C_3/C_4光合作用差异表达基因的鉴定与分析
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摘要
和C3植物相比,C4植物具有更高的光合作用效率。利用基因工程手段将C4核心循环相关酶导入C3植物被认为是提高C3植物光合作用效率的有效手段之一。但是对于潜在的C4光合作用调控机制(如光合作用组织的结构形成机制和叶肉(维管束鞘)细胞叶绿体分化与定位)却了解甚少。莎草属中有不少种在不同的生长环境中采用C3和C4两种不同光合作用模式,这些特征使其成为研究C3/C4光合作用分子调控机制方面的良好体系。本研究分别用抑制差减杂交和第二代测序技术鉴定Eleocharis baldwinii(陆生为C4模式,水生为C3-C4兼性模式)C3/C4差异表达基因。研究主要目的是分析C3/C4代谢水平差异,并为后续调控研究提供候选基因。主要研究结果如下：
1.以陆生cDNA为tester,水生cDNA为driver,构建陆生上调表达差减文库。用陆生和水生总cDNA为探针,筛选出64个陆生上升表达ESTs。通过生物信息学分析,共确认了56个单基因,其中52个具有注释,它们的功能主要涉及C4核心循环基因,转运子,光系统相关蛋白和调控基因,如转录因子。但是抑制差减杂交所能提供的信息相对有限；
2.利用第二代测序技术对陆生,ABA诱导和水生3种材料转录组进行深度测序。经过序列拼接,共获得61747条单一序列,长度分布在200bp-3000bp之间,平均长度为471bp。最后我们共得到24204条差异表达序列；
3.对差异表达基因进行聚类分析。结果显示ABA诱导样品的表达模式与陆生更为相近。同时根据表达谱的差异将差异基因分为9个cluster,其中Ⅰ,Ⅲ和Ⅵ类代表了C3/C4主要表达差异基因,而Ⅸ类则代表了可能跟环境相关的差异基因；
4.对代谢相关差异表达基因进行功能分析。结果发现：1)C4核心循环相关酶类和大批跟代谢物相关的转运子在陆生和ABA诱导材料中出现上调表达,表明这些转运子可能在C4光合作用代谢流和发育调控中起着重要作用；2)卡尔文循环,柠檬酸循环和糖酵解循环相关的酶也表现出C4上调表达,它们主要的功能可能是提高C4光合作用的碳固定能力及为C02固定提供部分碳骨架；3)核糖体复合体在C4条件下下调表达暗示着更少的蛋白质合成和更高的氮素利用效率；4)与光吸收相关的基因(如叶绿素结合蛋白基因,叶绿素合成基因,类胡萝卜素合成基因和光敏色素响应基因)和C2循环相关基因表现出水生环境(水生和ABA诱导)和陆生环境表达差异,这类基因反映了主要的环境差异,可能与C4光合作用代谢途径并没有直接的联系；5)ABA合成及分解代谢相关基因在陆生和ABA诱导材料中的表达差异暗示,可以通过提高ABA内源生物合成水平或体外补充,这两种不同的策略来维持体内ABA水平,进而对C4光合作用模式进行调控;
5.鉴定了1205个C3/C4调控类差异表达基因,包括830个转录因子和375个蛋白激酶等。Real-time表达量检测结果表明部分差异表达基因的表达模式与光合作用组织的发育进程和叶绿体的积累分化过程一致,这类基因可能参与光合作用组织发育调控,将作为主要的候选基因在后续的实验中做进一步的功能验证；
6.在C3/C4差异表达基因中检测到一些与表观修饰相关的基因。PPDK基因组DNA MSRE-PCR结果显示在水生和陆生条件下确实存在甲基化水平的差异。
Comparing to C3plants, C4plants have higher photosynthesis efficiency.and introducing the C4core cycle related enzymes into C3plants by genetic engineering was considered as one of the effective efficient strategy to increase its photosynthesis efficiency. However, the potential photosynthetic regulation mechanisms, such as the photosynthetic apparatus formation and the differentiation and positioning of mesophyll chloroplast and bundle sheath chloroplast, are remaining unknown. Many species in Eleochairs use different photosynthetic models in different environments and this feature make them to be an ideal system in C4regulatory research. In this study, SSH and NGS were used to identify the C3/C4differentially expressed genes in Eleocharis baldwinii. The main aims are to analysis the C3/C4metabolic differentiation and obtain candidate genes for C4regulatory research. The main results are as follow:
1. A terrestrial up regulated SSH library was constructed using terrestrial cDNA as the tester and submerged cDNA as the driver.64terrestrial up regulated ESTs were identified by the total cDNA probes of terrestrial and submerged. After bioinformatics assay,56unigenes were confirmed and52of them have GO annotations. These genes mainly involved in C4core cycle, metabolic transportation, photosystem and regulatory genes, such as transcription factor. However, the information that SSH supplied was very limited;
2. Three RNA samples including terrestrial, ABA induced and submerged were deeply sequenced by NGS (Next Generation Sequencing). After clean reads assembly, we totally obtained61747unigenes with an average length of471bp and the length distributed between200bp to3000bp. At last,24204DE (Differentially Expressed) genes were identified;
3. The clustering results of DE genes showed the gene expression profiles in ABA induced sample was more similar to those in terrestrial. At the same time, the DE genes can be divided into9clusters according the different expression profiles. The cluster I, III and VI represented the most of C3/C4differentiation and the genes in cluster IX might relate to the environment responding;
4. After gene functional assay, we found:1) The C4core cycle related enzymes and a huge of metabolic reporters were up regulated in terrestrial and ABA induced samples and these transporter may contribute to C4photosynthesis in both metabolism fluxes and developmental regulatory;2) The genes related to Calvin cycle, the citrate cycle and glycolysis were also up regulated in C4culms and their roles in C4photosynthesis may relate to the increasing photosynthetic efficiency and supply carbon skeleton for CO2fixation;3) The down regulated ribosome complex related genes suggested a less protein synthesis and a higher N use efficiency in C4culms;4) The different expression profiles of light harvesting and C2cycle related genes between terrestrial and under water (both submerged and ABA induced) may relate to the environment responding and not directly relate to C4photosynthesis, such as genes of chlorophyll binding protein, biosynthesis of chlorophyll and carotenoids and phytochrome responding genes;5) The different expression profiles of ABA biosynthesis and catabolism related genes in terrestrial and ABA induced sample indicated that an increasing endogenous ABA biosynthesis and additional exogenous ABA complementation were two different strategies to maintain endogenous ABA homeostasis in C4photosynthetic regulatory pathway in E. baldwinii.
5.1205C3/C4differentially accumulated regulation genes were identified including830transcriptional factors and375protein kinases. The Real-time results suggested that some regulation genes were co-expressed with the development procedure of photosynthetic apparatus and chloroplast accumulation and differentiation. These kind of genes may involve in the development controlling of photosynthetic apparatus and will be served as the candidate genes in the gene functional validation;
6. In this study, some genes related to epigenetic modification were also differentially expressed in C3/C4samples. The MSRE-PCR results of PPDK genomic DNA showed there were indeed different methylation levels in terrestrial and submerged environments.
1.以陆生cDNA为tester,水生cDNA为driver,构建陆生上调表达差减文库。用陆生和水生总cDNA为探针,筛选出64个陆生上升表达ESTs。通过生物信息学分析,共确认了56个单基因,其中52个具有注释,它们的功能主要涉及C4核心循环基因,转运子,光系统相关蛋白和调控基因,如转录因子。但是抑制差减杂交所能提供的信息相对有限；
2.利用第二代测序技术对陆生,ABA诱导和水生3种材料转录组进行深度测序。经过序列拼接,共获得61747条单一序列,长度分布在200bp-3000bp之间,平均长度为471bp。最后我们共得到24204条差异表达序列；
3.对差异表达基因进行聚类分析。结果显示ABA诱导样品的表达模式与陆生更为相近。同时根据表达谱的差异将差异基因分为9个cluster,其中Ⅰ,Ⅲ和Ⅵ类代表了C3/C4主要表达差异基因,而Ⅸ类则代表了可能跟环境相关的差异基因；
4.对代谢相关差异表达基因进行功能分析。结果发现：1)C4核心循环相关酶类和大批跟代谢物相关的转运子在陆生和ABA诱导材料中出现上调表达,表明这些转运子可能在C4光合作用代谢流和发育调控中起着重要作用；2)卡尔文循环,柠檬酸循环和糖酵解循环相关的酶也表现出C4上调表达,它们主要的功能可能是提高C4光合作用的碳固定能力及为C02固定提供部分碳骨架；3)核糖体复合体在C4条件下下调表达暗示着更少的蛋白质合成和更高的氮素利用效率；4)与光吸收相关的基因(如叶绿素结合蛋白基因,叶绿素合成基因,类胡萝卜素合成基因和光敏色素响应基因)和C2循环相关基因表现出水生环境(水生和ABA诱导)和陆生环境表达差异,这类基因反映了主要的环境差异,可能与C4光合作用代谢途径并没有直接的联系；5)ABA合成及分解代谢相关基因在陆生和ABA诱导材料中的表达差异暗示,可以通过提高ABA内源生物合成水平或体外补充,这两种不同的策略来维持体内ABA水平,进而对C4光合作用模式进行调控;
5.鉴定了1205个C3/C4调控类差异表达基因,包括830个转录因子和375个蛋白激酶等。Real-time表达量检测结果表明部分差异表达基因的表达模式与光合作用组织的发育进程和叶绿体的积累分化过程一致,这类基因可能参与光合作用组织发育调控,将作为主要的候选基因在后续的实验中做进一步的功能验证；
6.在C3/C4差异表达基因中检测到一些与表观修饰相关的基因。PPDK基因组DNA MSRE-PCR结果显示在水生和陆生条件下确实存在甲基化水平的差异。
Comparing to C3plants, C4plants have higher photosynthesis efficiency.and introducing the C4core cycle related enzymes into C3plants by genetic engineering was considered as one of the effective efficient strategy to increase its photosynthesis efficiency. However, the potential photosynthetic regulation mechanisms, such as the photosynthetic apparatus formation and the differentiation and positioning of mesophyll chloroplast and bundle sheath chloroplast, are remaining unknown. Many species in Eleochairs use different photosynthetic models in different environments and this feature make them to be an ideal system in C4regulatory research. In this study, SSH and NGS were used to identify the C3/C4differentially expressed genes in Eleocharis baldwinii. The main aims are to analysis the C3/C4metabolic differentiation and obtain candidate genes for C4regulatory research. The main results are as follow:
1. A terrestrial up regulated SSH library was constructed using terrestrial cDNA as the tester and submerged cDNA as the driver.64terrestrial up regulated ESTs were identified by the total cDNA probes of terrestrial and submerged. After bioinformatics assay,56unigenes were confirmed and52of them have GO annotations. These genes mainly involved in C4core cycle, metabolic transportation, photosystem and regulatory genes, such as transcription factor. However, the information that SSH supplied was very limited;
2. Three RNA samples including terrestrial, ABA induced and submerged were deeply sequenced by NGS (Next Generation Sequencing). After clean reads assembly, we totally obtained61747unigenes with an average length of471bp and the length distributed between200bp to3000bp. At last,24204DE (Differentially Expressed) genes were identified;
3. The clustering results of DE genes showed the gene expression profiles in ABA induced sample was more similar to those in terrestrial. At the same time, the DE genes can be divided into9clusters according the different expression profiles. The cluster I, III and VI represented the most of C3/C4differentiation and the genes in cluster IX might relate to the environment responding;
4. After gene functional assay, we found:1) The C4core cycle related enzymes and a huge of metabolic reporters were up regulated in terrestrial and ABA induced samples and these transporter may contribute to C4photosynthesis in both metabolism fluxes and developmental regulatory;2) The genes related to Calvin cycle, the citrate cycle and glycolysis were also up regulated in C4culms and their roles in C4photosynthesis may relate to the increasing photosynthetic efficiency and supply carbon skeleton for CO2fixation;3) The down regulated ribosome complex related genes suggested a less protein synthesis and a higher N use efficiency in C4culms;4) The different expression profiles of light harvesting and C2cycle related genes between terrestrial and under water (both submerged and ABA induced) may relate to the environment responding and not directly relate to C4photosynthesis, such as genes of chlorophyll binding protein, biosynthesis of chlorophyll and carotenoids and phytochrome responding genes;5) The different expression profiles of ABA biosynthesis and catabolism related genes in terrestrial and ABA induced sample indicated that an increasing endogenous ABA biosynthesis and additional exogenous ABA complementation were two different strategies to maintain endogenous ABA homeostasis in C4photosynthetic regulatory pathway in E. baldwinii.
5.1205C3/C4differentially accumulated regulation genes were identified including830transcriptional factors and375protein kinases. The Real-time results suggested that some regulation genes were co-expressed with the development procedure of photosynthetic apparatus and chloroplast accumulation and differentiation. These kind of genes may involve in the development controlling of photosynthetic apparatus and will be served as the candidate genes in the gene functional validation;
6. In this study, some genes related to epigenetic modification were also differentially expressed in C3/C4samples. The MSRE-PCR results of PPDK genomic DNA showed there were indeed different methylation levels in terrestrial and submerged environments.
引文
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