Bioinformatics and Expression Analysis of ERF Transcription Factor in Agropyron mongolicum Keng

doi:10.11733/j.issn.1007-0435.2022.11.008

Acta Agrestia Sinica ›› 2022, Vol. 30 ›› Issue (11): 2910-2921.DOI: 10.11733/j.issn.1007-0435.2022.11.008

Bioinformatics and Expression Analysis of ERF Transcription Factor in Agropyron mongolicum Keng

WU Jing¹, FAN Bo-bo¹, ZHANG Xue-feng¹, SONG Jin-wei¹, FANG Yong-yu², YU Zhuo¹, YAN Xiu-xiu¹, ZHAO Yan³, MA Yan-hong¹

1. College of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010019, China;
2. Inner Mongolia Academy of Agricultural&Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, China;
3. College of Grassland, Resources Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China

Received:2022-05-16 Revised:2022-07-24 Published:2022-12-02

蒙古冰草ERF转录因子生物信息学及其表达分析

吴婧¹, 范菠菠¹, 张学峰¹, 宋金微¹, 房永雨², 于卓¹, 闫秀秀¹, 赵彦³, 马艳红¹

1. 内蒙古农业大学农学院, 内蒙古呼和浩特 010019;
2. 内蒙古自治区农牧业科学院, 内蒙古呼和浩特 010031;
3. 内蒙古农业大学草原与资源环境学院, 内蒙古呼和浩特 010018

通讯作者: 马艳红,E-mail:mayanhong80@126.com
作者简介:吴婧(1998-)，女，汉族，内蒙古赤峰人，硕士研究生，主要从事牧草遗传育种研究，E-mail：jingwu530@126.com
基金资助:
国家自然科学基金(31860670)；内蒙古自治区草原英才创新团队资助

Abstract

Abstract: ERF is an important transcription factor family in plants,which are involved in plant growth,development and response to abiotic stresses. In order to screen ERF transcription factors related to drought resistance in A. mongolicum Keng,physicochemical properties,subcellular localization,conserved domain and motif,phylogenetic evolution,expression under different drought treatments and secondary and tertiary structures of ERF genes were analyzed via methods of bioinformatics. Eighteen ERF TFs with ERF structural characteristics were screened,and their protein size was ranged from 70 to 404 amino acid,molecular weight ranged from 7 447.54 to 43 654.9,and theoretical isoelectric point (PI) ranged from 4.53 to 11.10. Two of them were hydrophobic proteins,and the others were hydrophilic proteins. Most of them were localized in the nucleus. The secondary and tertiary structures of ERF TFs were mainly random coil. It was speculated that motif1,2 and 3 were the conserved motifs. Results of phylogenetic evolution analyses showed that the four ERF TFs,such as AmERF053,AmERF1B,AmERF4-1 and AmERF4-2,had high homology with known proteins related to drought resistance,and they were significantly differentially expressed in A.mongolicum under drought treatment.

Key words: Agropyron mongolicum Keng, ERF transcription factors, Drought resistance, Bioinformatics

摘要： ERF(Ethylene responsive factor)家族是植物中一种重要的转录因子，参与植物生长发育和逆境胁迫响应。为筛选蒙古冰草(Agropyron mongolicum Keng)抗旱相关的ERF转录因子，本研究利用生物信息学方法对其理化性质、亚细胞定位、保守基序、进化关系及其二、三级结构进行分析，同时对不同干旱处理下的ERF基因进行表达分析。结果显示：筛选得到18个具有ERF结构特征的蒙古冰草ERF转录因子，蛋白大小在70～404aa之间，分子质量在7447.54～43654.9之间，理论等电点(PI)在4.53～11.10之间，其中有2个疏水性蛋白，其余均为亲水性蛋白，大部分定位于细胞核。ERF转录因子的二、三级结构以无规则卷曲为主，推测motif1，motif2，motif3为保守基序。进化关系比对发现AmERF053，AmERF1B，AmERF4-1，AmERF4-2与已知具有抗旱功能的蛋白具有较高同源性，且在干旱处理的蒙古冰草中显著差异表达。

关键词: 蒙古冰草, ERF转录因子, 抗旱, 生物信息学分析

CLC Number:

S543+.9

WU Jing, FAN Bo-bo, ZHANG Xue-feng, SONG Jin-wei, FANG Yong-yu, YU Zhuo, YAN Xiu-xiu, ZHAO Yan, MA Yan-hong. Bioinformatics and Expression Analysis of ERF Transcription Factor in Agropyron mongolicum Keng[J]. Acta Agrestia Sinica, 2022, 30(11): 2910-2921.

