马铃薯StUOXs基因家族的生物信息学分析

doi:10.3969/j.issn.1004-1524.2020.09.01

浙江农业学报 ›› 2020, Vol. 32 ›› Issue (9): 1523-1532.DOI: 10.3969/j.issn.1004-1524.2020.09.01

马铃薯StUOXs基因家族的生物信息学分析

梁丽琴^a,b, 杨瑞^a, 郜刚^a,*

a.山西师范大学,生命科学学院,山西临汾 041004;
b.山西师范大学,文理学院,山西临汾 041004

收稿日期:2020-03-14 出版日期:2020-09-25 发布日期:2020-10-10
通讯作者: *郜刚,E-mail:ggsxnu@126.com
作者简介:梁丽琴(1979—),女,山西襄汾人,博士,副教授,主要从事蛋白质结构与功能,及真菌小RNA发生分子遗传机制研究。E-mail:lingliqin699@126.com
基金资助:
国家自然科学基金(31771858);山西师范大学文理学院基础研究基金(2019JCYJ21)

Bioinformatics analysis of StUOXs gene family in potato

LIANG Liqin^a,b, YANG Rui^a, GAO Gang^a,*

a. College of Life Sciences, Shanxi Normal University, Linfen 041004, China;
b. College of Arts and Sciences, Shanxi Normal University, Linfen 041004, China

Received:2020-03-14 Online:2020-09-25 Published:2020-10-10

摘要/Abstract

摘要： 马铃薯(Solanum tuberosum)是世界第三大粮食作物,其产量和品质受到生物与非生物胁迫的影响。泛醌氧化酶(ubiquinol oxidase,UOX)是一种由核基因编码的线粒体末端氧化酶,在植物生长发育及胁迫应答中发挥重要作用。为了解StUOXs在马铃薯抗病过程中发挥的应答反应,利用生物信息学方法在马铃薯基因组中鉴定出5个StUOXs基因,对其理化性质、染色体定位、三级结构、进化关系、保守结构域、启动子元件和表达谱尤其是受青枯菌(Ralstonia solanacearum)诱导的表达模式进行了分析。结果表明:马铃薯StUOXs基因编码的氨基酸数在279~366,相对分子质量为31~42 ku,亚细胞定位在线粒体中;系统进化分析发现,马铃薯StUOXs成员与番茄、辣椒的UOXs成员的亲缘关系最近,较之拟南芥、烟草亲缘关系稍远;FPKM数据分析发现,StUOXs主要受盐、激素和生物胁迫诱导而在叶片中表达,这与其启动子中的存在的激素应答等顺式作用元件相对应。青枯菌接种后的qRT-PCR实验表明,StUOX4参与马铃薯青枯病的早期应答反应。

关键词: 马铃薯, StUOXs, 序列特征, 生物信息学分析

Abstract: Potato(Solanum tuberosum) is the third largest food crop in the world, and its yield and quality are adversely affected by biotic and abiotic stresses. Ubiquinone oxidase(UOX), as a mitochondrial terminal oxidase encoded by nuclear genes, plays an important role in the regulation of plant growth and stress response. In order to understand the response of StUOXs in potato disease resistance, five StUOXs genes were identified in potato genome by bioinformatics methods, and their physical and chemical properties, chromosome location, tertiary structure, evolutionary relationship, conserved domain, promoter element and expression profile, especially the expression patterns induced by Ralstonia solanacearum were analyzed. The results showed that the number of amino acids encoded by potato StUOXs genes was between 279 and 366, the molecular weight was distributed between 31 and 42 ku, and the subcellular locations were located in mitochondria. Phylogenetic analysis showed that potato StUOXs members were closely related to tomato and pepper UOXs members, but slightly farther than Arabidopsis thaliana and tobacco. FPKM data analysis showed that StUOXs were mainly induced by salt, hormone and biological stress in leaves, which corresponded to the cis-acting elements such as hormone response in its promoter. The qRT-PCR test after inoculation with Ralstonia solanacearum showed that StUOX4 was involved in the early response to the bacterial wilt pathogens.

Key words: potato, StUOXs, sequences characteristics, bioinformatics analysis

中图分类号:

S532

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.

LIANG Liqin, YANG Rui, GAO Gang. Bioinformatics analysis of StUOXs gene family in potato[J]. , 2020, 32(9): 1523-1532.

