[1] Wu Haonan, Da Yao, Wei Jiawei, Jiang Peng, et al. Synonymous codon usage in Methanosarcina mazei str.Goe1and other Euryarchaeota microorganisms [J]. Journal of Southeast University (English Edition), 2007, 23 (2): 289-293. [doi:10.3969/j.issn.1003-7985.2007.02.027]
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Synonymous codon usage in Methanosarcina mazei str.Goe1and other Euryarchaeota microorganisms(
)
甲烷八叠球古菌及其他广古菌同义密码子使用偏好性
)Journal of Southeast University (English Edition)[ISSN:1003-7985/CN:32-1325/N]
- Volumn:
- 23
- Issue:
- 2007 2
- Page:
- 289-293
- Research Field:
- Biological Science and Medical Engineering
- Publishing date:
- 2007-06-30
Info
- Title:
- Synonymous codon usage in Methanosarcina mazei str.Goe1and other Euryarchaeota microorganisms
- 甲烷八叠球古菌及其他广古菌同义密码子使用偏好性
- Author(s):
- Wu Haonan; Da Yao; Wei Jiawei; Jiang Peng; Lu Zuhong
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
- PACS:
- Q617
- DOI:
- 10.3969/j.issn.1003-7985.2007.02.027
- Abstract:
- A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str.Goe1 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.Goe1 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 patterns.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 patterns.
- 比较分析了甲烷八叠球古菌(Methanosarcina mazei str.Goe1)和其他2种系统发育相关的广古细菌(嗜苦古菌(Picrophilus torridus str.DSM 9790)和盐碱古菌(Natronomonas pharaonis str.DSM 2160))的同义密码子使用偏好性.结果表明甲烷八叠球古菌的密码子使用偏好性很小, 并且与GC3S值有很高的相关性.这3种广古细菌的密码子使用模式在进化上很保守.通过分层聚类分析, 得出较之基因功能对密码子使用的影响, 这些广古菌密码子的使用更是由其物种所决定的.考虑到这3个物种生活在pH值差异很大的环境中, 推测其生活环境在很大程度上决定了这些微生物密码子的使用方式.
References:
[1] Deppenmeier U, Johann A, Hartsch T, et al.The genome of Methanosarcina mazei:evidence for lateral gene transfer between bacteria and archaea [J].J Mol Microbiol Biotechnol, 2002, 4(4):453-461.
[2] Futterer O, Angelov A, Liesegang H, et al.Genome sequence of Picrophilus torridus and its implications for life around pH 0 [J].Proc Natl Acad Sci USA, 2004, 101(24):9091-9096.
[3] Falb M, Pfeiffer F, Palm P, et al.Living with two extremes:conclusions from the genome sequence of Natronomonas pharaonis [J].Genome Res, 2005, 15(10):1336-1343.
[4] Wright F.The “effective number of codons” used in a gene [J].Gene, 1990, 87(1):23-29.
[5] Comeron J M, Aguade M.An evaluation of measures of synonymous codon usage bias [J].J Mol Evol, 1998, 47(3):268-274.
[6] Sharp P M, Li W H.Codon usage in regulatory genes in Escherichia coli does not reflect selection for “rare” codons [J].Nucleic Acids Res, 1986, 14(19):7737-7749.
[7] Gupta S K, Ghosh T C.Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa [J].Gene, 2001, 273(1):63-70.
[8] Lattin J M, Carroll J D, Green P E.Analyzing multivariate data [M].Beijing:Thomson Asia Pte Ltd and China Machine Press, 2003:31-80.
[9] Ma J M, Zhou T, Gu W J, et al.Cluster analysis of the codon use frequency of MHC genes from different species [J].Biosystems, 2002, 65(2/3):199-207.
Memo
- Memo:
- Biographies: Wu Haonan(1983—), male, undergraduate;Lu Zuhong(corresponding author), male, doctor, professor, zhlu@seu.edu.cn.