Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function

Abstract

Auxin plays a crucial role in the diverse cellular and developmental responses of plants across their lifespan. Plants can quickly sense and respond to changes in auxin levels, and these responses involve several major classes of auxin-responsive genes, including the Auxin/Indole-3-Acetic Acid (Aux/IAA) family, the auxin response factor (ARF) family, small auxin upregulated RNA (SAUR), and the auxin-responsive Gretchen Hagen3 (GH3) family. Aux/IAA proteins are short-lived nuclear proteins comprising several highly conserved domains that are encoded by the auxin early response gene family. These proteins have specific domains that interact with ARFs and inhibit the transcription of genes activated by ARFs. Molecular studies have revealed that Aux/IAA family members can form diverse dimers with ARFs to regulate genes in various ways. Functional analyses of Aux/IAA family members have indicated that they have various roles in plant development, such as root development, shoot growth, and fruit ripening. In this review, recently discovered details regarding the molecular characteristics, regulation, and protein-protein interactions of the Aux/IAA proteins are discussed. These details provide new insights into the molecular basis of the Aux/IAA protein functions in plant developmental processes.

Keywords: Aux/IAA gene family; auxin; function; regulation.

Figure 1

Domain architecture of the canonical Aux/IAA proteins. The canonical Aux/IAA proteins consist of four typical domains, namely, Domains I–IV. Domain I contains an “LxLxL” motif, which is called the ethylene response factor (ERF)-associated amphiphilic repression (EAR) motif. Between Domain I and II, a conserved “KR” motif was identified as a rate motif, and a bipartite nuclear localization signal (NLS) was located between the KR motif and Domain II. The “GWPPV” motif in Domain II is a degron, which controls the turnover of Aux/IAA proteins. Domain III and IV together form type I/II Phox and Bem1p (PB1) domains. Domain III comprises β1, β2, and α1, and the conserved “K” residue in β1 has been identified as a type II basic motif of PB1. Domain IV contains three β-sheets (β3–β5) and two α-helices (α2 and α3). One OPCA-like motif in this domain forms the other face of the ePB1 domain, and a conserved “GDVP” motif between β4 and α2 may facilitate electrostatic protein interactions. Another NLS was also observed in this domain [5,44,60].

Figure 2

Aux/IAA protein interaction network. The physical protein–protein interactions were obtained from the BioGRID database (v3.4.153, https://thebiogrid.org/) [76] and visualized in Cytoscape (version 3.5.0) [77]. The Aux/IAA, ARF, TPL/TPR and TIR1/AFB proteins were identified first, and the remaining proteins were classified into different functional categories using MapMan software (version 3.0.0) [78].

Figure 3

Aux/IAA proteins might be regulated at different levels. PKL, PICKLE; LAX2, LIKE AUXIN RESISTANT 2; GCN5, general control nonderepressible 5; PIF3, PHYTOCHROME INTERACTING FACTOR 3; PIF4, PHYTOCHROME INTERACTING FACTOR 4; PIF5, PHYTOCHROME INTERACTING FACTOR 5; CBF1, C-repeat binding factor 1; DREB2A, dehydration-responsive element binding protein 2A; bZIP11, basic leucine zipper 11; PHYA, PHYTOCHROME A; RGL3, RGA-LIKE3; UBC13, UBIQUITIN-CONJUGATING ENZYME 13; TIR1, TRA NSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX.

Figure 4

Summary of the functions of Aux/IAA genes in growth and development processes of Arabidopsis thaliana [18,19].