Rapid degradation of auxin/indoleacetic acid proteins requires conserved amino acids of domain II and is proteasome dependent

DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins

Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 ( drmy1 ), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.

Identification of potential Auxin Response Candidate genes for soybean rapid canopy coverage through comparative evolution and expression analysis

Glycine max, soybean, is an abundantly cultivated crop worldwide. Efforts have been made over the past decades to improve soybean production in traditional and organic agriculture, driven by growing demand for soybean-based products. Rapid canopy cover development (RCC) increases soybean yields and suppresses early-season weeds. Genome-wide association studies have found natural variants associated with RCC, however causal mechanisms are unclear. Auxin modulates plant growth and development and has been implicated in RCC traits. Therefore, modulation of auxin regulatory genes may enhance RCC. Here, we focus on the use of genomic tools and existing datasets to identify auxin signaling pathway RCC candidate genes, using a comparative phylogenetics and expression analysis approach. We identified genes encoding 14 TIR1/AFB auxin receptors, 61 Aux/IAA auxin co-receptors and transcriptional co-repressors, and 55 ARF auxin response factors in the soybean genome. We used Bayesian phylogenetic inference to identify soybean orthologs of Arabidopsis thaliana genes, and defined an ortholog naming system for these genes. To further define potential auxin signaling candidate genes for RCC, we examined tissue-level expression of these genes in existing datasets and identified highly expressed auxin signaling genes in apical tissues early in development. We identified at least 4 TIR1/AFB, 8 Aux/IAA, and 8 ARF genes with highly specific expression in one or more RCC-associated tissues. We hypothesize that modulating the function of these genes through gene editing or traditional breeding will have the highest likelihood of affecting RCC while minimizing pleiotropic effects.

Auxin response factors are keys to the many auxin doors

In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.

Structural Aspects of Auxin Signaling

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.

Auxin Distribution in Lateral Root Primordium Development Affects the Size and Lateral Root Diameter of Rice

Lateral roots (LRs) occupy a large part of the root system and play a central role in plant water and nutrient uptake. Monocot plants, such as rice, produce two types of LRs: the S-type (short and thin) and the L-type (long, thick, and capable of further branching). Because of the ability to produce higher-order branches, the L-type LR formation contributes to efficient root system expansion. Auxin plays a major role in regulating the root system development, but its involvement in developing different types of LRs is largely unknown. Here, we show that auxin distribution is involved in regulating LR diameter. Dynamin-related protein (DRP) genes were isolated as causative genes of the mutants with increased L-type LR number and diameter than wild-type (WT). In the drp mutants, reduced endocytic activity was detected in rice protoplast and LRs with a decreased OsPIN1b-GFP endocytosis in the protoplast. Analysis of auxin distribution using auxin-responsive promoter DR5 revealed the upregulated auxin signaling in L-type LR primordia (LRP) of the WT and the mutants. The application of polar auxin transport inhibitors enhanced the effect of exogenous auxin to increase LR diameter with upregulated auxin signaling in the basal part of LRP. Inducible repression of auxin signaling in the mOsIAA3-GR system suppressed the increase in LR diameter after root tip excision, suggesting a positive role of auxin signaling in LR diameter increase. A positive regulator of LR diameter, OsWOX10, was auxin-inducible and upregulated in the drp mutants more than the WT, and revealed as a potential target of ARF transcriptional activator. Therefore, auxin signaling upregulation in LRP, especially at the basal part, induces OsWOX10 expression, increasing LR diameter.

Morpho-physiological and molecular mechanisms of phenotypic root plasticity for rice adaptation to water stress conditions

Different types of water stress severely affect crop production, and the plant root system plays a critical role in stress avoidance. In the case of rice, a cereal crop cultivated under the widest range of soil hydrologic conditions, from irrigated anaerobic conditions to rainfed conditions, phenotypic root plasticity is of particular relevance. Recently, important plastic root traits under different water stress conditions, and their physiological and molecular mechanisms have been gradually understood. In this review, we summarize these plastic root traits and their contributions to dry matter production through enhancement of water uptake under different water stress conditions. We also discuss the physiological and molecular mechanisms regulating the phenotypic plasticity of root systems.

Ligand-receptor interactions in plant hormone signaling

Small-molecule plant hormones principally control plant growth, development, differentiation, and environmental responses. Nine types of plant hormones are ubiquitous in angiosperms, and the molecular mechanisms of their hormone actions have been elucidated during the last two decades by genomic decoding of model plants with genetic mutants. In particular, the discovery of hormone receptors has greatly contributed to the understanding of signal transduction systems. The three-dimensional structure of the ligand-receptor complex has been determined for eight of the nine hormones by X-ray crystal structure analysis, and ligand perception mechanisms have been revealed at the atomic level. Collective research has revealed the molecular function of plant hormones that act as either molecular glue or an allosteric regulator for activation of receptors. In this review, we present an overview of the respective hormone signal transduction and describe the structural bases of ligand-receptor interactions.

Arabidopsis RING-type E3 ubiquitin ligase XBAT35.2 promotes proteasome-dependent degradation of ACD11 to attenuate abiotic stress tolerance

Plants employ multiple mechanisms to cope with a constantly changing and challenging environment, including using the ubiquitin proteasome system (UPS) to alter their proteome to assist in initiating, modulating and terminating responses to stress. We previously reported that the ubiquitin ligase XBAT35.2 mediates the proteasome-dependent degradation of Accelerated Cell Death 11 (ACD11) to promote pathogen defense. Here, we demonstrate roles for XBAT35.2 and ACD11 in abiotic stress tolerance. As seen in response to pathogen infection, abiotic stress stabilizes XBAT35.2 and the abundance of ACD11 rose consistently with increasing concentrations of abscisic acid (ABA) and salt. Surprisingly, exposure to ABA and salt increased the stability of ACD11, and the overexpression of ACD11 improves plant survival of salt and drought stress, suggesting a role for ACD11 in promoting tolerance. Prolonged exposure to high concentrations of ABA or salt resulted in ubiquitination and the proteasome-dependent degradation of ACD11, however. The stress-induced turnover of ACD11 requires XBAT35.2, as degradation is slowed in the absence of the E3 ubiquitin ligase. Consistent with XBAT35.2 mediating the proteasome-dependent degradation of ACD11, the loss of E3 ubiquitin ligase function enhances the tolerance of salt and drought stress, whereas overexpression increases sensitivity. A model is presented where, upon the perception of abiotic stress, ACD11 abundance increases to promote tolerance. Meanwhile, XBAT35.2 accumulates and in turn promotes the degradation of ACD11 to attenuate the stress response. The results characterize XBAT35.2 as an E3 ubiquitin ligase with opposing roles in abiotic and biotic stress.

