An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis

Characterization the role of a UFC homolog, AtAuxRP3, in the regulation of Arabidopsis seedling growth and stress response

Auxin is a well-known, crucial regulator of the entire plant lifecycle, not only orchestrating many aspects of plant growth and development, but also playing various roles in biotic and abiotic stress. This study reports the isolation and functional characterization of a DUF-966 domain-containing gene, At3g46110, re-named AtAuxRP3. AtAuxRP3 overexpression in Arabidopsis increased the levels of endogenous indole-3-acetic acid, enhanced expression of the auxin-responsive reporter DR5:GUS near the vegetative shoot apex, and led to ectopic activation of auxin signaling, including dysmorphic (narrow, asymmetric) rosette leaves, abnormal emergence of inflorescence, inhibition of primary root elongation and arrest of dark-grown hypocotyls. AtAuxRP3-OX lines also showed decreased tolerance to NaCl and osmotic stress during Arabidopsis seeds germination and young seedling growth. Genome-wide transcriptomic analysis showed AtAuxRP3-OX seedlings displayed increases in the expression of genes that group in a variety of developmental categories, while other downregulated genes were associated with stress responses. Our results provide evidence for a regulatory role of AtAuxRP3 in endogenous auxin levels, leaf development, and initiation of inflorescence stems early in reproductive development during Arabidopsis seedling growth.

A tetraspanin gene regulating auxin response and affecting orchid perianth size and various plant developmental processes

The competition between L (lip) and SP (sepal/petal) complexes in P-code model determines the identity of complex perianth patterns in orchids. Orchid tetraspanin gene Auxin Activation Factor (AAF) orthologs, whose expression strongly correlated with the expansion and size of the perianth after P code established, were identified. Virus-induced gene silencing (VIGS) of OAGL6-2 in L complex resulted in smaller lips and the down-regulation of Oncidium OnAAF. VIGS of PeMADS9 in L complex resulted in the enlarged lips and up-regulation of Phalaenopsis PaAAF. Furthermore, the larger size of Phalaenopsis variety flowers was associated with higher PaAAF expression, larger and more cells in the perianth. Thus, a rule is established that whenever bigger perianth organs are made in orchids, higher OnAAF/PaAAF expression is observed after their identities are determined by P-code complexes. Ectopic expression Arabidopsis AtAAF significantly increased the size of flower organs by promoting cell expansion in transgenic Arabidopsis due to the enhancement of the efficiency of the auxin response and the subsequent suppression of the jasmonic acid (JA) biosynthesis genes (DAD1/OPR3) and BIGPETAL gene during late flower development. In addition, auxin-controlled phenotypes, such as indehiscent anthers, enhanced drought tolerance, and increased lateral root formation, were also observed in 35S::AtAAF plants. Furthermore, 35S::AtAAF root tips maintained gravitropism during auxin treatment. In contrast, the opposite phenotype was observed in palmitoylation-deficient AtAAF mutants. Our data demonstrate an interaction between the tetraspanin AAF and auxin/JA that regulates the size of flower organs and impacts various developmental processes.

A novel Ca2+-binding protein that can rapidly transduce auxin responses during root growth

Signaling cross talks between auxin, a regulator of plant development, and Ca2+, a universal second messenger, have been proposed to modulate developmental plasticity in plants. However, the underlying molecular mechanisms are largely unknown. Here, we report that in Arabidopsis roots, auxin elicits specific Ca2+ signaling patterns that spatially coincide with the expression pattern of auxin-regulated genes. We have identified the single EF-hand Ca2+-binding protein Ca2+-dependent modulator of ICR1 (CMI1) as an interactor of the Rho of plants (ROP) effector interactor of constitutively active ROP (ICR1). CMI1 expression is directly up-regulated by auxin, whereas the loss of function of CMI1 associates with the repression of auxin-induced Ca2+ increases in the lateral root cap and vasculature, indicating that CMI1 represses early auxin responses. In agreement, cmi1 mutants display an increased auxin response including shorter primary roots, longer root hairs, longer hypocotyls, and altered lateral root formation. Binding to ICR1 affects subcellular localization of CMI1 and its function. The interaction between CMI1 and ICR1 is Ca2+-dependent and involves a conserved hydrophobic pocket in CMI1 and calmodulin binding-like domain in ICR1. Remarkably, CMI1 is monomeric in solution and in vitro changes its secondary structure at cellular resting Ca2+ concentrations ranging between 10-9 and 10-8 M. Hence, CMI1 is a Ca2+-dependent transducer of auxin-regulated gene expression, which can function in a cell-specific fashion at steady-state as well as at elevated cellular Ca2+ levels to regulate auxin responses.