吴婧, 范菠菠, 张学峰, 宋金微, 房永雨, 于卓, 闫秀秀, 赵彦, 马艳红. 蒙古冰草ERF转录因子生物信息学及其表达分析[J]. 草地学报, 2022, 30(11): 2910-2921.

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URL: https://manu40.magtech.com.cn/Jweb_cdxb/EN/10.11733/j.issn.1007-0435.2022.11.008

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References

[1] 李科友,朱海兰. 植物非生物逆境胁迫DREB/CBF转录因子的研究进展[J]. 林业科学,2011,47(1):124-134
[2] 张麒,陈静,李俐,等. 植物AP2/ERF转录因子家族的研究进展[J]. 生物技术通报,2018,34(8):1-7
[3] AMALRAJ A,LUANG S,KUMAR M Y,et al. Change of Function of the Wheat Stress-responsive Transcriptional Repressor TaRAP2. 1L by Repressor Motif Modification[J]. Plant Biotechnol J,2016,14(2):820-832
[4] ZHUANG J,CAI B,PENG R H,et al. Genome-wide Analysis of the AP2/ERF Gene Family in Populus trichocarpa[J]. Biochemical&Biophysical Research Communications,2008,371(3):468-474
[5] MARSCH-MARTINEZ N,GRECO R,BECKER J D,et al. BOLITA,an Arabidopsis AP2/ERF-like Transcription Factor that Affects Cell Expansion and Proliferation Differentiation Pathways[J]. Plant Molecular Biology,2006,62 (6):825-843
[6] STOCKINGER E J,MAO Y,REGIER M K,et al. Arabidopsis thaliana CBF1 Encodes an AP2 domain-containing Transcriptional Activator that Binds to the C-repeat/DRE,a Cis-acting DNA Regulatory Element that Stimulates Transcription in Response to Low Temperature and Water Deficit[J]. Proceedings of the National Academy Sciences,USA,1997,94(3):1035-1040
[7] SARAH F,MICHAEL F. Thomashow. Arabidopsis Transcriptome Profiling Indicates that Multiple Regulatory Pathways are Activated during Cold Acclimation in Addition to the CBF Cold Response Athway[J]. The Plant Cell,2002,14(8):1675-1690
[8] LIU J G,ZHANG Z,QIN Q L,et al. Isolated and Characterization of a cDNA Encoding Ethylene-responsive Element Binding Protein (EREBP)/AP2-type Protein,RCBF2,in Oryza sativa L.[J]. Biotechnology Letters,2007,29(1):165-173
[9] 刘强,张贵友,陈受宜,等. 植物转录因子的结构与调控作用[J]. 科学通报,2000,45(14):1465-1474
[10] YAMAGUCHI S K,SHINOZAKI K,KAZUK,et al. Transcriptional Regulatory Networks in Cellular Responses and Tolerance to Dehydration and Cold Stresses[J]. Annual Review of Plant Physiology,2006,57(1):781-803
[11] 王凯悦,陈芳泉,黄五星,等. 植物干旱胁迫响应机制研究进展[J]. 中国农业科技导报,2019,21(2):19-25
[12] LIU Q,KASUGA M,SAKUMA Y. Two Transcription Factors,DREB1 and DREB2,with an EREBP/AP2 DNA Binding Domain Separate two Cellular Signal Transduction Pathways in Drought and Low-temperature-responsive Gene Expression,Respectively,in Arabidopsis[J]. The Plant Cell,1998,10 (8):1391-1406
