Bioinformatics Vol. 19 Suppl. 2 2003
page ii15
© 2003 Oxford University Press
Metabolic economics and microbial proteome evolution
Institute of Molecular Evolutionary Genetics, Department of Biology, 208 Mueller Laboratory, Penn State University, University Park, PA 16802, USA
Received on March 17, 2003
; accepted on June 9, 2003
Natural selection is thought to act upon protein structures to optimize biochemical properties related to their specific cellular function. Selection pressures related to efficient synthesis, rather than proper function, of proteins may act globally on the amino acid composition of the proteome, but are less firmly established. A substantial fraction of bacterial energy budgets are devoted to biosynthesis of amino acids, the building blocks of proteins. The fueling reactions of central metabolism provide precursor metabolites for synthesis of amino acids. Thus, synthesis of an amino acid entails a dual cost; energy is lost by diverting chemical intermediates from fueling reactions and additional energy is required to convert precursor metabolites to amino acids. Selection to reduce the energetic costs predicts increases in the abundance of less energetically costly amino acids in highly expressed proteins. Using synonymous codon usage bias as a measure of translation rates, we show that amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis reflects the action of natural selection to enhance metabolic efficiency. The primary structures of proteins may also reflect natural selection to enhance the rate and accuracy of their synthesis. Differences in cellular concentrations of tRNAs could lead to translation selection both within and among synonymous families. In yeast, usage of several amino acids show striking associations with gene expression. These changes in amino acid composition result in stronger correlations between amino acid usage and tRNA abundances in highly expressed genes than in less expressed loci. Proteome-wide patterns of amino acid composition in microbes appears to reflect natural selection to enhance the overall physiology of cells as well as the specific functions of proteins.
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