AXR3 and SHY2 interact to regulate root hair development

Auxin, the organizer of the hormonal/environmental signals for root hair growth

The root hair development is controlled by diverse factors such as fate-determining developmental cues, auxin-related environmental factors, and hormones. In particular, the soil environmental factors are important as they maximize their absorption by modulating root hair development. These environmental factors affect the root hair developmental process by making use of diverse hormones. These hormonal factors interact with each other to modulate root hair development in which auxin appears to form the most intensive networks with the pathways from environmental factors and hormones. Moreover, auxin action for root hair development is genetically located immediately upstream of the root hair-morphogenetic genes. These observations suggest that auxin plays as an organizing node for environmental/hormonal pathways to modulate root hair growth.

A map of cell type-specific auxin responses

In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin-responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue-specific transcriptional regulation of cell-identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin-response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome-level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.

SCF(TIR1/AFB)-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism

The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box(TIR1/AFB) (SCF(TIR1/AFB))-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth.

Nuclear glutathione

Glutathione (GSH) is a linchpin of cellular defences in plants and animals with physiologically-important roles in the protection of cells from biotic and abiotic stresses. Moreover, glutathione participates in numerous metabolic and cell signalling processes including protein synthesis and amino acid transport, DNA repair and the control of cell division and cell suicide programmes. While it is has long been appreciated that cellular glutathione homeostasis is regulated by factors such as synthesis, degradation, transport, and redox turnover, relatively little attention has been paid to the influence of the intracellular partitioning on glutathione and its implications for the regulation of cell functions and signalling. We focus here on the functions of glutathione in the nucleus, particularly in relation to physiological processes such as the cell cycle and cell death. The sequestration of GSH in the nucleus of proliferating animal and plant cells suggests that common redox mechanisms exist for DNA regulation in G1 and mitosis in all eukaryotes. We propose that glutathione acts as "redox sensor" at the onset of DNA synthesis with roles in maintaining the nuclear architecture by providing the appropriate redox environment for the DNA replication and safeguarding DNA integrity. In addition, nuclear GSH may be involved in epigenetic phenomena and in the control of nuclear protein degradation by nuclear proteasome. Moreover, by increasing the nuclear GSH pool and reducing disulfide bonds on nuclear proteins at the onset of cell proliferation, an appropriate redox environment is generated for the stimulation of chromatin decompaction. This article is part of a Special Issue entitled Cellular functions of glutathione.

Getting a grasp on domain III/IV responsible for Auxin Response Factor-IAA protein interactions

Auxin Response Factors (ARFs) and Indole Acetic Acid (IAA) proteins contain a similar carboxyl-terminal domain (domain III/IV) that facilitates interactions among these transcription factors as well as other proteins. The specificity of these interactions is controversial, and the mechanisms involved in these interactions have not been investigated. Here, we review some of the controversies about the specificities and requirements for ARF and IAA interactions and discuss some of the technical problems that might contribute to differences reported for these interactions. We make some preliminary conclusions that ARF activator-IAA, ARF activator-ARF activator, and ARF repressor-ARF repressor interactions are favored over ARF repressor-IAA and ARF repressor-ARF activator interactions, and we suggest that IAA-IAA interactions are largely indiscriminant. Based upon the predicted secondary structure of domain III/IV, we introduce a model for how ARF and IAA proteins might interact with one another through a ubiquitin-like β-grasp fold.

OsIAA13-mediated auxin signaling is involved in lateral root initiation in rice

The plant hormone auxin is essential for root formation. After auxin perception, transmission of the auxin signal progresses through the degradation of Aux/IAA proteins. In this study, we newly isolated and characterized a rice gain-of-function mutant, Osiaa13, containing a single amino acid substitution in the core sequence required for the degradation of the OsIAA13 protein. The Osiaa13 mutant displayed typical auxin-related phenotypes: the number of lateral roots was significantly reduced and the root gravitropic response was defective. Osiaa13 mutants also exhibited altered GUS staining controlled by the DR5 promoter in lateral root initiation sites. Furthermore, expression levels of several genes that might be associated with lateral root initiation were altered in Osiaa13. Taken together, our results indicate that OsIAA13 is involved in auxin signaling and controls the expression of genes that are required for lateral root initiation in rice.

The evolution of root hairs and rhizoids

BACKGROUND

Almost all land plants develop tip-growing filamentous cells at the interface between the plant and substrate (the soil). Root hairs form on the surface of roots of sporophytes (the multicellular diploid phase of the life cycle) in vascular plants. Rhizoids develop on the free-living gametophytes of vascular and non-vascular plants and on both gametophytes and sporophytes of the extinct rhyniophytes. Extant lycophytes (clubmosses and quillworts) and monilophytes (ferns and horsetails) develop both free-living gametophytes and free-living sporophytes. These gametophytes and sporophytes grow in close contact with the soil and develop rhizoids and root hairs, respectively.

SCOPE

Here we review the development and function of rhizoids and root hairs in extant groups of land plants. Root hairs are important for the uptake of nutrients with limited mobility in the soil such as phosphate. Rhizoids have a variety of functions including water transport and adhesion to surfaces in some mosses and liverworts.

CONCLUSIONS

A similar gene regulatory network controls the development of rhizoids in moss gametophytes and root hairs on the roots of vascular plant sporophytes. It is likely that this gene regulatory network first operated in the gametophyte of the earliest land plants. We propose that later it functioned in sporophytes as the diploid phase evolved a free-living habit and developed an interface with the soil. This transference of gene function from gametophyte to sporophyte could provide a mechanism that, at least in part, explains the increase in morphological diversity of sporophytes that occurred during the radiation of land plants in the Devonian Period.

