大白菜和甘蓝型油菜AP2/ERF家族转录因子的克隆与分析
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摘要
植物一生面临很多的生物和非生物胁迫,严重影响植物的生长发育,从而影响作物的产量。很多基因被这些胁迫诱导表达,以增强植物对逆境的抗性。转录因子是其中重要的一类调控基因,通过与顺式元件相互作用调节植物对各种环境胁迫的适应。AP2/ERF家族是植物中重要的一类转录因子,包含一个高度保守的AP2-DNA结合域,其基因编码的产物具有广泛的功能。
植物基因组分析是研究基因功能和基因进化的有效手段,目前植物基因功能解析很大程度上依赖模式植物拟南芥的研究信息。拟南芥、大白菜和油菜同属于十字花科,亲缘关系较为密切,因此可以利用拟南芥基因组研究的基因资源和生物信息资源,开展大白菜和油菜的功能基因组研究。本研究分析了大白菜和油菜一类重要的转录因子AP2/ERF,对于研究大白菜和油菜的逆境抗性、开花机制和果实发育等有重要的意义。
1、通过对大白菜EST数据库分析,使用拟南芥AP2/ERF家族转录因子氨基酸序列信息为探针,得到62个AP2/ERF家族基因。基于这些大白菜AP2/ERF家族转录因子的氨基酸序列,可以分为四个亚族(ERF、DREB、RAV和AP2),而且上述亚族的分类与拟南芥非常相似。进一步对大白菜AP2/ERF家族转录因子进行了一系列的生物信息学分析：cDNA和氨基酸序列、组成、理化性质、进化树、保守域序列和功能域。通过对EST数据进一步分析研究大白菜AP2/ERF家族转录因子的表达。研究发现,上述62个AP2/ERF转录因子家族成员在根中丰度最高,达到33%,接着是叶和种子,丰度均为21%。芽、花和长果角中的丰度相对较低,分别为：6%、8%和11%。大白菜AP2/ERF家族转录因子基因表达量最高的出现在根中,为BraERF-B2-5基因。
2、利用油菜UniGene数据库,通过电子克隆从一个UniGene中分离得到三个AP2/ERF转录因子(BnaERF1、BnaERF2和BnaERF3)。BnaERF1、BnaERF2和BnaERF3属于AP2/ERF家族转录因子ERF-B2亚族,是亲水性蛋白,蛋白质三级结构与AtERF1相似。蛋白质无序化分析发现,油菜BnaERF1、BnaERF2和BnaERF3无序化程度小于拟南芥AtERF1.通过PCR和RT-PCR方法分别从甘蓝型油菜“沪油15”的DNA和cDNA中扩增了上述基因,初步分析BnaERF2没有内含子,BnaERF1和BnaERF3有内含子。另外,通过EST丰度分析显示,该类转录因子表达最高峰在种子中,其次为花,在芽、茎和分生组织中没有检测到表达。
3、以拟南芥AP2/ERF-B3亚族转录因子保守序列为信息探针,分离得到2个油菜AP2/ERF-B3亚族的转录因子BnaERFB3-1和BnaERFB3-2.通过PCR和RT-PCR方法从甘蓝型油菜“沪油15”的DNA和cDNA中克隆了上述基因。序列分析显示,克隆的BnaERFB3-1-Hy15和BnaERFB3-2-Hy15转录因子都没有内含子,BnaERFB3-1-Hy15和BnaERFB3-2-Hy15是亲水性蛋白,蛋白质三级结构与AtERF5相似。BnaERFB3-1-Hy15和BnaERFB3-2-Hyl5蛋白无序化程度大于拟南芥AtERF5。EST丰度显示,BnaERFB3-1表达集中在种子中,而BnaERFB3-2表达集中在根中。另外,将上述基因分别构建入酵母表达载体和植物双元表达载体。
4、以拟南芥AP2/ERF-B4亚族转录因子保守序列为探针,分离得到一个UniGene (Bna.17538),进一步序列拼接得到一个油菜AP2/ERF-B4亚族转录因子BnaERFB4-1。分析结果显示BnaERFB4-1是亲水性蛋白,蛋白质三级结构与拟南芥RAP2.6L非常相似,蛋白质无序化程度大于拟南芥RAP2.6L.通过PCR和RT-PCR方法分别从甘蓝型油菜“沪油15”DNA和cDNA中分离了BnaERFB4-1基因。序列测定证实BnaERFB4-1-Hy15基因存在一个内含子。将BnaERFB4-1-Hy15基因通过Bam HI和Sac I酶切后分别插入酵母表达载体YK3302和植物双元表达载体pYF1404,构建了BnaERFB4-1-Hy15基因的酵母体内结合和植物转化载体。
5、以拟南芥CBF家族转录因子保守序列为信息探针,搜索油菜UniGene数据库,得到二个UniGene:Bna.2193和Bna.2260,序列拼接得到2个cDNA序列(BnaCBF-1和BnaCBF-2).通过PCR和RT-PCR方法分别从甘蓝型油菜“沪油15”DNA和cDNA中克隆了上述基因。序列分析显示,“沪油15”的BnaCBF-1-Hy15和BnaCBF-2-Hy15基因都没有内含子。BnaCBF-1-Hy15和BnaCBF-2-Hy15转录因子属于AP2/ERF家族中的DREB-A1亚族,是亲水性蛋白,在蛋白质的三级结构上与AtCBF1相似。
Plants are exposed to many types of abiotic stress and biotic stress during their life-cycle, such as drought, salinity, and high and low temperatures, which have adverse effects on growth and the productivity of crop plants. A variety of plant genes are induced by a single or multiple stresses, and their products are thought to function in stress tolerance and in the regulation of gene expression and signal transduction in stress responses. Transcription factors have critical roles in the regulation of gene expression. Various transcription factors and cis-acting elements in the stress-responsive promoters function in plant adaptation to environmental stress. AP2/ERF is a family of transcription factors containing the highly conserved ethylene-responsive-element-binding AP2 DNA-binding domain. The AP2/ERF family genes are involved in response to drought, high salt content, temperature change, disease resistance, and the flowering control pathway, and have been analyzed by a combination of genetic and molecular approaches.
