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Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms 被引量:2
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作者 江澎 孙啸 陆祖宏 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第3期275-284,共10页
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 Sulfol... 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 GC3s 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 hving 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. 展开更多
关键词 codon usage bias relative synonymous codon usage (RSCU) Aeropyrum pernix K1
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Synonymous codon usage in Methanosarcina mazei str.Goe1 and other Euryarchaeota microorganisms
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作者 吴昊男 笪遥 +2 位作者 魏镓伟 江澎 陆祖宏 《Journal of Southeast University(English Edition)》 EI CAS 2007年第2期289-293,共5页
A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms (Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160... A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms (Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160). Results revealed that synonymous codon usage in Methanosarcina mazei str. Goel was less biased, which was highly correlated with the GC3S value. And the codon usage patterns were phylogenetically conserved among those Euryarchaeota microorganisms. By employing a hierarchical clustering analysis, it can be seen that it is more the species than the gene function that determines their gene codon usage pattems. Considering that those microorganisms live in different environments where the pH conditions vary quite a lot, it can be presumed that their living environments, especially the pH conditions, play an important role in determining those microorganisms' codon usage pattems. 展开更多
关键词 codon usage bias relative synonymous codon usage (RSCU) methanosarcina mazei str. Goel
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Comparative Multivariate Analysis of Codon and Amino Acid Usage in Three Leishmania Genomes
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作者 Nutan Chauhan Ambarish Sharan Vidyarthi Raju Poddar 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2011年第6期218-228,共11页
Multivariate analysis of codon and amino acid usage was performed for three Leishmania species, including L. donovani, L. infantum and L. major. It was revealed that all three species are under mutational bias and tra... Multivariate analysis of codon and amino acid usage was performed for three Leishmania species, including L. donovani, L. infantum and L. major. It was revealed that all three species are under mutational bias and translational selection. Lower GC12 and higher GC3s in all three parasites suggests that the ancestral highly expressed genes (HEGs), compared to lowly expressed genes (LEGs), might have been rich in AT-content. This also suggests that there must have been a faster rate of evolution under GC-bias in LEGs. It was observed from the esti- mation of synonymous/non-synonymous substitutions in HEGs that the HEG dataset of L. donovani is much closer to L. major evolutionarily. This is also supported by the higher ds value as compared to ds between L. donovani and L. major, suggesting the conservation of synonymous codon positions between these two species and the role of translational selection in shaping the composition of protein-coding genes. 展开更多
关键词 LEISHMANIA relative synonymous codon usage multivariate analysis HYDROPATHY AROMATICITY
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