水牛瘦素受体基因密码子使用偏好性分析

doi:10.16431/j.cnki.1671-7236.2017.04.019

《中国畜牧兽医》 ›› 2017, Vol. 44 ›› Issue (4): 1069-1078.doi: 10.16431/j.cnki.1671-7236.2017.04.019

水牛瘦素受体基因密码子使用偏好性分析

范新阳¹, 欧阳依娜¹, 王鹏武², 张永云³, 滕晓红¹, 苗永旺¹

1. 云南农业大学动物科学技术学院, 昆明 650201;
2. 云南省大理州家畜繁育指导站, 大理 671000;
3. 云南农业大学, 农科专业基础实验教学示范中心, 昆明 650201

收稿日期:2016-09-05 出版日期:2017-04-20 发布日期:2017-05-03
通讯作者: 苗永旺 E-mail:yongwangmiao1@126.com
作者简介:范新阳(1991-),男,河北石家庄人,硕士生,研究方向:动物遗传学,E-mail:985402140@qq.com;欧阳依娜(1979-),女,云南昆明人,博士生,研究方向:分子遗传学,E-mail:yinaouyang@126.com范新阳和欧阳依娜对本文具有同等贡献,并列为第一作者
基金资助:
国家自然科学基金项目（31460582、30660024）；云南省应用基础研究重点项目（2014FA032、2007C0003Z）

Analysis of Codon Usage Bias of Leptin Receptor Gene in Buffalo

FAN Xin-yang¹, OUYANG Yi-na¹, WANG Peng-wu², ZHANG Yong-yun³, TENG Xiao-hong¹, MIAO Yong-wang¹

1. Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China;
2. Livestock Breeding Guidance Station of Dali Prefecture, Dali 671000, China;
3. Teaching Demonstration Center of the Basic Experiments of Agricultural Majors, Yunnan Agricultural University, Kunming 650201, China

Received:2016-09-05 Online:2017-04-20 Published:2017-05-03

摘要/Abstract

摘要：

试验选取27头河流型水牛和41头沼泽型水牛，以从NCBI数据库中下载的家牛、野牦牛、野牛、绵羊、山羊、小鼠和人的序列作对照，对编码瘦素受体（leptin receptor，LEPR）基因的密码子偏好性及水牛与其他物种间密码子使用的差异和进化关系进行了深入分析。结果发现，所有的密码子在河流型水牛和沼泽型水牛LEPR基因中均有使用，两种类型水牛偏好使用的密码子有28个，其中使用偏好性较强的密码子为AGA（RSCU≥2），表明河流型水牛和沼泽型水牛LEPR基因密码子使用特征相似。水牛及参考物种LEPR基因均偏好使用以A/U结尾的密码子，但水牛与其他参考物种间偏好使用密码子的种类和数目有差异。密码子使用偏好聚类分析表明，河流型水牛与沼泽型水牛亲缘关系最近，先聚为一类，然后与家牛、野牦牛和野牛聚为一类，再与绵羊、山羊、小鼠和人等物种聚为一类。在密码子使用频率上，河流型水牛LEPR基因与酵母密码子偏好性差异小于与大肠杆菌和小鼠密码子偏好性差异，从而揭示酵母更适合作为水牛LEPR基因的外源表达系统。

关键词: 河流型水牛; 沼泽型水牛; LEPR基因; 密码子使用偏好性

Abstract:

The experiment was aimed to study the synonymous codon usage features of leptin receptor (LEPR) gene in buffalos, the codon usage differences and evolutionary relationships between buffalo and other reference species. The coding region of LEPR gene from 27 river buffalo and 41 swamp buffalo were sequencing,and Bos taurus,Bos mutus,Bos bison,Ovis aries,Capra hircus,Mus musculus and Homo sapiens were chosen as reference species from NCBI database. The results showed that all synonymous codons were used in the LEPR gene of river buffalo and swamp buffalo. Two kinds of buffalo had 28 biased usage codons. Among them,strongly biased codon was AGA (RSCU≥2),which indicated that codon usage features were similar in LEPR gene of two types of buffalo. Furthermore,buffalo and the species compared in this study were bias toward the synonymous codons with A/U at the third codon position in LEPR gene.However,the types and numbers of bias usage codons were different between buffalo and the species compared. Clustering analysis showed that the relationship between river buffalo and swamp buffalo was the closest,and they gathered into one group firstly,then they gathered with Bos taurus,Bos mutus and Bos bison,and further gathered in turn with Ovis aries,Capra hircus,Mus musculus and Homo sapiens.The frequency differences of synonymous codon usage between buffalo LEPR gene and yeast genome were less than that between buffalo and E.coli,Mus musculus genome,suggesting that yeast might be more suitable as an external expression system for buffalo LEPR gene.

Key words: river buffalo; swamp buffalo; LEPR gene; codon usage bias

中图分类号:

范新阳, 欧阳依娜, 王鹏武, 张永云, 滕晓红, 苗永旺. 水牛瘦素受体基因密码子使用偏好性分析[J]. 《中国畜牧兽医》, 2017, 44(4): 1069-1078.

