樱桃谷鸭ATF4基因SNPs筛查及生物信息学分析

doi:10.3969/j.issn.1004-1524.2020.02.05

浙江农业学报 ›› 2020, Vol. 32 ›› Issue (2): 218-225.DOI: 10.3969/j.issn.1004-1524.2020.02.05

樱桃谷鸭ATF4基因SNPs筛查及生物信息学分析

谭光辉, 覃媛钰, 李杰章, 吴磊, 岳雍, 张依裕^*

贵州大学动物科学学院高原山地动物遗传育种与繁殖教育部重点实验室,贵州贵阳 550025

收稿日期:2019-08-30 出版日期:2020-02-25 发布日期:2020-03-13
通讯作者: *张依裕,E-mail:zyy8yyc@163.com
作者简介:谭光辉(1996—),男,贵州贵阳人,硕士研究生,主要从事动物遗传育种与繁殖研究。E-mail:1207080679@qq.com
基金资助:
国家自然科学基金(31760663); 贵州省科技人才补助项目(黔科合平台人才〔2017〕5788); 贵州省千层次创新型人才项目(701030174401)

Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks

TAN Guanghui, QIN Yuanyu, LI Jiezhang, WU Lei, YUE Yong, ZHANG Yiyu^*

Key Laboratory of Plateau and Mountain Animal Genetics and Breeding, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China

Received:2019-08-30 Online:2020-02-25 Published:2020-03-13

摘要/Abstract

摘要： 旨在在樱桃谷鸭群体中筛选出转录激活因子4(activating transcription factor 4,ATF4)基因突变个体,通过选育而培育具有优质蛋壳品质的优良家禽品种。以樱桃谷鸭为试验对象,构建DNA混合池,利用普通PCR分段扩增得到ATF4基因序列,并筛查其单核苷酸多态性(single nucleotide polymorphism sites, SNPs),进行生物信息学分析。结果显示:樱桃谷鸭ATF4基因编码区全长1 065 bp,可编码354个氨基酸,ATF4基因编码的蛋白为不稳定的可溶性蛋白,不存在信号肽,有2个N-糖基化位点;ATF4基因CDS区共筛查到4个SNPs,分别是A⁹⁰⁹G、G⁶³⁶A、G⁸¹³A和T⁸⁶⁷A,除T⁸⁶⁷A是错义突变外,其他3个SNPs均为同义突变,4个SNPs均引起mRNA二级结构和自由能和基因频率的改变;蛋白质的二级结构和三级结构主要元件为α-螺旋、无规则卷曲和延伸链,T⁸⁶⁷A突变后蛋白质的二、三级结构均发生了变化,其中α-螺旋、延伸链和β-折叠含量均增加,无规则卷曲含量减少。以上研究表明,樱桃谷鸭ATF4基因具有丰富的多态性,为提高樱桃谷鸭蛋壳品质的分子标记辅助选择提供了理论基础。

关键词: 樱桃谷鸭, ATF4基因, SNPs, 生物信息学

Abstract: To screen out the mutant individuals of activating transcription factor 4 (ATF4) gene in Cherry Valley duck population and breed excellent poultry breeds with good egg shell quality, a DNA mixing pool was constructed with Cherry Valley duck as the test object. The ATF4 gene coding sequence was obtained by common PCR fragmentation amplification and screening. single nucleotide polymorphism sites (SNPs) and bioinformatics analysis were examined. The results showed that the coding region of ATF4 gene of Cherry Valley duck was 1 065 bp in length, encoding 354 amino acids. The protein was unstable and soluble. There were no signal peptide but two N-glycosylation sites. Four SNPs were screened in the CDS region of ATF4 gene, namely A⁹⁰⁹G, G⁶³⁶A, G⁸¹³A and T⁸⁶⁷A, except that T⁸⁶⁷A was a missense mutation. All of them were synonymous mutations. Four SNPs caused changes in the secondary structure and free energy of RNA and gene frequency. The primary components of the secondary and tertiary structures of proteins were α-helix, random curl and extended chain. After T⁸⁶⁷A mutation, the secondary and tertiary structures of proteins had all changed, and the contents of α-helix, extended chain and β-fold had all increased, while the contents of random curl had decreased. In conclusion, ATF4 gene of Cherry Valley duck had abundant polymorphism, which provided a theoretical basis for molecular marker-assisted selection to improve the egg shell quality of Cherry Valley duck.

