The herpes simplex virus alkaline nuclease is required to maintain replication fork progression

ABSTRACT Herpes simplex virus is a large double-strand DNA virus that replicates in the nucleus of the host cell and interacts with host DNA replication and repair proteins. The viral 5′ to 3′ alkaline nuclease, UL12, is required for production of DNA that can be packaged into infectious virus. The UL12-deleted virus, AN-1, exhibits near wild-type levels of viral DNA replication, but the DNA cannot be packaged into capsids, suggesting it is structurally aberrant. To better understand the DNA replication defect observed in AN-1, we utilized isolation of proteins on nascent DNA (iPOND), a powerful tool to study all the proteins at a DNA replication fork. Combining iPOND with stable isotope labeling of amino acids in cell culture (SILAC) allows for a quantitative assessment of protein abundance when comparing wild type to mutant replication forks. We performed five replicates of iPOND-SILAC comparing AN-1 to the wild-type virus, KOS. We observed 60 proteins that were significantly lost from AN-1 forks out of over 1,000 quantified proteins. These proteins largely represent host DNA replication proteins including MCM2-7, RFC1-5, MSH2/6, MRN, and proliferating cell nuclear antigen. These observations are reminiscent of how these proteins behave at stalled human replication forks. We also observed similar protein changes when we stalled KOS forks with hydroxyurea. Additionally, we observed a decrease in the rate of AN-1 replication fork progression at the single-molecule level. These data indicate that UL12 is required for DNA replication fork progression and that forks stall in the absence of UL12. IMPORTANCE Herpes simplex virus 1 (HSV-1) is a near-ubiquitous pathogen within the global population, causing a lifelong latent infection with sporadic reactivation throughout the life of the host. Within at-risk and immunocompromised communities, HSV-1 infection can cause serious morbidities including herpes keratitis and encephalitis. With the possibility of herpesviruses to evade established antiviral therapies and there being no approved HSV-1 vaccine, there comes a need to investigate potential targets for intervention against infection and subsequent disease. UL12 is the viral 5'–3' exonuclease, which is required for the production of infectious progeny. In this study, we show that in the absence of UL12, viral replication fork progression is abrogated. These data point to UL12 as an attractive target for intervention, which could lead to better clinical outcomes of HSV-1-associated disease in the future.