Evolutionary analysis of two complement C4 genes: Ancient duplication and conservation during jawed vertebrate evolution

The complement C4 is a thioester-containing protein, and a histidine (H) residue catalyzes the cleavage of the thioester to allow covalent binding to carbohydrates on target cells. Some mammalian and teleost species possess an additional isotype where the catalytic H is replaced by an aspartic acid (D), which binds preferentially to proteins. We found the two C4 isotypes in many other jawed vertebrates, including sharks and birds/reptiles. Phylogenetic analysis suggested that C4 gene duplication occurred in the early days of the jawed vertebrate evolution. The D-type C4 of bony fish except for mammals formed a cluster, termed D-lineage. The D-lineage genes were located in a syntenic region outside MHC, and evolved conservatively. Mammals lost the D-lineage before speciation, but D-type C4 was regenerated by recent gene duplication in some mammalian species or groups. Dual C4 molecules with different substrate specificities would have contributed to development of the antibody-dependent classical pathway. •Two C4 isotypes were found in various jawed vertebrates, including sharks and birds/reptiles.•C4 gene duplication occurred in the early days of the jawed vertebrate evolution.•Two divergent C4 lineages, termed H-lineage and D-lineage, were found in bony vertebrates.•The D-lineage genes were located in a syntenic region outside MHC.•In mammals, the D-lineage was lost before speciation, but D-type C4 was regenerated in some species or groups.