13种哺乳动物MUC4基因密码子使用模式分析  

Analysis of Codon Usage Patterns of MUC4 Gene in 13 Species of Mammals

作　　者：冯海悦 张羽 吴正常[1] 吴圣龙[1,2] 包文斌 FENG Hai-Yue;ZHANG Yu;WU Zheng-Chang;WU Sheng-Long;BAO Wen-Bin(Key Laboratory for Animal Genetics,Breeding,Reproduction and Molecular Design of Jiangsu Province,Yangzhou University,Yangzhou 225009,China;Jiangsu Engineering Research Center for the Reproduction and Healthy Breeding of Boar,Yangzhou 225009,China)

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]江苏省种猪繁育和健康养殖工程技术研究中心,扬州225009

出　　处：《农业生物技术学报》2018年第9期1546-1556,共11页Journal of Agricultural Biotechnology

基　　金：国家自然科学基金(No.31572360);苏州市科技局攻关项目(No.SNG201628)

摘　　要：大肠杆菌(Escherichia coli)是导致人类和初生幼畜腹泻的重要人畜共患型病原体,而产肠毒素大肠杆菌F4是引起腹泻最常见的病原之一。前期已有研究表明4型黏蛋白基因(Mucin 4 gene,MUC4)可能作为大肠杆菌F4ab/F4ac的重要受体基因。研究密码子的使用特性有助于进一步了解某一特定基因的分子机制和进化关系。为了揭示MUC4基因密码子的使用模式,本研究选取13种哺乳动物MUC4基因的编码序列,计算其碱基组成、有效密码子数、同义密码子相对使用度(relative synonymous codon usage,RSCU)等相关参数,同时分析了影响MUC4基因密码子使用偏好性的因素。结果表明:不同物种MUC4基因偏好使用以G或C结尾的密码子,RSCU值分析发现,不同物种中CUG、AGG、GCC、AUC、GUG、ACA为最优密码子(RSCU值>1.6);此外,MUC4基因密码子偏好性主要受密码子第3位碱基的GC含量(GC3s)的影响;聚类分析发现,猪(Sus scrofa)与家猫(Felis catus)聚为一类,人(Homo sapiens)与家犬(Canis lupus familiaris)聚为一类,与系统分类关系不一致。本研究系统揭示了MUC4基因密码子的使用模式,为今后MUC4基因在动物遗传改良中选择合适的受体动物,以及通过基因工程和密码子优化途径提高外源基因表达水平进而提高机体对大肠杆菌F4ab/F4ac病原菌感染的抗性提供理论依据。Escherichia coli served as an important zoonotic pathogen that cause diarrhea in human and neonatal livestock, and the E. coli with fimbriae of the F4 family are one of the major causes of diarrhea. Previous study showed that the Mucin 4 gene （MUC4） was likely to be the receptor of E. coli F4ab/F4ac. Analysis of codon usage patterns contribute to a better understanding of the molecular mechanism and the evolution of a particular gene. To reveal the codon usage patterns of MUC4 gene, this study performed codon usage bias analysis of the complete coding sequences of the MUC4 gene from 13 different mammals. The indexes of codon usage bias of the MUC4 gene including nucleotide composition, effective number of codon and relative synonymous codon usage were calculated. Meanwhile, the analysis of codon usage bias parameter were performed to investigate the main factors that influence the codon usage bias of the MUC4 gene. The results showed that the codons ending with G or C were preferentially used in the MUC4 gene of all the analyzed species. RSCU analysis showed that all of these species had 6 optimal codons, whose biased strongly codons were CUG, AGG, GCC, AUC, GUG, ACA. Moreover, the codon usage patterns of the MUC4 gene were found to be mainly influenced by GC content at the third position. Clustering analysis by RSCU values demonstrated that Sus scrofa and Felis catus, Homo sapiens and Canis lupus familiaris were clustered respectively, which disagreed with taxonomic relationship. In conclusion, this study systematically provides insights into the codon usage patterns of the MUC4 gene. These results can provide the scientific basis for selecting a suitable recipient animal in animal genetic improvement, enhancing exogenous expression level of the MUC4 gene to improve the resistance to E. coli F4ab/F4ac infection by the methods of gene engineering and codon optimization.

关 键 词：4型黏蛋白基因(MUC4) 密码子偏好性 外源表达 

分 类 号：S813.3[农业科学—畜牧学]