Drought-induced protein (Di19-3) plays a role in auxin signaling by interacting with IAA14 in Arabidopsis

The members of early auxin response gene family, Aux/IAA, encode negative regulators of auxin signaling but play a central role in auxin-mediated plant development. Here we report the interaction of an Aux/IAA protein, AtIAA14, with Drought-induced-19 (Di19-3) protein and its possible role in auxin signaling. The Atdi19-3 mutant seedlings develop short hypocotyl, both in light and dark, and are compromised in temperature-induced hypocotyl elongation. The mutant plants accumulate more IAA and also show altered expression of NIT2, ILL5, and YUCCA genes involved in auxin biosynthesis and homeostasis, along with many auxin responsive genes like AUX1 and MYB77. Atdi19-3 seedlings show enhanced root growth inhibition when grown in the medium supplemented with auxin. Nevertheless, number of lateral roots is low in Atdi19-3 seedlings grown on the basal medium. We have shown that AtIAA14 physically interacts with AtDi19-3 in yeast two-hybrid (Y2H), bimolecular fluorescence complementation, and in vitro pull-down assays. However, the auxin-induced degradation of AtIAA14 in the Atdi19-3 seedlings was delayed. By expressing pIAA14::mIAA14-GFP in Atdi19-3 mutant background, it became apparent that both Di19-3 and AtIAA14 work in the same pathway and influence lateral root development in Arabidopsis. Gain-of-function slr-1/iaa14 (slr) mutant, like Atdi19-3, showed tolerance to abiotic stress in seed germination and cotyledon greening assays. The Atdi19-3 seedlings showed enhanced sensitivity to ethylene in triple response assay and AgNO3, an ethylene inhibitor, caused profuse lateral root formation in the mutant seedlings. These observations suggest that AtDi19-3 interacting with AtIAA14, in all probability, serves as a positive regulator of auxin signaling and also plays a role in some ethylene-mediated responses in Arabidopsis.

SIGNIFICANCE STATEMENT

This study has demonstrated interaction of auxin responsive Aux/IAA with Drought-induced 19 (Di19) protein and its possible implication in abiotic stress response.

Non-canonical AUX/IAA protein IAA33 competes with canonical AUX/IAA repressor IAA5 to negatively regulate auxin signaling

The phytohormone auxin controls plant growth and development via TIR1-dependent protein degradation of canonical AUX/IAA proteins, which normally repress the activity of auxin response transcription factors (ARFs). IAA33 is a non-canonical AUX/IAA protein lacking a TIR1-binding domain, and its role in auxin signaling and plant development is not well understood. Here, we show that IAA33 maintains root distal stem cell identity and negatively regulates auxin signaling by interacting with ARF10 and ARF16. IAA33 competes with the canonical AUX/IAA repressor IAA5 for binding to ARF10/16 to protect them from IAA5-mediated inhibition. In contrast to auxin-dependent degradation of canonical AUX/IAA proteins, auxin stabilizes IAA33 protein via MITOGEN-ACTIVATED PROTEIN KINASE 14 (MPK14) and does not affect IAA33 gene expression. Taken together, this study provides insight into the molecular functions of non-canonical AUX/IAA proteins in auxin signaling transduction.

Regulation of auxin transcriptional responses

The plant hormone auxin acts as a signaling molecule to regulate a vast number of developmental responses throughout all stages of plant growth. Tight control and coordination of auxin signaling is required for the generation of specific auxin‐response outputs. The nuclear auxin signaling pathway controls auxin‐responsive gene transcription through the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F‐BOX pathway. Recent work has uncovered important details into how regulation of auxin signaling components can generate unique and specific responses to determine auxin outputs. In this review, we discuss what is known about the core auxin signaling components and explore mechanisms important for regulating auxin response specificity.

A review of recent updates to our understanding of auxin signaling.

Identification and characterization of a new dwarf locus DS-4 encoding an Aux/IAA7 protein in Brassica napus

A dominant dwarfing gene, ds - 4 , encodes an Aux/IAA protein that negatively regulates plant stature through an auxin signaling pathway. Dwarfism is an important agronomic trait affecting yield in many crop species. The molecular mechanisms underlying dwarfism in oilseed rape (Brassica napus) are poorly understood, restricting the progress of breeding dwarf varieties in this species. Here, we identified and characterized a new dwarf locus, DS-4, in B. napus. Next-generation sequencing-assisted genetic mapping and candidate gene analysis found that DS-4 encodes a nucleus-targeted auxin/indole-3-acetic acid (Aux/IAA) protein. A substitution (P87L) was found in the highly conserved degron motif of the Aux/IAA7 protein in the ds-4 mutant. This mutation co-segregated with the phenotype of individuals in the BC₁F₂ population. The P87L substitution was confirmed as the cause of the extreme dwarf phenotype by ectopic expression of the mutant allele BnaC05.iaa7 (equivalent to ds-4) in Arabidopsis. The P87L substitution blocked the interaction of BnaC05.iaa7 with TRANSPORT INHIBITOR RESPONSE 1 in the presence of auxin. The BnaC05.IAA7 gene is highly expressed in the cotyledons, hypocotyls, stems and leaves, but weakly in the roots and seeds of B. napus. Our findings provide new insights into the molecular mechanisms underlying dominant (gain-of-function) dwarfism in B. napus. Our identification of a distinct gene locus controlling plant height may help to improve lodging resistance in oilseed rape.

TMK1-mediated auxin signalling regulates differential growth of the apical hook

The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)^1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin-TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes.

