The march of the PINs: developmental plasticity by dynamic polar targeting in plant cells

Modelling auxin efflux carrier phosphorylation and localization

Regulation of the activity and localization of PIN-FORMED (PIN) membrane proteins, which facilitate efflux of the plant hormone auxin from cells, is important for plants to respond to environmental stimuli and to develop new organs. The protein kinase PINOID (PID) is involved in regulating PIN phosphorylation, and this is thought to affect PIN localization by biasing recycling towards shootwards (apical) (rather than rootwards (basal)) membrane domains. PID has been observed to undergo transient internalization following auxin treatment, and it has been suggested that this may be a result of calcium-dependent sequestration of PID by the calcium-binding protein TOUCH3 (TCH3). We present a mathematical formulation of these processes and examine the resulting steady-state and time-dependent behaviours in response to transient increases in cytosolic calcium. We further combine this model with one for the recycling of PINs in polarized cells and also examine its behaviour. The results provide insight into the behaviour observed experimentally and provide the basis for subsequent studies of the tissue-level implications of these subcellular processes for phenomena such as gravitropism.

Endocytic trafficking towards the vacuole plays a key role in the auxin receptor SCF(TIR)-independent mechanism of lateral root formation in A. thaliana

Plants' developmental plasticity plays a pivotal role in responding to environmental conditions. One of the most plastic plant organs is the root system. Different environmental stimuli such as nutrients and water deficiency may induce lateral root formation to compensate for a low level of water and/or nutrients. It has been shown that the hormone auxin tunes lateral root development and components for its signaling pathway have been identified. Using chemical biology, we discovered an Arabidopsis thaliana lateral root formation mechanism that is independent of the auxin receptor SCF(TIR). The bioactive compound Sortin2 increased lateral root occurrence by acting upstream from the morphological marker of lateral root primordium formation, the mitotic activity. The compound did not display auxin activity. At the cellular level, Sortin2 accelerated endosomal trafficking, resulting in increased trafficking of plasma membrane recycling proteins to the vacuole. Sortin2 affected Late endosome/PVC/MVB trafficking and morphology. Combining Sortin2 with well-known drugs showed that endocytic trafficking of Late E/PVC/MVB towards the vacuole is pivotal for Sortin2-induced SCF(TIR)-independent lateral root initiation. Our results revealed a distinctive role for endosomal trafficking in the promotion of lateral root formation via a process that does not rely on the auxin receptor complex SCF(TIR).

The phosphorylation code is implicated in cell type-specific trafficking of PIN-FORMEDs

The subcellular polarity of PIN-FORMEDs (PINs) is critical for directional cell-to-cell transport of auxin. Phosphorylation of PIN proteins plays an important role in generating and maintaining specific PIN polarity. In a recent study, we have shown that phosphorylation in certain conserved residues of the PIN3 hydrophilic loop (HL) modulates its subcellular localization and polarity in a cell type-specific manner in different root tissues. Here, we additionally show that the phosphorylation code of PIN3-HL is operational for the determination of PIN3 polarity in the Arabidopsis guard cell and is deciphered in a differential way even in a single tobacco cell for the intracellular trafficking of PIN3. On the other hand, PIN3 localization often remained unaltered in certain cell types irrespective of its phosphorylation status. These findings, together with previous reports, indicate that the phosphorylation code of the PIN-HL along with cell type-specific factors, kinases, and developmental/environmental cues is instrumental for the PIN trafficking to different subcellular compartments as well as different plasma membrane domains.

Systems analysis of shoot apical meristem growth and development: integrating hormonal and mechanical signaling

The shoot apical meristem (SAM) is a small population of stem cells that continuously generates organs and tissues. This review covers our current understanding of organ initiation by the SAM in Arabidopsis thaliana. Meristem function and maintenance involves two major hormones, cytokinins and auxins. Cytokinins appear to play a major role in meristem maintenance and in controlling meristematic properties, such as cell proliferation. Self-organizing transport processes, which are still only partially understood, lead to the patterned accumulation of auxin at particular positions, where organs will grow out. A major downstream target of auxin-mediated growth regulation is the cell wall, which is a determinant for both growth rates and growth distribution, but feedbacks with metabolism and the synthetic capacity of the cytoplasm are crucial as well. Recent work has also pointed at a potential role of mechanical signals in growth coordination, but the precise mechanisms at work remain to be elucidated.

A small molecule inhibitor partitions two distinct pathways for trafficking of tonoplast intrinsic proteins in Arabidopsis

Tonoplast intrinsic proteins (TIPs) facilitate the membrane transport of water and other small molecules across the plant vacuolar membrane, and members of this family are expressed in specific developmental stages and tissue types. Delivery of TIP proteins to the tonoplast is thought to occur by vesicle–mediated traffic from the endoplasmic reticulum to the vacuole, and at least two pathways have been proposed, one that is Golgi-dependent and another that is Golgi-independent. However, the mechanisms for trafficking of vacuolar membrane proteins to the tonoplast remain poorly understood. Here we describe a chemical genetic approach to unravel the mechanisms of TIP protein targeting to the vacuole in Arabidopsis seedlings. We show that members of the TIP family are targeted to the vacuole via at least two distinct pathways, and we characterize the bioactivity of a novel inhibitor that can differentiate between them. We demonstrate that, unlike for TIP1;1, trafficking of markers for TIP3;1 and TIP2;1 is insensitive to Brefeldin A in Arabidopsis hypocotyls. Using a chemical inhibitor that may target this BFA-insensitive pathway for membrane proteins, we show that inhibition of this pathway results in impaired root hair growth and enhanced vacuolar targeting of the auxin efflux carrier PIN2 in the dark. Our results indicate that the vacuolar targeting of PIN2 and the BFA-insensitive pathway for tonoplast proteins may be mediated in part by common mechanisms.

