大豆miRNA的鉴定与在抗疫霉根腐病中的功能分析
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摘要
由大豆疫霉菌(Phytophthora sojae Kaufinann&Gerdemann, P. sojae)引起的大豆疫霉根腐病是大豆生产上的毁灭性土传病害之一。研究大豆疫霉根腐病的抗病机制,是培育广谱、稳定、高效、持久抗病品种的基础。microRNA(miRNA)是真核生物中发现的一类内源性的具有调控功能的非编码小分子RNA,通过碱基互补配对的方式识别靶标mRNA,并根据互补程度的不同指导沉默复合体降解靶标mRNA或者抑制靶标mRNA的翻译。miRNA在植物生长发育和病害防御中起着重要的作用。
本研究首先证明植物基因沉默系统对卵茵的抗性具有重要的作用。利用同源搜索方法对栽培大豆中的miRNA进行预测；以大豆疫霉根腐病抗病、耐病和感病品种为材料,通过人工接种和miRNA芯片技术,鉴定与大豆疫霉菌侵染相关和抗病类型相关的miRNA;通过生物信息学方法预测miRNA的靶标基因并进行功能分析。根据miRNA在抗病、耐病和感病材料之间的表达差异,分析miRNA在抗大豆疫霉根腐病途径中的机制和作用,为培育和改良大豆疫霉根腐病抗性品种奠定基础。主要研究结果如下：
1.植物基因沉默系统对卵茵抗性的作用
利用烟草疫霉菌Pp025和辣椒疫霉菌Pc35接种拟南芥基因沉默突变体zippy, ago1-27、sgs3-11、rdr6-11,发现突变体的抗病性与野生型相比,略有增强。利用烟草瞬时转化系统,将p19注射至烟草叶片,然后接种Pp025,发现与对照GFP相比,病斑长度明显增长。利用发根农杆菌K599介导的大豆瞬时转化系统,将p19转入大豆,然后接种大豆疫霉菌P6497,发现转化p19的阳性根毛对疫霉菌的抗病性有轻微的下降。结果初步显示,植物的基因沉默系统与卵菌抗性之间存在着密切的关系。
2.栽培大豆中miRNA的预测
通过比对拟南芥、水稻、苜蓿等所有植物中已知的miRNA成熟体序列与栽培大豆的EST序列,经过层层严格筛选,鉴定到48条新的miRNA,并利用RT-PCR对预测的部分miRNA进行实验验证。使用植物靶基因预测软件psRNAtarget,将该48个miRNA与大豆的基因组数据库进行比对,寻找可能的靶标基因,一共获得323个潜在的miRNA靶标。根据基因的功能注释,发现靶基因编码产物类型多样,其中包括转录因子、抗性蛋白等。同时还分析了包含有候选miRNA的EST的来源,结果发现有部分EST与胁迫响应有关,推测来源于这些EST的miRNA可能受胁迫的调控。
3.大豆中保守miRNA的表达分析
选择7个保守的miRNA进行表达分析。8个大豆品种进行大豆疫霉菌P6497处理,通过Northern blotting技术,对这7个miRNA进行检测。结果发现,有6个miRNA在这8个品种中都有表达。
4.与大豆疫霉菌侵染相关和抗性相关的miRNA的鉴定
为了鉴定与大豆疫霉菌侵染相关的miRNA,我们利用生物芯片检测了三个对P6497具有不同抗性反应的大豆品种(Williams,感病品种；Conrad,耐病品种；Williams82,抗病品种,含有Rpsl-k)接种P. sojae前后miRNA的表达模式,找到97个受P. sojae调控的miRNA,同时分析了与抗性类型相关的miRNA.利用qRT-PCR对芯片中有显著表达的9个miRNA进行了验证,结果发现定量结果与芯片结果的一致性较高。
5. miRNA靶基因的预测及功能分析
通过BLAST比对,对miRNA的靶标进行预测,并与前人已发表的大豆-大豆疫霉菌互作的基因芯片数据进行比较,找到与miRNA表达趋势相反的靶标基因,并利用实时定量PCR方法进行验证。利用Gateway技术将与卵茵侵染显著相关的10个miRNA前体构建至植物表达载体pEarleyGate103中,并在烟草和大豆中进行遗传转化,初步结果表明过表达miRNA能影响大豆疫霉菌的致病性。
通过上述研究,我们初步明确了植物基因沉默系统在抗卵茵病害过程中具有重要作用,鉴定了48个大豆新型miRNA并对它们的特性进行了分析,同时利用基因芯片技术分析了所有已知植物的miRNA在大豆不同抗性品种中的表达规律,发现了一批与疫霉根腐病抗性和病原菌侵染相关的大豆miRNA,并对它们的靶标基因进行了预测,实验证明大豆miRNA可以调节这些基因的表达来进一步影响大豆的抗病性。
Phytophthora. root and stem rot (PRR) of soybean caused by Phytophthora sojae is a destructive disease affecting soybean production regions throughout the world. To breed new varieties with efficient, broad-spectrum and stable resistance to the soybean PRR, understanding of resistance mechanism is of great importance. The utilization of resistant cultivars is the most economical and environmentally safe method for controlling this disease.
