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Adenovirus Genome

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Patrick Hearing – One of the best experts on this subject based on the ideXlab platform.

  • Adenovirus major core protein condenses dna in clusters and bundles modulating Genome release and capsid internal pressure
    Nucleic Acids Research, 2019
    Co-Authors: Natalia Martingonzalez, Philomena Ostapchuk, Patrick Hearing, Mercedes Hernandoperez, Gabriela N Condezo, Marta Perezillana, Antonio Siber, David Reguera, Carmen San Martin, Pedro J De Pablo
    Abstract:

    Some viruses package dsDNA together with large amounts of positively charged proteins, thought to help condense the Genome inside the capsid with no evidence. Further, this role is not clear because these viruses have typically lower packing fractions than viruses encapsidating naked dsDNA. In addition, it has recently been shown that the major Adenovirus condensing protein (polypeptide VII) is dispensable for Genome encapsidation. Here, we study the morphology and mechanics of Adenovirus particles with (Ad5-wt) and without (Ad5-VII-) protein VII. Ad5-VII- particles are stiffer than Ad5-wt, but DNA-counterions revert this difference, indicating that VII screens repulsive DNA-DNA interactions. Consequently, its absence results in increased internal pressure. The core is slightly more ordered in the absence of VII and diffuses faster out of Ad5-VII- than Ad5-wt fractured particles. In Ad5-wt unpacked cores, dsDNA associates in bundles interspersed with VII-DNA clusters. These results indicate that protein VII condenses the Adenovirus Genome by combining direct clustering and promotion of bridging by other core proteins. This condensation modulates the virion internal pressure and DNA release from disrupted particles, which could be crucial to keep the Genome protected inside the semi-disrupted capsid while traveling to the nuclear pore.

  • Adenovirus Early Proteins and Host Sumoylation
    mBio, 2016
    Co-Authors: Sook-young Sohn, Patrick Hearing
    Abstract:

    The human Adenovirus Genome is transported into the nucleus, where viral gene transcription, viral DNA replication, and virion assembly take place. Posttranslational modifications by small ubiquitin-like modifiers (SUMOs) are implicated in the regulation of diverse cellular processes, particularly nuclear events. It is not surprising, therefore, that Adenovirus modulates and utilizes the host sumoylation system. Adenovirus early proteins play an important role in establishing optimal host environments for virus replication within infected cells by stimulating the cell cycle and counteracting host antiviral defenses. Here, we review findings on the mechanisms and functional consequences of the interplay between human Adenovirus early proteins and the host sumoylation system.

  • The use of chromatin immunoprecipitation (ChIP) to study the binding of viral proteins to the Adenovirus Genome in vivo.
    Methods in molecular biology (Clifton N.J.), 2013
    Co-Authors: Yueting Zheng, Patrick Hearing
    Abstract:

    The encapsidation of Adenovirus (Ad) DNA into virus particles depends on cis-acting sequences located at the left end of the viral Genome. Repeated DNA sequences in the packaging domain contribute to viral DNA encapsidation and several viral proteins bind to these repeats when analyzed using in vitro DNA-protein binding assays. In this chapter, we describe a chromatin immunoprecipitation (ChIP) approach to study the binding of viral proteins to packaging sequences in vivo. This assay permits accurate quantification over a wide range of DNA concentrations. The use of formaldehyde cross-linking to stabilize DNA-protein and proteinprotein complexes formed in vivo allows the identification of macromolecular complexes found in living cells.

Göran Wadell – One of the best experts on this subject based on the ideXlab platform.

