A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin

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.

MiR393 regulation of auxin signaling and redox-related components during acclimation to salinity in Arabidopsis

One of the most striking aspects of plant plasticity is the modulation of development in response to environmental changes. Plant growth and development largely depend on the phytohormone auxin that exerts its function through a partially redundant family of F-box receptors, the TIR1-AFBs. We have previously reported that the Arabidopsis double mutant tir1 afb2 is more tolerant to salt stress than wild-type plants and we hypothesized that down-regulation of auxin signaling might be part of Arabidopsis acclimation to salinity. In this work, we show that NaCl-mediated salt stress induces miR393 expression by enhancing the transcription of AtMIR393A and leads to a concomitant reduction in the levels of the TIR1 and AFB2 receptors. Consequently, NaCl triggers stabilization of Aux/IAA repressors leading to down-regulation of auxin signaling. Further, we report that miR393 is likely involved in repression of lateral root (LR) initiation, emergence and elongation during salinity, since the mir393ab mutant shows reduced inhibition of emergent and mature LR number and length upon NaCl-treatment. Additionally, mir393ab mutant plants have increased levels of reactive oxygen species (ROS) in LRs, and reduced ascorbate peroxidase (APX) enzymatic activity compared with wild-type plants during salinity. Thus, miR393 regulation of the TIR1 and AFB2 receptors could be a critical checkpoint between auxin signaling and specfic redox-associated components in order to coordinate tissue and time-specific growth responses and tolerance during acclimation to salinity in Arabidopsis.

Hormonal networks involved in apical hook development in darkness and their response to light

In darkness, the dicot seedlings produce an apical hook as result of differential cell division and extension at opposite sides of the hypocotyl. This hook protects the apical meristem from mechanical damage during seedling emergence from the soil. In darkness, gibberellins act via the DELLA-PIF (PHYTOCHROME INTERACTING FACTORs) pathway, and ethylene acts via the EIN3/EIL1 (ETHYLENE INSENSITIVE 3/EIN3 like 1)-HLS1 (HOOKLESS 1) pathway to control the asymmetric accumulation of auxin required for apical hook formation and maintenance. These core pathways form a network with multiple points of connection. Light perception by phytochromes and cryptochromes reduces the activity of PIFs and (COP1) CONSTITUTIVE PHOTOMORPHOGENIC 1-both required for hook formation in darkness-, lowers the levels of gibberellins, and triggers hook opening as a component of the switch between heterotrophic and photoautotrophic development. Apical hook opening is thus a suitable model to study the convergence of endogenous and exogenous signals on the control of cell division and cell growth.

Molecular locks and keys: the role of small molecules in phytohormone research

Plant adaptation, growth and development rely on the integration of many environmental and endogenous signals that collectively determine the overall plant phenotypic plasticity. Plant signaling molecules, also known as phytohormones, are fundamental to this process. These molecules act at low concentrations and regulate multiple aspects of plant fitness and development via complex signaling networks. By its nature, phytohormone research lies at the interface between chemistry and biology. Classically, the scientific community has always used synthetic phytohormones and analogs to study hormone functions and responses. However, recent advances in synthetic and combinational chemistry, have allowed a new field, plant chemical biology, to emerge and this has provided a powerful tool with which to study phytohormone function. Plant chemical biology is helping to address some of the most enduring questions in phytohormone research such as: Are there still undiscovered plant hormones? How can we identify novel signaling molecules? How can plants activate specific hormone responses in a tissue-specific manner? How can we modulate hormone responses in one developmental context without inducing detrimental effects on other processes? The chemical genomics approaches rely on the identification of small molecules modulating different biological processes and have recently identified active forms of plant hormones and molecules regulating many aspects of hormone synthesis, transport and response. We envision that the field of chemical genomics will continue to provide novel molecules able to elucidate specific aspects of hormone-mediated mechanisms. In addition, compounds blocking specific responses could uncover how complex biological responses are regulated. As we gain information about such compounds we can design small alterations to the chemical structure to further alter specificity, enhance affinity or modulate the activity of these compounds.

