2025年 01期

Bioinformatics Identification and Analysis of Ethylene Responsive Factor Subfamily in Maize

摘要(Abstract):

为了全面了解玉米APETALA2/乙烯响应因子(AP2/ERF)超家族中ERF亚家族成员在玉米生长发育和逆境过程中的作用,利用生物信息学手段鉴定和分析玉米Zea mays L.B73基因组ERF亚家族成员。结果表明:共鉴定到87个ERF基因且不均匀地分布在玉米的10条染色体上,蛋白序列长度为124~603 aa,蛋白质分子质量为13.23~65.44 kDa,理论等电点为4.44~10.84,亚细胞定位于细胞核;进化树分析显示,ERF基因被分为5个组,各组内的基因结构和保守基序的数量、分布等相似,但各组之间存在较大的差异,多数没有内含子,有内含子的基因占比为20.69%; ERF亚家族成员共有10个保守基序,其中前2个保守基序最为保守,且通常以串联方式存在于多数ERF亚家族成员中;启动子分析显示ZmERF基因含有大量光响应、激素响应、胁迫响应和生长发育相关元件,表明玉米ERF亚家族成员在玉米生长发育及非生物胁迫、生物胁迫方面发挥作用。

关键词(KeyWords): 生物信息学;玉米;乙烯响应因子;转录因子;

基金项目(Foundation): 国家自然科学基金项目(41800333)

作者(Author): 李焰榕,谭孝婷,车荣会

DOI: 10.13349/j.cnki.jdxbn.20240423.001

参考文献(References):

[1] BOYER J S.Plant productivity and environment[J].Science,1982,218(4571):443.

[2] DIMOVA D K,STEVAUX O,FROLOV M V,et al.Cell cycle-dependent and cell cycle-independent control of transcription by the Drosophila E2F/RB pathway[J].Genes & Development,2003,17(18):2308.

[3] SHARMA M K,KUMAR R,SOLANKE A U,et al.Identification,phylogeny,and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato[J].Molecular Genetics and Genomics,2010,284(6):455.

[4] JIN J P,TIAN F,YANG D C,et al.PlantTFDB 4.0:toward a central hub for transcription factors and regulatory interactions in plants[J].Nucleic Acids Research,2017,45(D1):D1040.

[5] SINGH K,FOLEY R C,O?ATE-SáNCHEZ L.Transcription factors in plant defense and stress responses[J].Current Opinion in Plant Biology,2002,5(5):430.

[6] SEO E,CHOI D.Functional studies of transcription factors involved in plant defenses in the genomics era[J].Briefings in Functional Genomics,2015,14(4):260.

[7] MIZOI J,SHINOZAKI K,YAMAGUCHI-SHINOZAKI K.AP2/ERF family transcription factors in plant abiotic stress responses[J].Biochimica et Biophysica Acta,2012,1819(2):86.

[8] RIECHMANN J L,HEARD J,MARTIN G,et al.Arabidopsis transcription factors:genome-wide comparative analysis among eukaryotes[J].Science,2000,290(5499):2105.

[9] 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(2):411.

[10] SWAMINATHAN K,PETERSON K,JACK T.The plant B3 superfamily[J].Trends in Plant Science,2008,13(12):647.

[11] ZHUANG J,CAI B,PENG R H,et al.Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa[J].Biochemical and Biophysical Research Communications,2008,371(3):468.

[12] LICAUSI F,GIORGI F M,ZENONI S,et al.Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera[J].BMC Genomics,2010,11:719.

[13] SAKUMA Y,LIU Q,DUBOUZET J G,et al.DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs,trans-cription factors involved in dehydration- and cold-inducible gene expression[J].Biochemical and Biophysical Research Communications,2002,290(3):998.

[14] YAMAGUCHI-SHINOZAKI K,SHINOZAKI K.Characterization of the expression of a desiccation-responsive rd29 gene of Arabidopsis thalianaand analysis of its promoter in transgenic plants[J].Molecular Genetics and Genomics,1993,236(2/3):331.

[15] STOCKINGER E J,GILMOUR S J,THOMASHOW M F.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 of Sciences of the United States of America,1997,94(3):1035.

[16] JIANG C,IU B,SINGH J.Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus[J].Plant Molecular Biology,1996,30(3):679.

