奶牛CSF3基因遗传多态性筛查及其生物信息学分析

doi:10.3969/j.issn.1004-1524.2020.06.06

浙江农业学报 ›› 2020, Vol. 32 ›› Issue (6): 986-993.DOI: 10.3969/j.issn.1004-1524.2020.06.06

奶牛CSF3基因遗传多态性筛查及其生物信息学分析

吴佳, 陈朗, 姜涛, 黄国明, 李倬, 李耀东, 张丽, 刘丽霞^*

西北民族大学生命科学与工程学院,甘肃兰州 730030

收稿日期:2019-10-13 出版日期:2020-06-25 发布日期:2020-06-24
通讯作者: *刘丽霞,E-mail: skllx@xbmu.edu.cn
作者简介:吴佳(1998—),女,宁夏石嘴山人,本科生,研究方向为生物化学与分子生物学。E-mail: 15109660012@163.com
基金资助:
西北民族大学中央高校基本科研业务费资金(31920190025,31920200074); 西北民族大学本科生科研创新项目(XBMU-BYL19127); 西北民族大学引进人才科研项目(xbmuyjrc201413)

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

WU Jia, CHEN Lang, JIANG Tao, HUANG Guoming, LI Zhuo, LI Yaodong, ZHANG Li, LIU Lixia^*

College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China

Received:2019-10-13 Online:2020-06-25 Published:2020-06-24

摘要/Abstract

摘要： 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。

关键词: 奶牛, CSF3, SNP, 生物信息学分析

Abstract: 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.

Key words: dairy cow, CSF3, SNP, bioinformatics analysis

中图分类号:

S823.9⁺1

吴佳, 陈朗, 姜涛, 黄国明, 李倬, 李耀东, 张丽, 刘丽霞. 奶牛CSF3基因遗传多态性筛查及其生物信息学分析[J]. 浙江农业学报, 2020, 32(6): 986-993.

WU Jia, CHEN Lang, JIANG Tao, HUANG Guoming, LI Zhuo, LI Yaodong, ZHANG Li, LIU Lixia. Genetic polymorphism screening of CSF3 gene in dairy cow and its bioinformatics analysis[J]. , 2020, 32(6): 986-993.

