Detecting and quantifying oligomerization of ARF PB1 Domains

Abstract

Auxin response factors (ARFs) are a family of transcription factors within plants that serve to regulate the plant’s response to auxin, a growth initiating hormone. ARFs can either serve as transcription activators or repressors to auxin regulation in the presence of auxin. The majority ARFs have 3 domains: a PB1 protein interaction domain, the low‐complexity middle region, and a DNA binding domain. Major differences between ARF activators and repressors lay in large sequence differences in the middle region, but sequence analysis of the PB1s domains show key differences with implications for their role in transcription regulation. PB1 domains are responsible the interactions necessary for auxin regulation. All ARF PB1 domains are type I/II meaning they contain both a positive and negative residue on opposite sides for electrostatic interactions with copies of themselves or other PB1 domains. The potential for bidentate interaction interfaces complicates the model of auxin response by requiring us to consider oligomerization through the PB1 domain including the potential for hetero‐oligomerizatin between ARF activators and repressors. The work examines the degree of oligomerization and quantifies dimerization affinity in both the wild‐type ARF5 PB1, a transcription activator, and the ARF1 PB1, a transcription repressor. More specifically, to answer these questions crosslinking, gel filtration, and fluorescence anisotropy were used to compare a broad range of concentrations for analysis as well as to improve quantification. Both wild‐type ARF5 and ARF1 self‐associated as expected under varying conditions, forming small oligomers, but ARF5 remained primarily in the dimer state. This work suggests a more nuanced model of transcriptional regulation depending on the specific population of regulatory PB1s present.