玉米中绒毡层发育调控基因ZmUdt1克隆的生物信息学分析
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摘要
为了研究玉米中绒毡层发育调控基因Udt1的功能与作用,进行生物信息学分析,通过利用Udt1基因培育雄性不育的玉米新品种,来提高杂交种纯度和种质质量并缩短育种年限。该试验采用已知的水稻OsUdt1基因(AY953870.1)为参考序列,使用同源克隆的方式在玉米基因组中得到同源性最高的基因BT068494.1(GenBank),并利用生物信息学方法预测该基因的各级结构以及生物学功能等,同时使用MEGA 7.0程序软件构建分子系统进化树。ZmUdt1基因位于玉米的第2条染色体上,ZmUdt1蛋白由219个氨基酸构成,蛋白的相对分子量为24.48 ku,等电点为5.35,属于亲水蛋白;主要由α-螺旋与无规则卷曲构成二级结构,其三级结构与水稻OsUdt1蛋白的三级结构基本一致,属于HLH超级家族,没有信号肽以及跨膜结构;亚细胞定位预测该蛋白位于细胞核中的可能性较大;通过预测,该蛋白具有翻译、复制与转录、转录调控信号转导等功能,具有17个磷酸化修饰位点,而是否具有其他功能尚没有确定。系统进化树表明,玉米与水稻、高粱等物种遗传距离最近,且与拟南芥的DYT1蛋白也有一定的遗传相关性。通过预测和比较,ZmUdt1和OsUdt1蛋白在结构和功能上具有极高的相似性。研究结果可为进一步研究ZmUdt1蛋白的功能与作用,以及创新玉米的雄性不育系提供理论依据。
In order to study the function and action of the tapetum developmental regulatory gene Udt1 in maize,bioinformatics analysis was carried out in this experiment. By using Udt1 gene to cultivate new male sterile maize varieties,to improve the purity of hybrids and the quality of germplasm and shorten the breeding years. The study used the known rice OsUdt1 gene( AY953870. 1) as the reference sequence,using homologous cloning,the highest homology gene BT068494. 1( GenBank) was obtained in maize genome,and bioinformatics was used to predict the structure and biological function of the gene. At the same time,the molecular phylogenetic tree was constructed by using MEGA 7. 0 software. The ZmUdt1 gene was located on second chromosomes of maize,ZmUdt1 protein was composed of 219 amino acids. The relative molecular weight of the protein was 24. 48 ku and the isoelectric point was 5. 35,belonging to hydrophilic protein. It was mainly composed of alpha helix and regular coil,forming two structures. The three stage structure was basically consistent with the three stage structure of OsUdt1 protein in rice,belong to the HLH super family. There were no signal peptides and transmembrane structures; Subcellular localization predicts that the protein had more likely to be located in the nucleus. It was predicted that the protein had functions of translation,replication and transcription,transcriptional regulation and signal transduction,and it had 17 phosphorylation sites,whether it had any other function had not been determined. Phylogenetic tree showed that the genetic distance between maize and rice,sorghum and other species was the closest,and also had a certain genetic correlation with Arabidopsis thaliana DYT1 protein. By comparison and prediction,the structure and function of ZmUdt1 and OsUdt1 proteins were highly similar. This experiment provides a theoretical basis for further research on the function and function of ZmUdt1 protein and the innovation of male sterile lines of maize.
In order to study the function and action of the tapetum developmental regulatory gene Udt1 in maize,bioinformatics analysis was carried out in this experiment. By using Udt1 gene to cultivate new male sterile maize varieties,to improve the purity of hybrids and the quality of germplasm and shorten the breeding years. The study used the known rice OsUdt1 gene( AY953870. 1) as the reference sequence,using homologous cloning,the highest homology gene BT068494. 1( GenBank) was obtained in maize genome,and bioinformatics was used to predict the structure and biological function of the gene. At the same time,the molecular phylogenetic tree was constructed by using MEGA 7. 0 software. The ZmUdt1 gene was located on second chromosomes of maize,ZmUdt1 protein was composed of 219 amino acids. The relative molecular weight of the protein was 24. 48 ku and the isoelectric point was 5. 35,belonging to hydrophilic protein. It was mainly composed of alpha helix and regular coil,forming two structures. The three stage structure was basically consistent with the three stage structure of OsUdt1 protein in rice,belong to the HLH super family. There were no signal peptides and transmembrane structures; Subcellular localization predicts that the protein had more likely to be located in the nucleus. It was predicted that the protein had functions of translation,replication and transcription,transcriptional regulation and signal transduction,and it had 17 phosphorylation sites,whether it had any other function had not been determined. Phylogenetic tree showed that the genetic distance between maize and rice,sorghum and other species was the closest,and also had a certain genetic correlation with Arabidopsis thaliana DYT1 protein. By comparison and prediction,the structure and function of ZmUdt1 and OsUdt1 proteins were highly similar. This experiment provides a theoretical basis for further research on the function and function of ZmUdt1 protein and the innovation of male sterile lines of maize.
