猪FASN基因功能性单核苷酸多态性的生物信息学分析

Bioinformatics analysis of functional SNPs in pig FASN genes

为了筛选出猪FASN基因中具有生物学功能的非同义单核苷酸多态性(non-synonymous single nucleotide polymorphisms,nsSNPs)位点,试验采用生物信息学方法对FASN基因的nsSNPs位点进行了研究。首先利用Ensembl数据库分析FASN基因nsSNPs位点的相关信息,然后利用SIFT、Polyphen2和Provean三种方法预测nsSNPs位点的有害性,再利用ConSurf server、I-Mutant 3.0、Mupro、BDM-PUB、SUMO plotTM、NetPhos 2.0 Server等在线软件对nsSNPs位点的进化保守位点、蛋白质稳定性、泛素化位点、磷酸化位点进行预测,SOPMA和MutPred2在线软件分析nsSNPs位点对FASN蛋白二级结构和三级结构的影响,最后使用Phyre2和VMD软件预测和构建野生型和突变型FASN蛋白的空间结构。结果表明:FASN基因有2个转录子,共38个nsSNPs位点,其中有7个位点被SIFT、Polyphen2和Provean三种方法均预测为有害突变位点,分别是L215F、V560G、R409C、F494L、L560R、R872W、R1123W。L215F、F494L位点属于高保守性位点;7个位点都可降低FASN蛋白的稳定性且不存在泛素化修饰,只有L215F位点存在磷酸化修饰;7个位点都可能参与了FASN蛋白二级结构的形成;L215F、V560G、L560R位点对FASN蛋白的三级结构有影响。说明L215F位点可能是猪FASN基因的潜在功能性位点。

In order to screen out the non-synonymous single nucleotide polymorphisms(nsSNPs)with biological functions in the pig FASN genes,the nsSNPs of FASN gene was studied by bioinformatics method.First of all,the relevant information of the nsSNPs in pig FASN gene was analyzed by Ensembl database.Then the harmworthiness of nsSNPs was predicted by using SIFT,Polyphen-2 and Provean.Softwares such as ConSurf server,I-Mutant 3.0,Mupro,BDM-PUB,SUMO plotTM and NetPhos 2.0 Server were used to predict the evolutionary conservation sites,protein stability,ubiquitination sites and phosphorylation sites of the nsSNPs.SOPMA and MutPred2 online software were used to analyze the effects of the nsSNPs on the secondary and 3D structure of FASN protein,respectively.At last,Phyre2 and VMD software were used to establish the 3D structure of FASN protein.The resutls showed that FASN gene had two transcripts and 38 nsSNPs,among which 7 detelerious mutation sites(L215F,V560G,R409C,F494L,L560R,R872W,R1123W)were predicted by SIFT,Polyphen2 and Provean methods.L215F and F494L were highly conserved sites.All the 7 nsSNPs could reduce the stability of FASN protein,but there was no ubiquitination modification sites,while only L215F had phosphorylation modification.All the 7 nsSNPs might be involved in the formation of the secondary structure of FASN protein.L215F,V560G and L560R had effects on the tertiary structure of FASN protein.These results suggested that L215F might be potential functional site of pig FASN genes.