Structural Aspects of Auxin Signaling

Abstract

Auxin signaling regulates growth and developmental processes in plants. The core of nuclear auxin signaling relies on just three components: TIR1/AFBs, Aux/IAAs, and ARFs. Each component is itself made up of several domains, all of which contribute to the regulation of auxin signaling. Studies of the structural aspects of these three core signaling components have deepened our understanding of auxin signaling dynamics and regulation. In addition to the structured domains of these components, intrinsically disordered regions within the proteins also impact auxin signaling outcomes. New research is beginning to uncover the role intrinsic disorder plays in auxin-regulated degradation and subcellular localization. Structured and intrinsically disordered domains affect auxin perception, protein degradation dynamics, and DNA binding. Taken together, subtle differences within the domains and motifs of each class of auxin signaling component affect signaling outcomes and specificity.

Figure 1.

The canonical nuclear auxin signaling pathway. The core nuclear auxin signaling pathway is made up of three components: TIR1/AFBs, AUX/IAAs, and ARFs. (A) High auxin levels; (B) Low/no auxin. Under low auxin conditions, the AUX/IAAs interact with ARFs via the carboxy-terminal PB1 domain found in both protein families and prevent transcription of auxin-responsive genes. As auxin levels increase, the F-box protein and auxin-receptor TIR1 binds the molecule, which stabilizes interactions with its target, the AUX/IAAs. The AUX/IAAs are polyubiquitinated and degraded by the 26S proteasome, relieving the ARFs of repression and allowing auxin-responsive transcription to occur. (DBD) DNA-binding domain.

Figure 2.

TIR1 is the auxin receptor. (A) The TIR1 protein encodes a 48-amino-acid F-box domain at its amino-terminus that is required for interactions with the SCF complex. (B) The TIR1 crystal structure (tan) in complex with the SCF adaptor component ASK1 (cyan) was resolved by Tan et al. (2007). The F-box domain (magenta) contacts the helices of ASK1 at several points and disturbing this interaction results in a dominant-negative form of TIR1. (C) Critical residues in the auxin-binding pocket of TIR1 are required for its function. This region was targeted to generate the synthetic ccvTIR1 form. (D) Upon auxin (green) binding, TIR1 (tan) can strongly interact with the degron (DII) of the AUX/IAA (pale blue) that seals in the auxin molecule.

Figure 3.

The AUX/IAAs are modular proteins with only a single structured domain. (A) An idealized motif and domain structure based on the Pisum sativum IAA4 protein. The only globular domain is the carboxy-terminal PB1 domain that mediates interactions with other AUX/IAAs and the ARFs. Both the degron (DII) and the EAR motif (DI) are short linear motifs that mediate interactions with TIR1 and the TPL corepressor family, respectively. (B) The atomic structure of the PsIAA4 PB1 domain here, resolved by Dinesh et al. (2015), shows that each face of the PB1 domain is enriched for either positively (blue) or negatively (red) charged residues that facilitate head-to-tail interactions with one another. (C) The current model for TIR1–AUX/IAA interactions now incorporates the intrinsically disordered regions that flank the degron. Key residues on both TIR1 and the AUX/IAA help stabilize the degron-mediated interaction and ensure downstream degradation and auxin signaling as shown in Niemeyer et al. (2020).

Figure 4.

The ARFs are defined by three major domains. (A) The ARFs are defined by two globular domains, the amino-terminal DNA-binding domain (DBD) and the carboxy-terminal PB1 domain, and an intrinsically disordered middle region that lies between them, based on the Arabidopsis ARF7 protein model. (B) The crystal structure of the class B ARF1 DBD binding an ER7 AuxRE, resolved by Boer et al. (2014), shows dimerization contact points (yellow) that stabilize the interactions with TGTCTC consensus sequence (purple) in an antiparallel manner. (C) The ARF7 PB1 domain crystal structure resolved by Korasick et al. (2014), like the AUX/IAA PB1 domain, has both a positively and negatively charged face. (D) These faces interact in a head-to-tail fashion to generate strings of PB1 domains in the crystal structure. The lysine residue on the positive face interacts with the aspartic and glutamic acid residues on the negative face similar to a bar magnet. Perturbing these residues results in the loss of PB1 domain interactions along that face.

Figure 5.

Auxin signaling relies on abundant, nuclear class A ARFs. (A) Powers et al. (2019) show that auxin signaling is absent in tissues in which ARF19 has moved out of the nucleus into cytoplasmic condensates. This effect can be eliminated if ARF19 remains nuclear. (B) As data in Kato et al. (2020) show, auxin signaling is present in the tissues that express class A ARF1 in Marchantia and absent in the tissues that express class B ARF2. Taken together, these two studies present a model in which high abundance of nuclear localized class A ARFs define auxin-responsive tissues, whereas tissues lacking class A ARFs entirely or from the nucleus are generally auxin insensitive.