玉米氮素营养相关小分子非编码RNA的克隆及miRNA169的功能鉴定
摘要
氮素作为作物需求量最大的元素与作物的产量和品质密切相关,相关研究多集中于氮素吸收与同化过程,而相应的调控机制还很不清楚,调控机制研究的滞后严重限制了人们应用基因工程手段培育可行的氮素高效利用的作物品种。小分子非编码RNA作为重要的上游调控因子,其发现也吸引了植物营养分子生物学家的注意,有证据表明有miRNA参与植物适应氮胁迫的过程,但是具体路径及机制有待于进一步深入研究。
本课题以禾本科重要的模式作物——玉米为试材,结合拟南芥,运用RNA组学技术、生物信息学和分子生物学等手段,挖掘受氮胁迫影响的miRNA,从小分子非编码RNA的角度深入研究植物氮素吸收和同化过程的调控机制。主要结果和结论如下：
1.通过对缺氮处理下的玉米幼苗组成的4个小RNA文库和一个降解组库进行深度测序,我们新发现了47个1niRNA家族,将玉米中的miRNA数量由150提高到249。此外,我们分别发现了miR171、miR169和miR398家族的3、5和1个新成员。
2.通过降解组分析发现了miR164f*, miR167g*/h*/i*, miR169r*, miR168a*/b*以及miR827*的潜在靶标,表明miRNA*链并不是像原先认为的在生物体内无功能,而是可以通过对潜在靶基因的切割来参与植物各种生理代谢过程。
3.根据small RNA深度测序、Q-PCR,小RNA Northern blot、5'-RACE等结果,我们鉴定了八个在低氮胁迫下上调或下调的miRNA(5个保守：miRNA家族和3个新发现miRNA家族),并总结了玉米应答低氮胁迫可能的miRNA功能网络。低氮胁迫显著降低miR169、 miR395、miR827和miRC1的表达,它们通过对靶基因表达量的调控直接参与玉米适应氮胁迫的过程；而低氮条件下,miR171、miR528、miRC39和miRC37的表达量上调,其靶基因很可能参与缺氮信号在玉米体内的转导过程。
4.选取了物种间保守的miR169在拟南芥中进行功能验证。基于对miR169前体的分析发现,只有MIR169a的表达量同时在缺氮状况下的根和地上部中发生了下降。35S::MR169a转基因植株在所有生长条件(水培、培养基生长、土培)下对于缺氮都高度敏感,并且都出现了叶片发黄的症状；而miR169的靶基因NFYA5过表达植株在缺氮条件下表现出了更加耐受胁迫的现象,并且生物量也显著高于野生型。这些均表明miR169a通过调控靶基因NFYA5的表达量参与了植物适应氮胁迫的过程。
5.在缺氮条件下,35S::MIR169a转基因植株根部的总氮含量为4.5%,明显低于野生型(5%),在地上部也有相同的变化趋势。此外,35S::MIR169a转基因植株中发现硝酸盐转运蛋白AtNRT1:1和AtNRT2:1的表达都比野生型要低,这其中至少有一部分原因是由于在35S::MIR169a转基因植株中,氮吸收系统遭到破坏所致。这些结果指出,miR169在帮助植物应对土壤中的氮素有效性波动过程中起作用。
Nitrogen (N) is closely related to crop's yeild and quality, and it is the most required element of crop, related research has focused on nitrogen uptake and assimilation, while the corresponding regulatory mechanism is still unclear. Lagged study of regulatory mechanism severely limit researchers breed nitrogen efficient use crop by genetic engineering techniques. As an important upstream regulatory factor, the finding of plant miRNAs attracted the attention of molecular plant nutrition biologists. Although recent studies indicated that miRNAs regulate plant adaptive responses to nutrient deprivation, the functional significance of miRNAs in adaptive responses to N-limitation remains to be explored.