Analysis of plant genomes can also facilitate the study of genome and gene evolution. Until relatively recently, gene functional dissection of plant has depended largely on molecular characterization of individual genes from various species. Companied with complete genome sequences, technologies of bioinformatic analysis have advanced so that the information stored in the various genomes of plants can be explored to search information that regulate plant growth and development. Brassica rapa, B. napus and Arabidopsis thaliana are members of the crucifereae and the protein coding sequences are conserved among the three species. In this study, we cloned and analyzed an important plant transcription factor family, AP2/ERF from Chinese cabbage, oilseed and compared them with the model plant species, Arabidopsis. Since AP2/ERF gene family are involved in regulating stress responses and flowering, and relatively few genes of this gene family from Chinese cabbage and oilseed have been characterized in detail, these bioinformatic analyses will help scientists to make use of information from other species to study those plants stress resistance and flowering and fruit development, such as orthorlogous relationship of a particular stress response gene.
1. Starting from a large database of B. rapa expressed sequence tags (ESTs),62 putative AP2/ERF family genes were identified by in silico cloning using the amino acid sequence of A. thaliana as a probe. Based on the number of AP2/ERF domains and functions of the genes, the AP2/ERF transcription factors from B. rapa were classified into four subfamilies as ERF, DREB, RAV and AP2. Nearly all the genes were similar to those defined earlier as AP2/ERF from A. thaliana. The following properties and attributes were predicted and analyzed:cDNA and deduced amino acid sequence, composition, physical and chemical characterization, phylogenetic tree, conserved domain sequences, and function domain. Using large-scale transcriptome analysis and available EST information as a source of expression data for digital expression profiling, differentially expressed genes were identified among diverse plant tissues. Roots contained the largest number of transcripts of the AP2/ERF family genes, followed by leaves and seeds. Only a few of the 62 AP2/ERF family genes were expressed in all tissues:most were expressed only in some tissues but not in others. Some AP2/ERF family genes were constitutive and expressed in all the six kinds of tissues investigated namely seeds, siliques, buds, flowers, leaves, and roots. The maximum expression was that of BraERF-B2-5, and it was recorded from seed tissue.
2. Three AP2/ERF family transcriptional regulators (BnaERFl, BnaERF2 and BnaERF3) were isolated from B. napus by in silico cloning method using the conserved domain amino acid sequence of A. thaliana ERF as probe. Then, BnaERFl, BnaERF2 and BnaERF3 genes were isolated from B. napus L. Huyoul5 by RT-PCR and PCR using cDNA and DNA as template.
