AtPIN4 mediates sink-driven auxin gradients and root patterning in Arabidopsis

The polarly localized D6 PROTEIN KINASE is required for efficient auxin transport in Arabidopsis thaliana

The phytohormone auxin is a major determinant of plant growth and differentiation. Directional auxin transport and auxin responses are required for proper embryogenesis, organ formation, vascular development, and tropisms. Members of several protein families, including the PIN auxin efflux facilitators, have been implicated in auxin transport; however, the regulation of auxin transport by signaling proteins remains largely unexplored. We have studied a family of four highly homologous AGC protein kinases, which we designated the D6 protein kinases (D6PKs). We found that d6pk mutants have defects in lateral root initiation, root gravitropism, and shoot differentiation in axillary shoots, and that these phenotypes correlate with a reduction in auxin transport. Interestingly, D6PK localizes to the basal(lower) membrane of Arabidopsis root cells, where it colocalizes with PIN1, PIN2 and PIN4. D6PK and PIN1 interact genetically, and D6PK phosphorylates PIN proteins in vitro and in vivo. Taken together, our data show that D6PK is required for efficient auxin transport and suggest that PIN proteins are D6PK phosphorylation targets.

Cytokinins modulate auxin-induced organogenesis in plants via regulation of the auxin efflux

Postembryonic de novo organogenesis represents an important competence evolved in plants that allows their physiological and developmental adaptation to changing environmental conditions. The phytohormones auxin and cytokinin (CK) are important regulators of the developmental fate of pluripotent plant cells. However, the molecular nature of their interaction(s) in control of plant organogenesis is largely unknown. Here, we show that CK modulates auxin-induced organogenesis (AIO) via regulation of the efflux-dependent intercellular auxin distribution. We used the hypocotyl explants-based in vitro system to study the mechanism underlying de novo organogenesis. We show that auxin, but not CK, is capable of triggering organogenesis in hypocotyl explants. The AIO is accompanied by endogenous CK production and tissue-specific activation of CK signaling. CK affects differential auxin distribution, and the CK-mediated modulation of organogenesis is simulated by inhibition of polar auxin transport. CK reduces auxin efflux from cultured tobacco cells and regulates expression of auxin efflux carriers from the PIN family in hypocotyl explants. Moreover, endogenous CK levels influence PIN transcription and are necessary to maintain intercellular auxin distribution in planta. Based on these findings, we propose a model in which auxin acts as a trigger of the organogenic processes, whose output is modulated by the endogenously produced CKs. We propose that an important mechanism of this CK action is its effect on auxin distribution via regulation of expression of auxin efflux carriers.

The RPN5 subunit of the 26s proteasome is essential for gametogenesis, sporophyte development, and complex assembly in Arabidopsis

The 26S proteasome is an essential multicatalytic protease complex that degrades a wide range of intracellular proteins, especially those modified with ubiquitin. Arabidopsis thaliana and other plants use pairs of genes to encode most of the core subunits, with both of the isoforms often incorporated into the mature complex. Here, we show that the gene pair encoding the regulatory particle non-ATPase subunit (RPN5) has a unique role in proteasome function and Arabidopsis development. Homozygous rpn5a rpn5b mutants could not be generated due to a defect in male gametogenesis. While single rpn5b mutants appear wild-type, single rpn5a mutants display a host of morphogenic defects, including abnormal embryogenesis, partially deetiolated development in the dark, a severely dwarfed phenotype when grown in the light, and infertility. Proteasome complexes missing RPN5a are less stable in vitro, suggesting that some of the rpn5a defects are caused by altered complex integrity. The rpn5a phenotype could be rescued by expression of either RPN5a or RPN5b, indicating functional redundancy. However, abnormal phenotypes generated by overexpression implied that paralog-specific functions also exist. Collectively, the data point to a specific role for RPN5 in the plant 26S proteasome and suggest that its two paralogous genes in Arabidopsis have both redundant and unique roles in development.

Role of AUX1 in the control of organ identity during in vitro organogenesis and in mediating tissue specific auxin and cytokinin interaction in Arabidopsis

Classic plant tissue culture experiments have shown that exposure of cell culture to a high auxin to cytokinin ratio promotes root formation and a low auxin to cytokinin ratio leads to shoot regeneration. It has been widely accepted that auxin and cytokinin play an antagonistic role in the control of organ identities during organogenesis in vitro. Since the auxin level is highly elevated in the shoot meristem tissues, it is unclear how a low auxin to cytokinin ratio promotes the regeneration of shoots. To identify genes mediating the cytokinin and auxin interaction during organogenesis in vitro, three allelic mutants that display root instead of shoot regeneration in response to a low auxin to cytokinin ratio are identified using a forward genetic approach in Arabidopsis. Molecular characterization shows that the mutations disrupt the AUX1 gene, which has been reported to regulate auxin influx in plants. Meanwhile, we find that cytokinin substantially stimulates auxin accumulation and redistribution in calli and some specific tissues of Arabidopsis seedlings. In the aux1 mutants, the cytokinin regulated auxin accumulation and redistribution is substantially reduced in both calli and specific tissues of young seedlings. Our results suggest that auxin elevation and other changes stimulated by cytokinin, instead of low auxin or exogenous auxin directly applied, is essential for shoot regeneration.

Root system architecture from coupling cell shape to auxin transport

Lateral organ position along roots and shoots largely determines plant architecture, and depends on auxin distribution patterns. Determination of the underlying patterning mechanisms has hitherto been complicated because they operate during growth and division. Here, we show by experiments and computational modeling that curvature of the Arabidopsis root influences cell sizes, which, together with tissue properties that determine auxin transport, induces higher auxin levels in the pericycle cells on the outside of the curve. The abundance and position of the auxin transporters restricts this response to the zone competent for lateral root formation. The auxin import facilitator, AUX1, is up-regulated by auxin, resulting in additional local auxin import, thus creating a new auxin maximum that triggers organ formation. Longitudinal spacing of lateral roots is modulated by PIN proteins that promote auxin efflux, and pin2,3,7 triple mutants show impaired lateral inhibition. Thus, lateral root patterning combines a trigger, such as cell size difference due to bending, with a self-organizing system that mediates alterations in auxin transport.