Quantitative trait loci analysis of hormone levels in Arabidopsis roots

Quantitative trait loci (QTL) analyses for five groups of hormones, including cytokinins in Arabidopsis roots were performed using recombinant inbred lines (Ler×Cvi). Significant QTLs were detected for cytokinins, jasmonic acid and salicylic acid. Separate analysis of two sub-populations, viz., vegetative and flowering plants revealed that many of the QTLs were development-specific. Using near-isogenic lines, several significant QTLs were confirmed; three co-localized QTL regions were responsible for determining several cytokinin metabolites. Using a knock-out plant, a functional role of zeatin N-glucosyltransferase gene (UGT76C2) underlying a large-effect QTL for levels of tZ-N-glucosides and tZRMP was evaluated in the metabolism of cytokinins. Pleotropic effects of this gene were found for cytokinin levels in both roots and leaves, but significant changes of morphological traits were observed only in roots. Hormone QTL analysis reveals development-specific and organ-dependent aspects of the regulation of plant hormone content and metabolism.

Opsin 1 and Opsin 2 of the Corn Smut Fungus Ustilago maydis Are Green Light-Driven Proton Pumps

In fungi, green light is absorbed by rhodopsins, opsin proteins carrying a retinal molecule as chromophore. The basidiomycete Ustilago maydis, a fungal pathogen that infects corn plants, encodes three putative photoactive opsins, called ops1 (UMAG_02629), ops2 (UMAG_00371), and ops3 (UMAG_04125). UmOps1 and UmOps2 are expressed during the whole life cycle, in axenic cultures as well as in planta, whereas UmOps3 was recently shown to be absent in axenic cultures but highly expressed during plant infection. Here we show that expression of UmOps1 and UmOps2 is induced by blue light under control of white collar 1 (Wco1). UmOps1 is mainly localized in the plasma membrane, both when expressed in HEK cells and U. maydis sporidia. In contrast, UmOps2 was mostly found intracellularly in the membranes of vacuoles. Patch-clamp studies demonstrated that both rhodopsins are green light-driven outward rectifying proton pumps. UmOps1 revealed an extraordinary pH dependency with increased activity in more acidic environment. Also, UmOps1 showed a pronounced, concentration-dependent enhancement of pump current caused by weak organic acids (WOAs), especially by acetic acid and indole-3-acetic acid (IAA). In contrast, UmOps2 showed the typical behavior of light-driven, outwardly directed proton pumps, whereas UmOps3 did not exhibit any electrogenity. With this work, insights were gained into the localization and molecular function of two U. maydis rhodopsins, paving the way for further studies on the biological role of these rhodopsins in the life cycle of U. maydis.