FAN Xin-yang, OUYANG Yi-na, WANG Peng-wu, ZHANG Yong-yun, TENG Xiao-hong, MIAO Yong-wang. Analysis of Codon Usage Bias of Leptin Receptor Gene in Buffalo[J]. , 2017, 44(4): 1069-1078.

参考文献

[1] 王春艳,杜瑞平,张兴夫,等.瘦素及其生理功能概述[J].动物营养学报,2012,24(3):423-427.
[2] Feuermann Y,Mabjeesh S J,Shamay A. Leptin affects prolactin action on milk protein and fat synthesis in the bovine mammary gland[J].J Dairy Sci,2004,87(9):2941-2946.
[3] Kita A,Uotani S,Kuwahara H,et al. Vanadate enhances leptin-induced activation of JAK/STAT pathway in CHO cells[J].Biochemical and Biophysical Research Communications,2003,302(4):805-809.
[4] 徐利娟,钟金城,杨万远,等.牦牛mtDNA编码蛋白质的基因密码子偏好性研究及聚类分析[J].西北农业学报,2010,19(6):13-17.
[5] Bulmer M. The selection-mutation-drift theory of synonymous codon usage[J].Genetics,1991,129(3):897-907.
[6] Marin M. Folding at the rhythm of the rare codon beat[J].Biotechnology Journal,2008,3(8):1047-1057.
[7] Chamary J V,Parmley J L,Hurst L D. Hearing silence:Non-neutral evolution at synonymous sites in mammals[J].Nature Reviews Genetics,2006,7(2):98-108.
[8] Saunders R,Deane C M. Synonymous codon usage influences the local protein structure observed[J]. Nucleic Acids Research,2010,38(19):6719-6728.
[9] Angov E. Codon usage:Nature's roadmap to expression and folding of proteins[J].Biotechnology Journal,2011,6(6):650-659.
[10] 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.
[11] 李思银,杨亮宇,杨玉艾,等.德宏水牛与尼里拉菲水牛及其杂交水牛的细胞遗传学研究[J]. 中国畜牧兽医,2013,40(4):184-189.
[12] Tamura K,Peterson D,Peterson N,et al. MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J]. Molecular Biology and Evolution,2011,28(10):2731-2739.
[13] Sharp P M,Li W H. An evolutionary perspective on synonymous codon usage in unicellular organisms[J]. J Mol Evol,1986,24(1-2):28-38.
[14] 吴正常,王靖,赵乔辉,等.猪脂多糖结合蛋白基因(LBP)的密码子偏好性分析[J].农业生物技术学报,2013,21(10):1135-1144.
[15] 晁岳恩,吴政卿,杨会民,等.11种植物psbA基因的密码子偏好性及聚类分析[J].核农学报,2011,25(5):927-932.
[16] 刘汉梅,赵耀,顾勇,等.几种植物waxy基因的密码子用法特性分析[J].核农学报,2010,24(3):476-481.
[17] Behura S K,Severson D W. Codon usage bias:Causative factors,quantification methods and genome-wide patterns:With emphasis on insect genomes[J].Biological Reviews,2013,88(1):49-61.
[18] Behura S K,Stanke M,Desjardins C A,et al. Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods,and relation to codon usage bias[J].Insect Molecular Biology,2010,19:49-58.
[19] Behura S K,Severson D W. Coadaptation of isoacceptortRNA genes and codon usage bias for translation efficiency in Aedes aegypti and Anopheles gambiae[J].Insect Molecular Biology,2011,20(2):177-187.
[20] Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes[J].J MolBiol,1981,146(1):1-21.
[21] Sharp P M,Emery L R,Zeng K. Forces that influence the evolution of codon bias[J].Philos Trans R Soc Lond B Biol Sci,2010,365(1544):1203-1212.
[22] Hey J,Kliman R M. Interactions between natural selection,recombination and gene density in the genes of Drosophila[J].Genetics,2002,160(2):595-608.
[23] 李平,白云凤,冯瑞云,等.籽粒苋苹果酸酶(NAD-ME)基因密码子偏好性分析[J].应用与环境生物学报,2011,17(1):12-17.
[24] 郭秀丽,王玉,杨路成,等.茶树CBF1基因密码子使用特性分析[J].遗传,2012,34(12):1614-1623.

水牛瘦素受体基因密码子使用偏好性分析

Analysis of Codon Usage Bias of Leptin Receptor Gene in Buffalo

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 3

编辑推荐

Metrics

本文评价

[1]	李芳芳, 龙开旭, 俸祥仁, 黄项生, 潘堂峰, 江明生, 王国利, 邓祝新, 蒋钦扬, 郭亚芬. 河流型水牛热休克蛋白70的原核表达及其对精液抗冻性的影响[J]. 《中国畜牧兽医》, 2018, 45(9): 2417-2424.
[2]	戴开宇, 黄焱杰, 吴丽思, 包文斌, 吴圣龙. 猪FUT2基因密码子使用偏好性分析及优化[J]. 《中国畜牧兽医》, 2018, 45(7): 1863-1872.
[3]	邓继贤;杨秀荣;韦英明;蒋和生;. 沼泽型水牛卵泡抑素基因的真核表达研究[J]. , 2011, 38(9): 57-60.