The ethylene pathway contributes to root hair elongation induced by the beneficial bacteria Phyllobacterium brassicacearum STM196

In Arabidopsis roots, some epidermal cells differentiate into root hair cells. Auxin regulates root hair positioning, while ethylene controls cell elongation. Phyllobacterium brassicacearum STM196, a beneficial strain of plant growth promoting rhizobacteria (PGPR) isolated from the roots of field-grown oilseed rape, stimulates root hair elongation in Arabidopsis thaliana seedlings. We investigated the role of ethylene in the response of root hair cells to STM196 inoculation. While we could not detect a significant increase in ethylene biosynthesis, we could detect a slight activation of the ethylene signalling pathway. Consistent with this, an exhaustive survey of the root hair elongation response of mutants and transgenic lines affected in the ethylene pathway showed contrasting root hair sensitivities to STM196. We propose that local ethylene emission contributes to STM196-induceed root hair elongation.

A gain-of-function mutation in IAA16 confers reduced responses to auxin and abscisic acid and impedes plant growth and fertility

Auxin regulates many aspects of plant development, in part, through degradation of the Aux/IAA family of transcriptional repressors. Consequently, stabilizing mutations in several Aux/IAA proteins confer reduced auxin responsiveness. However, of the 29 apparent Aux/IAA proteins in Arabidopsis thaliana, fewer than half have roles established through mutant analysis. We identified iaa16-1, a dominant gain-of-function mutation in IAA16 (At3g04730), in a novel screen for reduced root responsiveness to abscisic acid. The iaa16-1 mutation also confers dramatically reduced auxin responses in a variety of assays, markedly restricts growth of adult plants, and abolishes fertility when homozygous. We compared iaa16-1 phenotypes with those of dominant mutants defective in the closely related IAA7/AXR2, IAA14/SLR, and IAA17/AXR3, along with the more distantly related IAA28, and found overlapping but distinct patterns of developmental defects. The identification and characterization of iaa16-1 provides a fuller understanding of the IAA7/IAA14/IAA16/IAA17 clade of Aux/IAA proteins and the diverse roles of these repressors in hormone response and plant development.

The interaction and integration of auxin signaling components

IAA, a naturally occurring auxin, is a simple signaling molecule that regulates many diverse steps of plant development. Auxin essentially coordinates plant development through transcriptional regulation. Auxin binds to TIR1/AFB nuclear receptors, which are F-box subunits of the SCF ubiquitin ligase complex. The auxin signal is then modulated by the quantitative and qualitative responses of the Aux/IAA repressors and the auxin response factor (ARF) transcription factors. The specificity of the auxin-regulated gene expression profile is defined by several factors, such as the expression of these regulatory proteins, their post-transcriptional regulation, their stability and the affinity between these regulatory proteins. Auxin-binding protein 1 (ABP1) is a candidate protein for an auxin receptor that is implicated in non-transcriptional auxin signaling. ABP1 also affects TIR1/AFB-mediated auxin-responsive gene expression, implying that both the ABP1 and TIR1/AFB signaling machineries coordinately control auxin-mediated physiological events. Systematic approaches using the comprehensive mapping of the expression and interaction of signaling modules and computational modeling would be valuable for integrating our knowledge of auxin signals and responses.

AUX/LAX family of auxin influx carriers-an overview

Auxin regulates several aspects of plant growth and development. Auxin is unique among plant hormones for exhibiting polar transport. Indole-3-acetic acid (IAA), the major form of auxin in higher plants, is a weak acid and its intercellular movement is facilitated by auxin influx and efflux carriers. Polarity of auxin movement is provided by asymmetric localization of auxin carriers (mainly PIN efflux carriers). PIN-FORMED (PIN) and P-GLYCOPROTEIN (PGP) family of proteins are major auxin efflux carriers whereas AUXIN1/LIKE-AUX1 (AUX/LAX) are major auxin influx carriers. Genetic and biochemical evidence show that each member of the AUX/LAX family is a functional auxin influx carrier and mediate auxin related developmental programmes in different organs and tissues. Of the four AUX/LAX genes, AUX1 regulates root gravitropism, root hair development and leaf phyllotaxy whereas LAX2 regulates vascular development in cotyledons. Both AUX1 and LAX3 have been implicated in lateral root (LR) development as well as apical hook formation whereas both AUX1 and LAX1 and possibly LAX2 are required for leaf phyllotactic patterning.

Distinguishing possible mechanisms for auxin-mediated developmental control in Arabidopsis: models with two Aux/IAA and ARF proteins, and two target gene-sets

New models of gene transcriptional responses to auxin signalling in Arabidopsis are presented. This work extends a previous model of auxin signalling to include networks of gene-sets which may control developmental responses along auxin gradients. Key elements of this new study include models of signalling pathways and networks involving two Aux-IAA proteins (IAAs), auxin response factors (ARFs) and gene targets. Hypotheses for the gene network topologies which may be involved in developmental responses have been tested against experimental observations for root hair growth in particular. In studying these models, we provide a framework for the analysis of auxin signalling with multiple IAAs and ARFs, and discuss the implications of bistability in such systems.

