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MBE Advance Access published online on June 5, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl029
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted May 25, 2006

Research Article

Amino Acid Cost and Codon Usage Biases in Six Prokaryotic Genomes: A Whole Genome Analysis

Esley M. Heizer Jr. 1, Douglas W. Raiford 2, Michael L. Raymer 2, Travis E. Doom 2, Robert V. Miller 3, and Dan E. Krane 1 *

1 Department of Biological Sciences, Wright State University, Dayton, OH
2 Department of Computer Science and Engineering, Wright State University, Dayton, OH
3 Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK

* To whom correspondence should be addressed.
Dan E. Krane, E-mail: Dan.Krane{at}wright.edu


  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 seven-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 four 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 six organisms is inversely correlated with a coding region's average amino acid biosynthetic cost in a fashion that is independent of chemoheterophic, photoautotrophic, or thermophilic life style. 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.

Keywords: codon usage bias; amino acid cost; prokaryote; genome; bioinformatics.
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