Parasitic nematodes modulate PIN-mediated auxin transport to facilitate infection

Plant-parasitic nematodes are destructive plant pathogens that cause significant yield losses. They induce highly specialized feeding sites (NFS) in infected plant roots from which they withdraw nutrients. In order to establish these NFS, it is thought that the nematodes manipulate the molecular and physiological pathways of their hosts. Evidence is accumulating that the plant signalling molecule auxin is involved in the initiation and development of the feeding sites of sedentary plant-parasitic nematodes. Intercellular transport of auxin is essential for various aspects of plant growth and development. Here, we analysed the spatial and temporal expression of PIN auxin transporters during the early events of NFS establishment using promoter-GUS/GFP fusion lines. Additionally, single and double pin mutants were used in infection studies to analyse the role of the different PIN proteins during cyst nematode infection. Based on our results, we postulate a model in which PIN1-mediated auxin transport is needed to deliver auxin to the initial syncytial cell, whereas PIN3 and PIN4 distribute the accumulated auxin laterally and are involved in the radial expansion of the NFS. Our data demonstrate that cyst nematodes are able to hijack the auxin distribution network in order to facilitate the infection process.

Cytokinin signaling during root development

The cytokinin class of phytohormones regulates division and differentiation of plant cells. They are perceived and signaled by a phosphorelay mechanism similar to those observed in prokaryotes. Research into the components of phosphorelay had previously been marred by genetic redundancy. However, recent studies have addressed this with the creation of high-order mutants. In addition, several new elements regulating cytokinin signaling have been identified. This has uncovered many roles in diverse developmental and physiological processes. In this review, we look at these processes specifically in the context of root development. We focus on the formation and maintenance of the root apical meristem, primary and secondary vascular development, lateral root emergence and development, and root nodulation. We believe that the root is an ideal organ with which to investigate cytokinin signaling in a wider context.

Visualizing auxin transport routes in Arabidopsis leaf primordia

The phytohormone auxin plays a pivotal role in plant development, regulating a myriad of processes including embryo patterning, root patterning, organ initiation, and vein patterning. Auxin is unique among the plant hormones as it is actively transported from cell to cell in a polar fashion. It has recently been discovered that polar auxin transport generates dynamic, local auxin gradients within plant tissues that appear to provide positional information in patterning processes. Visualization of apparent auxin transport patterns has largely been facilitated by the recent creation of translational fusions of GFP to members of the Arabidopsis (At)PIN family of auxin efflux associated proteins. Confocal visualization of these fusion products (PIN:GFPs) enables the tracking of apparent auxin transport patterns in a huge number of samples. This visualization method can be combined with experimental interference, such as local auxin application and inhibition of auxin transport, to deduce possible self-organizing auxin-dependent patterning mechanisms and to make them amenable to mathematical modeling.

Post-transcriptional regulation of auxin transport proteins: cellular trafficking, protein phosphorylation, protein maturation, ubiquitination, and membrane composition

Auxin concentration gradients, established by polar transport of auxin, are essential for the establishment and maintenance of polar growth and morphological patterning. Three families of cellular transport proteins, PIN-formed (PIN), P-glycoprotein (ABCB/PGP), and AUXIN RESISTANT 1/LIKE AUX1 (AUX1/LAX), can independently and co-ordinately transport auxin in plants. Regulation of these proteins involves intricate and co-ordinated cellular processes, including protein-protein interactions, vesicular trafficking, protein phosphorylation, ubiquitination, and stabilization of the transporter complexes on the plasma membrane.

Rice shoot branching requires an ATP-binding cassette subfamily G protein

* Shoot branching is important for the establishment of plant architecture and productivity. * Here, characterization of rice (Oryza sativa) reduced culm number 1 (rcn1) mutants revealed that Rcn1 positively controls shoot branching by promoting the outgrowth of lateral shoots. Molecular studies revealed that Rcn1 encodes a novel member of ATP-binding cassette protein subfamily G (ABCG subfamily), also known as the white-brown complex (WBC) subfamily, and is designated OsABCG5. * Rcn1 is expressed in leaf primordia of main and axillary shoots, and in the vascular cells and leaf epidermis of older leaves. In addition, Rcn1 is expressed in the crown root primordia, endodermis, pericycle and stele in the root. No effect on Rcn1 expression in shoots or roots was seen when the roots were treated with auxins. Phenotypic analyses of rcn1 and tillering dwarf 3 (d3) double mutants at the seedling stage clarified that Rcn1 works independently of D3 in the branching inhibitor pathway. * Rcn1 is the first functionally defined plant ABCG protein gene that controls shoot branching and could thus be significant in future breeding for high-yielding rice.

Polar targeting and endocytic recycling in auxin-dependent plant development

Plant development is characterized by a profound phenotypic plasticity that often involves redefining of the developmental fate and polarity of cells within differentiated tissues. The plant hormone auxin and its directional intercellular transport play a major role in these processes because they provide positional information and link cell polarity with tissue patterning. This plant-specific mechanism of transport-dependent auxin gradients depends on subcellular dynamics of auxin transport components, in particular on endocytic recycling and polar targeting. Recent insights into these cellular processes in plants have revealed important parallels to yeast and animal systems, including clathrin-dependent endocytosis, retromer function, and transcytosis, but have also emphasized unique features of plant cells such as diversity of polar targeting pathways; integration of environmental signals into subcellular trafficking; and the link between endocytosis, cell polarity, and cell fate specification. We review these advances and focus on the translation of the subcellular dynamics to the regulation of whole-plant development.

