Marine biology

Analysis on codon usage bias of fatty acid delta-6 desaturase genes from different algae

Expand
  • Engineering Research Center of Industrial Microbiology, Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350108, China
赵薇(1984—), 女, 福建省福州市人, 硕士, 主要从事微生物生物技术的研究, 现工作单位: 福建省微生物研究所

Received date: 2009-07-31

  Revised date: 2009-11-08

  Online published: 2010-05-24

Supported by

福建省教育厅项目(JA09061); 福建省科技厅重点项目(2007I0039, 2008I0047); 教育部留学回国人员科研启动基金资助项目

Abstract

Delta-6 desaturases are the key enzymes required for the synthesis of unsaturated fatty acids, which introduce double bond at the position of 18C in algae. In this study, the authors investigate codon usage bias and base composition variations in nine available complete desaturase gene sequences from Bacillariophyta, Chlorophyta and Cyanophyta. The results showed that △6 desaturase genes of T. pseudonana and P. tricornutum (Bacillariophyta) as well as Ostreococcus tauri (Chlorophyta) prefer to use the codons ended with G or C, with GC content as high as 61.61%; while △6 desaturase genes of three algae of Cyanophyta prefer to use the codons ended with A or U, with GC content 39.1%. Codon usage bias in alga △6 desaturase gene was very small, which was mainly determined by base compositions on the third codon position and the value of effective number of codons (ENC). It was implied that △6 desaturase genes were phylogenetically conservative. The results of comparing algae △6 desaturase genes to genomic codon usage of E.coli, yeast and Arabidopsis thaliana preference revealed that codon usage pattern among them was significantly different. In order to significantly increase the efficiency of algae △6 desaturase gene expression, partial codon in gene’s open reading frame needs to be reconstituted. The findings presented in this study offer guidance for expressing algae △6 desaturase gene in prokaryotic and eukaryotic expression systems.

Cite this article

ZHAO Wei,CHEN Bi-lian,WANG Ming-zi,HUANG Jian-zhong . Analysis on codon usage bias of fatty acid delta-6 desaturase genes from different algae[J]. Journal of Tropical Oceanography, 2010 , 29(3) : 126 -134 . DOI: 10.11978/j.issn.1009-5470.2010.03.126

References

[1] COMERON J M, AGUADE M. An evaluation of measures of synonymous codon usage bias[J]. Journal of Molecular Evolution, 1998, 47(3): 268-274.
[2] ZHOU T, GU W, MA J, et al. Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses[J]. Biosystems, 2005, 81(1): 77-86.
[3] SHARP P M, STENICO M, PEDEN J F, et al. Codon usage: mutational bias, translational selection, or both? [J]. Biochemical Society Transactions, 1993, 21(4): 835-841.
[4] LIVINGSTONE F B. Genetic drift and polygenic inheritance[J]. American Journal of Physical Anthropology, 1972, 37(1): 117-126.
[5] 石秀凡, 黄京飞, 柳树群, 等. 人类基因同义密码子偏好的特征以及与基因GC含量的关系[J]. 生物化学与生物物理进展, 2002, 29 (3): 411-414.
[6] DURET L, MOUCHIROUD D. Expression pattern and surprisingly gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
[J]. Proceedings of the National Academy of Sciences, 1999, 96(8): 4 482-4 487.
[7] SAKAI H, WASHIO T, SATIO R, et al. Correlation between sequence conservation of the 5? untranslated region and codon usage bias in Mus musculus genes[J]. Gene, 2001, 276(1/2): 101-105.
[8] 顾万君, 马建民, 周童, 等. 不同结构的蛋白编码基因的密码子偏性研究[J]. 生物物理学报, 2002, 18(1): 81-86.
[9] 石秀凡, 黄京飞, 梁宠荣, 等. 人类基因中同义密码子的偏好与密码子-反密码子间的结合强度密切相关吗? [J]. 科学通报, 2000, 45 (23): 2 520-2 525.
[10] ZHAO S, ZHANG Q, LIU X, et al. Analysis of synonymous codon usage in 11 human bocavirus isolates [J]. Biosystems, 2008, 92(3): 207-214.
[11] 赵耀, 刘汉梅, 顾勇, 等. 玉米waxy基因密码子偏好性分析[J]. 玉米科学, 2008, 16(2): 16-21.
[12] 吴宪明, 吴松锋, 任大明, 等. 密码子偏性的分析方法及相关研究进展[J]. 遗传, 2007, 29(4): 420-426.
[13] POWELL J P, SEZZI E, MORIYAMA E N, et al. Analysis of a shift in codon usage in Drosophila[J]. Journal of Molecular Evolution, 2003, 57: 214-225.
[14] BULMER M. The selection-mutation-drift theory of    synonymous codon usage[J]. Genetics, 1991, 129(3): 897-907.
[15] 王侃, 刘次全, 曹槐, 等. 大肠杆菌mRNA编码区长度、形成二级结构倾向与密码子偏好性的关系[J]. 微生物学报, 2006, 46 (6): 895-899.
[16] 张文娟. 基于密码子水平的生物信息学分析及进化研究[D]. 上海: 复旦大学生命科学学院, 2006.
 

Outlines

/