Polar Auxin Transport Determines Adventitious Root Emergence and Growth in Rice

Flooding is a severe limitation for crop production worldwide. Unlike other crop plants, rice (Oryza sativa L.) is well adapted to partial submergence rendering it a suitable crop plant to understand flooding tolerance. Formation of adventitious roots (ARs), that support or replace the main root system, is a characteristic response to flooding. In rice, AR emergence is induced by ethylene and in the dark where roots grow upward. We used the synthetic auxins 2,4-D and α-NAA, and the auxin transport inhibitor naphthylphtalamic acid (NPA) to study emergence, growth rate and growth angle of ARs. While α-NAA had no effect, NPA and 2,4-D reduced the root elongation rate and the angle with a stronger effect on root angle in the dark than in the light. Furthermore, NPA delayed emergence of AR primordia suggesting that efflux carrier-mediated auxin transport is required for all aspects of directed AR growth. Expression analysis using OsPIN:GUS reporter lines revealed that OsPIN1b and OsPIN1c promoters were active in the stele and root cap in accord with their predicted role in acropetal auxin transport. OsPIN2 was expressed at the root tip and was reduced in the presence of NPA. Auxin activity, detected with DR5:VENUS, increased in primordia following growth induction. By contrast, auxin activity was high in epidermal cells above primordia and declined following growth induction suggesting that auxin levels are antagonistically regulated in AR primordia and in epidermal cells above AR primordia suggesting that auxin signaling contributes to the coordinated processes of epidermal cell death and AR emergence.

Cytokinin-Dependent Control of GH3 Group II Family Genes in the Arabidopsis Root

The Arabidopsis root is a dynamic system where the interaction between different plant hormones controls root meristem activity and, thus, organ growth. In the root, a characteristic graded distribution of the hormone auxin provides positional information, coordinating the proliferating and differentiating cell status. The hormone cytokinin shapes this gradient by positioning an auxin minimum in the last meristematic cells. This auxin minimum triggers a cell developmental switch necessary to start the differentiation program, thus, regulating the root meristem size. To position the auxin minimum, cytokinin promotes the expression of the IAA-amido synthase group II gene GH3.17, which conjugates auxin with amino acids, in the most external layer of the root, the lateral root cap tissue. Since additional GH3 genes are expressed in the root, we questioned whether cytokinin to position the auxin minimum also operates via different GH3 genes. Here, we show that cytokinin regulates meristem size by activating the expression of GH3.5 and GH3.6 genes, in addition to GH3.17. Thus, cytokinin activity provides a robust control of auxin activity in the entire organ necessary to regulate root growth.

Stem cells within the shoot apical meristem: identity, arrangement and communication

Stem cells are specific cells that renew themselves and also provide daughter cells for organ formation. In plants, primary stem cell populations are nurtured within shoot and root apical meristems (SAM and RAM) for the production of aerial and underground parts, respectively. This review article summarizes recent progress on control of stem cells in the SAM from studies of the model plant Arabidopsis thaliana. To that end, a brief overview of the RAM is provided first to emphasize similarities and differences between the two apical meristems, which would help in better understanding of stem cells in the SAM. Subsequently, we will discuss in depth how stem cells are arranged in an organized manner in the SAM, how dynamically the stem cell identity is regulated, what factors participate in stem cell control, and how intercellular communication by mobile signals modulates stem cell behaviors within the SAM. Remaining questions and perspectives are also presented for future studies.

Arabidopsis γ-glutamylcyclotransferase affects glutathione content and root system architecture during sulfur starvation

γ-Glutamylcyclotransferase initiates glutathione degradation to component amino acids l-glutamate, l-cysteine and l-glycine. The enzyme is encoded by three genes in Arabidopsis thaliana, one of which (GGCT2;1) is transcriptionally upregulated by starvation for the essential macronutrient sulfur (S). Regulation by S-starvation suggests that GGCT2;1 mobilizes l-cysteine from glutathione when there is insufficient sulfate for de novo l-cysteine synthesis. The response of wild-type seedlings to S-starvation was compared to ggct2;1 null mutants. S-starvation causes glutathione depletion in S-starved wild-type seedlings, but higher glutathione is maintained in the primary root tip than in other seedling tissues. Although GGCT2;1 is induced throughout seedlings, its expression is concentrated in the primary root tip where it activates the γ-glutamyl cycle. S-starved wild-type plants also produce longer primary roots, and lateral root growth is suppressed. While glutathione is also rapidly depleted in ggct2;1 null seedlings, much higher glutathione is maintained in the primary root tip compared to the wild-type. S-starved ggct2;1 primary roots grow longer than the wild-type, and lateral root growth is not suppressed. These results point to a role for GGCT2;1 in S-starvation-response changes to root system architecture through activity of the γ-glutamyl cycle in the primary root tip. l-Cysteine mobilization from glutathione is not solely a function of GGCT2;1.