Analysis of the protein expression profiling during rice callus differentiation under different plant hormone conditions

Plant hormones function to coordinate plant growth and development. While the plant hormones, mainly auxin and cytokinin, are exogenously added to various plant tissue cultures, their effects on the organogenesis are apparent, but little is known concerning the molecular mechanisms by which they function in cultured cells. Rice, as a model plant in monocots, is also suitable to tissue culture studies. Here, we used four types of regeneration mediums with different relative concentrations of cytokinin and auxin for rice callus differentiation, the calli at different differentiation stages were collected for proteomic analysis. 2-dimensional electrophoresis revealed that 213 protein spots significantly differentially expressed during callus differentiation under different hormone conditions. By using mass spectrometry, 183 differentially expressed protein spots were identified to match 157 unique proteins. Most of these differential proteins were cellular/metabolic process-related proteins, whose different expression patterns may be correlated with the cytokinin and auxin regulation. Several hormone-related proteins were prominently featured in differentiated calli as compared with the initiated calli, such as alpha-amylase isoforms, mannose-binding rice lectin, putative dehydration stress-induced protein, cysteine endopeptidase and cystatin. All these results provide a novel insight into how the two plant hormones effect the callus differentiation in rice on the proteomic level.

Differential degradation of PIN2 auxin efflux carrier by retromer-dependent vacuolar targeting

All eukaryotic cells present at the cell surface a specific set of plasma membrane proteins that modulate responses to internal and external cues and whose activity is also regulated by protein degradation. We characterized the lytic vacuole-dependent degradation of membrane proteins in Arabidopsis thaliana by means of in vivo visualization of vacuolar targeting combined with quantitative protein analysis. We show that the vacuolar targeting pathway is used by multiple cargos including PIN-FORMED (PIN) efflux carriers for the phytohormone auxin. In vivo visualization of PIN2 vacuolar targeting revealed its differential degradation in response to environmental signals, such as gravity. In contrast to polar PIN delivery to the basal plasma membrane, which depends on the vesicle trafficking regulator ARF-GEF GNOM, PIN sorting to the lytic vacuolar pathway requires additional brefeldin A-sensitive ARF-GEF activity. Furthermore, we identified putative retromer components SORTING NEXIN1 (SNX1) and VACUOLAR PROTEIN SORTING29 (VPS29) as important factors in this pathway and propose that the retromer complex acts to retrieve PIN proteins from a late/pre-vacuolar compartment back to the recycling pathways. Our data suggest that ARF GEF- and retromer-dependent processes regulate PIN sorting to the vacuole in an antagonistic manner and illustrate instrumentalization of this mechanism for fine-tuning the auxin fluxes during gravitropic response.

Cell polarity signaling: focus on polar auxin transport

Polar auxin transport, which is required for the formation of auxin gradients and directional auxin flows that are critical for plant pattern formation, morphogenesis, and directional growth response to vectorial cues, is mediated by polarized sub-cellular distribution of PIN-FORMED Proteins (PINs, auxin efflux carriers), AUX1/AUX1-like proteins (auxin influx facilitators), and multidrug resistance P-glycoproteins (MDR/PGP). Polar localization of these proteins is controlled by both developmental and environmental cues. Recent studies have revealed cellular (endocytosis, transcytosis, and endosomal sorting and recycling) and molecular (PINOID kinase, protein phosphatase 2A) mechanisms underlying the polar distribution of these auxin transport proteins. Both TIR1-mediated auxin signaling and TIR1-independent auxin-mediated endocytosis have been shown to regulate polar PIN localization and auxin flow, implicating auxin as a self-organizing signal in directing polar transport and directional flows.

Cellular and molecular requirements for polar PIN targeting and transcytosis in plants

The polar, sub-cellular localization of PIN auxin efflux carriers determines the direction of intercellular auxin flow, thus defining the spatial aspect of auxin signalling. Dynamic, transcytosis-like relocalizations of PIN proteins occur in response to external and internal signals, integrating these signals into changes in auxin distribution. Here, we examine the cellular and molecular mechanisms of polar PIN delivery and transcytosis. The mechanisms of the ARF-GEF-dependent polar targeting and transcytosis are well conserved and show little variations among diverse Arabidopsis ecotypes consistent with their fundamental importance in regulating plant development. At the cellular level, we refine previous findings on the role of the actin cytoskeleton in apical and basal PIN targeting, and identify a previously unknown role for microtubules, specifically in basal targeting. PIN protein delivery to different sides of the cell is mediated by ARF-dependent trafficking with a previously unknown complex level of distinct ARF-GEF vesicle trafficking regulators. Our data suggest that alternative recruitment of PIN proteins by these distinct pathways can account for cell type- and cargo-specific aspects of polar targeting, as well as for polarity changes in response to different signals. The resulting dynamic PIN positioning to different sides of cells defines a three-dimensional pattern of auxin fluxes within plant tissues.

