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Ascovirus P64 Homologs: A Novel Family of Large Cationic Proteins That Condense Viral Genomic DNA for Encapsidation. BIOLOGY 2018; 7:biology7030044. [PMID: 30208603 PMCID: PMC6163548 DOI: 10.3390/biology7030044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/01/2018] [Accepted: 09/07/2018] [Indexed: 01/05/2023]
Abstract
Eukaryotic dsDNA viruses use small basic protamine-like proteins or histones, typically <15 kDa, to condense and encapsidate their genomic (g)DNAs during virogenesis. Ascoviruses are large dsDNA (~100⁻200 kbp) viruses that are pathogenic to lepidopteran larvae. Little is known about the molecular basis for condensation and encapsidation of their gDNAs. Previous proteomic analysis showed that Spodoptera frugiperda ascovirus (SfAV-1a) virions contain a large unique DNA-binding protein (P64; 64 kDa, pI = 12.2) with a novel architecture proposed to condense its gDNA. Here we used physical, biochemical, and transmission electron microscopy techniques to demonstrate that P64's basic C-terminal domain condenses SfAV-1a gDNA. Moreover, we demonstrate that only P64 homologs in other ascovirus virions are unique in stably binding DNA. As similar protein families or subfamilies were not identified in extensive database searches, our collective data suggest that ascovirus P64 homologs comprise a novel family of atypical large viral gDNA condensing proteins.
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2
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Alqahtani A, Heesom K, Bramson JL, Curiel D, Ugai H, Matthews DA. Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics. J Gen Virol 2014; 95:2504-2511. [PMID: 25096814 PMCID: PMC4202269 DOI: 10.1099/vir.0.068221-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We used SILAC (stable isotope labelling of amino acids in cell culture) and high-throughput quantitative MS mass spectrometry to analyse the protein composition of highly purified WT wild type adenoviruses, mutant adenoviruses lacking an internal protein component (protein V) and recombinant adenoviruses of the type commonly used in gene therapy, including one virus that had been used in a clinical trial. We found that the viral protein abundance and composition were consistent across all types of virus examined except for the virus lacking protein V, which also had reduced amounts of another viral core protein, protein VII. In all the samples analysed we found no evidence of consistent packaging or contamination with cellular proteins. We believe this technique is a powerful method to analyse the protein composition of this important gene therapy vector and genetically engineered or synthetic virus-like particles. The raw data have been deposited at proteomexchange, identifer PXD001120.
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Affiliation(s)
- Ali Alqahtani
- College of Applied Medical Sciences, Najran University, Najran 1983, Saudi Arabia.,School of Cellular and Molecular Medicine, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Kate Heesom
- Proteomics Facility, Faculty of Medical and Veterinary Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Jonathan L Bramson
- McMaster Immunology Research Centre, 4016 Michael DeGroote Centre for Learning & Discovery, McMaster University, Hamilton, L8S 4L8 Ontario, Canada
| | - David Curiel
- Biologic Therapeutics Center, School of Medicine, Washington University in St Louis, 4511 Forest Park Medical Building, St Louis, MO 63108, USA.,Cancer Biology Division, Department of Radiation Oncology, School of Medicine, Washington University in St Louis, 4511 Forest Park Medical Building, St Louis, MO 63108, USA
| | - Hideyo Ugai
- Cancer Biology Division, Department of Radiation Oncology, School of Medicine, Washington University in St Louis, 4511 Forest Park Medical Building, St Louis, MO 63108, USA
| | - David A Matthews
- School of Cellular and Molecular Medicine, University Walk, University of Bristol, Bristol BS8 1TD, UK
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3
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Samad MA, Komatsu T, Okuwaki M, Nagata K. B23/nucleophosmin is involved in regulation of adenovirus chromatin structure at late infection stages, but not in virus replication and transcription. J Gen Virol 2012; 93:1328-1338. [PMID: 22337638 DOI: 10.1099/vir.0.036665-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
B23/nucleophosmin has been identified in vitro as a stimulatory factor for replication of adenovirus DNA complexed with viral basic core proteins. In the present study, the in vivo function of B23 in the adenovirus life cycle was studied. It was found that both the expression of a decoy mutant derived from adenovirus core protein V that tightly associates with B23 and small interfering RNA-mediated depletion of B23 impeded the production of progeny virions. However, B23 depletion did not significantly affect the replication and transcription of the virus genome. Chromatin immunoprecipitation analyses revealed that B23 depletion significantly increased the association of viral DNA with viral core proteins and cellular histones. These results suggest that B23 is involved in the regulation of association and/or dissociation of core proteins and cellular histones with the virus genome. In addition, these results suggest that proper viral chromatin assembly, regulated in part by B23, is crucial for the maturation of infectious virus particles.
