引用本文:穆阳杰,詹玉洁,许卫锋,夏天雨.高pH胁迫下拟南芥根转录组学与网络应答[J].土壤学报,2020,57(3):691-701. DOI:10.11766/trxb201902160084
MU Yangjie,ZHAN Yujie,XU Weifeng,XIA Tianyu.Transcriptome and Network Response of Arabidopsis Root Under High pH Stress[J].Acta Pedologica Sinica,2020,57(3):691-701. DOI:10.11766/trxb201902160084
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高pH胁迫下拟南芥根转录组学与网络应答
穆阳杰, 詹玉洁, 许卫锋, 夏天雨
福建农林大学生命科学学院
摘要:
土壤碱化是影响作物产量的重要因素。为进一步了解植物应答土壤碱化的转录调控机制,利用转录组测序技术对正常pH(pH 6.0)和高pH(pH 8.0)条件下生长的拟南芥根进行全基因表达谱分析,共筛选出1 129个差异表达基因。基因本体论GO(Gene Ontology)功能注释显示,差异表达基因主要与胁迫应答、转录、细胞组织发生、运输、蛋白质代谢和信号转导等生物学过程相关。其中,参与离子运输、细胞壁合成、钙离子信号和植物激素等过程的基因表达量发生了显著性变化,暗示这些基因参与植物对高pH胁迫的响应。转录调控网络预测分析表明,花卉同源蛋白质2/乙烯反应元件结合蛋白AP2-EREBP(APETALA2/Ethylene-responsive element binding proteins)、髓母细胞瘤病毒致癌基因同源物MYB(Myeloblastosis viral oncogene homolog)、具有高度保守结构域的转录调控因子WRKY和无顶端分生组织,拟南芥转录激活因子NAC(No apical meristem,Arabidopsis transcription activation factor and Cup-shaped cotyledon)家族转录因子与高pH胁迫响应基因存在密切的转录调控关系。本研究为植物耐碱分子机理的解析和耐碱品种的培育提供了方向和依据。
关键词:  高pH胁迫  转录组  调控网络  离子运输  细胞壁合成  信号传导
基金项目:国家重点研发计划项目(2017YFE0118100,2018YFD02003025)和国家自然科学基金项目(31872169)资助
Transcriptome and Network Response of Arabidopsis Root Under High pH Stress
MU Yangjie, ZHAN Yujie, XU Weifeng, XIA Tianyu
College of Life Sciences, Fujian Agriculture and Forestry University
Abstract:
【Objective】Soil alkalinity is a widespread environmental problem that limits crop yield. Up to 831 million hectares of land are under salt stress on the earth, and about half are being alkalinized. Under alkali stress, plants are exposed to both salt and high pH. Moreover, high pH stress is a more significant factor in limiting plant growth than salt stress. High pH stress inhibits plant growth by imposing adverse effect on roots, such as increasing ion imbalance, disrupting cellular pH stability and decreasing nutrient solubility. However, it remains unknown how transcription responds to high pH stress for regulation and its mechanism. Therefore, this paper tries to elucidate molecular mechanism of high pH tolerances of Arabidopsis with the aid of high throughput biotechnology. The research is essential to breeding high and stable yield crops. 【Method】 In recent years, high throughput sequencing has been rapidly developed and used in genome-wide gene expression profiling of Arabidopsis, rice and soybean. In this paper, a stable pH experiment system was established and transcriptional profiling of the root of Arabidopsis cultivated in high pH medium for 7 days was conucted using RNA-seq. Then differently expressed genes (DEGs) in response to high pH stress were presented and annotated. In the end, important high pH responsive genes and their putative upstream transcription factors were identified.【Result】The following findings were obtained. It was found that under high pH stress, growth of the primary root of Arabidopsis was significantly limited. Transcriptome sequencing of Arabidopsis root under normal pH (6.0) and high pH (8.0) were performed. Of the 1129 DEGs analyzed, 329 were identified as up-regulated genes and 800 as down-regulated genes. GO (Gene Ontology) functional categorization shows that these DEGs are highly related to abiotic stimulus, transcription, cell organizations and biogenesis, ion transport, protein metabolism and signal transduction. In addition, several genes were determined to be responsive to high pH identified. For example, water channel gene PIP2;4 and PIP2;5 , Al-activated malate transporter gene ALMT1 , K+ transporter gene HAK5 and calcium exchanger gene CAX7 were down-regulated after high pH treatment. Several encoding calcium binding proteins and calmodulin protein genes, such as MSS3, CBL7, CML23, CML37, CML38, were also down-regulated under high pH stress. Auxin responsive genes SAUR16, SAUR40, IAA4 and transport genes PIN5, PIN-LIKES7 and cytokinin biosynthesis genes LOG2 , LOG5, LOG6, LOG9 were expressed differently under high pH stress, suggesting that auxin and cytokinin play important roles in response to high pH. Meanwhile, identification of 97 differently expressed transcription factors (DE TFs) under high pH condition was performed. These DE TFs were included in 20 TF families, such as AP2/EREBP, MYB, WRKY, NAC, bHLH. Then a transcriptional regulatory network between DE TFs and important high pH responsive genes was constructed. It was found that DE TFs belonged to AP2/EREBP, WRKY, NAC and MYB TF families, such as DREB2A, WRKY45 , NAC045 and MYB107 acted as the hub genes in this high pH responsive network.【Conclusion】In this paper, a comprehensive overview was presented of the transcriptomes of Arabidopsis root under high pH stress. Among them a total of 1129 genes were identified as high pH responsive DEGs, and frequently involved in transcription regulation, ion transport, cell wall organizations, Ca2+ signaling and hormones pathway. Furthermore, regulatory relationship between the DE TFs and high pH responsive genes were predicted. DE TFs belongimg to AP2/EREBP, WRKY, NAC and MYB families played core roles in this regulatory network, suggesting that these TFs play important roles in high pH stress response in Arabidopsis. Overall, all the findings in this study may serve as a important theoretical basis for breeding of alkaline-tolerant crops.
Key words:  High pH stress  Transcriptome  Regulatory network  Ion transport  Cell wall synthesis  Signal transduction