent DNA. The additional detection of the viral DNA-dependent RNA polymerase and intermediate and late transcription factors provided evidence for a temporal coupling of replication and transcription. Further studies are needed to assess the potential roles of host proteins, including topoisomerases IIα and IIβ and PCNA, which were found associated with nascent DNA.
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83
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Dembowski JA, Deluca NA. Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins. J Vis Exp 2017. [PMID: 28892026 DOI: 10.3791/56374] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The goal of this protocol is to isolate herpes simplex virus type 1 (HSV-1) DNA from infected cells for the identification of associated viral and cellular proteins by mass spectrometry. Although proteins that interact with viral genomes play major roles in determining the outcome of infection, a comprehensive analysis of viral genome associated proteins was not previously feasible. Here we demonstrate a method that enables the direct purification of HSV-1 genomes from infected cells. Replicating viral DNA is selectively labeled with modified nucleotides that contain an alkyne functional group. Labeled DNA is then specifically and irreversibly tagged via the covalent attachment of biotin azide via a copper(I)-catalyzed azide-alkyne cycloaddition or click reaction. Biotin-tagged DNA is purified on streptavidin-coated beads and associated proteins are eluted and identified by mass spectrometry. This method enables the selective targeting and isolation of HSV-1 replication forks or whole genomes from complex biological environments. Furthermore, adaptation of this approach will allow for the investigation of various aspects of herpesviral infection, as well as the examination of the genomes of other DNA viruses.
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Affiliation(s)
- Jill A Dembowski
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine;
| | - Neal A Deluca
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine;
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84
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Olias P, Etheridge RD, Zhang Y, Holtzman MJ, Sibley LD. Toxoplasma Effector Recruits the Mi-2/NuRD Complex to Repress STAT1 Transcription and Block IFN-γ-Dependent Gene Expression. Cell Host Microbe 2017; 20:72-82. [PMID: 27414498 DOI: 10.1016/j.chom.2016.06.006] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/09/2016] [Accepted: 06/09/2016] [Indexed: 12/12/2022]
Abstract
Interferon gamma (IFN-γ) is an essential mediator of host defense against intracellular pathogens, including the protozoan parasite Toxoplasma gondii. However, prior T. gondii infection blocks IFN-γ-dependent gene transcription, despite the downstream transcriptional activator STAT1 being activated and bound to cognate nuclear promoters. We identify the parasite effector that blocks STAT1-dependent transcription and show it is associated with recruitment of the Mi-2 nucleosome remodeling and deacetylase (NuRD) complex, a chromatin-modifying repressor. This secreted effector, toxoplasma inhibitor of STAT1-dependent transcription (TgIST), translocates to the host cell nucleus, where it recruits Mi-2/NuRD to STAT1-dependent promoters, resulting in altered chromatin and blocked transcription. TgIST is conserved across strains, underlying their shared ability to block IFN-γ-dependent transcription. TgIST deletion results in increased parasite clearance in IFN-γ-activated cells and reduced mouse virulence, which is restored in IFN-γ-receptor-deficient mice. These findings demonstrate the importance of both IFN-γ responses and the ability of pathogens to counteract these defenses.
