二氧化硫胁迫下拟南芥miRNA表达谱分析
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摘要
以拟南芥为材料,利用高通量测序技术并结合生物信息学分析方法,检测二氧化硫(SO_2)处理后拟南芥植株的小分子RNA表达谱,筛选SO_2胁迫响应microRNAs(miRNAs)分子,研究植物miRNAs对逆境胁迫的应答机制.结果发现,30 mg·m~(-3) SO_2处理72 h后,拟南芥地上组织小分子RNA长度分布发生改变,在对照组和SO_2组中均有大量特有的小分子RNA序列,说明SO_2胁迫可诱导拟南芥小分子RNA的表达改变.SO_2胁迫诱导186个保守miRNA和16个新miRNA分子差异表达,其靶基因主要涉及转录调控、信号转导、代谢、刺激响应等生理过程.差异表达的miR160和miR393可通过生长素信号途径调控植株生长发育,参与植物对SO_2的胁迫响应.本研究揭示了植物中参与SO_2胁迫应答的miRNA种类及作用机制,进一步阐明了miRNAs在植物抗逆应答过程中的作用.
MicroRNAs(miRNAs) are a class of small non-coding RNAs that play important regulative roles in response to environmental stress. Sulfur dioxide(SO_2) is one of the most common and harmful air pollutants. In this study, we investigated the miRNAs expression profiles to indentify SO_2-responsive miRNAs in Arabidopsis thaliana shoots by using deep sequencing. The results showed that the length distribution and the abundance of small RNAs(sRNAs) were changed in Arabidopsis shoots after exposed to 30 mg·m~(-3) SO_2 for 72 h. Meanwhile, there were many specific sRNAs sequences in both the control and SO_2-treated Arabidopsis shoots. Our results indicated that SO_2 exposure induced the changes in expression levels of sRNAs in Arabidopsis. A total of 186 conserved miRNAs and 16 novel miRNAs are expressed differentially under SO_2 stress. Functional analysis showed that the target genes of SO_2-responsive miRNAs were involved in transcription regulation, signal transduction, metabolism and stress response. The expression levels of miR160 and miR393 were significantly up-regulated in response to SO_2 stress, which would affect plant growth and development through regulating auxin signaling pathway. This study revealed the miRNAs that involved in SO_2 stress response and the regulatory mechanisms, and further clarified the role of miRNAs in plant defense responses.
MicroRNAs(miRNAs) are a class of small non-coding RNAs that play important regulative roles in response to environmental stress. Sulfur dioxide(SO_2) is one of the most common and harmful air pollutants. In this study, we investigated the miRNAs expression profiles to indentify SO_2-responsive miRNAs in Arabidopsis thaliana shoots by using deep sequencing. The results showed that the length distribution and the abundance of small RNAs(sRNAs) were changed in Arabidopsis shoots after exposed to 30 mg·m~(-3) SO_2 for 72 h. Meanwhile, there were many specific sRNAs sequences in both the control and SO_2-treated Arabidopsis shoots. Our results indicated that SO_2 exposure induced the changes in expression levels of sRNAs in Arabidopsis. A total of 186 conserved miRNAs and 16 novel miRNAs are expressed differentially under SO_2 stress. Functional analysis showed that the target genes of SO_2-responsive miRNAs were involved in transcription regulation, signal transduction, metabolism and stress response. The expression levels of miR160 and miR393 were significantly up-regulated in response to SO_2 stress, which would affect plant growth and development through regulating auxin signaling pathway. This study revealed the miRNAs that involved in SO_2 stress response and the regulatory mechanisms, and further clarified the role of miRNAs in plant defense responses.
引文
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Rajagopalan R,Vaucheret H,Trejo J,et al.2006.A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana [J].Gene & Development,20:3407-3425
Schmitz R J,Zhang X.2011.High-throughput approaches for plant epigenomic studies[J].Current Opinion in Plant Biology,14:130-136
Song J B,Huang S Q,Dalmay T,et al.2012.Regulation of leaf morphology by microRNA394 and its target Leaf Curling Responsiveness [J].Plant and Cell Physiology,53:1283-1294
Sunkar R,Zhu J K.2004.Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis [J].The Plant Cell,16(8):2001-2019
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王海波,王莎莎,龚明.2013.植物miRNA的分子特征及其在逆境中的响应机制[J].基因组学与应用生物学,32(1):121-126
Xia Z,Zhao Z,Li M,et al.2018.Identification of miRNAs and their targets in maize in response to Sugarcane mosaic virus infection [J].Plant Physiology and Biochemistry,125:143-152
Xue M Z,Yi H L.2018.Enhanced Arabidopsis disease resistance against Botrytis cinerea induced by sulfur dioxide [J].Ecotoxicology and Environmental Safety,147:523-529
Yi H,Yin J,Liu X,et al.2012.Sulfur dioxide induced programmed cell death in Vicia guard cells [J].Ecotoxicology and Environmental Safety,78(1):281-286
Zhang B H.2015.MicroRNA:a new target for improving plant tolerance to abiotic stress [J].Journal of Experiment Botany,66(7):1749-1761
Zhou Z S,Song J B,Yang Z M.2012.Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium [J].Journal of Experiment Botany,63(12):4597-4613
曾幼玲,杨瑞瑞.2016.植物miRNA的生物学特性及在环境胁迫中的作用[J].中国农业科学,49(19):3671-3682
Chen C,Ridzon D A,Broomer A J,et al.2005.Real-time quantification of microRNAs by stem-loop RT-PCR [J].Nucleic Acids Research,33 (20):e179
Chien P,Chiang C,Wang Z,et al.2017.MicroRNA-mediated signaling and regulation of nutrient transport and utilization [J].Current Opinion in Plant Biology,39:73-79
Choi D,Toda H,Kim Y,et al.2014.Effect of sulfur dioxide (SO2) on growth and physiological activity in Alnus sieboldiana at Miyakejima Island in Japan [J].Ecological Research,29(1):103-110
杜康兮,沈文辉,董爱武.2018.表观遗传调控植物响应非生物胁迫的研究进展[J].植物学报,53(5):581-593
黄儒,苍晶,于晶,等.2014.冬小麦小RNA高通量测序及生物信息学分析[J].植物学报,49(1):8-18
Islam W,Qasim M,Noman A,et al.2018.Plant microRNAs:Front line players against invading pathogens [J].Microbial Pathogenesis,118:9-17
Jagadeeswaran G,Li Y F,Sunkar R.2014.Redox signaling mediates the expression of a sulfate-deprivation-inducible microRNA395 in Arabidopsis [J].Plant Journal,77:85-96
Knauer S,Holt A L,Rubio-Somoza I,et al.2013.A protodermal miR394 signal defines a region of stem cell competence in the Arabidopsis shoot meristem [J].Development Cell,24:125-132
Li L H,Yi H L.2012.Differential expression of Arabidopsis defense-related genes in response to sulfur dioxide [J].Chemosphere,78:718-724
Liang G,He H,Yu D.2012.Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana [J].PLoS ONE,7(11):e48951
Livak K J,Schmittgen T D.2001.Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method [J].Methods,25 (4):402-408
Megha S,Basu U,Kav N N V.2018.Regulation of low temperature stress in plants by microRNAs [J].Plant Cell and Environment,41:1-15
Rajagopalan R,Vaucheret H,Trejo J,et al.2006.A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana [J].Gene & Development,20:3407-3425
Schmitz R J,Zhang X.2011.High-throughput approaches for plant epigenomic studies[J].Current Opinion in Plant Biology,14:130-136
Song J B,Huang S Q,Dalmay T,et al.2012.Regulation of leaf morphology by microRNA394 and its target Leaf Curling Responsiveness [J].Plant and Cell Physiology,53:1283-1294
Sunkar R,Zhu J K.2004.Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis [J].The Plant Cell,16(8):2001-2019
宋顺,黄冬梅,王安邦,等.2018.作物抗逆相关miRNA的研究进展 [J].分子植物育种,16(7):2180-2186
王海波,王莎莎,龚明.2013.植物miRNA的分子特征及其在逆境中的响应机制[J].基因组学与应用生物学,32(1):121-126
Xia Z,Zhao Z,Li M,et al.2018.Identification of miRNAs and their targets in maize in response to Sugarcane mosaic virus infection [J].Plant Physiology and Biochemistry,125:143-152
Xue M Z,Yi H L.2018.Enhanced Arabidopsis disease resistance against Botrytis cinerea induced by sulfur dioxide [J].Ecotoxicology and Environmental Safety,147:523-529
Yi H,Yin J,Liu X,et al.2012.Sulfur dioxide induced programmed cell death in Vicia guard cells [J].Ecotoxicology and Environmental Safety,78(1):281-286
Zhang B H.2015.MicroRNA:a new target for improving plant tolerance to abiotic stress [J].Journal of Experiment Botany,66(7):1749-1761
Zhou Z S,Song J B,Yang Z M.2012.Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium [J].Journal of Experiment Botany,63(12):4597-4613
曾幼玲,杨瑞瑞.2016.植物miRNA的生物学特性及在环境胁迫中的作用[J].中国农业科学,49(19):3671-3682