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Background  APOBEC3 (A3) proteins deaminate DNA cytosines and block the replication of retroviruses and retrotransposons. Each  A3  gene encodes a protein with one or two conserved zinc-coordinating motifs (Z1, Z2 or Z3). The presence of one  A3  gene in mice (Z2–Z3) and seven in humans,  A3A-H  (Z1a, Z2a-Z1b, Z2b, Z2c-Z2d, Z2e-Z2f, Z2g-Z1c, Z3), suggests extraordinary evolutionary flexibility. To gain insights into the mechanism and timing of  A3  gene expansion and into the functional modularity of these genes, we analyzed the genomic sequences, expressed cDNAs and activities of the full  A3  repertoire of three artiodactyl lineages: sheep, cattle and pigs.    Results  Sheep and cattle have three  A3  genes,  A3Z1 ,  A3Z2  and A3Z3, whereas pigs only have two,  A3Z2  and A3Z3. A comparison between domestic and wild pigs indicated that  A3Z1  was deleted in the pig lineage. In all three species, read-through transcription and alternative splicing also produced a catalytically active double domain A3Z2-Z3 protein that had a distinct cytoplasmic localization. Thus, the three  A3  genes of sheep and cattle encode four conserved and active proteins. These data, together with phylogenetic analyses, indicated that a similar, functionally modular  A3  repertoire existed in the common ancestor of artiodactyls and primates ( i.e ., the ancestor of placental mammals). This mammalian ancestor therefore possessed the minimal  A3  gene set, Z1-Z2-Z3, required to evolve through a remarkable series of eight recombination events into the present day eleven Z domain human repertoire.    Conclusion  The dynamic recombination-filled history of the mammalian  A3  genes is consistent with the modular nature of the locus and a model in which most of these events (especially the expansions) were selected by ancient pathogenic retrovirus infections.

bmc molecular biology

The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals