水稻高温逆境下全基因组差异基因表达谱分析与特异启动子的功能鉴定
摘要
水稻作为全世界最重要的粮食作物之一,受到高温、干旱、病虫害等多种逆境的影响也越来越大,因此而造成的损失已经引起全世界的关注。为此,改善和提高水稻抗逆性就成为全球性的重大课题。通过筛选和克隆逆境相关基因和启动子并鉴定其功能就成为借助基因工程手段改良水稻性状的重要内容。
本论文利用水稻全基因组微阵列技术平台,开展了水稻幼穗和剑叶的高温全基因组表达谱数据的分析和挖掘,取得了一些有意义的成果。在此基础上,利用转基因技术,进一步分析了3个高温显著响应基因的启动子在经高温和干旱处理的水稻幼穗和剑叶中的表达活性。结果如下：
(1)在利用HCL等方法进行数据质量控制和评价的基础上,分别获得了水稻幼穗和剑叶在高温条件下的差异表达基因。对各个时间点的差异表达基因数目分析发现,高温处理2h可能是水稻响应高温逆境的一个重要转折点；GO分析及基因表达规律分析的结果表明,来自幼穗和剑叶的热激响应基因主要与转运蛋白、蛋白结合、抗氧化、催化、转录调控、逆境响应等相关；且对两个组织中受高温显著调控的包括Hsf、AP2/ERF、bHLH、bZIP、Myb、WRKY、NAC和C2H2等在内的转录因子和Hsp家族基因的表达特征进行了比较分析。这些研究结果将为组织特异性的高温响应基因和启动子的筛选与鉴定提供重要线索；
(2)发现水稻幼穗中高温响应的ROS相关基因的复杂而显著的表达变化有助于维持ROS的平衡；与生长素、ABA和乙烯代谢与信号传导相关的基因均表达下调,而与光、钙离子相关的蛋白基因和G蛋白编码基因则有显著上调；
(3)对水稻幼穗中共表达基因的启动子进行了分析和挖掘,发现GCC box、 CE3、ABRE和HSE等在早期上调的聚类中显著富集,而GCC box和CE3还成为两个共现网络的中心,且HSE和ABRE与这两个元件关系密切,具有显著的共现特征；
(4)构建了以ROS为中心的调控模型,利用水稻幼穗全基因组微阵列数据和ROS定量分析的结果阐述了ROS平衡机制在水稻幼穗高温响应中的重要性；
(5)阐述了高温对水稻剑叶中糖酵解与TCA代谢通路、次生代谢、UPS及光合作用中的光反应等相关基因的表达的影响；发现高温显著促进酵解和UPS,但抑制TCA通路、次生代谢、光合作用等生理学过程；
(6)在对微阵列数据进行筛选和逆境诱导基因表达水平进行qRT-PCR验证及启动子生物信息学分析的基础上,克隆了3个逆境响应元件较为集中的目的启动子片段,转化水稻日本晴,并进行了阳性转基因水稻的筛选。对成熟期转基因水稻分别进行了高温和干旱处理,并利用组织化学染色和MU荧光测定法、qRT-PCR等对幼穗和剑叶中的GUS酶活和基因表达水平进行了分析,结果表明,在3个候选启动子中,Hsfp在高温和干旱条件下的幼穗中具有最高水平的活性,但在剑叶中没有表现出明显的活性；Dehp在干旱或高温处理的水稻剑叶和幼穗中均没有显著的活性变化；Putp在干旱处理的幼穗中的活性较强,而其在干旱的剑叶和高温条件下的活性则不明显。
As one of the most important crops in the world, rice has been encountering varous adverse environmental factors such as heat, drought, disease, which has attracted more and more attentions all around the world. Consequently, it becomes an important task to improve rice resistence to various stresses based on gene engineering via cloning and characterizing stress-related genes and promoters.