3. Two AP2/ERF family transcriptional regulators (BnaERFB3-1 and BnaERFB3-2) were isolated from B. napus by in silico cloning method using the conserved domain amino acid sequence of A. thaliana AP2/ERF-B3 subfamily as probe. Based on the sequences of BnaERFB3-1 and BnaERFB3-2, we isolated the BnaERFB3-1-Hy15 gene and BnaERFB3-2-Hy15 gene from winter and spring type B. napus L. cv Huyoul5 by RT-PCR and PCR using cDNA and DNA as template. No intron localized on the two genes from Huyou15, respectively. BnaERFB3-1-Hy15 and BnaERFB3-2-Hy15 were hydrophilic protein. The two proteins and AtERF5 have similar three-dimension structure. The disordered residues of protein BnaERFB3-1-Hy15 and BnaERFB3-2-Hy15 were higher than that of AtERF5. BnaERFB3-1 was mainly expression in seed, while BnaERFB3-2 was mainly expression in root. Moreover, those genes were successfully constructed into the recombinant plasmids of plant expression vector and yeast expression vector.
4. One AP2/ERF family transcriptional regulators (Named BnaERFB4-1) was isolated from B. napus by in silico cloning method using the conserved domain amino acid sequence of A. thaliana ERF-B4 subfamily as probe. BnaERFB4-1 was hydrophilic protein. The protein and RAP2.6L have similar three-dimension structure. The disordered residues of protein BnaERFB4-1 was higher than that of RAP2.6L. We isolated the BnaERFB4-1 gene from winter and spring type B. napus L. cv Huyou15 by RT-PCR and PCR using cDNA and DNA as template. DNA sequencing and analyzing indicated that there only three amino acid residues difference between BnaERFB4-1-Hy15 and BnaERFB4-1. Moreover, the gene was ligated into expression vectors, respectively. It was successful to construct the recombinant plasmids of plant expression vector and yeast expression vector.
5. Two CBF family transcriptional regulators were isolated from B. napus by in silico cloning method using the conserved domain amino acid sequence of AtCBF1 as probe. Based on the sequences of BnaCBF-1 and BnaCBF-2 from Bna.2193 and Bna.2260, the BnaCBF-1-Hy15 and BnaCBF-2-Hy15 genes were isolated from B. napus L. cv Huyou15 by RT-PCR and PCR using cDNA and DNA as template. No intron localized on the two genes from Huyou15, respectively. BnaCBF-1-Hy15 and BnaCBF-2-Hy15 were part of the DREB-A1 subfamily, and were hydrophilic protein. The two proteins and AtCBF1 have similar three-dimension structure.
植物基因组分析是研究基因功能和基因进化的有效手段,目前植物基因功能解析很大程度上依赖模式植物拟南芥的研究信息。拟南芥、大白菜和油菜同属于十字花科,亲缘关系较为密切,因此可以利用拟南芥基因组研究的基因资源和生物信息资源,开展大白菜和油菜的功能基因组研究。本研究分析了大白菜和油菜一类重要的转录因子AP2/ERF,对于研究大白菜和油菜的逆境抗性、开花机制和果实发育等有重要的意义。
1、通过对大白菜EST数据库分析,使用拟南芥AP2/ERF家族转录因子氨基酸序列信息为探针,得到62个AP2/ERF家族基因。基于这些大白菜AP2/ERF家族转录因子的氨基酸序列,可以分为四个亚族(ERF、DREB、RAV和AP2),而且上述亚族的分类与拟南芥非常相似。进一步对大白菜AP2/ERF家族转录因子进行了一系列的生物信息学分析：cDNA和氨基酸序列、组成、理化性质、进化树、保守域序列和功能域。通过对EST数据进一步分析研究大白菜AP2/ERF家族转录因子的表达。研究发现,上述62个AP2/ERF转录因子家族成员在根中丰度最高,达到33%,接着是叶和种子,丰度均为21%。芽、花和长果角中的丰度相对较低,分别为：6%、8%和11%。大白菜AP2/ERF家族转录因子基因表达量最高的出现在根中,为BraERF-B2-5基因。
2、利用油菜UniGene数据库,通过电子克隆从一个UniGene中分离得到三个AP2/ERF转录因子(BnaERF1、BnaERF2和BnaERF3)。BnaERF1、BnaERF2和BnaERF3属于AP2/ERF家族转录因子ERF-B2亚族,是亲水性蛋白,蛋白质三级结构与AtERF1相似。蛋白质无序化分析发现,油菜BnaERF1、BnaERF2和BnaERF3无序化程度小于拟南芥AtERF1.通过PCR和RT-PCR方法分别从甘蓝型油菜“沪油15”的DNA和cDNA中扩增了上述基因,初步分析BnaERF2没有内含子,BnaERF1和BnaERF3有内含子。另外,通过EST丰度分析显示,该类转录因子表达最高峰在种子中,其次为花,在芽、茎和分生组织中没有检测到表达。
