Cysteine-rich sperm protamines arose independently at least twice on a deeply conserved, intrinsically disordered scaffold in amniotes.

Abstract

Every amniote must compact and shield the paternal genome, but the chemistry differs. In placental mammals, sperm chromatin is locked by protamine disulfide bridges, and the cysteine-rich form is considered the "mammalian" protamine. Analyzing 46 tetrapod protamine-1 orthologs on a time-calibrated phylogeny, we find it neither confined to eutherians nor of single origin: dasyurid marsupials (Planigale) carry cysteine-bearing protamines nested among cysteine-free marsupials. Ancestral-state reconstruction recovers cysteine-free as the ancestral state (root probability 0.99), with cysteine-bearing protamine arising independently at least twice (eutherian stem and Planigale; three gains, zero losses). Alignment and a gene tree confirm the Planigale proteins are dasyurid PRM1 orthologs whose cysteines occupy homologous positions within the genus, replacing tyrosine or arginine, at sites distinct from eutherian cysteines. All 46 protamines show sequence characteristics consistent with intrinsic disorder and none is folded by three structure predictors; confidence rises with disorder because poly-arginine is modelled as spurious helix, even in alignment-free AlphaFold3. Cysteine-free protamines carry marginally higher charge density across both origins (PGLS beta = + 0.044, p = 0.046) but not robustly; because the gained cysteines derive from tyrosine rather than arginine, and the difference is independent of PRM2, the pattern is consistent with, but not proof of, electrostatic compensation. The disulfide protamine is thus a convergent elaboration on a conserved, disordered polyarginine scaffold, not a mammalian baseline. Because protamine integrity underlies sperm DNA integrity and fertility, this polarity reframes the central question: how ancestral cysteine-free lineages, birds among them, protect the genome without covalent cross-links.