  • two closely related Adenovirus Genome types with kidney or respiratory tract tropism differ in their binding to epithelial cells of various origins
    Virology, 1998
    Co-Authors: Ya-fang Mei, Kristina Lindman, Göran Wadell
    Abstract:

    Abstract The host–cell interactions of the Genome types Ad11p and Ad11a of human Adenovirus serotype 11, displaying kidney or respiratory tropism, were compared using FACS analysis. Kinetic experiments indicated that the virus binding started immediately and reached a plateau after 30 min. The binding of biotinylated virions to seven continuous cell lines: A549, A498, J82, HeLa, CHO, MDCK, and human diploid fibroblasts (HEDF), was quantitated by FACS analysis. The binding capacities of the two viruses to all human cell lines but A549 cells appeared to differ. Ad11p virions manifested high affinities, whereas Ad11a virions presented low affinities. Neither of the two viruses bound to CHO or MDCK cells. Reciprocal competition experiments showed that the Ad11a virions could be weakly blocked by the Ad11p virions, whereas the Ad11p virions could not be competed at all by the Ad11a virions. The binding of the Ad11p virions to cells could be blocked by the rfiber antiserum of Ad11p, but not by the corresponding antiserum against Ad11a or Ad35p. A comparison of the cytopathogenicity of the seven cell lines infected by Ad11p and Ad11a demonstrated that the efficiency of the initial event of an Adenovirus infection directly affects the outcome of the viral infection. The Ad11a in the A498, J82, HeLa, or HEDF cells that presented lower affinity and receptor concentration showed 100 times less infectivity than that in A549 cells displaying high affinity and receptor concentration. These results indicate that the cell susceptibility to Ad11p and Ad11a infection strongly depends on both the number of fiber receptors on the host cells and the receptor affinity for ligands on the fiber knob. Our findings also suggest that the receptors for Ad11p and Ad11a on the surface of different cell types may be different or on different sites.

  • Sequence Analysis of the E3 Region and Fiber Gene of Human Adenovirus Genome Type 7h
    Virology, 1996
    Co-Authors: Adriana E. Kajon, Göran Wadell
    Abstract:

    Adenovirus type 7h is currently the predominant virulent Genome type of serotype 7 isolated in Argentina, Chile, and Uruguay in association with severe infantile pneumonia. In order to characterize possible molecular determinants of pathogenicity, the nucleotide sequence of a 5904-bp fragment (76 to 93 mu) containing the entire E3 region and the fiber gene of Ad7h was established. The organization of the ORFs within the E3 region was similar to that reported for the prototype strains of Ad7 and Ad3. A comparison of the nucleotide and amino acid sequences of all ORFs revealed a higher homology between Ad7h and Ad7p than between Ad7h and Ad3 for 12.0K and 16.1K, whereas the 15.3K ORF and the adjacent fiber gene were strikingly more homologous to those of Ad3 (99.5 vs 81.1% and 98.2 vs 66.6%, respectively). The equivalent to ORF 7.7K in Ad7p was missing in Ad7h due to a deletion and a mutation affecting the start codon (ATG–>ATT). Although the hemagglutinin of the Ad7h fiber could not be characterized due to its lack of activity on monkey erythrocytes, our results indicate that Ad7h is an intermediate strain 7-3.

  • Highly heterogeneous fiber genes in the two closely related Adenovirus Genome types Ad35p and Ad34a.
    Virology, 1995
    Co-Authors: Ya-fang Mei, Göran Wadell
    Abstract:

    Two Adenovirus isolates from urine, Ad35p (from a bone marrow recipient) and Ad34a (from a hemorrhagic cystitis patient), were compared regarding their fiber gene organization and hemagglutinating capacity. The fiber serves as the ligand between the virus capsid and the host cell receptor. The Ad35p fiber gene encoded a 323-amino-acid protprotein, and the Ad34a fiber gene a 325 amino acidacid protprotein. The two fibers manifested 62.4% overall amino acid sequence homology, the differences predominantly occurring within the knob region where sequence homology was only 49.5%. The knob region of Ad34a was virtually identical to that of Ad11p which also causes hemorrhagic cystitis. Unlike all other known subgenus B Adenoviruses, in the Ad35p fiber an asparagine constituted the C-terminus. Although both Ad34a and Ad35p viruses can hemagglutinate monkey erythrocytes, the hemagglutination inhibition test showed them to differ from each other in the epitopes expressed on the fibers.

Kyosuke Nagata – One of the best experts on this subject based on the ideXlab platform.

