Human cytomegalovirus regulates host DNA repair machinery for viral genome integrity

ABSTRACT The DNA damage response (DDR) encompasses a multitude of interconnected pathways that serve as a cellular defense to protect genome integrity. Dysregulation or failure of these pathways results in cancers and genetic disease. DNA viruses, including the herpesvirus cytomegalovirus (CMV), activate DDR signaling during their replicative program. The mechanisms by which they commandeer these responses for replication of their genome is less well understood. Here, we define a viral protein, UL138, that modulates the activity of host DDR pathways. The loss of UL138 results in structural variants, including inversion, deletions, duplication, with signature of homology-directed repair and other DDR pathways. The actions of UL138 are due, in part, to its modulation of pathways regulated by the cellular deubiquitinating complex that targets proliferating cell nuclear antigen (PCNA) and Fanconi Anemia effectors, FANCD2 and FANCI. However, we also show that UL138 accesses pathways independent of USP1-PCNA/FANCD2/FANCI. Disruption of UL138 or these pathways impacts viral genome replication and had consequences for viral genome integrity. This work provides mechanistic insight into the long-standing questions of how DNA viruses recruit, modulate and use cellular DDR pathways. It also puts forth CMV as a model system for further defining these pathways in human cells. GRAPHICAL ABSTRACT Major findings UL138 protects HCMV genome integrity through its interaction with USP1-PCNA/FANCD2/FANCI and repeat sequence-mediated pathways UL138 protects HCMV genome integrity in the UL region by mechanisms independent of repeat sequences and USP1-PCNA/FANCD2/FANCI Collectively, US and UL regions of the HCMV genome have fundamentally different pathways acting on them and UL138 modulates DNA damage and repair pathway choice.