The expression profile in rice panicle and flag leaf under heat stress was analyzed through rice microarray. Furthermore, using transgenic technology, the expression activity of the three promoters from the highly heat-inducible genes in rice panicle and flag leaf under heat and drought was detected. The major results are as followed:
(1) The differentially expressed genes (DEGs) in rice panicle and flag leaf under heat treatment were obtained under the condition of quality control and evaluation using HCL. The analysis on the DEGs showed the time point2h of heat treatment may be an important transition for rice response to heat stress. The results from GO retrieve and gene expression pattern analysis showed the heat-responsive (HR) genes in rice panicle and flag leaf are mainly involved in transporter, protein binding, antioxidation, catalysis, transcription regulation and stress response. The comprehensive statement and primary comparison on the HR transcription factors such as Hsf, AP2/ERF, bHLH, bZIP, Myb, WRKY, NAC and C2H2as well as Hsp family genes from both tissues was carried out. These work provided important clues for the characterization and identification of tissue-specific heat-responsive genes and promoters.
(2) The expression profile analysis showed that the complicated changes of ROS-related genes in rice panicle under heat stress helps maintain ROS balance, and that the genes related to auxin, ABA and ethylene metabolism and signal transduction were mainly down-regulated, and the ones involved in light, calcium and G-protein were up-regulated.
(3) The analysis on the promoters of co-regulated genes in rice panicle showed that GCC box, CE3, ABRE and HSE are significantly enriched in the early-regulated cluster, and GCC box and CE3are the centers of the two co-occurrence network, with which HSE and ABRE significantly co-occured, respectively.
(4) A regulation model central to ROS was established, and the data from the rice panicle microarray and ROS quantification help elucidate the importance of ROS balance in the rice panicle response to heat shock.
(5) The pathway analysis on the HR genes in rice flag leaf showed that heat shock significantly promoted glycolysis and UPS, and repressed TCA, secondary metabolism, and photosynthesis via inhibiting light reaction.
(6) Based on the screening microarray data, qRT-PCR idenfitication and bioinformatics analysis on promoters, the three candidate promoters for the highly heat-inducible genes were cloned, transformed into rice, and the positive transgenic lines were characterized using PCR. After heat and drought treatment on the mature transgenic rice, GUS enzyme activity and expression level was detected using histochemical staining, fluorescence quantification and qRT-PCR in rice panicle and flag leaf. The results showed that, among the three candidate promoters, Hsfp exhibited highest activity in rice panicle under heat and drought, bu none in flag leaf; Dehp had no activity in both tissues under stress conditions; Putp showed higher activity only in panicle under drought.
本论文利用水稻全基因组微阵列技术平台,开展了水稻幼穗和剑叶的高温全基因组表达谱数据的分析和挖掘,取得了一些有意义的成果。在此基础上,利用转基因技术,进一步分析了3个高温显著响应基因的启动子在经高温和干旱处理的水稻幼穗和剑叶中的表达活性。结果如下：
(1)在利用HCL等方法进行数据质量控制和评价的基础上,分别获得了水稻幼穗和剑叶在高温条件下的差异表达基因。对各个时间点的差异表达基因数目分析发现,高温处理2h可能是水稻响应高温逆境的一个重要转折点；GO分析及基因表达规律分析的结果表明,来自幼穗和剑叶的热激响应基因主要与转运蛋白、蛋白结合、抗氧化、催化、转录调控、逆境响应等相关；且对两个组织中受高温显著调控的包括Hsf、AP2/ERF、bHLH、bZIP、Myb、WRKY、NAC和C2H2等在内的转录因子和Hsp家族基因的表达特征进行了比较分析。这些研究结果将为组织特异性的高温响应基因和启动子的筛选与鉴定提供重要线索；
(2)发现水稻幼穗中高温响应的ROS相关基因的复杂而显著的表达变化有助于维持ROS的平衡；与生长素、ABA和乙烯代谢与信号传导相关的基因均表达下调,而与光、钙离子相关的蛋白基因和G蛋白编码基因则有显著上调；
(3)对水稻幼穗中共表达基因的启动子进行了分析和挖掘,发现GCC box、 CE3、ABRE和HSE等在早期上调的聚类中显著富集,而GCC box和CE3还成为两个共现网络的中心,且HSE和ABRE与这两个元件关系密切,具有显著的共现特征；
(4)构建了以ROS为中心的调控模型,利用水稻幼穗全基因组微阵列数据和ROS定量分析的结果阐述了ROS平衡机制在水稻幼穗高温响应中的重要性；
(5)阐述了高温对水稻剑叶中糖酵解与TCA代谢通路、次生代谢、UPS及光合作用中的光反应等相关基因的表达的影响；发现高温显著促进酵解和UPS,但抑制TCA通路、次生代谢、光合作用等生理学过程；
