Due to the nature of their genetic material, many DNA viruses share an intimate relationship with the host cell nucleus and are at least partially dependent on host cell machinery, or the perturbation of it for the efficient completion of their lifecycle. For this reason, the study of how DNA viruses manipulate the nuclear environment has been particularly important for our understanding of DNA replication, recombination, and repair. Analysis of host machinery targeted by viral gene products has provided a plethora of valuable insights as to their normal cellular functions and has led to the discovery and characterization of such important host molecules as p300/CBP and p53. There is no doubt that further analysis of DNA viruses and their interactions with the host cell will continue to provide us with important insights concerning basic biology and viral pathogenesis and contribute to the development of viruses as therapeutic agents.
In order to ensure their survival, DNA viruses must efficiently and accurately replicate their genomes in the inhospitable environment of the host cell. With some notable exceptions such as Vaccinia virus, DNA viruses transport their genetic material into the nucleus where it is replicated by differing combinations of host cell and virally encoded proteins. DNA viruses such as simian virus-40 (SV40) are almost completely dependent upon host cell proteins for replication while others, like herpes simplex virus-1 (HSV-1), utilize predominantly virally encoded replication apparatus. The parvovirus, adeno-associated virus (AAV), can utilize a wide variety of conditions and protein combinations to replicate its genome. The study of viral DNA replication and the in vitro reconstitution of many of these systems have been instrumental for developing our current understanding of eukaryotic DNA replication.
Fig. 1 DNA virus infection and replication.
The replication of DNA viruses results m the reorganization of the host nuclear environment and causes the disruption of a variety of structures including the nucleolus, promyelocytic leukemia (PML) oncogenic domains (PODs), splicing domains, and centromeres. POD domains are a common target of many viruses. These macromolecular nuclear structures contain a number of proteins involved in diverse aspects of cellular metabolism, such as cell cycle control, apoptosis, transcription, genomic stability, the immune response, and the response to stress.
In addition to modifying pre-existing structures, viruses such as adenovirus (Ad) and HSV-1 establish discrete replication centers in the nucleus where viral DNA synthesis takes place. Cytological analysis of these centers has been valuable for identifying host cell proteins that are affected by the lifecycle of a number of viruses. Viral proteins can modulate the activity of host cell proteins that affect replication by a number of means, including exclusion from replication centers, targeted degradation, or inactivation by direct interaction. The modulation of host protein activities by viruses not only interferes with normal cellular functions, such as DNA replication, it has the potential to lead to more severe consequences, such as the induction of genomic instability and the development of cancer.
In addition to potentially disrupting the functions of important host nuclear machinery, viral replication in the nucleus presents the host cell with a number of foreign and otherwise abnormal DNA structures. These may represent targets for the host cell apparatus that recognizes and repairs damaged DNA. Many viruses, such as HSV-1, Ad and AAV contain repeated sequences that can undergo rearrangements or form secondary structures that are predicted substrates for repair machinery. For example, the AAV genome is flanked by inverted terminal repeats (ITRs) that form hairpin structures to prime DNA replication. Repetitive sequences in the genomes of many organisms have been shown to cause recombination hotspots or lead to DNA damage and secondary structure that is processed by host-cell machinery. Little is known about the interactions between replicating DNA viruses and the host damage machinery. Presumably, the inappropriate processing of viral genomes could represent a problem for replication efficiency and DNA viruses would need to deal with this insult by some means.