World Journal of Microbiology and Biotechnology

, Volume 24, Issue 8, pp 1585–1592

The factors dictating the codon usage variation among the genes in the genome of Burkholderia pseudomallei

Original Paper

DOI: 10.1007/s11274-007-9652-8

Cite this article as:
Zhao, S., Zhang, Q., Chen, Z. et al. World J Microbiol Biotechnol (2008) 24: 1585. doi:10.1007/s11274-007-9652-8


Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. Codon usage biases of all protein-coding genes (length greater than or equal to 300 bp) from the complete genome of B. pseudomallei K96243 have been analyzed. As B. pseudomallei is a GC-rich organism (68.5%), overall codon usage data analysis indicates that indeed codons ending in G and/or C are predominant in this organism. But multivariate statistical analysis indicates that there is a single major trend in the codon usage variation among the genes in this organism, which has a strong positively correlation with the expressivities of the genes. The majority of the lowly expressed genes are scattered towards the negative end of the major axis whereas the highly expressed genes are clustered towards the positive end. At the same time, from the results that there were two significant correlations between axis 1 coordinates and the GC, GC3s content at silent sites of each sequence, and clearly significant negatively correlations between the ‘Effective Number of Codons’ values and GC, GC3s content, we inferred that codon usage bias was affected by gene nucleotide composition also. In addition, some other factors such as the lengths of the genes as well as the hydrophobicity of genes also influence the codon usage variation among the genes in this organism in a minor way. At the same time, notably, 21 codons have been defined as ‘optimal codons’ of the B. pseudomallei. In summary, our work have provided a basic understanding of the mechanisms for codon usage bias and some more useful information for improving the expression of target genes in vivo and in vitro.


Burkholderia pseudomallei K96243Codon usageCorrespondence analysis



Base pair


Foot-and-mouth disease


Foot-and-mouth disease virus


Relative synonymous codon usage


Effective number of codons


Correspondence analysis


The frequency of G+C at the synonymous third position of sense codons

A3S, T3S, G3S and C3S

The adenine, thymine, guanine and cytosine content at synonymous third positions


Open reading frame


Standard deviation

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Jingchu University of TechnologyJingmenP.R. China
  2. 2.College of Life Science and TechnologySouthwest University for NationalitiesChengduP.R. China