3、以拟南芥AP2/ERF-B3亚族转录因子保守序列为信息探针,分离得到2个油菜AP2/ERF-B3亚族的转录因子BnaERFB3-1和BnaERFB3-2.通过PCR和RT-PCR方法从甘蓝型油菜“沪油15”的DNA和cDNA中克隆了上述基因。序列分析显示,克隆的BnaERFB3-1-Hy15和BnaERFB3-2-Hy15转录因子都没有内含子,BnaERFB3-1-Hy15和BnaERFB3-2-Hy15是亲水性蛋白,蛋白质三级结构与AtERF5相似。BnaERFB3-1-Hy15和BnaERFB3-2-Hyl5蛋白无序化程度大于拟南芥AtERF5。EST丰度显示,BnaERFB3-1表达集中在种子中,而BnaERFB3-2表达集中在根中。另外,将上述基因分别构建入酵母表达载体和植物双元表达载体。
4、以拟南芥AP2/ERF-B4亚族转录因子保守序列为探针,分离得到一个UniGene (Bna.17538),进一步序列拼接得到一个油菜AP2/ERF-B4亚族转录因子BnaERFB4-1。分析结果显示BnaERFB4-1是亲水性蛋白,蛋白质三级结构与拟南芥RAP2.6L非常相似,蛋白质无序化程度大于拟南芥RAP2.6L.通过PCR和RT-PCR方法分别从甘蓝型油菜“沪油15”DNA和cDNA中分离了BnaERFB4-1基因。序列测定证实BnaERFB4-1-Hy15基因存在一个内含子。将BnaERFB4-1-Hy15基因通过Bam HI和Sac I酶切后分别插入酵母表达载体YK3302和植物双元表达载体pYF1404,构建了BnaERFB4-1-Hy15基因的酵母体内结合和植物转化载体。
5、以拟南芥CBF家族转录因子保守序列为信息探针,搜索油菜UniGene数据库,得到二个UniGene:Bna.2193和Bna.2260,序列拼接得到2个cDNA序列(BnaCBF-1和BnaCBF-2).通过PCR和RT-PCR方法分别从甘蓝型油菜“沪油15”DNA和cDNA中克隆了上述基因。序列分析显示,“沪油15”的BnaCBF-1-Hy15和BnaCBF-2-Hy15基因都没有内含子。BnaCBF-1-Hy15和BnaCBF-2-Hy15转录因子属于AP2/ERF家族中的DREB-A1亚族,是亲水性蛋白,在蛋白质的三级结构上与AtCBF1相似。
Plants are exposed to many types of abiotic stress and biotic stress during their life-cycle, such as drought, salinity, and high and low temperatures, which have adverse effects on growth and the productivity of crop plants. A variety of plant genes are induced by a single or multiple stresses, and their products are thought to function in stress tolerance and in the regulation of gene expression and signal transduction in stress responses. Transcription factors have critical roles in the regulation of gene expression. Various transcription factors and cis-acting elements in the stress-responsive promoters function in plant adaptation to environmental stress. AP2/ERF is a family of transcription factors containing the highly conserved ethylene-responsive-element-binding AP2 DNA-binding domain. The AP2/ERF family genes are involved in response to drought, high salt content, temperature change, disease resistance, and the flowering control pathway, and have been analyzed by a combination of genetic and molecular approaches.
Analysis of plant genomes can also facilitate the study of genome and gene evolution. Until relatively recently, gene functional dissection of plant has depended largely on molecular characterization of individual genes from various species. Companied with complete genome sequences, technologies of bioinformatic analysis have advanced so that the information stored in the various genomes of plants can be explored to search information that regulate plant growth and development. Brassica rapa, B. napus and Arabidopsis thaliana are members of the crucifereae and the protein coding sequences are conserved among the three species. In this study, we cloned and analyzed an important plant transcription factor family, AP2/ERF from Chinese cabbage, oilseed and compared them with the model plant species, Arabidopsis. Since AP2/ERF gene family are involved in regulating stress responses and flowering, and relatively few genes of this gene family from Chinese cabbage and oilseed have been characterized in detail, these bioinformatic analyses will help scientists to make use of information from other species to study those plants stress resistance and flowering and fruit development, such as orthorlogous relationship of a particular stress response gene.