Generation of cell polarity in plants links endocytosis, auxin distribution and cell fate decisions

Dynamically polarized membrane proteins define different cell boundaries and have an important role in intercellular communication-a vital feature of multicellular development. Efflux carriers for the signalling molecule auxin from the PIN family are landmarks of cell polarity in plants and have a crucial involvement in auxin distribution-dependent development including embryo patterning, organogenesis and tropisms. Polar PIN localization determines the direction of intercellular auxin flow, yet the mechanisms generating PIN polarity remain unclear. Here we identify an endocytosis-dependent mechanism of PIN polarity generation and analyse its developmental implications. Real-time PIN tracking showed that after synthesis, PINs are initially delivered to the plasma membrane in a non-polar manner and their polarity is established by subsequent endocytic recycling. Interference with PIN endocytosis either by auxin or by manipulation of the Arabidopsis Rab5 GTPase pathway prevents PIN polarization. Failure of PIN polarization transiently alters asymmetric auxin distribution during embryogenesis and increases the local auxin response in apical embryo regions. This results in ectopic expression of auxin pathway-associated root-forming master regulators in embryonic leaves and promotes homeotic transformation of leaves to roots. Our results indicate a two-step mechanism for the generation of PIN polar localization and the essential role of endocytosis in this process. It also highlights the link between endocytosis-dependent polarity of individual cells and auxin distribution-dependent cell fate establishment for multicellular patterning.

Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development

The signalling molecule auxin controls plant morphogenesis via its activity gradients, which are produced by intercellular auxin transport. Cellular auxin efflux is the rate-limiting step in this process and depends on PIN and phosphoglycoprotein (PGP) auxin transporters. Mutual roles for these proteins in auxin transport are unclear, as is the significance of their interactions for plant development. Here, we have analysed the importance of the functional interaction between PIN- and PGP-dependent auxin transport in development. We show by analysis of inducible overexpression lines that PINs and PGPs define distinct auxin transport mechanisms: both mediate auxin efflux but they play diverse developmental roles. Components of both systems are expressed during embryogenesis, organogenesis and tropisms, and they interact genetically in both synergistic and antagonistic fashions. A concerted action of PIN- and PGP-dependent efflux systems is required for asymmetric auxin distribution during these processes. We propose a model in which PGP-mediated efflux controls auxin levels in auxin channel-forming cells and, thus, auxin availability for PIN-dependent vectorial auxin movement.

Transcriptional networks in root cell fate specification

Cell fate in the Arabidopsis root is determined by positional information mediated by plant hormones and interpreted by transcriptional networks. In this review, we summarize recent advances in our understanding of the regulatory networks that control cell fate within the root meristem, and in the interplay of these networks with phytohormones. Recent work describing the importance of chromatin organization in tissue patterning is also highlighted. A new, high resolution root expression map detailing the transciptome of nearly all cell types in the Arabidopsis root across developmental timepoints will provide a framework for understanding these networks.

ARF GEF-dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis

Cell polarity manifested by the polar cargo delivery to different plasma-membrane domains is a fundamental feature of multicellular organisms. Pathways for polar delivery have been identified in animals; prominent among them is transcytosis, which involves cargo movement between different sides of the cell [1]. PIN transporters are prominent polar cargoes in plants, whose polar subcellular localization determines the directional flow of the signaling molecule auxin [2, 3]. In this study, we address the cellular mechanisms of PIN polar targeting and dynamic polarity changes. We show that apical and basal PIN targeting pathways are interconnected but molecularly distinct by means of ARF GEF vesicle-trafficking regulators. Pharmacological or genetic interference with the Arabidopsis ARF GEF GNOM leads specifically to apicalization of basal cargoes such as PIN1. We visualize the translocation of PIN proteins between the opposite sides of polarized cells in vivo and show that this PIN transcytosis occurs by endocytic recycling and alternative recruitment of the same cargo molecules by apical and basal targeting machineries. Our data suggest that an ARF GEF-dependent transcytosis-like mechanism is operational in plants and provides a plausible mechanism to trigger changes in PIN polarity and hence auxin fluxes during embryogenesis and organogenesis.

Auxin influx carriers stabilize phyllotactic patterning

One of the most striking features of plant architecture is the regular arrangement of leaves and flowers around the stem, known as phyllotaxis. Peaks in concentration of the plant hormone auxin, generated by the polar localization of the PIN1 auxin efflux carrier, provide the instructive signal for primordium initiation. This mechanism generates the spacing between neighboring primordia, which results in regular phyllotaxis. Studies of the role of auxin transport in phyllotactic patterning have focused on PIN1-mediated efflux. Recent computer simulations indicate an additional role for transporter-mediated auxin uptake. Mutations in the AUX1 auxin influx carrier have not, however, been reported to cause an aerial phenotype. Here, we study the role of AUX1 and its paralogs LAX1, LAX2, and LAX3. Analysis of the quadruple mutant reveals irregular divergence angles between successive primordia. A highly unusual aspect of the phenotype is the occurrence of clusters of primordia, in violation of classical theory. At the molecular level, the sharp peaks in auxin levels and coordinated PIN polarization are reduced or lost. In addition, the increased penetrance of the phenotype under short-day conditions suggests that the AUX LAX transporters act to buffer the PIN-mediated patterning mechanism against environmental or developmental influences.

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.

Effects of conditional IPT-dependent cytokinin overproduction on root architecture of Arabidopsis seedlings

Cytokinin (CK) has been known to inhibit primary root elongation and suggested to act as an auxin antagonist in the regulation of lateral root (LR) formation. While the role of auxin in root development has been thoroughly studied, the detailed and overall description of CK effects on root system morphology, particularly that of developing lateral root primordia (LRPs), and hence its role in organogenesis is still in progress. Here we examine the effects of conditional endogenous CK overproduction on root architecture and consider its temporal aspect during the early development of Arabidopsis thaliana. We employed the pOp/LhGR system to induce ectopic ipt overexpression with a glucocorticoid dexamethasone at designated developmental points. The transient CaMV 35S>GR>ipt transactivation greatly enhanced levels of biologically active CKs of zeatin (Z)-type and identified a distinct developmental interval during which primary root elongation is susceptible to increases in endogenous CK production. Long-term CK overproduction inhibited primary root elongation by reducing quantitative parameters of primary root meristem, disturbed a characteristic graded distribution pattern of auxin response in LRPs and impaired their development. Our findings indicate the impact of perturbed endogenous CK on the regulation of asymmetric auxin distribution during LRP development and imply that there is cross-talk between auxin and CK during organogenesis in A. thaliana.

