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Issue No.02 - April-June (2010 vol.7)
pp: 238-250
Douglas W. Raiford , University of Montana, Missoula
Dan E. Krane , Wright State University, Dayton
Travis E. Doom , Wright State University, Dayton
Michael L. Raymer , Wright State University, Dayton
Genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale; however, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons are preferred. Detection of this bias is an important tool in the analysis of genomic data, particularly as a predictor of gene expressivity. Methods for identifying codon usage bias in genomic data that rely solely on genomic sequence data are susceptible to being confounded by the presence of several factors simultaneously influencing codon selection. Presented here is a new technique for removing the effects of one of the more common confounding factors, GC(AT)-content, and of visualizing the search-space for codon usage bias through the use of a solution landscape. This technique successfully isolates expressivity-related codon usage trends, using only genomic sequence information, where other techniques fail due to the presence of GC(AT)-content confounding influences.
Codon usage bias, GC-content, strand bias, translational efficiency.
Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer, "Automated Isolation of Translational Efficiency Bias That Resists the Confounding Effect of GC(AT)-Content", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, no. 2, pp. 238-250, April-June 2010, doi:10.1109/TCBB.2008.65
[1] M. Bulmer, "The Selection-Mutation-Drift Theory of Synonymous Codon Usage," Genetics, vol. 129, no. 3, pp. 897-907, Nov. 1991.
[2] S. Varenne, J. Buc, R. Lloubes, and C. Lazdunski, "Translation is a Non-Uniform Process. Effect of tRNA Availability on the Rate of Elongation of Nascent Polypeptide Chains," J. Molecular Biology, vol. 180, no. 3, pp. 549-576, Dec. 1984.
[3] R. Grantham, C. Gautier, M. Gouy, R. Mercier, and A. Pavé, "Codon Catalog Usage and the Genome Hypothesis," Nucleic Acids Research, vol. 8, no. 1, pp. r49-r62, http://nar.oupjournals. org/cgi/content/ abstract/9/1r43, 1981.
[4] R. Grantham, C. Gautier, M. Gouy, M. Jacobzone, and R. Mercier, "Codon Catalog Usage is a Genome Strategy Modulated for Gene Expressivity," Nucleic Acids Research, vol. 9, no. 1, pp. r43-74, 9/1r43, 1981.
[5] T. Ikemura, "Correlation between the Abundance of Escherichia coli Transfer RNAs and the Occurrence of the Respective Codons in Its Protein Genes," J. Molecular Biology, vol. 146, pp. 1-21, 1981.
[6] M. Gouy and C. Gautier, "Codon Usage in Bacteria: Correlation with Gene Expressivity," Nucleic Acids Research, vol. 10, no. 22, pp. 7055-7074, http://www.pubmedcentral.nih.govarticlerender.fcgi?tool=pubmed&pubmedid=6760125 , 1982.
[7] P.M. Sharp, E. Cowe, D.G. Higgins, D.C. Shields, K.H. Wolfe, and F. Wright, "Codon Usage Patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens: A Review of the Considerable Within-Species Diversity," Nucleic Acids Research, vol. 16, no. 17, pp. 8207-8211, Sept. 1988.
[8] F. Wright, "The "Effective Number of Codons" Used in a Gene," Gene, vol. 87, pp. 23-29, 1990.
[9] R.J. Grocock and P.M. Sharp, "Synonymous Codon Usage in Pseudomonas aeruginosa PA01," Gene, vol. 289, noS. 1/2, pp. 131-139, May 2002.
[10] A. Carbone, F. Képès, and A. Zinovyev, "Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle," Molecular Biology and Evolution, vol. 22, no. 3, pp. 547-561,, Mar. 2005.
[11] B. Lafay, A.T. Lloyd, M.J. McLean, K.M. Devine, P.M. Sharp, and K.H. Wolfe, "Proteome Composition and Codon Usage in Spirochaetes: Species-Specific and DNA Strand-Specific Mutational Biases," Nucleic Acids Research, vol. 27, no. 7, pp. 1642-1649, Apr. 1999.
[12] R. Jain, M.C. Rivera, J.E. Moore, and J.A. Lake, "Horizontal Gene Transfer in Microbial Genome Evolution," Theoretical Population Biology, vol. 61, no. 4, pp. 489-495, June 2002.
[13] S. Waack, O. Keller, R. Asper, T. Brodag, C. Damm, W.F. Fricke, K. Surovcik, P. Meinicke, and R. Merkl, "Score-Based Prediction of Genomic Islands in Prokaryotic Genomes Using Hidden Markov Models," BMC Bioinformatics, vol. 7, p. 142, , 2006.
[14] P.M. Sharp and W.H. Li, "An Evolutionary Perspective on Synonymous Codon Usage in Unicellular Organisms," J. Molecular Evolution, vol. 24, no. 1/2, pp. 28-38, 1986.
[15] J. Precup and J. Parker, "Missense Misreading of Asparagine Codons as a Function of Codon Identity and Context," J. Biological Chemistry, vol. 262, no. 23, pp. 11351-11355, Aug. 1987.
[16] D.C. Shields and P.M. Sharp, "Synonymous Codon Usage in Bacillus Subtilis Reflects Both Translational Selection and Mutational Biases," Nucleic Acids Research, vol. 15, no. 19, pp. 8023-8040, 15/198023, 1987.
