title: Cost-minimization of amino acid usage.
abstract: The negative correlation between the frequencies of usage of amino acids and their biosynthetic cost suggests that organisms minimize costs of protein biosynthesis. Empirical results support that: (1) free-living organisms (Archaea, Bacteria, and Eucaryota) minimize the usage of heavy amino acids more than intracellular organisms (viruses, chloroplasts, and mitochondria), a result confirmed by comparing intracellular Bacteria with other Bacteria; (2) avoidance of amino acids with low impact on protein structure (Chou-Fasman indices) is greater than for those with equal molecular weight but greater structural impact: constraints on protein function limit cost-minimization; (3) amino acid weight minimization (WM) for a protein correlates positively with the protein's expression level and with its size; (4) preliminary results suggest that for different proteins, the evolutionary rate of amino acid replacements correlates negatively with WM in these proteins; (5) results suggest that WM decreases with genome-size; and (6) developmental rates correlate positively with WM (within primates and rodents), even after confounding factors were accounted for. Effects of biosynthetic cost-minimization at whole-organism levels vary with metabolic and ecological strategies. Biosynthetic cost-minimization is an adaptive hypothesis that yields a semi-mechanistic explanation for small differences in allele fitness.
authors.affiliation: Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. Herve@uchicago.edu
authors.forename: Hervé
authors.initials: H
authors.lastname: Seligmann
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism*; D000818:Animals; D001105:Archaea / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001482:Base Composition; D003062:Codon; D004734:Energy Metabolism / Q000502:physiology*; D005057:Eukaryotic Cells / Q000502:physiology; D016678:Genome; D008954:Models, Biological; D008970:Molecular Weight; D014176:Protein Biosynthesis; D011506:Proteins / Q000737:chemistry
chemical_list: D000596:Amino Acids; D003062:Codon; D011506:Proteins