番茄RNA沉默体系的鉴定及其抗病毒新方法的研究
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摘要
RNA沉默利用负调控手段,在基因的转录和转录后水平,介导的序列特异性的基因沉默；其在植物生长发育、基因组的稳定、对逆境和胁迫的响应与防御等方面发挥着重要作用。RNA沉默途径具有多样性,涉及的关键基因也比较多,在拟南芥等模式植物上研究的比较清楚。番茄是果实发育研究的重要的模式生物,但对其RNA沉默系统的认识还不系统和完整。在番茄生产栽培中,病毒(如番茄黄化曲叶病毒,TYLCV和黄瓜花叶病毒,CMV)的危害很严重。寄主直接抵抗病毒的分子机制主要有RNA沉默和抗性基因这两大类,而二者之间的差异与联系研究较少。本研究通过对番茄RNA沉默系统核心蛋白,sRNA组学特征及其功能和耐感(针对TYLCV)品种间RNA沉默系统特征的比较,来全面地认识番茄RNA沉默系统及与病毒抗性关系。另外,还开展了系统性基因沉默增强嫁接番茄病毒抗性的研究。获得了如下主要研究结果：
1、本文研究了番茄RNA沉默系统的核心基因：在番茄中鉴定了7个DCL、15个AGO和6个RDR基因。系统进化树分析,认为这些基因均可被分类为4类。比较了这些基因的结构和序列相似性、对其进行了番茄基因组上的定位,并且利用网络数据库和半定量RT-PCR,鉴定了不同组织或器官以及在不同非生物胁迫和在TYLCV病毒胁迫下的表达。在非生物胁迫和TYLCV侵染后,发现一些特定基因的表达获得了提高。从SlDCL2s的串联重复和表达模式来看,DCL2家族在番茄进化过程中可能具有重要作用。
2、调查了番茄内源sRNA组和降解组组学特征：利用高通量测序方法,比较了内源sRNA在不同耐(含Ty-1)感品种及TYLCV病毒侵染前后差异；鉴定了30个保守的：miRNA,预测了1666个新的1niRNA。首次,利用降解组鉴定出了番茄所有保守miRNA以及1575条新的miRNA的切割靶标。利用较严格的标准,对耐感样本接种病毒前后miRNA表达差异的比较发现,大部分保守miRNA和新的miRNA对病毒产生了响应,靶标功能分析证明这些niRNA可能与植物抗性或症状形成相关。本研究对样本中siRNA也进行了详细分析,各样本间siRNA变化差异较大,表明寄主内源siRNA对病毒的侵染做出了响应。对siRNA靶标预测发现,众多siRNA的靶标都与抗病相关。这暗示siRNA具有作为植物免疫系统调控的重要功能。以上数据与分析为番茄的RNA沉默系统的全面认识提供重要基础。
3、深入分析了侵染TYLCV后抗感品种中vsRNA及其功能差异：利用高通量测序方法,首次比较了耐病品种相对于感病品种中vsRNA的生产与功能差异。结果发现：vsRNA的产生没有碱基偏好；不同长度vsRNA连续分布于病毒基因组;vsRNA的分布存在热点,可能与转录本的重叠和转录本二级结构相关。首次利用降解组为vsRNA提供了直接的病毒转录本切割/降解证据。利用BSP调查了病毒DNA的甲基化情况,发现抗感品种编码区均呈现低甲基化；而在IR区互补链具有高度甲基化,暗示24nt vsRNA可能介导了IR区甲基化。本研究通过比较病毒DNA.mRNA与vsRNA的表达量与趋势,提出在寄主诱导的病毒抗性作用中,RNA介导的病毒免疫要滞后于Ty-1基因的作用,且其对病害的抑制作用是有限的。
4、进行了RNA沉默与嫁接技术结合获得病毒(CMV)抗性材料的实践：分别以CMV的5个基因为靶标,通过农杆菌介导的转化,成功获得53株Kan抗性及PCR阳性植株。通过对扦插苗接种CMV鉴定抗性发现,1A-CP中存在不同程度的抗性,其中1A和3A共有6株、2A有7株、2B有8株以及5株CP转基因番茄展现出对CMV的高抗。本研究利用扦插的方法,获得了大量的砧木后代,在生产上对于抗性材料的繁殖是十分有益的。以高抗的转基因植株作为砧木嫁接非转基因番茄品种,发现其病毒抗性可进行有效传递。而嫁接接穗成功获得病毒抗性,为园艺植物嫁接育种提供了依据。另外,砧木中超表达的NptⅡ基因的rnRNA并未在接穗中检测到,这可能为消除消费者对GMO生物安全性的忧虑提供新的途径。
本研究的意义在于：1、为理解番茄的RNA沉默体系,研究其核心基因在番茄生长发育或不同逆境条件下的功能,提供了重要信息；2、为理解植物sRNA特征及其功能提供数据；3、为认识Ty-1基因和RNA沉默介导的病毒抗性之间的异同提供了证据；4、实践了RNA沉默技术在病毒抗性上的应用,提出了高效安全的转基因抗病毒新策略。
RNA silencing is a negative control, mediating specific gene silencing via complementarity principle, at the gene transcriptional and posttranscriptional level. It plays an important role in plant growth and development, the stability of the genome, and response and defence to adversity and stress. By studying for the model plant such as Arabidopsis, researchers realized that plant RNA silencing pathways are diverse and involve many core genes. Tomato is an important model plant for fruit development, but their understanding of RNA silencing system is not systematic and complete. In tomato cultivation, virus infection (such as TYLCV and CMV) is very serious. The molecular mechanism of host plant resistance to virus, directly, is mainly used by RNA silence and resistance gene. Nevertheless, the difference and relationship of these two mechanism are acquainted scarce.