The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development

Root growth and development in Arabidopsis thaliana are sustained by a specialised zone termed the meristem, which contains a population of dividing and differentiating cells that are functionally analogous to a stem cell niche in animals. The hormones auxin and cytokinin control meristem size antagonistically. Local accumulation of auxin promotes cell division and the initiation of a lateral root primordium. By contrast, high cytokinin concentrations disrupt the regular pattern of divisions that characterises lateral root development, and promote differentiation. The way in which the hormones interact is controlled by a genetic regulatory network. In this paper, we propose a deterministic mathematical model to describe this network and present model simulations that reproduce the experimentally observed effects of cytokinin on the expression of auxin regulated genes. We show how auxin response genes and auxin efflux transporters may be affected by the presence of cytokinin. We also analyse and compare the responses of the hormones auxin and cytokinin to changes in their supply with the responses obtained by genetic mutations of SHY2, which encodes a protein that plays a key role in balancing cytokinin and auxin regulation of meristem size. We show that although shy2 mutations can qualitatively reproduce the effect of varying auxin and cytokinin supply on their response genes, some elements of the network respond differently to changes in hormonal supply and to genetic mutations, implying a different, general response of the network. We conclude that an analysis based on the ratio between these two hormones may be misleading and that a mathematical model can serve as a useful tool for stimulate further experimental work by predicting the response of the network to changes in hormone levels and to other genetic mutations.

Apoplastic alkalinization is instrumental for the inhibition of cell elongation in the Arabidopsis root by the ethylene precursor 1-aminocyclopropane-1-carboxylic acid

In Arabidopsis (Arabidopsis thaliana; Columbia-0) roots, the so-called zone of cell elongation comprises two clearly different domains: the transition zone, a postmeristematic region (approximately 200-450 μm proximal of the root tip) with a low rate of elongation, and a fast elongation zone, the adjacent proximal region (450 μm away from the root tip up to the first root hair) with a high rate of elongation. In this study, the surface pH was measured in both zones using the microelectrode ion flux estimation technique. The surface pH is highest in the apical part of the transition zone and is lowest at the basal part of the fast elongation zone. Fast cell elongation is inhibited within minutes by the ethylene precursor 1-aminocyclopropane-1-carboxylic acid; concomitantly, apoplastic alkalinization occurs in the affected root zone. Fusicoccin, an activator of the plasma membrane H(+)-ATPase, can partially rescue this inhibition of cell elongation, whereas the inhibitor N,N'-dicyclohexylcarbodiimide does not further reduce the maximal cell length. Microelectrode ion flux estimation experiments with auxin mutants lead to the final conclusion that control of the activity state of plasma membrane H(+)-ATPases is one of the mechanisms by which ethylene, via auxin, affects the final cell length in the root.

Sending mixed messages: auxin-cytokinin crosstalk in roots

Despite their relatively simple appearance, roots are incredibly complex organs that are highly adapted to differing environments. Many aspects of root development are co-ordinated by subtle spatial differences in the concentrations of the phytohormones auxin and cytokinin. Events from the formation of a root during embryogenesis to the determination of the network of lateral roots are controlled by interactions between these hormones. Recently, interactions have been defined where auxin signaling promotes the expression of cytokinin signaling inhibitors, cytokinin signaling promotes the expression of auxin signaling inhibitors and finally where cytokinin signaling regulates the complex network of auxin transport proteins to position zones of high auxin signaling. We are witnessing a period of discovery in which we are beginning to understand how these hormonal pathways communicate to regulate root formation.

Plant development: early events in lateral root initiation

How are the lateral root founder cells specified in the pericycle to initiate lateral root development? An Aux/IAA28 signaling module activates transcription factor GATA23 to control founder cell identity.

New insights into the mechanism of development of Arabidopsis root hairs and trichomes

Epidermis cell differentiation in Arabidopsis thaliana is a model system for understanding the mechanisms leading to the developmental end state of plant cells. Both root hairs and trichomes differentiate from epidermal cells and molecular genetic analyses using Arabidopsis mutants have demonstrated that the differentiation of root hairs and trichomes is regulated by similar molecular mechanisms. Molecular-genetic approaches have led to the identification of many genes that are involved in epidermal cell differentiation, most of which encode transcription factors that induce the expression of genes active in both root hair and trichome development. Control of cell growth after fate determination has also been studied using Arabidopsis mutants.

Quantifying degradation rates of transmembrane receptor kinases

Transmembrane receptor-kinases are widespread throughout eukaryotes and their activities are known to regulate all kinds of cellular responses in diverse organs and cell types. In order to guarantee the correct amplitude and duration of signals, receptor levels at the cellular surface need to be tightly controlled. The regulation of receptor degradation is the most direct way to achieve this and elaborate mechanisms are in place to control this process. Therefore, the rate of receptor degradation is a parameter of central importance for understanding the dynamics of a signal transduction cascade. Unfortunately, degradation of transmembrane receptors is a complicated multistep process that involves internalization from the plasma membrane, invagination into the lumen of endosomal compartments, and finally fusion with the vacuole for degradation by vacuolar proteases. Therefore, degradation should be measured in an as noninvasive way as possible, such as not to interfere with the complicated transport processes. Here, a method for minimally invasive, in vivo turn-over measurements in intact organs is provided. This technique was used for quantifying the turn-over rates of the Brassinosteroid receptor kinase BRI1 (BRASSINOSTEROID INSENSITIVE 1) in Arabidopsis thaliana root meristems. Pulse-chase expression of a fluorescently labeled BRI1 variant was used and its turn-over rate was determined by quantitative confocal microscopy. This method is well suited to measure turn-over of transmembrane kinases, but can evidently be extended to measure turn-over of any types of transmembrane proteins.

Context, specificity, and self-organization in auxin response

Auxin is a simple molecule with a remarkable ability to control plant growth, differentiation, and morphogenesis. The mechanistic basis for this versatility appears to stem from the highly complex nature of the networks regulating auxin metabolism, transport and response. These heavily feedback-regulated and inter-dependent mechanisms are complicated in structure and complex in operation giving rise to a system with self-organizing properties capable of generating highly context-specific responses to auxin as a single, generic signal.

