拟南芥F-box基因AtPP2-B11的功能分析及苹果RING finger型泛素连接酶E3的家族分析
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摘要
泛素/26S蛋白酶体途径是一类重要的翻译后修饰过程,它能有效地调节功能蛋白质的选择性降解,是生命过程进行精确时空调控的重要环节之一。其中,泛素连接酶E3是在底物的特异性选择降解过程中作用最为关键成员。拟南芥基因组中大约5%的基因(大约1400多个基因)编码泛素连接酶。在众多的泛素连接酶类型中,F-box型和RING finger型是家族成员最多的两大类。本文通过对F-box和RING finger型基因的功能和结构的分析,揭示了泛素连接酶E3在基因表达调控中的重要作用。结果如下:
(1)本文首先分析了一个拟南芥F-box类型蛋白的功能。利用生物信息学的方法,在拟南芥1488个泛素连接酶E3中分离到了31个含有DRE元件的E3,通过RT-PCR的方法确定了它们在干旱处理下的表达量变化情况,并从中挑出了一个受干旱诱导较明显的F-box基因AtPP2-B11进行了进一步的研究。
(2)qRT-PCR的实验证明,AtPP2-B11受到干旱的诱导。GUS活性实验表明,AtPP2-B11基因上游启动子区域的DRE元件对于干旱响应起到了一定作用。同时,实验证明AtPP2-B11基因还受到ABA的部分诱导,表明AtPP2-B11基因可能是通过依赖ABA和不依赖ABA两种途径参与对干旱的响应。
(3)将AtPP2-B11基因转入野生型拟南芥中进行干旱处理实验,发现超表达AtPP2-B11基因明显的减弱了植株的干旱抗性。qRT-PCR检测LEA14,COR15a,RD29A等下游干旱响应基因时发现,在干旱处理时下游基因的RNA水平均降低,干旱处理后下游基因发生了不同程度的下调,表明AtPP2-B11基因可能通过影响这些下游基因从而改变了植株的抗旱性。
(4)通过酵母双杂交系统,我们以AtPP2-B11蛋白为诱饵,筛选了拟南芥干旱诱导的cDNA文库,共得到约20个阳性克隆,测序后发现可以与AtPP2-B11蛋白发生相互作用的蛋白包括LEA14,HSP70等蛋白。利用酵母双杂交和双分子荧光互补技术进一步分析发现,AtPP2-B11蛋白可以与LEA14蛋白发生相互作用,暗示了AtPP2-B11基因很可能作为一个负调因子,通过调节LEA14基因的活性来影响植株的干旱抗性。
(5)另外,我们还利用生物信息学的方法对苹果中的RING finger型蛋白进行了数量和结构的预测及鉴定。我们发现在苹果的基因组中有688个RING finger结构域分布于634个RING型蛋白中。根据其结构特征我们将苹果中的688个RING finger结构域分为9大类:367个RING-H2,208个RING-HC,10个RING-C2,35个RING-v,1个RING-D,11个RING-S/T,2个RING-G,10个RING-mH2和44个RING-mHC。其中,前7类是在拟南芥中曾经出现过的,后2类是在苹果中首次发现的。结构分析描述了每一种RING型结构域的典型特征。同时还鉴定了RING型蛋白中除了RING结构域以外的其他结构域,为将来RING finger蛋白的功能研究奠定基础。
The ubiquitin (Ub)/26S pathway is a major system for protein degradation that is conserved in all eukaryotes cells. The specificity of ubiquitination is largely determined by the many isoforms of E3 that recruits specific target protein(s). In Arabidopsis thaliana more than 1400 genes (~5%of the proteome) encode subunits of the E3 ubiquitin ligases, which confer substrate specificity to the pathway. F-box and RING finger genes are the most common family genes in Arabidopsis. The fuction and structure analysis of F-box in Arabidopsis and RING finger proteins in apple provide valuable information for understanding the classification and putative functions of the E3 gene family in higher plants. The obtained results are as follows:
(1) First, an F-box-containing gene was analyzed. Using bioinformatics approaches, 31 E3s containing DRE (dehydration responsive element) motif were isolated from 1488 E3s in Arabidopsis, in which an F-box gene (AtPP2-B11) were extremely induced by drought treatment.
(2) GUS activity assay showed that the DRE motif in the promoter region of AtPP2-B11 played partial roles in drought response. AtPP2-B11 also showed slightly increased expression treated by ABA, indicating that AtPP2-B11 may respons to drought both in ABA-independent and ABA-dependent pathways.
(3) Transgenic plants overexpressing AtPP2-B11 exhibited decreased drought tolerance. Quantitative RT-PCR showed that the expression levels of a number of key ABA and drought stress marker genes such as LEA14,COR15a,RD29A in transgeneic plants were altered in drought treatment.
(4) Interactive proteins were screened from drought-treatment cDNA library with the full-length of AtPP2-B11 as bait protein by Yeast Two-Hybrid System. More than 80 positive clones were identified by PCR colony screening and the representative clones were sequenced. Among them 20 clones were selected which interacted with full-length AtPP2-B11. Further Yeast Two-Hybrid assay and Bimolecular Fluorescenc Complementation (BiFC) assay showed that AtPP2-B11 protein interacted with LEA14 protein, indicating that AtPP2-B11 gene may fuction as a novel drought tolerance repressor by regulating the level of LEA14.
