Amino acid metabolism conflicts with protein diversity

TL;DR

This paper presents a model explaining amino acid abundance in proteomes as a trade-off between metabolic cost and sequence diversity, aligning well with observed data across many species.

Contribution

It introduces a simple cost-diversity trade-off model that accounts for amino acid abundances and explains proteome diversity and size.

Findings

Model explains amino acid abundance patterns

Proteomes balance size and diversity optimally

Cost function including chemical decay fits data well

Abstract

The twenty protein coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, sequence diversity is necessary for protein folding, function and evolution. Here we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data is remarkably well explained when the cost function accounts for amino acid chemical decay. More than one hundred proteomes reach comparable solutions to the trade-off by different combinations of cost and diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse.