基于基因组鉴定小桐子Dof转录因子家族及其表达分析
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摘要
Dof蛋白是植物特有的C2-C2型锌指蛋白类转录因子,在植物碳氮代谢、次生物质合成、种子萌发及抗逆性等方面发挥重要作用。为全面解析小桐子Dof基因的特征,本研究基于小桐子基因组数据,对Dof基因家族进行了鉴定,并对其系统进化、基因结构、保守结构域及差异表达特性等进行了分析。结果表明,在小桐子基因组中共鉴定到24个Dof基因,GSDS基因结构分析显示都包含1(9个)或2(15个)个外显子,聚类分析结果将24个小桐子Dof蛋白分属于4个亚族及7个亚组,其中,有16个(66.7%)Dof蛋白的等电点偏碱性。荧光定量表达分析显示,JcDof1.4L与JcDof5.4L分别在茎与根中高表达,且两者都属于低温诱导表达基因,分别在低温胁迫3 h与24 h达到最大表达量,较对照分别提高4.06倍、8.96倍(p<0.01)。本研究结果为进一步开展小桐子Dof基因的克隆与功能鉴定提供了依据。
The Dof protein is a plant-specific type of C2-C2 zinc finger protein transcription factor, which plays an important role in plant carbon/nitrogen metabolism, secondary substance synthesis, seed germination, and stress resistance. To investigate the characteristics of Dof gene(Jc Dof) in Jatropha curcas genome, we identified the Dof gene family and analyzed the phylogenetic evolution, gene structure, conserved motifs, and differential expression characterization. The results showed that a total of 24 JcDof genes with 1(9) or 2(15) exons were identified in J.curcas, and they were phylogenetically clustered into 4 subfamilies and 7 subgroup. Prot Param program analysis showed that 16(66.7%) members shared alkalinity-tendency isoelectric point. q RT-PCR analysis showed that JcDof1.4 L and JcDof5.4 L were highly expressed in stems and roots respectively, both belonged to cold-induced expression gene, and reached the highest expression level at low-temperature stress after 3 h and 24 h, increased by4.06 times and 8.96 times(p<0.01) of the control group. The results of this study might provide a foundation for further studies on the gene cloning and functional verification of Dof gene family in J. curcas.
The Dof protein is a plant-specific type of C2-C2 zinc finger protein transcription factor, which plays an important role in plant carbon/nitrogen metabolism, secondary substance synthesis, seed germination, and stress resistance. To investigate the characteristics of Dof gene(Jc Dof) in Jatropha curcas genome, we identified the Dof gene family and analyzed the phylogenetic evolution, gene structure, conserved motifs, and differential expression characterization. The results showed that a total of 24 JcDof genes with 1(9) or 2(15) exons were identified in J.curcas, and they were phylogenetically clustered into 4 subfamilies and 7 subgroup. Prot Param program analysis showed that 16(66.7%) members shared alkalinity-tendency isoelectric point. q RT-PCR analysis showed that JcDof1.4 L and JcDof5.4 L were highly expressed in stems and roots respectively, both belonged to cold-induced expression gene, and reached the highest expression level at low-temperature stress after 3 h and 24 h, increased by4.06 times and 8.96 times(p<0.01) of the control group. The results of this study might provide a foundation for further studies on the gene cloning and functional verification of Dof gene family in J. curcas.