To elucidate the regulatory mechanism of plant nitrogen uptake and assimilation from the perspective of miRNAs, we use maize and Arabidopsis as model plant, and use the RNA genomics technology, the bioinformatics, and the molecular biology to explore the plant miRNAs that affected by N-limitation. The main results are as follows:
1. We discovered a total of99absolutely new loci belonging to47miRNA families by small RNA deep sequencing and degradome sequencing, as well as9new loci were the paralogs of previously reported miR169, miR171, and miR398, significantly expanding the reported150high confidence genes within26miRNA families in maize.
2. Through the degradome we detected the potential targets of miR164f*, miR167g*/h*/i*, miR169r*, miR168a*/b*and miR827*, suggesting that miRNA*could play important roles in plant physiological metabolism processes by mediated mRNA cleavage, which are far from former consider.
3. Small RNA deep sequencing, Q-PCR, small RNA northern blot and5'-RACE analysis identified eight miRNA families (five conserved and three newly identified) differentially expressed under the N-deficient condition, and we summarized a potential function network of miRNA that responses to N-limitation in maize. The expression of miR169, miR395, miR827and miRC1are down-regulated by N-limitation, they directly involved in maize nitrogen stress adaptation by regulate the expression of their targets; miR.171, miR528, miRC19and miRC37are up-regulated under N-limitation condition, their targets are suggested to involved in the N-limitation singal transduction in maize.
4. Further research are carried in Arabidopsis as functional verification, we chose miR169and its target NFYA5, which is a conserved miRNA between plant species. Analysis of the expression of miR169precursors showed that MIR169a was substantially down-regulated in both roots and shoots by N-limitation.35S::MIR169a transgenic plants are hypersensitive to N starvation in hydroponic solution, agar medium and soil, and in all these conditions35S::MIR169a transgenic plants emerge a symptom:the leaves turn yellow. However,35S::NFYA5transgenic plants are more tolerance to the N-limitation, and35S::NFYA5transgenic plants can gain more biomass than wild type, suggesting miR169is involved in the N-limitation responses by regulated the expression of its target in plant.
5. Under N-limiting conditions, the total N contents in roots of35S::MIR169a transgenic plants were c.4.5%, which was lower than that of the wild-type (5%). Furthermore, compare to wild-type, the expression of AtNRT1:1and AtNRT2:1are less in35S::MIR169a transgenic plants. These results provide evidence that miRNAs have functional roles in helping plants to cope with fluctuations in N availability in the soil.
本课题以禾本科重要的模式作物——玉米为试材,结合拟南芥,运用RNA组学技术、生物信息学和分子生物学等手段,挖掘受氮胁迫影响的miRNA,从小分子非编码RNA的角度深入研究植物氮素吸收和同化过程的调控机制。主要结果和结论如下：
1.通过对缺氮处理下的玉米幼苗组成的4个小RNA文库和一个降解组库进行深度测序,我们新发现了47个1niRNA家族,将玉米中的miRNA数量由150提高到249。此外,我们分别发现了miR171、miR169和miR398家族的3、5和1个新成员。
2.通过降解组分析发现了miR164f*, miR167g*/h*/i*, miR169r*, miR168a*/b*以及miR827*的潜在靶标,表明miRNA*链并不是像原先认为的在生物体内无功能,而是可以通过对潜在靶基因的切割来参与植物各种生理代谢过程。
3.根据small RNA深度测序、Q-PCR,小RNA Northern blot、5'-RACE等结果,我们鉴定了八个在低氮胁迫下上调或下调的miRNA(5个保守：miRNA家族和3个新发现miRNA家族),并总结了玉米应答低氮胁迫可能的miRNA功能网络。低氮胁迫显著降低miR169、 miR395、miR827和miRC1的表达,它们通过对靶基因表达量的调控直接参与玉米适应氮胁迫的过程；而低氮条件下,miR171、miR528、miRC39和miRC37的表达量上调,其靶基因很可能参与缺氮信号在玉米体内的转导过程。
4.选取了物种间保守的miR169在拟南芥中进行功能验证。基于对miR169前体的分析发现,只有MIR169a的表达量同时在缺氮状况下的根和地上部中发生了下降。35S::MR169a转基因植株在所有生长条件(水培、培养基生长、土培)下对于缺氮都高度敏感,并且都出现了叶片发黄的症状；而miR169的靶基因NFYA5过表达植株在缺氮条件下表现出了更加耐受胁迫的现象,并且生物量也显著高于野生型。这些均表明miR169a通过调控靶基因NFYA5的表达量参与了植物适应氮胁迫的过程。