We expect a comprehensive investigation of tomato RNA silencing system and its relationship to viral resistance via compared the core proteins of RNA silencing system, characteristics of sRNAs and its function between tolerant and susceptible varieties for TYLCV. In addition, we also using RNA silencing boned with grafting technique to obtain high-efficiency virus-resistant material and get the following main results:
1, This study investigated the core genes of the tomato RNA silencing system. We identified seven DCL,15AGO and six RDR genes. The phylogenetic tree shows that these genes can be classified into four subfamily. Comprehensive analyses of gene structure, genomic localization and similarity between these genes were performed. Their expression patterns were investigated by means of expressive models in different tissues/organs, abiotic stress and TYLCV infection using online data and semi-quantitative RT-PCR. Many of the candidate genes were up-regulated in response to TYLCV infection and abiotic stresses. Expression models of tandem gene duplications among SlDCL2s indicated the DCL2family plays an important role in the evolution of tomato.
2, utilizing high-throughput sequencing methods, we compared endogenous sRNA difference before and after infection between TYLCV tolerant (encompass Ty-1) to susceptible tomato varieties. We identified30conserved tomato miRNA and predicted1666novel miRNA. For the first time, we employed degradome to identified the cleaved targets of all the conserved miRNA and1575new miRNA. Utilized a stringent standard, we compared the different expressions among samples of tolerant and susceptible plants that before or after inoculated with TYLCV. Results show that the most conserved and novel miRNA were responsive virus infection. Target function analysis proves that these miRNA may be related to plant resistance or symptoms formation. We also performed a detailed analysis the siRNA expressions and these predicted targets, and the data imply that siRNA is an essential function as a plant immune system regulation. All of above data and analysis provide an important basis for a comprehensive understanding of the tomato RNA silencing system.
3, using high-throughput sequencing strategy, we compare the differences of viral-derived small RNA (vsRNA) generation and function of TYLCV tolerant to susceptible varieties. The results showed that1) no nucleotide preference in vsRNA generated;2) vsRNAs provide continuous coverage of every genomic position of TYLCV;3) the hot spots of vsRNA distribution may be associated with the overlap and secondary structure of viral transcripts. We employed degradome data to provide direct evidence for vsRNA cleave/degradation targets. Using BSP investigated viral DNA methylation, we found that there is hypomethylation in both tolerant and susceptible varieties, while hypermethylation in the complementary strand of the IR region. These results implied the24nt vsRNA may be mediated methylation on IR region. We also compare the expression trend of viral DNA, mRNA and vsRNA. According to the result, we proposed that in host-induced viral resistance, the function of RNA-based antiviral immunity is restricted and lags behind the Ty-1resistance gene.
4, RNA silencing and grafting techniques were combined for obtaining virus (CMV) resistant materials:The current study combined RNA silencing of five genes of CMV and grafting techniques to construct five intron-spliced hairpin RNA (ihpRNA) plant expression vectors. Transgenic tomatoes were obtained53Kan resistances and PCR positive plants by Agrobacterium-mediated transformation with expression vectors. Highly resistant generations of transgenic plants were employed as rootstocks and grafted onto non-transgenic tomato plants that resulted in the successful transfer of resistance to the scions. In this study, six lines of lA and3A, eight of2B, seven of2A, and five CP transgenic plants were shown to be highly resistant. Further, this method produces scions that can remain undetectable for transgenic resistance marker genes that may provide novel mechanisms to evade collective concerns about genetically-modified organism (GMO) biosafety.
