A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network

PLoS One. 2015 Feb 26;10(2):e0116973. doi: 10.1371/journal.pone.0116973. eCollection 2015.

Abstract

Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) mutation has a larger impact on APETALA1 (AP1), which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY) which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1) by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / growth & development
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Flowers / genetics*
  • Flowers / growth & development
  • Gene Expression Regulation, Plant*
  • Gene Regulatory Networks*
  • MADS Domain Proteins / genetics
  • MADS Domain Proteins / metabolism
  • Models, Genetic
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • AGL20 protein, Arabidopsis
  • AP1 protein, Arabidopsis
  • Arabidopsis Proteins
  • FLF protein, Arabidopsis
  • LFY protein, Arabidopsis
  • MADS Domain Proteins
  • Transcription Factors

Grant support

This work was supported by a Max Planck postdoctoral fellowship to DP, an EMBO Long-Term postdoctoral fellowship to MCK, a Deutsche Forschungsgemeinschaft (DFG) grant (ERA-PG “BloomNet”, SCHM1560/7-1) to MS and the Max Planck Society, a Netherlands Organisation for Scientific Research (NWO) VENI grant (863.08.027) to ADJvD, the SYSFLO Marie Curie Initial Training Network (FLV), and by the Netherlands Consortium for Systems Biology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. RvH is employed by Keygene N.V. Keygene N.V. provided support in the form of salary for author RvH, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section.