参考文献

[1] MATSUTANI M, FUKUSHIMA K, KAYAMA C, et al.Replacement of a terminal cytochrome C oxidase by ubiquinol oxidase during the evolution of acetic acid bacteria[J]. Biochimica et Biophysica Acta, 2014, 1837(10):1810-1820.
[2] BR?NDÉN G, GENNIS R B, BRZEZINSKI P. Transmembrane proton translocation by cytochrome C oxidase[J]. Biochimica et Biophysica Acta, 2006, 1757(8):1052-1063.
[3] 苏明慧, 汪一荣, 杨艳梅, 等. 细胞色素C氧化酶亚基Cox4的克隆及高效表达[J].江苏农业科学,2018, 46(15):31-34.
SU M H, WANG Y R, YANG Y M, et al.Cloning and high expression of cytochrome C oxidase subunit Cox4[J]. Jiangsu Agricultural Sciences, 2018, 46(15):31-34. (in Chinese)
[4] ROGOV A G, ZVYAGILSKAYA R A.Physiological role of alternative oxidase (from yeasts to plants)[J]. Biochemistry (Moscow), 2015, 80(4):400-407.
[5] VANLERBERGHE G C, MCINTOSH L.ALTERNATIVE OXIDASE: from gene to function[J]. Annual Review of Plant Physiology and Plant Molecular Biology, 1997, 48:703-734.
[6] ITO Y, SAISHO D, NAKAZONO M, et al.Transcript levels of tandem-arranged alternative oxidase genes in rice are increased by low temperature[J]. Gene, 1997, 203(2):121-129.
[7] MOORE A L, SHIBA T, YOUNG L, et al.Unraveling the heater: new insights into the structure of the alternative oxidase[J]. Annual Review of Plant Biology, 2013, 64:637-663.
[8] SWEETMAN C, SOOLE K L, JENKINS C L D, et al. Genomic structure and expression of alternative oxidase genes in legumes[J]. Plant, Cell & Environment, 2019, 42(1):71-84.
[9] ARMSTRONG A F, BADGER M R, DAY D A, et al.Dynamic changes in the mitochondrial electron transport chain underpinning cold acclimation of leaf respiration[J]. Plant, Cell & Environment, 2008, 31(8):1156-1169.
[10] WATANABE C K, HACHIYA T, TERASHIMA I, et al.The lack of alternative oxidase at low temperature leads to a disruption of the balance in carbon and nitrogen metabolism, and to an up-regulation of antioxidant defence systems in Arabidopsis thaliana leaves[J]. Plant, Cell & Environment, 2008, 31(8):1190-1202.
[11] BARTOLI C G, GOMEZ F, GERGOFF G, et al.Up-regulation of the mitochondrial alternative oxidase pathway enhances photosynthetic electron transport under drought conditions[J]. Journal of Experimental Botany, 2005, 56(415):1269-1276.
[12] GIRAUD E, HO L H M, CLIFTON R, et al. The absence of ALTERNATIVE OXIDASE1a in Arabidopsis results in acute sensitivity to combined light and drought stress[J]. Plant Physiology, 2008, 147(2):595-610.
[13] MAXWELL D P, WANG Y, MCINTOSH L.The alternative oxidase lowers mitochondrial reactive oxygen production in plant cells[J]. Proceedings of the National Academy of Sciences of the United States of America, 1999, 96(14):8271-8276.
[14] YOSHIDA K, NOGUCHI K.Differential gene expression profiles of the mitochondrial respiratory components in illuminated Arabidopsis leaves[J]. Plant & Cell Physiology, 2009, 50(8):1449-1462.
[15] BIRCH P R J, BRYAN G, FENTON B, et al. Crops that feed the world 8: potato: are the trends of increased global production sustainable?[J]. Food Security, 2012, 4(4):477-508.
[16] SELVA KUMAR S, RAM KRISHNA RAO M, DEEPAK KUMAR R, et al. Biocontrol by plant growth promoting rhizobacteria against black scurf and stem canker disease of potato caused by Rhizoctonia solani[J]. Archives of Phytopathology and Plant Protection, 2013, 46(4):487-502.
[17] 冯耀斌. 山西省马铃薯产业发展分析[J]. 中国马铃薯, 2018, 32(5):315-318.
FENG Y B.Analysis of potato industry development in Shanxi Province[J]. Chinese Potato Journal, 2018, 32(5):315-318.(in Chinese with English abstract)