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Affiliation(s)
- Mohammad Abdus Samad
- Department of Applied Nutrition and Food Technology, Faculty of Applied Science and Technology, Islamic University, Kushtia, Bangladesh.,Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, 1-1-1 Tennohdai, Tsukuba 305-8575, Japan
| | - Tetsuro Komatsu
- Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, 1-1-1 Tennohdai, Tsukuba 305-8575, Japan
| | - Mitsuru Okuwaki
- Initiatives for the Promotion of Young Scientists' Independent Research, University of Tsukuba, 1-1-1 Tennohdai, Tsukuba 305-8577, Japan.,Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, 1-1-1 Tennohdai, Tsukuba 305-8575, Japan
| | - Kyosuke Nagata
- Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, 1-1-1 Tennohdai, Tsukuba 305-8575, Japan
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4
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Momose F, Sekimoto T, Ohkura T, Jo S, Kawaguchi A, Nagata K, Morikawa Y. Apical transport of influenza A virus ribonucleoprotein requires Rab11-positive recycling endosome. PLoS One 2011; 6:e21123. [PMID: 21731653 PMCID: PMC3120830 DOI: 10.1371/journal.pone.0021123] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Accepted: 05/19/2011] [Indexed: 12/31/2022] Open
Abstract
Influenza A virus RNA genome exists as eight-segmented ribonucleoprotein complexes containing viral RNA polymerase and nucleoprotein (vRNPs). Packaging of vRNPs and virus budding take place at the apical plasma membrane (APM). However, little is known about the molecular mechanisms of apical transport of newly synthesized vRNP. Transfection of fluorescent-labeled antibody and subsequent live cell imaging revealed that punctate vRNP signals moved along microtubules rapidly but intermittently in both directions, suggestive of vesicle trafficking. Using a series of Rab family protein, we demonstrated that progeny vRNP localized to recycling endosome (RE) in an active/GTP-bound Rab11-dependent manner. The vRNP interacted with Rab11 through viral RNA polymerase. The localization of vRNP to RE and subsequent accumulation to the APM were impaired by overexpression of Rab binding domains (RBD) of Rab11 family interacting proteins (Rab11-FIPs). Similarly, no APM accumulation was observed by overexpression of class II Rab11-FIP mutants lacking RBD. These results suggest that the progeny vRNP makes use of Rab11-dependent RE machinery for APM trafficking.
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Affiliation(s)
- Fumitaka Momose
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan.
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5
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Stepwise loss of fluorescent core protein V from human adenovirus during entry into cells. J Virol 2010; 85:481-96. [PMID: 21047958 DOI: 10.1128/jvi.01571-10] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human adenoviruses (Ads) replicate and assemble particles in the nucleus. They organize a linear double-strand DNA genome into a condensed core with about 180 nucleosomes, by the viral proteins VII (pVII), pX, and pV attaching the DNA to the capsid. Using reverse genetics, we generated a novel, nonconditionally replicating Ad reporter by inserting green fluorescent protein (GFP) at the amino terminus of pV. Purified Ad2-GFP-pV virions had an oversized complete genome and incorporated about 38 GFP-pV molecules per virion, which is about 25% of the pV levels in Ad2. GFP-pV cofractionated with the DNA core, like pV, and newly synthesized GFP-pV had a subcellular localization indistinguishable from that of pV, indicating that GFP-pV is a valid reporter for pV. Ad2-GFP-pV completed the replication cycle, although at lower yields than Ad2. Incoming GFP-pV (or pV) was not imported into the nucleus. Virions lost GFP-pV at two points during the infection process: at entry into the cytosol and at the nuclear pore complex, where capsids disassemble. Disassembled capsids, positive for the conformation-specific antihexon antibody R70, were devoid of GFP-pV. The loss of GFP-pV was reduced by the macrolide antibiotic leptomycin B (LMB), which blocks nuclear export and adenovirus attachment to the nuclear pore complex. LMB inhibited the appearance of R70 epitopes on Ad2 and Ad2-GFP-pV, indicating that the loss of GFP-pV from Ad2-GFP-pV is an authentic step in the adenovirus uncoating program. Ad2-GFP-pV is genetically complete and hence enables detailed analyses of infection and spreading dynamics in cells and model organisms or assessment of oncolytic adenoviral potential.
