Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis Export

@article{heizer2006, 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. 10.1093/molbev/msl029}, author = {Heizer, Esley M. and Raiford, Douglas W. and Raymer, Michael L. and Doom, Travis E. and Miller, Robert V. and Krane, Dan E.}, citeulike-article-id = {1236432}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/molbev/msl029}, citeulike-linkout-1 = {http://mbe.oxfordjournals.org/cgi/content/abstract/23/9/1670}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16754641}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16754641}, day = {1}, doi = {10.1093/molbev/msl029}, journal = {Molecular Biology and Evolution}, keywords = {amino-acid-usage, cost-minimisation, gene-characteristics, mdb-manuscript-1, mdb-thesis}, month = {September}, number = {9}, pages = {1670--1680}, posted-at = {2009-02-03 15:33:06}, priority = {2}, title = {Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis}, url = {http://dx.doi.org/10.1093/molbev/msl029}, volume = {23}, year = {2006} }

TY - JOUR ID - heizer2006 L3 - citeulike-article-id:1236432 N2 - 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. 10.1093/molbev/msl029 IS - 9 JF - Molecular Biology and Evolution EP - 1680 TI - Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis VL - 23 SP - 1670 KW - amino-acid-usage KW - cost-minimisation KW - gene-characteristics KW - mdb-manuscript-1 KW - mdb-thesis AU - Heizer, Esley AU - Raiford, Douglas AU - Raymer, Michael AU - Doom, Travis AU - Miller, Robert AU - Krane, Dan PY - 2006/09/01/ UR - http://dx.doi.org/10.1093/molbev/msl029 ER -