谷子Dof转录因子家族分析及功能预测
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摘要
Dof转录因子是植物所特有的转录因子,在植物生长发育和基因表达调控过程中具有重要的作用,本研究利用一系列生物信息学方法对谷子全基因组Dof基因的保守结构域、系统进化关系、保守motif、基因结构、表达模式和蛋白互作进行了分析。结果表明:谷子中共有35个Dof类型基因,通过Clustal X进行分析后,可以看出这35个基因都含有一个明显的锌指结构。通过MEGA6.0对谷子、高粱、水稻和玉米进行系统进化树的分析表明该家族基因在植物中具有高度同源性。而通过MEME进一步进行分析后,分析结果与聚类分析具有一致性。利用基因结构显示系统GSDS对Dof转录因子家族进行分析,了解其基因结构,进一步验证了之前的分析结果。结合生物芯片数据,在Cluster和Treeview软件中根据在不同组织的表达结果进行Heatmap图示,结果显示部分Dof基因在根、茎、叶和花序组织呈现高表达,推测这些Dof基因可能参与这些特定组织的发育。通过STRING对Dof蛋白互作进行分析,发现大部分Dof蛋白基因的进化速度较快,且与谷子中其他蛋白没有互作关系,只有少数Dof蛋白与谷子中其他蛋白在功能上相关联。本研究为Dof转录因子基因功能进一步的研究提供了经验和基础。
Dof transcription factor is unique in pl ants, which plays an important role in plant growth and development and gene expression regulation. In this paper, a series of bioinformatics methods were used to analyze the conserved domain, phylogenetic relationship, conserved motif, gene structure, expression pattern and protein interaction of Dof gene in millet. The results showed that there were 35 types of Dof gene in the millet, anf after Clustal X analysis, it was obvious that these 35 genes contained a distinct zinc finger structure. Phylogenetic tree analysis of millet, sorghum, rice and maize by MEGA6.0 indicated that this family genes had high homology in plants. After further analysis by MEME, the results were consistent with cluster analysis. The gene structure display system(GSDS) was used to analyze the Dof transcription factor family, aiming to investigate its gene structure and further verify the former results. Combined with biochip data, Heatmap diagrams were performed in cluster and treeview software according to the expression results in different tissues. The results showed that part of the Dof gene was highly expressed in root, stem, leaves and inflorescence tissues. Implying that these Dof genes might be involved in the development of these specific tissues. By STRING analysis of Dof protein interaction, it was found that most Dof protein genes evolved faster and had no interaction with other proteins in millet. Only a few Dof proteins were functionally related to other proteins in millet. This study could provide experience and basis for the further research on the gene function of Dof transcription factor.
Dof transcription factor is unique in pl ants, which plays an important role in plant growth and development and gene expression regulation. In this paper, a series of bioinformatics methods were used to analyze the conserved domain, phylogenetic relationship, conserved motif, gene structure, expression pattern and protein interaction of Dof gene in millet. The results showed that there were 35 types of Dof gene in the millet, anf after Clustal X analysis, it was obvious that these 35 genes contained a distinct zinc finger structure. Phylogenetic tree analysis of millet, sorghum, rice and maize by MEGA6.0 indicated that this family genes had high homology in plants. After further analysis by MEME, the results were consistent with cluster analysis. The gene structure display system(GSDS) was used to analyze the Dof transcription factor family, aiming to investigate its gene structure and further verify the former results. Combined with biochip data, Heatmap diagrams were performed in cluster and treeview software according to the expression results in different tissues. The results showed that part of the Dof gene was highly expressed in root, stem, leaves and inflorescence tissues. Implying that these Dof genes might be involved in the development of these specific tissues. By STRING analysis of Dof protein interaction, it was found that most Dof protein genes evolved faster and had no interaction with other proteins in millet. Only a few Dof proteins were functionally related to other proteins in millet. This study could provide experience and basis for the further research on the gene function of Dof transcription factor.
