Amino acid usage versus anaerobic expression data across the entire proteome

Range Table - link
Organism Budding yeast Saccharomyces cerevisiae
Reference Raiford DW, Heizer EM Jr, Miller RV, Akashi H, Raymer ML, Krane DE. Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae? J Mol Evol. 2008 Dec67(6):621-30. p.625 table 2PubMed ID18937004
Method P.623 left column bottom paragraph: "The approach taken to calculate biosynthetic costs was first employed by Craig and Weber (1998), and by Akashi and Gojobori (2002 PMID 11904428), and it exploited the near-universality of biosynthetic pathways to determine the number of high energy phosphate bonds (~PO4) required to synthesize amino acids."
Comments P.628 left column 2nd paragraph: "The most biosynthetically expensive amino acid utilizing anaerobic costs is Met, which also exhibits no significant trend (Table 2). The other aromatic amino acids (Tyr and Phe) which also are aerobically biosynthetically expensive generally show no significant trend in usage vs. expression data acquired under aerobic conditions (Tyr has a significant negative trend with respect to aerobic transcript abundance however, the Mantel-Haenszel statistic is not significant, indicating that the trend is not consistent across functional categories) (Tables 1 and 2). Additionally, there are several amino acids with a low biosynthetic cost that exhibit negative correlations with all three expressivity measures (Ser for anaerobic costs and Arg, Asn, Cys, His, and Ser, e.g., for aerobic) (Tables 1 and 2)."
Entered by Uri M
ID 107585