Tryptophan Metabolism in Caenorhabditis elegans Links Aggregation Behavior to Nutritional Status

Caenorhabditis elegans uses aggregation pheromones to communicate its nutritional status and recruit fellow members of its species to food sources. These aggregation pheromones include the IC-ascarosides, ascarosides modified with an indole-3-carbonyl (IC) group on the 4'-position of the ascarylose sugar. Nothing is known about the biosynthesis of the IC modification beyond the fact that it is derived from tryptophan. Here, we show that C. elegans produces endogenously several indole-containing metabolites, including indole-3-pyruvic acid (IPA), indole-3-acetic acid (IAA; auxin), and indole-3-carboxylic acid, and that these metabolites are intermediates in the biosynthetic pathway from tryptophan to the IC group. Stable isotope-labeled IPA and IAA are incorporated into the IC-ascarosides. Importantly, we show that flux through the biosynthetic pathway is affected by the activity of the pyruvate dehydrogenase complex (PDC). Knockdown of the PDC by RNA interference leads to an accumulation of upstream metabolites and a reduction in downstream metabolites in the pathway. Our results show that production of aggregation pheromones is linked to PDC activity and that aggregation behavior may reflect a favorable metabolic state in the worm. Lastly, we show that treatment of  C. elegans with indole-containing metabolites in the pathway induces the biosynthesis of the IC-ascarosides. Because the natural environment of C. elegans is rotting plant material, indole-containing metabolites in this environment could potentially stimulate pheromone biosynthesis and aggregation behavior in the worm. Thus, there may be important links between tryptophan metabolism in C. elegans and in plants and bacteria that enable interkingdom signaling.

A bacterial assay for rapid screening of IAA catabolic enzymes

BACKGROUND

Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl-l-aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and in planta feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays.

RESULTS

In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC-ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein.

CONCLUSIONS

This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.

Root Tropisms: Investigations on Earth and in Space to Unravel Plant Growth Direction

Root tropisms are important responses of plants, allowing them to adapt their growth direction. Research on plant tropisms is indispensable for future space programs that envisage plant-based life support systems for long-term missions and planet colonization. Root tropisms encompass responses toward or away from different environmental stimuli, with an underexplored level of mechanistic divergence. Research into signaling events that coordinate tropistic responses is complicated by the consistent coincidence of various environmental stimuli, often interacting via shared signaling mechanisms. On Earth the major determinant of root growth direction is the gravitational vector, acting through gravitropism and overruling most other tropistic responses to environmental stimuli. Critical advancements in the understanding of root tropisms have been achieved nullifying the gravitropic dominance with experiments performed in the microgravity environment. In this review, we summarize current knowledge on root tropisms to different environmental stimuli. We highlight that the term tropism must be used with care, because it can be easily confused with a change in root growth direction due to asymmetrical damage to the root, as can occur in apparent chemotropism, electrotropism, and magnetotropism. Clearly, the use of Arabidopsis thaliana as a model for tropism research contributed much to our understanding of the underlying regulatory processes and signaling events. However, pronounced differences in tropisms exist among species, and we argue that these should be further investigated to get a more comprehensive view of the signaling pathways and sensors. Finally, we point out that the Cholodny-Went theory of asymmetric auxin distribution remains to be the central and unifying tropistic mechanism after 100 years. Nevertheless, it becomes increasingly clear that the theory is not applicable to all root tropistic responses, and we propose further research to unravel commonalities and differences in the molecular and physiological processes orchestrating root tropisms.

