Structural basis for oligomerization of auxin transcriptional regulators

Abstract

The plant hormone auxin is a key morphogenetic regulator acting from embryogenesis onwards. Transcriptional events in response to auxin are mediated by the auxin response factor (ARF) transcription factors and the Aux/IAA (IAA) transcriptional repressors. At low auxin concentrations, IAA repressors associate with ARF proteins and recruit corepressors that prevent auxin-induced gene expression. At higher auxin concentrations, IAAs are degraded and ARFs become free to regulate auxin-responsive genes. The interaction between ARFs and IAAs is thus central to auxin signalling and occurs through the highly conserved domain III/IV present in both types of proteins. Here, we report the crystal structure of ARF5 domain III/IV and reveal the molecular determinants of ARF-IAA interactions. We further provide evidence that ARFs have the potential to oligomerize, a property that could be important for gene regulation in response to auxin.

Structural basis for the auxin-induced transcriptional regulation by Aux/IAA17

“…The essential residues at the dimer interface of PB1 were highly conserved in domain III−IV of Aux/ IAA and ARF family proteins, suggesting that they would be important for oligomerization. Indeed, mutation of the conserved residues has recently allowed for determination of the crystal structure of domain III−IV in ARF family proteins (14,15). Here we report, to our knowledge, the first solution structure of domain III−IV of Arabidopsis Aux/IAA17 (IAA17), and characterize the Significance Auxin is the central hormone that governs diverse developmental processes in plants.…”

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

“…A crystal structure of an ARF bound to an ER AuxRE showed that the 15-18 bp spacing allowed the bound ARF homodimer to stabilize through interaction of the ARF dimerization domain (DD) (Boer et al, 2014). Similarly, the DR spacing preference may be explained by stabilizing interactions through a second dimerization domain, the III/IV domain ( Figure 6B) (Nanao et al, 2014). Importantly, although substantial evidence supports a role for motif dimers in ARF binding and auxin response regulation, no comprehensive model yet exists to explain or predict ARF binding site preferences (Farcot et al, 2015).…”

“…We also identified novel binding events at IR repeats, which showed similar spacing preferences to those seen for ER-TGTC repeats but had only two spacing groups (15-16 and 25-27 bp). To explain homodimer binding at this third repeat type, we propose a model in which a third isoform of the ARF5 homodimer, with interactions between positively and negatively charged sides of the III/IV dimerization domain (Nanao et al, 2014), stabilizes the complex at specific spacing of the IR-TGTC ( Figure S5C). To summarize, we observed three repeat-specific patterns of ARF binding that may be explained by three different ARF dimerization models.…”

“…See also Figure S3 and Table S1. (Nanao et al, 2014) and at an ER by the dimerization domain (bottom) (Boer et al, 2014). (C) Relative frequencies of DAP-seq peaks at DR, ER, and IR pairs for Arabidopsis (AtARF5 and AtARF2) and maize (ARF5/ZmARF29) proteins interrogating Arabidopsis (At-gDNA) or maize (Zm-gDNA) DAP-seq libraries.…”

Recapitulation of the forward nuclear auxin response pathway in yeast

“…The inherent modularity of the ARC lends itself to adding additional layers of complexity and quantitative analysis of other challenging features of auxin response, such as feedback or higher-order complexes between ARFs and IAAs. Indeed, recent structural studies indicate the potential for higher-order ARF-IAA complexes than previously suspected (37)(38)(39). ARC Sc may be a useful tool for quantifying the impact of this structural complexity on response dynamics.…”