引文
Bau mann K.,De Paolis A.,Costantino P.,and Gualberti G.,1999,The DNA binding site of the Dof protein NtB BF1 is essential for tissue-specific and auxin-regulated expression of the rol B oncogene in plants,Plant Cell,11(3):323-334
Cai X.,Zhang Y.,Zhang C.,Zhang T.,Hu T.,Ye J.,Zhang J.,Wang T.,Li H.,and Ye Z.,2013,Genome-wide analysis of plant-specific Dof transcription factor family in tomato,J.Integr.Plant Biol.,55(6):552-566
Cominelli E.,Galbiati M.,Albertini A.,Fornara F.,Conti L.,Coupland G.,and Tonelli C.,2011,Dof-binding sites additively contribute to guard cell-specificity of At MYB60 promoter,BMC Plant Biol.,11:162
Corrales A.R.,Nebauer S.G.,Carrillo L.,Fernandez-Nohales P.,Marqués J.,Renau-Morata B.,Granell A.,Pollmann S.,Vicente-Carbajosa J.,Molina R.V.,and Medina J.,2014,Characterization of tomato cycling Dof factors reveals conserved and new functions in the control of flowering time and abiotic stress responses,J.Exp.Bot.,65(4):995-1012
Diaz I.,Vicente-Carbajosa J.,Abraham Z.,Martinez M.,Isabel-La Moneda I.,and Carbonero P.,2002,The GAMYBprotein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development,Plant J.,29(4):453-464
Gar diner J.,Sherr I.,and Scarpella E.,2010,Expression of Dof genes identifies early stages of vascular development in Arabidopsis leaves,Int.J.Dev.Biol.,54(8-9):1389-1396
Guo Y.,and Qiu L.J.,2013,Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics,PLo S One,8(9):e76809
Guo Y.,Qin G.,Gu H.,and Qu L.J.,2009,Dof5.6/HCA2,a Dof transcription factor gene,regulates interfascicular cambium formation and vascular tissue development in Arabidopsis,Plant Cell,21(11):3518-3534
Hernando-Amado S.,Gonzalez-Calle V.,Carbonero P.,and Barrero-Sicilia C.,2012,The family of Dof transcription factors in Brachypodium distachyon:phylogenetic comparison with rice and barley Dofs and expression profiling,BMC Plant Biol.,12:202
Isabel-La Moneda I.,Diaz I.,Martinez M.,Mena M.,and Carbonero P.,2003,SAD:a new DOF protein from barley that activates transcription of a cathepsin B-Iike thiol protease gene in the aleurone of germinating seeds,Plant J.,33(2):329-340
Iwamoto M.,Higo K.,and Takano M.,2009,Circadian clock-and phytochrome-regulated Dof-like gene,Rdd1,is associated with grain size in rice,Plant Cell Environ.,32(5):592-603
Kang H.G.,and Singh K.B.,2000,Characterization of salicylic acid-responsive,Arabidopsis Dof domain proteins:overexpression of OBP3 leads to growth defects,Plant J.,21(4):329-339
Kang H.G.,Foley R.C.,Onate-Sanchez L.,Lin C.,and Singh K.B.,2003,Target genes for OBP3,a Dof transcription factor,include novel basic helix-loop-helix domain proteins inducible by salicylic acid,Plant J.,35(3):362-372
Kisu Y.,Ono T.,Shimofurutani N.,Suzuki M.,and Esaka M.,1998,Characterization and expression of a new class of zinc finger protein that binds to silencer region of ascorbate oxidase gene,Plant Cell Physiol.,39(10):1054-1064
Kushwaha H.,Gupta S.,Singh V.K.,Rastogi S.,and Yadav D.,2011,Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis,Mol.Biol.Rep.,38(8):5037-5053
Li Z.G.,and Gong M.,2010,Effects of different chemical disinfectant on seed germination and seedling growth of Jatropha curcas L.,Zhongzi(Seed),30(2):4-7(李忠光,龚明,2010,不同化学消毒剂对小桐子种子萌发和幼苗生长的影响,种子,30(2):4-7)