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Affiliation(s)
- Philipp Olias
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ronald D Etheridge
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yong Zhang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Holtzman
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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85
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Zhao Z, Tang KW, Muylaert I, Samuelsson T, Elias P. CDK9 and SPT5 proteins are specifically required for expression of herpes simplex virus 1 replication-dependent late genes. J Biol Chem 2017; 292:15489-15500. [PMID: 28743741 PMCID: PMC5602406 DOI: 10.1074/jbc.m117.806000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Indexed: 12/02/2022] Open
Abstract
DNA replication greatly enhances expression of the herpes simplex virus 1 (HSV-1) γ2 late genes by still unknown mechanisms. Here, we demonstrate that 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB), an inhibitor of CDK9, suppresses expression of γ2 late genes with an IC50 of 5 μm, which is at least 10 times lower than the IC50 value required for inhibition of expression of early genes. The effect of DRB could not be explained by inhibition of DNA replication per se or loading of RNA polymerase II to late promoters and subsequent reduction of transcription. Instead, DRB reduces accumulation of γ2 late mRNA in the cytoplasm. In addition, we show that siRNA-mediated knockdown of the transcription factor SPT5, but not NELF-E, also gives rise to a specific inhibition of HSV-1 late gene expression. Finally, addition of DRB reduces co-immunoprecipitation of ICP27 using an anti-SPT5 antibody. Our results suggest that efficient expression of replication-dependent γ2 late genes is, at least in part, regulated by CDK9 dependent co- and/or post-transcriptional events involving SPT5 and ICP27.
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Affiliation(s)
- Zhiyuan Zhao
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, SE-405 30 Gothenburg, Sweden
| | - Ka-Wei Tang
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, SE-405 30 Gothenburg, Sweden
| | - Isabella Muylaert
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, SE-405 30 Gothenburg, Sweden
| | - Tore Samuelsson
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, SE-405 30 Gothenburg, Sweden
| | - Per Elias
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, SE-405 30 Gothenburg, Sweden
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86
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Abstract
Herpes simplex virus 1 (HSV-1) genes are transcribed by cellular RNA polymerase II (RNA Pol II). While four viral immediate early proteins (ICP4, ICP0, ICP27, and ICP22) function in some capacity in viral transcription, the mechanism by which ICP22 functions remains unclear. We observed that the FACT complex (comprised of SSRP1 and Spt16) was relocalized in infected cells as a function of ICP22. ICP22 was also required for the association of FACT and the transcription elongation factors SPT5 and SPT6 with viral genomes. We further demonstrated that the FACT complex interacts with ICP22 throughout infection. We therefore hypothesized that ICP22 recruits cellular transcription elongation factors to viral genomes for efficient transcription elongation of viral genes. We reevaluated the phenotype of an ICP22 mutant virus by determining the abundance of all viral mRNAs throughout infection by transcriptome sequencing (RNA-seq). The accumulation of almost all viral mRNAs late in infection was reduced compared to the wild type, regardless of kinetic class. Using chromatin immunoprecipitation sequencing (ChIP-seq), we mapped the location of RNA Pol II on viral genes and found that RNA Pol II levels on the bodies of viral genes were reduced in the ICP22 mutant compared to wild-type virus. In contrast, the association of RNA Pol II with transcription start sites in the mutant was not reduced. Taken together, our results indicate that ICP22 plays a role in recruiting elongation factors like the FACT complex to the HSV-1 genome to allow for efficient viral transcription elongation late in viral infection and ultimately infectious virion production. HSV-1 interacts with many cellular proteins throughout productive infection. Here, we demonstrate the interaction of a viral protein, ICP22, with a subset of cellular proteins known to be involved in transcription elongation. We determined that ICP22 is required to recruit the FACT complex and other transcription elongation factors to viral genomes and that in the absence of ICP22 viral transcription is globally reduced late in productive infection, due to an elongation defect. This insight defines a fundamental role of ICP22 in HSV-1 infection and elucidates the involvement of cellular factors in HSV-1 transcription.
