辣椒BES1基因家族鉴定及表达分析
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摘要
BES1基因是油菜素内酯信号途径中的关键转录因子。为了解辣椒中BES1基因家族功能,以已测序辣椒CM334为试验材料,根据已公布辣椒基因组数据,本研究利用生物信息学方法对辣椒BES1基因家族进行鉴定,并对基因结构、结构域、系统进化关系、基因表达模式和生物非生物胁迫表达情况进行分析。结果表明,辣椒中有9个候选BES1基因,根据BES1基因结构可将其分为ClassⅠ和ClassⅡ2大类,ClassⅠ和ClassⅡ在结构上差异较大。辣椒BES1编码蛋白介于181～713个氨基酸范围内,分子量为20.22～78.23 kDa,等电点介于5.48～9.23。转录组数据分析发现,辣椒BES1基因在辣椒中表达具有差异性。在脱落酸、低温、高温、茉莉酸甲酯和疫病胁迫下CA04g20150和CA12g17430均被诱导上调,表明其在生物和非生物胁迫中发挥作用。本研究结果为进一步探究BES1基因家族调控植物抗逆的分子机制奠定了基础。
BES1 is the key transcription factors of brassinosteroid( BR) signaling. In order to understand the function of BES1 gene family in pepper,bioinformatic analysis was used to identify the BES1 gene family according to the released pepper whole-genome sequences. Gene structure,protein domain,phylogenetic relationship,gene expression pattern and biotic and abiotic stress were analyzed to characterize the function of BES1 gene family. The results showed that there were 9 candidate BES1 genes in pepper. According to the structure of BES1,they were divided into 2 categories:ClassⅠand ClassⅡ,with great difference in structure. The BES1 encoding proteins were range from 181 to 713 amino acids,the molecular weights of BES1 encoding proteins were 20.22 ～ 78.23 k Da,and the range of isoelectric point was5.48 ～ 9.23. The result of RNA-seq data indicated that the expression of the BES1 gene in pepper is different. Under the stress of ABA, cold, heat, Me and Phytophthora blight, both CA04 g20150 and CA12 g17430 were induced to upregulated,indicating that they may played a role in biotic and abiotic stress. The study laid foundation for exploring the molecular mechanism of the BES1 gene family regulating plant stress resistance.
BES1 is the key transcription factors of brassinosteroid( BR) signaling. In order to understand the function of BES1 gene family in pepper,bioinformatic analysis was used to identify the BES1 gene family according to the released pepper whole-genome sequences. Gene structure,protein domain,phylogenetic relationship,gene expression pattern and biotic and abiotic stress were analyzed to characterize the function of BES1 gene family. The results showed that there were 9 candidate BES1 genes in pepper. According to the structure of BES1,they were divided into 2 categories:ClassⅠand ClassⅡ,with great difference in structure. The BES1 encoding proteins were range from 181 to 713 amino acids,the molecular weights of BES1 encoding proteins were 20.22 ～ 78.23 k Da,and the range of isoelectric point was5.48 ～ 9.23. The result of RNA-seq data indicated that the expression of the BES1 gene in pepper is different. Under the stress of ABA, cold, heat, Me and Phytophthora blight, both CA04 g20150 and CA12 g17430 were induced to upregulated,indicating that they may played a role in biotic and abiotic stress. The study laid foundation for exploring the molecular mechanism of the BES1 gene family regulating plant stress resistance.
