甘草生长素反应因子(ARF)基因家族的鉴定及表达分析

doi:10.11924/j.issn.1000-6850.casb2020-0304

中国农学通报 ›› 2021, Vol. 37 ›› Issue (29): 20-27.doi: 10.11924/j.issn.1000-6850.casb2020-0304

所属专题：生物技术

甘草生长素反应因子(ARF)基因家族的鉴定及表达分析

关思静¹(), 高静¹(), 徐蓉蓉¹, 葛甜甜¹, 王楠², 颜永刚¹, 张岗¹, 陈莹¹, 刘阿萍¹, 程萌格¹

¹陕西中医药大学药学院/陕西省秦岭中草药应用开发工程技术研究中心,陕西西安 712046
²陕西中医药大学/陕西中药资源产业化省部共建协同创新中心,陕西咸阳 712083

收稿日期:2020-07-30 修回日期:2020-10-19 出版日期:2021-10-15 发布日期:2021-10-29
通讯作者: 高静
作者简介:关思静,女,1995年出生,陕西安康人,硕士,研究方向：中药资源的开发与利用研究。通信地址：712083 陕西省咸阳市秦都区渭阳中路陕西中医药大学协同创新中心,Tel：029-38035207,E-mail： gsj127810@163.com。
基金资助:
国家自然科学基金项目“根际真菌提高甘草水分和磷利用率的生理机制研究”(31600320);陕西省社会发展科技攻关项目“甘草高产优质品种选育及其配套栽培技术研究”(2018SF-338);陕西中医药大学“秦药”品质评价及资源开发学科创新团队项目(2019-QN01)

Auxin Response Factor (ARF) Gene Family in Glycyrrhiza uralensis Fisch.: Identification and Expression Analysis

Guan Sijing¹(), Gao Jing¹(), Xu Rongrong¹, Ge Tiantian¹, Wang Nan², Yan Yonggang¹, Zhang Gang¹, Chen Ying¹, Liu Aping¹, Cheng Mengge¹

¹College of Pharmacy, Shaanxi University of Chinese Medicine/Shaanxi Qinling Chinese Herbal Medicine Application Development Engineering Technology Research Center, Xi’an Shaanxi 712046
²Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry, Shaanxi University of Chinese Medicine, Xianyang Shaanxi 712083

Received:2020-07-30 Revised:2020-10-19 Online:2021-10-15 Published:2021-10-29
Contact: Gao Jing

摘要/Abstract

摘要：

本研究旨在鉴定甘草ARF基因家族并分析其在非生物胁迫下的表达模式。以乌拉尔甘草(Glycyrrhiza uralensis Fisch.)为研究对象,利用生物信息学方法对ARF基因家族进行鉴定,并对其蛋白质理化性质、保守结构域、基因结构、进化关系、顺式作用元件和表达模式分析。鉴定得到10个甘草ARF基因。其蛋白氨基酸序列长度在301~945 aa之间,分子量约为33.07~104.37kDa,等电点为5.93~8.50。亚细胞定位分析显示甘草ARF蛋白均位于细胞核。保守结构域分析显示GuARF蛋白大多包含B3、Auxin_resp和Aux/IAA结构域。基因结构发现外显子数量从6个到22个不等。在甘草ARF基因启动子区还存在5类不同的顺式调控元件。系统进化分析表明甘草ARF蛋白分为3类。转录组数据分析显示,10个GuARF基因在非生物胁迫下具有一定表达特异性。上述结果显示甘草ARF基因家族可能参与多种生物过程,这为进一步研究植物对非生物胁迫的生理和分子反应提供了有价值的信息。

关键词: 乌拉尔甘草, 生长素反应因子, 系统进化, 基因表达, 表达模式分析

Abstract:

The purpose of the study is to identify the auxin response factor (ARF) gene family in Glycyrrhiza uralensis Fisch. and analyze their expression patterns under abiotic stress. G. Uralensis Fisch. was taken as the object. We identified the ARF gene family by bioinformatics tools, and analyzed the physicochemical properties of proteins, conserved motifs, gene structure, evolutionary relationships, cis-elements and expression profiles. 10 ARF genes (GuARFs) were identified. The length of these ARF proteins ranges from 301 to 945 amino acids and the relative molecular weight varies from 33.07 to 104.37 kDa, with PIs in the range of 5.93 to 8.50. Subcellular localization assays shows that the GuARF proteins are located in the nucleus. The conserved domain analysis indicates that most of GuARF proteins contain B3, Auxin_resp and Aux/IAA domain. Gene structure analysis reveals that the exon number of GuARF genes ranges from 6 to 22. There are 5 different types of cis-elements in the promoter region of GuARF genes. Phylogenetic analysis reveals that the GuARF proteins are clustered into 3 groups. RNA-seq data show that the expression level of 10 GuARF genes is different under abiotic stresses. The results indicate that the GuARF gene family may involve in multiple biological processes, and the study could provide valuable information for further research on physiological and molecular response of plants to abiotic stresses.

