Hormone-mediated modulation of gene activation or repression through transcription factors is central to all organisms. AUXIN RESPONSE FACTOR (ARF) transcription factors are critical modulators of plant growth and provide an ideal model for exploring hormone control of gene activation and repression. Of the 23-member ARF family, five are considered transcriptional activators and 18 are considered transcriptional repressors, allowing for study of both of these activities in a single family. Under low auxin concentrations, Aux/IAA proteins repress ARF transcription factors via direct interaction and recruitment of chromatin remodeling factors. When auxin concentrations are high, a co-receptor complex, comprised of an F-box protein from the TRANSPORT INHIBITOR REPONSE1 (TIR1) family and an Aux/IAA repressor protein, directly binds auxin. The F-box protein participates in a Skp1-Cullin-F-box (SCF) E3 ubiquitin ligase, which targets the Aux/IAA protein for degradation. This degradation event relieves ARF transcription factor repression, allowing auxin-regulated transcription. This receptor-ligand interaction allows a very short signal transduction chain to facilitate rapid transcriptional responses to auxin. To understand the molecular underpinnings of ARF-ARF and ARF-Aux/IAA interactions, our lab solved the structure of the domain driving these interactions, finding that it folds into a Type I/II Phox and Bem1 (PB1) domain. Within this domain, there is a positively charged and a negatively charged electrostatic face on opposing sides, creating a Janus-like protein fold. This allows for front-to-back ARF oligomerization (similar to a set of bar magnets) in the packed crystal, in solution, and in the plant. In addition to the well-studied repression ? derepression mechanism of regulation, our lab has discovered that activity of a subset of ARFs can be regulated by protein phase transition driven by the combination of PB1 oligomerization and an intrinsically disordered region. Phase transition of these ARFs appears to modulate responsiveness to auxin in a developmentally relevant context. We have further found that many ARFs are regulated by proteasomal degradation and have identified an E3 ubiquitin ligase involved in this process. Finally, ARF interactions can be easily manipulated using PB1 domain point mutations, allowing us to direct ARF interactions for study. Using ARFs as a model will allow us to interrogate transcription factor function in an easily manipulated system to yield broad insight into many transcription factors. We are aided in our efforts by our multidisciplinary approach, extensive auxin-related molecular toolkit, and unique reagents generated by our lab. Our lab's expertise in genetics and biochemistry/biophysics, combined with our recent discoveries of ARF condensation and proteasomal degradation, makes us well positioned to drive forward our understanding of phase transition and other mechanisms in regulation of transcription factor activity.
Our research is relevant to the NIH mission to seek fundamental knowledge about the nature and behavior of living systems. We seek to understand hormone-mediated modulation of gene activation or repression through transcription factors. Because this process is central to all systems, identifying mechanisms that regulate transcriptional activity in one organism may be broadly informative to all organisms.