茶树密码子用法分析

doi:10.13305/j.cnki.jts.2011.04.013

茶叶科学 ›› 2011, Vol. 31 ›› Issue (4): 319-325.doi: 10.13305/j.cnki.jts.2011.04.013

茶树密码子用法分析

赵洋, 杨阳^*, 刘振, 杨培迪

湖南省农业科学院茶叶研究所,湖南长沙 410125

收稿日期:2010-10-18 修回日期:2011-03-03 出版日期:2011-08-15 发布日期:2019-09-09
通讯作者: yangyangsir@126.com
作者简介:赵洋（1979— ）,女,湖南长沙人,助理研究员,主要从事茶树遗传育种和分子生物学研究。
基金资助:
国家茶叶产业技术体系建设专项（tycytx-23）、湖南省农业科学院科技创新项目（2010茶树特异种质资源引进与利用研究）

Analysis of Codon Usage in Tea Plant (Camellia sinensis)

ZHAO Yang, YANG Yang^*, LIU Zhen, YANG Pei-di

Hunan Tea Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China

Received:2010-10-18 Revised:2011-03-03 Online:2011-08-15 Published:2019-09-09

摘要/Abstract

摘要： 运用CodonW软件和CUSP程序对筛选的134个茶树蛋白质编码基因序列进行了分析、计算密码子使用频率,并将它与人、果蝇、酵母、大肠杆菌这4种代表性生物及拟南芥、大豆、棉花、水稻、小麦等单、双子叶植物进行比较。结果显示茶树密码子偏爱性与人、果蝇、酵母、大肠杆菌有不同程度的差异,与单子叶植物水稻、小麦的密码子使用频率差异较大,与双子叶植物拟南芥、大豆、棉花的密码子偏爱性一致,分析结果对茶树基因转化及高效表达系统的选择等具有重要指导意义。

关键词: 茶树（Camellia sinensis）, 密码子用法, 密码子偏爱性

Abstract: The coding sequence of 134 selected proteins in tea plant (Camellia sinensis) were analyzed by CodonW and CUSP program in this investigation, and the frequency of codon usage which encoded amino acids was calculated and compared with four classes of representative organisms including human (Homo sapiens), yeast (Saccharomyces cerevisiae), Escherichia coli. Bacteria and fruit fly (Drosophila melanogaster). These results showed that codon preference of tea plant was differed in various degrees with these model organisms. Accomparison of codon usage frequency of tea plant with dicotyledons and monocotyledons plants including Arabidopsis thaliana, soybean (Glycine max), cotton (Gossypium hirsutum), rice (Oryza sativa), wheat (Triticum aestivum), the consequence indicated that codon usage frequency of tea plant was obviously differed from these monocotyledons such as Oryza sativa and Triticum aestivum, but had a consistency in codon preference with these dicotyledons such as Arabidopsis thaliana, Glycine max and Gossypium hirsutum. These results showed an important guidance for tea plant gene-transforming and the selection of the high-efficient expression system.

Key words: tea plant(Camellia sinensis), codon usage, codon preference

中图分类号:

S571.1
Q786

赵洋, 杨阳, 刘振, 杨培迪. 茶树密码子用法分析[J]. 茶叶科学, 2011, 31(4): 319-325. doi: 10.13305/j.cnki.jts.2011.04.013.

ZHAO Yang, YANG Yang, LIU Zhen, YANG Pei-di. Analysis of Codon Usage in Tea Plant (Camellia sinensis)[J]. Journal of Tea Science, 2011, 31(4): 319-325. doi: 10.13305/j.cnki.jts.2011.04.013.

参考文献

[1] Gustafsson C, Govindarajan S, Minshull J.Codon bias and heterologous protein expression[J]. Trends Biotechnol, 2004, 22(7): 346-353.
[2] 刘汉梅,何瑞,赵耀, 等. 玉米密码子用法分析[J]. 核农学报, 2008, 22(2): 141-147.
[3] 刘庆坡, 谭军, 薛庆忠. 籼稻品种93-11同义密码子的使用偏性[J]. 遗传学报, 2003, 30(4): 335-340.
[4] Ingvarsson PK.Molecular evolution of synonymous codon usage in Populus[J]. BMC Evol Biol, 2008, 8: 307.
[5] Liu HM, He R, Zhang H, et al. Analysis of synonymous codon usage in Zea mays[J]. Mol Biol Rep, 2010, 37(2): 677-684.
[6] Chiapello H, Lisacek E, Caboche M, ,et al. Codon usage. Codon usage and gene function are related in sequences of Arabidopsis thaliana [J]. Gene, 1998, 209(1/2): GC1-GC38.
[7] 胡桂兵, 张上隆, 徐昌杰, 等. 柑橘密码子用法分析[J]. 果树学报, 2006, 23(3): 479-485.
[8] Liu QP, Ying Feng, Zhao XA, et al. Synonymous Codon Usage Bias in Oryza sativa[J]. Plant Sci, 2004, 167: 101-105.
[9] 周猛, 童春发, 施季森. 杨树同义密码子用法的初步分析[J]. 植物生理与分子生物学学报, 2007, 33(4): 285-293.
[10] 马建民, 顾万君, 周童, 等. 一种基于密码子使用偏性的检测型基因芯片设计方法[J]. 东南大学学报: 自然科学版, 2002, 32(4): 58l-585.
[11] Paul MS, Elizabeth C.Synonymous codon usage in Saccharomyces cerevisiae[J]. Yeast, 1991(7): 657-678.
[12] Carlini DB, Chen Y, Stephan W.The relationship between third codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr[J]. Genetics, 2001, 159(2): 623-633.
[13] Najafabadi HS, Goodarzi H, Salavati R.Universal function-specificity of codon usage[J]. Nucleic Acids Res, 2009, 37(21): 7014-7023.
[14] Stenstrom CM, Jin HN, Major LL, et al. Codon bias at the 3`side of the initiation codon is correlated with translation initiation eficiency in Escherichia coli[J]. Gene, 2001, 263(1/2): 273-284.
[15] 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.
[16] Duret L, Mouehireud D.Expression pattern and surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila and Arabidopsis[J]. Proc Natl Acad Sci USA, 1999, 96(8): 4482-487.
[17] Moriyama EN, Powell JR.Gene length and codon usage bias in Drosophila melanogaster,Saecharomyces cerevisiae and Eseherichia coli[J]. Nucleic Acids Res, 1998, 26(13): 3188-3193.
[18] Moriyama EN, Powell JR.Codon usage bias and tRNA abundance in Drosophila[J]. J Mol Evol, 1997, 45(5): 514-523.
[19] Najafabadi HS, Salavati R.Sequence-based prediction of protein-protein interactions by means of codon usage[J]. Genome Biol, 2008, 9(5): R87.
[20] Gupta SK, Bhattacharya TK.Studies on the relationships between the synonymous codon usage and protein secondary structural units[J]. Biochem Bioph Res Co, 2000, 269(3): 692-696.
[21] Grantham R, Gautier C, Gouy M, et al. Codon catalog usage and the genome hypothesis[J]. Nucleic Acids Res, 1980, 8(1): 49-62.
[22] Kawabe A, Miyashita NT.Patterns of codon usage bias in three dicot and four monocot plant species[J]. Genes Genet Syst, 2003, 78(5): 343-352.

茶树密码子用法分析

Analysis of Codon Usage in Tea Plant (Camellia sinensis)

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