Lateral root organogenesis - from cell to organ

Unlike locomotive organisms capable of actively approaching essential resources, sessile plants must efficiently exploit their habitat for water and nutrients. This involves root-mediated underground interactions allowing plants to adapt to soils of diverse qualities. The root system of plants is a dynamic structure that modulates primary root growth and root branching by continuous integration of environmental inputs, such as nutrition availability, soil aeration, humidity, or salinity. Root branching is an extremely flexible means to rapidly adjust the overall surface of the root system and plants have evolved efficient control mechanisms, including, firstly initiation, when and where to start lateral root formation; secondly lateral root primordia organogenesis, during which the development of primordia can be arrested for a certain time; and thirdly lateral root emergence. Our review will focus on the most recent advances in understanding the molecular mechanisms involved in the regulation of lateral root initiation and organogenesis with the main focus on root system of the model plant Arabidopsis thaliana.

ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis

Spatial distribution of the plant hormone auxin regulates multiple aspects of plant development. These self-regulating auxin gradients are established by the action of PIN auxin transporters, whose activity is regulated by their constitutive cycling between the plasma membrane and endosomes. Here, we show that auxin signaling by the auxin receptor AUXIN-BINDING PROTEIN 1 (ABP1) inhibits the clathrin-mediated internalization of PIN proteins. ABP1 acts as a positive factor in clathrin recruitment to the plasma membrane, thereby promoting endocytosis. Auxin binding to ABP1 interferes with this action and leads to the inhibition of clathrin-mediated endocytosis. Our study demonstrates that ABP1 mediates a nontranscriptional auxin signaling that regulates the evolutionarily conserved process of clathrin-mediated endocytosis and suggests that this signaling may be essential for the developmentally important feedback of auxin on its own transport.

Expression and regulation of the early auxin-responsive Aux/IAA genes during strawberry fruit development

The plant hormone auxin transcriptionally activates Aux/IAA genes. Auxin plays an important role in regulating fruit growth and ripening of strawberry and Aux/IAA genes have been extensively studied in Arabidopsis, rice and tomato, but little information is available on strawberry fruit. In the present work, two full-length of early auxin-responsive Aux/IAA genes, termed FaAux/IAA1 and FaAux/IAA2 respectively, were isolated and characterized from strawberry fruit. Moreover, the expression profiles of two FaAux/IAA genes during fruit development, and the effect of naphthalene acetic acid (NAA) on their expressions of fruits at two different developmental stages were also investigated. The results showed that the levels of FaAux/IAA1 and FaAux/IAA2 transcripts were very high at early stage of fruit development, and decreased sharply at ripening stage (after white stage). In addition, NAA applied at the stage of large green and white fruit obviously increased the accumulations of FaAux/IAA1 and FaAux/IAA2 transcripts. These data suggested that the expressions of both FaAux/IAA1 and FaAux/IAA2 genes were likely to be involved in early fruit development, and the enhancement of FaAux/IAAs transcripts might be attributed at least or partially to auxin-induced fruit growth and delayed fruit ripening of strawberry.

The rate of cell differentiation controls the Arabidopsis root meristem growth phase

Upon seed germination, apical meristems grow as cell division prevails over differentiation and reach their final size when division and differentiation reach a balance. In the Arabidopsis root meristem, this balance results from the interaction between cytokinin (promoting differentiation) and auxin (promoting division) through a regulatory circuit whereby the ARR1 cytokinin-responsive transcription factor activates the gene SHY2, which negatively regulates the PIN genes encoding auxin transport facilitators. However, it remains unknown how the final meristem size is set, i.e., how a change in the relative rates of cell division and differentiation is brought about to cause meristem growth to stop. Here, we show that during meristem growth, expression of SHY2 is driven by another cytokinin-response factor, ARR12, and that completion of growth is brought about by the upregulation of SHY2 caused by both ARR12 and ARR1: this leads to an increase in cell differentiation rate that balances it with division, thus setting root meristem size. We also show that gibberellins selectively repress expression of ARR1 at early stages of meristem development, and that the DELLA protein REPRESSOR OF GA 1-3 (RGA) mediates this negative control.

Auxin control of root development

A plant's roots system determines both the capacity of a sessile organism to acquire nutrients and water, as well as providing a means to monitor the soil for a range of environmental conditions. Since auxins were first described, there has been a tight connection between this class of hormones and root development. Here we review some of the latest genetic, molecular, and cellular experiments that demonstrate the importance of generating and maintaining auxin gradients during root development. Refinements in the ability to monitor and measure auxin levels in root cells coupled with advances in our understanding of the sources of auxin that contribute to these pools represent important contributions to our understanding of how this class of hormones participates in the control of root development. In addition, we review the role of identified molecular components that convert auxin gradients into local differentiation events, which ultimately defines the root architecture.

A basic helix-loop-helix transcription factor controls cell growth and size in root hairs

Postmitotic cell growth defines cell shape and size during development. However, the mechanisms regulating postmitotic cell growth in plants remain unknown. Here we report the discovery of a basic helix-loop-helix (bHLH) transcription factor called RSL4 (ROOT HAIR DEFECTIVE 6-LIKE 4) that is sufficient to promote postmitotic cell growth in Arabidopsis thaliana root-hair cells. Loss of RSL4 function resulted in the development of very short root hairs. In contrast, constitutive RSL4 expression programmed constitutive growth, resulting in the formation of very long root hairs. Hair-cell growth signals, such as auxin and low phosphate availability, modulate hair cell extension by regulating RSL4 transcript and protein levels. RSL4 is thus a regulator of growth that integrates endogenous developmental and exogenous environmental signals that together control postmitotic growth in root hairs. The control of postmitotic growth by transcription factors may represent a general mechanism for regulating cell size across diverse organisms.