[13] ZHANG G Y,CHEN M,LI L C,et al. Overexpression of the Soybean GmERF3 Gene,an AP2/ERF Type Transcription Factor for Increased Tolerances to Salt,Drought,and Diseases in Transgenic Tobacco[J]. Journal of Experimental Botany,2009,60(13):3781-3796
[14] 翟莹,张军,赵艳,等. 大豆5个新发现ERF基因的生物信息学及表达分析[J]. 浙江农业学报,2016,28(10):61644-61649
[15] 赵艳红,郎明林,王小龙,等. 纤毛鹅观草DREB类基因RcDREB1的克隆及其蛋白结合干旱应答元件DRE的功能验证[J]. 植物遗传资源学报,2013,14(5):857-863
[16] XU Z S,XIA L Q,CHEN M,et al. Isolation and Molecular Characterization of the Triticum aestivum L. Ethylene-responsive Factor 1(TaERF1) that Increases Multiple Stress Tolerance[J]. Plant Molecular Biology,2007,65(6):719-732
[17] XIONG H Y,YU J P,LI Z C,et al. Natural Variation in OsLG3 Increases Drought Tolerance in Rice by Inducing ROS Scavenging[J]. Plant Physiology,2018,178(1):451-467
[18] ZHANG H,ZHANG J,QUAN R,et al. EAR Motif Mutation of Rice OsERF3 Alters the Regulation of Ethylene Biosynthesis and Drought Tolerance[J]. Planta,2013,237(6):1443-1451
[19] 马艳红,刘旭婷,张旭婷,等.蒙古冰草MYB转录因子基因的序列分析[J]. 基因组学与应用生物学,2019,38(5):2167-2174
[20] 范菠菠,张学峰,马艳红,等. 与蒙古冰草抗旱相关的NAC转录因子生物信息学及其表达分析[J]. 草地学报,2021,29(6):1183-1192
[21] GASTEIGER E,HOOGLAND C,GATTIKER A,et al. Protein Identification and Analysis Tools on the ExPASy Server[M]. To towa:The Proteomics Protocols Handbook,Human Press,2005:571-607
[22] CHOU K C,SHEN H B. Cell-PLoc a Package of Web Servers for Predicting Subcellular Localization of Proteins in Various Organisms[J]. Nature Protocols,2008,3(2):153-162
[23] BAILEY T L,JOHNSON J,GRANT C E, et al. The MEME Suite[J]. Nucleic Acids Research,2015,43(1):39-49
[24] CROOKS G E,HON G,CHANDONIA J M,et al. Weblogo:a Sequence Logo Generator[J]. Genome Research,2004,14(04):1188-1190
[25] KUMAR S,STECHER G,TAMURA K. MEGA7:Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets[J]. Molecular Biology & Evolution,2015,33(7):1870-1874
[26] HE Z L,ZHANG H K,GAO S H,et al. Evolview v2:an Online Visualization and Management Tool for Customized and Annotated Phylogenetic Trees[J]. Nucleic Acids Research,2016,44(1):236-241
[27] 刘文平. 玉米抗旱相关基因的挖掘及其功能鉴定[D]. 哈尔滨:东北农业大学,2020:45-56
[28] ZHANG G,CHEN M,CHEN X,et al. Isolation and Characterization of a Novel EAR-motif-containing Gene GmERF4 from Soybean (Glycine max L.)[J]. Molecular Biology Reports,2010,37(2):809-818
[29] 翟莹,赵艳,杨晓杰,等. 大豆乙烯响应因子GmERF6的功能分析[J]. 生物技术通报,2013,12(5):73-77
[30] 贺文辉. 马铃薯ERF1基因克隆及其功能研究[D]. 兰州:甘肃农业大学,2014:44-47
[31] 刘秉焱,韩翠英,刘虎岐,等. 4个小麦抗旱相关转录因子基因的表达及其与抗旱生理生化指标的相关性[J]. 西北农业学报,2016,25(4):530-537
[32] Cheng M C,HSIEH E J,CHEN J H,et al. Arabidopsis RGLG2,Functioning as a RING E3 Ligase,Interacts with AtERF53 and Negatively Regulates the Plant Drought Stress Response[J]. Plant Physiology,2012,158(1):363-375