引文
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[9]付海辉,辛培尧,许玉兰,等.几种经济植物UFGT基因的生物信息学分析[J].基因组学与应用生物学,2011,30(1):92-102.
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[14]张智敏,叶娟英,龙海飞,等.玉米早期花药蛋白质组和磷酸化蛋白质组分析[J].生物工程学报,2016,32(7):937-955.
[15]甄艳,李春映,陆叶,等.植物磷酸化蛋白质组研究进展[J].基因组学与应用生物学,2014,33(6):1405-1414.
[16]Ye J Y,Zhang Z B,Long H F,et al.Proteomic and phosphoproteomic analyses reveal extensive phosphorylation of regulatory proteins in developing rice anthers[J].Plant Journal,2015,84(3):527-544.
[17]Guan Y E,Meng X Z,Khanna R,et al.Phosphorylation of a WRKY transcription factor by MAPKs is required for pollen development and function in Arabidopsis[J].PLo S Genetics,2014,10(5):e1004384.
[18]李旭娟,刘洪博,林秀琴,等.甘蔗KNOX基因(Sckn1)的电子克隆及生物信息学分析[J].基因组学与应用生物学,2015,4(1):136-142.
[19]鲍思元.水稻Os UVR8基因电子克隆及生物信息学分析[J].生物技术,2016(2):169-175.
[20]Liu Z H,Bao W J,Liang W Q,et al.Identification of gamyb-4 and analysis of the regulatory role of GAMYB in rice anther development[J].Journal of Integrative Plant Biology,2010,52(7):670-678.
[21]Rousset F.Handbook of statistical genetics[M].Third Edition.USA:Wildy-Interscience,2008:945-979.
[22]李建义,童坦君.螺旋-环区-螺旋蛋白质-DNA结合蛋白的新类型[J].生物化学与生物物理进展,1993(1):11-14,73.
[23]李晓星,蒋海雄,黄青云,等.水稻b HLH基因家族成员表达模式分析[J].厦门大学学报:自然科学版,2006,45(S):73-77.
[24]夏杰.拟南芥转录因子DYT1、TDF1和AMS功能的初步比较[D].上海:上海师范大学,2012.
[25]Zhu J,Chen H,Li H,et al.Defective in tapetal development and function 1 is essential for anther development and tapetal function for microspore maturation in Arabidopsis[J].The Plant Journal:for Cell and Molecular Biology,2008,55(2):266-277.
[26]Zhu J,Lou Y E,Xu X F,et al.A genetic pathway for tapetum development and function in Arabidopsis[J].Journal of Integrative Plant Biology,2011,53(11):892-900.
[27]Fujii S,Yamada M,Toriyama K.Cytoplasmic male sterilityrelated protein kinase,Os Nek3,is regulated downstream of mitochondrial protein phosphatase 2C,DCW11[J].Plant and Cell Physiology,2009,50(4):828-837.
[28]孟超敏,姬俊华,李雪林,等.小麦CPP转录因子基因的电子克隆及生物信息学分析[J].生物技术,2014(4):39-42.
[29]Feng B M,Lu D H,Ma X,et al.Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development[J].Plant Journal,2012,72(4):612-624.
[30]Zhang F,Yao J,Ke J Y,et al.Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling[J].Nature,2015,525:269.
[2]顾敬楠.拟南芥绒毡层发育重要转录因子DYT1转录调控研究[D].上海:上海师范大学,2014.
[3]张增川.玉米雄性不育系泰玉D2的类型鉴定及不育机理的细胞学研究[D].泰安:山东农业大学,2009.
[4]Fu Z Z,Yu J,Cheng X W,et al.The rice basic HelixLoop-Helix transcription factor TDR interacting protein2is a central Switch in early anther development[J].Plant Cell,2014,26(4):1512-1524.
