title: The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China. yuexun@sdau.edu.cn.|State Key Laboratory of Crop Biology, College of Information Sciences and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China. yuexun@sdau.edu.cn.
authors: Xun
authors: X
authors: Yue
authors: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
authors: Xing Guo
authors: XG
authors: Li
authors: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
authors: Xin-Qi
authors: XQ
authors: Gao
authors: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
authors: Xiang Yu
authors: XY
authors: Zhao
authors: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
authors: Yu Xiu
authors: YX
authors: Dong
authors: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
authors: Chao
authors: C
authors: Zhou
mesh_terms: D017360:Arabidopsis / Q000166:cytology / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D003583:Cytokinins / Q000378:metabolism; D006706:Homeostasis; D007210:Indoleacetic Acids / Q000378:metabolism; D008954:Models, Biological; D010937:Plant Growth Regulators / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; D003583:Cytokinins; D007210:Indoleacetic Acids; D010937:Plant Growth Regulators; D014157:Transcription Factors
keywords: Arabidopsis; Circular control units; Metabolic route; Network; Pathway; Phytohormone crosstalk