(6)在对微阵列数据进行筛选和逆境诱导基因表达水平进行qRT-PCR验证及启动子生物信息学分析的基础上,克隆了3个逆境响应元件较为集中的目的启动子片段,转化水稻日本晴,并进行了阳性转基因水稻的筛选。对成熟期转基因水稻分别进行了高温和干旱处理,并利用组织化学染色和MU荧光测定法、qRT-PCR等对幼穗和剑叶中的GUS酶活和基因表达水平进行了分析,结果表明,在3个候选启动子中,Hsfp在高温和干旱条件下的幼穗中具有最高水平的活性,但在剑叶中没有表现出明显的活性；Dehp在干旱或高温处理的水稻剑叶和幼穗中均没有显著的活性变化；Putp在干旱处理的幼穗中的活性较强,而其在干旱的剑叶和高温条件下的活性则不明显。
As one of the most important crops in the world, rice has been encountering varous adverse environmental factors such as heat, drought, disease, which has attracted more and more attentions all around the world. Consequently, it becomes an important task to improve rice resistence to various stresses based on gene engineering via cloning and characterizing stress-related genes and promoters.
The expression profile in rice panicle and flag leaf under heat stress was analyzed through rice microarray. Furthermore, using transgenic technology, the expression activity of the three promoters from the highly heat-inducible genes in rice panicle and flag leaf under heat and drought was detected. The major results are as followed:
(1) The differentially expressed genes (DEGs) in rice panicle and flag leaf under heat treatment were obtained under the condition of quality control and evaluation using HCL. The analysis on the DEGs showed the time point2h of heat treatment may be an important transition for rice response to heat stress. The results from GO retrieve and gene expression pattern analysis showed the heat-responsive (HR) genes in rice panicle and flag leaf are mainly involved in transporter, protein binding, antioxidation, catalysis, transcription regulation and stress response. The comprehensive statement and primary comparison on the HR transcription factors such as Hsf, AP2/ERF, bHLH, bZIP, Myb, WRKY, NAC and C2H2as well as Hsp family genes from both tissues was carried out. These work provided important clues for the characterization and identification of tissue-specific heat-responsive genes and promoters.
(2) The expression profile analysis showed that the complicated changes of ROS-related genes in rice panicle under heat stress helps maintain ROS balance, and that the genes related to auxin, ABA and ethylene metabolism and signal transduction were mainly down-regulated, and the ones involved in light, calcium and G-protein were up-regulated.
(3) The analysis on the promoters of co-regulated genes in rice panicle showed that GCC box, CE3, ABRE and HSE are significantly enriched in the early-regulated cluster, and GCC box and CE3are the centers of the two co-occurrence network, with which HSE and ABRE significantly co-occured, respectively.
(4) A regulation model central to ROS was established, and the data from the rice panicle microarray and ROS quantification help elucidate the importance of ROS balance in the rice panicle response to heat shock.
(5) The pathway analysis on the HR genes in rice flag leaf showed that heat shock significantly promoted glycolysis and UPS, and repressed TCA, secondary metabolism, and photosynthesis via inhibiting light reaction.
(6) Based on the screening microarray data, qRT-PCR idenfitication and bioinformatics analysis on promoters, the three candidate promoters for the highly heat-inducible genes were cloned, transformed into rice, and the positive transgenic lines were characterized using PCR. After heat and drought treatment on the mature transgenic rice, GUS enzyme activity and expression level was detected using histochemical staining, fluorescence quantification and qRT-PCR in rice panicle and flag leaf. The results showed that, among the three candidate promoters, Hsfp exhibited highest activity in rice panicle under heat and drought, bu none in flag leaf; Dehp had no activity in both tissues under stress conditions; Putp showed higher activity only in panicle under drought.
引文
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