Composition, roles, and regulation of cullin-based ubiquitin e3 ligases

Due to their sessile nature, plants depend on flexible regulatory systems that allow them to adequately regulate developmental and physiological processes in context with environmental cues. The ubiquitin proteasome pathway, which targets a great number of proteins for degradation, is cellular tool that provides the necessary flexibility to accomplish this task. Ubiquitin E3 ligases provide the needed specificity to the pathway by selectively binding to particular substrates and facilitating their ubiquitylation. The largest group of E3 ligases known in plants is represented by CULLIN-REALLY INTERESTING NEW GENE (RING) E3 ligases (CRLs). In recent years, a great amount of knowledge has been generated to reveal the critical roles of these enzymes across all aspects of plant life. This review provides an overview of the different classes of CRLs in plants, their specific complex compositions, the variety of biological processes they control, and the regulatory steps that can affect their activities.

Unraveling plant hormone signaling through the use of small molecules

Plants have acquired the capacity to grow continuously and adjust their morphology in response to endogenous and external signals, leading to a high architectural plasticity. The dynamic and differential distribution of phytohormones is an essential factor in these developmental changes. Phytohormone perception is a fast but complex process modulating specific developmental reprogramming. In recent years, chemical genomics or the use of small molecules to modulate target protein function has emerged as a powerful strategy to study complex biological processes in plants such as hormone signaling. Small molecules can be applied in a conditional, dose-dependent and reversible manner, with the advantage of circumventing the limitations of lethality and functional redundancy inherent to traditional mutant screens. High-throughput screening of diverse chemical libraries has led to the identification of bioactive molecules able to induce plant hormone-related phenotypes. Characterization of the cognate targets and pathways of those molecules has allowed the identification of novel regulatory components, providing new insights into the molecular mechanisms of plant hormone signaling. An extensive structure-activity relationship (SAR) analysis of the natural phytohormones, their designed synthetic analogs and newly identified bioactive molecules has led to the determination of the structural requirements essential for their bioactivity. In this review, we will summarize the so far identified small molecules and their structural variants targeting specific phytohormone signaling pathways. We will highlight how the SAR analyses have enabled better interrogation of the molecular mechanisms of phytohormone responses. Finally, we will discuss how labeled/tagged hormone analogs can be exploited, as compelling tools to better understand hormone signaling and transport mechanisms.

Defining the selectivity of processes along the auxin response chain: a study using auxin analogues

The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.

Jasmonate signalling: a copycat of auxin signalling?

Plant hormones regulate almost all aspects of plant growth and development. The past decade has provided breakthrough discoveries in phytohormone sensing and signal transduction, and highlighted the striking mechanistic similarities between the auxin and jasmonate (JA) signalling pathways. Perception of auxin and JA involves the formation of co-receptor complexes in which hormone-specific E3-ubiquitin ligases of the SKP1-Cullin-F-box protein (SCF) type interact with specific repressor proteins. Across the plant kingdom, the Aux/IAA and the JASMONATE-ZIM DOMAIN (JAZ) proteins correspond to the auxin- and JA-specific repressors, respectively. In the absence of the hormones, these repressors form a complex with transcription factors (TFs) specific for both pathways. They also recruit several proteins, among which the general co-repressor TOPLESS, and thereby prevent the TFs from activating gene expression. The hormone-mediated interaction between the SCF and the repressors targets the latter for 26S proteasome-mediated degradation, which, in turn, releases the TFs to allow modulating hormone-dependent gene expression. In this review, we describe the similarities and differences in the auxin and JA signalling cascades with respect to the protein families and the protein domains involved in the formation of the pathway-specific complexes.