Lijavetzky D.,Carbonero P.,and Vicente-Carbajosa J.,2003,Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families,BMC Evol.Biol.,3:17
Mena M.,Cejudo F.J.,Isabel-Lamoneda I.,and Carbonero P.,2002,A role for the Dof transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone,Plant Physiol.,130(1):111-119
Moreno-Risueno M.A.,Martinez M.,Vicente-Carbajosa J.,and Carbonero P.,2007,The family of Dof transcription factors:from green unicellular algae to vascular plants,Mol.Genet.Genomics,277(4):379-390
Riechmann J.L.,Heard J.,Martin G.,Reuber L.,Jiang C.,Keddie J.,Adam L.,Pineda O.,Ratcliffe O.J.,Samaha R.R.,Creelman R.,Pilgrim M.,Broun P.,Zhang J.Z.,Ghandehari D.,Sherman B.K.,and Yu G.,2000,Arabidopsis transcription factors:genome-wide comparative analysis among eukaryotes,Science,290(5499):2105-2110
Rueda-L仵pez M.,Crespillo R.,Canovas F.M.,and Avila C.,2008,Differential regulation of two glutamine synthetase genes by a single Dof transcription factor,Plant J.,56(1):73-85
Sato S.,Hirakawa H.,Isobe S.,Fukai E.,Watanabe A.,Kato M.,Kawashima K.,Minami C.,Muraki A.,Nakazaki N.,Takahashi C.,Nakayama S.,Kishida Y.,Kohara M.,Yamada M.,Tsuruoka H.,Sasamoto S.,Tabata S.,Aizu T.,Toyoda A.,Shin-i T.,Minakuchi Y.,Kohara Y.,Fujiyama A.,Tsuchimoto S.,Kajiyama S.,Makigano E.,Ohmido N.,Shibagaki N.,Cartagena J.A.,Wada N.,Kohinata T.,Atefeh A.,Yuasa S.,Matsunaga S.,and Fukui K.,2011,Sequence analysis of the genome of an oil-bearing tree,Jatropha curcas L.,DNARes.,18(1):65-76
Shaw L.M.,Mc Intyre C.L.,Gresshoff P.M.,and Xue G.P.,2009,Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation,Funct Integr Genomic,9(4):485-498
Skirycz A.,Reichelt M.,Burow M.,Birkemeyer C.,Rolcik J.,Kopka J.,Zanor M.I.,Gershenzon J.,Strnad M.,Szopa J.,Mueller-Roeber B.,and Witt I.,2006,Dof transcription factor At Dof1.1(OBP2)is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis,Plant J.,47(1):10-24
Umemura Y.,Ishiduka T.,Yamamoto R.,and Esaka M.,2004,The Dof domain,a zinc finger DNA-binding domain conserved only in higher plants,truly functions as a Cys2/Cys2Zn finger domain,Plant J.,37(5):741-749
Wei P.C.,Tan F.,Gao X.Q.,Zhang X.Q.,Wang G.Q.,Xu H.,Li L.J.,Chen J.,and Wang X.C.,2010,Overexpression of At DOF4.7,an Arabidopsis Dof family transcription factor,induces floral organ abscission deficiency in Arabidopsis,Plant Physiol.,153(3):1031-1045
Yanagisawa S.,2002,The Dof family of plant transcription factors,Trends Plant Sci.,7(12):555-560
Yanagisawa S.,2004,Dof domain proteins:plant-specific transcription factors associated with diverse phenomena unique to plants,Plant Cell Physiol.,45(4):386-391
Yanagisawa S.,and Izui K.,1993,Molecular cloning of two DNA-binding proteins of maize that are structurally different but interact with the same sequence motif,J.Biol.Chem.,268(21):16028-16036
Yanagisawa S.,and Schmidt R.J.,1999,Diversity and similarity among recognition sequences of Dof transcription factors,Plant J.,17(2):209-214
Yang X.H.,Tuskan G.A.,and Cheng M.Z.,2006,Divergence of the Dof gene families in poplar,Arabidopsis,and rice suggests multiple modes of gene evolution after duplication,Plant Physiol.,142(3):820-830
Zhang H.,Zhu Y.Y.,Shao X.,Wang Y.,Li Y.Q.,and Guo W.D.,2015,Isolation and characterization of Ppc CBF CBF/DREBtranscription factor c DNA of Chinese cherry(Prunus pseudocerasus),Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(1):149-154(张弘,朱友银,邵姁,王月,李永强,郭卫东,2015,中国樱桃CBF/DREB转录因子Ppc CBF的克隆与表达分析,基因组学与应用生物学,34(1):149-154)
