A model of the ethylene signaling pathway and its gene response in Arabidopsis thaliana: pathway cross-talk and noise-filtering properties.
Dynamic models of molecular networks and pathways enable in silico evaluations of the consistency of proposed interactions and the outcomes of perturbations as well as of hypotheses on system-level structure and function. We postulate a continuous model of the activation dynamics of the ethylene response factor 1 (ERF1) gene in response to ethylene signaling. This activation elicits the response of the plant defensin 1 (PDF1) gene, which also responds to jasmonic acid, and the inhibition of the putative auxin responsive factor 2 (ARF2) gene, that also responds to auxin. Our model allows the effect of different ethylene concentrations in eliciting contrasting genetic and phenotypic responses to be evaluated allows the effect of different ethylene concentrations in eliciting contrasting genetic and phenotypic responses to be evaluated and seems to consider key components of the ethylene pathway because the ERF1 dose-response curve that we predict has the same qualitative form as the phenotypic dose-response curves obtained experimentally. Therefore, our model suggests that the phenotypic dose-response curves obtained experimentally could be due, at least in part, to ERF1 changes to different ethylene concentrations. Stability analyses show that the model's results are robust to parameter estimates. Of interest is that our model predicts that the ethylene pathway may filter stochastic and rapid chaotic fluctuations in ethylene availability. This novel approach may be applied to any cellular signaling and response pathway in plants and animals.
Díaz
José
J
Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecologia Funcional, Instituto de Ecologia, UNAM, CU., Mexico D.F. 04510, Mexico.
Alvarez-Buylla
Elena R
ER
D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005030:Ethylenes / Q000378:metabolism*; D005246:Feedback / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D008954:Models, Biological; D015233:Models, Statistical; D010940:Plant Proteins / Q000378:metabolism*; D012097:Repressor Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D013269:Stochastic Processes
C503421:ARF2 protein, Arabidopsis; D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; D005030:Ethylenes; C121819:PDF1 protein, Arabidopsis; D010940:Plant Proteins; D012097:Repressor Proteins; C093680:ethylene-responsive element binding protein; C036216:ethylene