A mathematical model for the coreceptors SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1 and SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE3 in BRASSINOSTEROID INSENSITIVE1-mediated signaling

Brassinosteroids (BRs) are key regulators in plant growth and development. The main BR-perceiving receptor in Arabidopsis (Arabidopsis thaliana) is BRASSINOSTEROID INSENSITIVE1 (BRI1). Seedling root growth and hypocotyl elongation can be accurately predicted using a model for BRI1 receptor activity. Genetic evidence shows that non-ligand-binding coreceptors of the SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) family are essential for BRI1 signal transduction. A relatively simple biochemical model based on the properties of SERK loss-of-function alleles explains complex physiological responses of the BRI1-mediated BR pathway. The model uses BRI1-BR occupancy as the central estimated parameter and includes BRI1-SERK interaction based on mass action kinetics and accurately describes wild-type root growth and hypocotyl elongation. Simulation studies suggest that the SERK coreceptors primarily act to increase the magnitude of the BRI1 signal. The model predicts that only a small number of active BRI1-SERK complexes are required to carry out BR signaling at physiological ligand concentration. Finally, when calibrated with single mutants, the model predicts that roots of the serk1serk3 double mutant are almost completely brassinolide (BL) insensitive, while the double mutant hypocotyls remain sensitive. This points to residual BRI1 signaling or to a different coreceptor requirement in shoots.

A quantitative ratiometric sensor for time-resolved analysis of auxin dynamics

Time-resolved quantitative analysis of auxin-mediated processes in plant cells is as of yet limited. By applying a synergistic mammalian and plant synthetic biology approach, we have developed a novel ratiometric luminescent biosensor with wide applicability in the study of auxin metabolism, transport, and signalling. The sensitivity and kinetic properties of our genetically encoded biosensor open new perspectives for the analysis of highly complex auxin dynamics in plant growth and development.

Flower development under drought stress: morphological and transcriptomic analyses reveal acute responses and long-term acclimation in Arabidopsis

Drought dramatically affects plant growth and crop yield, but previous studies primarily examined responses to drought during vegetative development. Here, to study responses to drought during reproductive development, we grew Arabidopsis thaliana plants with limited water, under conditions that allowed the plants to initiate and complete reproduction. Drought treatment from just after the onset of flowering to seed maturation caused an early arrest of floral development and sterility. After acclimation, plants showed reduced fertility that persisted throughout reproductive development. Floral defects included abnormal anther development, lower pollen viability, reduced filament elongation, ovule abortion, and failure of flowers to open. Drought also caused differential expression of 4153 genes, including flowering time genes flowering locus t, suppressor of overexpression of CO1, and leafy, genes regulating anther and pistil development, and stress-related transcription factors. Mutant phenotypes of hypersensitivity to drought and fewer differentially expressed genes suggest that dehydration response element B1A may have an important function in drought response in flowers. A more severe filament elongation defect under drought in myb21 plants demonstrated that appropriate stamen development requires MYB domain protein 21 under drought conditions. Our study reveals a regulatory cascade in reproductive responses and acclimation under drought.

Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid

The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.

From perception to attenuation: auxin signalling and responses

The plant hormone auxin is essential for growth, development, and responses to environmental factors. Recently, Auxin Binding Protein 1 was shown to mediate non-transcriptional auxin signalling at the cell periphery. This has provoked reexamination of the paradigm that all auxin perception is intracellular and is mediated by the TIR1/AFB-Aux/IAA co-receptors for which auxin functions as a concentration-dependent molecular glue. Further, another F-box protein, SKP2a, was shown to bind auxin in the same way as TIR1/AFB, which provides a link to the role of auxin in the cell cycle. New work on auxin signalling and homeostasis include D6 PROTEIN KINASE activation of PINFORMED (PIN) auxin carriers, ROP-GTPase mediation of PIN localization, endoplasmic reticulum localization PIN and PIN-LIKES auxin carriers, and auxin biosynthesis and metabolism.