An auxin signaling gene BnaA3.IAA7 contributes to improved plant architecture and yield heterosis in rapeseed

Plant architecture is the key factor affecting overall yield in many crops. The genetic basis underlying plant architecture in rapeseed (Brassica napus), a key global oil crop, is elusive. We characterized an ethyl methanesulfonate (EMS)-mutagenized rapeseed mutant, sca, which had multiple phenotypic alterations, including crinkled leaves, semi-dwarf stature, narrow branch angles and upward-standing siliques. We identified the underlying gene, which encodes an Aux/IAA protein (BnaA3.IAA7). A G-to-A mutation changed the glycine at the 84^th position to glutamic acid (G84E), disrupting the conserved degron motif GWPPV and reducing the affinity between BnaA3.IAA7 and TIR1 (TRANSPORT INHIBITOR RESPONSE 1) in an auxin dosage-dependent manner. This change repressed the degradation of BnaA3.IAA7 and therefore repressed auxin signaling at low levels of auxin that reduced the length of internodes. The G84E mutation reduced branch angles by enhancing the gravitropic response. The heterozygote +/sca closely resembled a proposed ideal plant architecture, displaying strong yield heterosis through single-locus overdominance by improving multiple component traits. Our findings demonstrate that a weak gain-of-function mutation in BnaA3.IAA7 contributes to yield heterosis by improving plant architecture and would be valuable for breeding superior rapeseed hybrid cultivars and such a mutation may increase the yield in other Brassica crops.

Methods for studying the regulation of membrane traffic by ubiquitin and the ESCRT pathway

Covalent modification of proteins with ubiquitin dynamically regulates their function and fate. The ubiquitination of most plasma membrane proteins initiates endocytosis and ESCRT-mediated sorting to the lysosomal lumen for degradation. Powerful genetic approaches in the budding yeast Saccharomyces cerevisiae have been particularly instrumental in the discovery and elucidation of these molecular mechanisms, which are conserved in all eukaryotes. Here we provide two detailed protocols and tools for studying ubiquitination-dependent membrane trafficking mechanisms in yeast. The first utilizes fusions between a protein of interest and an auxotrophic marker to screen for mutants that affect ubiquitin-mediated endocytosis. The second method artificially ubiquitinates a protein of interest, allowing downstream trafficking steps to be studied independently from the regulatory signals that initiate endocytosis.

Translating auxin responses into ovules, seeds and yield: Insight from Arabidopsis and the cereals

Grain production in cereal crops depends on the stable formation of male and female gametes in the flower. In most angiosperms, the female gamete is produced from a germline located deep within the ovary, protected by several layers of maternal tissue, including the ovary wall, ovule integuments and nucellus. In the field, germline formation and floret fertility are major determinants of yield potential, contributing to traits such as seed number, weight and size. As such, stimuli affecting the timing and duration of reproductive phases, as well as the viability, size and number of cells within reproductive organs can significantly impact yield. One key stimulant is the phytohormone auxin, which influences growth and morphogenesis of female tissues during gynoecium development, gametophyte formation, and endosperm cellularization. In this review we consider the role of the auxin signaling pathway during ovule and seed development, first in the context of Arabidopsis and then in the cereals. We summarize the gene families involved and highlight distinct expression patterns that suggest a range of roles in reproductive cell specification and fate. This is discussed in terms of seed production and how targeted modification of different tissues might facilitate improvements.

TaWRKY51 promotes lateral root formation through negative regulation of ethylene biosynthesis in wheat (Triticum aestivum L.)

Common wheat (Triticum aestivum L.) is an important staple food crop worldwide. Lateral roots (LRs), as the major component of root architecture, affect water and nutrient uptake in wheat. The phytohormone ethylene is known to affect LR formation; however, the factor(s) modulating ethylene during this process have not yet been elucidated in wheat. Here we identified wheat TaWRKY51 as a key factor that functions in LR formation by modulating ethylene biosynthesis. Wheat TaWRKY51RNA interference lines (TaWRKY51-RNAi) and the homozygous mutants tawrky51-2a and tawrky51-2b all produced fewer LRs than the wild type and negative transgenic plants, whereas the TaWRKY51 overexpression lines (TaWRKY51-OE) had the opposite phenotype. Transcription analysis revealed that 1-aminocyclopropane-1-carboxylic acid synthase (ACS) genes (TaACS2, TaACS7 and TaACS8) involved in ethylene biosynthesis were downregulated in TaWRKY51-OE lines but upregulated in TaWRKY51-RNAi lines. The rate of ethylene production also decreased in TaWRKY51-OE lines but increased in TaWRKY51-RNAi lines compared with their respective negative transgenic controls. Electrophoretic mobility shift and transient expression assays revealed that TaWRKY51 inhibits the expression of ACS genes by binding to the W-box cis-element present in their promoter region. Moreover, overexpression of ACS2 or exogenous application of 1-aminocyclopropane-1-carboxylic acid reversed the phenotype of enhanced LR number in TaWRKY51-OE Arabidopsis lines, and overexpression of TaWRKY51 in the ethylene-overproducing mutant eto1-1 rescued its LR defect phenotype. In addition, genetic evidence demonstrates that TaWRKY51-regulated LR formation is also dependent on ethylene and auxin signaling pathways. Our findings reveal a molecular genetic mechanism by which a WRKY gene coordinates ethylene production and LR formation in wheat.

The Role of Auxin in Cell Wall Expansion

Plant cells are surrounded by cell walls, which are dynamic structures displaying a strictly regulated balance between rigidity and flexibility. Walls are fairly rigid to provide support and protection, but also extensible, to allow cell growth, which is triggered by a high intracellular turgor pressure. Wall properties regulate the differential growth of the cell, resulting in a diversity of cell sizes and shapes. The plant hormone auxin is well known to stimulate cell elongation via increasing wall extensibility. Auxin participates in the regulation of cell wall properties by inducing wall loosening. Here, we review what is known on cell wall property regulation by auxin. We focus particularly on the auxin role during cell expansion linked directly to cell wall modifications. We also analyze downstream targets of transcriptional auxin signaling, which are related to the cell wall and could be linked to acid growth and the action of wall-loosening proteins. All together, this update elucidates the connection between hormonal signaling and cell wall synthesis and deposition.

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

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.

Evolution of nuclear auxin signaling: lessons from genetic studies with basal land plants

Auxin plays critical roles in growth and development through the regulation of cell differentiation, cell expansion, and pattern formation. The auxin signal is mainly conveyed through a so-called nuclear auxin pathway involving the receptor TIR1/AFB, the transcriptional co-repressor AUX/IAA, and the transcription factor ARF with direct DNA-binding ability. Recent progress in sequence information and molecular genetics in basal plants has provided many insights into the evolutionary origin of the nuclear auxin pathway and its pleiotropic roles in land plant development. In this review, we summarize the latest knowledge of the nuclear auxin pathway gained from studies using basal plants, including charophycean green algae and two major model bryophytes, Marchantia polymorpha and Physcomitrella patens. In addition, we discuss the functional implication of the increase in genetic complexity of the nuclear auxin pathway during land plant evolution.

Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

BACKGROUND

Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known.

RESULTS

In this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes. Evolutionary and comparative analysis revealed that 111 (94.1%) B. napus Aux/IAA genes were multiplied due to ancestral Brassica genome triplication and recent allotetraploidy from B. rapa and B. oleracea. Phylogenetic analysis indicated seven subgroups containing 29 orthologous gene sets and two Brassica-specific gene sets. Structures of genes and proteins varied across different genes but were conserved among homologous genes in B. napus. Furthermore, analysis of transcriptional profiles revealed that the expression patterns of Aux/IAA genes in B. napus were tissue dependent. Auxin-responsive elements tend to be distributed in the proximal region of promoters, and are significantly associated with early exogenous auxin up-regulation.

CONCLUSIONS

Members of the Aux/IAA gene family were identified and analyzed comprehensively in the allotetraploid B. napus genome. This analysis provides a deeper understanding of diversification of the Aux/IAA gene family and will facilitate further dissection of Aux/IAA gene function in B. napus.

Rice Inositol Polyphosphate Kinase (OsIPK2) Directly Interacts with OsIAA11 to Regulate Lateral Root Formation

The plant hormone auxin controls many aspects of plant growth and development by promoting the degradation of Auxin/Indole-3-acetic acid (Aux/IAA) proteins. The domain II (DII) of Aux/IAA proteins is sufficient for eliciting the degradation by directly interacting with the auxin receptor F-box protein TIR1 to form a TIR1/AFBs-Aux/IAA complex in an auxin-dependent manner. However, the underlying mechanisms of fine-tuning Aux/IAA degradation by auxin stimuli remain to be elucidated. Here, we show that OsIPK2, a rice (Oryza sativa) inositol polyphosphate kinase, directly interacts with an Aux/IAA protein OsIAA11 to repress its degradation. In a rice protoplast transient expression system, the auxin-induced degradation of Myc-OsIAA11 fusion was delayed by co-expressed GFP-OsIPK2 proteins. Furthermore, expressing additional OsIPK2 or its N-terminal amino acid sequence enhanced the accumulation of OsIAA11 proteins in transgenic plants, which in turn caused defects in lateral root formation and auxin response. Taken together, we identify a novel co-factor of Aux/IAA in auxin signaling and demonstrate its role in regulating lateral root development.

Identification of critical functional residues of receptor-like kinase ERECTA

In plants, extracellular signals are primarily sensed by plasma membrane-localized receptor-like kinases (RLKs). ERECTA is a leucine-rich repeat RLK that together with its paralogs ERECTA-like 1 (ERL1) and ERL2 regulates multiple aspects of plant development. ERECTA forms complexes with a range of co-receptors and senses secreted cysteine-rich small proteins from the EPF/EPFL family. Currently the mechanism of the cytoplasmic domain activation and transmission of the signal by ERECTA is unclear. To gain a better understanding we performed a structure-function analysis by introducing altered ERECTA genes into erecta and erecta erl1 erl2 mutants. These experiments indicated that ERECTA's ability to phosphorylate is functionally significant, and that while the cytoplasmic juxtamembrane domain is important for ERECTA function, the C-terminal tail is not. An analysis of multiple putative phosphorylation sites identified four amino acids in the activation segment of the kinase domain as functionally important. Homology of those residues to functionally significant amino acids in multiple other plant RLKs emphasizes similarities in RLK function. Specifically, our data predicts Thr812 as a primary site of phosphor-activation and potential inhibitory phosphorylation of Tyr815 and Tyr820. In addition, our experiments suggest that there are differences in the molecular mechanism of ERECTA function during regulation of stomata development and in elongation of above-ground organs.

Auxin-induced expression divergence between Arabidopsis species may originate within the TIR1/AFB-AUX/IAA-ARF module

Auxin is an essential regulator of plant growth and development, and auxin signaling components are conserved among land plants. Yet, a remarkable degree of natural variation in physiological and transcriptional auxin responses has been described among Arabidopsis thaliana accessions. As intraspecies comparisons offer only limited genetic variation, we here inspect the variation of auxin responses between A. thaliana and A. lyrata. This approach allowed the identification of conserved auxin response genes including novel genes with potential relevance for auxin biology. Furthermore, promoter divergences were analyzed for putative sources of variation. De novo motif discovery identified novel and variants of known elements with potential relevance for auxin responses, emphasizing the complex, and yet elusive, code of element combinations accounting for the diversity in transcriptional auxin responses. Furthermore, network analysis revealed correlations of interspecies differences in the expression of AUX/IAA gene clusters and classic auxin-related genes. We conclude that variation in general transcriptional and physiological auxin responses may originate substantially from functional or transcriptional variations in the TIR1/AFB, AUX/IAA, and ARF signaling network. In that respect, AUX/IAA gene expression divergence potentially reflects differences in the manner in which different species transduce identical auxin signals into gene expression responses.

Rice Dwarf Virus P2 Protein Hijacks Auxin Signaling by Directly Targeting the Rice OsIAA10 Protein, Enhancing Viral Infection and Disease Development

The phytohormone auxin plays critical roles in regulating myriads of plant growth and developmental processes. Microbe infection can disturb auxin signaling resulting in defects in these processes, but the underlying mechanisms are poorly understood. Auxin signaling begins with perception of auxin by a transient co-receptor complex consisting of an F-box transport inhibitor response 1/auxin signaling F-box (TIR1/AFB) protein and an auxin/indole-3-acetic acid (Aux/IAA) protein. Auxin binding to the co-receptor triggers ubiquitination and 26S proteasome degradation of the Aux/IAA proteins, leading to subsequent events, including expression of auxin-responsive genes. Here we report that Rice dwarf virus (RDV), a devastating pathogen of rice, causes disease symptoms including dwarfing, increased tiller number and short crown roots in infected rice as a result of reduced sensitivity to auxin signaling. The RDV capsid protein P2 binds OsIAA10, blocking the interaction between OsIAA10 and OsTIR1 and inhibiting 26S proteasome-mediated OsIAA10 degradation. Transgenic rice plants overexpressing wild-type or a dominant-negative (degradation-resistant) mutant of OsIAA10 phenocopy RDV symptoms are more susceptible to RDV infection; however, knockdown of OsIAA10 enhances the resistance of rice to RDV infection. Our findings reveal a previously unknown mechanism of viral protein reprogramming of a key step in auxin signaling initiation that enhances viral infection and pathogenesis.