microRNAs (miRNAs) are20-24nucleotides non-coding RNAs, serving as a class of post-transcriptional regulators in eukaryotic organism. Dicer ribonucleases process miRNAs from their precursor hairpins. Then, the mature miRNA is incorporated into the RNA-induced silencing complex (RISC). Within this complex, miRNA targets the mRNA for cleavage or repression its productive translation based on the match between miRNA muture sequence and mRNA sequence. miRNAs regulate gene network in plants, including development, organ formation, cell proliferation and senescence, biotic and abiotic stresses.
Here, we present evidences that plant gene silencing system plays an important role in the resistance during oomycetes-plant interactions. New miRNAs were predicted in Glycine max using bioinformatics approaches. miRNAs of soybean under the stress of P. sojae by artifical inoculation were identified from tolerant, resistant and susceptive cultivars by microarray, and miRNAs related to P. sojae and genotype were assayed, and target genes of miRNA were predicted and functional analyzed. Accordingly, the role of the miRNAs in resistance pathway of PRR was discussed, which lay the foundation for breeding and improving the resistant varieties in soybean by biotechnology method. The main results were as follows:1. Gene silencing system function in plant resistance to ooraycetes infection
RNA silencing is a common strategy shared by eukaryotic organisms to regulate gene expression, and also can operate as a defense mechanism against biotic stress. In Arabidopsis thaliana, several genes have been identified for RNA silencing, including SGS3(suppressor of gene silencing3), A GO1(Argonaute1), HEN1(Hua enhancer1), RDR6(RNA-dependent Polymerase6) and ZIPPY (ZIP). Here, Arabidopsis gene silencing mutants (zippy, ago1-27, sgs3-11and rdr6-11) were inoculated by Pp025and Pc35. The results showed that compared with the wildtype, phenotype of mutants was more resistant. Using PVX-mediated transformation system, p19was transformed into tobacco leaves and found that p19may be interfered plant gene silencing system, p19was transgened into soybean cultivar Williams, the positive roots were inoculated by P6497, and found that the resistance were repressed compared with the control. These results showed that there was relationship between RNA silencing and oomycetes resistance.
2. miRNA prediction of Glycine max
Soybean is one of the most important crops with high economic value. Up to now, miRNAs in soybean have been identified by computational analysis or high-throughput sequencing. However, this number is very limited. Soybean ESTs were searched with non-redundant plant mature miRNAs by BLASTn approach, and removed coding gene support; finally,48putative soybean novel miRNAs were identified. To experimentally validate the prediction, poly(A)-tailed RT-RNA was used to amplified the three miRNAs, and the software psRNAtarget was also adopted to search the potential targets of the miRNAs. Based on the gene annotation, we found that many targets coded for different proteins, including resistant proteins and transcriptional factors. In addition, we analysed the source of ESTs containing potential miRNAs. The results showed that some ESTs containing potential miRNAs were involved in stresses, indicating that these miRNAs may be regulated by stresses.
3. Expression analysis of conserved miRNAs
Seven conserved miRNAs were selected to analyse the expression levels. Eight soybean cultivars inoculated with P6497were extracted small RNA and miRNA was detected by Northern blotting. The results showed that, six conserved miRNAs were expressed in eight cultivars in pre-and post-inoculation.
4. Identification of P. sojae involved and genotype-specific miRNAs
To identify miRNAs involving soybean which respond to P. sojae and correlate to the different resistance cultivars, microarray was designed to detect miRNA expression pattern. Three soybean cultivars:Williams (susceptible), Conrad (quantitative resistance) and Williams82(qualitative resistance, containing Rpsl-k) were assayed at two stages:3-day post inoculation (dpi) and mock, microarray data were further confirmed by qRT-PCR analysis.
5. Prediction of miRNA targets and functional analysis of miRNA
miRNA targets were predicted by tBLASTn. We took advantage of the available gene expression data of Williliams infected with P. sojae, and compared the expression pattern of miRNAs with that of their potential targets. We used qRT-PCR to validate the results. miRNA fragments are amplified from soybean genomic DNA by PCR, and construct them into overexpression vector pEarleyGate103. By Agrobacterium rhizogenes-mediated transform system, we found that overexpression of miRNA and silencing the target gene may influence plant resistance.