Seeing is better than believing: visualization of membrane transport in plants

Recently, the plant transport field has shifted their research focus toward a more integrative investigation of transport networks thought to provide the basis for long-range transport routes. Substantial progress was provided by of a series of elegant techniques that allow for a visualization or prediction of substrate movements in plant tissues in contrast to established quantitative methods offering low spatial resolution. These methods are critically evaluated in respect to their spatio-temporal resolution, invasiveness, dynamics and overall quality. Current limitations of transport route predictions-based on transporter locations and transport modeling are addressed. Finally, the potential of new tools that have not yet been fully implemented into plant research is indicated.

Regulatory networks controlling the development of the root system and the formation of lateral roots: a comparative analysis of the roles of pericycle and vascular cambium

Background

The production of a new lateral root from parental root primary tissues has been investigated extensively, and the most important regulatory mechanisms are now well known. A first regulatory mechanism is based on the synthesis of small peptides which interact ectopically with membrane receptors to elicit a modulation of transcription factor target genes. A second mechanism involves a complex cross-talk between plant hormones. It is known that lateral roots are formed even in parental root portions characterized by the presence of secondary tissues, but there is not yet agreement about the putative tissue source providing the cells competent to become founder cells of a new root primordium.

Scope

We suggest models of possible regulatory mechanisms for inducing specific root vascular cambium (VC) stem cells to abandon their activity in the production of xylem and phloem elements and to start instead the construction of a new lateral root primordium. Considering the ontogenic nature of the VC, the models which we suggest are the result of a comparative review of mechanisms known to control the activity of stem cells in the root apical meristem, procambium and VC. Stem cells in the root meristems can inherit various competences to play different roles, and their fate could be decided in response to cross-talk between endogenous and exogenous signals.

Conclusions

We have found a high degree of relatedness among the regulatory mechanisms controlling the various root meristems. This fact suggests that competence to form new lateral roots can be inherited by some stem cells of the VC lineage. This kind of competence could be represented by a sensitivity of specific stem cells to factors such as those presented in our models.

Flow Cytometry Has a Significant Impact on the Cellular Metabolome

The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyze the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signaling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry.

Auxins and Cytokinins-The Role of Subcellular Organization on Homeostasis

Plant hormones are master regulators of plant growth and development. Better knowledge of their spatial signaling and homeostasis (transport and metabolism) on the lowest structural levels (cellular and subcellular) is therefore crucial to a better understanding of developmental processes in plants. Recent progress in phytohormone analysis at the cellular and subcellular levels has greatly improved the effectiveness of isolation protocols and the sensitivity of analytical methods. This review is mainly focused on homeostasis of two plant hormone groups, auxins and cytokinins. It will summarize and discuss their tissue- and cell-type specific distributions at the cellular and subcellular levels.

Systems, variation, individuality and plant hormones

Inter-individual variation in plants and particularly in hormone content, figures strongly in evolution and behaviour. Homo sapiens and Arabidopsis exhibit similar and substantial phenotypic and molecular variation. Whereas there is a very substantial degree of hormone variation in mankind, reports of inter-individual variation in plant hormone content are virtually absent but are likely to be as large if not larger than that in mankind. Reasons for this absence are discussed. Using an example of inter-individual variation in ethylene content in ripening, the article shows how biological time is compressed by hormones. It further resolves an old issue of very wide hormone dose response that result directly from negative regulation in hormone (and light) transduction. Negative regulation is used because of inter-individual variability in hormone synthesis, receptors and ancillary proteins, a consequence of substantial genomic and environmental variation. Somatic mosaics have been reported for several plant tissues and these too contribute to tissue variation and wide variation in hormone response. The article concludes by examining what variation exists in gravitropic responses. There are multiple sensing systems of gravity vectors and multiple routes towards curvature. These are an aspect of the need for reliability in both inter-individual variation and unpredictable environments. Plant hormone inter-individuality is a new area for research and is likely to change appreciation of the mechanisms that underpin individual behaviour.