Auxin modulates the transition from the mitotic cycle to the endocycle in Arabidopsis

Amplification of genomic DNA by endoreduplication often marks the initiation of cell differentiation in animals and plants. The transition from mitotic cycles to endocycles should be developmentally programmed but how this process is regulated remains largely unknown. We show that the plant growth regulator auxin modulates the switch from mitotic cycles to endocycles in Arabidopsis; high levels of TIR1-AUX/IAA-ARF-dependent auxin signalling are required to repress endocycles, thus maintaining cells in mitotic cycles. By contrast, lower levels of TIR1-AUX/IAA-ARF-dependent auxin signalling trigger an exit from mitotic cycles and an entry into endocycles. Our data further demonstrate that this auxin-mediated modulation of the mitotic-to-endocycle switch is tightly coupled with the developmental transition from cell proliferation to cell differentiation in the Arabidopsis root meristem. The transient reduction of auxin signalling by an auxin antagonist PEO-IAA rapidly downregulates the expression of several core cell cycle genes, and we show that overexpressing one of the genes, CYCLIN A2;3 (CYCA2;3), partially suppresses an early initiation of cell differentiation induced by PEO-IAA. Taken together, these results suggest that auxin-mediated mitotic-to-endocycle transition might be part of the developmental programmes that balance cell proliferation and cell differentiation in the Arabidopsis root meristem.

A theoretical model for ROP localisation by auxin in Arabidopsis root hair cells

Background

Local activation of Rho GTPases is important for many functions including cell polarity, morphology, movement, and growth. Although a number of molecules affecting Rho-of-Plants small GTPase (ROP) signalling are known, it remains unclear how ROP activity becomes spatially organised. Arabidopsis root hair cells produce patches of ROP at consistent and predictable subcellular locations, where root hair growth subsequently occurs.

Methodology/Principal Findings

We present a mathematical model to show how interaction of the plant hormone auxin with ROPs could spontaneously lead to localised patches of active ROP via a Turing or Turing-like mechanism. Our results suggest that correct positioning of the ROP patch depends on the cell length, low diffusion of active ROP, a gradient in auxin concentration, and ROP levels. Our theory provides a unique explanation linking the molecular biology to the root hair phenotypes of multiple mutants and transgenic lines, including OX-ROP, CA-rop, aux1, axr3, tip1, eto1, etr1, and the triple mutant aux1 ein2 gnom^eb.

Conclusions/Significance

We show how interactions between Rho GTPases (in this case ROPs) and regulatory molecules (in this case auxin) could produce characteristic subcellular patterning that subsequently affects cell shape. This has important implications for research on the morphogenesis of plants and other eukaryotes. Our results also illustrate how gradient-regulated Turing systems provide a particularly robust and flexible mechanism for pattern formation.

Cytokinin-auxin crosstalk

Post-embryonic plant growth and development are sustained by meristems, a source of undifferentiated cells that give rise to the adult plant structures. Two hormones, cytokinin and auxin, are known to act antagonistically in controlling meristem activities. Here, we review recent significant progress in elucidating the molecular mechanisms through which these hormones interact to control specific aspects of plant development. For example, in the root meristem of Arabidopsis thaliana, cytokinin promotes cell differentiation by repressing both auxin signalling and transport, whereas auxin sustains root meristem activity by promoting cell division. The coordinated action of these two hormones is essential for maintaining root meristem size and for ensuring root growth.

Abscisic acid represses growth of the Arabidopsis embryonic axis after germination by enhancing auxin signaling

Under unfavorable environmental conditions, the stress phytohormone ABA inhibits the developmental transition from an embryo in a dry seed into a young seedling. We developed a genetic screen to isolate Arabidopsis thaliana mutants whose early seedling development is resistant to ABA. Here, we report the identification of a recessive mutation in AUXIN RESISTANT1 (AUX1), encoding a cellular auxin influx carrier. Although auxin is a major morphogenesis hormone in plants, little is known about ABA-auxin interactions during early seedling growth. We show that aux1 and pin2 mutants are insensitive to ABA-dependent repression of embryonic axis (hypocotyl and radicle) elongation. Genetic and physiological experiments show that this involves auxin transport to the embryonic axis elongation zone, where ABA enhances the activity of an auxin-responsive promoter. We propose that ABA represses embryonic axis elongation by potentiating auxin signaling in its elongation zone. This involves repression of the AUXIN INDUCIBLE (Aux/IAA) gene AXR2/IAA7, encoding a key component of ABA- and auxin-dependent responses during postgerminative growth.

The evolution of nuclear auxin signalling

BACKGROUND

The plant hormone auxin directs many aspects of plant growth and development. To understand the evolution of auxin signalling, we compared the genes encoding two families of crucial transcriptional regulators, AUXIN RESPONSE FACTOR (ARF) and AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA), among flowering plants and two non-seed plants, Physcomitrella patens and Selaginella moellendorffii.

RESULTS

Comparative analysis of the P. patens, S. moellendorffii and Arabidopsis thaliana genomes suggests that the well-established rapid transcriptional response to auxin of flowering plants, evolved in vascular plants after their divergence from the last common ancestor shared with mosses. An N-terminally truncated ARF transcriptional activator is encoded by the genomes of P. patens and S. moellendorffii, and suggests a supplementary mechanism of nuclear auxin signalling, absent in flowering plants. Site-specific analyses of positive Darwinian selection revealed relatively high rates of synonymous substitution in the A. thaliana ARFs of classes IIa (and their closest orthologous genes in poplar) and Ib, suggesting that neofunctionalization in important functional regions has driven the evolution of auxin signalling in flowering plants. Primary auxin responsive gene families (GH3, SAUR, LBD) show different phylogenetic profiles in P. patens, S. moellendorffii and flowering plants, highlighting genes for further study.