The endoplasmic reticulum localized PIN8 is a pollen-specific auxin carrier involved in intracellular auxin homeostasis

The plant hormone auxin is a mobile signal which affects nuclear transcription by regulating the stability of auxin/indole-3-acetic acid (IAA) repressor proteins. Auxin is transported polarly from cell to cell by auxin efflux proteins of the PIN family, but it is not as yet clear how auxin levels are regulated within cells and how access of auxin to the nucleus may be controlled. The Arabidopsis genome contains eight PINs, encoding proteins with a similar membrane topology. While five of the PINs are typically targeted polarly to the plasma membranes, the smallest members of the family, PIN5 and PIN8, seem to be located not at the plasma membrane but in endomembranes. Here we demonstrate by electron microscopy analysis that PIN8, which is specifically expressed in pollen, resides in the endoplasmic reticulum and that it remains internally localized during pollen tube growth. Transgenic Arabidopsis and tobacco plants were generated overexpressing or ectopically expressing functional PIN8, and its role in control of auxin homeostasis was studied. PIN8 ectopic expression resulted in strong auxin-related phenotypes. The severity of phenotypes depended on PIN8 protein levels, suggesting a rate-limiting activity for PIN8. The observed phenotypes correlated with elevated levels of free IAA and ester-conjugated IAA. Activation of the auxin-regulated synthetic DR5 promoter and of auxin response genes was strongly repressed in seedlings overexpressing PIN8 when exposed to 1-naphthalene acetic acid. Thus, our data show a functional role for endoplasmic reticulum-localized PIN8 and suggest a mechanism whereby PIN8 controls auxin thresholds and access of auxin to the nucleus, thereby regulating auxin-dependent transcriptional activity.

Functional identification of the phosphorylation sites of Arabidopsis PIN-FORMED3 for its subcellular localization and biological role

Directional cell-to-cell movement of auxin is mediated by asymmetrically localized PIN-FORMED (PIN) auxin efflux transporters. The polar localization of PINs has been reported to be modulated by phosphorylation. In this study, the function of the phosphorylation sites of the PIN3 central hydrophilic loop (HL) was characterized. The phosphorylation sites were located in two conserved neighboring motifs, RKSNASRRSF(/L) and TPRPSNL, where the former played a more decisive role than the latter. Mutations of these phosphorylatable residues disrupted in planta phosphorylation of PIN3 and its subcellular trafficking, and caused defects in PIN3-mediated biological processes such as auxin efflux activity, auxin maxima formation, root growth, and root gravitropism. Because the defective intracellular trafficking behaviors of phospho-mutated PIN3 varied according to cell type, phosphorylation codes in PIN3-HL are likely to operate in a cell-type-specific manner.

Small signaling peptides in Arabidopsis development: how cells communicate over a short distance

To sustain plants' postembryonic growth and development in a structure of cells fixed in cell walls, a tightly controlled short distance cell-cell communication is required. The focus on phytohormones, such as auxin, has historically overshadowed the importance of small peptide signals, but it is becoming clear that secreted peptide signals are important in cell-cell communication to coordinate and integrate cellular functions. However, of the more than 1000 potential secreted peptides, so far only very few have been functionally characterized or matched to a receptor. Here, we will describe our current knowledge on how small peptide signals can be identified, how they are modified and processed, which roles they play in Arabidopsis thaliana development, and through which receptors they act.

ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis

Auxin is a key coordinative signal required for many aspects of plant development and its levels are controlled by auxin metabolism and intercellular auxin transport. Here we find that a member of PIN auxin transporter family, PIN8 is expressed in male gametophyte of Arabidopsis thaliana and has a crucial role in pollen development and functionality. Ectopic expression in sporophytic tissues establishes a role of PIN8 in regulating auxin homoeostasis and metabolism. PIN8 co-localizes with PIN5 to the endoplasmic reticulum (ER) where it acts as an auxin transporter. Genetic analyses reveal an antagonistic action of PIN5 and PIN8 in the regulation of intracellular auxin homoeostasis and gametophyte as well as sporophyte development. Our results reveal a role of the auxin transport in male gametophyte development in which the distinct actions of ER-localized PIN transporters regulate cellular auxin homoeostasis and maintain the auxin levels optimal for pollen development and pollen tube growth.

Trying to make sense of retromer

Retromer is a cytosolic protein complex which binds to post-Golgi organelles involved in the trafficking of proteins to the lytic compartment of the cell. In non-plant organisms, retromer mediates the recycling of acid hydrolase receptors from early endosomal (EE) compartments. In plants, retromer components are required for the targeting of vacuolar storage proteins, and for the recycling of endocytosed PIN proteins. However, there are contradictory reports as to the localization of the sorting nexins and the core subunit of retromer. There is also uncertainty as to the identity of the organelles from which vacuolar sorting receptors (VSRs) and endocytosed plasma membrane (PM) proteins are recycled. In this review we try to resolve some of these conflicting observations.