(5) In addition, we analyzed the RING finger proteins in apple genome which were recently secquenced. In our study, 688 RING domains in 663 predicted proteins were identified in apple. Based on the characteristics of RING domains, nine RING type were identified: 367 RING-H2, 208 RING-HC, 10 RING-C2, 35 RING-v, 1 RING-D, 11 RING-S/T, 2 RING-G, 10 RING-mH2 and 44 RING-mHC, in which the first seven types were decribed previously in Arabidopsis, while the latter two types were newly identified in apple. Proteins containing RING finger motifs were further classified into 57 groups according to the different known or unknown domains outside the RING domains.
(1)本文首先分析了一个拟南芥F-box类型蛋白的功能。利用生物信息学的方法,在拟南芥1488个泛素连接酶E3中分离到了31个含有DRE元件的E3,通过RT-PCR的方法确定了它们在干旱处理下的表达量变化情况,并从中挑出了一个受干旱诱导较明显的F-box基因AtPP2-B11进行了进一步的研究。
(2)qRT-PCR的实验证明,AtPP2-B11受到干旱的诱导。GUS活性实验表明,AtPP2-B11基因上游启动子区域的DRE元件对于干旱响应起到了一定作用。同时,实验证明AtPP2-B11基因还受到ABA的部分诱导,表明AtPP2-B11基因可能是通过依赖ABA和不依赖ABA两种途径参与对干旱的响应。
(3)将AtPP2-B11基因转入野生型拟南芥中进行干旱处理实验,发现超表达AtPP2-B11基因明显的减弱了植株的干旱抗性。qRT-PCR检测LEA14,COR15a,RD29A等下游干旱响应基因时发现,在干旱处理时下游基因的RNA水平均降低,干旱处理后下游基因发生了不同程度的下调,表明AtPP2-B11基因可能通过影响这些下游基因从而改变了植株的抗旱性。
(4)通过酵母双杂交系统,我们以AtPP2-B11蛋白为诱饵,筛选了拟南芥干旱诱导的cDNA文库,共得到约20个阳性克隆,测序后发现可以与AtPP2-B11蛋白发生相互作用的蛋白包括LEA14,HSP70等蛋白。利用酵母双杂交和双分子荧光互补技术进一步分析发现,AtPP2-B11蛋白可以与LEA14蛋白发生相互作用,暗示了AtPP2-B11基因很可能作为一个负调因子,通过调节LEA14基因的活性来影响植株的干旱抗性。
(5)另外,我们还利用生物信息学的方法对苹果中的RING finger型蛋白进行了数量和结构的预测及鉴定。我们发现在苹果的基因组中有688个RING finger结构域分布于634个RING型蛋白中。根据其结构特征我们将苹果中的688个RING finger结构域分为9大类:367个RING-H2,208个RING-HC,10个RING-C2,35个RING-v,1个RING-D,11个RING-S/T,2个RING-G,10个RING-mH2和44个RING-mHC。其中,前7类是在拟南芥中曾经出现过的,后2类是在苹果中首次发现的。结构分析描述了每一种RING型结构域的典型特征。同时还鉴定了RING型蛋白中除了RING结构域以外的其他结构域,为将来RING finger蛋白的功能研究奠定基础。
The ubiquitin (Ub)/26S pathway is a major system for protein degradation that is conserved in all eukaryotes cells. The specificity of ubiquitination is largely determined by the many isoforms of E3 that recruits specific target protein(s). In Arabidopsis thaliana more than 1400 genes (~5%of the proteome) encode subunits of the E3 ubiquitin ligases, which confer substrate specificity to the pathway. F-box and RING finger genes are the most common family genes in Arabidopsis. The fuction and structure analysis of F-box in Arabidopsis and RING finger proteins in apple provide valuable information for understanding the classification and putative functions of the E3 gene family in higher plants. The obtained results are as follows:
(1) First, an F-box-containing gene was analyzed. Using bioinformatics approaches, 31 E3s containing DRE (dehydration responsive element) motif were isolated from 1488 E3s in Arabidopsis, in which an F-box gene (AtPP2-B11) were extremely induced by drought treatment.
(2) GUS activity assay showed that the DRE motif in the promoter region of AtPP2-B11 played partial roles in drought response. AtPP2-B11 also showed slightly increased expression treated by ABA, indicating that AtPP2-B11 may respons to drought both in ABA-independent and ABA-dependent pathways.
(3) Transgenic plants overexpressing AtPP2-B11 exhibited decreased drought tolerance. Quantitative RT-PCR showed that the expression levels of a number of key ABA and drought stress marker genes such as LEA14,COR15a,RD29A in transgeneic plants were altered in drought treatment.
(4) Interactive proteins were screened from drought-treatment cDNA library with the full-length of AtPP2-B11 as bait protein by Yeast Two-Hybrid System. More than 80 positive clones were identified by PCR colony screening and the representative clones were sequenced. Among them 20 clones were selected which interacted with full-length AtPP2-B11. Further Yeast Two-Hybrid assay and Bimolecular Fluorescenc Complementation (BiFC) assay showed that AtPP2-B11 protein interacted with LEA14 protein, indicating that AtPP2-B11 gene may fuction as a novel drought tolerance repressor by regulating the level of LEA14.
(5) In addition, we analyzed the RING finger proteins in apple genome which were recently secquenced. In our study, 688 RING domains in 663 predicted proteins were identified in apple. Based on the characteristics of RING domains, nine RING type were identified: 367 RING-H2, 208 RING-HC, 10 RING-C2, 35 RING-v, 1 RING-D, 11 RING-S/T, 2 RING-G, 10 RING-mH2 and 44 RING-mHC, in which the first seven types were decribed previously in Arabidopsis, while the latter two types were newly identified in apple. Proteins containing RING finger motifs were further classified into 57 groups according to the different known or unknown domains outside the RING domains.
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