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[1]孙晶,何涛,万闰兰,等.铁皮石斛尿苷二磷酸葡萄糖焦磷酸化酶基因(UGP)的密码子偏好性分析[J].应用与环境生物学报,2014,20(05):759-766.[doi:10.3724/SP.J.1145.2014.03041]
 SUN Jing,HE Tao,WAN Runlan,et al.The Codon usage bias of UDP-glucose pyrophosphorylase gene (UGP) in Dendrobium officinale[J].Chinese Journal of Applied & Environmental Biology,2014,20(05):759-766.[doi:10.3724/SP.J.1145.2014.03041]
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铁皮石斛尿苷二磷酸葡萄糖焦磷酸化酶基因(UGP)的密码子偏好性分析()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
20卷
期数:
2014年05期
页码:
759-766
栏目:
研究论文
出版日期:
2014-10-25

文章信息/Info

Title:
The Codon usage bias of UDP-glucose pyrophosphorylase gene (UGP) in Dendrobium officinale
作者:
孙晶 何涛 万闰兰 彭小凤 淳泽
1中国科学院成都生物研究所 成都 610041 2中国科学院大学 北京 100049
Author(s):
SUN Jing HE Tao WAN Runlan PENG Xiaofeng CHUN Ze
1Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China 2University of Chinese Academy of Sciences, Beijing 100049, China
关键词:
铁皮石斛尿苷二磷酸葡萄糖焦磷酸化酶基因(UGP)密码子偏好性聚类分析
Keywords:
Dendrobium officinale UDP-glucose pyrophosphorylase gene codon bias cluster analysis
分类号:
Q949.71+8.430.3
DOI:
10.3724/SP.J.1145.2014.03041
文献标志码:
A
摘要:
尿苷二磷酸葡萄糖焦磷酸化酶(UDP-Glucose pyrophosphorylase,UGPase)是糖代谢的主要酶类之一. 为了解铁皮石斛(Dendrobium officinale)尿苷二磷酸葡萄糖焦磷酸化酶基因(UGP)的密码子使用特性,运用CHIPS、CUSP 和CodonW在线程序分析自主克隆的铁皮石斛UGP基因(GenBank登录号:KF711982.1)的密码子偏好性,并与其他物种的UGP基因以及基因组进行比较. 结果显示,铁皮石斛UGP基因偏好使用A/T结尾的密码子,27 种偏好密码子(RSCU > 1)中偏好性较强的有TAA和CCU(RSCU ≥ 2). 与其他物种的UGP基因密码子使用对比后,发现不同物种UGP基因密码子使用偏好性存在一定差异. 在9个所选物种的聚类分析中,发现基于UGP基因CDS序列聚类的进化树比基于RSCU的聚类更与传统的系统发育观点接近. 与3种生物基因组密码子使用频率比较发现,与大肠杆菌基因组密码子使用频率差值较大的有23个,与酵母和拟南芥基因组差值较大的均有13个,这预示着铁皮石斛UGP基因在酵母和拟南芥中的表达效率较高. 本研究结果为铁皮石斛UGP基因选择最佳的外源表达系统以及提高其表达水平奠定了前期的研究基础.
Abstract:
UDP-glucose pyrophosphorylase is one of the key enzymes in the carbohydrate metabolic pathway. In order to understand the codon bias of Dendrobium officinale UDP-glucose pyrophosphorylase gene (UGP) and to select appropriate expression systems, the D. officinale UGP (GenBank Accession: KF711982.1) was analyzed by online Codon W, CHIPS, and CUSP programs, and then compared with UGP genes from other species and genomes. The results showed that the D. officinale UGP preferred to use codons ended with A or T. There were 27 biased codons (relative synonymous codon usage, RSCU > 1), among which TAA and CCU were highly frequently used codons with RSCU value more than 2. Comparative analysis of UGP genes from the selected species indicated that there existed differences in their codon bias. In comparison with the phylogenetic tree based on RSCU, the phylogenetic tree calculated with CDS sequence of the 9 species was more consistent with conventional developmental viewpoint. There were 23 codons showing distinct usage differences between UGP of D. officinale and genome of Escherichia coli, 13 between UGP of D. officinale and genome of Saccharomyces cerevisiae and Arabidopsis thaliana. Therefore, it might be more suitable for expression of D. officinale UGP in the Saccharomyces cerevisiae and Arabidopsis thaliana expression systems. Our study may provide a basis for selecting appropriate expression systems and improving the expression level of D. officinale UGP.

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备注/Memo

备注/Memo:
国家科技支撑计划项目(2011BAC09B04)、中国科学院知识创新工程及院地合作项目(XBCD-2011-007)、四川省“十二五”中药材育种攻关项目(2011NZ0098-12-10)、四川省应用基础研究和科技支撑计划项目(2013JY0133、2014JY0179、2014FZ0086)和四川省科技基础条件平台项目资助 Supported by the National Science and Technology Pillar Program of China (2011BAC09B04), the Knowledge Innovation and Cooperation Project of the Chinese Academy of Sciences (XBCD-2011-007), the Sichuan “12th Five-year Plan” Project of Chinese Herbal Breeding Research (2011NZ0098-12-10), the Applied Basic Research Project of Sichuan (2013JY0133, 2014JY0179), the Science and Technology Pillar Program of Sichuan (2014FZ0086) and the Sichuan Platform Construction Project for Science and Technology Condition
更新日期/Last Update: 2014-10-23