Cai X.,Zhang Y.,Zhang C.,Zhang T.,Hu T.,Ye J.,Zhang J.,Wang T.,Li H.,and Ye Z.,2013,Genome-wide analysis of plant-specific Dof transcription factor family in tomato,J.Integr.Plant Biol.,55(6):552-566
Cominelli E.,Galbiati M.,Albertini A.,Fornara F.,Conti L.,Coupland G.,and Tonelli C.,2011,Dof-binding sites additively contribute to guard cell-specificity of At MYB60 promoter,BMC Plant Biol.,11:162
Corrales A.R.,Nebauer S.G.,Carrillo L.,Fernandez-Nohales P.,Marqués J.,Renau-Morata B.,Granell A.,Pollmann S.,Vicente-Carbajosa J.,Molina R.V.,and Medina J.,2014,Characterization of tomato cycling Dof factors reveals conserved and new functions in the control of flowering time and abiotic stress responses,J.Exp.Bot.,65(4):995-1012
Diaz I.,Vicente-Carbajosa J.,Abraham Z.,Martinez M.,Isabel-La Moneda I.,and Carbonero P.,2002,The GAMYBprotein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development,Plant J.,29(4):453-464
Gar diner J.,Sherr I.,and Scarpella E.,2010,Expression of Dof genes identifies early stages of vascular development in Arabidopsis leaves,Int.J.Dev.Biol.,54(8-9):1389-1396
Guo Y.,and Qiu L.J.,2013,Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics,PLo S One,8(9):e76809
Guo Y.,Qin G.,Gu H.,and Qu L.J.,2009,Dof5.6/HCA2,a Dof transcription factor gene,regulates interfascicular cambium formation and vascular tissue development in Arabidopsis,Plant Cell,21(11):3518-3534
Hernando-Amado S.,Gonzalez-Calle V.,Carbonero P.,and Barrero-Sicilia C.,2012,The family of Dof transcription factors in Brachypodium distachyon:phylogenetic comparison with rice and barley Dofs and expression profiling,BMC Plant Biol.,12:202
Isabel-La Moneda I.,Diaz I.,Martinez M.,Mena M.,and Carbonero P.,2003,SAD:a new DOF protein from barley that activates transcription of a cathepsin B-Iike thiol protease gene in the aleurone of germinating seeds,Plant J.,33(2):329-340
Iwamoto M.,Higo K.,and Takano M.,2009,Circadian clock-and phytochrome-regulated Dof-like gene,Rdd1,is associated with grain size in rice,Plant Cell Environ.,32(5):592-603
Kang H.G.,and Singh K.B.,2000,Characterization of salicylic acid-responsive,Arabidopsis Dof domain proteins:overexpression of OBP3 leads to growth defects,Plant J.,21(4):329-339
Kang H.G.,Foley R.C.,Onate-Sanchez L.,Lin C.,and Singh K.B.,2003,Target genes for OBP3,a Dof transcription factor,include novel basic helix-loop-helix domain proteins inducible by salicylic acid,Plant J.,35(3):362-372
Kisu Y.,Ono T.,Shimofurutani N.,Suzuki M.,and Esaka M.,1998,Characterization and expression of a new class of zinc finger protein that binds to silencer region of ascorbate oxidase gene,Plant Cell Physiol.,39(10):1054-1064
Kushwaha H.,Gupta S.,Singh V.K.,Rastogi S.,and Yadav D.,2011,Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis,Mol.Biol.Rep.,38(8):5037-5053
Li Z.G.,and Gong M.,2010,Effects of different chemical disinfectant on seed germination and seedling growth of Jatropha curcas L.,Zhongzi(Seed),30(2):4-7(李忠光,龚明,2010,不同化学消毒剂对小桐子种子萌发和幼苗生长的影响,种子,30(2):4-7)
Lijavetzky D.,Carbonero P.,and Vicente-Carbajosa J.,2003,Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families,BMC Evol.Biol.,3:17