Plant E3 ligases: flexible enzymes in a sessile world

E3 ligases comprise a highly diverse and important group of enzymes that act within the 26S ubiquitin proteasome pathway. They facilitate the transfer of ubiquitin moieties to substrate proteins which may be marked for degradation by this step. As such, they serve as central regulators in many cellular and physiological processes in plants. The review provides an update on the multitude of different E3 ligases currently known in plants, and illustrates the central role in plant biology of specific examples.

Lateral root development in Arabidopsis: fifty shades of auxin

The developmental plasticity of the root system represents a key adaptive trait enabling plants to cope with abiotic stresses such as drought and is therefore important in the current context of global changes. Root branching through lateral root formation is an important component of the adaptability of the root system to its environment. Our understanding of the mechanisms controlling lateral root development has progressed tremendously in recent years through research in the model plant Arabidopsis thaliana (Arabidopsis). These studies have revealed that the phytohormone auxin acts as a common integrator to many endogenous and environmental signals regulating lateral root formation. Here, we review what has been learnt about the myriad roles of auxin during lateral root formation in Arabidopsis.

From models to ornamentals: how is flower senescence regulated?

Floral senescence involves an ordered set of events coordinated at the plant, flower, organ and cellular level. This review assesses our current understanding of the input signals, signal transduction and cellular processes that regulate petal senescence and cell death. In many species a visible sign of petal senescence is wilting. This is accompanied by remobilization of nutrients from the flower to the developing ovary or to other parts of the plant. In other species, petals abscise while still turgid. Coordinating signals for floral senescence also vary across species. In some species ethylene acts as a central regulator, in others floral senescence is ethylene insensitive and other growth regulators are implicated. Due to the variability in this coordination and sequence of events across species, identifying suitable models to study petal senescence has been challenging, and the best candidates are reviewed. Transcriptomic studies provide an overview of the MAP kinases and transcription factors that are activated during petal senescence in several species including Arabidopsis. Our understanding of downstream regulators such as autophagy genes and proteases is also improving. This gives us insights into possible signalling cascades that regulate initiation of senescence and coordination of cell death processes. It also identifies the gaps in our knowledge such as the role of microRNAs. Finally future prospects for using all this information from model to non-model species to extend vase life in ornamental species is reviewed.

Post-embryonic root organogenesis in cereals: branching out from model plants

The root architecture of higher plants is amazingly diverse. In this review, we compare the lateral root developmental programme in cereals and Arabidopsis thaliana. In cereals, cells in the endodermis are recruited to form the new root cap and overlying cortical cells divide to facilitate the emergence of the lateral root primordium. The TIR1/ABF2 auxin receptors and the AUX/IAA, ARF, and LBD transcriptional regulatory proteins are conserved in cereals and Arabidopsis. Several elements of this regulatory network are common to lateral and crown roots in cereals. Also, the ground meristem from which crown roots differentiate shows similarities with the root pericycle. Studies in cereals promise to give complementary insights into the mechanisms regulating the development of post-embryonic roots in plants.

Auxin: simply complicated

Auxin is a plant hormone involved in an extraordinarily broad variety of biological mechanisms. These range from basic cellular processes, such as endocytosis, cell polarity, and cell cycle control over localized responses such as cell elongation and differential growth, to macroscopic phenomena such as embryogenesis, tissue patterning, and de novo formation of organs. Even though the history of auxin research reaches back more than a hundred years, we are still far from a comprehensive understanding of how auxin governs such a wide range of responses. Some answers to this question may lie in the auxin molecule itself. Naturally occurring auxin-like substances have been found and they may play roles in specific developmental and cellular processes. The molecular mode of auxin action can be further explored by the utilization of synthetic auxin-like molecules. A second area is the perception of auxin, where we know of three seemingly independent receptors and signalling systems, some better understood than others, but each of them probably involved in distinct physiological processes. Lastly, auxin is actively modified, metabolized, and intracellularly compartmentalized, which can have a great impact on its availability and activity. In this review, we will give an overview of these rather recent and emerging areas of auxin research and try to formulate some of the open questions. Without doubt, the manifold facets of auxin biology will not cease to amaze us for a long time to come.