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6
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de Souza RF, Iyer LM, Aravind L. Diversity and evolution of chromatin proteins encoded by DNA viruses. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1799:302-18. [PMID: 19878744 PMCID: PMC3243496 DOI: 10.1016/j.bbagrm.2009.10.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/21/2009] [Accepted: 10/22/2009] [Indexed: 11/23/2022]
Abstract
Double-stranded DNA viruses display a great variety of proteins that interact with host chromatin. Using the wealth of available genomic and functional information, we have systematically surveyed chromatin-related proteins encoded by dsDNA viruses. The distribution of viral chromatin-related proteins is primarily influenced by viral genome size and the superkingdom to which the host of the virus belongs. Smaller viruses usually encode multifunctional proteins that mediate several distinct interactions with host chromatin proteins and viral or host DNA. Larger viruses additionally encode several enzymes, which catalyze manipulations of chromosome structure, chromatin remodeling and covalent modifications of proteins and DNA. Among these viruses, it is also common to encounter transcription factors and DNA-packaging proteins such as histones and IHF/HU derived from cellular genomes, which might play a role in constituting virus-specific chromatin states. Through all size ranges a subset of domains in viral chromatin proteins appears to have been derived from those found in host proteins. Examples include the Zn-finger domains of the E6 and E7 proteins of papillomaviruses, SET domain methyltransferases and Jumonji-related demethylases in certain nucleocytoplasmic large DNA viruses and BEN domains in poxviruses and polydnaviruses. In other cases, chromatin-interacting modules, such as the LXCXE motif, appear to have been widely disseminated across distinct viral lineages, resulting in similar retinoblastoma targeting strategies. Viruses, especially those with large linear genomes, have evolved a number of mechanisms to manipulate viral chromosomes in the process of replication-associated recombination. These include topoisomerases, Rad50/SbcC-like ABC ATPases and a novel recombinase system in bacteriophages utilizing RecA and Rad52 homologs. Larger DNA viruses also encode SWI2/SNF2 and A18-like ATPases which appear to play specialized roles in transcription and recombination. Finally, it also appears that certain domains of viral provenance have given rise to key functions in eukaryotic chromatin such as a HEH domain of chromosome tethering proteins and the TET/JBP-like cytosine and thymine hydroxylases.
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Affiliation(s)
- Robson F. de Souza
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States of America
| | - Lakshminarayan M. Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States of America
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States of America
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7
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Chen J, Morral N, Engel DA. Transcription releases protein VII from adenovirus chromatin. Virology 2007; 369:411-22. [PMID: 17888479 DOI: 10.1016/j.virol.2007.08.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 08/06/2007] [Accepted: 08/13/2007] [Indexed: 11/16/2022]
Abstract
Adenovirus protein VII is the major protein component of the viral nucleoprotein core. It is a nonspecific DNA-binding protein that condenses viral DNA inside the capsid. Protein VII remains associated with viral chromatin throughout early phase, indicating its continuing role during infection. Here we characterize the release of protein VII from infectious genomes during a time period that corresponds to the late phase of infection. Interestingly, the early viral transactivator E1A, but not other early gene products, is responsible for releasing protein VII by a mechanism that requires ongoing transcription but not viral DNA replication. Moreover transcription per se, in the absence of E1A, is also sufficient to trigger release. Accordingly, a recombinant genome containing only non-coding "stuffer" DNA is unable to support release of protein VII. Our data support a model in which early gene transcription results in a change in the structure of the viral chromatin.
