Amino acid metabolic origin as an evolutionary influence on protein sequence in yeast

Abstract

The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor's phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time.

Fig. 1

Amino acid composition bias profiles of the 221 largest GO groups. The fold abundance of each amino acid compared with the genomic average within the largest 221 GO groups is shown. Red/yellow indicates overrepresentation, and blue/cyan indicates underrepresentation. Rows are clustered by the similarity in bias profiles of each group, and columns are clustered by similarity in amino acid abundance across GO groups. Distance trees indicate the similarities of values in rows and columns, but they do not imply historic relations. Meta-GO groups that are inferred from groups within the GO clustering are labeled on the left

Fig. 2

Metabolic origin determines the greatest diversity in composition bias across GO groups. a The clustering of amino acids by similarity in bias profiles is shown in tree format. Amino acids derived metabolically from the oxidative portion of cellular respiration are yellow, whereas those derived from the reductive portion are green. Red outlines indicate polar amino acids. b Metabolic network of amino acid synthesis in yeast. c PCA of the bias profile across the 221 largest GO groups. Shown are the PC2 versus PC1 values of each GO group, along with the amino acid terms contributing to each PC. GO group points are colored according to membership in the listed meta-GOs

Fig. 3

Amino acid abundances in periodic proteins follow the phases of their synthesis. a The same high-level functional groups seen in Fig. 1 in a ternary plot indicating their YMC phase expression biases. Color indicates PC1 value. Cell-cycle is shown for reference (blue). b The fraction of periodic genes expressed in the Ox (red) and RB (blue) phases are correlated with PC1 across the 75 GO groups exhibiting the most nonuniform YMC expression; p = 0.0042 and 0.00024, respectively, by Bonferroni-corrected Spearman rank correlation. c Composition bias trees (as in Fig. 2a). Yellow indicates oxidative amino acids, green indicates reductive amino acids, and red indicates polar amino acids. See Fig. S4 for remaining species. d Significance of separation of amino acids by polarity, metabolic source, and metabolic cost across divisions of the composition bias trees. Bars indicate SEM across all trees divisions, leaving ≥5 amino acids on each “half.” Polarity, source, and cost were tested with Fisher’s exact, Fisher’s exact, and Mann–Whitney U-tests, respectively. Asterisks indicate facultative organisms. Obligate aerobes: Pseudomonas aeruginosa and Sulfolobus acidocaldarius. Obligate anaerobes: Clostridium acetobutylicum, Fusobacterium nucleatum, and M. jannaschii. Facultative species: Halobacterium salinarium and Bacillus subtilis