A role for uracil in innate immunity to HIV-1 infection

The nucleobase uracil is a common component of RNA, but can also be found within the context of DNA as a DNA lesion. A major source of uracil in DNA is the simple hydroylsis of cytosine bases. This process occurs spontaneously in the cell and generates premutagenic U:G mispairs that will lead to C/G → T/A transition mutations if not repaired prior to DNA replication. Cytosine is also enzymatically converted to uracil by the APOBEC family of cytosine deaminases. This purposeful introduction of uracil into DNA is an obligate step in the mechanisms of these enzymes in the acquired and innate immune response pathways. In addition to cytosine deamination, uracil can also be introduced into DNA through misincorporation of the uracil deoxynucleoside triphosphate, dUTP. dUTP is an important precursor to the cannonical DNA nucleotide dTTP, and like dTTP, can be incorporated into DNA by DNA polymerases opposite dA. While dUTP incorporation is not inherently mutagenic, rampant uracil incorporation does lead to genomic instability and fragmentation. To keep dUTP levels low, all free living organisms express the enzyme dUTPase, which hydrolyzes dUTP into dUMP. dUTPase is robustly expressed during the replicative stages of the cell cycle, where there threat of dUTP misincorporation in the greatest. However, dUTPase activity is barely detectable in quiescent stages of the cell cycle, leading to high steady state dUTP concentrations in non-dividing cells. Many viruses whose tropism includes non-dividing cells encode dUTPase to prevent uracil misincorporation into their DNA. Perplexingly, non-primate lentiviruses such as HIV-1 do not encode dUTPase, but are still capable of infecting quiescent macrophages. To adders this paradox, the studies herein provide an analytical assessment of the effect of dUTP misincorporation on HIV-1 and reveal that uracil misincorporation has antiviral effects at the integration and post integration stages. In addition, these studies define the uracil base excision repair enzyme UNG2 as a restriction factor for HIV-1, but only under conditions of high dUTP. These findings reconcile why studies performed in different model systems have lead to contradictory hypotheses for the role for UNG2 in HIV-1 replication.