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Affiliation(s)
- Jiangning Chen
- Department of Microbiology, University of Virginia Health System, PO Box 800734, Charlottesville, VA 22908-0734, USA
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8
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Spector DJ. Default assembly of early adenovirus chromatin. Virology 2007; 359:116-25. [PMID: 17034827 DOI: 10.1016/j.virol.2006.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 08/23/2006] [Accepted: 09/06/2006] [Indexed: 11/17/2022]
Abstract
In adenovirus particles, the viral nucleoprotein is organized into a highly compacted core structure. Upon delivery to the nucleus, the viral nucleoprotein is very likely to be remodeled to a form accessible to the transcription and replication machinery. Viral protein VII binds to intra-nuclear viral DNA, as do at least two cellular proteins, SET/TAF-Ibeta and pp32, components of a chromatin assembly complex that is implicated in template remodeling. We showed previously that viral DNA-protein complexes released from infecting particles were sensitive to shearing after cross-linking with formaldehyde, presumably after transport of the genome into the nucleus. We report here the application of equilibrium-density gradient centrifugation to the analysis of the fate of these complexes. Most of the incoming protein VII was recovered in a form that was not cross-linked to viral DNA. This release of protein VII, as well as the binding of SET/TAF-Ibeta and cellular transcription factors to the viral chromatin, did not require de novo viral gene expression. The distinct density profiles of viral DNA complexes containing protein VII, compared to those containing SET/TAF-Ibeta or transcription factors, were consistent with the notion that the assembly of early viral chromatin requires both the association of SET/TAF-1beta and the release of protein VII.
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Affiliation(s)
- David J Spector
- Department of Microbiology and Immunology, Pennsylvania State University College of Hershey, PA 17033, USA.
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9
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Haruki H, Okuwaki M, Miyagishi M, Taira K, Nagata K. Involvement of template-activating factor I/SET in transcription of adenovirus early genes as a positive-acting factor. J Virol 2006; 80:794-801. [PMID: 16378981 PMCID: PMC1346848 DOI: 10.1128/jvi.80.2.794-801.2006] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Accepted: 10/21/2005] [Indexed: 02/04/2023] Open
Abstract
The adenovirus genome complexed with viral core protein VII (adenovirus DNA-protein VII complex) at least is the bona fide template for transcription of adenovirus early genes. It is believed that the highly basic protein VII, like cellular histones, is a negative regulator for genome functions. Analyses with in vitro replication and transcription systems using the adenovirus DNA-protein VII complex have revealed that remodeling of the complex is crucial for efficient DNA replication and transcription. We identified host acidic proteins, template-activating factor I (TAF-I), TAF-II, and TAF-III as stimulatory factors for replication from the adenovirus DNA-protein VII complex. Recently, it was reported that the adenovirus DNA interacts with TAF-I and pp32, another host acidic protein (Y. Xue, J. S. Johnson, D. A. Ornelles, J. Lieberman, and D. A. Engel, J. Virol. 79:2474-2483, 2005). We found that TAF-I interacts and colocalizes with protein VII in adenovirus-infected cells during the early phases of infection, but pp32 does not. Although pp32 had the potential ability to interact with protein VII, pp32 did not remodel the adenovirus DNA-protein VII complex in vitro. Small interfering RNA-mediated knockdown of TAF-I expression leads to the delay of the transcription timing of early genes. These results provide evidence that TAF-I plays an important role in the early stages of the adenovirus infection cycle.
