Abstract
It is generally believed that the effect of translational selection on codon usage bias is related to the number of transfer RNA genes in bacteria, which is more with respect to the high expression genes than the whole genome. Keeping this in the background, we analyzed codon usage bias with respect to asparagine, isoleucine, phenylalanine, and tyrosine amino acids. Analysis was done in seventeen bacteria with the available gene expression data and information about the tRNA gene number. In most of the bacteria, it was observed that codon usage bias and tRNA gene number were not in agreement, which was unexpected. We extended the study further to 199 bacteria, limiting to the codon usage bias in the two highly expressed genes rpoB and rpoC which encode the RNA polymerase subunits β and β′, respectively. In concordance with the result in the high expression genes, codon usage bias in rpoB and rpoC genes was also found to not be in agreement with tRNA gene number in many of these bacteria. Our study indicates that tRNA gene numbers may not be the sole determining factor for translational selection of codon usage bias in bacterial genomes.
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Acknowledgments
We thank Dr. Supek, the Rudjer Boskovic Institute, Croatia, for providing information for retrieving transcriptome data from the NCBI. We extend our thanks to Mrs. Madhusmita Dash, Qr. No. C-83, Tezpur University, for writing the C program for rank calculation. We also thank Dr. B.R. Powdel, Darang College, Tezpur, for his comments on the manuscript. We thank the two anonymous reviewers for their helpful comments on the previous version of this manuscript.
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Satapathy, S.S., Dutta, M., Buragohain, A.K. et al. Transfer RNA Gene Numbers may not be Completely Responsible for the Codon Usage Bias in Asparagine, Isoleucine, Phenylalanine, and Tyrosine in the High Expression Genes in Bacteria. J Mol Evol 75, 34–42 (2012). https://doi.org/10.1007/s00239-012-9524-1
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DOI: https://doi.org/10.1007/s00239-012-9524-1