Mena M.,Cejudo F.J.,Isabel-Lamoneda I.,and Carbonero P.,2002,A role for the Dof transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone,Plant Physiol.,130(1):111-119
Moreno-Risueno M.A.,Martinez M.,Vicente-Carbajosa J.,and Carbonero P.,2007,The family of Dof transcription factors:from green unicellular algae to vascular plants,Mol.Genet.Genomics,277(4):379-390
Riechmann J.L.,Heard J.,Martin G.,Reuber L.,Jiang C.,Keddie J.,Adam L.,Pineda O.,Ratcliffe O.J.,Samaha R.R.,Creelman R.,Pilgrim M.,Broun P.,Zhang J.Z.,Ghandehari D.,Sherman B.K.,and Yu G.,2000,Arabidopsis transcription factors:genome-wide comparative analysis among eukaryotes,Science,290(5499):2105-2110
Rueda-L仵pez M.,Crespillo R.,Canovas F.M.,and Avila C.,2008,Differential regulation of two glutamine synthetase genes by a single Dof transcription factor,Plant J.,56(1):73-85
Sato S.,Hirakawa H.,Isobe S.,Fukai E.,Watanabe A.,Kato M.,Kawashima K.,Minami C.,Muraki A.,Nakazaki N.,Takahashi C.,Nakayama S.,Kishida Y.,Kohara M.,Yamada M.,Tsuruoka H.,Sasamoto S.,Tabata S.,Aizu T.,Toyoda A.,Shin-i T.,Minakuchi Y.,Kohara Y.,Fujiyama A.,Tsuchimoto S.,Kajiyama S.,Makigano E.,Ohmido N.,Shibagaki N.,Cartagena J.A.,Wada N.,Kohinata T.,Atefeh A.,Yuasa S.,Matsunaga S.,and Fukui K.,2011,Sequence analysis of the genome of an oil-bearing tree,Jatropha curcas L.,DNARes.,18(1):65-76
Shaw L.M.,Mc Intyre C.L.,Gresshoff P.M.,and Xue G.P.,2009,Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation,Funct Integr Genomic,9(4):485-498
Skirycz A.,Reichelt M.,Burow M.,Birkemeyer C.,Rolcik J.,Kopka J.,Zanor M.I.,Gershenzon J.,Strnad M.,Szopa J.,Mueller-Roeber B.,and Witt I.,2006,Dof transcription factor At Dof1.1(OBP2)is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis,Plant J.,47(1):10-24
Umemura Y.,Ishiduka T.,Yamamoto R.,and Esaka M.,2004,The Dof domain,a zinc finger DNA-binding domain conserved only in higher plants,truly functions as a Cys2/Cys2Zn finger domain,Plant J.,37(5):741-749
Wei P.C.,Tan F.,Gao X.Q.,Zhang X.Q.,Wang G.Q.,Xu H.,Li L.J.,Chen J.,and Wang X.C.,2010,Overexpression of At DOF4.7,an Arabidopsis Dof family transcription factor,induces floral organ abscission deficiency in Arabidopsis,Plant Physiol.,153(3):1031-1045
Yanagisawa S.,2002,The Dof family of plant transcription factors,Trends Plant Sci.,7(12):555-560
Yanagisawa S.,2004,Dof domain proteins:plant-specific transcription factors associated with diverse phenomena unique to plants,Plant Cell Physiol.,45(4):386-391
Yanagisawa S.,and Izui K.,1993,Molecular cloning of two DNA-binding proteins of maize that are structurally different but interact with the same sequence motif,J.Biol.Chem.,268(21):16028-16036
Yanagisawa S.,and Schmidt R.J.,1999,Diversity and similarity among recognition sequences of Dof transcription factors,Plant J.,17(2):209-214
Yang X.H.,Tuskan G.A.,and Cheng M.Z.,2006,Divergence of the Dof gene families in poplar,Arabidopsis,and rice suggests multiple modes of gene evolution after duplication,Plant Physiol.,142(3):820-830
Zhang H.,Zhu Y.Y.,Shao X.,Wang Y.,Li Y.Q.,and Guo W.D.,2015,Isolation and characterization of Ppc CBF CBF/DREBtranscription factor c DNA of Chinese cherry(Prunus pseudocerasus),Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(1):149-154(张弘,朱友银,邵姁,王月,李永强,郭卫东,2015,中国樱桃CBF/DREB转录因子Ppc CBF的克隆与表达分析,基因组学与应用生物学,34(1):149-154)