A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation

Somatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates but is especially prominent in higher plants, where it has been postulated to be essential for cell growth and fate maintenance. However, a comprehensive understanding of the physiological significance of plant endopolyploidy has remained elusive. Here, we modeled and experimentally verified a high-resolution DNA endoploidy map of the developing Arabidopsis thaliana root, revealing a remarkable spatiotemporal control of DNA endoploidy levels across tissues. Fitting of a simplified model to publicly available data sets profiling root gene expression under various environmental stress conditions suggested that this root endoploidy patterning may be stress-responsive. Furthermore, cellular and transcriptomic analyses revealed that inhibition of endoreplication onset alters the nuclear-to-cellular volume ratio and the expression of cell wall-modifying genes, in correlation with the appearance of cell structural changes. Our data indicate that endopolyploidy might serve to coordinate cell expansion with structural stability and that spatiotemporal endoreplication pattern changes may buffer for stress conditions, which may explain the widespread occurrence of the endocycle in plant species growing in extreme or variable environments.

Quantitative 3D imaging of cell level auxin and cytokinin response ratios in soybean roots and nodules

Legume-Rhizobium symbiosis results in root nodules where rhizobia fix atmospheric nitrogen into plant usable forms in exchange for plant-derived carbohydrates. The development of these specialized root organs involves a set of carefully orchestrated plant hormone signalling. In particular, a spatio-temporal balance between auxin and cytokinin appears to be crucial for proper nodule development. We put together a construct that carried nuclear localized fluorescence sensors for auxin and cytokinin and used two photon induced fluorescence microscopy for concurrent quantitative 3-dimensional imaging to determine cellular level auxin and cytokinin outputs and ratios in root and nodule tissues of soybean. The use of nuclear localization signals on the markers and nuclei segmentation during image processing enabled accurate monitoring of outputs in 3D image volumes. The ratiometric method used here largely compensates for variations in individual outputs due to sample turbidity and scattering, an inherent issue when imaging thick root and nodule samples typical of many legumes. Overlays of determined auxin/cytokinin ratios on specific root zones and cell types accurately reflected those predicted based on previously reported outputs for each hormone individually. Importantly, distinct auxin/cytokinin ratios corresponded to distinct nodule cell types indicating a key role for these hormones in nodule cell type identity.

AtBET5 is essential for exine pattern formation and apical meristem organization in Arabidopsis

BET5 is a component of trafficking protein particle (TRAPP) which has been studied extensively in non-plant organisms where they are involved in membrane trafficking within Golgi and between Golgi and early endosomes. Recent analysis of TRAPP in different classes of organisms indicates that TRAPP function might exhibit differences among organisms. A single copy of the BET5 gene named AtBET5 was found in the Arabidopsis genome based on sequence similarity. Developmental phenotype and the underlying mechanisms have been characterized upon transcriptional knock-down lines generated by both T-DNA insertion and RNAi. Pollen grains of the T-DNA insertional line present reduced fertility and pilate exine instead of tectate exine. Perturbation of the AtBET5 expression by RNAi leads to apical meristematic organization defects and reduced fertility as well. The reduced fertility was due to the pollination barrier caused by an altered composition and structure of pollen walls. Auxin response in root tip cells is altered and there is a severe disruption in polar localization of PIN1-GFP, but to a less extent of PIN2-GFP in the root tips, which causes the apical meristematic organization defects and might also be responsible for the secretion of sporopollenin precursor or polar targeting of sporopollenin precursor transporters.

Involvement of phytohormones in root elongation activity of isoprothiolane in Arabidopsis

Isoprothiolane (diisopropyl 1,3-dithiolan-2-ylidenemalonate, IPT), an active ingredient of "Fuji-one," has been used as a plant growth regulating agent to control non-parasitic damping-off (MURENAE disease) of rice seedlings. To understant plant growth regulating activity of IPT, its effect on root development was investigated in Arabidopsis. IPT enhanced root elongation at a lower concentration (12.5 µg/mL) but suppressed it at a higher concentration (75 µg/mL). Analysis using phytohormone-related mutants and chemical inhibitors revealed that the enhancement of root elongation by IPT required auxin, jasmonic acid, and ethylene signal transduction. Activation of the signal transduction mediated by these three phytohormones was confirmed by gene expression analysis. More detailed mechanisms of IPT's effect on root development were demonstrated via investigation using Arabidopsis and chemical inhibitors.