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.

The role of auxin in shaping shoot architecture

The variety of plant architectures observed in nature is predominantly determined by vegetative and reproductive branching patterns, the positioning of lateral organs, and differential stem elongation. Branches, lateral organs, and stems are the final products of the activity of meristems, groups of stem cells whose function is genetically determined and environmentally influenced. Several decades of studies in different plant species have shed light on the essential role of the hormone auxin in plant growth and development. Auxin influences stem elongation and regulates the formation, activity, and fate of meristems, and has therefore been recognized as a major hormone shaping plant architecture. Increasing our knowledge of the molecular mechanisms that regulate auxin function is necessary to understand how different plant species integrate a genetically determined developmental programme, the establishment of a body plan, with constant inputs from the surrounding environment. This information will allow us to develop the molecular tools needed to modify plant architecture in several crop species and in rapidly changing environments.

Micro-regulators of auxin action

microRNAs (miRs) are 21- to 24-nucleotide-long RNA molecules that are mainly involved in regulating the gene expression at the post-transcriptional levels. They are present in a variety of organisms from algae to plants and play an important role in gene regulation. The identification of several diverging and converging functions of miRs indicates that they play versatile roles in regulating plant development including differentiation, organ development, phase change, signalling, disease resistance and response to environmental stresses. This article provides a concise update on the plant miR functions and their targets in the auxin pathway with focus on the interactions between miRs and auxin signalling to intricately regulate the plant responses.

Auxin and self-organization at the shoot apical meristem

Plants continuously generate new tissues and organs throughout their life cycle, due to the activity of populations of specialized tissues containing stem cells called meristems. The shoot apical meristem (SAM) generates all the aboveground organs of the plant, including leaves and flowers, and plays a key role in plant survival and reproduction. Organ production at the SAM occurs following precise spatio-temporal patterns known as phyllotaxis. Because of the regularity of these patterns, phyllotaxis has been the subject of investigations from biologists, physicists, and mathematicians for several centuries. Both experimental and theoretical works have led to the idea that phyllotaxis results from a self-organizing process in the meristem via long-distance interactions between organs. In recent years, the phytohormone auxin has emerged not only as the central regulator of organogenesis at the SAM, but also as a major determinant of the self-organizing properties of phyllotaxis. Here, we discuss both the experimental and theoretical evidence for the implication of auxin in the control of organogenesis and self-organization of the SAM. We highlight how several layers of control acting at different scales contribute together to the function of the auxin signal in SAM dynamics. We also indicate a role for mechanical forces in the development of the SAM, supported by recent interdisciplinary studies.

Auxin and the Arabidopsis thaliana gynoecium

Recent research is beginning to reveal how intricate networks of hormones and transcription factors coordinate the complex patterning of the gynoecium, the female reproductive structure of flowering plants. This review summarizes recent advances in understanding of how auxin biosynthesis, transport, and responses together generate specific gynoecial domains. This review also highlights areas where future research endeavours are likely to provide additional insight into the homeostatic molecular mechanisms by which auxin regulates gynoecium development.

Structure and function of abscisic acid receptors

The phytohormone abscisic acid (ABA) plays a crucial role in adaptive responses to environmental stresses, such as drought and high salinity, as well as in plant development, such as seed maturation and dormancy. PYR/PYL/RCAR has been identified as a bona fide ABA receptor (ABAR) that constitutes the core regulatory component of ABA signaling networks in plants. Here, we review recent structural and functional studies of the ABAR that have elucidated its activation mechanism, early signaling components, and physiological responses. A crucial event in the receptor's activation was found to be an open-to-closed conformational change in the gate loop of the receptor protein. More recent progress has provided strategies for controlling the gate's closure using chemical agonists or protein engineering approaches.