The significances of this study are as follows:1) It is provide important information for the understanding of the tomato RNA silencing system and for the function of their core genes in tomato growth and development or under different stress conditions;2) It is provide data for the understanding plant sRNA characteristics and its functions;3) It is provide the evidence for the understanding of the similarities and differences between the resistance gene and RNA-based antiviral immunity;4) we practiced the application of RNA silencing in viral resistance, and put forward a new strategy for efficient and safe antiviral transgenic engineering.
1、本文研究了番茄RNA沉默系统的核心基因：在番茄中鉴定了7个DCL、15个AGO和6个RDR基因。系统进化树分析,认为这些基因均可被分类为4类。比较了这些基因的结构和序列相似性、对其进行了番茄基因组上的定位,并且利用网络数据库和半定量RT-PCR,鉴定了不同组织或器官以及在不同非生物胁迫和在TYLCV病毒胁迫下的表达。在非生物胁迫和TYLCV侵染后,发现一些特定基因的表达获得了提高。从SlDCL2s的串联重复和表达模式来看,DCL2家族在番茄进化过程中可能具有重要作用。
2、调查了番茄内源sRNA组和降解组组学特征：利用高通量测序方法,比较了内源sRNA在不同耐(含Ty-1)感品种及TYLCV病毒侵染前后差异；鉴定了30个保守的：miRNA,预测了1666个新的1niRNA。首次,利用降解组鉴定出了番茄所有保守miRNA以及1575条新的miRNA的切割靶标。利用较严格的标准,对耐感样本接种病毒前后miRNA表达差异的比较发现,大部分保守miRNA和新的miRNA对病毒产生了响应,靶标功能分析证明这些niRNA可能与植物抗性或症状形成相关。本研究对样本中siRNA也进行了详细分析,各样本间siRNA变化差异较大,表明寄主内源siRNA对病毒的侵染做出了响应。对siRNA靶标预测发现,众多siRNA的靶标都与抗病相关。这暗示siRNA具有作为植物免疫系统调控的重要功能。以上数据与分析为番茄的RNA沉默系统的全面认识提供重要基础。
3、深入分析了侵染TYLCV后抗感品种中vsRNA及其功能差异：利用高通量测序方法,首次比较了耐病品种相对于感病品种中vsRNA的生产与功能差异。结果发现：vsRNA的产生没有碱基偏好；不同长度vsRNA连续分布于病毒基因组;vsRNA的分布存在热点,可能与转录本的重叠和转录本二级结构相关。首次利用降解组为vsRNA提供了直接的病毒转录本切割/降解证据。利用BSP调查了病毒DNA的甲基化情况,发现抗感品种编码区均呈现低甲基化；而在IR区互补链具有高度甲基化,暗示24nt vsRNA可能介导了IR区甲基化。本研究通过比较病毒DNA.mRNA与vsRNA的表达量与趋势,提出在寄主诱导的病毒抗性作用中,RNA介导的病毒免疫要滞后于Ty-1基因的作用,且其对病害的抑制作用是有限的。
4、进行了RNA沉默与嫁接技术结合获得病毒(CMV)抗性材料的实践：分别以CMV的5个基因为靶标,通过农杆菌介导的转化,成功获得53株Kan抗性及PCR阳性植株。通过对扦插苗接种CMV鉴定抗性发现,1A-CP中存在不同程度的抗性,其中1A和3A共有6株、2A有7株、2B有8株以及5株CP转基因番茄展现出对CMV的高抗。本研究利用扦插的方法,获得了大量的砧木后代,在生产上对于抗性材料的繁殖是十分有益的。以高抗的转基因植株作为砧木嫁接非转基因番茄品种,发现其病毒抗性可进行有效传递。而嫁接接穗成功获得病毒抗性,为园艺植物嫁接育种提供了依据。另外,砧木中超表达的NptⅡ基因的rnRNA并未在接穗中检测到,这可能为消除消费者对GMO生物安全性的忧虑提供新的途径。
本研究的意义在于：1、为理解番茄的RNA沉默体系,研究其核心基因在番茄生长发育或不同逆境条件下的功能,提供了重要信息；2、为理解植物sRNA特征及其功能提供数据；3、为认识Ty-1基因和RNA沉默介导的病毒抗性之间的异同提供了证据；4、实践了RNA沉默技术在病毒抗性上的应用,提出了高效安全的转基因抗病毒新策略。
RNA silencing is a negative control, mediating specific gene silencing via complementarity principle, at the gene transcriptional and posttranscriptional level. It plays an important role in plant growth and development, the stability of the genome, and response and defence to adversity and stress. By studying for the model plant such as Arabidopsis, researchers realized that plant RNA silencing pathways are diverse and involve many core genes. Tomato is an important model plant for fruit development, but their understanding of RNA silencing system is not systematic and complete. In tomato cultivation, virus infection (such as TYLCV and CMV) is very serious. The molecular mechanism of host plant resistance to virus, directly, is mainly used by RNA silence and resistance gene. Nevertheless, the difference and relationship of these two mechanism are acquainted scarce.