[17] M.A. Freire-Picos, M.I. Gonzalez-Siso, E. Rodriguez-Belmonte, A.M. Rodriguez-Torre, E. Ramil, and M.E. Cerdan, "Codon Usage in Kluyveromyces lactis and in Yeast Cytochrome C-Encoding Genes," Gene, vol. 139, pp. 43-49, 1994.
[18] S. Kanaya, Y. Yamada, Y. Kudo, and T. Ikemura, "Studies of Codon Usage and tRNA Genes of 18 Unicellular Organisms and Quantification of Bacillus subtilis tRNAs: Gene Expression Level and Species-Specific Diversity of Codon Usage Based on Multivariate Analysis," Gene, vol. 238, pp. 143-155, 1999.
[19] P.M. Sharp and W.H. Li, "The Codon Adaptation Index—A Measure of Directional Synonymous Codon Usage Bias, and Its Potential Applications," Nucleic Acids Research, vol. 15, pp. 1281-1295, 1987.
[20] A. Carbone, A. Zinovyev, and F. Kepes, "Codon Adaptation Index as a Measure of Dominating Codon Bias," Bioinformatics, vol. 19, no. 16, pp. 2005-2015, content/abstract/19/162005, 2003.
[21] A.C. McHardy, A. Pühler, J. Kalinowski, and F. Meyer, "Comparing Expression Level-Dependent Features in Codon Usage with Protein Abundance: An Analysis of "Predictive Proteomics"," Proteomics, vol. 4, no. 1, pp. 46-58, 2004.
[22] A. Carbone, "Computational Prediction of Genomic Functional Cores Specific to Different Microbes," J. Molecular Evolution, vol. 63, no. 6, pp. 733-746, , Dec. 2006.
[23] H. Hotelling, "Analysis of a Complex of Statistical Variables into Principal Components," J. Educational Psychology, vol. 24, pp. 417-441, 1933.
[24] P. Sharp, T. Tuohy, and K. Mosurski, "Codon Usage in Yeast: Cluster Analysis Clearly Differentiates Highly and Lowly Expressed Genes," Nucleic Acids Research, vol. 14, no. 13, pp. 5125-5143, 14/135125, 1986.
[25] A. Ghosh, S. Tsutsui, and S. Tusutsui, Advances in Evolutionary Computing. Springer, 2003.
[26] V.K. Vassilev, T.C. Fogarty, and J.F. Miller, "Smoothness, Ruggedness and Neutrality of Fitness Landscapes: From Theory to Application," Advances in Evolutionary Computing: Theory and Applications, pp. 3-44, 2003.
[27] E.D. Weinberger, "Correlated and Uncorrelated Fitness Landscapes and How to Tell the Difference," Biological Cybernetics, vol. 63, pp. 325-336, 1990.
[28] S. Wright, "The Roles of Mutation, Inbreeding, Crossbreeding, and Selection in Evolution," Proc. Sixth Int'l Congress on Genetics, pp. 355-366, 1932.
[29] C.B. Barber, D.P. Dobkin, and H. Huhdanpaa, "The Quickhull Algorithm for Convex Hulls," ACM Trans. Math. Software, vol. 22, no. 4, pp. 469-483, 1996.
[30] S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, "Basic Local Alignment Search Tool," J. Molecular Biology, vol. 215, pp. 403-410, 1990.
[31] W. Press, S. Teukolsky, W.T. Vetterling, and B. Flannery, Numerical Recipes in C, the Art of Scientific Computing, second ed. Cambridge Univ. Press, 1999.
[32] A. Zinovyev and A. Carbone, "CAIJava," Calculates Codon Frequencies and CAI-Values of All Genes,\ , 2002.
[33] T. Barrett, D.B. Troup, S.E. Wilhite, P. Ledoux, D. Rudnev, C. Evangelista, I.F. Kim, A. Soboleva, M. Tomashevsky, and R. Edgar, "NCBI GEO: Mining Tens of Millions of Expression Profiles-Database and Tools Update," Nucleic Acids Research, vol. 35, database issue, pp. D760-D765, http://www.ncbi.nlm. nih.govgeo/, Jan. 2007.
[34] R. Wünschiers and H. Eckes, HyDaBa Hydrogen Database: Nostoc, http://www.hydaba.uni-koeln.deindex.php, Apr. 2005.
[35] NCBI, Nat'l Center for Biotechnology Information, http:/, May 2005.
[36] R.A. Fisher, "Frequency Distribution of the Values of the Correlation Coefficient in Samples from an Indefinitely Large Population," Biometrika, vol. 10, no. 4, pp. 507-521, May 1915.
[37] E.C. Fieller, H.O. Hartley, and E.S. Pearson, "Tests for Rank Correlation Coefficients. I," Biometrika, vol. 3, no. 4, pp. 470-481, Dec. 1957.
[38] A. Otero and M. Vincenzini, "Extracellular Polysaccharide Synthesis by Nostoc Strains as Affected by n Source and Light Intensity," J. Biotechnology, vol. 102, no. 2, pp. 143-152, Apr. 2003.
[39] M. dos Reis, R. Savva, and L. Wernisch, "Solving the Riddle of Codon Usage Preferences: A Test for Translational Selection," Nucleic Acids Research, vol. 32, no. 17, pp. 5036-5044, http://dx., 2004.
[40] P. Puigbò, I.G. Bravo, and S. Garcia-Vallvé, "E-CAI: A Novel Server to Estimate an Expected Value of Codon Adaptation Index (ECAI)," BMC Bioinformatics, vol. 9, p. 65, 11861471-2105-9-65 , 2008.
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