鸡IFIT5基因编码区多态性及生物信息学分析  

Polymorphisms Detection and Bioinformatics Analysis of Coding Domain Sequence of IFIT5 Gene in Chicken

作　　者：张贝[1] 孟婕 任一帆 杨晴[1] 巩静 张传生[1] 耿立英[1] 李祥龙[1] ZHANG Bei;MENG Jie;REN Yifan;YANG Qing;GONG Jing;ZHANG Chuansheng;GENG Liying;LI Xianglong(Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation(under planning),Hebei Normal University of Science and Technology,Qinhuangdao,Hebei 066004)

机构地区：[1]河北科技师范学院河北省特色动物种质资源挖掘与创新重点实验室(筹),河北秦皇岛066004

出　　处：《中国家禽》2021年第10期17-24,共8页China Poultry

基　　金：河北省教育厅重点项目(ZD2018034);河北省现代农业产业技术体系(HBCT2018150201);河北省鸡现代种业创新团队(21326303D-5);秦皇岛市科学技术研究与发展计划(201903B001);河北科技师范学院博士启动基金(2018YB002)。

摘　　要：为探究鸡IFIT5基因多态性,预测其蛋白质的结构并分析功能特征,采用PCR技术对IFIT5的CDS进行扩增,并结合多种生物信息学等方法对蛋白的理化性质及蛋白结构功能进行系统性预测分析。结果显示:通过PCR成功克隆了IFIT5外显子2的CDS区域,测序结果为1 411 bp;经分析得到完整的IFIT5 CDS区为1 440 bp,共编码479个氨基酸,测序比对结果准确。IFIT5蛋白为不稳定的、小分子的、非分泌型的亲水蛋白,且具有磷酸化和糖基化位点;二级结构主要以α-螺旋为主,结构域以TPR结构域为主。研究发现了12个SNP,其中SNP1(g.405 G>A)和SNP9(g.1 124 G>A)在原鸡为A,在家鸡中已固定为G;只有SNP8(g.110 8 A>G)和SNP12(g.1 273 A>G)位点具有中度多态性,其他位点是低度。12个SNP位点中存在4个nsSNP位点(D370N、Y375C、N402K和G425R)。其中D370N、Y375C和N402K位点被预测为有害性位点;并且D370N和N402K突变可能改变相关氨基酸的氢键数目和蛋白的高级结构,进而影响蛋白的结构和功能。这些nsSNP位点,特别是D370N和N402K可尝试作为鸡先天免疫的候选分子标记,为遗传资源的保护及抗病性分子育种提供理论依据。To elucidate the polymorphism of IFIT5 gene coding region and the protein structural and func tional characteristics in chicken, the PCR technique was used to clone sequence of IFIT5 coding region, and many bioinformatics methods were used to systematically predict and analyze the physi cochemical characteristics, protein structure and function. The results showed that the CDS of IFIT5-Exon2 was successfully cloned by PCR, which was 1 411 bp. By analysis, the complete CDS of IFIT5 was 1 440 bp, and encodes 479 amino acids. IFIT5 protein was an unstable, small,non-secretory, hydrophilic proteins with phosphorylation and glycosylation sites. The secondary structure was mainlyα-helix and the domain was mainly TPR. We found 12 SNP, of which SNP1(g.405 G>A) and SNP9(g.1 124 G>A) were A in Gallus gallus, but they had been fixed as G in domestic chickens. Only SNP8(g.1 108 A>G) and SNP12(g.1 273 A>G) sites were moderately polymorphic, other sites were low. Interestingly, there were 4 nsSNPs(D370N, Y375C,N402K, and G425 R) among the 12 SNP sites. Among them, D370N, Y375C and N402K are predicted to be harmful sites. Also, D370N and N402K mutations might change the number of hydrogen bonds of related amino acids and the higher structure of the protein, thus affected the structure and function of the protein. These nsSNP sites, especially D370N and N402K, can be used as candidate molecular markers for chicken innate immunity, which provides a theoretical basis for the protection of chicken genetic resources and the disease resistance molecular breeding.

关 键 词：鸡 IFIT5基因 多态性 蛋白质结构 生物信息学分析 

分 类 号：S831.2[农业科学—畜牧学]