Candidate Roles for Initiator Methionine Processing in Ribosome Assembly and Function: A Cross-Species Census

How initiator methionine processing relates to ribosomal protein interfaces remains incompletely understood. This study integrated 68 ribosome structures from 61 species (1873 family–species records, 95 families) and characterized termini and published assembly intermediates to examine comparative associations and identify specific candidate interfaces. Residue-2 predictions agreed with 388 out of 393 characterized termini in 12 species. In 58 switching families, the burial-based RNA only versus exposed odds ratio for predicted retention was 0.31 (95% confidence interval 0.18–0.53) with family strata, 0.64 (0.32–1.29) with family by domain strata, and 0.76 (0.29–1.99) with family by clade strata; the reconstructed family by clade estimate was 1.21 (0.48–3.07). Common position scoring preserved the pooled RNA association, whereas matched phylogenetic estimates remained inconclusive and protein contact contrasts depended strongly on the scored position. An exploratory analysis of 21,485 reference proteomes identified a bacterial association at order, one out of five ranks tested, surviving within-domain but not three-domain multiplicity adjustment. Conserved permissive families showed no detected difference between RNA-contacting and protein-packed groups, and observed bS16 retention opposed a uniform cleavage requirement. At individual interfaces, uL15 and eL24 exhibited alternative terminal contact registers, while yeast uS12 and eS27 occupied supported RNA and protein interfaces, respectively, in pre-40S and mature particles. These comparisons extend processing-associated functional studies by identifying specific molecular interfaces and their assembly contexts. They prioritize uS12 and eS27 for investigating how terminal processing influences ribosome organization and function; the functional consequences at each site remain to be established.