奶牛CSF3基因遗传多态性筛查及其生物信息学分析

为探究奶牛集落刺激因子3(CSF3)基因的遗传免疫功能,采用DNA混合池扩增后用直接测序法对奶牛CSF3基因的5个外显子进行单核苷酸多态性(SNP)位点筛选,并采用生物信息学方法对CSF3基因开放阅读框(ORF)区、编码蛋白质信号肽跨膜区、氨基酸理化性质、蛋白质亲/疏水性、mRNA二级结构、蛋白质二级和三级结构进行预测分析。结果显示,奶牛CSF3基因外显子2上存在3个SNP位点,分别为T⁶⁶C、C⁶⁷A、C¹¹⁸A,全部为错义突变,分别导致丝氨酸(Ser)、脯氨酸(Pro)变为组氨酸(His)。mRNA二级结构预测结果表明,T⁶⁶C和C⁶⁷A降低了奶牛CSF3基因mRNA二级结构稳定性,而C¹¹⁸A增大了其稳定性。理化特征分析结果表明,奶牛CSF3基因全长为1 460 bp,共编码195个氨基酸,是一种混合型可溶蛋白,编码产物存在信号肽跨膜区,其二级结构的主要成分为α-螺旋和无规则卷曲。

Genetic polymorphism screening of CSF3 gene in dairy cow and its bioinformatics analysis

In order to explore the genetic immunization function of colony-stimulating factor 3 (CSF3) gene in dairy cows, the single nucleotide polymorphism (SNP) of 5 exons of CSF3 gene in dairy cows were screened by direct sequencing after amplification by DNA pool, and the open reading frame (ORF) region of CSF3 gene was encoded by bioinformatics. Signal peptide transmembrane region, amino acid physicochemical properties, protein affinity/hydrophobicity, mRNA secondary structure, protein secondary and tertiary structure were predicted and analyzed. The results showed that there were three SNPs in exon 2 of CSF3 gene in cows, which were T⁶⁶C, C⁶⁷A and C¹¹⁸A, all of which were missense mutations, and led to the changes of serine (Ser) and proline (Pro) to histidine (His). The results of mRNA secondary structure prediction showed that T⁶⁶C and C⁶⁷A reduced the secondary structure stability of CSF3 gene mRNA in dairy cows, while C¹¹⁸A increased its stability. The results of physicochemical analysis showed that the CSF3 gene of cows was 1 460 bp in length and encoded a total of 195 amino acids. It is a mixed soluble protein with a signal peptide transmembrane region. The main components of its secondary structure are α-helix and random coli.