Cellular auxin homeostasis: gatekeeping is housekeeping

The phytohormone auxin is essential for plant development and contributes to nearly every aspect of the plant life cycle. The spatio-temporal distribution of auxin depends on a complex interplay between auxin metabolism and cell-to-cell auxin transport. Auxin metabolism and transport are both crucial for plant development; however, it largely remains to be seen how these processes are integrated to ensure defined cellular auxin levels or even gradients within tissues or organs. In this review, we provide a glance at very diverse topics of auxin biology, such as biosynthesis, conjugation, oxidation, and transport of auxin. This broad, but certainly superficial, overview highlights the mutual importance of auxin metabolism and transport. Moreover, it allows pinpointing how auxin metabolism and transport get integrated to jointly regulate cellular auxin homeostasis. Even though these processes have been so far only separately studied, we assume that the phytohormonal crosstalk integrates and coordinates auxin metabolism and transport. Besides the integrative power of the global hormone signaling, we additionally introduce the hypothetical concept considering auxin transport components as gatekeepers for auxin responses.

The endodermis--development and differentiation of the plant's inner skin

Controlling external compound entrance is essential for plant survival. To set up an efficient and selective sorting of nutrients, free diffusion via the apoplast in vascular plants is blocked at the level of the endodermis. Although we have learned a lot about endodermal specification in the last years, information regarding its differentiation is still very limited. A differentiated endodermal cell can be defined by the presence of the "Casparian strip" (CS), a cell wall modification described first by Robert Caspary in 1865. While the anatomical description of CS in many vascular plants has been very detailed, we still lack molecular information about the establishment of the Casparian strips and their actual function in roots. The recent isolation of a novel protein family, the CASPs, that localizes precisely to a domain of the plasma membrane underneath the CS represents an excellent point of entry to explore CS function and formation. In addition, it has been shown that the endodermis contains transporters that are localized to either the central (stele-facing) or peripheral (soil-facing) plasma membranes. These features suggest that the endodermis functions as a polar plant epithelium.

The role of PIN auxin efflux carriers in polar auxin transport and accumulation and their effect on shaping maize development

In plants, proper seed development and the continuing post-embryonic organogenesis both require that different cell types are correctly differentiated in response to internal and external stimuli. Among internal stimuli, plant hormones and particularly auxin and its polar transport (PAT) have been shown to regulate a multitude of plant physiological processes during vegetative and reproductive development. Although our current auxin knowledge is almost based on the results from researches on the eudicot Arabidopsis thaliana, during the last few years, many studies tried to transfer this knowledge from model to crop species, maize in particular. Applications of auxin transport inhibitors, mutant characterization, and molecular and cell biology approaches, facilitated by the sequencing of the maize genome, allowed the identification of genes involved in auxin metabolism, signaling, and particularly in polar auxin transport. PIN auxin efflux carriers have been shown to play an essential role in regulating PAT during both seed and post-embryonic development in maize. In this review, we provide a summary of the recent findings on PIN-mediated polar auxin transport during maize development. Similarities and differences between maize and Arabidopsis are analyzed and discussed, also considering that their different plant architecture depends on the differentiation of structures whose development is controlled by auxins.

Polar auxin transport: an early invention

In higher plants, cell-to-cell polar auxin transport (PAT) of the phytohormone auxin, indole-3-acetic acid (IAA), generates maxima and minima that direct growth and development. Although IAA is present in all plant phyla, PAT has only been detected in land plants, the earliest being the Bryophytes. Charophyta, a group of freshwater green algae, are among the first multicellular algae with a land plant-like phenotype and are ancestors to land plants. IAA has been detected in members of Charophyta, but its developmental role and the occurrence of PAT are unknown. We show that naphthylphthalamic acid (NPA)-sensitive PAT occurs in internodal cells of Chara corallina. The relatively high velocity (at least 4-5 cm/h) of auxin transport through the giant (3-5 cm) Chara cells does not occur by simple diffusion and is not sensitive to a specific cytoplasmic streaming inhibitor. The results demonstrate that PAT evolved early in multicellular plant life. The giant Chara cells provide a unique new model system to study PAT, as Chara allows the combining of real-time measurements and mathematical modelling with molecular, developmental, cellular, and electrophysiological studies.

A PP6-type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis

The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation.

The evolution of reproductive structures in seed plants: a re-examination based on insights from developmental genetics

The study of developmental genetics is providing insights into how plant morphology can and does evolve, and into the fundamental nature of specific organs. This new understanding has the potential to revise significantly the way we think about seed plant evolution, especially with regard to reproductive structures. Here, we have sought to take a step in bridging the divide between genetic data and critical fields such as paleobotany and systematics. We discuss the evidence for several evolutionarily important interpretations, including the possibility that ovules represent meristematic axes with their own type of lateral determinate organs (integuments) and a model that considers carpels as analogs of complex leaves. In addition, we highlight the aspects of reproductive development that are likely to be highly labile and homoplastic, factors that have major implications for the understanding of seed plant relationships. Although these hypotheses may suggest that some long-standing interpretations are misleading, they also open up whole new avenues for comparative study and suggest concrete best practices for evolutionary analyses of development.

