甜菜NAC转录因子鉴定及其在水分胁迫下的表达分析
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摘要
植物特异性NAC转录因子是植物特有的、最大的转录因子家族之一,在响应植物干旱胁迫反应等过程中发挥着重要作用。本研究以NAC保守结构域序列为检索序列通过HMM和BLAST在甜菜(Beta vulgaris)基因组数据中进行同源性搜索,对甜菜NAC转录因子基因(BvNAC)家族成员进行鉴定。利用ExPASy、MEGA 6.0、Mapinspect、GSDS 2.0、MEME等生物信息学分析工具对甜菜NAC转录因子家族成员进行蛋白质氨基酸组分和理化性质分析、系统进化关系分析、基因染色体定位及蛋白质结构域序列保守性预测;通过RNA-seq和qRT-PCR分析甜菜NAC基因在水分胁迫下的表达情况。结果表明:甜菜NAC家族基因共有52个成员,其中50个在9条染色体上不均等分布, 2个目前尚未定位;其编码的蛋白所含氨基酸残基数从48到711不等,其中17个为碱性蛋白质, 4个为亲水性蛋白质;系统进化分析将52个成员分为2类, Ⅰ类有38个成员, Ⅱ类有14个成员; NAC保守域分析表明同类成员有相近的保守元件,而外显子和内含子数目具有高变异性;在干旱胁迫下甜菜NAC家族成员中共有23个基因上调表达。研究结果为揭示甜菜耐旱分子机理和发掘甜菜耐旱基因提供了理论依据。
Plant-specific NAC transcription factors are one of the plant-specific and largest family of transcription factors and play an important role in response of plant to drought stress. In this study, the NAC conserved domain sequence was used as a search sequence to search for the homologous in sugar beet(Beta vulgaris) genome data by HMM and BLAST, and sugar beet NAC transcription factor family members were identified by using bioinformatics analysis tools such as ExPASy, MEGA 6.0, Mapinspect, GSDS 2.0, and MEME to analyze protein amino acid composition and physicochemical properties, phylogenetic relationship analysis, gene chromosomal localization, and protein domain sequence conservation prediction of beet NAC transcription factor family members. The expression of sugar beet NAC gene under water stress was analyzed by RNA-seq and qRT-PCR. The results showed that there were 52 members of sugar beet NAC family gene, 50 of which were unevenly distributed on 9 chromosomes, and 2 were not currently located. The encoded protein contained amino acid residues ranging from 48 to 711, of which 17 were basic proteins, four are hydrophilic proteins. The phylogenetic analysis divided 52 members into 2 categories, class Ⅰ had 38 members, and class Ⅱ had 14 members. NAC conserved domain analysis indicated that similar members had similar conserved elements, while the number of neutrons and introns had high variability. Under water stress, 23 genes were up-regulated in the NAC family members of sugar beet.
Plant-specific NAC transcription factors are one of the plant-specific and largest family of transcription factors and play an important role in response of plant to drought stress. In this study, the NAC conserved domain sequence was used as a search sequence to search for the homologous in sugar beet(Beta vulgaris) genome data by HMM and BLAST, and sugar beet NAC transcription factor family members were identified by using bioinformatics analysis tools such as ExPASy, MEGA 6.0, Mapinspect, GSDS 2.0, and MEME to analyze protein amino acid composition and physicochemical properties, phylogenetic relationship analysis, gene chromosomal localization, and protein domain sequence conservation prediction of beet NAC transcription factor family members. The expression of sugar beet NAC gene under water stress was analyzed by RNA-seq and qRT-PCR. The results showed that there were 52 members of sugar beet NAC family gene, 50 of which were unevenly distributed on 9 chromosomes, and 2 were not currently located. The encoded protein contained amino acid residues ranging from 48 to 711, of which 17 were basic proteins, four are hydrophilic proteins. The phylogenetic analysis divided 52 members into 2 categories, class Ⅰ had 38 members, and class Ⅱ had 14 members. NAC conserved domain analysis indicated that similar members had similar conserved elements, while the number of neutrons and introns had high variability. Under water stress, 23 genes were up-regulated in the NAC family members of sugar beet.