In conclusion, gene silencing system plays an important role in plants resistance to oomycetes;48novel miRNAs were identified and characterized in G.max; using microarray, we analysed the miRNA expression pattern involving P. sojae and genotype, and target genes of miRNAs were predicted by Blast. These results suggest that the target genes involving soybean resistance may be regulated by miRNA.
本研究首先证明植物基因沉默系统对卵茵的抗性具有重要的作用。利用同源搜索方法对栽培大豆中的miRNA进行预测；以大豆疫霉根腐病抗病、耐病和感病品种为材料,通过人工接种和miRNA芯片技术,鉴定与大豆疫霉菌侵染相关和抗病类型相关的miRNA;通过生物信息学方法预测miRNA的靶标基因并进行功能分析。根据miRNA在抗病、耐病和感病材料之间的表达差异,分析miRNA在抗大豆疫霉根腐病途径中的机制和作用,为培育和改良大豆疫霉根腐病抗性品种奠定基础。主要研究结果如下：
1.植物基因沉默系统对卵茵抗性的作用
利用烟草疫霉菌Pp025和辣椒疫霉菌Pc35接种拟南芥基因沉默突变体zippy, ago1-27、sgs3-11、rdr6-11,发现突变体的抗病性与野生型相比,略有增强。利用烟草瞬时转化系统,将p19注射至烟草叶片,然后接种Pp025,发现与对照GFP相比,病斑长度明显增长。利用发根农杆菌K599介导的大豆瞬时转化系统,将p19转入大豆,然后接种大豆疫霉菌P6497,发现转化p19的阳性根毛对疫霉菌的抗病性有轻微的下降。结果初步显示,植物的基因沉默系统与卵菌抗性之间存在着密切的关系。
2.栽培大豆中miRNA的预测
通过比对拟南芥、水稻、苜蓿等所有植物中已知的miRNA成熟体序列与栽培大豆的EST序列,经过层层严格筛选,鉴定到48条新的miRNA,并利用RT-PCR对预测的部分miRNA进行实验验证。使用植物靶基因预测软件psRNAtarget,将该48个miRNA与大豆的基因组数据库进行比对,寻找可能的靶标基因,一共获得323个潜在的miRNA靶标。根据基因的功能注释,发现靶基因编码产物类型多样,其中包括转录因子、抗性蛋白等。同时还分析了包含有候选miRNA的EST的来源,结果发现有部分EST与胁迫响应有关,推测来源于这些EST的miRNA可能受胁迫的调控。
3.大豆中保守miRNA的表达分析
选择7个保守的miRNA进行表达分析。8个大豆品种进行大豆疫霉菌P6497处理,通过Northern blotting技术,对这7个miRNA进行检测。结果发现,有6个miRNA在这8个品种中都有表达。
4.与大豆疫霉菌侵染相关和抗性相关的miRNA的鉴定
为了鉴定与大豆疫霉菌侵染相关的miRNA,我们利用生物芯片检测了三个对P6497具有不同抗性反应的大豆品种(Williams,感病品种；Conrad,耐病品种；Williams82,抗病品种,含有Rpsl-k)接种P. sojae前后miRNA的表达模式,找到97个受P. sojae调控的miRNA,同时分析了与抗性类型相关的miRNA.利用qRT-PCR对芯片中有显著表达的9个miRNA进行了验证,结果发现定量结果与芯片结果的一致性较高。
5. miRNA靶基因的预测及功能分析
通过BLAST比对,对miRNA的靶标进行预测,并与前人已发表的大豆-大豆疫霉菌互作的基因芯片数据进行比较,找到与miRNA表达趋势相反的靶标基因,并利用实时定量PCR方法进行验证。利用Gateway技术将与卵茵侵染显著相关的10个miRNA前体构建至植物表达载体pEarleyGate103中,并在烟草和大豆中进行遗传转化,初步结果表明过表达miRNA能影响大豆疫霉菌的致病性。
通过上述研究,我们初步明确了植物基因沉默系统在抗卵茵病害过程中具有重要作用,鉴定了48个大豆新型miRNA并对它们的特性进行了分析,同时利用基因芯片技术分析了所有已知植物的miRNA在大豆不同抗性品种中的表达规律,发现了一批与疫霉根腐病抗性和病原菌侵染相关的大豆miRNA,并对它们的靶标基因进行了预测,实验证明大豆miRNA可以调节这些基因的表达来进一步影响大豆的抗病性。
Phytophthora. root and stem rot (PRR) of soybean caused by Phytophthora sojae is a destructive disease affecting soybean production regions throughout the world. To breed new varieties with efficient, broad-spectrum and stable resistance to the soybean PRR, understanding of resistance mechanism is of great importance. The utilization of resistant cultivars is the most economical and environmentally safe method for controlling this disease.
microRNAs (miRNAs) are20-24nucleotides non-coding RNAs, serving as a class of post-transcriptional regulators in eukaryotic organism. Dicer ribonucleases process miRNAs from their precursor hairpins. Then, the mature miRNA is incorporated into the RNA-induced silencing complex (RISC). Within this complex, miRNA targets the mRNA for cleavage or repression its productive translation based on the match between miRNA muture sequence and mRNA sequence. miRNAs regulate gene network in plants, including development, organ formation, cell proliferation and senescence, biotic and abiotic stresses.