  • Imaging analysis of nuclear antiviral factors through direct detection of incoming Adenovirus Genome complexes.
    Biochemical and biophysical research communications, 2016
    Co-Authors: Tetsuro Komatsu, Kyosuke Nagata, Hans Will, Harald Wodrich
    Abstract:

    Recent studies involving several viral systems have highlighted the importance of cellular intrinsic defense mechanisms through nuclear antiviral proteins that restrict viral propagation. These factors include among others components of PML nuclear bodies, the nuclear DNA sensor IFI16, and a potential restriction factor PHF13/SPOC1. For several nuclear replicating DNA viruses, it was shown that these factors sense and target viral Genomes immediately upon nuclear import. In contrast to the anticipated view, we recently found that incoming adenoviral Genomes are not targeted by PML nuclear bodies. Here we further explored cellular responses against adenoviral infection by focusing on specific conditions as well as additional nuclear antiviral factors. In line with our previous findings, we show that neither interferon treatment nor the use of specific isoforms of PML nuclear body components results in co-localization between incoming adenoviral Genomes and the subnuclear domains. Furthermore, our imaging analyses indicated that neither IFI16 nor PHF13/SPOC1 are likely to target incoming adenoviral Genomes. Thus our findings suggest that incoming adenoviral Genomes may be able to escape from a large repertoire of nuclear antiviral mechanisms, providing a rationale for the efficient initiation of lytic replication cycle.

  • DNA replication-dependent binding of CTCF plays a critical role in Adenovirus Genome functions
    Scientific reports, 2013
    Co-Authors: Tetsuro Komatsu, Takeshi Sekiya, Kyosuke Nagata
    Abstract:

    The expression of Adenovirus late genes is shown to require viral DNA replication, but its mechanism remains elusive. Here we found that knockdown of CTCF suppresses viral DNA replication as well as late, but not early, gene expression. Chromatin immunoprecipitation assays indicated that CTCF binds to viral chromatin depending on viral DNA replication. These findings depict CTCF as a critical regulator for Adenovirus Genome functions in late phases of infection.

  • Stimulation of DNA Transcription by the Replication Factor from the Adenovirus Genome in a Chromatin-like Structure
    The Journal of biological chemistry, 1995
    Co-Authors: Ken Matsumoto, Mitsuru Okuwaki, Hiroyuki Kawase, Hiroshi Handa, Fumio Hanaoka, Kyosuke Nagata
    Abstract:

    Adenovirus (Ad) Genome DNA is complexed with viral core proteins in the virus particle and in host cells during the early stages of infection. This DNA protein complex, called Ad core, is thought to be the template for transcription and DNA replication in infected cells. The Ad core functioned as template for DNA replication in the cell-free system consisting of viral replication proteins, uninfected HeLa nuclear extracts, and a novel factor, template activating factor-I (TAF-I) that we have isolated from uninfected HeLa cytoplasmic fractions. The Ad core did not function as an efficient template in the cell-free transcription system with nuclear extracts of uninfected HeLa cells. The addition of TAF-I resulted in the stimulation of transcription from E1A and ML promoters on the Ad core. TAF-I was required, at least, for the formation of preinitiation complexes. These observations suggest that, in addition to factors essential for transcription on naked DNA template, the factor such as TAF-I needed for replication of the Ad core is also required for transcription from the Ad Genome in a chromatin-like structure.

Matthew D Weitzman – One of the best experts on this subject based on the ideXlab platform.

  • repair of protein linked dna double strand breaks using the Adenovirus Genome as a model substrate in cell based assays
    DNA Repair, 2019
    Co-Authors: Brandon J Lamarche, Matthew D Weitzman, Nicole I Orazio, Brittany Goben, Jill Meisenhelder, Zhongsheng You, Tony Hunter
    Abstract:

    Abstract The DNA double strand breaks (DSBs) created during meiotic recombination and during some types of chemotherapy contain protein covalently attached to their 5′ termini. Removal of the end-blocking protein is a prerequisite to DSB processing by non-homologous end-joining or homologous recombination. One mechanism for removing the protein involves CtIP-stimulated Mre11-catalyzed nicking of the protein-linked strand distal to the DSB terminus, releasing the end-blocking protein while it remains covalently attached to an oligonucleotide. Much of what is known about this repair process has recently been deciphered through in vitro reconstitution studies. We present here a novel model system based on Adenovirus (Ad), which contains the Ad terminal protein covalently linked to the 5′ terminus of its dsDNA Genome, for studying the repair of 5′ protein-linked DSBs in vivo. It was previously shown that the Genome of Ad mutants that lack early region 4 (E4) can be joined into concatemers in vivo, suggesting that the Ad terminal protein had been removed from the Genome termini prior to ligation. Here we show that during infection with the E4-deleted Ad mutant dl1004, the Ad terminal protein is removed in a manner that recapitulates removal of end-blocking proteins from cellular DSBs. In addition to displaying a dependence on CtIP, and Mre11 acting as the endonuclease, the protein-linked oligonucleotides that are released from the viral Genome are similar in size to the oligos that remain attached to Spo11 and Top2 after they are removed from the 5′ termini of DSBs during meiotic recombination and etoposide chemotherapy, respectively. The single nucleotide resolution that is possible with this assay, combined with the single sequence context in which the lesion is presented, make it a useful tool for further refining our mechanistic understanding of how blocking proteins are removed from the 5′ termini of DSBs.

  • Adenovirus core protein vii downregulates the dna damage response on the host Genome
    Journal of Virology, 2017
    Co-Authors: Daphne C Avgousti, Matthew D Weitzman, Ashley N Della Fera, Clayton J Otter, Christin Herrmann, Neha J Pancholi
    Abstract:

    Viral manipulation of cellular proteins allows viruses to suppress host defenses and generate infectious progeny. Due to the linear double-stranded DNA nature of the Adenovirus Genome, the cellular DNA damage response (DDR) is considered a barrier to successful infection. The Adenovirus Genome is packaged with protein VII, a virally encoded histone-like core protprotein that is suggested to protect incoming viral Genomes from detection by the cellular DNA damage machinery. We showed that protein VII localizes to host chromatin during infection, leading us to hypothesize that protein VII may affect DNA damage responses on the cellular Genome. Here we show that protein VII at cellular chromatin results in a significant decrease in accumulation of phosphorylated H2AX (γH2AX) following irradiation, indicating that protein VII inhibits DDR signaling. The oncoprotein SET was recently suggested to modulate the DDR by affecting access of repair proteins to chromatin. Since protein VII binds SET, we investigated a role for SET in DDR inhibition by protein VII. We show that knockdown of SET partially rescues the protein VII-induced decrease in γH2AX accumulation on the host Genome, suggesting that SET is required for inhibition. Finally, we show that knockdown of SET also allows ATM to localize to incoming viral Genomes bound by protein VII during infection with a mutant lacking early region E4. Together, our data suggest that the protein VII-SET interaction contributes to DDR evasion by Adenovirus. Our results provide an additional example of a strategy used by Adenovirus to abrogate the host DDR and show how viruses can modify cellular processes through manipulation of host chromatin.IMPORTANCE The DNA damage response (DDR) is a cellular network that is crucial for maintaining Genome integrity. DNA viruses replicating in the nucleus challenge the resident Genome and must overcome cellular responses, including the DDR. Adenoviruses are prevalent human pathogens that can cause a multitude of diseases, such as respiratory infections and conjunctivitis. Here we describe how a small Adenovirus core protprotein that localizes to host chromatin during infection can globally downregulate the DDR. Our study focuses on key players in the damage signaling pathway and highlights how viral manipulation of chromatin may influence access of DDR proteins to the host Genome.

Philomena Ostapchuk – One of the best experts on this subject based on the ideXlab platform.