引文
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Bu QY,Jiang HL,Li CB,et al(2008).Role of the Arabidopsis thaliana NAC transcription factors ANAC019 and ANAC055 in regulating jasmonic acid-signaled defense responses.Cell Res,18(5):756-767
Christianson JA,Dennis ES,Llewellyn DJ,et al(2010).Ataf NAC transcription factors:regulators of plant stress signaling.Plant Signal Behav,5(4):428-432
Dai TT,Yao XZ,Lv LT,et al(2018).Cloning and droughtresistant function analysis of NAC4 gene in tobacco(Nicotiana tabacum).J Agric Biotechnol,26(5):764-773(in Chinese with English abstract)[代婷婷,姚新转,吕立堂等(2018).烟草NAC4基因的克隆及其抗旱功能分析.农业生物技术学报,26(5):764-773]
Hu HH,Dai MQ,Yao JL,et al(2006).Overexpressing a NAM,ATAF,and CUC(NAC)transcription factor enhances drought resistance and salt tolerance in rice.Proc Natl Acad Sci USA,103(35):12987-12992
Huang H,Wang Y,Wang SL,et al(2012).Transcriptome-wide survey and expression analysis of stress-responsive NACgenes in Chrysanthemum lavandulifolium.Plant Sci,193-194(3):18-27
Kim YS,Kim SG,Park JE,et al(2007).A membrane-bound NAC transcription factor regulates cell division in Arabidopsis.Plant Cell,18(1):3132-3144
Li GL,Wu HX,Wen L,et al(2011).Study on screening of drought resistance assessment indices and comprehensive evaluation of sugarbeet during seedling stage.Agric Res Arid Areas,29(4):69-74(in Chinese with English abstract)[李国龙,吴海霞,温丽等(2011).甜菜苗期抗旱鉴定指标筛选及其综合评价.干旱地区农业研究,29(4):69-74]
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Liu TM,Zhu SY,Tang QM,et al(2014).Identification of 32full-length NAC transcription factors in ramie(Boehmeria nivea L.Gaud)and characterization of the expression pattern of these genes.Mol Genet Genomics,289(4):675-684
Lu PL,Chen NZ,An R,et al(2006).A novel drought-inducible gene,ATAF1,encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis.Plant Mol Biol,63(2):289-305
Mao XG,Chen SS,Li A,et al(2014).Novel NAC transcription factor TaNAC67 confers enhanced multi-abiotic stress tolerances in Arabidopsis.PLoS ONE,9(1):e84359
Nakashima K,Tran LP,Nguyen DV,et al(2007).Functional analysis of a NAC-type transcription factor OsNAC6involved in abiotic and biotic stress-responsive gene expression in rice.Plant J,51(4):617-630
Nakashima K,Takasaki H,Mizoi J,et al(2012).NAC transcription factors in plant abiotic stress responses.Biochim Biophys Acta,1819(2):97-103
Nuruzzaman M,Manimekalai R,Sharoni AM,et al(2010).Genome-wide analysis of nac transcription factor family in rice.Gene,465(1):30-44
Ooka H,Tatoh K,Doi K,et al(2003).Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.DNA Res,10(6):239-247
Redillas MC,Jeong JS,Kim YS,et al(2012).The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions.Plant Biotechnol J,10(7):792-805
Sablowski RWM,Meyerowitz EM(1998).A Homolog of NOAPICAL MERISTEM,is an immediate target of the floral homeotic genes APETALA3/PISTILLATA.Cell,92(1):93-103
Shiriga K,Sharma R,Kumar K,et al(2014).Genome-wide identification and expression pattern of drought-responsive members of the NAC family in maize.Meta Gene,2(1):407-417
Shang HH,Li W,Zou CS,et al(2013).Analyses of the NACtranscription factor gene family in Gossypium raimondii ulbr:chromosomal location,structure,phylogeny,and expression patterns.J Integr Plant Biol,55(7):663-676
Souer E,Houwelingen AV,Kloos D,et al(1996).The NOAPICAL MERISTEM gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries.Cell,85(2):159-170
Sun LJ,Li DY,Zhang HJ,et al(2012).Functions of NACtranscription factors in biotic and abiotic stress responses in plants.Hereditas,34(8):993-1002(in Chinese with English abstract)[孙利军,李大勇,张慧娟等(2012).NAC转录因子在植物抗病和抗非生物胁迫反应中的作用.遗传,34(8):993-1002]