Here, we present evidences that plant gene silencing system plays an important role in the resistance during oomycetes-plant interactions. New miRNAs were predicted in Glycine max using bioinformatics approaches. miRNAs of soybean under the stress of P. sojae by artifical inoculation were identified from tolerant, resistant and susceptive cultivars by microarray, and miRNAs related to P. sojae and genotype were assayed, and target genes of miRNA were predicted and functional analyzed. Accordingly, the role of the miRNAs in resistance pathway of PRR was discussed, which lay the foundation for breeding and improving the resistant varieties in soybean by biotechnology method. The main results were as follows:1. Gene silencing system function in plant resistance to ooraycetes infection
RNA silencing is a common strategy shared by eukaryotic organisms to regulate gene expression, and also can operate as a defense mechanism against biotic stress. In Arabidopsis thaliana, several genes have been identified for RNA silencing, including SGS3(suppressor of gene silencing3), A GO1(Argonaute1), HEN1(Hua enhancer1), RDR6(RNA-dependent Polymerase6) and ZIPPY (ZIP). Here, Arabidopsis gene silencing mutants (zippy, ago1-27, sgs3-11and rdr6-11) were inoculated by Pp025and Pc35. The results showed that compared with the wildtype, phenotype of mutants was more resistant. Using PVX-mediated transformation system, p19was transformed into tobacco leaves and found that p19may be interfered plant gene silencing system, p19was transgened into soybean cultivar Williams, the positive roots were inoculated by P6497, and found that the resistance were repressed compared with the control. These results showed that there was relationship between RNA silencing and oomycetes resistance.
2. miRNA prediction of Glycine max
Soybean is one of the most important crops with high economic value. Up to now, miRNAs in soybean have been identified by computational analysis or high-throughput sequencing. However, this number is very limited. Soybean ESTs were searched with non-redundant plant mature miRNAs by BLASTn approach, and removed coding gene support; finally,48putative soybean novel miRNAs were identified. To experimentally validate the prediction, poly(A)-tailed RT-RNA was used to amplified the three miRNAs, and the software psRNAtarget was also adopted to search the potential targets of the miRNAs. Based on the gene annotation, we found that many targets coded for different proteins, including resistant proteins and transcriptional factors. In addition, we analysed the source of ESTs containing potential miRNAs. The results showed that some ESTs containing potential miRNAs were involved in stresses, indicating that these miRNAs may be regulated by stresses.
3. Expression analysis of conserved miRNAs
Seven conserved miRNAs were selected to analyse the expression levels. Eight soybean cultivars inoculated with P6497were extracted small RNA and miRNA was detected by Northern blotting. The results showed that, six conserved miRNAs were expressed in eight cultivars in pre-and post-inoculation.
4. Identification of P. sojae involved and genotype-specific miRNAs
To identify miRNAs involving soybean which respond to P. sojae and correlate to the different resistance cultivars, microarray was designed to detect miRNA expression pattern. Three soybean cultivars:Williams (susceptible), Conrad (quantitative resistance) and Williams82(qualitative resistance, containing Rpsl-k) were assayed at two stages:3-day post inoculation (dpi) and mock, microarray data were further confirmed by qRT-PCR analysis.
5. Prediction of miRNA targets and functional analysis of miRNA
miRNA targets were predicted by tBLASTn. We took advantage of the available gene expression data of Williliams infected with P. sojae, and compared the expression pattern of miRNAs with that of their potential targets. We used qRT-PCR to validate the results. miRNA fragments are amplified from soybean genomic DNA by PCR, and construct them into overexpression vector pEarleyGate103. By Agrobacterium rhizogenes-mediated transform system, we found that overexpression of miRNA and silencing the target gene may influence plant resistance.
In conclusion, gene silencing system plays an important role in plants resistance to oomycetes;48novel miRNAs were identified and characterized in G.max; using microarray, we analysed the miRNA expression pattern involving P. sojae and genotype, and target genes of miRNAs were predicted by Blast. These results suggest that the target genes involving soybean resistance may be regulated by miRNA.
引文
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