猪脂多糖结合蛋白基因(LBP)的密码子偏好性分析  

Analysis of Codon Bias of Lipopolysaccharide-binding Protein Gene(LBP) in Pigs(Sus scrofa)

作　　者：吴正常[1] 王靖[1] 赵乔辉[1] 朱世平[1] 訾臣[1] 吴圣龙[1,2] 包文斌[1,2] 

机构地区：[1]扬州大学动物科学与技术学院,江苏省动物遗传繁育与分子设计重点实验室,扬州225009 [2]江苏省现代种猪分子选育工程技术研究中心,常州213149

出　　处：《农业生物技术学报》2013年第10期1135-1144,共10页Journal of Agricultural Biotechnology

基　　金：国家自然科学基金(No.31172183);江苏省科技支撑计划(农业)(No.BE2012330,BE2010371,BE2013345);江苏省产学研前瞻性联合研究项目(No.BY2012157)

摘　　要：脂多糖结合蛋白(lipopolysaccharide-binding protein,LBP)是机体识别革兰氏阴性菌内毒素并启动免疫反应的关键因子。为了了解LBP基因的密码子使用特性,为其选择合适的受体动物以及最佳外源表达系统提供依据,本研究运用CHIPS、CUSP和CodonW在线程序分析自主电子克隆的猪(Sus scrofa)LBP基因(GenBank登录号:NM-001128435.1)的密码子偏好性,并与猪8种抗病相关基因、模式生物基因组以及其他物种LBP基因相比较。结果表明,猪LBP基因大部分偏好使用以G/C结尾的密码子,27种偏好密码子(相对使用度(RSCU)>1)中偏好性较强的有GCC、CAC、CTG和TCC(RSCU≥2),而猪8种抗病相关基因有23种偏好密码子,全部以G/C结尾,并且偏好性较强的密码子有GCC、ATC、CTG和GTG;通过比较14种动物的LBP基因密码子偏好性,发现14个物种的LBP基因表达水平一般,并且都偏好以G/C结尾的密码子;聚类分析发现,偶蹄目猪与2种食肉目动物(猫(Felis catus)和狗(Canis))聚为一类,与系统分类关系不一致;在密码子的使用频率上,猪LBP基因与小鼠(Mus musculus)基因组的差异小于大肠杆菌(Escherichia coli)和酵母菌(Saccharomyces)等2种模式生物基因组,故小鼠更适合作为该LBP基因的外源表达宿主。本研究结果为LBP基因在动物遗传改良中选择合适的受体动物、选择最佳的外源表达系统以及提高其表达水平提供一定的理论依据。Lipopolysaccharide-binding protein（LBP） is key factor in identifying endotoxin of gram-negative bacterium and starting immune response. The aim of this study was to understand LBP gene codon use features and provide foundation for selecting appropriate receptor animals and expression systems. In this research, pig（Sus scrofa） LBP gene（GenBank Accession： NM-001128435.1） based on electronic cloning sequence was analyzed by Codon W, CHIPS, and CUSP programs online, and then compared with eight disease resistance-related genes, genomes in model organisms and LBP genes from 14 animal species. The results showed that most of pig LBP genes were bias toward the synonymous codons with G and C at the third codon position. There were twenty-seven biased codons （relative synonymous codon usage（RSCU）〉 1）, whose biased strongly codons were GCC, CAC, CTG and TCC （RSCU~〉2）. However, all of eight disease resistance-related genes were bias toward codons with G and C, and had twenty-three biased codons, whose biased strongly codons were GCC, ATC, CTG and GTG. The comparative analysis results of LBP genes from 14 animal species also showed that gene expression level was general in 14 animal species, and all of the LBP genes were bias toward the synonymous codons with G and C at the third codon position, which was possible due to special functions of these genes. Clustering analysis showed that pigs belonging to artiodactyla and animals belonging to carnivora were together for a class, which disagreed with taxonomic relationship. The differences in codon usage frequency between pig LBP gene and genome of Mus musculus were less than other two kinds of model organisms＇ （Escheriehia coli and Saccharomyces Yeast） genome. Therefore, Mus musculus expression systems might be more suitable for expression of LBP gene. This study can provide certain theoretical basis for selecting the appropriate receptor animals in animal genetic improvement, selecting appropriate expression systems and improving t

关 键 词：猪 脂多糖结合蛋白基因(tsp) 密码子偏好性 

分 类 号：Q513[生物学—生物化学]