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Article
Amino Acid Cost and Codon-Usage Biases in 6 Prokaryotic Genomes: A Whole-Genome Analysis
Molecular Biology and Evolution
  • Esley M. Heizer, Wright State University - Main Campus
  • Douglas W. Raiford, Wright State University - Main Campus
  • Michael L. Raymer, Wright State University - Main Campus
  • Travis E. Doom, Wright State University - Main Campus
  • Robert V. Miller
  • Dan E. Krane, Wright State University - Main Campus
Document Type
Article
Publication Date
9-1-2006
Abstract
For most prokaryotic organisms, amino acid biosynthesis represents a significant portion of their overall energy budget. The difference in the cost of synthesis between amino acids can be striking, differing by as much as 7-fold. Two prokaryotic organisms, Escherichia coli and Bacillus subtilis, have been shown to preferentially utilize less costly amino acids in highly expressed genes, indicating that parsimony in amino acid selection may confer a selective advantage for prokaryotes. This study confirms those findings and extends them to 4 additional prokaryotic organisms: Chlamydia trachomatis, Chlamydophila pneumoniae AR39,Synechocystis sp. PCC 6803, and Thermus thermophilus HB27. Adherence to codon-usage biases for each of these 6 organisms is inversely correlated with a coding region's average amino acid biosynthetic cost in a fashion that is independent of chemoheterotrophic, photoautotrophic, or thermophilic lifestyle. The obligate parasites C. trachomatis and C. pneumoniae AR39 are incapable of synthesizing many of the 20 common amino acids. Removing auxotrophic amino acids from consideration in these organisms does not alter the overall trend of preferential use of energetically inexpensive amino acids in highly expressed genes.
DOI
10.1093/molbev/msl029
Citation Information
Esley M. Heizer, Douglas W. Raiford, Michael L. Raymer, Travis E. Doom, et al.. "Amino Acid Cost and Codon-Usage Biases in 6 Prokaryotic Genomes: A Whole-Genome Analysis" Molecular Biology and Evolution Vol. 23 Iss. 9 (2006) p. 1670 - 1680 ISSN: 07374038
Available at: http://works.bepress.com/travis_doom/41/