小麦抗逆相关转录因子DREB密码子偏好性特征分析
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摘要
DREB(dehydration responsive element binding)转录因子在植物抵抗干旱、高盐、低温等非生物逆境中发挥着重要作用。为探究普通小麦抗逆相关转录因子DREB密码子的偏好性特征,本研究运用CodonW、CHIPS和CUSP软件程序分析了小麦DREB基因的密码子使用特性,并与13种植物的DREB密码子偏性进行比较。结果表明,小麦DREB基因主要偏好以GC结尾的密码子;根据RSCU值,确定小麦DREB基因的高频密码子有14个;不同作物间DREB基因的密码子选用偏好性存在一定差异;基于DREB编码序列的聚类分析比基于密码子使用偏性聚类分析更能准确地反映物种间的亲缘关系;属于真核生物的酵母菌比属于原核生物的大肠杆菌更适宜作为DREB基因表达的异源受体。小麦DREB与模式植物基因组之间密码子使用偏性差异较小,拟南芥可能比烟草和番茄更适合作为该基因转基因研究的理想受体。小麦DREB密码子偏性分析为该基因的异源表达及分子遗传研究提供了一定的理论依据。
DREB transcription factors play an important role in plant resistance to abiotic stresses,such as drought,high salt and low temperature.In order to explore the codon bias of stress-resistant related transcription factor DREB in wheat,in this study the DREB were analyzed with CodonW,CHIPS and CUSP programs,compared with DREB from 13 plant species.The results showed that TaDREB was bias toward the synonymous codons with G and C.According to the RSCU value,14 codons showed high-frequency.Comparison of the codon usage preference of homologous genes with other crops suggests that there is a certain difference in codon usage preference among DREB genes in different crops.The cluster analysis based on DREB coding sequences can more accurately reflect the geneticrelationship between species,compared with the biased cluster analysis based on codon usage.Based on the codon bias result,the eukaryote yeast expression system is more suitable for heterologous expression of TaDREBthan the prokaryote E.coli.There is less difference in codon usage bias between TaDREBand model plant genomes.Arabidopsis thalianais more suitable for transgenesis of this than Nicotiana tabacumand Lycopersicon esculentum Mill.This analysis of wheat DREB codon bias provides a theoretical basis for the heterologous expression and molecular genetic studies of this gene.
DREB transcription factors play an important role in plant resistance to abiotic stresses,such as drought,high salt and low temperature.In order to explore the codon bias of stress-resistant related transcription factor DREB in wheat,in this study the DREB were analyzed with CodonW,CHIPS and CUSP programs,compared with DREB from 13 plant species.The results showed that TaDREB was bias toward the synonymous codons with G and C.According to the RSCU value,14 codons showed high-frequency.Comparison of the codon usage preference of homologous genes with other crops suggests that there is a certain difference in codon usage preference among DREB genes in different crops.The cluster analysis based on DREB coding sequences can more accurately reflect the geneticrelationship between species,compared with the biased cluster analysis based on codon usage.Based on the codon bias result,the eukaryote yeast expression system is more suitable for heterologous expression of TaDREBthan the prokaryote E.coli.There is less difference in codon usage bias between TaDREBand model plant genomes.Arabidopsis thalianais more suitable for transgenesis of this than Nicotiana tabacumand Lycopersicon esculentum Mill.This analysis of wheat DREB codon bias provides a theoretical basis for the heterologous expression and molecular genetic studies of this gene.
引文
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[17]赵洋,刘振,杨培迪,等.茶树CsActin1基因密码子偏性分析[J].茶叶通讯,2014,41(4):14.ZHAO Y,LIU Z,YANG P D,et al.Analysis of codon bias of CsActin1 of Camellia sinesis[J].Journal of Tea Communication,2014,41(4):14.
[18]WONG G K,WANG J,TAO L,et al.Compositional gradients in Gramineae genes[J].Genome Research,2002,12:851.
[19]周晓明,赵慧芳,陆嘉良,等.甲型流感病毒基因变异与生存选择压力相关性分析[J].中华传染病杂志,2005,23(4):221.ZHOU X M,ZHAO H F,LU J L,et al.Correlation analysis of type A influenza virus genetic variation characteristic with survival selective pressure[J].Chinese Journal of Infectious Diseases,2005,23(4):221.