引文
Altschul S.F.,Madden T.L.,Schffer A.A.,Zhang J.,Zhang Z.,Miller W.,and Lipman D.J.,1997,Gapped BLAST and PSI-BLAST a new generation of protein database search programs,Nucleic Acids Res.,25(17):3389-3402
Bailey T.L.,and Elkan C.,1994,Fitting a mixture model by expectation maximization to discover motifs in biopolymers,Proc.Int.Conf.Intell.Syst.Mol.Biol.,2:28-36
Cavalar M.,Mller C.,Offermann S.,Krohn N.M.,Grasser K.D.,and Peterhnsel C.,2003,The interaction of DOF transcription factors with nucleosomes depends on the positioning of the binding site and is facilitated by maize HMGB5,Biochemistry,42(7):2149-2157
Ge M.,Lv Y.D.,Li T.,Zhang T.F.,Zhang X.L.,and Zhao H.,2014,Genome-wide identification and analysis of Dof transcription factor family in maize,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),47(23):4563-4572(葛敏,吕远大,李坦,张体付,张晓林,赵涵,2014,玉米Dof转录因子家族的全基因组鉴定与分析,中国农业科学,47(23):4563-4572)
Guo X.F.,and Yan H.Y.,2005,Dof protein and Dof transcription factor family in plants,Zhiwu Shenglixue Tongxun,41(4):419-423(郭晓芳,严海燕,2005,植物中的Dof蛋白和Dof转录因子家族,植物生理学通讯,41(4):419-423)
Hu B.,Jin J.P.,Guo A.Y.,Zhang H.,Luo J.C.,and Gao G.,2015,GSDS 2.0 an upgraded gene feature visualization server,Bioinformatics,31(8):1296-1297
Jin J.,Tian F.,Yang D.C.,Meng Y.Q.,Kong L.,Luo J.,and Gao G.,2017,PlantTFDB 4.0 toward a central hub for transcription factors and regulatory interactions in plants,Nucleic Acids Res.,45(D):1040-1045
Kim J.,and Kim H.Y.,2006,Functional analysis of a calcium-binding transcription factor involved in plant salt stress signaling,FEBS Letters,580(22):5251-5256
Larkin M.A.,Blackshields G.,Brown N.P.,Chenna R.,Mcgettigan P.A.,Mcwilliam H.,Valentin F.,Wallace I.M.,Wilm A.,and Lopez R.,2007,Clustal W and Clustal X version 2.0,Bioinformatics,23(21):2947-2948
Li B.Y.,Hu S.L.,Cao Y.,and Xu G.,2015,Bioinformatics analysis of NAC transcription factor family in Phyllostachys edulis,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(8):1769-1777(黎帮勇,胡尚连,曹颖,徐刚,2015,毛竹NAC转录因子家族生物信息学分析,基因组学与应用生物学,34(8):1769-1777)
LijavetzkyD.,Carbonero P.,and Vicentecarbajosa J.,2003,Genomewide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families,BMC Evol.Biol.,3:17
Mackay J.P.,and Crossley M.,1998,Zinc fingers are sticking together,Trends in Biochem.Sci.,23(1):1-4
Morenorisueno M.A.,Díaz I.,Carrillo L.,Fuentes R.,and Carbonero P.,2010,The Hv DOF19 transcription factor mediates the abscisic acid-dependent repression of hydrolase genes in germinating barley aleurone,Plant J.,51(3):352-365
Nakano T.,Suzuki K.,Ohtsuki N.,Tsujimoto Y.,Fujimura T.,and Shinshi H.,2006,Identification of genes of the plantspecific transcription-factor families cooperatively regulated by ethylene and jasmonate in Arabidopsis thaliana,J.Plant Res.,119(4):407-413
Riechmann J.L.,Heard J.,Martin G.,Reuber L.,Jiang C.Z.,Keddie J.,Adam L.,Pineda O.,Ratcliffe O.J.,and Samaha R.R.,2000,Arabidopsis transcription factors genome-wide comparative analysis among eukaryotes,Science,290(5499):2105-2110
Szklarczyk D.,Morris J.H.,Cook H.,Kuhn M.,Wyder S.,Simonovic M.,Santos A.,Doncheva N.T.,Roth A.,and Bork P.,2017,The STRING database in 2017 quality-controlled protein-protein association networks,made broadly accessible,Nucleic Acids Res.,45(1):362-368
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
Wang H.W.,Zhang B.,Hao Y.J.,Huang J.,Tian A.G.,Liao Y.,Zhang J.S.,and Chen S.Y.,2007,The soybean Dof-type transcription factor genes,GmDof4 and GmDof11,enhance lipid content in the seeds of transgenic Arabidopsis plants,Plant J.,52(4):716-729
Yanagisawa S.,1995,A novel DNA-binding domain that may form a single zinc finger motif,Nucleic Acids Res.,23(17):3403-3410
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
Zhang L.,Liu B.,Zheng G.,Zhang A.,and Li R.,2017,Genomewide characterization of the SiDof gene family in foxtail millet(Setaria italica),Biosystems,151:27-33