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Affiliation(s)
- Hirohito Haruki
- Department of Infection Biology, Graduate School of Comprehensive Human Sciences and Institute of Basic Medical Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
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10
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Xue Y, Johnson JS, Ornelles DA, Lieberman J, Engel DA. Adenovirus protein VII functions throughout early phase and interacts with cellular proteins SET and pp32. J Virol 2005; 79:2474-83. [PMID: 15681448 PMCID: PMC546597 DOI: 10.1128/jvi.79.4.2474-2483.2005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adenovirus protein VII is the major component of the viral nucleoprotein core. It is a highly basic nonspecific DNA-binding protein that condenses viral DNA inside the capsid. We have investigated the fate and function of protein VII during infection. "Input" protein VII persisted in the nucleus throughout early phase and the beginning of DNA replication. Chromatin immunoprecipitation revealed that input protein VII remained associated with viral DNA during this period. Two cellular proteins, SET and pp32, also associated with viral DNA during early phase. They are components of two multiprotein complexes, the SET and INHAT complexes, implicated in chromatin-related activities. Protein VII associated with SET and pp32 in vitro and distinct domains of protein VII were responsible for binding to the two proteins. Interestingly, protein VII was found in novel nuclear dot structures as visualized by immunofluorescence. The dots likely represent individual infectious genomes in association with protein VII. They appeared within 30 min after infection and localized in the nucleus with a peak of intensity between 4 and 10 h postinfection. After this, their intensity decreased and they disappeared between 16 and 24 h postinfection. Interestingly, disappearance of the dots required ongoing RNA synthesis but not DNA synthesis. Taken together these data indicate that protein VII has an ongoing role during early phase and the beginning of DNA replication.
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Affiliation(s)
- Yuming Xue
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908, USA
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11
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Abstract
Gene therapy holds promise for the treatment of a range of inherited diseases, such as cystic fibrosis. However, efficient delivery and expression of the therapeutic transgene at levels sufficient to result in phenotypic correction of cystic fibrosis pulmonary disease has proved elusive. There are many reasons for this lack of progress, both macroscopically in terms of airway defence mechanisms and at the molecular level with regard to effective cDNA delivery. This review of approaches to cystic fibrosis gene therapy covers these areas in detail and highlights recent progress in the field. For gene therapy to be effective in patients with cystic fibrosis, the cDNA encoding the cystic fibrosis transmembrane conductance regulator protein must be delivered effectively to the nucleus of the epithelial cells lining the bronchial tree within the lungs. Expression of the transgene must be maintained at adequate levels for the lifetime of the patient, either by repeat dosage of the vector or by targeting airway stem cells. Clinical trials of gene therapy for cystic fibrosis have demonstrated proof of principle, but gene expression has been limited to 30 days at best. Results suggest that viral vectors such as adenovirus and adeno-associated virus are unsuited to repeat dosing, as the immune response reduces the effectiveness of each subsequent dose. Nonviral approaches, such as cationic liposomes, appear more suited to repeat dosing, but have been less effective. Current work regarding non-viral gene delivery is now focused on understanding the mechanisms involved in cell entry, endosomal escape and nuclear import of the transgene. There is now increasing evidence to suggest that additional ligands that facilitate endosomal escape or contain a nuclear localization signal may enhance liposome-mediated gene delivery. Much progress in this area has been informed by advances in our understanding of the mechanisms by which viruses deliver their genomes to the nuclei of host cells.
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Affiliation(s)
- Tim W R Lee
- School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, UK.
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Johnson JS, Osheim YN, Xue Y, Emanuel MR, Lewis PW, Bankovich A, Beyer AL, Engel DA. Adenovirus protein VII condenses DNA, represses transcription, and associates with transcriptional activator E1A. J Virol 2004; 78:6459-68. [PMID: 15163739 PMCID: PMC416553 DOI: 10.1128/jvi.78.12.6459-6468.2004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Adenovirus protein VII is the major protein component of the viral nucleoprotein core. It is highly basic, and an estimated 1070 copies associate with each viral genome, forming a tightly condensed DNA-protein complex. We have investigated DNA condensation, transcriptional repression, and specific protein binding by protein VII. Xenopus oocytes were microinjected with mRNA encoding HA-tagged protein VII and prepared for visualization of lampbrush chromosomes. Immunostaining revealed that protein VII associated in a uniform manner across entire chromosomes. Furthermore, the chromosomes were significantly condensed and transcriptionally silenced, as judged by the dramatic disappearance of transcription loops characteristic of lampbrush chromosomes. During infection, the protein VII-DNA complex may be the initial substrate for transcriptional activation by cellular factors and the viral E1A protein. To investigate this possibility, mRNAs encoding E1A and protein VII were comicroinjected into Xenopus oocytes. Interestingly, whereas E1A did not associate with chromosomes in the absence of protein VII, expression of both proteins together resulted in significant association of E1A with lampbrush chromosomes. Binding studies with proteins produced in bacteria or human cells or by in vitro translation showed that E1A and protein VII can interact in vitro. Structure-function analysis revealed that an N-terminal region of E1A is responsible for binding to protein VII. These studies define the in vivo functions of protein VII in DNA binding, condensation, and transcriptional repression and indicate a role in E1A-mediated transcriptional activation of viral genes.
