Reduced Amino Acid Substitution Matrices Find Traces of Ancient Coding Alphabets in Modern Day Proteins.

ABSTRACT: All known living systems make proteins from the same 20 canonically coded amino acids, but this was not always the case. Early genetic coding systems likely operated with a restricted pool of amino acid types and limited means to distinguish between them. Despite this, amino acid substitution models like LG and WAG all assume a constant coding alphabet over time. That makes them especially inappropriate for the aminoacyl-tRNA synthetases (aaRS)-the enzymes that govern translation. To address this limitation, we created a class of substitution models that account for evolutionary changes in the coding alphabet size by defining the transition from 19 states in a past epoch to 20 now. We use a Bayesian phylogenetic framework to improve phylogeny estimation and testing of this two-alphabet hyp

SUBMITTER: Douglas J 

PROVIDER: S-EPMC12402984 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature