Two distinct replication compartments provide viral genomes for either transcription or packaging into progeny virions

For adenoviruses (AdV) as for many other viruses, the viral life cycle requires the dynamic conversion of viral genomes into distinct physiological forms. During entry AdV genomes (vDNAs) are delivered as highly condensed, transcriptionally inactive chromatin, stored inside the viral capsid and devoid of cellular histones. Decondensation and initial transcription of viral genes post genome delivery is achieved through association with cellular host chromatin factors, including histones. Incoming vDNAs then have to replicate, new virions have to be produced from expressed viral genes and the replicated genomes have to be condensed and packed histone free into progeny virions.

In our recent manuscript we used pulse-chase labeling of viral DNA with nucleotide analogs allowing us to follow the fate of newly replicated viral genomes over time. This analysis has identified the existence of two distinct replication compartments that are organized in a spatio-temporal manner. Our results suggest that early replication compartments replicate genomes dedicated to viral gene expression presumably following chromatinization with cellular histones. An unidentified switch then triggers conversion into morphologically and functionally different late replication compartments that replicate genomes for packaging into progeny virions. Late replicated vDNAs accumulate in distinct subnuclear domains, which we termed ViPR bodies (Virus-induced-post-replication bodies). ViPR bodies are devoid of cellular histones and specifically associate with viral chromatin markers and a nucleolar factor Mybbp1a supporting the idea that these vDNAs are subject to packaging into progeny virions.

Thus our work suggests timed control of replication to generate two classes of viral genomes, one for transcription and one for transport.
(1) Tracking adenovirus genomes identifies morphologically distinct late DNA replication compartments. Komatsu T, Robinson DR, Hisaoka M, Ueshima S, Okuwaki M, Nagata K, Wodrich H. Traffic. 2016 Aug 5.

Single viral genome analysis reveals escape mechanisms for adenoviruses from nuclear antiviral sensors and effectors (Komatsu et al. 1-3)

Latency and lytic replication are two hallmarks of nuclear replicating DNA viruses. In recent years it became evident that the chromatin structure of the viral genome is the underlying cause to distinguish between repressive/latent state and transcriptional active/lytic state. In this context the first hours of an infection have been suggested to play a crucial role in how the cell nucleus perceives and reacts to an invading genome. Based on studies in the herpes simplex virus it was suggested that PML nuclear bodies and its constituents such as the chromatin remodeling complex Daxx/ATRX, SP100 or PML are major effectors targeting incoming genomes to establish a repressive chromatin structure on the viral genome with the goal to suppress viral gene expression. The observation that knockdown of individual PML-NB components and/or nuclear DNA sensors such as IFI16 have pro-viral functions and the observation that viral genomes of other viral families also associate with PML nuclear bodies was used to generalize the notion that PML nuclear bodies are ubiquitous, IFN inducible antiviral factors against invading viral genomes.

In this series of three manuscripts by Komatsu et al. we oppose this generalized view. First we developed (1) an imaging system for individual incoming adenoviral genomes to study the nuclear antiviral response. In subsequent studies we show that for adenoviruses (2) neither PML nuclear bodies nor (3) IFN treatment nor other known antiviral factors such as IFI16, PH13/SPOC or SP100 isoforms target invading adenovirus genomes. We conclude that adenoviruses, different from herpesviruses, have developed mechanisms to evade a large repertoire of nuclear antiviral sensors and effectors providing a rational for their efficient lytic replication. Our data also show that PML nuclear bodies react differentially to viral genomes when exposed to different virus families and show the need for detailed in depth studies and the requirement for developing suitable experimental systems to visualize individual viral genomes at the single cell level.

(1) A Method for Visualization of Incoming Adenovirus Chromatin Complexes in Fixed and Living Cells. Komatsu T, Dacheux D, Kreppel F, Nagata K, Wodrich H. PLoS One. 2015 Sep 2;10(9)

(2) An Adenovirus DNA Replication Factor, but Not Incoming Genome Complexes, Targets PML Nuclear Bodies. Komatsu T, Nagata K, Wodrich H. J Virol. 2015 Nov 25;90(3):1657-67. doi: 10.1128/JVI.02545-15.

(3) Imaging analysis of nuclear antiviral factors through direct detection of incoming adenovirus genome complexes. Komatsu T, Will H, Nagata K, Wodrich H. Biochem Biophys Res Commun. 2016 Mar 22.