引文
[1] Clouse S D. Molecular genetic studies confirm the role of brassinosteroids in plant growth and development[J]. The Plant Journal:for Cell and Molecular Biology,1996,10(1):1-8
[2] Mandava N B. Plant growth-promoting brassinosteroids[J]. Annual Review of Plant Biology,1988,39(1):23-52
[3] Li J,Chory J. Brassinosteroid actions in plants[J]. Journal of Experimental Botany,1999,50(332):275-282
[4] He J X,Gendron J M,Sun Y,Gampala S S L,Gendron N,Sun C Q,Wang Z Y. BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses[J]. Science,2005,307(5715):1634
[5] Guo R F,Qian H M,Shen W S,Liu L H,Zhang M,Cai C X,Zhao Y T,Qiao J J,Wang Q M. BZR1 and BES1 participate in regulation of glucosinolate biosynthesis by brassinosteroids in Arabidopsis[J]. Journal of Experimental Botany,2013,64(8):2401
[6] Ryu H,Cho H,Bae W H,Wang I. Control of early seedling development by BES1/TPL/HDA19-mediated epigenetic regulation of ABI3[J]. Nature Communications,2014,5:4138
[7] Jiang J,Zhang C,Wang X. A recently evolved isoform of the transcription factor BES1 promotes brassinosteroid signaling and development in Arabidopsis thaliana[J]. The Plant Cell,2015,27(2):361-374
[8] Yin Y,Wang Z Y,Moragarcia S,Li J,Yoshida S,Asami T,Chory J. BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation[J]. Cell,2002,109(2):181-191
[9] Wang Z Y,Nakano T,Gendron J,He J,Chen M,Vafeados D,Yang Y,Fujioka S,Yoshida S,Asami T. Nuclear-localized BZR1mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis[J]. Developmental Cell,2002,2(4):505-513
[10] Kim T W,Wang Z Y. Brassinosteroid signal transduction from receptor kinases to transcription factors[J]. Annual Review of Plant Biology,2010,61(1):681-704
[11] Qin C,Yu C S,Shen Y,et al. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization[J]. Proceedings of the National Academy of Sciences,2014,111(14):5135-5140
[12] Kim S,Park M,Yeom S I,et al. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species[J]. Nature Genetics,2014,46(3):270-278
[13]魏小春,姚秋菊,原玉香,赵艳艳,王志勇,姜俊,蒋武生,张晓伟.辣椒CaWRKY13基因克隆及非生物胁迫下表达分析[J].分子植物育种,2016,14(10):2582-2588
[14] Xu Q,Dunbrack R L J. Assignment of protein sequences to existing domain and family classification systems:Pfam and the PDB[J].Bioinformatics,2012,28(21):2763-2772
[15] Artimo P,Jonnalagedda M,Arnold K,Baratin D,Csardi G,de Castro E,Duvaud S,FlegelⅤ,Fortier A,Gasteiger E,Grosdidier A,Hernandez C,IoannidisⅤ,Kuznetsov D,Liechti R,Moretti S,Mostaguir K,Redaschi N,Rossier G,XenariosⅠ,Stockinger H.ExPASy:SIB bioinformatics resource portal[J]. Nucleic Acids Research,2012,40:597-603
[16] Hu B,Jin J P,Guo A F,Zhang H,Luo J C,Gao G. GSDS 2.0:an upgraded gene feature visualization server[J]. Bioinformatics,2015,31(8):1296-1297
[17] Livak K J,Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔGtMethod[J].Methods,2001,25(4):402-408
[18] Wu P,Song X M,Wang Z,Duan W K,Hu R,Wang W L,Li Y,Hou X L. Genome-wide analysis of the BES1 transcription factor family in Chinese cabbage(Brassica rapa ssp. pekinensis)[J].Plant Growth Regulation,2016,80(3):291-301
[19]胡静静,李春金,杨启航,王彤,王振怡,宋小明.甘蓝型油菜BES1转录因子家族的鉴定及比较基因组学分析[J].分子植物育种,2017(6):2058-2065
[20] KhripachⅤ, ZhabinskiiⅤ, Groot A D. Twenty years of brassinosteroids:steroidal plant hormones warrant better crops for the XXI century[J]. Annals of Botany,2000,86(3):441-447
