郏县红牛POLB基因克隆及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2022.03.010

摘要/Abstract

摘要： 【目的】克隆郏县红牛DNA聚合酶β（DNA polymerase beta，POLB）基因，并对其进行生物信息学分析。【方法】以郏县红牛肌肉组织cDNA为模板，通过PCR方法克隆POLB基因完整CDS区序列；利用在线软件进行遗传距离分析并构建系统进化树，分析POLB蛋白的理化性质、疏水性、磷酸化位点、跨膜结构、信号肽、二级结构、三级结构和互作蛋白。【结果】郏县红牛POLB基因CDS区序列全长1 008 bp，编码335个氨基酸。系统进化树分析表明，郏县红牛POLB基因氨基酸序列与绵羊等反刍动物的亲缘关系最近，与其他哺乳类动物和禽类次之，与斑马鱼（鱼类）最远。郏县红牛POLB蛋白分子质量为38.26 ku，理论等电点（pI）为9.10，半衰期为30 h，不稳定系数为31.06，总平均亲水系数为－0.659，属于稳定的亲水性蛋白；磷酸化位点预测分析发现，郏县红牛POLB蛋白包含17个丝氨酸磷酸化位点、12个苏氨酸磷酸化位点和4个酪氨酸磷酸化位点；跨膜区和信号肽预测结果显示，郏县红牛POLB蛋白不属于跨膜蛋白和分泌型蛋白；二级结构和三级结构预测发现，其主要包含α-螺旋、β-转角、延伸链和无规则卷曲4种结构；在线软件预测结果表明，POLB蛋白与XRCC1、FEN1、PARP1和LIG3等为互作蛋白。【结论】本研究成功克隆了郏县红牛POLB基因CDS序列，其与绵羊亲缘关系最近；POLB蛋白为无跨膜结构、无信号肽的亲水性蛋白，与XRCC1蛋白互作程度最高，结果可为进一步探究POLB基因生物学功能提供参考。

关键词: 郏县红牛; POLB基因; 克隆; 生物信息学分析

Abstract: 【Objective】 The aim of this study was to clone Jiaxian Red cattle DNA polymerase beta (POLB) gene and analyze its bioinformatics.【Method】 The complete CDS region of cattle POLB gene was cloned by PCR with the cDNA of muscle tissue in Jiaxian Red cattle as the template.Genetic distance analysis and phylogenetic tree were constructed by online softwares to analyze the physical and chemical properties, hydrophobicity, phosphorylation sites, transmembrane structure, signal peptide, secondary structure, tertiary structure and interaction proteins of POLB protein.【Result】 The sequence of CDS region of Jiaxian Red cattle POLB gene was 1 008 bp, encoding 335 amino acids.Phylogenetic tree analysis showed that the amino acid sequence of Jiaxian Red cattle POLB gene was closest related to sheep and other ruminants, followed by other mammals and poultry, and was farthest related to zebrafish (fish).The molecular weight of Jiaxian Red cattle POLB protein was 38.26 ku, the theoretical isoelectric point (pI) was 9.10, the half-life was 30 h, the instability coefficient was 31.06, and the total average hydrophilic coefficient was -0.659, indicating that it was a stable hydrophilic protein.Predictive analysis of phosphorylation sites showed that Jiaxian Red cattle POLB protein contained 17 serine phosphorylation, 12 threonine phosphorylation and 4 tyrosine phosphorylation sites.The prediction results of transmembrane region and signal peptide showed that Jiaxian Red cattle POLB protein did not belong to transmembrane protein and secretory protein.The prediction of secondary structure and tertiary structure showed that the structure mainly consisted of alpha helix, beta turn, extended strand and random coil.POLB protein was predicted to interact with XRCC1, FEN1, PARP1 and LIG3 by online softwares.【Conclusion】 The CDS sequence of Jiaxian Red cattle POLB gene was successfully cloned in this study, and it was closest to sheep.POLB protein was a hydrophilic protein without transmembrane structure and signal peptide, and had the highest degree of interaction with XRCC1 protein.The results could provide references for further exploring the biological function of POLB gene.

Key words: Jiaxian Red cattle; POLB gene; cloning; bioinformatics analysis

中图分类号:

李玉龙, 吕世杰, 翟亚莹, 张志杰, 朱肖亭, 张子敬, 陈付英, 施巧婷, 王二耀. 郏县红牛POLB基因克隆及生物信息学分析[J]. 中国畜牧兽医, 2022, 49(3): 887-896.

LI Yulong, LYU Shijie, ZHAI Yaying, ZHANG Zhijie, ZHU Xiaoting, ZHANG Zijing, CHEN Fuying, SHI Qiaoting, WANG Eryao. Cloning and Bioinformatics Analysis of POLB Gene in Jiaxian Red Cattle[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(3): 887-896.

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