5.在缺氮条件下,35S::MIR169a转基因植株根部的总氮含量为4.5%,明显低于野生型(5%),在地上部也有相同的变化趋势。此外,35S::MIR169a转基因植株中发现硝酸盐转运蛋白AtNRT1:1和AtNRT2:1的表达都比野生型要低,这其中至少有一部分原因是由于在35S::MIR169a转基因植株中,氮吸收系统遭到破坏所致。这些结果指出,miR169在帮助植物应对土壤中的氮素有效性波动过程中起作用。
Nitrogen (N) is closely related to crop's yeild and quality, and it is the most required element of crop, related research has focused on nitrogen uptake and assimilation, while the corresponding regulatory mechanism is still unclear. Lagged study of regulatory mechanism severely limit researchers breed nitrogen efficient use crop by genetic engineering techniques. As an important upstream regulatory factor, the finding of plant miRNAs attracted the attention of molecular plant nutrition biologists. Although recent studies indicated that miRNAs regulate plant adaptive responses to nutrient deprivation, the functional significance of miRNAs in adaptive responses to N-limitation remains to be explored.
To elucidate the regulatory mechanism of plant nitrogen uptake and assimilation from the perspective of miRNAs, we use maize and Arabidopsis as model plant, and use the RNA genomics technology, the bioinformatics, and the molecular biology to explore the plant miRNAs that affected by N-limitation. The main results are as follows:
1. We discovered a total of99absolutely new loci belonging to47miRNA families by small RNA deep sequencing and degradome sequencing, as well as9new loci were the paralogs of previously reported miR169, miR171, and miR398, significantly expanding the reported150high confidence genes within26miRNA families in maize.
2. Through the degradome we detected the potential targets of miR164f*, miR167g*/h*/i*, miR169r*, miR168a*/b*and miR827*, suggesting that miRNA*could play important roles in plant physiological metabolism processes by mediated mRNA cleavage, which are far from former consider.
3. Small RNA deep sequencing, Q-PCR, small RNA northern blot and5'-RACE analysis identified eight miRNA families (five conserved and three newly identified) differentially expressed under the N-deficient condition, and we summarized a potential function network of miRNA that responses to N-limitation in maize. The expression of miR169, miR395, miR827and miRC1are down-regulated by N-limitation, they directly involved in maize nitrogen stress adaptation by regulate the expression of their targets; miR.171, miR528, miRC19and miRC37are up-regulated under N-limitation condition, their targets are suggested to involved in the N-limitation singal transduction in maize.
4. Further research are carried in Arabidopsis as functional verification, we chose miR169and its target NFYA5, which is a conserved miRNA between plant species. Analysis of the expression of miR169precursors showed that MIR169a was substantially down-regulated in both roots and shoots by N-limitation.35S::MIR169a transgenic plants are hypersensitive to N starvation in hydroponic solution, agar medium and soil, and in all these conditions35S::MIR169a transgenic plants emerge a symptom:the leaves turn yellow. However,35S::NFYA5transgenic plants are more tolerance to the N-limitation, and35S::NFYA5transgenic plants can gain more biomass than wild type, suggesting miR169is involved in the N-limitation responses by regulated the expression of its target in plant.
5. Under N-limiting conditions, the total N contents in roots of35S::MIR169a transgenic plants were c.4.5%, which was lower than that of the wild-type (5%). Furthermore, compare to wild-type, the expression of AtNRT1:1and AtNRT2:1are less in35S::MIR169a transgenic plants. These results provide evidence that miRNAs have functional roles in helping plants to cope with fluctuations in N availability in the soil.
引文
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