An increase in nutrient dose leads to proportional increases in crop biomass and
agricultural yield. However, the molecular underpinnings of this nutrient
dose-response are largely unknown. To investigate, we assayed changes in the
Arabidopsis root transcriptome to different doses of nitrogen (N)-a key plant
nutrient-as a function of time. By these means, we found that rate changes of
genome-wide transcript levels in response to N-dose could be explained by a
simple kinetic principle: the Michaelis-Menten (MM) model. Fitting the MM model
allowed us to estimate the maximum rate of transcript change (V max), as well as
the N-dose at which one-half of V max was achieved (K m) for 1,153
N-dose-responsive genes. Since transcription factors (TFs) can act in part as
the catalytic agents that determine the rates of transcript change, we
investigated their role in regulating N-dose-responsive MM-modeled genes. We
found that altering the abundance of TGA1, an early N-responsive TF, perturbed
the maximum rates of N-dose transcriptomic responses (V max), K m, as well as
the rate of N-dose-responsive plant growth. We experimentally validated that
MM-modeled N-dose-responsive genes included both direct and indirect TGA1
targets, using a root cell TF assay to detect TF binding and/or TF regulation
genome-wide. Taken together, our results support a molecular mechanism of
transcriptional control that allows an increase in N-dose to lead to a
proportional change in the rate of genome-wide expression and plant growth.