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87
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Sherry MR, Hay TJM, Gulak MA, Nassiri A, Finnen RL, Banfield BW. The Herpesvirus Nuclear Egress Complex Component, UL31, Can Be Recruited to Sites of DNA Damage Through Poly-ADP Ribose Binding. Sci Rep 2017; 7:1882. [PMID: 28507315 PMCID: PMC5432524 DOI: 10.1038/s41598-017-02109-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/07/2017] [Indexed: 12/20/2022] Open
Abstract
The herpes simplex virus (HSV) UL31 gene encodes a conserved member of the herpesvirus nuclear egress complex that not only functions in the egress of DNA containing capsids from the nucleus, but is also required for optimal replication of viral DNA and its packaging into capsids. Here we report that the UL31 protein from HSV-2 can be recruited to sites of DNA damage by sequences found in its N-terminus. The N-terminus of UL31 contains sequences resembling a poly (ADP-ribose) (PAR) binding motif suggesting that PAR interactions might mediate UL31 recruitment to damaged DNA. Whereas PAR polymerase inhibition prevented UL31 recruitment to damaged DNA, inhibition of signaling through the ataxia telangiectasia mutated DNA damage response pathway had no effect. These findings were further supported by experiments demonstrating direct and specific interaction between HSV-2 UL31 and PAR using purified components. This study reveals a previously unrecognized function for UL31 and may suggest that the recognition of PAR by UL31 is coupled to the nuclear egress of herpesvirus capsids, influences viral DNA replication and packaging, or possibly modulates the DNA damage response mounted by virally infected cells.
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Affiliation(s)
- Maxwell R Sherry
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Thomas J M Hay
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Michael A Gulak
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Arash Nassiri
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Renée L Finnen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Bruce W Banfield
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada.
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88
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Wiest NE, Tomkinson AE. Optimization of Native and Formaldehyde iPOND Techniques for Use in Suspension Cells. Methods Enzymol 2017. [PMID: 28645366 DOI: 10.1016/bs.mie.2017.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The isolation of proteins on nascent DNA (iPOND) technique developed by the Cortez laboratory allows a previously unparalleled ability to examine proteins associated with replicating and newly synthesized DNA in mammalian cells. Both the original, formaldehyde-based iPOND technique and a more recent derivative, accelerated native iPOND (aniPOND), have mostly been performed in adherent cell lines. Here, we describe modifications to both protocols for use with suspension cell lines. These include cell culture, pulse, and chase conditions that optimize sample recovery in both protocols using suspension cells and several key improvements to the published aniPOND technique that reduce sample loss, increase signal to noise, and maximize sample recovery. Additionally, we directly and quantitatively compare the iPOND and aniPOND protocols to test the strengths and limitations of both. Finally, we present a detailed protocol to perform the optimized aniPOND protocol in suspension cell lines.
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Affiliation(s)
- Nathaniel E Wiest
- University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Alan E Tomkinson
- University of New Mexico School of Medicine, Albuquerque, NM, United States.
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89
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Abstract
DNA replication in a human cell involves hundreds of proteins that copy the DNA accurately and completely each cell division cycle. In addition to the core DNA copying machine (the replisome), accessory proteins work to respond to replication stress, correct errors, and repackage the DNA into appropriate chromatin structures. New proteomic tools have been invented in the past few years to facilitate the purification, identification, and quantification of the replication, chromatin maturation, and replication stress response machineries. These tools, including iPOND (isolation of proteins on nascent DNA) and NCC (nascent chromatin capture), have yielded discoveries of new proteins involved in these processes and insights into the dynamic regulatory processes ensuring genome and chromatin integrity. In this review, I will introduce these experimental approaches and examine how they have been utilized to define the replication fork proteome.
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Affiliation(s)
- David Cortez
- Vanderbilt University School of Medicine, Nashville, TN, United States.
