Refining the nuclear auxin response pathway through structural biology
Graphical abstract
Introduction
The phytohormone auxin (indole-3-acetic acid, IAA) is a master regulator of plant growth and development through control of cell division and expansion [1]. Because auxin potently impacts growth and development, auxin regulation must be precise. A variety of auxin regulatory strategies, ranging from biosynthesis and metabolism control [2, 3, 4] to transport and localization within the plant [5, 6], influence plant growth and development. Ultimately, auxin sensing triggers the myriad of gene expression changes required for plant growth and development.
Nuclear auxin response pathway components were identified using molecular and genetic approaches to uncover three major families of proteins that intimately link hormone perception and gene expression. Discovery of these protein families — for example, the auxin binding F-box proteins (TIR1; TRANSPORT INHIBITOR RESPONSE 1 and AFB1–5; AUXIN SIGNALING F-BOX PROTEINS 1–5), the AUXIN RESPONSE FACTOR (ARF) transcription factors, and AUXIN/INDOLE 3-ACETIC ACID INDUCIBLE (Aux/IAA) repressor proteins — employed a combination of screens and phylogenetics [7, 8, 9, 10, 11].
Integration of these proteins into a pathway from auxin perception to gene expression occurred through a series of creative studies. Protoplast and seedling-based assays, established the canonical ‘domain’ organization of the ARF transcription factors as an N-terminal DNA-binding domain (DBD), a middle region (MR) conferring either activation or repression properties, and a C-terminal region containing two sequence motifs (III/IV) [12] (Figure 1a). Subsequent studies determined that the III/IV motif of ARF and Aux/IAA proteins mediates ARF•ARF, Aux/IAA•Aux/IAA, and ARF•Aux/IAA interactions [8, 13]; that the Aux/IAA motif I facilitates interaction with TOPLESS (TPL) co-repressors [14]; and that the Aux/IAA motif II contains a degron that controls protein stability [15]. These investigations also established Aux/IAA proteins as ARF repressors [16] and defined two ARF subfamilies — positive and negative transcriptional regulators [12]. Further, molecular biology-focused studies suggested TIR1 as an auxin receptor [17, 18].
Various features of these three protein families led to a general model for plant auxin responses (Figure 1b). Under low auxin, Aux/IAA proteins repress ARF-mediated auxin-responsive gene transcription. Upon increased auxin, IAA binds an auxin-perceiving F-box protein, permitting Aux/IAA interaction. TIR1/AFB•auxin•Aux/IAA complex formation leads to Aux/IAA ubiquitylation and degradation and frees ARF proteins to regulate auxin-responsive gene expression [19].
A series of recent structural biology studies revealed salient features that guide the molecular interplay between IAA and auxin signaling components. This review summarizes current structural biology contributions to the establishment, dissection, and refinement of the auxin response pathway.
Section snippets
Structural identification of auxin signal perception by SCFTIR1/AFB
The TIR1/AFB F-box protein family provides a mechanism for auxin perception and mediates Aux/IAA protein ubiquitylation for proteasomal degradation [11, 20, 21]. After initial studies identified TIR1 as an auxin receptor [17, 18], the landmark structural study by Tan et al. [22••] introduced a new mechanism for auxin perception and Aux/IAA degradation (Figure 2). The TIR1•auxin•Aux/IAA complex X-ray crystal structure revealed how auxin binds to TIR1 to mediate interaction with the IAA7 degron
Mechanistic clues of auxin responsive gene transcription through binding of AuxREs
ARF proteins are central players in the nuclear auxin response pathway. Initially discovered in a yeast one-hybrid screen for proteins that bind the canonical auxin response element (AuxRE) [7, 30], these proteins modulate auxin-responsive gene transcription. The Arabidopsis genome encodes 22 ARF proteins with a three-domain architecture (Figure 1a), consisting of an N-terminal B3 type DBD, middle region, and interaction domain. B3 domains are plant-specific DBD [31]. The ARF MR can be enriched
ARF and Aux/IAA PB1 domain structures introduce a multimerization option
ARF and Aux/IAA proteins interact through two C-terminal regions of sequence homology (i.e., sequence motifs III and IV) [8]. X-ray crystal structures of the C-terminal regions of Arabidopsis ARF7 [39••] and ARF5 [40••] demonstrate that region III/IV adopts a type I/II Phox/Bem1p (PB1) domain structure (Figure 4a), as suggested by bioinformatic analysis [41]. Likewise, NMR structures of the PB1 domains of Arabidopsis IAA17 [42••] and Pisum sativum IAA4 [43••] confirm a similar architecture in
Conclusions
Structural biology provided new insights that define and refine the auxin response pathway. The first views of the TIR1•auxin•Aux/IAA complex established the ‘molecular glue’ mechanism for auxin perception; ARF DBD structural analyses revealed a molecular basis for AuxRE recognition; and ARF and Aux/IAA PB1 domain structures led to insight into how protein interactions attenuate auxin responses in plants and raises the possibility of ARF and/or Aux/IAA multimerization. Together, these studies
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
Support from the National Science Foundation Graduate Research Fellowship Program (2011101911 to D.A.K.), the United States Department of Agriculture – National Institute of Food and Agriculture Fellowship Program (MOW-2014-01877 to D.A.K.), the National Institutes of Health (R00 GM089987-03 to L.C.S.), and the National Science Foundation (MCB-1157771 to J.M.J. and IOS-1453750 to L.C.S.) is acknowledged.
