A key question in auxin biology is how auxin, a relatively simple molecule is able to elicit many different plant developmental responses. We describe how the family of DNA-binding ARF transcription factors act as a source of variation in auxin output specificity.
We consider three levels at which ARFs may differ: differential interactions with Aux/IAA inhibitors or with other ARFs, assembly into different protein complexes and binding to different genomic target sites and regulation of different families of proteins. We use genetic analysis, in vivo protein-protein interactions using a dynamic FRET-based interaction assay and mass-spectrometry based proteomics, and demonstrate both shared and unique protein interactions among the ARFs proteins. These results identify new regulators of auxin response and offer a plausible explanation for the unique and overlapping functions in auxin-dependent plant development.