[5]易洪杨.玉米新选CMS材料及CMS-C亚组材料的细胞学观察和遗传多样性分析[D].雅安:四川农业大学,2016.
[6]蔡慈峰.Os TDF1功能的研究揭示了水稻与拟南芥绒毡层发育过程中存在着保守的机制[D].上海:上海师范大学,2015.
[7]Goldberg R B,Beals T P,Sanders P M.Anther development:basic principles and practical applications[J].Plant Cell,1993,5(10):1217.
[8]江华.拟南芥花药发育相关基因MPS1和AMS功能的初步研究[D].上海:复旦大学,2009.
[9]付海辉,辛培尧,许玉兰,等.几种经济植物UFGT基因的生物信息学分析[J].基因组学与应用生物学,2011,30(1):92-102.
[10]原晓龙,周军,辛培尧,等.8种植物CHI基因的生物信息学分析[J].西南林业大学学报,2013,33(2):88-95.
[11]王明亮,陈鹏,郝明超,等.黄牛FSHR基因的生物信息学分析[J].甘肃农业大学学报,2012,47(4):7-13.
[12]李亚娟,王慧,张世栋,等.奶牛粘合素蛋白的生物信息学分析[J].中国农学通报,2017,33(5):101-106.
[13]宋江华,张立新.植物跨膜蛋白研究进展[J].生物学杂志,2009,26(6):62-64.
[14]张智敏,叶娟英,龙海飞,等.玉米早期花药蛋白质组和磷酸化蛋白质组分析[J].生物工程学报,2016,32(7):937-955.
[15]甄艳,李春映,陆叶,等.植物磷酸化蛋白质组研究进展[J].基因组学与应用生物学,2014,33(6):1405-1414.
[16]Ye J Y,Zhang Z B,Long H F,et al.Proteomic and phosphoproteomic analyses reveal extensive phosphorylation of regulatory proteins in developing rice anthers[J].Plant Journal,2015,84(3):527-544.
[17]Guan Y E,Meng X Z,Khanna R,et al.Phosphorylation of a WRKY transcription factor by MAPKs is required for pollen development and function in Arabidopsis[J].PLo S Genetics,2014,10(5):e1004384.
[18]李旭娟,刘洪博,林秀琴,等.甘蔗KNOX基因(Sckn1)的电子克隆及生物信息学分析[J].基因组学与应用生物学,2015,4(1):136-142.
[19]鲍思元.水稻Os UVR8基因电子克隆及生物信息学分析[J].生物技术,2016(2):169-175.
[20]Liu Z H,Bao W J,Liang W Q,et al.Identification of gamyb-4 and analysis of the regulatory role of GAMYB in rice anther development[J].Journal of Integrative Plant Biology,2010,52(7):670-678.
[21]Rousset F.Handbook of statistical genetics[M].Third Edition.USA:Wildy-Interscience,2008:945-979.
[22]李建义,童坦君.螺旋-环区-螺旋蛋白质-DNA结合蛋白的新类型[J].生物化学与生物物理进展,1993(1):11-14,73.
[23]李晓星,蒋海雄,黄青云,等.水稻b HLH基因家族成员表达模式分析[J].厦门大学学报:自然科学版,2006,45(S):73-77.
[24]夏杰.拟南芥转录因子DYT1、TDF1和AMS功能的初步比较[D].上海:上海师范大学,2012.
[25]Zhu J,Chen H,Li H,et al.Defective in tapetal development and function 1 is essential for anther development and tapetal function for microspore maturation in Arabidopsis[J].The Plant Journal:for Cell and Molecular Biology,2008,55(2):266-277.
[26]Zhu J,Lou Y E,Xu X F,et al.A genetic pathway for tapetum development and function in Arabidopsis[J].Journal of Integrative Plant Biology,2011,53(11):892-900.
[27]Fujii S,Yamada M,Toriyama K.Cytoplasmic male sterilityrelated protein kinase,Os Nek3,is regulated downstream of mitochondrial protein phosphatase 2C,DCW11[J].Plant and Cell Physiology,2009,50(4):828-837.
[28]孟超敏,姬俊华,李雪林,等.小麦CPP转录因子基因的电子克隆及生物信息学分析[J].生物技术,2014(4):39-42.
[29]Feng B M,Lu D H,Ma X,et al.Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development[J].Plant Journal,2012,72(4):612-624.
[30]Zhang F,Yao J,Ke J Y,et al.Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling[J].Nature,2015,525:269.