Default assembly of early adenovirus chromatin

Adenovirus - a blueprint for gene delivery

A central quest in gene therapy and vaccination is to achieve effective and long-lasting gene expression at minimal dosage. Adenovirus vectors are widely used therapeutics and safely deliver genes into many cell types. Adenoviruses evolved to use elaborate trafficking and particle deconstruction processes, and efficient gene expression and progeny formation. Here, we discuss recent insights into how human adenoviruses deliver their double-stranded DNA genome into cell nuclei, and effect lytic cell killing, non-lytic persistent infection or vector gene expression. The mechanisms underlying adenovirus entry, uncoating, nuclear transport and gene expression provide a blueprint for the emerging field of synthetic virology, where artificial virus-like particles are evolved to deliver therapeutic payload into human cells without viral proteins and genomes.

Human adenoviral DNA association with nucleosomes containing histone variant H3.3 during the early phase of infection is not dependent on viral transcription or replication

Adenovirus (Ad) DNA undergoes dynamic changes in protein association as the virus progresses through its replicative cycle. Within the virion, the Ad DNA associates primarily with the virus-encoded, protamine-like protein VII. During the early phase of infection (∼6 h), the viral DNA showed declining association with VII, suggesting that VII was removed from at least some regions of the viral DNA. Within 6 h, the viral DNA was wrapped into a repeating nucleosome-like array containing the histone variant H3.3. Transcription elongation was not required to strip VII from the viral DNA or for deposition of H3.3. H3.1 did not associate with the viral DNA at any point during infection. During the late phase of infection (i.e., active DNA replication ∼12-24 h), association with H3 was dramatically reduced and the repeating nucleosome-like pattern was no longer evident. Thus, we have uncovered some of the changes in nucleoprotein structure that occur during lytic Ad infection.

Design of a molecular imprinting biosensor with multi-scale roughness for detection across a broad spectrum of biomolecules

The molecular imprinting technique has tremendous applications in artificial enzymes, bioseparation, and sensor devices.

B23/nucleophosmin is involved in regulation of adenovirus chromatin structure at late infection stages, but not in virus replication and transcription

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.

Mass spectrometry based proteomic studies on viruses and hosts--a review

In terms of proteomic research in the 21st century, the realm of virology is still regarded as an enormous challenge mainly brought by three aspects, namely, studying on the complex proteome of the virus with unexpected variations, developing more accurate analytical techniques as well as understanding viral pathogenesis and virus-host interaction dynamics. Progresses in these areas will be helpful to vaccine design and antiviral drugs discovery. Mass spectrometry based proteomics have shown exceptional display of capabilities, not only precisely identifying viral and cellular proteins that are functionally, structurally, and dynamically changed upon virus infection, but also enabling us to detect important pathway proteins. In addition, many isolation and purification techniques and quantitative strategies in conjunction with MS can significantly improve the sensitivity of mass spectrometry for detecting low-abundant proteins, replenishing the stock of virus proteome and enlarging the protein-protein interaction maps. Nevertheless, only a small proportion of the infectious viruses in both of animal and plant have been studied using this approach. As more virus and host genomes are being sequenced, MS-based proteomics is becoming an indispensable tool for virology. In this paper, we provide a brief review of the current technologies and their applications in studying selected viruses and hosts.

DNA-tumor virus entry--from plasma membrane to the nucleus

DNA-tumor viruses comprise enveloped and non-enveloped agents that cause malignancies in a large variety of cell types and tissues by interfering with cell cycle control and immortalization. Those DNA-tumor viruses that replicate in the nucleus use cellular mechanisms to transport their genome and newly synthesized viral proteins into the nucleus. This requires cytoplasmic transport and nuclear import of their genome. Agents that employ this strategy include adenoviruses, hepadnaviruses, herpesviruses, and likely also papillomaviruses, and polyomaviruses, but not poxviruses which replicate in the cytoplasm. Here, we discuss how DNA-tumor viruses enter cells, take advantage of cytoplasmic transport, and import their DNA genome through the nuclear pore complex into the nucleus. Remarkably, nuclear import of incoming genomes does not necessarily follow the same pathways used by the structural proteins of the viruses during the replication and assembly phases of the viral life cycle. Understanding the mechanisms of DNA nuclear import can identify new pathways of cell regulation and anti-viral therapies.

Adenoviruses: update on structure and function

Adenoviruses have been studied intensively for over 50 years as models of virus-cell interactions and latterly as gene vectors. With the advent of more sophisticated structural analysis techniques the disposition of most of the 13 structural proteins have been defined to a reasonable level. This review seeks to describe the functional properties of these proteins and shows that they all have a part to play in deciding the outcome of an infection and act at every level of the virus's path through the host cell. They are primarily involved in the induction of the different arms of the immune system and a better understanding of their overall properties should lead to more effective ways of combating virus infections.

Chromatin organization and virus gene expression

Many viruses introduce DNA into the host-cell nucleus, where they must either embrace or confront chromatin factors as a support or obstacle to completion of their life cycle. Compared to the eukaryotic cell, viruses have compact and rapidly evolving genomes. Despite their smaller size, viruses have complex life cycles that involve dynamic changes in DNA structure. Nuclear entry, transcription, replication, genome stabilization, and virion packaging involve complex changes in chromosome organization and structure. Chromatin dynamics and epigenetic modifications play major roles in viral and host chromosome biology. In some cases, viruses may use novel or viral-specific epigenetic modifying activities, which may reflect variant pathways that distinguish their behavior from the bulk of the cellular chromosome. This review examines several recent discoveries that highlight the role of chromatin dynamics in the life cycle of DNA viruses.

Adeno-associated virus vector genomes persist as episomal chromatin in primate muscle

Recombinant adeno-associated virus (rAAV) vectors are capable of mediating long-term gene expression following administration to skeletal muscle. In rodent muscle, the vector genomes persist in the nucleus in concatemeric episomal forms. Here, we demonstrate with nonhuman primates that rAAV vectors integrate inefficiently into the chromosomes of myocytes and reside predominantly as episomal monomeric and concatemeric circles. The episomal rAAV genomes assimilate into chromatin with a typical nucleosomal pattern. The persistence of the vector genomes and gene expression for years in quiescent tissues suggests that a bona fide chromatin structure is important for episomal maintenance and transgene expression. These findings were obtained from primate muscles transduced with rAAV1 and rAAV8 vectors for up to 22 months after intramuscular delivery of 5 x 10(12) viral genomes/kg. Because of this unique context, our data, which provide important insight into in situ vector biology, are highly relevant from a clinical standpoint.

Transcription releases protein VII from adenovirus chromatin

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.