Auxin regulates plant growth and development through auxin signaling, which begins with the interaction of an F-box transport inhibitor response 1/auxin signaling F-box (TIR1/AFB) protein and an auxin/indole-3-acetic acid (Aux/IAA) protein co-receptor. Auxin binding to the co-receptor complex triggers ubiquitination and 26S proteasome degradation of Aux/IAA proteins, leading to a downstream signaling cascade that induces the expression of auxin-responsive genes. Auxin signaling is manipulated by plant pathogens to maximize their own multiplication, but the underlying mechanisms are poorly understood. Here we report that the P2 capsid protein encoded by Rice dwarf virus (RDV) sabotages auxin signaling by interacting with the rice Aux/IAA protein, OsIAA10, thereby shielding it from degradation and causing infected plants to display typical RDV symptoms including dwarfism, excessive tillering and stunted crown roots. Importantly, these symptoms are phenocopied by transgenic rice plants overexpressing OsIAA10 or its degradation-resistant mutant. Conversely, down-regulating OsIAA10 expression in rice led to milder RDV infection. Together these findings reveal a novel mechanism by which RDV reprograms auxin signaling, leading to enhanced viral infection.

ahg12 is a dominant proteasome mutant that affects multiple regulatory systems for germination of Arabidopsis

The ubiquitin-proteasome system is fundamentally involved in myriad biological phenomena of eukaryotes. In plants, this regulated protein degradation system has a pivotal role in the cellular response mechanisms for both internal and external stimuli, such as plant hormones and environmental stresses. Information about substrate selection by the ubiquitination machinery has accumulated, but there is very little information about selectivity for substrates at the proteasome. Here, we report characterization of a novel abscisic acid (ABA)-hypersensitive mutant named ABA hypersensitive germination12 (ahg12) in Arabidopsis. The ahg12 mutant showed a unique pleiotropic phenotype, including hypersensitivity to ABA and ethylene, and hyposensitivity to light. Map-based cloning identified the ahg12 mutation to cause an amino acid conversion in the L23 loop of RPT5a, which is predicted to form the pore structure of the 19S RP complex of the proteasome. Transient expression assays demonstrated that some plant-specific signaling components accumulated at higher levels in the ahg12 mutant. These results suggest that the ahg12 mutation led to changes in the substrate preference of the 26S proteasome. The discovery of the ahg12 mutation thus will contribute to elucidate the characteristics of the regulated protein degradation system.

Transcriptional Responses to the Auxin Hormone

Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.

Structural Biology of Nuclear Auxin Action

Auxin coordinates plant development largely via hierarchical control of gene expression. During the past decades, the study of early auxin genes paired with the power of Arabidopsis genetics have unraveled key nuclear components and molecular interactions that perceive the hormone and activate primary response genes. Recent research in the realm of structural biology allowed unprecedented insight into: (i) the recognition of auxin-responsive DNA elements by auxin transcription factors; (ii) the inactivation of those auxin response factors by early auxin-inducible repressors; and (iii) the activation of target genes by auxin-triggered repressor degradation. The biophysical studies reviewed here provide an impetus for elucidating the molecular determinants of the intricate interactions between core components of the nuclear auxin response module.

Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate

Reprogramming of cell identities during development frequently requires changes in the chromatin state that need to be restricted to the correct cell populations. Here we identify an auxin hormone-regulated chromatin state switch that directs reprogramming from transit amplifying to primordium founder cell fate in Arabidopsis inflorescences. Upon auxin sensing, the MONOPTEROS transcription factor recruits SWI/SNF chromatin remodeling ATPases to increase accessibility of the DNA for induction of key regulators of flower primordium initiation. In the absence of the hormonal cue, auxin sensitive Aux/IAA proteins bound to MONOPTEROS block recruitment of the SWI/SNF chromatin remodeling ATPases in addition to recruiting a co-repressor/histone deacetylase complex. This simple and elegant hormone-mediated chromatin state switch is ideally suited for iterative flower primordium initiation and orchestrates additional auxin-regulated cell fate transitions. Our findings establish a new paradigm for nuclear response to auxin. They also provide an explanation for how this small molecule can direct diverse plant responses.

Solanum lycopersicum IAA15 functions in the 2,4-dichlorophenoxyacetic acid herbicide mechanism of action by mediating abscisic acid signalling

2,4-Dichlorophenoxyacetic acid (2,4-D), an important plant growth regulator, is the herbicide most commonly used worldwide to control weeds. However, broad-leaf fruits and vegetables are extremely sensitive to herbicides, which can cause damage and result in lost crops when applied in a manner inconsistent with the directions. Despite detailed knowledge of the mechanism of 2,4-D, the regulation of auxin signalling is still unclear. For example, although the major mediators of auxin signalling, including auxin/indole acetic acid (AUX/IAA) proteins and auxin response factors (ARFs), are known to mediate auxinic herbicides, the underlying mechanisms are still unclear. In this study, the effects of 2,4-D on AUX/IAA gene expression in tomato were investigated, and the two most notably up-regulated genes, SlIAA15 and SlIAA29, were selected for further study. Western blotting revealed the substantial accumulation of both SlIAA15 and SlIAA29, and the expression levels of the corresponding genes were increased following abscisic acid (ABA) and ethylene treatment. Overexpressing SlIAA15, but not SlIAA29, induced a 2,4-D herbicide damage phenotype. The 35S::SlIAA15 line exhibited a strong reduction in leaf stomatal density and altered expression of some R2R3 MYB genes that are putatively involved in the regulation of stomatal differentiation. Further study revealed that root elongation in 35S::SlIAA15 was sensitive to ABA treatment, and was most probably due to the altered expression of an ABA signal transduction gene. In addition, the altered auxin sensitivities of SlIAA15 transformants were also explored. These results suggested that SlIAA15 plays an important role in determining the effects of the herbicide 2,4-D.