Key words: Glycyrrhiza Uralensis Fisch., auxin response factor, phylogeny, gene expression, expression pattern analysis

中图分类号:

S567.2

关思静, 高静, 徐蓉蓉, 葛甜甜, 王楠, 颜永刚, 张岗, 陈莹, 刘阿萍, 程萌格. 甘草生长素反应因子(ARF)基因家族的鉴定及表达分析[J]. 中国农学通报, 2021, 37(29): 20-27.

Guan Sijing, Gao Jing, Xu Rongrong, Ge Tiantian, Wang Nan, Yan Yonggang, Zhang Gang, Chen Ying, Liu Aping, Cheng Mengge. Auxin Response Factor (ARF) Gene Family in Glycyrrhiza uralensis Fisch.: Identification and Expression Analysis[J]. Chinese Agricultural Science Bulletin, 2021, 37(29): 20-27.

图/表 7

参考文献 28

[1]	李艳林, 高志红, 宋娟, 等. 植物生长素响应因子ARF与生长发育[J]. 植物生理学报, 2017, 53(10):1842-1858.
[2]	Singh V K, Rajkumar M S, Garg R, et al. Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea[J]. Scientific Reports, 2017, 7(1):10895. doi: 10.1038/s41598-017-11327-5 URL
[3]	Tiwari S B, Hagen G, Guilfoyle T. The roles of auxin response factor domains in auxin-responsive transcription[J]. The Plant Cell, 2003, 15(2):533-543. doi: 10.1105/tpc.008417 URL
[4]	Liscum E, Reed J W. Genetics of Aux/IAA and ARF action in plant growth and development[J]. Plant Molecular Biology, 2002, 49(3-4):387-400. pmid: 12036262
[5]	Lim P O, Lee I C, Kim J, et al. Auxin response factor 2 (ARF2) plays a major role in regulating auxin-mediated leaf longevity[J]. Journal of Experimental Botany, 2010, 61(5):1419-1430. doi: 10.1093/jxb/erq010 URL
[6]	Ellis C M, Nagpal P, Young J C, et al. AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana[J]. Development (Cambridge, England), 2005, 132(20):4563-4574. doi: 10.1242/dev.02012 URL
[7]	Kelley D R, Arreola A, Gallagher T L, et al. ETTIN (ARF3) physically interacts with KANADI proteins to form a functional complex essential for integument development and polarity determination in Arabidopsis[J]. Development (Cambridge, England), 2012, 139(6):1105-1109. doi: 10.1242/dev.067918 URL
[8]	Liu Z N, Miao L, Huo R X, et al. ARF2-ARF4 and ARF5 are essential for female and male gametophyte development in Arabidopsis[J]. Plant & cell Physiology, 2018, 59(1):179-189.
[9]	Wu Y F, Reed G W, Tian C Q. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction[J]. Development (Cambridge, England), 2006, 133(21):4211-4218. doi: 10.1242/dev.02602 URL
[10]	Goetz M, Vivian-Smith A, Johnson S D, et al. AUXIN RESPONSE FACTOR8 is a negative regulator of fruit initiation in Arabidopsis[J]. The Plant Cell, 2006, 18(8):1873-1886. doi: 10.1105/tpc.105.037192 URL
[11]	Wang B, Xue J S, Yu Y H, et al. Fine regulation of ARF17 for anther development and pollen formation[J]. BMC Plant Biology, 2017, 17(1):243. doi: 10.1186/s12870-017-1185-1 pmid: 29258431
[12]	Finet C, Berne-Dedieu A, Scutt C P, et al. Evolution of the ARF gene family in land plants: old domains, new tricks[J]. Molecular Biology and Evolution, 2013, 30(1):45-56. doi: 10.1093/molbev/mss220 URL
[13]	Wilmoth J C, Wang S, Tiwari S B, et al. NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation[J]. Plant Journal for Cell & Molecular Biology, 2010, 43(1):118-130.
[14]	Feng Z H, Zhu J, Du X L, et al. Effects of three auxin-inducible LBD members on lateral root formation in Arabidopsis thaliana[J]. Planta, 2012, 236(4):1227-1237. doi: 10.1007/s00425-012-1673-3 URL
[15]	Wang J W, Wang L J, Mao Y B, et al. Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis[J]. The Plant Cell, 2005, 17(8):2204-2216. doi: 10.1105/tpc.105.033076 URL
[16]	Mochida K, Sakurai T, Seki H, et al. Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume[J]. The Plant Journal, 2017, 89(2):181-194. doi: 10.1111/tpj.13385 URL
[17]	Chen C J, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 2020, 13(8):1194-1202. doi: 10.1016/j.molp.2020.06.009 URL
[18]	Wang D, Pei K, Fu Y, et al. Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa)[J]. Gene, 2007, 394(1):13-24. doi: 10.1016/j.gene.2007.01.006 URL
[19]	Zouine M, Fu Y Y, Wang H, et al. Characterization of the tomato ARF gene family uncovers a multi-levels post-transcriptional regulation including alternative splicing[J]. PloS one, 2014, 9(1):e84203. doi: 10.1371/journal.pone.0084203 URL
[20]	Shen C J, Yue R Q, Sun T, et al. Genome-wide identification and expression analysis of auxin response factor gene family in Medicago truncatula[J]. Frontiers in Plant Science, 2015, 6:73.
[21]	赵艳, 瓮巧云, 马海莲, 等. 谷子ARF基因家族的鉴定与生物信息学分析[J]. 植物遗传资源学报, 2017, 17(3):547-554.
[22]	Singh V K, Rajkumar M S, Garg R, et al. Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea[J]. Scientific Reports, 2017, 7(1):10895. doi: 10.1038/s41598-017-11327-5 URL
[23]	Okushima Y, Overvoorde P J, Arima K, et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19[J]. The Plant Cell, 2005, 17(2):444-463. doi: 10.1105/tpc.104.028316 URL
[24]	Pekker I, Alvarez J P, Eshed Y. Auxin response factors mediate Arabidopsis organ asymmetry via modulation of KANADI activity[J]. The Plant cell, 2005, 17(11):2899-2910. doi: 10.1105/tpc.105.034876 URL
[25]	Park J E, Park J Y, Kim Y S, et al. GH3-mediated auxin homeostasis links growth regulation with stress adaptation response in Arabidopsis[J]. Journal of Biological Chemistry, 2007, 282(13):10036-10046. doi: 10.1074/jbc.M610524200 URL
[26]	Huang D Q, Wu W R, Abrams S R, et al. The relationship of drought-related gene expression in Arabidopsis thaliana to hormonal and environmental factors[J]. Journal of Experimental Botany, 2008, 59:2991-3007. doi: 10.1093/jxb/ern155 URL
[27]	Chen L, Ren F, Zhong H, et al. Identification and expression analysis of genes in response to high-salinity and drought stresses in Brassica napus[J]. Acta Biochimica et Biophysica Sinica, 2010, 42(2):154-164. doi: 10.1093/abbs/gmp113 URL
[28]	Seki M, Narusaka M, Ishida J, et al. Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray[J]. The Plant Journal, 2002, 31(3):279-292. doi: 10.1046/j.1365-313X.2002.01359.x URL