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Affiliation(s)
- Jeffrey S Johnson
- Department of Microbiology, University of Virginia Health System, P.O. Box 800734, Charlottesville, VA 22908, USA
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13
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Haruki H, Gyurcsik B, Okuwaki M, Nagata K. Ternary complex formation between DNA-adenovirus core protein VII and TAF-Ibeta/SET, an acidic molecular chaperone. FEBS Lett 2004; 555:521-7. [PMID: 14675767 DOI: 10.1016/s0014-5793(03)01336-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The adenovirus (Ad) genome complexed with viral core proteins designated Ad core is the template for transcription of early genes and the first round of replication in Ad-infected cells. A cellular protein designated template-activating factor-I (TAF-I) is found to be involved in remodeling of the Ad core in vitro. Here we found that TAF-I interacts with the Ad DNA through core protein VII in infected cells in early phases of infection. In vitro binding assays using recombinant proteins showed that TAF-I forms ternary complexes with DNA-protein VII complexes.
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Affiliation(s)
- Hirohito Haruki
- Department of Infection Biology, Institute of Basic Medical Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
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14
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Lee TWR, Blair GE, Matthews DA. Adenovirus core protein VII contains distinct sequences that mediate targeting to the nucleus and nucleolus, and colocalization with human chromosomes. J Gen Virol 2003; 84:3423-3428. [PMID: 14645923 DOI: 10.1099/vir.0.19546-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During adenovirus infection, following capsid dissociation, core protein VII enters the host cell nucleus complexed with adenovirus DNA. In order to determine whether protein VII may have an active role in this nuclear import, regions of the preVII gene were amplified by PCR, and further oligonucleotide mutants were designed with site-directed mutation of codons for the basic amino acids arginine and lysine. Fragments were cloned into a mammalian expression plasmid to express the peptides as N-terminal fusions to enhanced green fluorescent protein. Results demonstrate that preVII protein contains both nuclear and nucleolar targeting sequences. Such signals may be important in the delivery of adenovirus DNA to the host cell nucleus during adenovirus infection. Furthermore, the data suggest that protein VII may bind to human chromosomes by means of two distinct domains, one sharing homology with the N-terminal regulatory tail of histone H3.
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Affiliation(s)
- Tim W R Lee
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - G Eric Blair
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David A Matthews
- Department of Pathology and Microbiology, School of Medicine, University of Bristol, Bristol BS8 1TD, UK
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15
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Dobner T, Büchner D, Zeller T, Wolf H, Niller HH. Specific nucleoprotein complexes within adenovirus capsids. Biol Chem 2001; 382:1373-7. [PMID: 11688720 DOI: 10.1515/bc.2001.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Adenoviral DNA was examined within capsids by dimethyl sulfate footprinting. Protein-DNA interactions were visualized through ligation-mediated PCR (LM-PCR). Signals for protein binding were found adjacent to both inverted terminal repeats (ITR). There were no indications of close protein binding at several other loci of the viral genome. Therefore, adenovirus type 5 seems to contain sequence- or locus-specific DNA binding proteins within the virion.