Key words: Cherry Valley ducks, ATF4 gene, SNPs, bioinformatics

中图分类号:

S834

谭光辉, 覃媛钰, 李杰章, 吴磊, 岳雍, 张依裕. 樱桃谷鸭ATF4基因SNPs筛查及生物信息学分析[J]. 浙江农业学报, 2020, 32(2): 218-225.

TAN Guanghui, QIN Yuanyu, LI Jiezhang, WU Lei, YUE Yong, ZHANG Yiyu. Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks[J]. , 2020, 32(2): 218-225.

参考文献

[1] WORTEL I M N, VAN DER MEER L T, KILBERG M S, et al. Surviving stress: modulation of ATF4-mediated stress responses in normal and malignant cells[J]. Trends in Endocrinology & Metabolism, 2017, 28(11): 794-806.
[2] HARDING H P, ZHANG Y H, ZENG H, et al.An integrated stress response regulates amino acid metabolism and resistance to oxidative stress[J]. Molecular Cell, 2003, 11(3): 619-633.
[3] NOVOA I, ZHANG Y H, ZENG H Q, et al.Stress-induced gene expression requires programmed recovery from translational repression[J]. The EMBO Journal, 2003, 22(5): 1180-1187.
[4] LIN H K, CHEN Z, WANG G, et al.Skp2 targeting suppresses tumorigenesis by Arf-p53-independent cellular senescence[J]. Nature, 2010, 464(7287):374-379.
[5] AMERI K, HARRIS A L.Activating transcription factor 4[J]. International Journal of Biochemistry & Cell Biology, 2008, 40(1):14-21.
[6] ADAMS C M, EBERT S M, DYLE M C.Role of ATF4 in skeletal muscle atrophy[J]. Current Opinion in Clinical Nutrition and Metabolic Care, 2017, 20(3): 164-168.
[7] RZYMSKI T, MILANI M, SINGLETON D C, et al.Role of ATF4 in regulation of autophagy and resistance to drugs and hypoxia[J]. Cell Cycle, 2009, 8(23): 3838-3847.
[8] SUN C J, QU L, YI G Q, et al.Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population[J]. BMC Genomics, 2015, 16: 565.
[9] VOLOSHANENKO O, SCHWARTZ U, KRANZ D, et al.Β-catenin-independent regulation of Wnt target genes by RoR2 and ATF2/ATF4 in colon cancer cells[J]. Scientific Reports, 2018, 8(1): 3178.
[10] ACKERS I, MALGOR R.Interrelationship of canonical and non-canonical Wnt signalling pathways in chronic metabolic diseases[J]. Diabetes & Vascular Disease Research, 2018, 15(1): 3-13.
[11] DE A.Wnt/Ca²+ signaling pathway: a brief overview[J]. Acta Biochimica ET Biophysica Sinica, 2011, 43(10):745-756.
[12] COUASNAY G, BON N, DEVIGNES C S, et al.PiT1/Slc20a1 is required for endoplasmic reticulum homeostasis, chondrocyte survival and skeletal development.[J]. Journal of bone and mineral research, 2019, 34(2):387-398.
[13] 杨永江, 吴恩芸, 任稳稳, 等. 中国荷斯坦牛TLR2基因SNPS快速筛查及等位基因频率估算[J]. 中国奶牛, 2018(5): 20-23.
YANG Y J, WU E Y, REN W W, et al.SNP screening and allele frequency estimation of TLR2 gene in Chinese Holstein cattle[J]. China Dairy Cattle, 2018(5): 20-23.(in Chinese with English abstract)
[14] 张丽, 刘丽霞, 戴洪伟, 等. 静宁鸡肌肉生长抑制素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), 2018, 44(5): 629-637.
ZHANG L, LIU L X, DAI H W, et al.Single nucleotide polymorphism screening and bioinformatics analysis of myostatin gene in Jingning chicken[J]. Journal of Zhejiang University(Agriculture & Life Sciences), 2018, 44(5): 629-637.(in Chinese with English abstract)
[15] 彭帅, 陈朗, 郑天宇, 等. 大通牦牛TLR2基因SNP位点筛选及生物信息学分析[J]. 浙江农业学报, 2019, 31(8): 1280-1285.
PENG S, CHEN L, ZHENG T Y, et al.SNP site screening and bioinformatics analysis of TLR2 gene in Datong yak[J]. Acta Agriculturae Zhejiangensis, 2019, 31(8): 1280-1285.(in Chinese with English abstract)
[16] 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)
[17] LITYŃSKA A, PRZYBY ĹO M, POCHE Ć E, et al. Comparison of the lectin-binding pattern in different human melanoma cell lines[J]. Melanoma Research, 2001, 11(3): 205-212.
[18] CARBAUGH D L, BARIC R S, LAZEAR H M, et al.Envelope protein glycosylation mediates Zika virus pathogenesis[J]. Journal of Virology, 2019, 93(12): e00113-19.
[19] CHEN C, WU W J, XIONG Y Z.Association of porcine ATF4 gene polymorphism and pro-duction traits and analysis of gene expression[J]. Hereditas, 2011, 33(12): 1347-1352.
[20] QU M, TANG F L, WANG L F, et al.Associations of ATF4 gene polymorphisms with schizophrenia in male patients[J]. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 2008, 147B(6): 732-736.
[21] GURUPRASAD K, REDDY B, PANDIT M W.Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence[J]. Protein Engineering, 1990, 4(2): 155-161.
[22] 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)