Modeling a cortical auxin maximum for nodulation: different signatures of potential strategies

Lateral organ formation from plant roots typically requires the de novo creation of a meristem, initiated at the location of a localized auxin maximum. Legume roots can form both root nodules and lateral roots. From the basic principles of auxin transport and metabolism only a few mechanisms can be inferred for increasing the local auxin concentration: increased influx, decreased efflux, and (increased) local production. Using computer simulations we investigate the different spatio-temporal patterns resulting from each of these mechanisms in the context of a root model of a generalized legume. We apply all mechanisms to the same group of preselected cells, dubbed the controlled area. We find that each mechanism leaves its own characteristic signature. Local production by itself can not create a strong auxin maximum. An increase of influx, as is observed in lateral root formation, can result in an auxin maximum that is spatially more confined than the controlled area. A decrease of efflux on the other hand leads to a broad maximum, which is more similar to what is observed for nodule primordia. With our prime interest in nodulation, we further investigate the dynamics following a decrease of efflux. We find that with a homogeneous change in the whole cortex, the first auxin accumulation is observed in the inner cortex. The steady state lateral location of this efflux reduced auxin maximum can be shifted by slight changes in the ratio of central to peripheral efflux carriers. We discuss the implications of this finding in the context of determinate and indeterminate nodules, which originate from different cortical positions. The patterns we have found are robust under disruption of the (artificial) tissue layout. The same patterns are therefore likely to occur in many other contexts.

Lysine63-linked ubiquitylation of PIN2 auxin carrier protein governs hormonally controlled adaptation of Arabidopsis root growth

Cross-talk between plant cells and their surroundings requires tight regulation of information exchange at the plasma membrane (PM), which involves dynamic adjustments of PM protein localization and turnover to modulate signal perception and solute transport at the interface between cells and their surroundings. In animals and fungi, turnover of PM proteins is controlled by reversible ubiquitylation, which signals endocytosis and delivery to the cell's lytic compartment, and there is emerging evidence for related mechanisms in plants. Here, we describe the fate of Arabidopsis PIN2 protein, required for directional cellular efflux of the phytohormone auxin, and identify cis- and trans-acting mediators of PIN2 ubiquitylation. We demonstrate that ubiquitin acts as a principal signal for PM protein endocytosis in plants and reveal dynamic adjustments in PIN2 ubiquitylation coinciding with variations in vacuolar targeting and proteolytic turnover. We show that control of PIN2 proteolytic turnover via its ubiquitylation status is of significant importance for auxin distribution in root meristems and for environmentally controlled adaptations of root growth. Moreover, we provide experimental evidence indicating that PIN2 vacuolar sorting depends on modification specifically by lysine(63)-linked ubiquitin chains. Collectively, our results establish lysine(63)-linked PM cargo ubiquitylation as a regulator of polar auxin transport and adaptive growth responses in higher plants.

Posttranslational modification and trafficking of PIN auxin efflux carriers

Cell-to-cell communication is absolutely essential for multicellular organisms. Both animals and plants use chemicals called hormones for intercellular signaling. However, multicellularity of plants and animals has evolved independently, which led to establishment of distinct strategies in order to cope with variations in an ever-changing environment. The phytohormone auxin is crucial to plant development and patterning. PIN auxin efflux carrier-driven polar auxin transport regulates plant development as it controls asymmetric auxin distribution (auxin gradients), which in turn modulates a wide range of developmental processes. Internal and external cues trigger a number of posttranslational PIN auxin carrier modifications that were demonstrated to decisively influence variations in adaptive growth responses. In this review, we highlight recent advances in the analysis of posttranslational modification of PIN auxin efflux carriers, such as phosphorylation and ubiquitylation, and discuss their eminent role in directional vesicle trafficking, PIN protein de-/stabilization and auxin transport activity. We conclude with updated models, in which we attempt to integrate the mechanistic relevance of posttranslational modifications of PIN auxin carriers for the dynamic nature of plant development.

Never too many? How legumes control nodule numbers

Restricted availability of nitrogen compounds in soils is often a major limiting factor for plant growth and productivity. Legumes circumvent this problem by establishing a symbiosis with soil-borne bacteria, called rhizobia that fix nitrogen for the plant. Nitrogen fixation and nutrient exchange take place in specialized root organs, the nodules, which are formed by a coordinated and controlled process that combines bacterial infection and organ formation. Because nodule formation and nitrogen fixation are energy-consuming processes, legumes develop the minimal number of nodules required to ensure optimal growth. To this end, several mechanisms have evolved that adapt nodule formation and nitrogen fixation to the plant's needs and environmental conditions, such as nitrate availability in the soil. In this review, we give an updated view on the mechanisms that control nodulation.

Stress homeostasis - the redox and auxin perspective

Under environmental stresses, plant development is adaptively modulated. This modulation is influenced by the steady-state balance (homeostasis) between reactive oxygen species (ROS) and phytohormones. Frequently observed symptoms in plant stress adaptation responses include growth retardation, reduced metabolism and photosynthesis, reallocation of metabolic resources and increased antioxidant activities to maximize plant survival under adverse environmental conditions. In view of stress-induced morphogenetic changes during adaptation, ROS and auxin are the main players in the regulatory networks because both are strongly affected by exposure to environmental cues. However, the mechanisms underlying the crosstalk between ROS and auxin are poorly understood. In this review, we aim at surveying how the integration of environmental stress-related signals is modulated by crosstalk between ROS and auxin regulatory networks.

Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis

Gradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds known as flavonols have been shown to act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the Auxin Response Factor 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis.

