Shubhajit Das: Quantitative understanding of a dynamic protein network

The plant hormone auxin steers various complex growth and developmental processes through a comparatively simpler nuclear signaling pathway that mostly acts via transcriptional gene regulation. The nuclear auxin signaling pathway (NAP) has only three set of components: the nuclear auxin receptor TIR1, the repressor Aux/IAA and the ARF transcription factors. However, the genetic redundancy of each NAP components in higher model plants (e.g. Arabidopsis thaliana with 6 TIR1,29 Aux/IAA,23 ARF) makes this signaling pathway complicated to understand in its entirety.


With almost centuries of research on auxin, today we have a lot of qualitative information about this pivotal plant hormone signaling pathway. However, there is very limited example of any quantitative data that can provide sufficient comprehension. In my project the objective is to investigate the quantitative aspect of the auxin response protein (TIR1, Aux/IAA, ARF) interaction network. We are interested to look into the interplay of all auxin response proteins to have a quantitative overview of this dynamic protein network as a whole. To this end we are using various microscopic and spectroscopic tools to determine the in vivo protein concentration, their interactions, dissociation constants of each protein-protein and protein-DNA interactions. With all this quantitative imaging data, we are aiming to develop a mathematical model that would identify the critical factors involved in the final signal output of the pathway.
The model plant that we are using for our study is a liverwort Marchantia polymorpha which has the simplest NAP among all land plants with only 1 TIR1, 1 AuxIAA and 3 ARFs (each representing 3 different ARF classes present in higher plants). We expect this project to yield adequate quantitative cognizance of auxin signaling and reveal the key quantitative factors involved in auxin mediated plant growth and development.