title: Translational selection and yeast proteome evolution.
abstract: The primary structures of peptides may be adapted for efficient synthesis as well as proper function. Here, the Saccharomyces cerevisiae genome sequence, DNA microarray expression data, tRNA gene numbers, and functional categorizations of proteins are employed to determine whether the amino acid composition of peptides reflects natural selection to optimize the speed and accuracy of translation. Strong relationships between synonymous codon usage bias and estimates of transcript abundance suggest that DNA array data serve as adequate predictors of translation rates. Amino acid usage also shows striking relationships with expression levels. Stronger correlations between tRNA concentrations and amino acid abundances among highly expressed proteins than among less abundant proteins support adaptation of both tRNA abundances and amino acid usage to enhance the speed and accuracy of protein synthesis. Natural selection for efficient synthesis appears to also favor shorter proteins as a function of their expression levels. Comparisons restricted to proteins within functional classes are employed to control for differences in amino acid composition and protein size that reflect differences in the functional requirements of proteins expressed at different levels.
authors.affiliation: Institute of Molecular Evolutionary Genetics and Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA. akashi@psu.edu
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Akashi
mesh_terms: D000222:Adaptation, Physiological; D000595:Amino Acid Sequence / Q000235:genetics; D003062:Codon / Q000235:genetics; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal; D007700:Kinetics; D020411:Oligonucleotide Array Sequence Analysis; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D014176:Protein Biosynthesis; D020543:Proteome; D012333:RNA, Messenger / Q000032:analysis; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D012641:Selection, Genetic; D013045:Species Specificity
chemical_list: D003062:Codon; D010455:Peptides; D020543:Proteome; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; D012343:RNA, Transfer