[20]CHIAPELLO H,LISACEK F,CABOCHE M,et al.Codon usage and gene function are related in sequences of Arabidopsis thaliana[J].Gene,1998,209(1-2):GC1-GC38.
[21]王海波,郭俊云,姚晴晴,等.植物质体型ω-3脂肪酸去饱和酶7基因的密码子偏性分析[J].基因组学与应用生物学,2015,34(11):2448.WANG H B,GUO J Y,YAO Q Q,et al.Codon bias analysis of plant typeω-3fatty acid desaturase 7gene[J].Genomics ang Aplied Biology,2015,34(11):2448.
[22]MURRAY E E,LOTZER J,EBERLE M.Codon usage in plant genes[J].Nucleic Acids Research,1989,17(2):477.
[23]NOVEMBRE J A.Accounting for background nucleotide composition when measuring codon usage bias[J].Molecular Biology&Evolution,2002,19(8):1390.
[24]赖瑞联,林玉玲,钟春水,等.龙眼生长素受体基因TIR1密码子偏好性分析[J].园艺学报,2016,43(4):775.LAI R L,LIN Y L,ZHONG C S,et al.Analysis of codon bias of auxin receptor gene TIR1in Dimocarpus longan[J].Acta Horticulturae Sinica,2016,43(4):775.
[25]晁岳恩,吴政卿,杨会民,等.11种植物psbA基因的密码子偏好性及聚类分析[J].核农学报,2011,25(5):929.CHAO Y E,WU Z Q,YANG H M,et al.Cluster analysis and codon usage bias studieson psbA genes from 11plant species[J].Journal of Nuclear Agricultural Sciences,2011,25(5):929.
[26]WANG J W,YANG F P,CHEN X Q.Induced expression of DREB transcriptional factor and study on its physiologycal effects of drought tolerance in transgenic wheat[J].Acta Genetica Sinica,2006,33(5):468.
[2]AN D,MA Q,YAN W,ZHOU W,et al.Divergent regulation of CBF regulon on cold tolerance and plant phenotype in cassava over expressing Arabidopsis CBF3 gene[J].Front Plant Sci,2016,7:1866.
[3]MATSUKURA S,MIZOI J,YOSHIDA T,et al.Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes[J].Molecular Genetics Genomics,2010,283:185.
[4]LIAO X,GUO X,WANG Q,et al.Overexpression of MsDREB6.2 results in cytokinin-deficient developmental phenotypes and enhances drought tolerance in transgenic apple plants[J].Palnt Journal,2017,89:510.
[5]周伟,吴宪,贾承国,等.山葡萄转录因子基因VaDREB的克隆及其抗逆功能分析[J].植物生理学报,2014,50(10):1563.ZHOU W,WU X,JIA C G,et al.Cloning and analysis of resistance function of VaDREBtranscription factor fromVitis amurensis[J].Plant Physiology Journal,2014,50(10):1563.
[6]KIDOKORO S,WATANABE K,OHORI T,et al.Soybean DREB1/CBF-type transcription factors function in heat and drought as well as cold stress-responsive gene expression[J].Plant Journal,2015,81:505.
[7]QIN F,SAKUMA Y,LI J,et al.Cloning and functional analysis of a novel DREB1/CBF transcription factor involved in cold-responsive gene expression in Zea mays L.[J].Plant Cell Physiology,2004,45(8):1042.
[8]MONDINI L,NACHIT M M,PAGNOTTA M A.Allelic variants in durum wheat(Triticum turgidum L.var.durum)DREBgenes conferring tolerance to abiotic stresses[J].Molecular Genetics Genomics,2015,290(2):531.
[9]吴宪明,吴松峰,任大明,等.密码子偏性的分析方法及相关研究进展[J].遗传,2007,29(4):420.WU X M,WU S F,REN D M,et al.The analysis method and progress in the study of codon bias[J].Hereditas,2007,29(4):420.
[10]LIU Q P,HU H C,WANG H.Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice(Oryza sativa L.)[J].Molecular Genetics and Genomics,2015,290(2):650.
[11]MUHAMMAD Y K B,ABDUL G K,MUHAMMAD D.The relationship between codon usage bias and salt resistant genes in Arabidopsis thaliana and Oryza sativa[J].Pure&Applied Biology,2012,1(2):48.