Polar localization and endocytic degradation of a boron transporter, BOR1, is dependent on specific tyrosine residues

Boron (B) is essential for plants, but is toxic in excess. Plants have to strictly regulate the uptake and translocation of B. In Arabidopsis thaliana root cells, a boric acid channel, NIP5;1, and a boric acid/borate exporter, BOR1, localize to the outer (facing soil) and inner plasma membrane domains, respectively, under B limitation. The opposite polar localizations of the importer and exporter would enable plant roots to transport B efficiently towards the xylem. In addition, accumulation of the B transporters is controlled by B conditions. When plants are shifted from low to high B conditions, NIP5;1 transcript accumulation is down-regulated through mRNA degradation. The BOR1 protein is transported to the trans-Golgi network/early endosome and multivesicular body and finally degraded in the vacuole. We have recently shown that both the polar localization and the endocytic degradation of BOR1 are controlled by at least two tyrosine residues in a large loop located in the cytosol. We also showed that ubiquitination is required for the endocytic degradation of BOR1. Here, we analyzed possible involvement of an additional tyrosine residue (Y414) in the loop region and discuss the pathway of the BOR1 trafficking for polar localization and endocytic degradation of BOR1.

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.

Structure and function of endosomes in plant cells

Endosomes are a heterogeneous collection of organelles that function in the sorting and delivery of internalized material from the cell surface and the transport of materials from the Golgi to the lysosome or vacuole. Plant endosomes have some unique features, with an organization distinct from that of yeast or animal cells. Two clearly defined endosomal compartments have been studied in plant cells, the trans-Golgi network (equivalent to the early endosome) and the multivesicular body (equivalent to the late endosome), with additional endosome types (recycling endosome, late prevacuolar compartment) also a possibility. A model has been proposed in which the trans-Golgi network matures into a multivesicular body, which then fuses with the vacuole to release its cargo. In addition to basic trafficking functions, endosomes in plant cells are known to function in maintenance of cell polarity by polar localization of hormone transporters and in signaling pathways after internalization of ligand-bound receptors. These signaling functions are exemplified by the BRI1 brassinosteroid hormone receptor and by receptors for pathogen elicitors that activate defense responses. After endocytosis of these receptors from the plasma membrane, endosomes act as a signaling platform, thus playing an essential role in plant growth, development and defense responses. Here we describe the key features of plant endosomes and their differences from those of other organisms and discuss the role of these organelles in cell polarity and signaling pathways.

Photomorphogenesis

As photoautotrophs, plants are exquisitely sensitive to their light environment. Light affects many developmental and physiological responses throughout plants' life histories. The focus of this chapter is on light effects during the crucial period of time between seed germination and the development of the first true leaves. During this time, the seedling must determine the appropriate mode of action to best achieve photosynthetic and eventual reproductive success. Light exposure triggers several major developmental and physiological events. These include: growth inhibition and differentiation of the embryonic stem (hypocotyl); maturation of the embryonic leaves (cotyledons); and establishment and activation of the stem cell population in the shoot and root apical meristems. Recent studies have linked a number of photoreceptors, transcription factors, and phytohormones to each of these events.

Plant endosomal trafficking pathways

Endosomes regulate both the recycling and degradation of plasma membrane (PM) proteins, thereby modulating many cellular responses triggered at the cell surface. Endosomes also play a role in the biosynthetic pathway by taking proteins to the vacuole and recycling vacuolar cargo receptors. In plants, the trans-Golgi network (TGN) acts as an early/recycling endosome whereas prevacuolar compartments/multivesicular bodies (MVBs) take PM proteins to the vacuole for degradation. Recent studies have demonstrated that some of the molecular complexes that mediate endosomal trafficking, such as the retromer, the ADP-ribosylation factor (ARF) machinery, and the Endosomal Sorting Complexes Required for Transport (ESCRTs) have both conserved and specialized functions in plants. Whereas there is disagreement on the subcellular localization of the plant retromer, its function in recycling vacuolar sorting receptors (VSRs) and modulating the trafficking of PM proteins has been well established. Studies on Arabidopsis ESCRT components highlight the essential role of this complex in cytokinesis, plant development, and vacuolar organization. In addition, post-translational modifications of plant PM proteins, such as phosphorylation and ubiquitination, have been demonstrated to act as sorting signals for endosomal trafficking.

Analysis of subcellular localization of auxin carriers PIN, AUX/LAX and PGP in Sorghum bicolor

Auxin transport at least correlates to the three gene families: efflux carriers PIN-formed (PIN), p-glycoprotein (PGP), and influx carrier auxin resistant 1/like aux1(AUX/LAX) in Arabidopsis thaliana. In monocotyledon Sorghum bicolor, the biological function of these genes retains unclear. Our previous study reported that the member analysis, organ-specific expression and expression profiles of the auxin transporter PIN, PGP and AUX/LAX gene families in Sorghum bicolor under IAA, brassinosteroid, polar auxin transport inhibitors and abiotic stresses. Here we further supply the prediction of subcellular localization of SbPIN, SbLAX and SbPGP proteins and discuss the potential relationship between the subcellular localization and stress response. The predicted results showed that the most of SbPIN, SbLAX and SbPGP proteins are localized to the plasma membrane, except few localized to vacuolar membrane and endoplasmic reticulum. This data set provides novel information for investigation of auxin transporters in Sorghum bicolor.