OsIAA6, a member of the rice Aux/IAA gene family, is involved in drought tolerance and tiller outgrowth

Auxin signaling is a fundamental part of many plant growth processes and stress responses and operates through Aux/IAA protein degradation and the transmission of the signal via auxin response factors (ARFs). A total of 31 Aux/IAA genes have been identified in rice (Oryza sativa), some of which are induced by drought stress. However, the mechanistic link between Aux/IAA expression and drought responses is not well understood. In this study we found that the rice Aux/IAA gene OsIAA6 is highly induced by drought stress and that its overexpression in transgenic rice improved drought tolerance, likely via the regulation of auxin biosynthesis genes. We observed that OsIAA6 was specifically expressed in the axillary meristem of the basal stem, which is the tissue that gives rise to tillers. A knock-down mutant of OsIAA6 showed abnormal tiller outgrowth, apparently due to the regulation of the auxin transporter OsPIN1 and the rice tillering inhibitor OsTB1. Our results confirm that the OsIAA6 gene is involved in drought stress responses and the control of tiller outgrowth.

Peptidyl-prolyl isomerization targets rice Aux/IAAs for proteasomal degradation during auxin signalling

In plants, auxin signalling is initiated by the auxin-promoted interaction between the auxin receptor TIR1, an E3 ubiquitin ligase, and the Aux/IAA transcriptional repressors, which are subsequently degraded by the proteasome. Gain-of-function mutations in the highly conserved domain II of Aux/IAAs abolish the TIR1-Aux/IAA interaction and thus cause an auxin-resistant phenotype. Here we show that peptidyl-prolyl isomerization of rice OsIAA11 catalysed by LATERAL ROOTLESS2 (LRT2), a cyclophilin-type peptidyl-prolyl cis/trans isomerase, directly regulates the stability of OsIAA11. NMR spectroscopy reveals that LRT2 efficiently catalyses the cis/trans isomerization of OsIAA11. The lrt2 mutation reduces OsTIR1-OsIAA11 interaction and consequently causes the accumulation of a higher level of OsIAA11 protein. Moreover, knockdown of the OsIAA11 expression partially rescues the lrt2 mutant phenotype in lateral root development. Together, these results illustrate cyclophilin-catalysed peptidyl-prolyl isomerization promotes Aux/IAA degradation, as a mechanism regulating auxin signalling.

Auxin activity: Past, present, and future

Long before its chemical identity was known, the phytohormone auxin was postulated to regulate plant growth. In the late 1800s, Sachs hypothesized that plant growth regulators, present in small amounts, move differentially throughout the plant to regulate growth. Concurrently, Charles Darwin and Francis Darwin were discovering that light and gravity were perceived by the tips of shoots and roots and that the stimulus was transmitted to other tissues, which underwent a growth response. These ideas were improved upon by Boysen-Jensen and Paál and were later developed into the Cholodny-Went hypothesis that tropisms were caused by the asymmetric distribution of a growth-promoting substance. These observations led to many efforts to identify this elusive growth-promoting substance, which we now know as auxin. In this review of auxin field advances over the past century, we start with a seminal paper by Kenneth Thimann and Charles Schneider titled "The relative activities of different auxins" from the American Journal of Botany, in which they compare the growth altering properties of several auxinic compounds. From this point, we explore the modern molecular understanding of auxin-including its biosynthesis, transport, and perception. Finally, we end this review with a discussion of outstanding questions and future directions in the auxin field. Over the past 100 yr, much of our progress in understanding auxin biology has relied on the steady and collective advance of the field of auxin researchers; we expect that the next 100 yr of auxin research will likewise make many exciting advances.

Auxin-induced degradation dynamics set the pace for lateral root development

Auxin elicits diverse cell behaviors through a simple nuclear signaling pathway initiated by degradation of Aux/IAA co-repressors. Our previous work revealed that members of the large Arabidopsis Aux/IAA family exhibit a range of degradation rates in synthetic contexts. However, it remained an unresolved issue whether differences in Aux/IAA turnover rates played a significant role in plant responses to auxin. Here, we use the well-established model of lateral root development to directly test the hypothesis that the rate of auxin-induced Aux/IAA turnover sets the pace for auxin-regulated developmental events. We did this by generating transgenic plants expressing degradation rate variants of IAA14, a crucial determinant of lateral root initiation. Progression through the well-established stages of lateral root development was strongly correlated with the engineered rates of IAA14 turnover, leading to the conclusion that Aux/IAAs are auxin-initiated timers that synchronize developmental transitions.

Diversity of stability, localization, interaction and control of downstream gene activity in the Maize Aux/IAA protein family

AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins are central regulators of auxin signal transduction. They control many aspects of plant development, share a conserved domain structure and are localized in the nucleus. In the present study, five maize Aux/IAA proteins (ZmIAA2, ZmIAA11, ZmIAA15, ZmIAA20 and ZmIAA33) representing the evolutionary, phylogenetic and expression diversity of this gene family were characterized. Subcellular localization studies revealed that ZmIAA2, ZmIAA11 and ZmIAA15 are confined to the nucleus while ZmIAA20 and ZmIAA33 are localized in both the nucleus and the cytoplasm. Introduction of specific point mutations in the degron sequence (VGWPPV) of domain II by substituting the first proline by serine or the second proline by leucine stabilized the Aux/IAA proteins. While protein half-life times between ∼11 min (ZmIAA2) to ∼120 min (ZmIAA15) were observed in wild-type proteins, the mutated forms of all five proteins were almost as stable as GFP control proteins. Moreover, all five maize Aux/IAA proteins repressed downstream gene expression in luciferase assays to different degrees. In addition, bimolecular fluorescence complementation (BiFC) analyses demonstrated interaction of all five Aux/IAA proteins with RUM1 (ROOTLESS WITH UNDETECTABLE MERISTEM 1, ZmIAA10) while only ZmIAA15 and ZmIAA33 interacted with the RUM1 paralog RUL1 (RUM-LIKE 1, ZmIAA29). Moreover, ZmIAA11, ZmIAA15 ZmIAA33 displayed homotypic interaction. Hence, despite their conserved domain structure, maize Aux/IAA proteins display a significant variability in their molecular characteristics which is likely associated with the wide spectrum of their developmental functions.