[21] Bajguz A,Hayat S. Effects of brassinosteroids on the plant responses to environmental stresses[J]. Plant Physiology&Biochemistry,2009,47(1):1-8
[22] Campos M L,Almeida M D,Rossi M L,Martinelli A P,Junior C G L,Figueira A,Vendramim J D,BeneditoⅤA,Peres L E P.Brassinosteroids interact negatively with jasmonates in the formation of anti-herbivory traits in tomato[J]. Journal of Experimental Botany,2009,60(15):4347
[23] Yang D H,Hettenhausen C,Baldwin I T,Wu J Q. BAK1 regulates the accumulation of jasmonic acid and the levels of trypsin proteinase inhibitors in Nicotiana attenuata's responses to herbivory[J].Journal of Experimental Botany,2011,62(2):641-652
[24] Sun Y,Fan X Y,Cao D M,Tang W,He K,Zhu J Y,Bai M Y,Zhu S,Oh E,Patil S,Kim T W,Ji H,Wong W H,Rhee S Y,Wang Z Y. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis[J].Developmental Cell,2010,19(5):765-777
[25] Yu X,Li L,Li L,Guo M,Chory J,Yin Y. Modulation of brassinosteroid-regulated gene expression by Jumonji domaincontaining proteins ELF6 and REF6 in Arabidopsis[J]. Proceedings of the National Academy of Sciences of the United States of America,2008,105(21):7618-7623
[26] Li Q F,Lu J,Yu J W,Zhang C Q,He J X,Liu Q Q. The brassinosteroid-regulated transcription factors BZR1/BES1 function as a coordinator in multisignal-regulated plant growth[J]. Biochim Biophys Acta,2018,1861(6):561-571
[27] Yu X,Li L,Zola J,Aluru M,Ye H,Foudree A,Guo H,Anderson S,Aluru S,Liu P,Rodermel S,Yin Y. A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana[J]. The Plant Journal:for Cell and Molecular Biology,2011,65(4):634-46
[28] Saito M,Kondo Y,Fukuda H. BES1 and BZR1 redundantly promote phloem and xylem differentiation[J]. Plant Cell Phsiology,2018,59(3):590-600
[2] Mandava N B. Plant growth-promoting brassinosteroids[J]. Annual Review of Plant Biology,1988,39(1):23-52
[3] Li J,Chory J. Brassinosteroid actions in plants[J]. Journal of Experimental Botany,1999,50(332):275-282
[4] He J X,Gendron J M,Sun Y,Gampala S S L,Gendron N,Sun C Q,Wang Z Y. BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses[J]. Science,2005,307(5715):1634
[5] Guo R F,Qian H M,Shen W S,Liu L H,Zhang M,Cai C X,Zhao Y T,Qiao J J,Wang Q M. BZR1 and BES1 participate in regulation of glucosinolate biosynthesis by brassinosteroids in Arabidopsis[J]. Journal of Experimental Botany,2013,64(8):2401
[6] Ryu H,Cho H,Bae W H,Wang I. Control of early seedling development by BES1/TPL/HDA19-mediated epigenetic regulation of ABI3[J]. Nature Communications,2014,5:4138
[7] Jiang J,Zhang C,Wang X. A recently evolved isoform of the transcription factor BES1 promotes brassinosteroid signaling and development in Arabidopsis thaliana[J]. The Plant Cell,2015,27(2):361-374
[8] Yin Y,Wang Z Y,Moragarcia S,Li J,Yoshida S,Asami T,Chory J. BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation[J]. Cell,2002,109(2):181-191
[9] Wang Z Y,Nakano T,Gendron J,He J,Chen M,Vafeados D,Yang Y,Fujioka S,Yoshida S,Asami T. Nuclear-localized BZR1mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis[J]. Developmental Cell,2002,2(4):505-513
[10] Kim T W,Wang Z Y. Brassinosteroid signal transduction from receptor kinases to transcription factors[J]. Annual Review of Plant Biology,2010,61(1):681-704
