Journal of Molecular Evolution

, Volume 75, Issue 1–2, pp 34–42 | Cite as

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

  • Siddhartha Sankar Satapathy
  • Malay Dutta
  • Alak Kumar Buragohain
  • Suvendra Kumar Ray
Article

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.

Keywords

Codon usage bias Gene expression Translational selection tRNA gene number 

Supplementary material

239_2012_9524_MOESM1_ESM.doc (700 kb)
Supplementary material 1 (DOC 700 kb)
239_2012_9524_MOESM2_ESM.doc (58 kb)
Supplementary material 2 (DOC 57 kb)

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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Siddhartha Sankar Satapathy
    • 1
  • Malay Dutta
    • 1
  • Alak Kumar Buragohain
    • 2
  • Suvendra Kumar Ray
    • 2
  1. 1.Departments of Computer Science and EngineeringTezpur UniversityTezpurIndia
  2. 2.Departments of Molecular Biology and BiotechnologyTezpur UniversityTezpurIndia

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