An AGAMOUS-related MADS-box gene, XAL1 (AGL12), regulates root meristem cell proliferation and flowering transition in Arabidopsis

MADS-box genes are key components of the networks that control the transition to flowering and flower development, but their role in vegetative development is poorly understood. This article shows that the sister gene of the AGAMOUS (AG) clade, AGL12, has an important role in root development as well as in flowering transition. We isolated three mutant alleles for AGL12, which is renamed here as XAANTAL1 (XAL1): Two alleles, xal1-1 and xal1-2, are in Columbia ecotype and xal1-3 is in Landsberg erecta ecotype. All alleles have a short-root phenotype with a smaller meristem, lower rate of cell production, and abnormal root apical meristem organization. Interestingly, we also encountered a significantly longer cell cycle in the strongest xal1 alleles with respect to wild-type plants. Expression analyses confirmed the presence of XAL1 transcripts in roots, particularly in the phloem. Moreover, XAL1beta-glucuronidase expression was specifically up-regulated by auxins in this tissue. In addition, mRNA in situ hybridization showed that XAL1 transcripts were also found in leaves and floral meristems of wild-type plants. This expression correlates with the late-flowering phenotypes of the xal1 mutants grown under long days. Transcript expression analysis suggests that XAL1 is an upstream regulator of SOC, FLOWERING LOCUS T, and LFY. We propose that XAL1 may have similar roles in both root and aerial meristems that could explain the xal1 late-flowering phenotype.

Modeling of branching patterns in plants

A major determinant of plant architecture is the arrangement of branches around the stem, known as phyllotaxis. However, the specific form of branching conditions is not known. Here we discuss this question and suggest a branching model which seems to be in agreement with biological observations.Recently, a number of models connected with the genetic network or molecular biology regulation of the processes of pattern formation appeared. Most of these models consider the plant hormone, auxin, transport and distribution in the apical meristem as the main factors for pattern formation and phyllotaxis. However, all these models do not take into consideration the whole plant morphogenesis, concentrating on the events in the shoot or root apex. On the other hand, other approaches for modeling phyllotaxis, where the whole plant is considered, usually are mostly phenomenological, and due to it, do not describe the details of plant growth and branching mechanism. In this work, we develop a mathematical model and study pattern formation of the whole, though simplified, plant organism where the main physiological factors of plant growth and development are taken into consideration. We model a growing plant as a system of intervals, which we will consider as branches. We assume that the number and location of the branches are not given a priori, but appear and grow according to certain rules, elucidated by the application of mathematical modeling. Four variables are included in our model: concentrations of the plant hormones auxin and cytokinin, proliferation and growth factor, and nutrients-we observe a wide variety of plant forms and study more specifically the involvement of each variable in the branching process. Analysis of the numerical simulations shows that the process of pattern formation in plants depends on the interaction of all these variables. While concentrations of auxin and cytokinin determine the appearance of a new bud, its growth is determined by the concentrations of nutrients and proliferation factors. Possible mechanisms of apical domination in the frame of our model are discussed.

Cortical microtubule arrays in the Arabidopsis seedling

Advances in live-cell imaging technology have provided an unprecedented look at the dynamic behaviors of the plant microtubule cytoskeleton. Recent studies revisit the classic question of how plants create cell shape through the patterned construction of the cell wall. Visualization of the cellulose synthase complex traveling in the plasma membrane has brought a watershed of new information about cellulose deposition. Observation of the cellulose synthase complex tracking precisely over the underlying cortical microtubules has provided clear evidence that the microtubule array pattern serves as a spatial template for cellulose microfibril extrusion. Understanding how the microtubules are organized into specific array patterns remains a challenge, though new ideas are arising from genetic and cell biological studies. Long-term time-lapse observations of the microtubule arrays in light-grown hypocotyl cells have revealed a striking process of microtubule patterning possibly linked to the creation of polylamellate cell walls.

Dichotomization of mycorrhizal and NPA-treated short roots in Pinus sylvestris

Conifers like Scots pine (Pinus sylvestris) have a complicated root system consisting of morphologically and anatomically different root types, of which the short roots have a very limited ability to elongate. Short roots have an important role in nature since they are able to establish ectomycorrhizal symbiosis, in which the growth of fungal mycelium between the epidermal cells and in the intercellular space between cortical cells leads to formation of dichotomous short roots, which may, through further splitting of the meristem, form coralloid root structures. Dichotomous short roots have been suggested to result from changes in either auxin or ethylene concentrations due to the fungal growth inside the root. NPA, the inhibitor of polar auxin transport, enhances the dichotomization of P. sylvestris short root tips similarly to the fungal growth in the root, thus confirming that auxin plays a role in short root morphogenesis. Ethylene is also known to have an important role in the regulation of root morphogenesis. In future the research dealing with the root system and ectomycorrhiza development in P. sylvestris must take into account that both auxin and ethylene are involved and that there is no contradiction in obtaining the same phenotype with both hormones. The expression analysis of PIN proteins, auxin efflux carriers, could give valuable information about the role of auxin transport in regulating the root growth and morphogenesis of coniferous root system and mycorrhiza.