[11] Qin C,Yu C S,Shen Y,et al. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization[J]. Proceedings of the National Academy of Sciences,2014,111(14):5135-5140
[12] Kim S,Park M,Yeom S I,et al. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species[J]. Nature Genetics,2014,46(3):270-278
[13]魏小春,姚秋菊,原玉香,赵艳艳,王志勇,姜俊,蒋武生,张晓伟.辣椒CaWRKY13基因克隆及非生物胁迫下表达分析[J].分子植物育种,2016,14(10):2582-2588
[14] Xu Q,Dunbrack R L J. Assignment of protein sequences to existing domain and family classification systems:Pfam and the PDB[J].Bioinformatics,2012,28(21):2763-2772
[15] Artimo P,Jonnalagedda M,Arnold K,Baratin D,Csardi G,de Castro E,Duvaud S,FlegelⅤ,Fortier A,Gasteiger E,Grosdidier A,Hernandez C,IoannidisⅤ,Kuznetsov D,Liechti R,Moretti S,Mostaguir K,Redaschi N,Rossier G,XenariosⅠ,Stockinger H.ExPASy:SIB bioinformatics resource portal[J]. Nucleic Acids Research,2012,40:597-603
[16] Hu B,Jin J P,Guo A F,Zhang H,Luo J C,Gao G. GSDS 2.0:an upgraded gene feature visualization server[J]. Bioinformatics,2015,31(8):1296-1297
[17] Livak K J,Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔGtMethod[J].Methods,2001,25(4):402-408
[18] Wu P,Song X M,Wang Z,Duan W K,Hu R,Wang W L,Li Y,Hou X L. Genome-wide analysis of the BES1 transcription factor family in Chinese cabbage(Brassica rapa ssp. pekinensis)[J].Plant Growth Regulation,2016,80(3):291-301
[19]胡静静,李春金,杨启航,王彤,王振怡,宋小明.甘蓝型油菜BES1转录因子家族的鉴定及比较基因组学分析[J].分子植物育种,2017(6):2058-2065
[20] KhripachⅤ, ZhabinskiiⅤ, Groot A D. Twenty years of brassinosteroids:steroidal plant hormones warrant better crops for the XXI century[J]. Annals of Botany,2000,86(3):441-447
[21] Bajguz A,Hayat S. Effects of brassinosteroids on the plant responses to environmental stresses[J]. Plant Physiology&Biochemistry,2009,47(1):1-8
[22] Campos M L,Almeida M D,Rossi M L,Martinelli A P,Junior C G L,Figueira A,Vendramim J D,BeneditoⅤA,Peres L E P.Brassinosteroids interact negatively with jasmonates in the formation of anti-herbivory traits in tomato[J]. Journal of Experimental Botany,2009,60(15):4347
[23] Yang D H,Hettenhausen C,Baldwin I T,Wu J Q. BAK1 regulates the accumulation of jasmonic acid and the levels of trypsin proteinase inhibitors in Nicotiana attenuata's responses to herbivory[J].Journal of Experimental Botany,2011,62(2):641-652
[24] Sun Y,Fan X Y,Cao D M,Tang W,He K,Zhu J Y,Bai M Y,Zhu S,Oh E,Patil S,Kim T W,Ji H,Wong W H,Rhee S Y,Wang Z Y. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis[J].Developmental Cell,2010,19(5):765-777
[25] Yu X,Li L,Li L,Guo M,Chory J,Yin Y. Modulation of brassinosteroid-regulated gene expression by Jumonji domaincontaining proteins ELF6 and REF6 in Arabidopsis[J]. Proceedings of the National Academy of Sciences of the United States of America,2008,105(21):7618-7623
[26] Li Q F,Lu J,Yu J W,Zhang C Q,He J X,Liu Q Q. The brassinosteroid-regulated transcription factors BZR1/BES1 function as a coordinator in multisignal-regulated plant growth[J]. Biochim Biophys Acta,2018,1861(6):561-571
[27] Yu X,Li L,Zola J,Aluru M,Ye H,Foudree A,Guo H,Anderson S,Aluru S,Liu P,Rodermel S,Yin Y. A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana[J]. The Plant Journal:for Cell and Molecular Biology,2011,65(4):634-46
[28] Saito M,Kondo Y,Fukuda H. BES1 and BZR1 redundantly promote phloem and xylem differentiation[J]. Plant Cell Phsiology,2018,59(3):590-600