Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms

Peng Jiang; Xiao Sun; Zuhong Lu

doi:10.1016/S1673-8527(07)60029-0

Volume 34 Issue 3

Mar. 2007

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Article Navigation > Journal of Genetics and Genomics > 2007 > 34(3): 275-284

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Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms

doi: 10.1016/S1673-8527(07)60029-0

State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China

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Corresponding author: E-mail address: zhlu@seu.edu.cn (Zuhong Lu)
Received Date: 2006-06-02
Accepted Date: 2006-08-22

Available Online: 2007-05-09

Publish Date: 2007-03-20

Abstract

Abstract

In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms (i.e., Pyrobaculum aerophilum str. IM2 and Sulfolobus acidocaldarius DSM 639). The results indicated that the synonymous codon usage in A. pernix K1 was less biased, which was highly correlated with the GC_3S value. The codon usage patterns were phylogenetically conserved among these Crenarchaeota microorganisms. Comparatively, it is the species function rather than the gene function that determines their gene codon usage patterns. A. pernix K1, P. aerophilum str. IM2, and S. acidocaldarius DSM 639 live in differently extreme conditions. It is presumed that the living environment played an important role in determining the codon usage pattern of these microorganisms. Besides, there was no strain-specific codon usage among these microorganisms. The extent of codon bias in A. pernix K1 and S. acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. aerophilum str. IM2 genomes.
- codon usage bias,
- relative synonymous codon usage (RSCU)

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References(29)

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