Host factor KAP1 coordinates temporal control between transcription and replication

Abstract

Temporal control of transcription and replication is necessary for efficient Epstein–Barr virus reactivation. Xu et al. identified the KAP1/EA-D/ATM axis as a critical regulator of these processes. This discovery illuminates the collaboration between host and viral factors as an essential interaction for viral reactivation.

Epstein–Barr virus (EBV), a pervasive human gamma-herpesvirus infecting approximately 95% of the global population, switches between a dormant latent and an active lytic cycle. The ability of the virus to emerge from latency by environmental cues and resume the lytic cycle is fundamental for viral propagation. During latency, EBV’s genome relies on the host replication machinery for propagation to daughter cells. However, during viral reactivation the host’s DNA replication is blocked, requiring transcription of the viral genes encoding the products necessary for replication. During the EBV lytic phase, the viral genome is both heavily transcribed and used as a template for viral replication. Simultaneous execution of these two processes creates the potential for disastrous physical encounters between the transcriptional and replication machineries leading to DNA breaks and deleterious rearrangements. EBV strategically navigates this challenge through strict temporal control. Immediate-early and early gene products important for DNA replication are first transcribed from the parental viral genomes, followed by DNA replication using these newly translated gene products. Finally, these newly synthesized genomes lack heterochromatin which ostensibly allows late transcription of structural gene products for virion production [1].

While herpesviruses, including EBV, meticulously orchestrate the temporal order during lytic reactivation, it is incompletely understood how such DNA viruses switch from transcription to replication of the same template. In a noteworthy addition to the research, Xu et al. unveil a critical role for a host and viral protein complex in the sequence of events at the viral replisome for efficient replication [2]. The research team leveraged protein purification on newly synthesized DNA (iPOND) technique in reactivated cells to determine the composition of viral replication forks. Notably, EBV DNA replication proteins dominated, excluding the host DNA polymerases due to the blockade of host DNA replication during lytic reactivation. Over 200 host proteins were found at these viral replication forks enriched in pathways involved in DNA replication and repair, chromatin modification and transcriptional repression, RNA processing, and the proteasome, emphasizing the significance of the host factors [2].

Emerging as a critical player in the switch from transcription to replication, KRAB-associated protein 1 (KAP1) is a host protein involved in transcriptional repression and chromatin organization. KAP1 serves as an essential transcriptional repressor in establishing latency by turning off lytic transcription in newly infected cells. During the lytic phase, the host’s DNA damage-response kinase ATM (ataxia-telangiectasia mutated) triggers a dynamic chromatin remodeling cascade on the viral genome. ATM phosphorylates and activates KAP1, a SUMO2-ligase. This results in SUMOylation of EBV processivity factor (EA-D) by KAP1 to recruit the histone loader CAF1 and the histone methyltransferase SETDB1, responsible for laying down H3K9 trimethyl marks [2]. Ultimately, the unique interplay between the host and lytic viral factors results in increased H3K9 trimethylation, a key epigenetic mark associated with chromatin condensation and transcriptional repression. Phosphorylation of KAP1 is a common event regulating the lytic phase among the herpesvirus family where it is phosphorylated by a viral protein in Kaposi’s sarcoma-associated herpesvirus [3], mammalian target of rapamycin in human cytomegalovirus [4], and ATM (but not mTOR) in EBV [5]. This versatility positions KAP1 as a potential integrator of internal and external cues, adapting to signals from different kinases. Interestingly, KAP1 is also found at HSV-1 lytic forks and may serve more broadly as a mediator in the switch between transcription and replication for other herpesviruses. This switch from transcription to replication is a key event in the replication of DNA viruses.

KAP1 serves a role in silencing lytic transcription during latency [6], and it seems necessary that the loss of KAP1 repression is required for initiating lytic transcription [7]; however, the dynamics of KAP1 regulation from the start of lytic reactivation is only partially clear. Additionally, the recruitment and activation of ATM at the viral replisome are unknown. Possibly, initial friction between the transcription and replication machineries, resulting in DNA damage, is the signal required to recruit ATM. A previous report showed that the EBV viral protein kinase (vPK, BGLF4 product) phosphorylates ATM and it is perfectly positioned at viral replication forks to interact with ATM [2,8]. Looking beyond EBV, this study highlights a potential role in EBV-negative cells for ATM, through phosphorylation of KAP1, to prevent transcription–replication collisions on the cellular genome.

Altogether, these studies demonstrate how EBV hijacks the hosts biology to maintain temporal order of transcription and replication during the lytic phase. EBV encodes the viral gene products necessary for autonomous DNA replication yet requires coordination between host epigenetic regulators and other cellular components which are indispensable for the strict regulation of viral transcription preceding DNA replication. EBV persists as a multicopy genome with epigenetically diverse programs and patterns [9] which may aid or disrupt the temporal control during the lytic phase. While much of the work has been performed in B lymphocyte lineages, understanding EBV infection of epithelial cells is equally crucial since it also leads to cancer. It will be interesting to see how KAP1-mediated transcriptional silencing is orchestrated with potentially different host factors from differing cell types. By recognizing the pivotal role of viral replication in the overall viral infection cycle, deciphering these underlying mechanisms may unveil opportunities for intervention, allowing nuanced differences between viral and host replication to be exploited for therapeutic targets.