Identifying Host Factors Associated with DNA Replicated During Virus Infection

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.

Replication Compartments of DNA Viruses in the Nucleus: Location, Location, Location

“…Other approaches have utilized the isolation of proteins on nascent DNA (iPOND), specifically labeling replicating viral DNA during infection with HSV-1, HAdV, or a cytoplasmic-replicating pox virus, and isolating labeled DNA in association with proteins. Similarly to the immunoprecipitation of ICP8, these studies identified host proteins involved in DNA replication, chromatin remodeling, DNA repair, transcription, and RNA processing, as well as nucleolar proteins [18,118,119]. Furthermore, this approach has provided insight into host factors that are excluded from VRCs to prevent the restriction of viral replication [18].…”

“…Since the discovery that the polyomavirus simian virus 40 (SV40) and human adenovirus (HAdV) initiated VRC formation at the periphery of PML NBs, a wealth of evidence now suggests that for many DNA viruses including members of the Herpesviridae, Adenoviridae, Parvoviridae, Polyomaviridae and Papillomviridae, VRC formation and many subsequent viral processes take place at these sites. Much of this evidence comes from the localization of viral proteins, viral nucleic acid, and even incoming viral genomes [6,11,14,[16][17][18]. One notable exception may be the autonomous parvoviruses.…”

Epigenetics and the dynamics of chromatin during adenovirus infections

“…The interaction between E4orf3 and E1A is likely direct since purified E1A co-immunoprecipitates with GST-tagged and purified E4orf3 in vitro. Given that both E1A and E4orf3 have previously been associated with regulators of host genome transcription (see E1A section of this review and [83,141]), it is plausible that the interaction of E1A and E4orf3 may impact transcription from viral DNA. During E1AD11-13 virus infection, histone occupancy is higher, E1A occupancy reduced, and transcription is lower at specific early-transcribed adenovirus genes as well as at the late gene promoter, suggesting that E4orf3 represses transcription from the viral genome.…”

“…Based on these observations, E4orf3 seems to facilitate the association of host histone proteins with viral genomes and therefore modulate transcription. Given that both E1A and E4orf3 have previously been associated with regulators of host genome transcription (see E1A section of this review and [83,141]), it is plausible that the interaction of E1A and E4orf3 may impact transcription from viral DNA. While many mechanistic details of this process remain unknown, these recent studies of E4orf3 make it clear that there is still much to be learned about E4orf3 and its interaction with host factors.…”

“…In the case of E4orf3-driven sequestration of the MRN complex, repair complex proteins are directed away from VRCs to prevent the host DSB repair machinery from ligating linear viral genomes. Mass spectrometry analysis of proteins associated with nascent viral DNA during adenovirus replication has provided a comprehensive view of which host factors are selectively excluded or enriched at VRCs [141]. E4orf3 sequesters other host factors besides PML body proteins and DNA repair factors.…”