Light plays an essential role in intracellular distribution of auxin efflux carrier PIN2 in Arabidopsis thaliana

Background

Light plays a key role in multiple plant developmental processes. It has been shown that root development is modulated by shoot-localized light signaling and requires shoot-derived transport of the plant hormone, auxin. However, the mechanism by which light regulates root development is not largely understood. In plants, the endogenous auxin, indole-3-acetic acid, is directionally transported by plasma-membrane (PM)-localized auxin influx and efflux carriers in transporting cells. Remarkably, the auxin efflux carrier PIN proteins exhibit asymmetric PM localization, determining the polarity of auxin transport. Similar to PM-resident receptors and transporters in animal and yeast cells, PIN proteins undergo constitutive cycling between the PM and endosomal compartments. Auxin plays multiple roles in PIN protein intracellular trafficking, inhibiting PIN2 endocytosis at some concentrations and promoting PIN2 degradation at others. However, how PIN proteins are turned over in plant cells is yet to be addressed.

Methodology and Principle Findings

Using laser confocal scanning microscopy, and physiological and molecular genetic approaches, here, we show that in dark-grown seedlings, the PM localization of auxin efflux carrier PIN2 was largely reduced, and, in addition, PIN2 signal was detected in vacuolar compartments. This is in contrast to light-grown seedlings where PIN2 was predominantly PM-localized. In light-grown plants after shift to dark or to continuous red or far-red light, PIN2 also accumulated in vacuolar compartments. We show that PIN2 vacuolar targeting was derived from the PM via endocytic trafficking and inhibited by HY5-dependent light signaling. In addition, the ubiquitin 26S proteasome is involved in the process, since its inhibition by mutations in COP9 and a proteasome inhibitor MG132 impaired the process.

Conclusions and Significance

Collectively, our data indicate that light plays an essential role in PIN2 intracellular trafficking, promoting PM-localization in the presence of light and, on the other hand, vacuolar targeting for protein degradation in the absence of light. Based on these results, we postulate that light regulation of root development is mediated at least in part by changes in the intracellular distribution of auxin efflux carriers, PIN proteins, in response to the light environment.

Oxidative stress and formation and maintenance of root stem cells

The hypothesis of L. Feldman and his coworkers, according to which a more oxidizing environment in the cells of root quiescent center results from high activity of ascorbate oxidase activated by indoleacetic acid (IAA) accumulating in these cells, is discussed. The high activity of ascorbate oxidase is responsible for lowered concentrations of the reduced form of ascorbic acid and glutathione and high content of reactive oxygen species in quiescent center cells. The oxidative stress represses proliferation of the cells. Inhibitors of IAA transport attenuate the oxidative stress, thus suggesting a role of IAA as an activator of ascorbate oxidase. Interestingly, the high concentration of IAA in dividing cap cells adjacent to the quiescent center cells did not cause retardation of cell proliferation and oxidative state in these cells.

Auxin: the looping star in plant development

The phytohormone auxin is a key factor in plant growth and development. Forward and reverse genetic strategies have identified important molecular components in auxin perception, signaling, and transport. These advances resulted in the identification of some of the underlying regulatory mechanisms as well as the emergence of functional frameworks for auxin action. This review focuses on the feedback loops that form an integrative part of these regulatory mechanisms.

Arabidopsis embryogenesis

Embryogenesis in higher plants consists of two major phases, morphogenesis and maturation. Morphogenesis involves the establishment of the embryo's body plan, whereas maturation involves cell expansion and accumulation of storage macromolecules to prepare for desiccation, germination and early seedling growth. Arabidopsis mutants showing defects in embryogenesis have provided information for understanding the events that govern embryo formation through molecular, genetic and biochemical analyses. Thus, many of the processes that underlie embryogenesis are beginning to be understood. In this chapter, we focus on genes that play key roles in the morphogenesis phase of Arabidopsis embryogenesis.

Embryonic patterning in Arabidopsis thaliana

Early embryonic development in the flowering plant Arabidopsis thaliana follows a predictable sequence of cell divisions. Anatomical hallmarks and the expression of marker genes in dynamic patterns indicate that new cell fates are established with virtually every round of mitosis. Although some of the factors regulating these early patterning events have been identified, the overall process remains relatively poorly understood. Starting at the globular stage, when the embryo has approximately 100 cells, the organization of development appears to be taken over by programs that regulate postembryonic patterning throughout the life cycle.

Auxin transport is sufficient to generate a maximum and gradient guiding root growth

The plant growth regulator auxin controls cell identity, cell division and cell expansion. Auxin efflux facilitators (PINs) are associated with auxin maxima in distal regions of both shoots and roots. Here we model diffusion and PIN-facilitated auxin transport in and across cells within a structured root layout. In our model, the stable accumulation of auxin in a distal maximum emerges from the auxin flux pattern. We have experimentally tested model predictions of robustness and self-organization. Our model explains pattern formation and morphogenesis at timescales from seconds to weeks, and can be understood by conceptualizing the root as an 'auxin capacitor'. A robust auxin gradient associated with the maximum, in combination with separable roles of auxin in cell division and cell expansion, is able to explain the formation, maintenance and growth of sharply bounded meristematic and elongation zones. Directional permeability and diffusion can fully account for stable auxin maxima and gradients that can instruct morphogenesis.

Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux

In plants, cell polarity and tissue patterning are connected by intercellular flow of the phytohormone auxin, whose directional signaling depends on polar subcellular localization of PIN auxin transport proteins. The mechanism of polar targeting of PINs or other cargos in plants is largely unidentified, with the PINOID kinase being the only known molecular component. Here, we identify PP2A phosphatase as an important regulator of PIN apical-basal targeting and auxin distribution. Genetic analysis, localization, and phosphorylation studies demonstrate that PP2A and PINOID both partially colocalize with PINs and act antagonistically on the phosphorylation state of their central hydrophilic loop, hence mediating PIN apical-basal polar targeting. Thus, in plants, polar sorting by the reversible phosphorylation of cargos allows for their conditional delivery to specific intracellular destinations. In the case of PIN proteins, this mechanism enables switches in the direction of intercellular auxin fluxes, which mediate differential growth, tissue patterning, and organogenesis.

