Ankita Abnave , Jerrin John , Erich Grotewold , Andrea I. Doseff , John Gray
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These regulators were further examined by co-expression analyses, and a subset of protein-DNA interactions (PDIs) validated <em>in vivo</em> by ChIP-qPCR and luciferase reporter assays in maize protoplasts. This study reveals a comprehensive GRN composed of 429 PDIs that exhibits hubs with high connectivity and cross hierarchical regulation of PEP genes in different branches of the pathway. The core GRN includes TFs that are conserved in other plant species and that are implicated in phenolic gene regulation including ZmMYB40/53/100, ZmMADS9, and ZmWD40.1/PAC1. The GRN also includes conserved TFs (<em>e.g.,</em> ZmC3H9, ZmHB20/79, ZmNAC103/123, ZmMYB19/26, ZmMYBR87, ZmDOF3, ZmbZIP67, ZmTCP30, and ZmbHLH128) which indicate that maize PEP genes are developmentally regulated but also fall under the control of biotic and abiotic stress signals. 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This study reveals a comprehensive GRN composed of 429 PDIs that exhibits hubs with high connectivity and cross hierarchical regulation of PEP genes in different branches of the pathway. The core GRN includes TFs that are conserved in other plant species and that are implicated in phenolic gene regulation including ZmMYB40/53/100, ZmMADS9, and ZmWD40.1/PAC1. The GRN also includes conserved TFs (<em>e.g.,</em> ZmC3H9, ZmHB20/79, ZmNAC103/123, ZmMYB19/26, ZmMYBR87, ZmDOF3, ZmbZIP67, ZmTCP30, and ZmbHLH128) which indicate that maize PEP genes are developmentally regulated but also fall under the control of biotic and abiotic stress signals. 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引用次数: 0
摘要
人们对破译支配植物特殊代谢的基因调控网络(GRN)以帮助植物育种有着浓厚的兴趣。在这里,我们研究了支配酚类生物合成途径的基因调控网络。此前已确定,玉米中 19 个主要表达的酚类(PEP)基因足以解释该途径核心苯丙酚、单木质素和黄酮类分支中 70% 的代谢通量。采用酵母-1-杂交(Y1H)基因中心筛选方法发现了玉米 PEP 基因的上层(2、3 和 4 级)调控因子。通过共表达分析进一步研究了这些调控因子,并在玉米原生质体中通过 ChIP-qPCR 和荧光素酶报告实验验证了蛋白质-DNA 相互作用(PDI)的子集。这项研究揭示了一个由 429 个 PDIs 组成的综合性 GRN,该 GRN 显示了具有高度连接性的枢纽,并对通路不同分支中的 PEP 基因进行交叉分层调控。核心 GRN 包括在其他植物物种中保守的、与酚类基因调控有关的 TF,包括 ZmMYB40/53/100、ZmMADS9 和 ZmWD40.1/PAC1。GRN 还包括保守的 TF(如 ZmC3H9、ZmHB20/79、ZmNAC103/123、ZmMYB19/26、ZmMYBR87、ZmDOF3、ZmbZIP67、ZmTCP30 和 ZmbHLH128),这表明玉米 PEP 基因受发育调控,但也受生物和非生物胁迫信号的控制。总之,玉米 PEP GRN 提供了一个复杂的调控机制,该机制在进化过程中协调调控许多酚类基因以响应多种内部和外部信号,并可指导旨在操纵植物酚类水平的工作,从而实现有针对性的育种改良。
Upper level and cross hierarchical regulation of predominantly expressed phenolic genes in maize
There is strong interest in deciphering the gene regulatory networks (GRNs) that govern plant specialized metabolism to assist in plant breeding. Here, we investigated the GRN governing phenolic biosynthesis pathways from which ∼ 8000 secondary metabolites are derived in plants. Previously it was established that 19 predominantly expressed phenolic (PEP) genes in maize are sufficient to explain >70 % of the metabolic flux through the core phenylpropanoid, monolignol, and flavonoid branches of this pathway. A yeast-1-hybrid (Y1H) gene centric screening approach was employed to discover upper level (tier 2, 3, and 4) regulators of maize PEP genes. These regulators were further examined by co-expression analyses, and a subset of protein-DNA interactions (PDIs) validated in vivo by ChIP-qPCR and luciferase reporter assays in maize protoplasts. This study reveals a comprehensive GRN composed of 429 PDIs that exhibits hubs with high connectivity and cross hierarchical regulation of PEP genes in different branches of the pathway. The core GRN includes TFs that are conserved in other plant species and that are implicated in phenolic gene regulation including ZmMYB40/53/100, ZmMADS9, and ZmWD40.1/PAC1. The GRN also includes conserved TFs (e.g., ZmC3H9, ZmHB20/79, ZmNAC103/123, ZmMYB19/26, ZmMYBR87, ZmDOF3, ZmbZIP67, ZmTCP30, and ZmbHLH128) which indicate that maize PEP genes are developmentally regulated but also fall under the control of biotic and abiotic stress signals. Together, the maize PEP GRN provides a complex regulatory mechanism that has evolved to coordinately regulate many phenolic genes in response to multiple internal and external signals and can guide efforts aimed at manipulating phenolic levels in plants towards targeted breeding improvement.
期刊介绍:
Current Plant Biology aims to acknowledge and encourage interdisciplinary research in fundamental plant sciences with scope to address crop improvement, biodiversity, nutrition and human health. It publishes review articles, original research papers, method papers and short articles in plant research fields, such as systems biology, cell biology, genetics, epigenetics, mathematical modeling, signal transduction, plant-microbe interactions, synthetic biology, developmental biology, biochemistry, molecular biology, physiology, biotechnologies, bioinformatics and plant genomic resources.