[17] YAMAGUCHI-SHINOZAKI K,SHINOZAKI K.A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought,low-temperature,or high-salt stress[J].Plant Cell,1994,6(2):251.

[18] OHME-TAKAGI M,SHINSHI H.Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element[J].Plant Cell,1995,7(2):173.

[19] YANG Z,TIAN L N,LATOSZEK-GREEN M,et al.Arabidopsis ERF4 is a transcriptional repressor capable of modulating ethylene and abscisic acid responses[J].Plant Molecular Biology,2005,58(4):585.

[20] YAO Y,HE R J,XIE Q L,et al.ETHYLENE RESPONSE FACTOR 74 (ERF74) plays an essential role in controlling a respiratory burst oxidase homolog D (RbohD)-dependent mechanism in response to different stresses in Arabidopsis[J].New Phytologist,2017,213(4):1667.

[21] PARK H Y,SEOK H Y,WOO D H,et al.AtERF71/HRE2 transcription factor mediates osmotic stress response as well as hypoxia response in Arabidopsis[J].Biochemical and Biophysical Research Communications,2011,414(1):135.

[22] 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.

[23] YANG C Y,HSU F C,LI J P,et al.The AP2/ERF transcription factor AtERF73/HRE1 modulates ethylene responses during hypoxia in Arabidopsis[J].Plant Physiology,2011,156(1):202.

[24] HSIEH E J,CHENG M C,LIN T P.Functional characterization of an abiotic stress-inducible transcription factor AtERF53 in Arabidopsis thaliana[J].Plant Molecular Biology,2013,82(3):223.

[25] YU Y,YU M,ZHANG S X,et al.Transcriptomic identification of wheat AP2/ERF transcription factors and functional characterization of TaERF-6-3A in response to drought and salinity stresses[J].International Journal of Molecular Sciences,2022,23(6):3272.

[26] RONG W,QI L,WANG A Y,et al.The ERF transcription factor TaERF3 promotes tolerance to salt and drought stresses in wheat[J].Plant Biotechnology Journal,2014,12(4):468.

[27] ZHANG L,LIU P,WU J,et al.Identification of a novel ERF gene,TaERF8,associated with plant height and yield in wheat[J].BMC Plant Biology,2020,20(1):263.

[28] JIN Y,PAN W Y,ZHENG X F,et al.OsERF101,an ERF family transcription factor,regulates drought stress response in reproductive tissues[J].Plant Molecular Biology,2018,98(1/2):51.

[29] LEE D K,JUNG H,JANG G,et al.Overexpression of the OsERF71 transcription factor alters rice root structure and drought resistance[J].Plant Physiology,2016,172(1):575.

[30] LOUREN?O T F,SERRA T S,CORDEIRO A M,et al.The rice E3-Ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 modulates the expression of ROOT MEANDER CURLING:a gene involved in root mechanosensing,through the interaction with two ETHYLENE-RESPONSE FACTOR transcription factors[J].Plant Physiology,2015,169(3):2275.

[31] RIVERO R M,MITTLER R,BLUMWALD E,et al.Developing climate-resilient crops:improving plant tolerance to stress combination[J].Plant Journal,2022,109(2):373.

[32] 曲悦,王姝瑶,郝鑫,等.盐胁迫诱导植物交叉适应及其信号转导[J].植物生理学报,2022,58(6):1045.

[33] BAILLO E H,KIMOTHO R N,ZHANG Z B,et al.Transcription factors associated with abiotic and biotic stress tolerance and their potential for crops improvement[J].Genes (Basel),2019,10(10):771.

[34] WANG J Z,ZHOU J X,ZHANG B L,et al.Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on sorghum[J].Journal of Integrative Plant Biology,2011,53(3):212.

[35] DIANE JOFUKU K,DEN BOER B G,VAN MONTAGU M,et al.Control of Arabidopsis flower and seed development by the homeotic gene APETALA2[J].Plant Cell,1994,6(9):1211.

[36] MISHRA S,PHUKAN U J,TRIPATHI V,et al.PsAP2 an AP2/ERF family transcription factor from Papaver somniferum enhances abiotic and biotic stress tolerance in transgenic tobacco[J].Plant Molecular Biology,2015,89(1/2):173.