A model for leaf initiation: determination of phyllotaxis by waves in the generative circle

A biophysical model is proposed for how leaf primordia are positioned on the shoot apical: meristem in both spiral and whorl phyllotaxes. Primordia are initiated by signals that propagate: in the epidermis in both azimuthal directions away from the cotyledons or the most recently: specified primordia. The signals are linear waves as inferred from the spatial periodicity of the: divergence angle and a temporal periodicity. The periods of the waves, which represent actively: transported auxin, are much smaller than the plastochron interval. Where oppositely directed: waves meet at one or more angular positions on the periphery of the generative circle, auxin: concentration builds and as in most models this stimulates local movement of auxin to: underlying cells, where it promotes polarized cell division and expansion. For higher order: spirals the wave model requires asymmetric function of auxin transport; that is, opposite wave: speeds differ. An algorithm for determination of the angular positions of leaves in common leaf: phyllotaxic configurations is proposed. The number of turns in a pattern repeat, number of leaves: per level and per pattern repeat, and divergence angle are related to speed of auxin transport and: radius of the generative circle. The rule for composition of Fibonacci or Lucas numbers: associated with some phyllotaxes is discussed. A subcellular model suggests how the shoot: meristem might specify either symmetric or asymmetric transport of auxin away from the: forming primordia that produce it. Biological tests that could make or break the mathematical: and molecular hypotheses are proposed.

Recycling, clustering, and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane

A combination of super-resolution microscopy in live cells and computational modeling provides new insights into the dynamic and interwoven mechanism that maintains the polar distribution of an important plant cargo.

Semi-quantitative and subdiffraction resolution fluorescence imaging in living plant cells provided unexpected insights into the mechanisms underlying dynamic maintenance of PIN polarity.

These experiments reveal super-polar targeting of PIN proteins to the center of polar domains, presumably by a TGN/endosome guided delivery mechanism.

PIN proteins are recruited to immobile membrane clusters that reduce lateral PIN mobility, and retrieved from the lateral cell side by spatially defined clathrin-dependent endocytosis.

In silico model simulations are consistent with these experimental observations and reveal the individual roles of these cellular processes in the organization of sharply defined polar plasma membrane domains.

Cell polarity reflected by asymmetric distribution of proteins at the plasma membrane is a fundamental feature of unicellular and multicellular organisms. It remains conceptually unclear how cell polarity is kept in cell wall-encapsulated plant cells. We have used super-resolution and semi-quantitative live-cell imaging in combination with pharmacological, genetic, and computational approaches to reveal insights into the mechanism of cell polarity maintenance in Arabidopsis thaliana. We show that polar-competent PIN transporters for the phytohormone auxin are delivered to the center of polar domains by super-polar recycling. Within the plasma membrane, PINs are recruited into non-mobile membrane clusters and their lateral diffusion is dramatically reduced, which ensures longer polar retention. At the circumventing edges of the polar domain, spatially defined internalization of escaped cargos occurs by clathrin-dependent endocytosis. Computer simulations confirm that the combination of these processes provides a robust mechanism for polarity maintenance in plant cells. Moreover, our study suggests that the regulation of lateral diffusion and spatially defined endocytosis, but not super-polar exocytosis have primary importance for PIN polarity maintenance.

Signaling and gene regulatory programs in plant vascular stem cells

A key question about the development of multicellular organisms is how they precisely control the complex pattern formation during their growth. For plants to grow for many years, a tight balance between pluripotent dividing cells and cells undergoing differentiation should be maintained within stem cell populations. In this process, cell-cell communication plays a central role by creating positional information for proper cell type patterning. Cell-type specific gene regulatory networks govern differentiation of cells into particular cell types. In this review, we will provide a comprehensive overview of emerging key signaling and regulatory programs in the stem cell population that direct morphogenesis of plant vascular tissues.

Signals and mechanisms affecting vesicular trafficking during root growth

Vesicular trafficking is mediated by distinct exocytic and endocytic routes in eukaryotic cells. These pathways involve RAB family proteins, ADP-ribosylation factor, RHO proteins of the Ras superfamily, and SNAREs (soluble N-ethylmaleimide-sensitive factor adaptors). Studies have shown that vesicular trafficking plays a crucial role in protein localization and movement, signal transduction, and multiple developmental processes. Here we summarize the role of vesicular trafficking in root and root hair growth and in auxin-mediated root development, focusing on the regulation of the polarized subcellular distribution of the PIN proteins (auxin efflux carriers).

Cell polarity in plants: when two do the same, it is not the same

In unicellular and multicellular organisms, cell polarity is essential for a wide range of biological processes. An important feature of cell polarity is the asymmetric distribution of proteins in or at the plasma membrane. In plants such polar localized proteins play various specific roles ranging from organizing cell morphogenesis, asymmetric cell division, pathogen defense, nutrient transport and establishment of hormone gradients for developmental patterning. Moreover, flexible respecification of cell polarities enables plants to adjust their physiology and development to environmental changes. Having evolved multicellularity independently and lacking major cell polarity mechanisms of animal cells, plants came up with alternative solutions to generate and respecify cell polarity as well as to regulate polar domains at the plasma membrane.