1. Starting from a large database of B. rapa expressed sequence tags (ESTs),62 putative AP2/ERF family genes were identified by in silico cloning using the amino acid sequence of A. thaliana as a probe. Based on the number of AP2/ERF domains and functions of the genes, the AP2/ERF transcription factors from B. rapa were classified into four subfamilies as ERF, DREB, RAV and AP2. Nearly all the genes were similar to those defined earlier as AP2/ERF from A. thaliana. The following properties and attributes were predicted and analyzed:cDNA and deduced amino acid sequence, composition, physical and chemical characterization, phylogenetic tree, conserved domain sequences, and function domain. Using large-scale transcriptome analysis and available EST information as a source of expression data for digital expression profiling, differentially expressed genes were identified among diverse plant tissues. Roots contained the largest number of transcripts of the AP2/ERF family genes, followed by leaves and seeds. Only a few of the 62 AP2/ERF family genes were expressed in all tissues:most were expressed only in some tissues but not in others. Some AP2/ERF family genes were constitutive and expressed in all the six kinds of tissues investigated namely seeds, siliques, buds, flowers, leaves, and roots. The maximum expression was that of BraERF-B2-5, and it was recorded from seed tissue.
2. Three AP2/ERF family transcriptional regulators (BnaERFl, BnaERF2 and BnaERF3) were isolated from B. napus by in silico cloning method using the conserved domain amino acid sequence of A. thaliana ERF as probe. Then, BnaERFl, BnaERF2 and BnaERF3 genes were isolated from B. napus L. Huyoul5 by RT-PCR and PCR using cDNA and DNA as template.
3. Two AP2/ERF family transcriptional regulators (BnaERFB3-1 and BnaERFB3-2) were isolated from B. napus by in silico cloning method using the conserved domain amino acid sequence of A. thaliana AP2/ERF-B3 subfamily as probe. Based on the sequences of BnaERFB3-1 and BnaERFB3-2, we isolated the BnaERFB3-1-Hy15 gene and BnaERFB3-2-Hy15 gene from winter and spring type B. napus L. cv Huyoul5 by RT-PCR and PCR using cDNA and DNA as template. No intron localized on the two genes from Huyou15, respectively. BnaERFB3-1-Hy15 and BnaERFB3-2-Hy15 were hydrophilic protein. The two proteins and AtERF5 have similar three-dimension structure. The disordered residues of protein BnaERFB3-1-Hy15 and BnaERFB3-2-Hy15 were higher than that of AtERF5. BnaERFB3-1 was mainly expression in seed, while BnaERFB3-2 was mainly expression in root. Moreover, those genes were successfully constructed into the recombinant plasmids of plant expression vector and yeast expression vector.
4. One AP2/ERF family transcriptional regulators (Named BnaERFB4-1) was isolated from B. napus by in silico cloning method using the conserved domain amino acid sequence of A. thaliana ERF-B4 subfamily as probe. BnaERFB4-1 was hydrophilic protein. The protein and RAP2.6L have similar three-dimension structure. The disordered residues of protein BnaERFB4-1 was higher than that of RAP2.6L. We isolated the BnaERFB4-1 gene from winter and spring type B. napus L. cv Huyou15 by RT-PCR and PCR using cDNA and DNA as template. DNA sequencing and analyzing indicated that there only three amino acid residues difference between BnaERFB4-1-Hy15 and BnaERFB4-1. Moreover, the gene was ligated into expression vectors, respectively. It was successful to construct the recombinant plasmids of plant expression vector and yeast expression vector.
5. Two CBF family transcriptional regulators were isolated from B. napus by in silico cloning method using the conserved domain amino acid sequence of AtCBF1 as probe. Based on the sequences of BnaCBF-1 and BnaCBF-2 from Bna.2193 and Bna.2260, the BnaCBF-1-Hy15 and BnaCBF-2-Hy15 genes were isolated from B. napus L. cv Huyou15 by RT-PCR and PCR using cDNA and DNA as template. No intron localized on the two genes from Huyou15, respectively. BnaCBF-1-Hy15 and BnaCBF-2-Hy15 were part of the DREB-A1 subfamily, and were hydrophilic protein. The two proteins and AtCBF1 have similar three-dimension structure.
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