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Affiliation(s)
- T Dobner
- Institut für Medizinische Mikrobiologie und Hygiene, Universität Regensburg, Germany
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16
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Newcomb WW, Brown JC. Use of Ar+ plasma etching to localize structural proteins in viruses: studies with adenovirus 2. Anal Biochem 1988; 169:279-86. [PMID: 3382003 DOI: 10.1016/0003-2697(88)90286-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The experiments described here were undertaken to test the idea that low energy Ar+ plasma etching could be employed as the basis of a method to order viral structural polypeptides according to their physical proximity to the virus surface. Since low energy (500 eV) Ar+ ions do not penetrate deeply into virus surfaces, one expects that the outermost proteins will be damaged before internal ones when intact virions are irradiated. To test this expectation, we exposed adenovirus 2 to a 500-eV Ar+ plasma and then employed sodium dodecyl sulfate-polyacryl-amide gel electrophoresis to assess the extent of damage to the major structural polypeptides. Gel analyses showed that the proteins exposed on the virus surface (proteins II, III, and IV) were degraded rapidly during the first 10 s of irradiation while protein VII, the major core polypeptide, was almost completely protected. Proteins located between the capsid and the core, such as proteins IIIa and VI, were degraded at intermediate rates. Quantitative measurements demonstrated that the observed decay rate differences were not due simply to differences in protein target size; distance to the virion surface made an important contribution. The plasma etching technique, therefore, appears to have considerable potential for the structural analysis of viruses and other macromolecular assemblies where the proximity of individual proteins to the particle surface is unknown.
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Affiliation(s)
- W W Newcomb
- Department of Microbiology, University of Virginia, School of Medicine, Charlottesville 22908
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17
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Abstract
The effects of the adenovirus type 2 (Ad2) structural proteins on Ad DNA synthesis in vitro have been examined. Both of the viral core proteins, polypeptides V and VII were shown to inhibit Ad2 DNA synthesis in vitro; however, only the major core protein, polypeptide VII, inhibited DNA synthesis at a ratio of protein to DNA proportional to the number of polypeptide VII molecules associated with the Ad2 DNA in the mature virion. In addition, fractions containing the precursor to polypeptide VII, pVII, were capable of inhibiting Ad2 DNA replication in vitro to the same extent as polypeptide VII. Purified polypeptide VII bound to double-stranded DNA with no apparent sequence specificity. In addition, polypeptide VII protected Ad2 DNA from digestion with micrococcal nuclease. The binding of polypeptide VII was probably responsible for the inhibition of Ad2 DNA synthesis in vitro by virtue of rendering the DNA inaccessible to viral replication proteins. These results suggest that the core proteins must be removed from the Ad2 genome before the template can function in genome replication and that assembly of pVII on Ad2 DNA can terminate the replication process.
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Weber J, Philipson L. Protein composition of adenovirus nucleoprotein complexes extracted from infected cells. Virology 1984; 136:321-7. [PMID: 6464354 DOI: 10.1016/0042-6822(84)90168-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A viral nucleoprotein complex was extracted from the nuclei of human cells 20 hr after infection with adenovirus type 2 or several of its temperature-sensitive mutants. In its sedimentation property, density in CsCl, and digestion pattern with micrococcal nuclease, the complex resembled viral cores. The polypeptides V, PVII, 11K, and 36K were found associated with this complex which is formed prior to or in the absence of virus assembly. The results suggest that this nucleoprotein complex is a direct precursor to virus assembly.
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Abstract
Ionic and nonionic interactions between the adenoviral histone-like proteins and DNA were examined by determining effects of ionic strength and urea concentration on disruption of viral nucleoprotein. The viral proteins were as susceptible to dissociation by salt in the presence of urea as histones. Nonionic interactions between viral proteins appeared more extensive than those between histones.
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20
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Burg JL, Schweitzer J, Daniell E. Introduction of superhelical turns into DNA by adenoviral core proteins and chromatin assembly factors. J Virol 1983; 46:749-55. [PMID: 6304339 PMCID: PMC256551 DOI: 10.1128/jvi.46.3.749-755.1983] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The interaction in vitro between adenoviral histone-like proteins and DNA in the presence of chromatin assembly factors was investigated. Viral core protein VII or its precursor pVII was incubated with DNA in the presence of an extract of HeLa cell chromatin, which mediates nucleosome assembly from histones and DNA. We have demonstrated that either protein can introduce superhelical turns into relaxed closed-circular DNA and that the presence of chromatin extract is necessary for the supertwisting effect. A greater density of superhelical turns was produced by pVII than by VII, but neither protein-DNA interaction resulted in the "physiological" amount of supertwisting produced by histones. The inhibition of histone-induced supercoiling by both proteins and the protection of turns in supertwisted starting material are also described. The nucleosome assembly factor, nucleoplasmin, fails to mediate the introduction of superhelical turns by VII or pVII.