Organogenesis from stem cells in planta: multiple feedback loops integrating molecular and mechanical signals

In multicellular organisms, the coordination of cell behaviors largely relies on biochemical and biophysical signals. Understanding how such signals control development is often challenging, because their distribution relies on the activity of individual cells and, in a feedback loop, on tissue behavior and geometry. This review focuses on one of the best-studied structures in biology, the shoot apical meristem (SAM). This tissue is responsible for the production of all the aerial parts of a plant. In the SAM, a population of stem cells continuously produces new cells that are incorporated in lateral organs, such as leaves, branches, and flowers. Organogenesis from stem cells involves a tight regulation of cell identity and patterning as well as large-scale morphogenetic events. The gene regulatory network controlling these processes is highly coordinated in space by various signals, such as plant hormones, peptides, intracellular mobile factors, and mechanical stresses. Many crosstalks and feedback loops interconnecting these pathways have emerged in the past 10 years. The plant hormone auxin and mechanical forces have received more attention recently and their role is more particularly detailed here. An integrated view of these signaling networks is also presented in order to help understanding how robust shape and patterning can emerge from these networks.

Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization

Carrier-dependent, intercellular auxin transport is central to the developmental patterning of higher plants (tracheophytes). The evolution of this polar auxin transport might be linked to the translocation of some PIN auxin efflux carriers from their presumably ancestral localization at the endoplasmic reticulum (ER) to the polar domains at the plasma membrane. Here we propose an eventually ancient mechanism of intercellular auxin distribution by ER-localized auxin transporters involving intracellular auxin retention and switch-like release from the ER. The proposed model integrates feedback circuits utilizing the conserved nuclear auxin signaling for the regulation of PIN transcription and a hypothetical ER-based signaling for the regulation of PIN-dependent transport activity at the ER. Computer simulations of the model revealed its plausibility for generating auxin channels and localized auxin maxima highlighting the possibility of this alternative mechanism for polar auxin transport.

PIN polarity regulation by AGC-3 kinases and ARF-GEF: a recurrent theme with context dependent modifications for plant development and response

The analysis of cell polarity in plants is fueled by the discovery and analysis of auxin efflux carrier PIN proteins that show polar localizations in various plant cell types in line with their roles in directional cell to cell auxin transport. As this asymmetry in cellular PIN localization drives directional auxin fluxes, abnormalities in PIN localizations modify auxin transport culminating into range of auxin distribution defective phenotypes. Because of this influence of PIN localization on plant development via changes in auxin distribution, mechanisms establishing, maintaining and altering PIN polarity are of intense interest in the plant field during the recent years. Recent findings suggest that two categories of molecules, namely AGC-3 kinase family members PINOID, WAG1, WAG2 and ARF-GEF family member GNOM predominantly influence the polar localization of PINs. The emerging mechanism for AGC-3 kinases and ARF-GEF action suggest that AGC-3 kinases predominantly phosphorylate PINs at the plasma membrane for eventual PIN internalization and PIN sorting into ARF-GEF GNOM independent polar recycling pathways. In case of mutant for AGC-3 kinases or mutations in AGC-3 kinase-targeted PIN residues, much less phosphorylated PINs are recruited into ARFGEF GNOM-dependent polar recycling pathway. When ARF-GEF GNOM is inactive, the bias is shifted for rerouting less efficiently phosphorylated PINs into GNOM-independent polar recycling pathways that generally prefer efficiently phosphorylated PINs. Thus, balance shifts between the extent of AGC-3 kinase mediated PIN phosphorylation and the functioning of ARFGEF instruct PIN polarity establishment and/or PIN polarity alterations. Recent studies report utilization of this AGC-3 kinase and ARF-GEF PIN polarity regulation module during diverse developmental and response programs including shoot patterning, root growth, phototropism, gravitropism, organogenesis, leaf epidermal cell indentations and fruit valve margin formation. Based on these findings the same theme of phosphorylated PIN sorting into differential polar recycling pathways for PIN polarity establishment and alteration seems to be employed in a context-dependent manner.

Inositol trisphosphate-induced Ca2+ signaling modulates auxin transport and PIN polarity

The phytohormone auxin is an important determinant of plant development. Directional auxin flow within tissues depends on polar localization of PIN auxin transporters. To explore regulation of PIN-mediated auxin transport, we screened for suppressors of PIN1 overexpression (supo) and identified an inositol polyphosphate 1-phosphatase mutant (supo1), with elevated inositol trisphosphate (InsP(3)) and cytosolic Ca(2+) levels. Pharmacological and genetic increases in InsP(3) or Ca(2+) levels also suppressed the PIN1 gain-of-function phenotypes and caused defects in basal PIN localization, auxin transport and auxin-mediated development. In contrast, the reductions in InsP(3) levels and Ca(2+) signaling antagonized the effects of the supo1 mutation and disrupted preferentially apical PIN localization. InsP(3) and Ca(2+) are evolutionarily conserved second messengers involved in various cellular functions, particularly stress responses. Our findings implicate them as modifiers of cell polarity and polar auxin transport, and highlight a potential integration point through which Ca(2+) signaling-related stimuli could influence auxin-mediated development.

Feedback models for polarized auxin transport: an emerging trend

The phytohormone auxin is vital to plant growth and development. A unique property of auxin among all other plant hormones is its cell-to-cell polar transport that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the substantial molecular insight into the cellular PIN polarization, the mechanistic understanding for developmentally and environmentally regulated PIN polarization is scarce. The long-standing belief that auxin modulates its own transport by means of a positive feedback mechanism has inspired both experimentalists and theoreticians for more than two decades. Recently, theoretical models for auxin-dependent patterning in plants include the feedback between auxin transport and the PIN protein localization. These computer models aid to assess the complexity of plant development by testing and predicting plausible scenarios for various developmental processes that occur in planta. Although the majority of these models rely on purely heuristic principles, the most recent mechanistic models tentatively integrate biologically testable components into known cellular processes that underlie the PIN polarity regulation. The existing and emerging computational approaches to describe PIN polarization are presented and discussed in the light of recent experimental data on the PIN polar targeting.