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90
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Wang Q, Li Y, Dong H, Wang L, Peng J, An T, Yang X, Tian Z, Cai X. Identification of host cellular proteins that interact with the M protein of a highly pathogenic porcine reproductive and respiratory syndrome virus vaccine strain. Virol J 2017; 14:39. [PMID: 28222748 PMCID: PMC5320790 DOI: 10.1186/s12985-017-0700-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) continues to pose one of the greatest threats to the swine industry. M protein is the most conserved and important structural protein of PRRSV. However, information about the host cellular proteins that interact with M protein remains limited. METHODS Host cellular proteins that interact with the M protein of HP-PRRSV were immunoprecipitated from MARC-145 cells infected with PRRSV HuN4-F112 using the M monoclonal antibody (mAb). The differentially expressed proteins were identified by LC-MS/MS. The screened proteins were used for bioinformatics analysis including Gene Ontology, the interaction network, and the enriched KEGG pathways. Some interested cellular proteins were validated to interact with M protein by CO-IP. RESULTS The PRRSV HuN4-F112 infection group had 10 bands compared with the control group. The bands included 219 non-redundant cellular proteins that interact with M protein, which were identified by LC-MS/MS with high confidence. The gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway bioinformatic analyses indicated that the identified proteins could be assigned to several different subcellular locations and functional classes. Functional analysis of the interactome profile highlighted cellular pathways associated with protein translation, infectious disease, and signal transduction. Two interested cellular proteins-nuclear factor of activated T cells 45 kDa (NF45) and proliferating cell nuclear antigen (PCNA)-that could interact with M protein were validated by Co-IP and confocal analyses. CONCLUSIONS The interactome data between PRRSV M protein and cellular proteins were identified and contribute to the understanding of the roles of M protein in the replication and pathogenesis of PRRSV. The interactome of M protein will aid studies of virus/host interactions and provide means to decrease the threat of PRRSV to the swine industry in the future.
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Affiliation(s)
- Qian Wang
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China
| | - Yanwei Li
- National Engineering Research Center of Veterinary Biologics, Harbin, 150001, China
| | - Hong Dong
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agribiotechnology, China Agricultural University, Beijing, 100193, China
| | - Li Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agribiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinmei Peng
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China
| | - Tongqing An
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China
| | - Xufu Yang
- North Guangdong Collaborative Innovation and Development Center of Pig Farming and Disease Control, Shaoguan University, Shaoguan, 512005, China
| | - Zhijun Tian
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China.
| | - Xuehui Cai
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China.
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91
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McBride AA. The Promise of Proteomics in the Study of Oncogenic Viruses. Mol Cell Proteomics 2017; 16:S65-S74. [PMID: 28104704 DOI: 10.1074/mcp.o116.065201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/16/2016] [Indexed: 12/30/2022] Open
Abstract
Oncogenic viruses are responsible for about 15% human cancers. This article explores the promise and challenges of viral proteomics in the study of the oncogenic human DNA viruses, HPV, McPyV, EBV and KSHV. These viruses have coevolved with their hosts and cause persistent infections. Each virus encodes oncoproteins that manipulate key cellular pathways to promote viral replication and evade the host immune response. Viral proteomics can identify cellular pathways perturbed by viral infection, identify cellular proteins that are crucial for viral persistence and oncogenesis, and identify important diagnostic and therapeutic targets.
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Affiliation(s)
- Alison A McBride
- From the ‡Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, 33 North Drive, MSC3209, National Institutes of Health, Bethesda, Maryland 20892
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92
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Replication-Coupled Recruitment of Viral and Cellular Factors to Herpes Simplex Virus Type 1 Replication Forks for the Maintenance and Expression of Viral Genomes. PLoS Pathog 2017; 13:e1006166. [PMID: 28095497 PMCID: PMC5271410 DOI: 10.1371/journal.ppat.1006166] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/27/2017] [Accepted: 01/03/2017] [Indexed: 01/13/2023] Open
Abstract
Herpes simplex virus type 1 (HSV-1) infects over half the human population. Much of the infectious cycle occurs in the nucleus of cells where the virus has evolved mechanisms to manipulate host processes for the production of virus. The genome of HSV-1 is coordinately expressed, maintained, and replicated such that progeny virions are produced within 4–6 hours post infection. In this study, we selectively purify HSV-1 replication forks and associated proteins from virus-infected cells and identify select viral and cellular replication, repair, and transcription factors that associate with viral replication forks. Pulse chase analyses and imaging studies reveal temporal and spatial dynamics between viral replication forks and associated proteins and demonstrate that several DNA repair complexes and key transcription factors are recruited to or near replication forks. Consistent with these observations we show that the initiation of viral DNA replication is sufficient to license late gene transcription. These data provide insight into mechanisms that couple HSV-1 DNA replication with transcription and repair for the coordinated expression and maintenance of the viral genome. HSV-1 is a ubiquitous human pathogen that causes persistent infections for the lifetime of the infected host. Of major interest are the mechanisms underlying how the virus utilizes cellular resources to rapidly replicate with high fidelity. We show that DNA repair and late transcription are coupled to genome replication by identifying the viral and cellular factors that associate with replicating viral DNA. In addition to transcription and repair, the results also describe how RNA processing and virion packaging are temporally coordinated relative to genome replication.