CONCLUSION

The genome of P. patens encodes all of the basic components necessary for a rapid auxin response. The spatial separation of the Q-rich activator domain and DNA-binding domain suggests an alternative mechanism of transcriptional control in P. patens distinct from the mechanism seen in flowering plants. Significantly, the genome of S. moellendorffii is predicted to encode proteins suitable for both methods of regulation.

Constitutive repression and activation of auxin signaling in Arabidopsis

Aux/IAA proteins are proposed to be transcriptional repressors that play a crucial role in auxin signaling by interacting with auxin response factors and repressing early/primary auxin response gene expression. In assays with transfected protoplasts, this repression was previously shown to occur when auxin concentrations in a cell are low, and derepression/activation was observed when auxin concentrations are elevated. Here we show that a stabilized version of the Arabidopsis (Arabidopsis thaliana) IAA17 repressor, when expressed constitutively or in a specific cell type in Arabidopsis plants, confers phenotypes similar to plants with decreased auxin levels. In contrast, a stabilized version of IAA17 that was converted to a transcriptional activator confers phenotypes similar to plants with increased auxin levels, when expressed under the same conditions in Arabidopsis plants. Free auxin levels were unchanged compared to control (DR5:beta-glucuronidase), however, in the seedlings expressing the IAA17 repressor and activator. These results together with our previous results carried out in transfected protoplasts suggest that the hormone auxin can be bypassed to regulate auxin signaling in a cell-autonomous manner in plants.

Hormone interactions at the root apical meristem

Plants exhibit an amazing developmental flexibility. Plant embryogenesis results in the establishment of a simple apical-basal axis represented by apical shoot and basal root meristems. Later, during postembryonic growth, shaping of the plant body continues by the formation and activation of numerous adjacent meristems that give rise to lateral shoot branches, leaves, flowers, or lateral roots. This developmental plasticity reflects an important feature of the plant's life strategy based on the rapid reaction to different environmental stimuli, such as temperature fluctuations, availability of nutrients, light or water and response resulting in modulation of developmental programs. Plant hormones are important endogenous factors for the integration of these environmental inputs and regulation of plant development. After a period of studies focused primarily on single hormonal pathways that enabled us to understand the hormone perception and signal transduction mechanisms, it became obvious that the developmental output mediated by a single hormonal pathway is largely modified through a whole network of interactions with other hormonal pathways. In this review, we will summarize recent knowledge on hormonal networks that regulate the development and growth of root with focus on the hormonal interactions that shape the root apical meristem.

Genome-wide analysis of the auxin-responsive transcriptome downstream of iaa1 and its expression analysis reveal the diversity and complexity of auxin-regulated gene expression

The AUXIN RESPONSE FACTORs (ARFs) and the Aux/IAA proteins regulate various auxin responses through auxin perception mediated by the F-box proteins TIR1/AFBs. ARFs are transcription factors that modulate expression of auxin response genes and are negatively regulated by the Aux/IAA proteins. To gain insight into the regulatory mechanisms of Aux/IAA-ARF action at the genome level, the transcriptome regulated downstream of iaa1, a stabilized IAA1 mutant protein, was identified using dexamethasone (DEX)-controlled nuclear translocation of iaa1 during the auxin response. The expression of the iaa1-regulated auxin-responsive genes selected from microarray data was analysed with RNA-gel blot analysis and it was shown that auxin-regulated expression of these genes was significantly inhibited by DEX treatment. While cycloheximide-inducible expression of a majority of these genes was also DEX-suppressible, expression of some genes could not be suppressed by treatment with DEX. Expression analysis in a variety of arf mutant backgrounds suggested that all iaa1-regulated auxin-response genes examined are controlled by ARFs to different extents and that the same ARF protein can regulate the expression of these genes in response to auxin in a positive or a negative manner. However, arf mutations did not affect auxin-mediated down-regulation, indicating that ARFs might not play a critical role in down-regulation. The decrease in auxin-responsive gene expression in arf7 arf19 mutants was more severe than that of tir1/afb quadruple mutants. These results show the diversity and complexity of mechanisms of Aux/IAA-ARF- and auxin-regulated gene expression. These data also provide the opportunity for functional analysis of genes mediating the auxin-response downstream of Aux/IAA-ARFs.

Auxin transport through non-hair cells sustains root-hair development

The plant hormone auxin controls root epidermal cell development in a concentration-dependent manner 1-3. Root hairs are produced on a subset of epidermal cells as they increase in distance from the root tip. Auxin is required for their initiation 4-7 and continued growth 8-11, but little is known about its distribution in this region of the root. Counter to the expectation that hair cells might require active auxin influx to ensure auxin supply, we did not detect the auxin-influx transporter AUX1 in root-hair cells. A high level of AUX1 expression was detected in adjacent non-hair cell files. Non-hair cells were necessary to achieve wild-type root-hair length, although an auxin response was not required in these cells. 3D modelling of auxin flow in the root tip suggests that AUX1-dependent transport through non-hair cells maintains an auxin supply to developing hair cells as they increase in distance from the root tip and sustains root-hair outgrowth. Experimental data support the hypothesis that, instead of moving uniformly though the epidermal cell layer 3,12, auxin is mainly transported through canals that extend longitudinally into the tissue.