ROS signaling: the new wave?

Reactive oxygen species (ROS) play a multitude of signaling roles in different organisms from bacteria to mammalian cells. They were initially thought to be toxic byproducts of aerobic metabolism, but have now been acknowledged as central players in the complex signaling network of cells. In this review, we will attempt to address several key questions related to the use of ROS as signaling molecules in cells, including the dynamics and specificity of ROS signaling, networking of ROS with other signaling pathways, ROS signaling within and across different cells, ROS waves and the evolution of the ROS gene network.

Seven things we think we know about auxin transport

Polar transport of the phytohormone auxin and the establishment of localized auxin maxima regulate embryonic development, stem cell maintenance, root and shoot architecture, and tropic growth responses. The past decade has been marked by dramatic progress in efforts to elucidate the complex mechanisms by which auxin transport regulates plant growth. As the understanding of auxin transport regulation has been increasingly elaborated, it has become clear that this process is involved in almost all plant growth and environmental responses in some way. However, we still lack information about some basic aspects of this fundamental regulatory mechanism. In this review, we present what we know (or what we think we know) and what we do not know about seven auxin-regulated processes. We discuss the role of auxin transport in gravitropism in primary and lateral roots, phototropism, shoot branching, leaf expansion, and venation. We also discuss the auxin reflux/fountain model at the root tip, flavonoid modulation of auxin transport processes, and outstanding aspects of post-translational regulation of auxin transporters. This discussion is not meant to be exhaustive, but highlights areas in which generally held assumptions require more substantive validation.

Amino acid export in plants: a missing link in nitrogen cycling

The export of nutrients from source organs to parts of the body where they are required (e.g. sink organs) is a fundamental biological process. Export of amino acids, one of the most abundant nitrogen species in plant long-distance transport tissues (i.e. xylem and phloem), is an essential process for the proper distribution of nitrogen in the plant. Physiological studies have detected the presence of multiple amino acid export systems in plant cell membranes. Yet, surprisingly little is known about the molecular identity of amino acid exporters, partially due to the technical difficulties hampering the identification of exporter proteins. In this short review, we will summarize our current knowledge about amino acid export systems in plants. Several studies have described plant amino acid transporters capable of bi-directional, facilitative transport, reminiscent of activities identified by earlier physiological studies. Moreover, recent expansion in the number of available amino acid transporter sequences have revealed evolutionary relationships between amino acid exporters from other organisms with a number of uncharacterized plant proteins, some of which might also function as amino acid exporters. In addition, genes that may regulate export of amino acids have been discovered. Studies of these putative transporter and regulator proteins may help in understanding the elusive molecular mechanisms of amino acid export in plants.

Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis

Plants exhibit daily rhythms in their growth, providing an ideal system for the study of interactions between environmental stimuli such as light and internal regulators such as the circadian clock. We previously found that two basic loop-helix-loop transcription factors, PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5, integrate light and circadian clock signaling to generate rhythmic plant growth in Arabidopsis (Arabidopsis thaliana). Here, we use expression profiling and real-time growth assays to identify growth regulatory networks downstream of PIF4 and PIF5. Genome-wide analysis of light-, clock-, or growth-correlated genes showed significant overlap between the transcriptomes of clock-, light-, and growth-related pathways. Overrepresentation analysis of growth-correlated genes predicted that the auxin and gibberellic acid (GA) hormone pathways both contribute to diurnal growth control. Indeed, lesions of GA biosynthesis genes retarded rhythmic growth. Surprisingly, GA-responsive genes are not enriched among genes regulated by PIF4 and PIF5, whereas auxin pathway and response genes are. Consistent with this finding, the auxin response is more severely affected than the GA response in pif4 pif5 double mutants and in PIF5-overexpressing lines. We conclude that at least two downstream modules participate in diurnal rhythmic hypocotyl growth: PIF4 and/or PIF5 modulation of auxin-related pathways and PIF-independent regulation of the GA pathway.

Transport and metabolism of the endogenous auxin precursor indole-3-butyric acid

Plant growth and morphogenesis depend on the levels and distribution of the plant hormone auxin. Plants tightly regulate cellular levels of the active auxin indole-3-acetic acid (IAA) through synthesis, inactivation, and transport. Although the transporters that move IAA into and out of cells are well characterized and play important roles in development, little is known about the transport of IAA precursors. In this review, we discuss the accumulating evidence suggesting that the IAA precursor indole-3-butyric acid (IBA) is transported independently of the characterized IAA transport machinery along with the recent identification of specific IBA efflux carriers and enzymes suggested to metabolize IBA. These studies have revealed important roles for IBA in maintaining IAA levels and distribution within the plant to support normal development.

Asymmetric cell division in land plants and algae: the driving force for differentiation

Asymmetric cell division generates two cells with different fates and has an important role in plant development. It produces distinct cell types and new organs, and maintains stem cell niches. To handle the constraints of having immobile cells, plants possess numerous unique features to obtain asymmetry, such as specific regulators of intrinsic polarity. Although several components have not yet been identified, new findings, together with knowledge from different developmental systems, now allow us to take an important step towards a mechanistic overview of asymmetric cell division in plants and algae. Strikingly, several key regulators are used for different developmental processes, and common mechanisms can be recognized.