In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples

High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is approximately 7 d, depending on the tissue used.

Regulation of the Arabidopsis root vascular initial population by LONESOME HIGHWAY

Complex organisms consist of a multitude of cell types arranged in a precise spatial relation to each other. Arabidopsis roots generally exhibit radial tissue organization; however, within a tissue layer, cells are not identical. Specific vascular cell types are arranged in diametrically opposed longitudinal files that maximize the distance between them and create a bilaterally symmetric (diarch) root. Mutations in the LONESOME HIGHWAY (LHW) gene eliminate bilateral symmetry and reduce the number of cells in the center of the root, resulting in roots with only single xylem and phloem poles. LHW does not appear to be required for the creation of any specific cell type, but coordinately controls the number of all vascular cell types by regulating the size of the pool of cells from which they arise. We cloned LHW and found that it encodes a protein with weak sequence similarity to basic helix-loop-helix (bHLH)-domain proteins. LHW is a transcriptional activator in vitro. In plants, LHW is nuclear-localized and is expressed in the root meristems, where we hypothesize it acts independently of other known root-patterning genes to promote the production of stele cells, but might also indirectly feed into established regulatory networks for the maintenance of the root meristem.

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.

Arabidopsis thaliana GH3.9 influences primary root growth

Auxins regulate a complex signal transduction network to direct plant development. Auxin-responsive genes fit into three major classes: the so-called auxin/indole-3-acetic acid (Aux/IAA), the GH3, and the small auxin-up RNA (SAUR) gene families. The 20-member Arabidopsis thaliana GH3 gene family has been subdivided into three groups. In vitro studies have shown that most Group II members function as IAA-amido synthetases to conjugate amino acids to the plant hormone auxin. Here we report the role of a previously uncharacterized GH3 gene family member, GH3.9, in root growth. Unlike most other Group II family members, GH3.9 expression was repressed by low concentrations of exogenous IAA in seedlings. Transgenic plants harboring a GH3.9 promoter::reporter gene construct indicate that GH3.9 is expressed in the root-hypocotyl junction, leaves and the shoot apical meristem of young seedlings, in mature embryos, and in the root vascular tissue. Expression was also observed in lateral root tips when seedlings were treated with exogenous IAA. Inverse PCR was used to identify an activation tagged T-DNA insertion in chromosome 2 near the 5'UTR region of At2g47750 (GH3.9). Plants homozygous for the T-DNA insertion (gh3.9-1 mutants) had reduced GH3.9 expression, no obvious effects on apical dominance or leaf morphology, greater primary root length, and increased sensitivity to indole-3-acetic acid (IAA)-mediated root growth inhibition. Additional T-DNA insertion alleles and transgenic plants with reduced GH3.9 transcript levels due to RNA-interference (RNAi) also showed these same phenotypes. Our results provide new information on the function of GH3.9 in roots where it is likely to control auxin activity through amino acid conjugation.

Arabidopsis inositol polyphosphate 6-/3-kinase (AtIpk2beta) is involved in axillary shoot branching via auxin signaling

The Arabidopsis (Arabidopsis thaliana) inositol polyphosphate 6-/3-kinase gene (AtIpk2beta) is known to participate in inositol phosphate metabolism. However, little is known about its physiological functions in higher plants. Here, we report that AtIpk2beta regulates Arabidopsis axillary shoot branching. By overexpressing AtIpk2beta in the wild type and mutants, we found that overexpression of AtIpk2beta leads to more axillary shoot branches. Further analysis of AtIpk2beta overexpression lines showed that axillary meristem forms earlier and the bud outgrowth rate is also accelerated, resulting in more axillary shoot branches. The AtIpk2beta promoter/beta-glucuronidase (GUS) fusion (AtIpk2betaGUS) expression pattern is similar to that of the auxin reporter DR5GUS. Moreover, AtIpk2beta can be induced in response to exogenous indole-3-acetic acid (IAA) treatments. In addition, AtIpk2beta overexpression plants exhibit IAA-related phenotypes and are more resistant to exogenous IAA treatments. Further analysis employing reverse transcription-polymerase chain reaction shows that some genes, including auxin-biosynthesis (CYP83B1), auxin-transport (PIN4), and auxin-mediated branching genes (MAX4 and SPS), are regulated by AtIpk2beta. Taken together, our data provide insights into a role for AtIpk2beta in axillary shoot branching through the auxin signaling pathway.

ATM-mediated transcriptional and developmental responses to gamma-rays in Arabidopsis

ATM (Ataxia Telangiectasia Mutated) is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT). To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT) and homozygous ATM-deficient mutants challenged with a dose of γ-rays (IR) that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of prolonged S-G2 phases that coincided with cell proliferation delay, or an anticipated subsequent auxin increase, accelerated cell differentiation or death, was used to link IR-regulated hallmark functions and tissue phenotypes after IR. The transcription burst was almost exclusively AtATM-dependent or weakly AtATR-dependent, and followed two major trends of expression in atm: (i)-loss or severe attenuation and delay, and (ii)-inverse and/or stochastic, as well as specific, enabling one to distinguish IR/ATM pathway constituents. Our data provide a large resource for studies on the interaction between plant checkpoints of the cell cycle, development, hormone response, and DNA repair functions, because IR-induced transcriptional changes partially overlap with the response to environmental stress. Putative connections of ATM to stem cell maintenance pathways after IR are also discussed.

Molecular and cellular aspects of auxin-transport-mediated development

The plant hormone auxin is frequently observed to be asymmetrically distributed across adjacent cells during crucial stages of growth and development. These auxin gradients depend on polar transport and regulate a wide variety of processes, including embryogenesis, organogenesis, vascular tissue differentiation, root meristem maintenance and tropic growth. Auxin can mediate such a perplexing array of developmental processes by acting as a general trigger for the change in developmental program in cells where it accumulates and by providing vectorial information to the tissues by its polar intercellular flow. In recent years, a wealth of molecular data on the mechanism of auxin transport and its regulation has been generated, providing significant insights into the action of this versatile coordinative signal.