A genetic framework for the control of cell division and differentiation in the root meristem

Plant growth and development are sustained by meristems. Meristem activity is controlled by auxin and cytokinin, two hormones whose interactions in determining a specific developmental output are still poorly understood. By means of a comprehensive genetic and molecular analysis in Arabidopsis, we show that a primary cytokinin-response transcription factor, ARR1, activates the gene SHY2/IAA3 (SHY2), a repressor of auxin signaling that negatively regulates the PIN auxin transport facilitator genes: thereby, cytokinin causes auxin redistribution, prompting cell differentiation. Conversely, auxin mediates degradation of the SHY2 protein, sustaining PIN activities and cell division. Thus, the cell differentiation and division balance necessary for controlling root meristem size and root growth is the result of the interaction between cytokinin and auxin through a simple regulatory circuit converging on the SHY2 gene.

Dissecting the molecular basis of the regulation of wood formation by auxin in hybrid aspen

Indole acetic acid (auxin) is a key regulator of wood formation, and an observed overlap between auxin concentration gradient and developing secondary xylem cells has led to the hypothesis that auxin regulates wood formation by acting as a morphogen. We dissected the role of auxin in wood formation by identifying the auxin-responsive transcriptome in wood-forming tissues and investigating alterations in wood formation in transgenic hybrid aspen plants (Populus tremula x Populus tremuloides) with perturbed auxin signaling. We showed that auxin-responsive genes in wood-forming tissues respond dynamically to changes in cellular auxin levels. However, the expression patterns of most of the auxin-responsive genes displayed limited correlation with the auxin concentration across this developmental zone. Perturbing auxin signaling by reducing auxin responsiveness reduced the cambial cell division activity, caused spatial deregulation of cell division of the cambial initials, and led to reductions in not only radial but also axial dimensions of fibers and vessels. We propose that, instead of acting as a morphogen, changes in auxin concentration in developing secondary xylem cells may provide important regulatory cues that modulate the expression of a few key regulators; these, in turn, may control the global gene expression patterns that are essential for normal secondary xylem development.

Degradation of the auxin response factor ARF1

Auxin-mediated gene expression is largely controlled through a family of DNA-binding proteins known as auxin response factors (ARF). Previous studies on the role of proteolytic regulation in auxin signaling have focused on degradation of their interacting partner, the Aux/IAA proteins. Aux/IAA family members with domain II sequences are rapidly degraded, show auxin-enhanced degradation rates, and interact with the related F-box proteins TIR1 and AFB1-3, which indicates that they are ubiquitylated by a CUL1-dependent E3 ligase. To date, limited data have been generated regarding degradation of ARFs. Here, we focus on the degradation rate of one ARF family member, Arabidopsis thaliana ARF1, and find that the half-lives of N-terminally HA-tagged ARF1 and C-terminally luciferase-tagged ARF1 are both approximately 3-4 h. This half-life appears to be conferred by a component of the middle region (MR), and degradation of the luciferase fusion with the MR is more rapid when the fusion includes an additional nuclear localization signal. ARF1 degradation is proteasome-dependent and rates are not altered in a CUL1 mutant background, suggesting that this ARF is targeted for proteasomal degradation via an alternative set of machinery to that used for Aux/IAA degradation. Consistent with this, exogenous indole acetic acid does not affect the degradation of ARF1. Given increasing evidence that the relative ratio of Aux/IAAs to ARFs rather than the absolute quantity within the cell appears to be the mode through which auxin signaling is modulated, this half-life is likely to be biologically relevant.

Proximal-distal patterns of transcription factor gene expression during Arabidopsis root development

The expression pattern of genes can identify the cells in which the respective proteins are active during development. As a step towards defining the genetic network that controls the development of roots, a high-throughput method of whole-mount in situ hybridization has been developed that does not require expensive equipment and allows the definition of the expression patterns of 137 transcription factor genes in young developing roots. Of the 137 transcription factors, 81.8% were expressed in the root while 18.2% showed no detectable expression. In all three proximal distal zones (meristem, elongation, and differentiation) of the root, 52.6% were expressed whereas 21.2% were expressed in only two zones. Eight percent of the genes were expressed in a single proximal distal zone. Cell-specific gene expression patterns were also detected. This rapid approach identified potential key regulators of cell differentiation and provides important spatial information for the expression patterns of a large number of transcriptional regulators that function during root development.

A genetic regulatory network in the development of trichomes and root hairs

Trichomes and root hairs differentiate from epidermal cells in the aerial tissues and roots, respectively. Because trichomes and root hairs are easily accessible, particularly in the model plant Arabidopsis, their development has become a well-studied model of cell differentiation and growth. Molecular genetic analyses using Arabidopsis mutants have demonstrated that the differentiation of trichomes and root hair/hairless cells is regulated by similar molecular mechanisms. Transcriptional complexes regulate differentiation into trichome cells and root hairless cells, and formation of the transcriptional complexes is inhibited in neighboring cells. Control of cell growth after fate determination has also been analyzed using Arabidopsis mutants. The progression of endoreduplication cycles, reorientation of microtubules, and organization of the actin cytoskeleton play important roles in trichome growth. Various cellular components such as ion channels, the actin cytoskeleton, microtubules and cell wall materials, and intracellular signal transduction act to establish and maintain root hair tip growth.

What Makes each Aux/IAA Gene Unique in its Gene Family, Expression Pattern or Properties of the Gene Product?

