Updated project metadata. Viruses must effectively remodel host cellular pathways to replicate and evade immune defenses, and they must do so with limited genomic coding capacity. Targeting post-translational modification (PTM) pathways provides a mechanism by which viruses can broadly and rapidly transform a hostile host environment into a hospitable one. We used mass spectrometry-based proteomics to quantify changes in protein abundance and two PTM types – phosphorylation and ubiquitination – in response to HIV-1 infection with viruses harboring targeted deletions of a subset of HIV-1 genes. PTM analysis revealed a requirement for Aurora kinase activity in HIV-1 infection and identified substrates of a phosphatase that is degraded during infection. Finally, we demonstrated that the Cullin4A-DDB1-DCAF1 E3 ubiquitin ligase ubiquitinates histone H1 somatic isoforms and that the HIV-1 Vpr protein inhibits this process, leading to defects in DNA repair.