On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes

Basak, Surajit; Roy, Sujata; Ghosh, Tapash Chandra

doi:10.1016/j.febslet.2007.11.054

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Volume 581, Issue 30 , Pages 5825-5830, 22 December 2007

On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes

Edited by Takashi Gojobori

Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India

Received 19 September 2007; received in revised form 14 November 2007; accepted 16 November 2007. published online 27 November 2007.

Abstract

Synonymous codon usage analysis between thermophilic and mesophilic prokaryotes has gained wide attention in recent years. Although it is known that thermophilic and mesophilic prokaryotes use different subset of synonymous codons, no reason for this difference is known so far. In the present communication, by analyzing a large number of thermophilic and mesophilic prokaryotes, we provide evidence that bias in the selection of synonymous codons between thermophilic and mesophilic prokaryotes is related to differential folding pattern of mRNA secondary structures. Moreover, we observe that error-minimizing property has significant influence in differentiating the synonymous codon usage between thermophilic and mesophilic prokaryotes. Biological implications of these results are discussed.

Keywords: Optimal growth temperature, Synonymous codon usage, Free folding energy, Error minimization, Z-score