In the auxin signal transduction, two protein families, Aux/IAAs and auxin response factors, play a crucial role just downstream of auxin F-box receptors. Distinct and overlapping phenotypes of the dominant Aux/IAA mutants suggest some functional differentiation of the Aux/IAA genes in auxin signaling. Taking advantage of unique phenotypes of the msg2/iaa19 mutants, we carried out promoter-exchange experiments, where cDNA of the msg2, axr2/iaa7 or slr/iaa14 gene was driven by the MSG2 or AXR2 promoter. The cDNAs were translationally fused to the green fluorescent protein gene to measure levels of expressed protein. Results showed that many abnormal phenotypes of the dominant Aux/IAA mutants were governed by their promoter activity, but some were dependent on their gene products. The latter result highlights the possible importance of Aux/IAA protein level controled by auxin F-box receptors.

Ethylene regulates root growth through effects on auxin biosynthesis and transport-dependent auxin distribution

In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery.

Endosomal signaling of plant steroid receptor kinase BRI1

The LRR receptor serine/threonine kinases are a major eukaryotic receptor family, for which the central regulatory mechanism of endosomal trafficking remains largely unadressed. We show that the steroid receptor BRI1 localizes to both plasma membrane and early endosomal compartments, even when observed at low, endogenous expression levels, and that its localization and turnover are independent of ligand. However, increasing endosomal localization of BRI1 enhances activation of the pathway and genomic responses. Our data indicate distinct signaling and trafficking mechanisms within this receptor class and show that the use of endosomes as signaling compartments is an unexpectedly broad phenomenon in eukaryotes.

pax1-1 partially suppresses gain-of-function mutations in Arabidopsis AXR3/IAA17

BACKGROUND

The plant hormone auxin exerts many of its effects on growth and development by controlling transcription of downstream genes. The Arabidopsis gene AXR3/IAA17 encodes a member of the Aux/IAA family of auxin responsive transcriptional repressors. Semi-dominant mutations in AXR3 result in an increased amplitude of auxin responses due to hyperstabilisation of the encoded protein. The aim of this study was to identify novel genes involved in auxin signal transduction by screening for second site mutations that modify the axr3-1 gain-of-function phenotype.

RESULTS

We present the isolation of the partial suppressor of axr3-1 (pax1-1) mutant, which partially suppresses almost every aspect of the axr3-1 phenotype, and that of the weaker axr3-3 allele. axr3-1 protein turnover does not appear to be altered by pax1-1. However, expression of an AXR3::GUS reporter is reduced in a pax1-1 background, suggesting that PAX1 positively regulates AXR3 transcription. The pax1-1 mutation also affects the phenotypes conferred by stabilising mutations in other Aux/IAA proteins; however, the interactions are more complex than with axr3-1.

CONCLUSION

We propose that PAX1 influences auxin response via its effects on AXR3 expression and that it regulates other Aux/IAAs secondarily.

From genes to patterns: Auxin distribution and auxin-dependent gene regulation in plant pattern formation

It has long been recognized that the plant hormone auxin plays integral roles in a variety of plant processes. More recently, it has become clear that these processes include some of the most basic pattern formation mechanisms needed to establish a functional plant body. Considerable insight into how this regulation plays out at the molecular level has been attained in recent years. Of special note are the complementary actions of the auxin efflux carrier proteins responsible for the formation of instructive auxin concentration gradients and the transcription factor complexes required for the appropriate interpretation of such instructions. The numerous players involved and the complexity of their regulation provide insight into how a single plant hormone can operate in such a multifunctional fashion. Many new features of auxin action can now be quantified and visualized, and three-dimensional models of auxin patterning can be tested and mathematically modeled. With these new advances, the developmental biology of auxin-mediated patterning has turned into a subject of plant systems biology research.

Vectorial information for Arabidopsis planar polarity is mediated by combined AUX1, EIN2, and GNOM activity

Cell polarity is commonly coordinated within the plane of a single tissue layer (planar polarity), and hair positioning has been exploited as a simple marker for planar polarization of animal epithelia . The root epidermis of the plant Arabidopsis similarly reveals planar polarity of hair localization close to root tip-oriented (basal) ends of hair-forming cells . Hair position is directed toward a concentration maximum of the hormone auxin in the root tip , but mechanisms driving this plant-specific planar polarity remain elusive. Here, we report that combinatorial action of the auxin influx carrier AUX1, ETHYLENE-INSENSITIVE2 (EIN2) , and GNOM genes mediates the vector for coordinate hair positioning. In aux1;ein2;gnom eb triple mutant roots, hairs display axial (apical or basal) instead of coordinate polar (basal) position, and recruitment of Rho-of-Plant (ROP) GTPases to the hair initiation site reveals the same polar-to-axial switch. The auxin concentration gradient is virtually abolished in aux1;ein2;gnom eb roots, where locally applied auxin can coordinate hair positioning. Moreover, auxin overproduction in sectors of wild-type roots enhances planar ROP and hair polarity over long and short distances. Hence, auxin may provide vectorial information for planar polarity that requires combinatorial AUX1, EIN2, and GNOM activity upstream of ROP positioning.

Patterning of Arabidopsis epidermal cells: epigenetic factors regulate the complex epidermal cell fate pathway

Cell fate determination in the Arabidopsis epidermis has been extensively studied for over a decade. Epidermal cells become either trichoblasts (hair-forming cells) or atrichoblasts (non-hair-forming cells). In Arabidopsis, two types of trichoblasts are formed in defined patterns: trichomes and root hairs. Both cell types are specified through the action of a common set of transcriptional regulators that define cell pattern. Recent studies also characterize epigenetic factors in the determination of cell fate in the root, suggesting a default pattern for epidermal cell fate that can be overridden by environmental stimuli. These results reveal how plant cell developmental plasticity is controlled at the molecular level.