Zheng Z.,Mosher S.L.,Fan B.,Klessig D.F.,and Chen Z.,2007,Functional analysis of Arabidopsis WRKY25 transcription factor in plant defense against Pseudomonas syringae,BMCPlant Biol.,7:2
Bailey T.L.,and Elkan C.,1994,Fitting a mixture model by expectation maximization to discover motifs in biopolymers,Proc.Int.Conf.Intell.Syst.Mol.Biol.,2:28-36
Cavalar M.,Mller C.,Offermann S.,Krohn N.M.,Grasser K.D.,and Peterhnsel C.,2003,The interaction of DOF transcription factors with nucleosomes depends on the positioning of the binding site and is facilitated by maize HMGB5,Biochemistry,42(7):2149-2157
Ge M.,Lv Y.D.,Li T.,Zhang T.F.,Zhang X.L.,and Zhao H.,2014,Genome-wide identification and analysis of Dof transcription factor family in maize,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),47(23):4563-4572(葛敏,吕远大,李坦,张体付,张晓林,赵涵,2014,玉米Dof转录因子家族的全基因组鉴定与分析,中国农业科学,47(23):4563-4572)
Guo X.F.,and Yan H.Y.,2005,Dof protein and Dof transcription factor family in plants,Zhiwu Shenglixue Tongxun,41(4):419-423(郭晓芳,严海燕,2005,植物中的Dof蛋白和Dof转录因子家族,植物生理学通讯,41(4):419-423)
Hu B.,Jin J.P.,Guo A.Y.,Zhang H.,Luo J.C.,and Gao G.,2015,GSDS 2.0 an upgraded gene feature visualization server,Bioinformatics,31(8):1296-1297
Jin J.,Tian F.,Yang D.C.,Meng Y.Q.,Kong L.,Luo J.,and Gao G.,2017,PlantTFDB 4.0 toward a central hub for transcription factors and regulatory interactions in plants,Nucleic Acids Res.,45(D):1040-1045
Kim J.,and Kim H.Y.,2006,Functional analysis of a calcium-binding transcription factor involved in plant salt stress signaling,FEBS Letters,580(22):5251-5256
Larkin M.A.,Blackshields G.,Brown N.P.,Chenna R.,Mcgettigan P.A.,Mcwilliam H.,Valentin F.,Wallace I.M.,Wilm A.,and Lopez R.,2007,Clustal W and Clustal X version 2.0,Bioinformatics,23(21):2947-2948
Li B.Y.,Hu S.L.,Cao Y.,and Xu G.,2015,Bioinformatics analysis of NAC transcription factor family in Phyllostachys edulis,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(8):1769-1777(黎帮勇,胡尚连,曹颖,徐刚,2015,毛竹NAC转录因子家族生物信息学分析,基因组学与应用生物学,34(8):1769-1777)
LijavetzkyD.,Carbonero P.,and Vicentecarbajosa J.,2003,Genomewide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families,BMC Evol.Biol.,3:17
Mackay J.P.,and Crossley M.,1998,Zinc fingers are sticking together,Trends in Biochem.Sci.,23(1):1-4
Morenorisueno M.A.,Díaz I.,Carrillo L.,Fuentes R.,and Carbonero P.,2010,The Hv DOF19 transcription factor mediates the abscisic acid-dependent repression of hydrolase genes in germinating barley aleurone,Plant J.,51(3):352-365
Nakano T.,Suzuki K.,Ohtsuki N.,Tsujimoto Y.,Fujimura T.,and Shinshi H.,2006,Identification of genes of the plantspecific transcription-factor families cooperatively regulated by ethylene and jasmonate in Arabidopsis thaliana,J.Plant Res.,119(4):407-413
Riechmann J.L.,Heard J.,Martin G.,Reuber L.,Jiang C.Z.,Keddie J.,Adam L.,Pineda O.,Ratcliffe O.J.,and Samaha R.R.,2000,Arabidopsis transcription factors genome-wide comparative analysis among eukaryotes,Science,290(5499):2105-2110
Szklarczyk D.,Morris J.H.,Cook H.,Kuhn M.,Wyder S.,Simonovic M.,Santos A.,Doncheva N.T.,Roth A.,and Bork P.,2017,The STRING database in 2017 quality-controlled protein-protein association networks,made broadly accessible,Nucleic Acids Res.,45(1):362-368
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
Wang H.W.,Zhang B.,Hao Y.J.,Huang J.,Tian A.G.,Liao Y.,Zhang J.S.,and Chen S.Y.,2007,The soybean Dof-type transcription factor genes,GmDof4 and GmDof11,enhance lipid content in the seeds of transgenic Arabidopsis plants,Plant J.,52(4):716-729
Yanagisawa S.,1995,A novel DNA-binding domain that may form a single zinc finger motif,Nucleic Acids Res.,23(17):3403-3410
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
Zhang L.,Liu B.,Zheng G.,Zhang A.,and Li R.,2017,Genomewide characterization of the SiDof gene family in foxtail millet(Setaria italica),Biosystems,151:27-33
Zheng Z.,Mosher S.L.,Fan B.,Klessig D.F.,and Chen Z.,2007,Functional analysis of Arabidopsis WRKY25 transcription factor in plant defense against Pseudomonas syringae,BMCPlant Biol.,7:2