We expect a comprehensive investigation of tomato RNA silencing system and its relationship to viral resistance via compared the core proteins of RNA silencing system, characteristics of sRNAs and its function between tolerant and susceptible varieties for TYLCV. In addition, we also using RNA silencing boned with grafting technique to obtain high-efficiency virus-resistant material and get the following main results:
1, This study investigated the core genes of the tomato RNA silencing system. We identified seven DCL,15AGO and six RDR genes. The phylogenetic tree shows that these genes can be classified into four subfamily. Comprehensive analyses of gene structure, genomic localization and similarity between these genes were performed. Their expression patterns were investigated by means of expressive models in different tissues/organs, abiotic stress and TYLCV infection using online data and semi-quantitative RT-PCR. Many of the candidate genes were up-regulated in response to TYLCV infection and abiotic stresses. Expression models of tandem gene duplications among SlDCL2s indicated the DCL2family plays an important role in the evolution of tomato.
2, utilizing high-throughput sequencing methods, we compared endogenous sRNA difference before and after infection between TYLCV tolerant (encompass Ty-1) to susceptible tomato varieties. We identified30conserved tomato miRNA and predicted1666novel miRNA. For the first time, we employed degradome to identified the cleaved targets of all the conserved miRNA and1575new miRNA. Utilized a stringent standard, we compared the different expressions among samples of tolerant and susceptible plants that before or after inoculated with TYLCV. Results show that the most conserved and novel miRNA were responsive virus infection. Target function analysis proves that these miRNA may be related to plant resistance or symptoms formation. We also performed a detailed analysis the siRNA expressions and these predicted targets, and the data imply that siRNA is an essential function as a plant immune system regulation. All of above data and analysis provide an important basis for a comprehensive understanding of the tomato RNA silencing system.
3, using high-throughput sequencing strategy, we compare the differences of viral-derived small RNA (vsRNA) generation and function of TYLCV tolerant to susceptible varieties. The results showed that1) no nucleotide preference in vsRNA generated;2) vsRNAs provide continuous coverage of every genomic position of TYLCV;3) the hot spots of vsRNA distribution may be associated with the overlap and secondary structure of viral transcripts. We employed degradome data to provide direct evidence for vsRNA cleave/degradation targets. Using BSP investigated viral DNA methylation, we found that there is hypomethylation in both tolerant and susceptible varieties, while hypermethylation in the complementary strand of the IR region. These results implied the24nt vsRNA may be mediated methylation on IR region. We also compare the expression trend of viral DNA, mRNA and vsRNA. According to the result, we proposed that in host-induced viral resistance, the function of RNA-based antiviral immunity is restricted and lags behind the Ty-1resistance gene.
4, RNA silencing and grafting techniques were combined for obtaining virus (CMV) resistant materials:The current study combined RNA silencing of five genes of CMV and grafting techniques to construct five intron-spliced hairpin RNA (ihpRNA) plant expression vectors. Transgenic tomatoes were obtained53Kan resistances and PCR positive plants by Agrobacterium-mediated transformation with expression vectors. Highly resistant generations of transgenic plants were employed as rootstocks and grafted onto non-transgenic tomato plants that resulted in the successful transfer of resistance to the scions. In this study, six lines of lA and3A, eight of2B, seven of2A, and five CP transgenic plants were shown to be highly resistant. Further, this method produces scions that can remain undetectable for transgenic resistance marker genes that may provide novel mechanisms to evade collective concerns about genetically-modified organism (GMO) biosafety.
The significances of this study are as follows:1) It is provide important information for the understanding of the tomato RNA silencing system and for the function of their core genes in tomato growth and development or under different stress conditions;2) It is provide data for the understanding plant sRNA characteristics and its functions;3) It is provide the evidence for the understanding of the similarities and differences between the resistance gene and RNA-based antiviral immunity;4) we practiced the application of RNA silencing in viral resistance, and put forward a new strategy for efficient and safe antiviral transgenic engineering.
引文
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