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21
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Abstract
We investigated the structure of adenovirus deoxyribonucleic acid (DNA)-protein complexes in nuclei of infected cells by using micrococcal nuclease. Parental (infecting) DNA was digested into multimers which had a unit fragment size that was indistinguishable from the size of the nucleosomal repeat of cellular chromatin. This pattern was maintained in parenteral DNA throughout infection. Similar repeating units were detected in hamster cells that were nonpermissive for human adenovirus and in cells pretreated with n-butyrate. Late in infection, the pattern of digestion of viral DNA was determined by two different experimental approaches. Nuclear DNA was electrophoresed, blotted, and hybridized with labeled viral sequences; in this procedure all virus-specific DNA was detected. This technique revealed a diffuse protected band of viral DNA that was smaller than 160 base pairs, but no discrete multimers. All regions of the genome were represented in the protected DNA. To examine the nuclease protection of newly replicated viral DNA, infected cells were labeled with [3H]thymidine after blocking of cellular DNA synthesis but not viral DNA synthesis. With this procedure we identified a repeating unit which was distinctly different from the cellular nucleosomal repeat. We found broad bands with midpoints at 200, 400, and 600 base pairs, as well as the limit digest material revealed by blotting. High-resolution acrylamide gel electrophoresis revealed that the viral species comprised a series of closely spaced bands ranging in size from less than 30 to 250 base pairs.
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22
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van der Ende A, Langeveld SA, Van Arkel GA, Weisbeek PJ. The interaction of the A and A* proteins of bacteriophage phi X174 with single-stranded and double-stranded phi X DNA in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 124:245-52. [PMID: 6212237 DOI: 10.1111/j.1432-1033.1982.tb06584.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The binding of the bacteriophage phi X 174-coded A and A* proteins to single-stranded (ssDNA) and double-stranded (dsDNA ) phi X DNA was studied by electron microscopy. The interaction of the A* protein with ssDNA and dsDNA was also studied by sedimentation velocity centrifugation. It was shown that the binding of the A and A* proteins to ssDNA occurs in a non-cooperative manner and requires no or very little sequence specificity under the conditions used here. Both protein-ssDNA complexes have the same compact structure caused by intrastrand cross-linking through the interaction of protein molecules with separate parts of the ssDNA molecule. The A protein does not bind to phi X dsDNA in the absence of divalent cations. The A* protein does bind to dsDNA, although it has a strong preference for binding to ssDNA. The structure of the A* protein-dsDNA complexes is different from that of the A* protein-ssDNA complexes, as the former have a rosette-like structure caused by protein-protein interactions. High ionic strengths favour the formation of large condensed aggregates.
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23
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Abstract
We investigated the structure of adenovirus deoxyribonucleic acid (DNA)-protein complexes in nuclei of infected cells by using micrococcal nuclease. Parental (infecting) DNA was digested into multimers which had a unit fragment size that was indistinguishable from the size of the nucleosomal repeat of cellular chromatin. This pattern was maintained in parenteral DNA throughout infection. Similar repeating units were detected in hamster cells that were nonpermissive for human adenovirus and in cells pretreated with n-butyrate. Late in infection, the pattern of digestion of viral DNA was determined by two different experimental approaches. Nuclear DNA was electrophoresed, blotted, and hybridized with labeled viral sequences; in this procedure all virus-specific DNA was detected. This technique revealed a diffuse protected band of viral DNA that was smaller than 160 base pairs, but no discrete multimers. All regions of the genome were represented in the protected DNA. To examine the nuclease protection of newly replicated viral DNA, infected cells were labeled with [3H]thymidine after blocking of cellular DNA synthesis but not viral DNA synthesis. With this procedure we identified a repeating unit which was distinctly different from the cellular nucleosomal repeat. We found broad bands with midpoints at 200, 400, and 600 base pairs, as well as the limit digest material revealed by blotting. High-resolution acrylamide gel electrophoresis revealed that the viral species comprised a series of closely spaced bands ranging in size from less than 30 to 250 base pairs.
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