[12]续晨,蔡小宁,钱保俐,等.葡萄基因组密码子使用偏好模式研究[J].西北植物学报,2012,32(2):410.XU C,CAI X N,QIAN B L,et al.Codon usage bias in Vitis vinifera[J].Acta Botanica Boreali-occidentalia Sinica,2012,32(2):410.
[13]张乐,金龙国,罗玲,等.大豆基因组和转录组的核基因密码子使用偏好性分析[J].作物学报,2011,37(6):966.ZHANG L,JIN L G,LUO L,et al.Analysis of nuclear gene codon bias on soybean genome and transcriptome[J].Acta Agronomica Sinica,2011,37(6):966.
[14]LIU Q,FENG Y,XUE Q.Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa[J].Mitochondrion,2004,4(4):313.
[15]时慧,王玉,杨路成,等.茶树抗寒调控转录因子ICE1密码子偏性分析[J].园艺学报,2012,39(7):1348.SHI H,WANG Y,YANG L C,et al.Analysis of codon bias of the cold regulated transcription factor ICE1in tea plant[J].Acta Horticulturae Sinica,2012,39(7):1348.
[16]李平,白云凤,冯瑞云,等.籽粒苋苹果酸酶(NAD-ME)基因密码子偏好性分析[J].应用与环境生物学报,2011,17(1):13.LI P,BAI Y F,FENG R Y,et al.Analysis of codon bias of NAD-ME gene in Amaranthus hypochondriacus[J].Chinese Journal of Applied and Environmental Biology,2011,17(1):13.
[17]赵洋,刘振,杨培迪,等.茶树CsActin1基因密码子偏性分析[J].茶叶通讯,2014,41(4):14.ZHAO Y,LIU Z,YANG P D,et al.Analysis of codon bias of CsActin1 of Camellia sinesis[J].Journal of Tea Communication,2014,41(4):14.
[18]WONG G K,WANG J,TAO L,et al.Compositional gradients in Gramineae genes[J].Genome Research,2002,12:851.
[19]周晓明,赵慧芳,陆嘉良,等.甲型流感病毒基因变异与生存选择压力相关性分析[J].中华传染病杂志,2005,23(4):221.ZHOU X M,ZHAO H F,LU J L,et al.Correlation analysis of type A influenza virus genetic variation characteristic with survival selective pressure[J].Chinese Journal of Infectious Diseases,2005,23(4):221.
[20]CHIAPELLO H,LISACEK F,CABOCHE M,et al.Codon usage and gene function are related in sequences of Arabidopsis thaliana[J].Gene,1998,209(1-2):GC1-GC38.
[21]王海波,郭俊云,姚晴晴,等.植物质体型ω-3脂肪酸去饱和酶7基因的密码子偏性分析[J].基因组学与应用生物学,2015,34(11):2448.WANG H B,GUO J Y,YAO Q Q,et al.Codon bias analysis of plant typeω-3fatty acid desaturase 7gene[J].Genomics ang Aplied Biology,2015,34(11):2448.
[22]MURRAY E E,LOTZER J,EBERLE M.Codon usage in plant genes[J].Nucleic Acids Research,1989,17(2):477.
[23]NOVEMBRE J A.Accounting for background nucleotide composition when measuring codon usage bias[J].Molecular Biology&Evolution,2002,19(8):1390.
[24]赖瑞联,林玉玲,钟春水,等.龙眼生长素受体基因TIR1密码子偏好性分析[J].园艺学报,2016,43(4):775.LAI R L,LIN Y L,ZHONG C S,et al.Analysis of codon bias of auxin receptor gene TIR1in Dimocarpus longan[J].Acta Horticulturae Sinica,2016,43(4):775.
[25]晁岳恩,吴政卿,杨会民,等.11种植物psbA基因的密码子偏好性及聚类分析[J].核农学报,2011,25(5):929.CHAO Y E,WU Z Q,YANG H M,et al.Cluster analysis and codon usage bias studieson psbA genes from 11plant species[J].Journal of Nuclear Agricultural Sciences,2011,25(5):929.
[26]WANG J W,YANG F P,CHEN X Q.Induced expression of DREB transcriptional factor and study on its physiologycal effects of drought tolerance in transgenic wheat[J].Acta Genetica Sinica,2006,33(5):468.