Rapid Depletion of Budding Yeast Proteins via the Fusion of an Auxin-Inducible Degron (AID)

The auxin-inducible degron (AID) system allows the rapid and reversible proteolysis of proteins of interest, and enables the generation of conditional mutants of budding yeast. The construction of budding yeast AID mutants is simple, and the effect of depletion of essential proteins on proliferation can be confirmed by analyzing their phenotype. In this protocol, we describe a procedure to generate AID mutants of budding yeast via a simple transformation using PCR-amplified DNA. We also describe methods to confirm the depletion of proteins of interest that are required for proliferation by serial-dilution and liquid-culture assays.

Auxin and the ubiquitin pathway. Two players-one target: the cell cycle in action

Plants are sessile organisms that have to adapt their growth to the surrounding environment. Concomitant with this adaptation capability, they have adopted a post-embryonic development characterized by continuous growth and differentiation abilities. Constant growth is based on the potential of stem cells to divide almost incessantly and on a precise balance between cell division and cell differentiation. This balance is influenced by environmental conditions and by the genetic information of the cell. Among the internal cues, the cross-talk between different hormonal signalling pathways is essential to control this division/differentiation equilibrium. Auxin, one of the most important plant hormones, regulates cell division and differentiation, among many other processes. Amazing advances in auxin signal transduction at the molecular level have been reported, but how this signalling is connected to the cell cycle is, so far, not well known. Auxin signalling involves the auxin-dependent degradation of transcription repressors by F-box-containing E3 ligases of ubiquitin. Recently, SKP2A, another F-box protein, was shown to bind auxin and to target cell-cycle repressors for proteolysis, representing a novel mechanism that links auxin to cell division. In this review, a general vision of what is already known and the most recent advances on how auxin signalling connects to cell division and the role of the ubiquitin pathway in plant cell cycle will be covered.

Intragenic suppressor of Osiaa23 revealed a conserved tryptophan residue crucial for protein-protein interactions

The Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) are two important families that play key roles in auxin signal transduction. Both of the families contain a similar carboxyl-terminal domain (Domain III/IV) that facilitates interactions between these two families. In spite of the importance of protein-protein interactions among these transcription factors, the mechanisms involved in these interactions are largely unknown. In this study, we isolated six intragenic suppressors of an auxin insensitive mutant, Osiaa23. Among these suppressors, Osiaa23-R5 successfully rescued all the defects of the mutant. Sequence analysis revealed that an amino acid substitution occurred in the Tryptophan (W) residue in Domain IV of Osiaa23. Yeast two-hybrid experiments showed that the mutation in Domain IV prevents the protein-protein interactions between Osiaa23 and OsARFs. Phylogenetic analysis revealed that the W residue is conserved in both OsIAAs and OsARFs. Next, we performed site-specific amino acid substitutions within Domain IV of OsARFs, and the conserved W in Domain IV was exchanged by Serine (S). The mutated OsARF(WS)s can be released from the inhibition of Osiaa23 and maintain the transcriptional activities. Expression of OsARF(WS)s in Osiaa23 mutant rescued different defects of the mutant. Our results suggest a previously unknown importance of Domain IV in both families and provide an indirect way to investigate functions of OsARFs.

A genetic screen for mutants defective in IAA1-LUC degradation in Arabidopsis thaliana reveals an important requirement for TOPOISOMERASE6B in auxin physiology

Many plant growth and developmental processes are modulated by the hormone auxin. Auxin-modulated proteolysis of Aux/IAAs, a family of transcriptional repressors, represents a major mode of auxin action. Auxin facilitates the interaction of Aux/IAAs with TIR1/AFB F-box proteins, promoting their ubiquitination by the SCF(TIR1/AFB) ubiquitin E3 ligase leading to subsequent degradation by the 26S proteasome. To identify new genes regulating Aux/IAA proteolysis in Arabidopsis thaliana, we took a genetic approach, identifying individuals with altered degradation of an IAA1-luciferase fusion protein (IAA1-LUC). A mutant with 2-fold slower IAA1-LUC degradation rate compared with wild-type was isolated. Positional cloning identified the mutant as an allele of TOPOISOMERASE6B, named top6b-7. TOP6B encodes a subunit of a plant and archea-specific enzyme regulating endoreduplication, DNA damage repair and transcription in plants. T-DNA insertion alleles (top6b-8 and top6b-9) were also analyzed. top6b-7 seedlings are less sensitive to exogenous auxin than wild-type siblings in primary root growth assays, and experiments with DR5:GUS. Additionally, top6b-7 seedlings have a 40% reduction in the amount of endogenous IAA. These data suggest that increased IAA1-LUC half-life in top6b-7 probably results from a combination of both lower endogenous IAA levels and reduced sensitivity to auxin.

An expanded tool kit for the auxin-inducible degron system in budding yeast

Fusion of inducible degradation signals, so-called degrons, to cellular proteins is an elegant method of controlling protein levels in vivo. Recently, a degron system relying on the plant hormone auxin has been described for use in yeast and vertebrate cells. We now report the construction of a series of vectors that significantly enhance the versatility of this auxin-inducible degron (AID) system in Saccharomyces cerevisiae. We have minimized the size of the degron and appended a series of additional epitope tags, allowing detection by commercial antibodies or fluorescence microscopy. The vectors are compatible with PCR-based genomic tagging strategies, allow for C- or N-terminal fusion of the degron, and provide a range of selection markers. Application to a series of yeast proteins, including essential replication factors, provides evidence for a general usefulness of the system.

Ectopic overexpression of an AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) gene OsIAA4 in rice induces morphological changes and reduces responsiveness to Auxin

Auxin has pleiotropic effects on plant growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins are short-lived transcriptional regulators that mediate auxin responses through interaction with an auxin receptor, the F-box protein transport inhibitor response 1 (TIR1). Most functions of Aux/IAA proteins have been identified in Arabidopsis by studying the gain-of-function mutants in domain II. In this study, we isolated and identified an Aux/IAA protein gene from rice, OsIAA4, whose protein contains a dominant mutation-type domain II. OsIAA4 has very low expression in the entire life cycle of rice. OsIAA4-overexpressing rice plants show dwarfism, increased tiller angles, reduced gravity response, and are less sensitive to synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D).