基因名称	基因号	氨基酸数/aa	分子量/kDa	等电点	不稳定系数	亚细胞定位
GuARF1	Glyur000846s00019247.1	301	33.07	5.93	56.52	Nucleus
GuARF2	Glyur000322s00020885.1	606	66.04	6.14	40.06	Nucleus
GuARF3	Glyur000066s00006209.1	749	82.15	7.59	47.87	Nucleus
GuARF4	Glyur000081s00006796.1	711	78.74	6.64	51.32	Nucleus
GuARF5	Glyur002712s00037647.1	665	73.65	8.50	43.03	Nucleus
GuARF6	Glyur001170s00029947.1	945	104.37	6.06	64.68	Nucleus
GuARF7	Glyur000250s00014115.1	646	72.05	7.68	57.28	Nucleus
GuARF8	Glyur000413s00015469.1	856	95.42	6.27	61.46	Nucleus
GuARF9	Glyur000325s00013489.1	725	80.45	7.81	52.50	Nucleus
GuARF10	Glyur000156s00011992.1	780	87.06	6.08	52.35	Nucleus

基因名称	基因号	氨基酸数/aa	分子量/kDa	等电点	不稳定系数	亚细胞定位
GuARF1	Glyur000846s00019247.1	301	33.07	5.93	56.52	Nucleus
GuARF2	Glyur000322s00020885.1	606	66.04	6.14	40.06	Nucleus
GuARF3	Glyur000066s00006209.1	749	82.15	7.59	47.87	Nucleus
GuARF4	Glyur000081s00006796.1	711	78.74	6.64	51.32	Nucleus
GuARF5	Glyur002712s00037647.1	665	73.65	8.50	43.03	Nucleus
GuARF6	Glyur001170s00029947.1	945	104.37	6.06	64.68	Nucleus
GuARF7	Glyur000250s00014115.1	646	72.05	7.68	57.28	Nucleus
GuARF8	Glyur000413s00015469.1	856	95.42	6.27	61.46	Nucleus
GuARF9	Glyur000325s00013489.1	725	80.45	7.81	52.50	Nucleus
GuARF10	Glyur000156s00011992.1	780	87.06	6.08	52.35	Nucleus

甘草生长素反应因子(ARF)基因家族的鉴定及表达分析

Auxin Response Factor (ARF) Gene Family in Glycyrrhiza uralensis Fisch.: Identification and Expression Analysis

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