  • Adenovirus major core protein condenses dna in clusters and bundles modulating Genome release and capsid internal pressure
    Nucleic Acids Research, 2019
    Co-Authors: Natalia Martingonzalez, Philomena Ostapchuk, Patrick Hearing, Mercedes Hernandoperez, Gabriela N Condezo, Marta Perezillana, Antonio Siber, David Reguera, Carmen San Martin, Pedro J De Pablo
    Abstract:

    Some viruses package dsDNA together with large amounts of positively charged proteins, thought to help condense the Genome inside the capsid with no evidence. Further, this role is not clear because these viruses have typically lower packing fractions than viruses encapsidating naked dsDNA. In addition, it has recently been shown that the major Adenovirus condensing protein (polypeptide VII) is dispensable for Genome encapsidation. Here, we study the morphology and mechanics of Adenovirus particles with (Ad5-wt) and without (Ad5-VII-) protein VII. Ad5-VII- particles are stiffer than Ad5-wt, but DNA-counterions revert this difference, indicating that VII screens repulsive DNA-DNA interactions. Consequently, its absence results in increased internal pressure. The core is slightly more ordered in the absence of VII and diffuses faster out of Ad5-VII- than Ad5-wt fractured particles. In Ad5-wt unpacked cores, dsDNA associates in bundles interspersed with VII-DNA clusters. These results indicate that protein VII condenses the Adenovirus Genome by combining direct clustering and promotion of bridging by other core proteins. This condensation modulates the virion internal pressure and DNA release from disrupted particles, which could be crucial to keep the Genome protected inside the semi-disrupted capsid while traveling to the nuclear pore.

  • The L4 22-Kilodalton Protein Plays a Role in Packaging of the Adenovirus Genome
    Journal of virology, 2006
    Co-Authors: Philomena Ostapchuk, Mary E. Anderson, Sharanya Chandrasekhar, Patrick Hearing
    Abstract:

    Packaging of the Adenovirus (Ad) Genome into a capsid is absolutely dependent upon the presence of a cis-acting region located at the left end of the Genome referred to as the packaging domain. The functionally significant sequences within this domain consist of at least seven similar repeats, referred to as the A repeats, which have the consensus sequence 5′ TTTG-N(8)-CG 3′. In vitro and in vivo binding studies have demonstrated that the Adenovirus protein IVa2 binds to the CG motif of the packaging sequences. In conjunction with IVa2, another virus-specific protein binds to the TTTG motifs in vitro. The efficient formation of these protein-DNA complexes in vitro was precisely correlated with efficient packaging activity in vivo. We demonstrate that the binding activity to the TTTG packaging sequence motif is the product of the L4 22-kDa open reading frame. Previously, no function had been ascribed to this protein. Truncation of the L4 22-kDa protein in the context of the viral Genome did not reduce viral gene expression or viral DNA replication but eliminated the production of infectious virus. We suggest that the L4 22-kDa protein, in conjunction with IVa2, plays a critical role in the recognition of the packaging domain of the Ad Genome that leads to viral DNA encapsidation. The L4 22-kDa protein is also involved in recognition of transcription elements of the Ad major late promoter.

  • Minimal cis-Acting Elements Required for Adenovirus Genome Packaging
    Journal of virology, 2003
    Co-Authors: Philomena Ostapchuk, Patrick Hearing
    Abstract:

    The design of drugs for treatment of virus infections and the exploitation of viruses as drugs for treatment of diseases could be made more successful by understanding the molecular mechanisms of virus-specific events. The process of assembly, and more specifically packaging of the Genome into a capsid, is an obligatory step leading to future infections. To enhance our understanding of the molecular mechanism of packaging, it is necessary to characterize the viral components necessary for the event. In the case of Adenovirus, sequences between nucleotides 200 and 400 at the left end of the Genome are essential for packaging. This region contains a series of redundant bipartite sequences, termed A repeats, that function in packaging. Synthetic packaging sequences made of multimers of a single A repeat substitute for the authentic Adenovirus packaging domain. A repeats are binding sites for the CCAAT displacement protein and the viral protprotein IVa2. Several lines of evidence implicate these proteins in the packaging process. It was not known, however, whether other cis-acting elements play a role in the packaging process as well. We utilized an in vivo approach to address the role of the inverted terminal repeats and the covalently linked terminal proteins in packaging of the Adenovirus Genome. Our results show that these elements are not necessary for efficient packaging of the viral Genome. A significant implication of these results applicable to gene therapy vector design is that the linkage of the Adenovirus packaging domain to heterologous DNA sequences should suffice for targeting to the viral capsid.