Tuning the auxin transcriptional response

How does auxin provoke such a diverse array of responses? This long-standing question is further complicated by a remarkably short nuclear auxin signalling pathway. To crack the auxin code, several potential sources of specificity need to be evaluated. These include: specificity of interactions among the core auxin response components, specificity resulting from higher order complex dynamics, and specificity in interactions with global factors controlling protein turnover and transcriptional repression. Here, we review recent progress towards characterizing and quantifying these interactions and highlight key gaps that remain.

Auxin: a master regulator in plant root development

The demand for increased crop productivity and the predicted challenges related to plant survival under adverse environmental conditions have renewed the interest in research in root biology. Various physiological and genetic studies have provided ample evidence in support of the role of plant growth regulators in root development. The biosynthesis and transport of auxin and its signaling play a crucial role in controlling root growth and development. The univocal role of auxin in root development has established it as a master regulator. Other plant hormones, such as cytokinins, brassinosteroids, ethylene, abscisic acid, gibberellins, jasmonic acid, polyamines and strigolactones interact either synergistically or antagonistically with auxin to trigger cascades of events leading to root morphogenesis and development. In recent years, the availability of biological resources, development of modern tools and experimental approaches have led to the advancement of knowledge in root development. Research in the areas of hormone signal perception, understanding network of events involved in hormone action and the transport of plant hormones has added a new dimension to root biology. The present review highlights some of the important conceptual developments in the interplay of auxin and other plant hormones and associated downstream events affecting root development.

A gain-of-function mutation in IAA8 alters Arabidopsis floral organ development by change of jasmonic acid level

Auxin regulates a variety of physiological processes via its downstream factors included Aux/IAAs. In this study, one of these Aux/IAAs, IAA8 is shown to play its role in Arabidopsis development with transgenic plants expressing GFP-mIAA8 under the control of IAA8 promoter, in which IAA8 protein was mutated by changing Pro170 to Leu170 in its conserved domain II. These transgenic dwarfed plants had more lateral branches, short primary inflorescence stems, decreased shoot apical dominance, curled leaves and abnormal flower organs (short petal and stamen, and bent stigmas). Further experiments revealed that IAA8::GFP-mIAA8 plants functioned as gain-of-function mutation to increase GFP-mIAA8 amount probably by stabilizing IAA8 protein against proteasome-mediated protein degradation with IAA8::GFP-IAA8 plants as control. The searching for its downstream factors indicated its interaction with both ARF6 and ARF8, suggesting that IAA8 may involve in flower organ development. This was further evidenced by analyzing the expression of jasmonic acid (JA) biosynthetic genes and JA levels because ARF6 and ARF8 are required for normal JA production. These results indicated that in IAA8::GFP-mIAA8 plants, JA biosynthetic genes including DAD1 (AT2G44810), AOS (AT5G42650) and ORP3 (AT2G06050) were dramatically down-regulated and JA level in the flowers was reduced to 70 % of that in wild-type. Furthermore, exogenous JA application can partially rescue short petal and stamen observed IAA8::GFP-mIAA8 plants. Thus, IAA8 plays its role in floral organ development by changes in JA levels probably via its interaction with ARF6/8 proteins.

Biosensors for phytohormone quantification: challenges, solutions, and opportunities

Fluorescent reporters are valuable tools for plant science research, particularly as sensors to monitor biological signals and developmental processes. Such biosensors are particularly useful to monitor the spatial and temporal distribution of small signalling molecules such as phytohormones. Knowledge of perception and signalling pathways can be exploited to design biosensors for estimating intracellular abundance of hormones. However, the nonlinear relationship between target molecule and reporter necessitates the development of parameterised mathematical models to quantitatively relate sensor fluorescence to hormone abundance. In this opinion article, we will discuss the use of transcriptional reporters, sensor design strategy, and the importance of mathematical modelling approaches and technological advances in the development of new techniques to allow truly quantitative analyses of hormone regulated processes.

Tissue-specific expression of SMALL AUXIN UP RNA41 differentially regulates cell expansion and root meristem patterning in Arabidopsis

Among the three primary auxin-induced gene families, Auxin/Indole-3-Acetic Acid (Aux/IAA), Gretchen Hagen3 (GH3) and SMALL AUXIN UP RNA (SAUR), the function of SAUR genes remains unclear. Arabidopsis SAUR genes have been phylogenetically classified into three clades. Recent work has suggested that SAUR19 (clade II) and SAUR63 (clade I) promote cell expansion through the modulation of auxin transport. Herein, we present our work on SAUR41, a clade III SAUR gene with a distinctive expression pattern in root meristems. SAUR41 was normally expressed in the quiescent center and cortex/endodermis initials; upon auxin stimulation, the expression was provoked in the endodermal layer. During lateral root development, SAUR41 was expressed in prospective stem cell niches of lateral root primordia and in expanding endodermal cells surrounding the primordia. SAUR41-EGFP (enhanced green fluorescent protein) fusion proteins localized to the cytoplasm. Overexpression of SAUR41 from the Cauliflower mosaic virus 35S promoter led to pleiotropic auxin-related phenotypes, including long hypocotyls, increased vegetative biomass and lateral root development, expanded petals and twisted inflorescence stems. Ectopic SAUR41 proteins were able to promote auxin transport in hypocotyls. Tissue-specific expression of SAUR41 from the PIN1, WOX5, PLT2 and ACR4 promoters induced the formation of new auxin accumulation/signaling peaks above the quiescent centers, whereas tissue-specific expression of SAUR41 from the PIN2 and PLT2 promoters enhanced root gravitropic growth. Cells in the root stem cell niches of these transgenic seedlings were differentially enlarged. The distinctive expression pattern of the SAUR41 gene and the explicit function of SAUR41 proteins implied that further investigations on the loss-of-function phenotypes of this gene in root development and environmental responses are of great interest.

Plant hormone signaling during development: insights from computational models

Recent years have seen an impressive increase in our knowledge of the topology of plant hormone signaling networks. The complexity of these topologies has motivated the development of models for several hormones to aid understanding of how signaling networks process hormonal inputs. Such work has generated essential insights into the mechanisms of hormone perception and of regulation of cellular responses such as transcription in response to hormones. In addition, modeling approaches have contributed significantly to exploring how spatio-temporal regulation of hormone signaling contributes to plant growth and patterning. New tools have also been developed to obtain quantitative information on hormone distribution during development and to test model predictions, opening the way for quantitative understanding of the developmental roles of hormones.