The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes.
The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes.
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拟南芥植物激素串扰网络涉及连续的代谢途径和调节酶编码基因的转录因子的循环控制单元
DOI：
10.1186/s12918-016-0333-9
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发表时间：
2016-09-02
影响因子：
--
通讯作者：
Zhou C
中科院分区：
文献类型：
--
作者：
Yue X;Li XG;Gao XQ;Zhao XY;Dong YX;Zhou C
背景：植物激素的协同作用和信号的相互依赖是植物发育生物学中的重要课题。植物激素串扰的生理学和遗传学实验证据不断积累，代表拟南芥代谢途径的基因组尺度的酶相关模型已经发表。结果：采用一种新颖的建模方法和先进的计算方法在生物合成水平构建了基于酶的拟南芥植物激素串扰网络(EAPCN)。EAPCN提供了植物激素生物合成途径的结构连接结构，并揭示了一个令人惊讶的结果：定位于高度连接的节点的酶形成了一条连续的代谢路线。此外，我们的分析表明，在连续的代谢途径中调节酶编码基因的转录因子(TF)形成了结构，我们将其描述为在转录水平上操作的循环控制单元。此外，还发现植物激素信号转导途径下游的转录因子参与了调控酶编码基因的循环控制单元。此外，EAPCN中的多种功能酶被发现参与离子和pH动态平衡、环境信号感知、细胞氧化还原动态平衡和生物钟。最后，以拟南芥根尖分生组织的转录图谱和蛋白质表达图谱为例验证了所提出的框架。结论：我们的结果揭示了激素串扰网络在协调内部发育过程和环境信号方面发挥中心作用的多个尺度的耦合机制，并提供了关于拟南芥植物激素串扰的更广泛的观点。我们还发现了潜在的关键调控因子，可以在未来的研究中进一步分析。
Background:Phytohormone synergies and signaling interdependency are important topics in plant developmental biology. Physiological and genetic experimental evidence for phytohormone crosstalk has been accumulating and a genome-scale enzyme correlation model representing the Arabidopsis metabolic pathway has been published. However, an integrated molecular characterization of phytohormone crosstalk is still not available.Results:A novel modeling methodology and advanced computational approaches were used to construct an enzyme-based Arabidopsis phytohormone crosstalk network (EAPCN) at the biosynthesis level. The EAPCN provided the structural connectivity architecture of phytohormone biosynthesis pathways and revealed a surprising result; that enzymes localized at the highly connected nodes formed a consecutive metabolic route. Furthermore, our analysis revealed that the transcription factors (TFs) that regulate enzyme-encoding genes in the consecutive metabolic route formed structures, which we describe as circular control units operating at the transcriptional level. Furthermore, the downstream TFs in phytohormone signal transduction pathways were found to be involved in the circular control units that included the TFs regulating enzyme-encoding genes. In addition, multiple functional enzymes in the EAPCN were found to be involved in ion and pH homeostasis, environmental signal perception, cellular redox homeostasis, and circadian clocks. Last, publicly available transcriptional profiles and a protein expression map of the Arabidopsis root apical meristem were used as a case study to validate the proposed framework.Conclusions:Our results revealed multiple scales of coupled mechanisms in that hormonal crosstalk networks that play a central role in coordinating internal developmental processes with environmental signals, and give a broader view of Arabidopsis phytohormone crosstalk. We also uncovered potential key regulators that can be further analyzed in future studies.
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