Proteome and cellular amino acid compositions may be mutually constrained and in a state of narrow convergence

Abstract

Proteins are composed of 20 amino acids, and their amino acid compositions are known to vary. Today, it is possible to examine all the amino acid compositions of all proteins in a proteome, and several reports have already reported on the differences in the compositions among the proteomes of different organisms. Meanwhile, the distribution of amino acid compositions within the proteome of a single organism has seldom been reported.

In this study, I examined the amino acid composition distribution of proteomic proteins based on publicly available information on human and Escherichia coli (E. coli) proteomes and found three things. First, each compositional distribution of all the examined amino acids showed a typical bell-shaped distribution. Second, the mean values of the distributions of each proteome were correlated with the measured amino acid compositions of human and E. coli cells, respectively. Third, in the distribution analysis of the distances between the protein compositions and their means, each proteome showed almost identical distributions in shape, and most of the proteins gathered toward the narrowed center near the mean.

The largest source of protein synthesis is intracellular proteins, and it is reasonable to assume that the source composition could constrain the proteome composition. On the other hand, proteome proteins consist of intracellular proteins, and therefore, the proteome composition likely constrains the intracellular composition. Hence, the bell-shaped narrow distributions of the amino acid compositions and the correlations with the actual cellular compositions seem to suggest that the amino acid compositions of proteome proteins are in a state of narrow convergence as a result of mutual constraint with the source amino acids of intracellular proteins.