参考文献

[1] 宋亚攀, 杨利国. 中国奶牛乳房炎防治研究进展[J]. 中国奶牛, 2010(12): 48-54.
SONG Y P, YANG L G.Research progress in prevention and treatment of mastitis in dairy cows in China[J]. China Dairy Cattle, 2010(12): 48-54.(in Chinese)
[2] 廖想想. 奶牛金黄色葡萄球菌人工诱导型乳腺炎基因表达谱分析[D]. 扬州: 扬州大学, 2014.
LIAO X X.Gene expression profiles of mastitis artifitially induced by Staphylococcus aureus in Chinese Holstein[D]. Yangzhou: Yangzhou University, 2014.(in Chinese with English abstract)
[3] YEGANEGI M, LEUNG C G, MARTINS A, et al.Lactobacillus rhamnosus GR-1 stimulates colony-stimulating factor 3 (granulocyte) (CSF₃) output in placental trophoblast cells in a fetal sex-dependent Manner1[J]. Biology of Reproduction, 2011, 84(1): 18-25.
[4] 魏玉好. 几个基因与LPS信号通路的关系及金英汤对其影响[D]. 贵阳: 贵州大学, 2018.
WEI Y H.The relationship between several genes with LPS signaling pathway and the influence of JYT on the gene expression in MECs[D]. Guiyang: Guizhou University, 2018.(in Chinese with English abstract)
[5] WANG H, FITZPATRICK M, WILSON N J, et al.CSF3R/CD114 mediates infection-dependent transition to severe asthma[J]. Journal of Allergy and Clinical Immunology, 2019, 143(2): 785-788.
[6] HOLLMÉN M, KARAMAN S, SCHWAGER S, et al. G-CSF regulates macrophage phenotype and associates with poor overall survival in human triple-negative breast cancer[J]. Oncoimmunology, 2016, 5(3): e1115177.
[7] GUTTULA P K, CHANDRASEKARAN G, GUPTA M K.Screening and insilico analysis of deleterious nsSNPs (missense) in human CSF3 for their effects on protein structure, stability and function[J]. Computational Biology and Chemistry, 2019, 82: 57-64.
[8] SHIFMAN S, PISANTÉ-SHALOM A, YAKIR B, et al.Quantitative technologies for allele frequency estimation of SNPs in DNA pools[J]. Molecular and Cellular Probes, 2002, 16(6): 429-434.
[9] 张丽, 刘丽霞, 李强子, 等. 天祝白牦牛MSTN基因编码区克隆及生物信息学分析[J]. 浙江农业学报, 2017, 29(4): 618-624.
ZHANG L, LIU L X, LI Q Z, et al.Cloning and bioinformatics analysis of MSTN gene of Tianzhu white yak[J]. Acta Agriculturae Zhejiangensis, 2017, 29(4): 618-624.(in Chinese with English abstract)
[10] 杨永江, 吴恩芸, 任稳稳, 等. 中国荷斯坦牛TLR2基因SNPs的快速筛查及等位基因频率的估算[J]. 浙江农业学报, 2018, 30(8): 1321-1327.
YANG Y J, WU E Y, REN W W, et al.SNP screening and protein function prediction of TLR2 gene in Chinese Holstein cattle[J]. Acta Agriculturae Zhejiangensis, 2018, 30(8): 1321-1327.(in Chinese with English abstract)
[11] 吴恩芸, 任稳稳, 李耀东, 等. 中国荷斯坦牛TLR1基因SNPs快速筛查及蛋白功能预测[J]. 核农学报, 2019, 33(10): 1940-1948.
WU E Y, REN W W, LI Y D, et al.Rapidly screening of TLR1 gene SNPs and prediction of protein function in Chinese Holstein cattle[J]. Journal of Nuclear Agricultural Sciences, 2019, 33(10): 1940-1948.(in Chinese with English abstract)
[12] 宁素恒, 徐军, 李强子, 等. 牛LF基因结构和功能的生物信息学分析[J]. 浙江农业科学, 2016, 57(6): 904-907.
NING S H, XU J, LI Q Z, et al.Bioinformatics analysis of LF gene structure and function in cattle[J]. Journal of Zhejiang Agricultural Sciences, 2016, 57(6): 904-907.(in Chinese)
[13] 李强子, 朱国强, 刘吴鑫, 等. 荷斯坦牛TLR6基因CDS区的生物信息学分析[J]. 江苏农业学报, 2016, 32(3): 608-614.
LI Q Z, ZHU G Q, LIU W X, et al.Bioinformatics analysis of CDS of TLR6 gene in Holstein cattle[J]. Jiangsu Journal of Agricultural Sciences, 2016, 32(3): 608-614.(in Chinese with English abstract)
[14] 李艳秋, 栗霄立, 王力宁, 等. 中性粒细胞集落刺激因子基因多态性与系统性红斑狼疮相关性的研究[J]. 中华风湿病学杂志, 2006(9):517-521.
LI Y Q, LI X L, WANG L N, et al.Granulocyte colony-stimulating factor gene polymorphism in patients with systemic lupus erythematosus in Northern Chinese[J].Chinese Journal of Rheumatology, 2006(9):517-521. (in Chinese with English abstract)
[15] GIBSON M S, KAISER P, FIFE M.Identification of chicken granulocyte colony-stimulating factor (G-CSF/CSF₃): the previously described myelomonocytic growth factor is actually CSF₃[J]. Journal of Interferon & Cytokine Research, 2009, 29(6): 339-344.
[16] 张灿. 荷斯坦奶牛细胞因子基因的克隆、表达及重组蛋白的应用[D]. 北京: 中国农业大学, 2005.
ZHANG C.Cloning, expression of Holstein cow cytokine genes and application of recombinant proteins[D]. Beijing: China Agricultural University, 2005.(in Chinese with English abstract)
[17] 张天, 孙素红, 姚新生. GM-CSF对乳腺癌患者化疗后外周血B细胞CDR3库的影响[C]//第九届全国免疫学学术大会论文集. 济南, 2014: 554-555.
[18] 赵淑清, 李军民. 粒细胞集落刺激因子及其受体与血液相关疾病[J]. 中国实验血液学杂志, 2015, 23(3): 871-877.
ZHAO S Q, LI J M.G-CSF and its receptor in hematonosis: review[J]. Journal of Experimental Hematology, 2015, 23(3): 871-877.(in Chinese with English abstract)
[19] 刘丽霞, 张丽, 田晓静, 等. 猪SLA-DRA基因SNP位点筛选及其生物信息学分析[J]. 浙江农业学报, 2017, 29(7): 1077-1085.
LIU L X, ZHANG L, TIAN X J, et al.SNP screening and bioinformatics analysis of SLA-DRA gene in pigs[J]. Acta Agriculturae Zhejiangensis, 2017, 29(7): 1077-1085.(in Chinese with English abstract)
[20] 张丽, 农伟伦, 卢建雄, 等. 八眉猪FABPs主要家族基因单核苷酸多态性筛查及生物信息学分析[J]. 浙江大学学报(农业与生命科学版), 2019, 45(1): 109-118.
ZHANG L, NONG W L, LU J X, et al.Single nucleotide polymorphism screening and bioinformatics analysis of the main family genes of FABPs in Bamei pig[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2019, 45(1): 109-118.(in Chinese with English abstract)
[21] 贾浩, 张小白, 宋晓峰. 人类胞内蛋白半衰期与其亚细胞定位的相关性研究[J]. 计算机与应用化学, 2011, 28(4): 411-414.
JIA H, ZHANG X B, SONG X F.Relationship between intracellular protein half-life and subcellular localization in human cells[J]. Computers and Applied Chemistry, 2011, 28(4): 411-414.(in Chinese with English abstract)
[22] ROST B, SANDER C.Combining evolutionary information and neural networks to predict protein secondary structure[J]. Proteins: Structure, Function, and Genetics, 1994, 19(1): 55-72.

奶牛CSF3基因遗传多态性筛查及其生物信息学分析

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

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