Mutations in the TIR1 auxin receptor that increase affinity for auxin/indole-3-acetic acid proteins result in auxin hypersensitivity

The phytohormone auxin regulates virtually every aspect of plant development. The hormone directly mediates the interaction between the two members of the auxin coreceptor complex, a TRANSPORT INHIBITOR RESPONSE (TIR1)/AUXIN SIGNALING F-BOX protein and an AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressor. To learn more about the interaction between these proteins, a mutant screen was performed using the yeast (Saccharomyces cerevisiae) two-hybrid system in Arabidopsis (Arabidopsis thaliana). Two tir1 mutations were identified that increased interaction with Aux/IAAs. The D170E and M473L mutations increase affinity between TIR1 and the degron motif of Aux/IAAs and enhance the activity of the SCF(TIR1) complex. This resulted in faster degradation of Aux/IAAs and increased transcription of auxin-responsive genes in the plant. Plants carrying the pTIR1:tir1 D170E/M473L-Myc transgene exhibit diverse developmental defects during plant growth and display an auxin-hypersensitive phenotype. This work demonstrates that changes in the leucine-rich repeat domain of the TIR1 auxin coreceptor can alter the properties of SCF(TIR1).

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.

Auxin 2012: a rich mea ho'oulu

In December 2012, scientists from around the world gathered in Waikoloa, Hawaii for 'Auxin 2012', a meeting organized by Paula McSteen (University of Missouri, USA), Ben Scheres (Utrecht University, The Netherlands) and Yunde Zhao (University of California, San Diego, USA). At the meeting, participants discussed the latest advances in auxin biosynthesis, transport and signaling research, in addition to providing context for how these pathways intersect with other aspects of plant physiology and development. Fittingly, the meeting began with a traditional Hawaiian ceremony that recognized the centrality of the harvest of plant life ('mea ho'oulu' in Hawaiian) for continued human survival.

Auxin metabolism and homeostasis during plant development

Auxin plays important roles during the entire life span of a plant. This small organic acid influences cell division, cell elongation and cell differentiation, and has great impact on the final shape and function of cells and tissues in all higher plants. Auxin metabolism is not well understood but recent discoveries, reviewed here, have started to shed light on the processes that regulate the synthesis and degradation of this important plant hormone.

Auxin regulation of embryonic root formation

The plant hormone auxin was initially identified as the bioactive substance that induces roots in plant tissue culture. In the past decades, mechanisms for auxin action, including its transport and response, have been described in detail. However, a molecular and cellular description of its role in root initiation is far from complete. In this review, we discuss recent advances in our understanding of auxin-dependent embryonic root formation. During this process, a root meristem is initiated in a precise and predictable position, and at a stage when the organism consists of relatively few cells. Recent studies have revealed mechanisms for local control of auxin transport, for cellular differences in auxin response components and cell type-specific chromatin regulation. The recent identification of biologically relevant target genes for auxin regulation during embryonic root initiation now also allows dissection of auxin-activated cellular processes. Finally, we discuss the potential for hormonal cross-regulation in embryonic root formation.

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.

Finding Missing Interactions of the Arabidopsis thaliana Root Stem Cell Niche Gene Regulatory Network

