Abstract
Methionine aminopeptidases remove the initiator methionine when residue 2 is small and uncharged. Loss of this activity is lethal in bacteria and yeast. This study asks whether the environment of a terminus predicts its processing class across lineages, whether it holds in sequences without structures, and whether the constrained termini are in place during subunit assembly. Across 68 ribosome structures from 61 species (1,873 records; 95 families, 58 switching class), termini embedded in rRNA without protein contact were predicted to retain methionine in 18% of records, against 45% of protein-contacted and 41% of exposed termini. Eight additional structures corroborated this pattern, which was attenuated under joint family-by-domain stratification. In 6,924 out-of-sample bacterial reference proteomes, exploratory clade-block tests supported an order-level residue-2 association sensitive to taxonomic rank and multiplicity; archaeal and eukaryotic tests were coverage-limited and inconclusive. In yeast assembly intermediates, the conserved uS12 and eS27 termini already occupy their mature environments. Twenty-five families are permissive in every sampled species, eleven threaded into rRNA. These findings indicate a conserved association between rRNA embedding and methionine removal and suggest that local compatibility of processed termini with rRNA contributes to it; the census is a resource for testing this hypothesis at named termini.