[33] OHTA M,MATSUI K,HIRATSU K,et al. Repression Domains of Class II ERF Transcriptional Repressors Share an Essential Motif for Active Repression[J]. The Plant Cell,2001,13(8):1959-1968
[34] LI Z,ZHANG L,YU Y,et al. The Ethylene Response Factor AtERF11 that is Transcriptionally Modulated by the bZIP Transcription Factor HY5 is a Crucial Repressor for Ethylene Biosynthesis in Arabidopsis[J]. The Plant Journal,2011,68(1):88-99
[35] LIVAK K J,SCHMITTGEN T D. Analysis of Relative Gene Expression Data Using Real-time Quantitative PCR and the 2^-ΔΔCT Method[J]. Methods. 2001,25(4):402-408
[36] 张计育,王庆菊,郭忠仁,等. 植物AP2/ERF类转录因子研究进展[J]. 遗传,2012,34(7):44-56
[37] 苟艳丽,张乐,郭欢,等. 植物AP2/ERF类转录因子研究进展[J]. 草业科学,2020,37(6):1150-1159
[38] 孙崇源,崔瑞凡,王瑞阳,等. 大豆ERF家族基因生物信息学分析及其对低磷胁迫的响应[J]. 大豆科学,2021,40(6):748-758
[39] 王丽娟,王毅,陆斌,等. 油橄榄AP2/ERF转录因子鉴定及水胁迫表达分析[J/OL]. 广西植物,https://kns.cnki.net/kcms/detail/45.1134.Q.20210818.1342.004.html,2021-08-18/2022-4-20
[40] NAKANO T,SUZUKI K,FUJIMURA T,et al. Genome-wide Analysis of the ERF Gene Family in Arabidopsis and Rice[J]. Plant Physiology,2006,140(1):411-432
[41] 赵雪惠,王庆杰,李晨,等. 桃ERF转录因子家族生物信息学分析及芽萌发相关基因筛选[J]. 植物学报,2018,53(5):612-624
[42] 沈兵琪,高晓宇,王大玮,等. 苹果DREB转录因子家族全基因组鉴定与分析[J]. 西北植物学报,2017,37(3):460-469
[43] FUJIMOTO S Y,OHTA M,USUI,et al. Arabidopsis Ethylene-Responsive Element Binding Factors Act as Transcriptional Activators or Repressors of GCC Box-Mediated Gene Expression[J]. The Plant Cell,2000,12(3):393-404
[44] 王芳芳,杨江伟,朱熙,等. 马铃薯StERF109基因的生物信息学及表达分析[J]. 农业生物技术学报,2021,29(11):2087-2098
[45] 林世扬,颜彦,田丽波,等. 木薯转录因子MeERF117的克隆及表达分析[J/OL]. 分子植物育种,http://kns.cnki.net/kcms/detail/46.1068.S.20220330.1619.010.html,2022-03-31/2022-05-10
[46] 赵云祥,徐兆师,陈明,等. 小麦ERF类转录因子W17的结合特异性及亚细胞定位分析[J]. 中国农业科学,2008,41(6):1575-1582
[47] 刘霖,许睿儿,程紫涵,等. 小黑杨ERF723基因的克隆表达及生物信息学分析[J]. 山西农业大学学报(自然科学版),2021,41(6):24-31
[48] 陈珂,张君,杨树琼,等. 绿豆AP2/ERF转录因子家族全的生物信息学鉴定与特征分析[J].分子植物育种,2020,18(20):6605-6617
[49] 高春艳,吴芮,袁玉,等. 植物AP2/ERF转录因子及其在非生物胁迫应答中的作用[J]. 江汉大学学报(自然科学版),2017,45(3):236-240
[50] 赵梦雨,杨迪,郝彦蓉,等. 苦荞转录因子FtDREB6基因克隆及其抗旱功能鉴定[J]. 植物遗传资源学报,2022,23(4):1132-1142
[51] 赵彦,陈雪英,石凤敏,等. 蒙古冰草MwDREB3基因的克隆及表达分析[J]. 草地学报,2015,23(2):377-382
[52] YU Y W,YANG D X,ZHOU S R,et al. The Ethylene Response Factor OsERF109 Negatively Affects Ethylene Biosynthesis and Drought Tolerance in Rice[J]. Protoplasma,2017,(254):401-408

Bioinformatics and Expression Analysis of ERF Transcription Factor in Agropyron mongolicum Keng

蒙古冰草ERF转录因子生物信息学及其表达分析

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