References (50)
- et al.
Enzyme action in the regulation of plant hormone responses
J Biol Chem
(2013) From perception to attenuation: auxin signalling and responses
Curr Opin Plant Biol
(2013)- et al.
Plant development is regulated by a family of auxin receptor F box proteins
Dev Cell
(2005) - et al.
Auxin response factors
Curr Opin Plant Biol
(2007) - et al.
Composite structure of auxin response elements
Plant Cell
(1995) - et al.
Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors
Cell
(2014) - et al.
ARF–Aux/IAA interactions through domain III/IV are not strictly required for auxin-responsive gene expression
Plant Signal Behav
(2013) - et al.
Integration of auxin and brassinosteroid pathways by Auxin Response Factor 2
Proc Natl Acad Sci U S A
(2008) - et al.
Auxin activity: past, present, and future
Am J Bot
(2015) Auxin biosynthesis and its role in plant development
Annu Rev Plant Biol
(2010)
Auxin biosynthesis and storage forms
J Exp Bot
PIN-dependent auxin transport: action, regulation, and evolution
Plant Cell
ARF1, a transcription factor that binds auxin response elements
Science
Protein–protein interactions among the Aux/IAA proteins
Proc Natl Acad Sci U S A
Changes in auxin response from mutations in an AUX/IAA gene
Science
The TIR1 protein of Arabidopsis functions in auxin response and is related to human SKP2 and yeast Grr1p
Genes Dev
Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements
Plant Cell
TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis
Science
A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin
Nat Chem Biol
The roles of auxin response factor domains in auxin-responsive transcription
Plant Cell
The F-box protein TIR1 is an auxin receptor
Nature
The Arabidopsis F-box protein TIR1 is an auxin receptor
Nature
SCFTIR1/AFB-based auxin perception: mechanism and role in plant growth and development
Plant Cell
Complex regulation of the TIR1/AFB family of auxin receptors
Proc Natl Acad Sci U S A
Auxin-induced, SCFTIR1-mediated poly-ubiquitination marks AUX/IAA proteins for degradation
Plant J
Cited by (39)
Determinants of PB1 Domain Interactions in Auxin Response Factor ARF5 and Repressor IAA17
2020, Journal of Molecular BiologyCitation Excerpt :Aux/IAA proteins have a co-repressor binding domain (Domain I), a degron domain (Domain II), and a C-terminal PB1 domain. The PB1 domain common to both ARF and Aux/IAA proteins mediates homomeric and heteromeric associations that are crucial for transcriptional control of auxin responsive genes [9,10]. At low auxin levels, Aux/IAA binds to ARFvia the PB1 domain and recruits TOPLESS (TPL) and TPL-relatedco-repressors to repress the transcriptional activity of ARF [11] (Figure 1(a)).
Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana
2019, Molecular CellCitation Excerpt :Auxins regulate diverse and critical aspects of cell division and expansion (Woodward and Bartel, 2005). Normal plant growth and development requires tight control of auxin responses, which are modulated by the auxin response factor (ARF) family of transcription factors (Korasick et al., 2015b; Wang and Estelle, 2014). In addition to ARFs, auxin-binding transport inhibitor response 1/auxin signaling F box (TIR1/AFB) proteins and the auxin/indole-3-acetic acid-inducible (Aux/IAA) repressor proteins act in the canonical auxin signaling system (Korasick et al., 2015b; Wang and Estelle, 2014).
Modification of auxinic phenoxyalkanoic acid herbicides by the acyl acid amido synthetase GH3.15 from Arabidopsis
2018, Journal of Biological ChemistryCitation Excerpt :At the molecular level, 2,4-D binds to the auxin receptor F-box protein TIR1, which facilitates interaction between the receptor and corepressor Aux/IAA proteins (11, 12). This leads to ubiquitination and degradation of the Aux/IAA proteins to modulate downstream interactions with auxin response factors that control transcription of auxin responsive genes (13, 14). Although both IAA and 2,4-D target the auxin receptor, 2,4-D is metabolized more slowly than IAA, which enhances herbicidal effects through elevated expression of auxin responsive genes leading to plant death (6, 15, 16).
Identification and expression profiling of the Aux/IAA gene family in Chinese hickory (Carya cathayensis Sarg.) during the grafting process
2018, Plant Physiology and BiochemistryGynoecium formation: an intimate and complicated relationship
2017, Current Opinion in Genetics and DevelopmentAuxins
2017, Hormone Metabolism and Signaling in Plants