Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold

Abstract Evolutionary arms races between cells and viruses drive the rapid diversification of antiviral genes in diverse life forms. Recent discoveries have revealed the existence of shared immune genes between prokaryotes and eukaryotes, showing molecular and mechanistic similarities in their response to viruses. However, the underlying evolutionary dynamics that explain the conservation and adaptation of these antiviral genes remain mostly unexplored. Here, we show that viperins constitute a highly conserved family of immune genes across diverse prokaryotes and eukaryotes, and uncover mechanisms by which they diversified in eukaryotes. Our findings indicate that viperins are enriched in Asgard archaea and widely distributed in all major eukaryotic clades, suggesting their presence in the Last Eukaryotic Common Ancestor (LECA). We show that viperins maintain their immune function by producing antiviral nucleotide analogs. We demonstrate that eukaryotic viperins diversified through serial innovations on the viperin gene, such as the emergence and selection of substrate specificity towards pyrimidine nucleotides, and through partnerships with genes maintained through genetic linkage, notably with nucleotide kinases. These findings unveil biochemical and genomic transitions underlying the adaptation of immune genes shared by prokaryotes and eukaryotes. Our study paves the way for the understanding of the conservation of immunity across domains of life.