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93
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The Role of Nuclear Antiviral Factors against Invading DNA Viruses: The Immediate Fate of Incoming Viral Genomes. Viruses 2016; 8:v8100290. [PMID: 27782081 PMCID: PMC5086622 DOI: 10.3390/v8100290] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
In recent years, it has been suggested that host cells exert intrinsic mechanisms to control nuclear replicating DNA viruses. This cellular response involves nuclear antiviral factors targeting incoming viral genomes. Herpes simplex virus-1 (HSV-1) is the best-studied model in this context, and it was shown that upon nuclear entry HSV-1 genomes are immediately targeted by components of promyelocytic leukemia nuclear bodies (PML-NBs) and the nuclear DNA sensor IFI16 (interferon gamma inducible protein 16). Based on HSV-1 studies, together with limited examples in other viral systems, these phenomena are widely believed to be a common cellular response to incoming viral genomes, although formal evidence for each virus is lacking. Indeed, recent studies suggest that the case may be different for adenovirus infection. Here we summarize the existing experimental evidence for the roles of nuclear antiviral factors against incoming viral genomes to better understand cellular responses on a virus-by-virus basis. We emphasize that cells seem to respond differently to different incoming viral genomes and discuss possible arguments for and against a unifying cellular mechanism targeting the incoming genomes of different virus families.
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94
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Ren K, Zhang W, Chen X, Ma Y, Dai Y, Fan Y, Hou Y, Tan RX, Li E. An Epigenetic Compound Library Screen Identifies BET Inhibitors That Promote HSV-1 and -2 Replication by Bridging P-TEFb to Viral Gene Promoters through BRD4. PLoS Pathog 2016; 12:e1005950. [PMID: 27764245 PMCID: PMC5072739 DOI: 10.1371/journal.ppat.1005950] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/22/2016] [Indexed: 12/22/2022] Open
Abstract
The human HSV-1 and -2 are common pathogens of human diseases. Both host and viral factors are involved in HSV lytic infection, although detailed mechanisms remain elusive. By screening a chemical library of epigenetic regulation, we identified bromodomain-containing protein 4 (BRD4) as a critical player in HSV infection. We show that treatment with pan BD domain inhibitor enhanced both HSV infection. Using JQ1 as a probe, we found that JQ1, a defined BD1 inhibitor, acts through BRD4 protein since knockdown of BRD4 expression ablated JQ1 effect on HSV infection. BRD4 regulates HSV replication through complex formation involving CDK9 and RNAP II; whereas, JQ1 promotes HSV-1 infection by allocating the complex to HSV gene promoters. Therefore, suppression of BRD4 expression or inhibition of CDK9 activity impeded HSV infection. Our data support a model that JQ1 enhances HSV infection by switching BRD4 to transcription regulation of viral gene expression from chromatin targeting since transient expression of BRD4 BD1 or BD1/2 domain had similar effect to that by JQ1 treatment. In addition to the identification that BRD4 is a modulator for JQ1 action on HSV infection, this study demonstrates BRD4 has an essential role in HSV infection.
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Affiliation(s)
- Ke Ren
- Medical School and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
- Jiangsu Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Wei Zhang
- Medical School and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
- Jiangsu Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Xiaoqing Chen
- The Hoffmann Institute of Immunology, Guangzhou Medical University, Guangzhou, China
| | - Yingyu Ma
- Medical School and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
- Jiangsu Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Yue Dai
- Jiangsu Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Yimei Fan
- Medical School and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yayi Hou
- Medical School and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Ren Xiang Tan
- Medical School and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
- Jiangsu Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
- Nanjing University of Chinese Medicine, Nanjing, China
- * E-mail: ;
| | - Erguang Li
- Medical School and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
- Jiangsu Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
- * E-mail: ;
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95
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Komatsu T, Robinson DR, Hisaoka M, Ueshima S, Okuwaki M, Nagata K, Wodrich H. Tracking adenovirus genomes identifies morphologically distinct late DNA replication compartments. Traffic 2016; 17:1168-1180. [PMID: 27492875 DOI: 10.1111/tra.12429] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/02/2016] [Accepted: 08/02/2016] [Indexed: 02/01/2023]
Abstract
In adenoviral virions, the genome is organized into a chromatin-like structure by viral basic core proteins. Consequently viral DNAs must be replicated, chromatinized and packed into progeny virions in infected cells. Although viral DNA replication centers can be visualized by virtue of viral and cellular factors, the spatiotemporal regulation of viral genomes during subsequent steps remains to be elucidated. In this study, we used imaging analyses to examine the fate of adenoviral genomes and to track newly replicated viral DNA as well as replication-related factors. We show de novo formation of a subnuclear domain, which we termed Virus-induced Post-Replication (ViPR) body, that emerges concomitantly with or immediately after disintegration of initial replication centers. Using a nucleoside analogue, we show that viral genomes continue being synthesized in morphologically distinct replication compartments at the periphery of ViPR bodies and are then transported inward. In addition, we identified a nucleolar protein Mybbp1a as a molecular marker for ViPR bodies, which specifically associated with viral core protein VII. In conclusion, our work demonstrates the formation of previously uncharacterized viral DNA replication compartments specific for late phases of infection that produce progeny viral genomes accumulating in ViPR bodies.
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Affiliation(s)
- Tetsuro Komatsu
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France.,Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Derrick R Robinson
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Miharu Hisaoka
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shuhei Ueshima
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mitsuru Okuwaki
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France.
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96
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Gu H, Zheng Y. Role of ND10 nuclear bodies in the chromatin repression of HSV-1. Virol J 2016; 13:62. [PMID: 27048561 PMCID: PMC4822283 DOI: 10.1186/s12985-016-0516-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/28/2016] [Indexed: 01/09/2023] Open
Abstract
Herpes simplex virus (HSV) is a neurotropic virus that establishes lifelong latent infection in human ganglion sensory neurons. This unique life cycle necessitates an intimate relation between the host defenses and virus counteractions over the long course of infection. Two important aspects of host anti-viral defense, nuclear substructure restriction and epigenetic chromatin regulation, have been intensively studied in the recent years. Upon viral DNA entering the nucleus, components of discrete nuclear bodies termed nuclear domain 10 (ND10), converge at viral DNA and place restrictions on viral gene expression. Meanwhile the infected cell mobilizes its histones and histone-associated repressors to force the viral DNA into nucleosome-like structures and also represses viral transcription. Both anti-viral strategies are negated by various HSV countermeasures. One HSV gene transactivator, infected cell protein 0 (ICP0), is a key player in antagonizing both the ND10 restriction and chromatin repression. On one hand, ICP0 uses its E3 ubiquitin ligase activity to target major ND10 components for proteasome-dependent degradation and thereafter disrupts the ND10 nuclear bodies. On the other hand, ICP0 participates in de-repressing the HSV chromatin by changing histone composition or modification and therefore activates viral transcription. Involvement of a single viral protein in two seemingly different pathways suggests that there is coordination in host anti-viral defense mechanisms and also cooperation in viral counteraction strategies. In this review, we summarize recent advances in understanding the role of chromatin regulation and ND10 dynamics in both lytic and latent HSV infection. We focus on the new observations showing that ND10 nuclear bodies play a critical role in cellular chromatin regulation. We intend to find the connections between the two major anti-viral defense pathways, chromatin remodeling and ND10 structure, in order to achieve a better understanding of how host orchestrates a concerted defense and how HSV adapts with and overcomes the host immunity.
