Cell type-specific differences in protein complex stoichiometry and transcriptional regulation affect the timing of stem cell division

Stem cells divide and differentiate to form all the specialized cell types and tissues in a multicellular organism. In the Arabidopsis root, stem cells are maintained in their undifferentiated state by a less mitotically dividing cell population known as the Quiescent Center (QC). However, what makes the QC fundamentally different than the actively-dividing, surrounding stem cell initials is not well understood. Here, we gained insight into differences between the QC and the Cortex Endodermis Initials (CEI) by studying the mobile transcription factor SHORTROOT (SHR) and its binding partner SCARECROW (SCR). To predict whether there are different, cell-type specific functions of SHR and SCR, we constructed an Ordinary Differential Equation (ODE) model of SHR and SCR concentrations in the QC and CEI. Using sensitivity analysis, we found that SHR and SCR complex stoichiometry as well as upstream regulation of SHR are important parameters in the model. We thus quantified SHR-SCR complex stoichiometry using scanning fluorescence correlation spectroscopy (Scanning FCS) and determined putative upstream SHR regulators using time course gene expression data. Our model prediction coupled with experimental validation showed that high levels of the SHR-SCR complex correlate with more CEI division but less QC division. Further, our model allowed us to predict the timing of QC and CEI division. Thus, our results suggest that protein complex stoichiometry and upstream transcriptional regulation modulate the division timing of different specialized cell types.