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.

Characterization of OsPID, the rice ortholog of PINOID, and its possible involvement in the control of polar auxin transport

PINOID, a serine threonine protein kinase in Arabidopsis, controls auxin distribution through a positive control of subcellular localization of PIN auxin efflux carriers. Compared with the rapid progress in understanding mechanisms of auxin action in dicot species, little is known about auxin action in monocot species. Here, we describe the identification and characterization of OsPID, the PINOID ortholog of rice. Phylogenetic analysis showed that the rice genome contains a single PID ortholog, OsPID. Constitutive overexpression of OsPID caused a variety of abnormalities, such as delay of adventitious root development, curled growth of shoots and agravitropism. Abnormalities observed in the plants that overexpress OsPID could be phenocopied by treatment with an inhibitor of active polar transport of auxin, indicating that OsPID could be involved in the control of polar auxin transport in rice. Analysis of OsPID mRNA distribution showed a complex pattern in shoot meristems, indicating that it probably plays a role in the pattern formation and organogenesis in the rice shoot.

Transcriptional profiling of the Arabidopsis embryo

We have used laser-capture microdissection to isolate RNA from discrete tissues of globular, heart, and torpedo stage embryos of Arabidopsis (Arabidopsis thaliana). This was amplified and analyzed by DNA microarray using the Affymetrix ATH1 GeneChip, representing approximately 22,800 Arabidopsis genes. Cluster analysis showed that spatial differences in gene expression were less significant than temporal differences. Time course analysis reveals the dynamics and complexity of gene expression in both apical and basal domains of the developing embryo, with several classes of synexpressed genes identifiable. The transition from globular to heart stage is associated in particular with an up-regulation of genes involved in cell cycle control, transcriptional regulation, and energetics and metabolism. The transition from heart to torpedo stage is associated with a repression of cell cycle genes and an up-regulation of genes encoding storage proteins, and pathways of cell growth, energy, and metabolism. The torpedo stage embryo shows strong functional differentiation in the root and cotyledon, as inferred from the classes of genes expressed in these tissues. The time course of expression of the essential EMBRYO-DEFECTIVE genes shows that most are expressed at unchanging levels across all stages of embryogenesis. We show how identified genes can be used to generate cell type-specific markers and promoter activities for future application in cell biology.

Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice

Most plant cells retain the capacity to differentiate into all the other cell and organ types that constitute a plant. However, genome-wide transcriptional activities underlying the process of cell differentiation are poorly understood, especially in monocot plants. Here we used a rice (Oryza sativa) cell culture system to generate somatic embryos, which were further induced into shoots and roots. The global transcriptional reorganization during the development of somatic embryos, shoots, and roots from cultured cells was studied using a rice whole genome microarray and verified by RNA blotting analysis of representative genes. Overall, only 1-3% of expressed genes were differentially regulated during each organogenesis process at the examined time point. Also metabolic pathways were minimally regulated. Thus the genes that dictating organ formation should be relatively small in number. Comparison of these three transcriptomes revealed little overlap during these three organogenesis processes. These results indicate that each organogenesis involves specific reorganization of genome expression.

KANADI and class III HD-Zip gene families regulate embryo patterning and modulate auxin flow during embryogenesis in Arabidopsis

Embryo patterning in Arabidopsis thaliana is highly affected when KANADI or Class III HD-Zip genes are compromised. Triple loss-of-function kan1 kan2 kan4 embryos exhibit striking defects in the peripheral-central axis, developing lateral leaf-like organs from the hypocotyls, whereas loss of Class III HD-Zip gene activity results in a loss of bilateral symmetry. Loss of KANADI activity in a Class III HD-Zip mutant background mitigates the defects in bilateral symmetry, implying that the two gene families act antagonistically during embryonic pattern formation. Dynamic patterns of auxin concentration and flux contribute to embryo patterning. Polar cellular distribution of PIN-FORMED1 (PIN1) mediates auxin flow throughout embryogenesis and is required for establishment of the apical-basal axis and bilateral symmetry. Defects in the pattern of PIN1 expression are evident when members of either the KANADI or Class III HD-Zip gene families are compromised. Abnormal expression patterns of PIN1 in KANADI or Class III HD-Zip multiple mutants and the phenotype of plants in which members of both gene families are mutated suggest that pattern formation along the central-peripheral axis results from interplay between auxin and the KANADI and Class III HD-Zip transcription factors, whose defined spatial and temporal expression patterns may also be influenced by auxin.

Interactions of PIN and PGP auxin transport mechanisms

Polarized transport of the plant hormone auxin influences multiple growth processes in plants and is regulated by plasma-membrane-localized efflux and uptake carriers. The PGP (P-glycoprotein) ABC transporters (ATP-binding-cassette transporters), PIN (pin-formed) subfamily of major facilitator proteins and members of AUX/LAX families have been shown to independently transport auxin both in planta and in heterologous systems. However, PIN- and PGP-mediated transport in heterologous systems exhibits decreased substrate specificity and inhibitor-sensitivity compared with what is seen in plants and plant cells. To determine whether PIN–PGP interactions enhance transport specificity, we analysed interactions of the representative auxin-transporting PGPs with PIN1 and AUX1 in planta and in heterologous systems. Here, we provide evidence that PINs and PGPs interact and function both independently and co-ordinately to control polar auxin transport and impart transport specificity and directionality. These interactions take place in protein complexes stabilized by PGPs in detergent-resistant microdomains.