Over the last few decades, the Arabidopsis thaliana root stem cell niche (RSCN) has become a model system for the study of plant development and stem cell niche dynamics. Currently, many of the molecular mechanisms involved in RSCN maintenance and development have been described. A few years ago, we published a gene regulatory network (GRN) model integrating this information. This model suggested that there were missing components or interactions. Upon updating the model, the observed stable gene configurations of the RSCN could not be recovered, indicating that there are additional missing components or interactions in the model. In fact, due to the lack of experimental data, GRNs inferred from published data are usually incomplete. However, predicting the location and nature of the missing data is a not trivial task. Here, we propose a set of procedures for detecting and predicting missing interactions in Boolean networks. We used these procedures to predict putative missing interactions in the A. thaliana RSCN network model. Using our approach, we identified three necessary interactions to recover the reported gene activation configurations that have been experimentally uncovered for the different cell types within the RSCN: (1) a regulation of PHABULOSA to restrict its expression domain to the vascular cells, (2) a self-regulation of WOX5, possibly by an indirect mechanism through the auxin signaling pathway, and (3) a positive regulation of JACKDAW by MAGPIE. The procedures proposed here greatly reduce the number of possible Boolean functions that are biologically meaningful and experimentally testable and that do not contradict previous data. We believe that these procedures can be used on any Boolean network. However, because the procedures were designed for the specific case of the RSCN, formal demonstrations of the procedures should be shown in future efforts.

Phloem-specific expression of a melon Aux/IAA in tomato plants alters auxin sensitivity and plant development

Phloem sap contains a large repertoire of macromolecules in addition to sugars, amino acids, growth substances and ions. The transcription profile of melon phloem sap contains over 1000 mRNA molecules, most of them associated with signal transduction, transcriptional control, and stress and defense responses. Heterografting experiments have established the long-distance trafficking of numerous mRNA molecules. Interestingly, several trafficking transcripts are involved in the auxin response, including two molecules coding for auxin/indole acetic acid (Aux/IAA). To further explore the biological role of the melon Aux/IAA transcript CmF-308 in the vascular tissue, a cassette containing the coding sequence of this gene under a phloem-specific promoter was introduced into tomato plants. The number of lateral roots was significantly higher in transgenic plants expressing CmF-308 under the AtSUC2 promoter than in controls. A similar effect on root development was obtained after transient expression of CmF-308 in source leaves of N. benthamiana plants. An auxin-response assay showed that CmF-308-transgenic roots are more sensitive to auxin than control roots. In addition to the altered root development, phloem-specific expression of CmF-308 resulted in shorter plants, a higher number of lateral shoots and delayed flowering, a phenotype resembling reduced apical dominance. In contrast to the root response, cotyledons of the transgenic plants were less sensitive to auxin than control cotyledons. The reduced auxin sensitivity in the shoot tissue was confirmed by lower relative expression of several Aux/IAA genes in leaves and an increase in the relative expression of a cytokinin-response regulator, TRR8/9b. The accumulated data suggest that expression of Aux/IAA in the phloem modifies auxin sensitivity in a tissue-specific manner, thereby altering plant development.

Functions of S-nitrosylation in plant hormone networks

In plants, a wide frame of physiological processes are regulated in liaison by both, nitric oxide (NO) and hormones. Such overlapping roles raise the question of how the cross-talk between NO and hormones trigger common physiological responses. In general, NO has been largely accepted as a signaling molecule that works in different processes. Among the most relevant ways NO and the NO-derived reactive species can accomplish their biological functions it is worthy to mention post-translational protein modifications. In the last years, S-nitrosylation has been the most studied NO-dependent regulatory mechanism. Briefly, S-nitrosylation is a redox-based mechanism for cysteine residue modification and is being recognized as a ubiquitous regulatory reaction comparable to phosphorylation. Therefore, it is emerging as a crucial mechanism for the transduction of NO bioactivity in plants and animals. In this mini-review, we provide an overview on S-nitrosylation of target proteins related to hormone networks in plants.

Phototropism: translating light into directional growth

Phototropism allows plants to align their photosynthetic tissues with incoming light. The direction of incident light is sensed by the phototropin family of blue light photoreceptors (phot1 and phot2 in Arabidopsis), which are light-activated protein kinases. The kinase activity of phototropins and phosphorylation of residues in the activation loop of their kinase domains are essential for the phototropic response. These initial steps trigger the formation of the auxin gradient across the hypocotyl that leads to asymmetric growth. The molecular events between photoreceptor activation and the growth response are only starting to be elucidated. In this review, we discuss the major steps leading from light perception to directional growth concentrating on Arabidopsis. In addition, we highlight links that connect these different steps enabling the phototropic response.

Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors

Upstream ORFs are elements found in the 5'-leader sequences of specific mRNAs that modulate the translation of downstream ORFs encoding major gene products. In Arabidopsis, the translational control of auxin response factors (ARFs) by upstream ORFs has been proposed as a regulatory mechanism required to respond properly to complex auxin-signaling inputs. In this study, we identify and characterize the aberrant auxin responses in specific ribosomal protein mutants in which multiple ARF transcription factors are simultaneously repressed at the translational level. This characteristic lends itself to the use of these mutants as genetic tools to bypass the genetic redundancy among members of the ARF family in Arabidopsis. Using this approach, we were able to assign unique functions for ARF2, ARF3, and ARF6 in plant development.

A complex systems approach to Arabidopsis root stem-cell niche developmental mechanisms: from molecules, to networks, to morphogenesis

Recent reports have shown that the molecular mechanisms involved in root stem-cell niche development in Arabidopsis thaliana are complex and contain several feedback loops and non-additive interactions that need to be analyzed using computational and formal approaches. Complex systems cannot be understood in terms of the behavior of their isolated components, but they emerge as a consequence of largely non-linear interactions among their components. The study of complex systems has provided a useful approach for the exploration of system-level characteristics and behaviors of the molecular networks involved in cell differentiation and morphogenesis during development. We analyzed the complex molecular networks underlying stem-cell niche patterning in the A. thaliana root in terms of some of the key dynamic traits of complex systems: self-organization, modularity and structural properties. We use these analyses to integrate the available root stem-cell niche molecular mechanisms data and postulate novel hypotheses, missing components and interactions and explain apparent contradictions in the literature.

Modeling regulatory networks to understand plant development: small is beautiful

We now have unprecedented capability to generate large data sets on the myriad genes and molecular players that regulate plant development. Networks of interactions between systems components can be derived from that data in various ways and can be used to develop mathematical models of various degrees of sophistication. Here, we discuss why, in many cases, it is productive to focus on small networks. We provide a brief and accessible introduction to relevant mathematical and computational approaches to model regulatory networks and discuss examples of small network models that have helped generate new insights into plant biology (where small is beautiful), such as in circadian rhythms, hormone signaling, and tissue patterning. We conclude by outlining some of the key technical and modeling challenges for the future.

A synthetic approach reveals extensive tunability of auxin signaling

Explaining how the small molecule auxin triggers diverse yet specific responses is a long-standing challenge in plant biology. An essential step in auxin response is the degradation of Auxin/Indole-3-Acetic Acid (Aux/IAA, referred to hereafter as IAA) repressor proteins through interaction with auxin receptors. To systematically characterize diversity in degradation behaviors among IAA|receptor pairs, we engineered auxin-induced degradation of plant IAA proteins in yeast (Saccharomyces cerevisiae). We found that IAA degradation dynamics vary widely, depending on which receptor is present, and are not encoded solely by the degron-containing domain II. To facilitate this and future studies, we identified a mathematical model able to quantitatively describe IAA degradation behavior in a single parameter. Together, our results demonstrate the remarkable tunability conferred by specific configurations of the auxin response pathway.

Auxology: when auxin meets plant evo-devo

Auxin is implicated throughout plant growth and development. Although the effects of this plant hormone have been recognized for more than a century, it is only in the past two decades that light has been shed on the molecular mechanisms that regulate auxin homeostasis, signaling, transport, crosstalk with other hormonal pathways as well as its roles in plant development. These discoveries established a molecular framework to study the role of auxin in land plant evolution. Here, we review recent advances in auxin biology and their implications in both micro- and macro-evolution of plant morphology. By analogy to the term 'hoxology', which refers to the critical role of HOX genes in metazoan evolution, we propose to introduce the term 'auxology' to take into account the crucial role of auxin in plant evo-devo.