DUF99 family proteins are novel endonucleases that cleave deoxyuridine on DNA substrates

DNA deamination occurs constantly in a cell and causes DNA damage. As this damage can be deleterious, organisms have evolved many systems to eliminate it, such as Endonuclease V (Endo V). DUF99 family protein contains a domain of unknown function similar to Endo V but has not been experimentally characterized to date. Here, we show that DUF99 family proteins cleave the 3'-side of deoxyuridine (dU) on DNA substrates. Based on phylogenetic analysis, we designated this new protein family as Endonuclease dU (Endo_dU). We also observed that Endo_dU coding gene frequently colocalizes with that of uracil-DNA glycosylase (UDG) in halophilic archaea, and we further performed gene knockout of Endo_dU gene on Haloferax volcanii. The transcription level of UDG gene on Endo_dU knockout strain was increased when induced by sodium bisulfite. Thus, we hypothesize that Endo_dU establishes a new endonuclease family with broad phylogenetic distribution and may participate in DNA repair.