樱桃谷鸭ATF4基因SNPs筛查及生物信息学分析

Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价

[1]	赵秀平, 王双, 闫星伊, 段强, 张帅, 陈永胜, 李国瑞. 稻瘟病菌MGG-01005的表达纯化与生物信息学分析[J]. 浙江农业学报, 2021, 33(3): 470-478.
[2]	梁丽琴, 杨瑞, 郜刚. 马铃薯StUOXs基因家族的生物信息学分析[J]. 浙江农业学报, 2020, 32(9): 1523-1532.
[3]	杜炎斌, 张港琛, 王瑜欣, 刘宝宝, 宫胜龙, 东笑, 汪洋. 猪链球菌rpoE基因克隆及生物信息学分析[J]. 浙江农业学报, 2020, 32(7): 1149-1154.
[4]	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.
[5]	王元红, 邢雪, 李传峰, 朱杰, 王勇, 刘光清. 猫传染性腹膜炎病毒AH1905株N基因的生物信息学分析及原核表达[J]. 浙江农业学报, 2020, 32(3): 406-414.
[6]	王小朋, 赵靓, 刘自敏, 白彩霞, 杨侃侃, 张达, 孙裴, 蒋书东, 李永东, 王勇. 猪细小病毒7型Cap基因原核表达与生物信息学分析[J]. 浙江农业学报, 2020, 32(2): 200-209.
[7]	秦玲, 张鑫, 荣春笑, 莫传园, 范露, 闫婕, 孟莹, 张满让. 苹果多胺氧化酶(PAO)基因家族鉴定与表达分析[J]. 浙江农业学报, 2020, 32(2): 262-273.
[8]	刘加林, 刘士力, 蒋文枰, 程顺, 迟美丽, 郑建波, 贾永义, 赵金良, 尹绍武, 顾志敏. 河川沙塘鳢GH基因及侧翼的克隆与生物信息学分析[J]. 浙江农业学报, 2019, 31(9): 1461-1470.
[9]	原晓龙, 李云琴, 王毅. 滇牡丹中3个类查尔酮合成酶基因的克隆与表达[J]. 浙江农业学报, 2019, 31(9): 1478-1484.
[10]	彭帅, 陈朗, 郑天宇, 陆会宁, 张丽, 刘丽霞. 大通牦牛TLR2基因SNP位点筛选及生物信息学分析[J]. 浙江农业学报, 2019, 31(8): 1280-1285.
[11]	刘正奎, 吴瑗, 陈琳, 王磊, 牟泓烨, 祝徐航, 王晓杜. 猪流行性腹泻病毒Nsp5基因的原核表达及生物信息学分析[J]. 浙江农业学报, 2019, 31(4): 532-538.
[12]	董新星, 李明丽, 崔艺佳, 兰国湘, 王孝义, 严达伟. 撒坝猪MCUR1基因克隆、生物信息学分析及其组织表达量检测[J]. 浙江农业学报, 2019, 31(11): 1825-1833.
[13]	张高峰, 杨侃侃, 张谦, 王元红, 俞赵荣, 张学琪, 鲁智敏, 刘自敏, 李永东, 王勇. 羊口疮病毒安徽株023基因的原核表达与生物信息学分析[J]. 浙江农业学报, 2019, 31(1): 30-38.
[14]	阮先乐, 王俊生, 刘红占, 陈良兵, 赵锦慧. 油菜miR169基因家族的生物信息学分析及靶基因预测[J]. 浙江农业学报, 2018, 30(8): 1273-1280.
[15]	农伟伦, 毕英杰, 李宏旭, 张丽. 甘肃黑猪H-FABP基因克隆、SNPs筛查及生物信息学分析[J]. 浙江农业学报, 2018, 30(3): 378-385.