Takada S,Hibara K,Ishida T,et al(2001).The CUP-SHAPEDCOTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation.Development,128(7):1127-1135
Tran LP,Nakashima K,Sakuma Y,et al(2004).Isolation and functional analysis of Arabidopsis stress-inducible NACtranscription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress1 promoter.Plant Cell,16(9):2481-2498
Tran LP,Nishiyama R,Yamaguchi-Shinozaki K,et al(2010).Potential utilization of nac transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach.GM Crops,1(1):32-39
Wang FT,Lin RM,Xu SC(2010).Cloning and characterization of three NAC-like transcription factor genes in wheat.Genomics Appl Biol,29(4):639-645(in Chinese with English abstract)[王凤涛,蔺瑞明,徐世昌(2010).小麦3个NAC转录因子基因克隆与功能分析.基因组学与应用生物学,29(4):639-645]
Wang JY,Wang JP,Yuan H(2013).A Populus euphratica NAC protein regulating Na+/K+homeostasis improves salt tolerance in Arabidopsis thaliana.Gene,521(2):265-273
Wang RF,Hu YS,Gao WR,et al(2014).Functions of NACtranscription factors family in stress responses in plants.Plant Physiol J,50(10):1494-1500(in Chinese with English abstract)[王瑞芳,胡银松,高文蕊等(2014).植物NAC转录因子家族在抗逆响应中的功能.植物生理学报,50(10):1494-1500]
Wang ZJ,Jin L,Xu ZD,et al(2014).Bioinformatics analysis of gene LEC1 from Jatropha curcas.J Biol,31(4):68-72(in Chinese with English abstract)[王占军,金伦,徐忠东等(2014).麻风树LEC1基因的生物信息学分析.生物学杂志,31(4):68-72]
Wu YR,Deng ZY,Lai JB,et al(2010).Dual function of Arabidopsis ATAF1 in abiotic and biotic stress responses.Cell Res,1279-1290
Zhang MQ,Chen RK(2005).Crop Drought Resistance Molecular Physiology And Genetic Improvement.Beijing:Science Press,22-23(in Chinese)[张木清,陈如凯(2005).作物抗旱分子生理与遗传改良.北京:科学出版社,22-23]
Zheng X,Chen B,Lu G,et al(2009).Overexpression of a nac transcription factor enhances rice drought and salt tolerance.Biochem Biophys Res Commun,379(4):985-989
Bu QY,Jiang HL,Li CB,et al(2008).Role of the Arabidopsis thaliana NAC transcription factors ANAC019 and ANAC055 in regulating jasmonic acid-signaled defense responses.Cell Res,18(5):756-767
Christianson JA,Dennis ES,Llewellyn DJ,et al(2010).Ataf NAC transcription factors:regulators of plant stress signaling.Plant Signal Behav,5(4):428-432
Dai TT,Yao XZ,Lv LT,et al(2018).Cloning and droughtresistant function analysis of NAC4 gene in tobacco(Nicotiana tabacum).J Agric Biotechnol,26(5):764-773(in Chinese with English abstract)[代婷婷,姚新转,吕立堂等(2018).烟草NAC4基因的克隆及其抗旱功能分析.农业生物技术学报,26(5):764-773]
Hu HH,Dai MQ,Yao JL,et al(2006).Overexpressing a NAM,ATAF,and CUC(NAC)transcription factor enhances drought resistance and salt tolerance in rice.Proc Natl Acad Sci USA,103(35):12987-12992
Huang H,Wang Y,Wang SL,et al(2012).Transcriptome-wide survey and expression analysis of stress-responsive NACgenes in Chrysanthemum lavandulifolium.Plant Sci,193-194(3):18-27
Kim YS,Kim SG,Park JE,et al(2007).A membrane-bound NAC transcription factor regulates cell division in Arabidopsis.Plant Cell,18(1):3132-3144
Li GL,Wu HX,Wen L,et al(2011).Study on screening of drought resistance assessment indices and comprehensive evaluation of sugarbeet during seedling stage.Agric Res Arid Areas,29(4):69-74(in Chinese with English abstract)[李国龙,吴海霞,温丽等(2011).甜菜苗期抗旱鉴定指标筛选及其综合评价.干旱地区农业研究,29(4):69-74]
Li W,Wan Q,Liu FZ,et al(2015).Allelic variation of transcription factor genes NAC4 in Arachis species.Acta Agron Sin,41(1):31-41(in Chinese with English abstract)[李文,万千,刘风珍等(2015).花生转录因子基因NAC4的等位变异分析.作物学报,41(1):31-41]
Liu TM,Zhu SY,Tang QM,et al(2014).Identification of 32full-length NAC transcription factors in ramie(Boehmeria nivea L.Gaud)and characterization of the expression pattern of these genes.Mol Genet Genomics,289(4):675-684
Lu PL,Chen NZ,An R,et al(2006).A novel drought-inducible gene,ATAF1,encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis.Plant Mol Biol,63(2):289-305
