Coalescing replication compartments provide the opportunity for recombination between coinfecting herpesviruses

Abstract

Homologous recombination (HR) is considered a major driving force of evolution because it generates and expands genetic diversity. Evidence of HR between coinfecting herpesvirus DNA genomes can be found frequently both in vitro and in clinical isolates. Each herpes simplex virus type 1 (HSV‐1) replication compartment (RC) derives from a single incoming genome and maintains a specific territory within the nucleus. This raises intriguing questions about where and when coinfecting viral genomes interact. To study the spatiotemporal requirements for intergenomic recombination, we developed an assay with dual‐color FISH that enables detection of HR between different pairs of coinfecting HSV‐1 genomes. Our results revealed that HR increases intermingling of RCs derived from different genomes. Furthermore, inhibition of RC movement reduces the rate of HR events among coinfecting viruses. Finally, we observed correlation between nuclear size and the number of RCs per nucleus. Our findings suggest that both viral replication and recombination are subject to nuclear spatial constraints. Other DNA viruses and cellular DNA are likely to encounter similar restrictions.—Tomer, E., Cohen, E. M., Drayman, N., Afriat, A., Weitzman, M. D., Zaritsky, A., Kobiler, O. Coalescing replication compartments provide the opportunity for recombination between coinfecting herpesviruses. FASEB J. 33, 9388–9403 (2019). http://www.fasebj.org

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

“…Under experimental conditions, DNA viruses typically initiate multiple VRCs with numbers anywhere between 1 and 20 per nucleus depending on the virus in question, experimental conditions such as multiplicity of infection (MOI), and the cell type infected [16,[61][62][63][64][65][66][67]. In the case of HAdV, the number of initiated VRCs correlates with MOI, up to a point of saturation where the addition of more virus does not result in an increase in VRC number [68].…”

“…This confirms that in the context of HSV-1 infection, the majority of VRCs likely initiate from a single genome. During co-infection with different pseudorabies viruses (PRV), PRV and HSV-1 in combination, or different HSV-1 recombinants, each virus is typically replicated within distinct territories [61,62,69]. Interestingly, this not only suggests that each VRC is initiated by a viral genome, but that each VRC contains only replicated progeny derived from the initial founder virus.…”

“…Although it is not entirely clear what dictates the upper limit of how many VRCs can form per nucleus, limitations on the availability of cellular factors required to initiate viral genome replication and the number of available sites viable for VRC initiation have been proposed as contributing factors [11,25,69]. Interestingly, both the number and size of HSV-1 VRCs correlates with nucleus size, suggesting that there may be spatial restraints to how many VRCs can form in an infected nucleus [62]. Indeed, it is possible that the upper limit of VRC number is restricted by availability of sites viable for the initiation and growth of VRCs.…”

“…In many cases, the accumulation of these viral proteins throughout the nucleoplasm can be detected prior to the formation of VRCs [16,68,85], suggesting that their formation is concentration dependent, which is another feature of LLPS [87][88][89][90]. HSV-1, CMV, PRV, and HAdV VRCs also coalesce as infection progresses and they grow, fusing together in a liquid-like manner [14,15,61,62,65,69,95,[102][103][104]. However, it was recently demonstrated that HSV-1 VRCs are not disrupted by treatment with 1,6-hexanediol, which is a feature of many other cellular BMCs.…”

Viral and cellular interactions during adenovirus DNA replication

“…It also implies that the cell is only capable of supporting a limited number of VRCs. Evidence in support of this model can also be extrapolated from studies of other DNA viruses . The factors limiting the maximum number of VRCs initiated within each nucleus is unknown.…”