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Affiliation(s)
- Haidong Gu
- Department of Biological Sciences, Wayne State University, 4117 Biological Science Building, 5047 Gullen Mall, Detroit, MI, 48202, USA.
| | - Yi Zheng
- Department of Biological Sciences, Wayne State University, 4117 Biological Science Building, 5047 Gullen Mall, Detroit, MI, 48202, USA
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97
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Szczubiałka K, Pyrć K, Nowakowska M. In search for effective and definitive treatment of herpes simplex virus type 1 (HSV-1) infections. RSC Adv 2016. [DOI: 10.1039/c5ra22896d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Herpes Simplex Virus type 1 (HSV-1) is a nuclear replicating enveloped virus.
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Affiliation(s)
| | - Krzysztof Pyrć
- Faculty of Biochemistry, Biophysics and Biotechnology
- Jagiellonian University
- 30-387 Kraków
- Poland
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Abrisch RG, Eidem TM, Yakovchuk P, Kugel JF, Goodrich JA. Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. J Virol 2015; 90:2503-13. [PMID: 26676778 PMCID: PMC4810688 DOI: 10.1128/jvi.02665-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Lytic infection by herpes simplex virus 1 (HSV-1) triggers a change in many host cell programs as the virus strives to express its own genes and replicate. Part of this process is repression of host cell transcription by RNA polymerase II (Pol II), which also transcribes the viral genome. Here, we describe a global characterization of Pol II occupancy on the viral and host genomes in response to HSV-1 infection using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). The data reveal near-complete loss of Pol II occupancy throughout host cell mRNA genes, in both their bodies and promoter-proximal regions. Increases in Pol II occupancy of host cell genes, which would be consistent with robust transcriptional activation, were not observed. HSV-1 infection induced a more potent and widespread repression of Pol II occupancy than did heat shock, another cellular stress that widely represses transcription. Concomitant with the loss of host genome Pol II occupancy, we observed Pol II covering the HSV-1 genome, reflecting a high level of viral gene transcription. Interestingly, the positions of the peaks of Pol II occupancy at HSV-1 and host cell promoters were different. IMPORTANCE We investigated the effect of herpes simplex virus 1 (HSV-1) infection on transcription of host cell and viral genes by RNA polymerase II (Pol II). The approach we used was to determine how levels of genome-bound Pol II changed after HSV-1 infection. We found that HSV-1 caused a profound loss of Pol II occupancy across the host cell genome. Increases in Pol II occupancy were not observed, showing that no host genes were activated after infection. In contrast, Pol II occupied the entire HSV-1 genome. Moreover, the pattern of Pol II at HSV-1 genes differed from that on host cell genes, suggesting a unique mode of viral gene transcription. These studies provide new insight into how HSV-1 causes changes in the cellular program of gene expression and how the virus coopts host Pol II for its own use.
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Affiliation(s)
- Robert G Abrisch
- University of Colorado, Department of Chemistry and Biochemistry, Boulder, Colorado, USA
| | - Tess M Eidem
- University of Colorado, Department of Chemistry and Biochemistry, Boulder, Colorado, USA
| | - Petro Yakovchuk
- University of Colorado, Department of Chemistry and Biochemistry, Boulder, Colorado, USA
| | - Jennifer F Kugel
- University of Colorado, Department of Chemistry and Biochemistry, Boulder, Colorado, USA
| | - James A Goodrich
- University of Colorado, Department of Chemistry and Biochemistry, Boulder, Colorado, USA
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