[18] DONLON T A, MORRIS B J.In silico analysis of human renin gene-gene interactions and neighborhood topologically associated domains suggests breakdown of insulators contribute to ageing-associated diseases[J]. Biogerontology, 2019, 20(6):857-869.
[19] FINN R D, BATEMAN A, CLEMENTS J, et al.Pfam: the protein families database[J]. Nucleic Acids Research, 2014, 42(D1):D222-D230.
[20] JIN J P, ZHANG H, KONG L, et al.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors[J]. Nucleic Acids Research, 2014, 42(Database issue):D1182-D1187.
[21] TAMURA K, STECHER G, PETERSON D, et al.MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Molecular Biology and Evolution, 2013, 30(12):2725-2729.
[22] CHEN C J, XIA R, CHEN H, et al. TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface[J/OL]. bioRxiv,[2020-03-14]. DOI:10.1101/289660.
[23] HE L.Characteristics of strains of Pseudomonas solanacearum from China[J]. Plant Disease, 1983, 67(12):1357-1361.
[24] 庞鹏湘, 常燕楠, 尉瑞敏, 等. 马铃薯StSRP1的克隆、表达及生物信息学分析[J]. 生物技术通报, 2019, 35(7):10-16.
PANG P X, CHANG Y N, YU R M, et al.Cloning, expression and bioinformatics analyses of StSRP1 gene in Solanum tuberosum[J]. Biotechnology Bulletin, 2019, 35(7):10-16.(in Chinese with English abstract)
[25] ZSIGMOND L, RIGÓ G, SZARKA A, et al.Arabidopsis PPR40 connects abiotic stress responses to mitochondrial electron transport[J]. Plant Physiology, 2008, 146(4):1721-1737.
[26] BREW-APPIAH R A T, YORK Z B, KRISHNAN V, et al. Genome-wide identification and analysis of the ALTERNATIVE OXIDASE gene family in diploid and hexaploid wheat[J]. PLoS One, 2018, 13(8):e0201439.
[27] BHAGI-DAMODARAN A, PETRIK I, LU Y.Using biosynthetic models of heme-copper oxidase and nitric oxide reductase in myoglobin to elucidate structural features responsible for enzymatic activities[J]. Israel Journal of Chemistry, 2016, 56(9/10):773-790.
[28] MOGI T, MINAGAWA J, HIRANO T, et al.Substitutions of conserved aromatic amino acid residues in subunit I perturb the metal centers of the Escherichia coli bo-type ubiquinol oxidase[J]. Biochemistry, 1998, 37(6):1632-1639.
[29] KAWASAKI M, MOGI T, ANRAKU Y.Substitutions of charged amino acid residues conserved in subunit I perturb the redox metal centers of the Escherichia coli bo-type ubiquinol oxidase[J]. Journal of Biochemistry, 1997, 122(2):422-429.
[30] CONSIDINE M J, HOLTZAPFFEL R C, DAY D A, et al.Molecular distinction between alternative oxidase from monocots and dicots[J]. Plant Physiology, 2002, 129(3):949-953.
[31] CLIFTON R, LISTER R, PARKER K L, et al.Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana[J]. Plant Molecular Biology, 2005, 58(2):193-212.
[32] BORECKY J, NOGUEIRA F T S, DE OLIVEIRA K A P, et al. The plant energy-dissipating mitochondrial systems: depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots[J]. Journal of Experimental Botany, 2006, 57(4):849-864.
[33] FENG H Q, WANG Y F, LI H Y, et al.Salt stress-induced expression of rice AOX1a is mediated through an accumulation of hydrogen peroxide[J]. Biologia, 2010, 65(5):868-873.
[34] MOHANAPRIYA G, BHARADWAJ R, NOCEDA C, et al.Alternative oxidase (AOX) senses stress levels to coordinate auxin-induced reprogramming from seed germination to somatic embryogenesis: a role relevant for seed vigor prediction and plant robustness[J]. Frontiers in Plant Science, 2019, 10:1134.

马铃薯StUOXs基因家族的生物信息学分析

Bioinformatics analysis of StUOXs gene family in potato

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