[37] FENG K,HOU X L,XING G M,et al.Advances in AP2/ERF super-family transcription factors in plant[J].Critical Reviews in Biotechnology,2020,40(6):750.

[38] 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.

[39] ROY S W,PENNY D.A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain[J].Molecular Biology and Evolution,2007,24(7):1447.

[40] SHU Y J,LIU Y,ZHANG J,et al.Genome-wide analysis of the AP2/ERF superfamily genes and their responses to abiotic stress in Medicago truncatula[J].Frontiers in Plant Science,2016,6:1247.

[41] HERNANDEZ-GARCIA C M,FINER J J.Identification and validation of promoters and cis-acting regulatory elements[J].Plant Science,2014,217/218:109.

[42] ZOU C,SUN K L,MACKALUSO J D,et al.Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana[J].Proceedings of the National Academy of Sciences of the United States of America,2011,108(36):14992.

[43] COLEBROOK E H,THOMAS S G,PHILLIPS A L,et al.The role of gibberellin signalling in plant responses to abiotic stress[J].Journal of Experimental Biology,2014,217(Pt 1):67.

[44] KAZAN K.Diverse roles of jasmonates and ethylene in abiotic stress tolerance[J].Trends in Plant Science,2015,20(4):219.

[45] TAO J J,CHEN H W,MA B,et al.The role of ethylene in plants under salinity stress[J].Frontiers in Plant Science,2015,6:1059.

[46] SAH S K,REDDY K R,LI J X.Abscisic acid and abiotic stress tolerance in crop plants[J].Frontiers in Plant Science,2016,7:571.

[47] NOLAN T M,BRENNAN B,YANG M R,et al.Selective autophagy of BES1 mediated by DSK2 balances plant growth and survival[J].Developmental Cell,2017,41(1):33.

[48] WILSON K,LONG D,SWINBURNE J,et al.A dissociation insertion causes a semidominant mutation that increases expression of TINY,an Arabidopsis gene related to APETALA2[J].Plant Cell,1996,8(4):659.

[49] CHUCK G,MUSZYNSKI M,KELLOGG E,et al.The control of spikelet meristem identity by the branched silkless1 gene in maize[J].Science,2002,298(5596):1238.

[50] KOMATSU M,CHUJO A,NAGATO Y,et al.FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets[J].Development,2003,130(16):3841.

[51] LIU M C,GOMES B L,MILA I,et al.Comprehensive profiling of ethylene response factor expression identifies ripening-associated ERF genes and their link to key regulators of fruit ripening in tomato[J].Plant Physiology,2016,170(3):1732.

[52] HAN Z Y,HU Y N,LV Y D,et al.Natural variation underlies differences in ETHYLENE RESPONSE FACTOR17 activity in fruit peel degreening[J].Plant Physiology,2018,176(3):2292.

[53] PARK D S,TILAHUN S,HEO J Y,et al.Quality and expression of ethylene response genes of “Daebong” persimmon fruit during ripening at different temperatures[J].Postharvest Biology and Technology,2017,133:57.

[54] MA R F,XIAO Y,LV Z Y,et al.AP2/ERF transcription factor,Ii049,positively regulates lignan biosynthesis in Isatis indigotica through activating salicylic acid signaling and lignan/lignin pathway genes[J].Frontiers in Plant Science,2017,8:1361.

[55] PAN Q F,WANG C Y,XIONG Z W,et al.CrERF5,an AP2/ERF transcription factor,positively regulates the biosynthesis of bisindole alkaloids and their precursors in Catharanthus roseus[J].Frontiers in Plant Science,2019,10:931.

[56] YU Z X,LI J X,YANG C Q,et al.The jasmonate-responsive AP2/ERF transcription factors AaERF1 and AaERF2 positively regulate artemisinin biosynthesis in Artemisia annua L.[J].Molecular Plant,2012,5(2):353.

[57] WELSCH R,MAASS D,VOEGEL T,et al.Transcription factor RAP2.2 and its interacting partner SINAT2:stable elements in the carotenogenesis of Arabidopsis leaves[J].Plant Physiology,2007,145(3):1073.

[58] AN J P,ZHANG X W,BI S Q,et al.The ERF transcription factor MdERF38 promotes drought stress-induced anthocyanin biosynthesis in apple[J].Plant Journal,2020,101(3):573.