Dynamics of auxin sensing by an SCF-E3 type ubiquitin ligase and its degradation targets

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Ubiquitin-dependent proteolysis (UPS) is essential to auxin perception and signaling, as the UPS machinery catalyzes hormone-dependent turnover of transcriptional regulators, mediating up- or down-regulation of the pathway. Auxin activates transcription of auxin response genes by promoting the degradation of AUX/IAA transcriptional repressors. We showed previously auxin is perceived by a co-receptor system formed by the F-box protein TRANSPORT INHIBITOR RESPONSE 1 (TIR1) or one of its paralogs AUXIN SIGNALING F-BOX 1-5 (AFB1-5) and its degradation targets, AUX/IAAs. Precisely, auxin enhances TIR1/AFB-AUX/IAA interaction by increasing hydrophobic contacts and acting as molecular glue. Thus, we biochemically determined that distinct TIR1/AFB-AUX/IAA co-receptor pairs are differentially perceptive to auxin and might constitute various auxin sensors in vivo. TIR1/AFBs act as substrate receptors of SCF-type E3 ligases, which bind to the degron of AUX/IAAs targeting them to proteasomal degradation. Whether regions besides the degron dictate auxin sensing and target recognition is still a puzzle. The diversity of AUX/IAA, as well as TIR1/AFB protein families in Arabidopsis gives rise to a repertoire of possible co-receptor combinations. Since different auxins and various auxin concentrations modulate plant plasticity, plant cells might perceive these differences via assembly of specific co-receptors with distinct auxin sensing properties. Ubiquitin-mediated protein degradation in response to hormones is the paragon for dynamics, as slight changes in hormone concentration not only imply the assembly and disassembly of target-receptor complexes, but determine when and where gene activation takes place. This dynamic system governs plant growth and development. Only a constant turnover of associations in response to internal cues and external signals allow plant cells to survive, adapt and thrive. As AUX/IAA target recognition by SCFTIR1/AFBs, auxin binding and target degradation are highly specific, timely regulated and dynamic processes; our research plan aims to gain biochemical and structural insights into auxin-dependent protein degradation to predict gene activation. The proposed work aims also to determine whether conformational transitions and competitive interactions take place during auxin sensing, and to characterize the determinants of substrate (AUX/IAA) processing by SCFTIR1/AFBs, and thereby by the 26S proteasome. With this project, we want to substantiate the regulatory mechanism of hormone sensing observed in vitro, and to investigate the structural determinants of small molecule-potentiated SCF activity.