Mao XG,Chen SS,Li A,et al(2014).Novel NAC transcription factor TaNAC67 confers enhanced multi-abiotic stress tolerances in Arabidopsis.PLoS ONE,9(1):e84359
Nakashima K,Tran LP,Nguyen DV,et al(2007).Functional analysis of a NAC-type transcription factor OsNAC6involved in abiotic and biotic stress-responsive gene expression in rice.Plant J,51(4):617-630
Nakashima K,Takasaki H,Mizoi J,et al(2012).NAC transcription factors in plant abiotic stress responses.Biochim Biophys Acta,1819(2):97-103
Nuruzzaman M,Manimekalai R,Sharoni AM,et al(2010).Genome-wide analysis of nac transcription factor family in rice.Gene,465(1):30-44
Ooka H,Tatoh K,Doi K,et al(2003).Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.DNA Res,10(6):239-247
Redillas MC,Jeong JS,Kim YS,et al(2012).The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions.Plant Biotechnol J,10(7):792-805
Sablowski RWM,Meyerowitz EM(1998).A Homolog of NOAPICAL MERISTEM,is an immediate target of the floral homeotic genes APETALA3/PISTILLATA.Cell,92(1):93-103
Shiriga K,Sharma R,Kumar K,et al(2014).Genome-wide identification and expression pattern of drought-responsive members of the NAC family in maize.Meta Gene,2(1):407-417
Shang HH,Li W,Zou CS,et al(2013).Analyses of the NACtranscription factor gene family in Gossypium raimondii ulbr:chromosomal location,structure,phylogeny,and expression patterns.J Integr Plant Biol,55(7):663-676
Souer E,Houwelingen AV,Kloos D,et al(1996).The NOAPICAL MERISTEM gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries.Cell,85(2):159-170
Sun LJ,Li DY,Zhang HJ,et al(2012).Functions of NACtranscription factors in biotic and abiotic stress responses in plants.Hereditas,34(8):993-1002(in Chinese with English abstract)[孙利军,李大勇,张慧娟等(2012).NAC转录因子在植物抗病和抗非生物胁迫反应中的作用.遗传,34(8):993-1002]
Takada S,Hibara K,Ishida T,et al(2001).The CUP-SHAPEDCOTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation.Development,128(7):1127-1135
Tran LP,Nakashima K,Sakuma Y,et al(2004).Isolation and functional analysis of Arabidopsis stress-inducible NACtranscription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress1 promoter.Plant Cell,16(9):2481-2498
Tran LP,Nishiyama R,Yamaguchi-Shinozaki K,et al(2010).Potential utilization of nac transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach.GM Crops,1(1):32-39
Wang FT,Lin RM,Xu SC(2010).Cloning and characterization of three NAC-like transcription factor genes in wheat.Genomics Appl Biol,29(4):639-645(in Chinese with English abstract)[王凤涛,蔺瑞明,徐世昌(2010).小麦3个NAC转录因子基因克隆与功能分析.基因组学与应用生物学,29(4):639-645]
Wang JY,Wang JP,Yuan H(2013).A Populus euphratica NAC protein regulating Na+/K+homeostasis improves salt tolerance in Arabidopsis thaliana.Gene,521(2):265-273
Wang RF,Hu YS,Gao WR,et al(2014).Functions of NACtranscription factors family in stress responses in plants.Plant Physiol J,50(10):1494-1500(in Chinese with English abstract)[王瑞芳,胡银松,高文蕊等(2014).植物NAC转录因子家族在抗逆响应中的功能.植物生理学报,50(10):1494-1500]
Wang ZJ,Jin L,Xu ZD,et al(2014).Bioinformatics analysis of gene LEC1 from Jatropha curcas.J Biol,31(4):68-72(in Chinese with English abstract)[王占军,金伦,徐忠东等(2014).麻风树LEC1基因的生物信息学分析.生物学杂志,31(4):68-72]
Wu YR,Deng ZY,Lai JB,et al(2010).Dual function of Arabidopsis ATAF1 in abiotic and biotic stress responses.Cell Res,1279-1290
Zhang MQ,Chen RK(2005).Crop Drought Resistance Molecular Physiology And Genetic Improvement.Beijing:Science Press,22-23(in Chinese)[张木清,陈如凯(2005).作物抗旱分子生理与遗传改良.北京:科学出版社,22-23]
Zheng X,Chen B,Lu G,et al(2009).Overexpression of a nac transcription factor enhances rice drought and salt tolerance.Biochem Biophys Res Commun,379(4):985-989