A Local Auxin Gradient Regulates Root Cap Self-Renewal and Size Homeostasis

Organ size homeostasis, compensatory growth to replace lost tissue, requires constant measurement of size and adjustment of growth rates. Morphogen gradients control organ and tissue sizes by regulating stem cell activity, cell differentiation, and removal in animals [1-3]. In plants, control of tissue size is of specific importance in root caps to protect the growing root tip from mechanical damage [4]. New root cap tissue is formed by the columella and lateral root-cap-epidermal stem cells, whose activity is regulated through non-dividing niche-like cells, the quiescent center (QC) [4, 5]. Columella daughter cells in contact with the QC retain the potency to divide, while derivatives oriented toward the mature cap undergo differentiation. The outermost columella layers are sequentially separated from the root body, involving remodeling of cell walls [6]. Factors regulating the balance between cell division, elongation, and separation to keep root cap size constant are currently unknown [4]. Here, we report that stem cell proliferation induced cell separation at the periphery of the root cap, resulting in tissue size homeostasis. An auxin response gradient with a maximum in the QC and a minimum in the detaching layer was established prior to the onset of cell separation. In agreement with a mathematical model, tissue size was positively regulated by the amount of auxin released from the source. Auxin transporters localized non-polarly to plasma membranes of the inner cap, partly isolating separating layers from the auxin source. Together, these results are in support of an auxin gradient measuring and regulating tissue size.

Plant Hormonomics: Multiple Phytohormone Profiling by Targeted Metabolomics

Phytohormones are physiologically important small molecules that play essential roles in intricate signaling networks that regulate diverse processes in plants. We present a method for the simultaneous targeted profiling of 101 phytohormone-related analytes from minute amounts of fresh plant material (less than 20 mg). Rapid and nonselective extraction, fast one-step sample purification, and extremely sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry enable concurrent quantification of the main phytohormone classes: cytokinins, auxins, brassinosteroids, gibberellins, jasmonates, salicylates, and abscisates. We validated this hormonomic approach in salt-stressed and control Arabidopsis (Arabidopsis thaliana) seedlings, quantifying a total of 43 endogenous compounds in both root and shoot samples. Subsequent multivariate statistical data processing and cross-validation with transcriptomic data highlighted the main hormone metabolites involved in plant adaptation to salt stress.

Combined fine mapping, genetic diversity, and transcriptome profiling reveals that the auxin transporter gene ns plays an important role in cucumber fruit spine development

Map-based cloning was used to identify the ns gene, which was involved in the formation of cucumber numerous fruit spines together with other genes under regulation by plant hormone signal transduction. The cucumber (Cucumis sativus) fruit spine density has an important impact on the commercial value. However, little is known about the regulatory mechanism for the fruit spine formation. Here, we identified NUMEROUS SPINES (NS), which regulate fruit spine development by modulating the Auxin signaling pathway. We fine-mapped the ns using a 2513 F₂ population derived from NCG122 (numerous fruit spines line) and NCG121 (few fruit spines line), and showed that NS encoded auxin transporter-like protein 3. Genetic diversity analysis of the NS gene in natural populations revealed that one SNP and one InDel in the coding region of ns are co-segregated with the fruit spine density. The NS protein sequence was highly conserved among plants, but its regulation of fruit spine development in cucumber seems to be a novel function. Transcriptome profiling indicated that the plant hormone signal transduction-related genes were highly enriched in the up-regulated genes in NCG122 versus NCG121. Moreover, expression pattern analysis of the auxin signal pathway-related genes in NCG122 versus NCG121 showed that upstream genes of the pathway (like ns candidate gene Csa2M264590) are down-regulated, while the downstream genes are up-regulated. Quantitative reverse transcription PCR confirmed the differential expression during the fruit spine development. Therefore, reduced expression of ns may promote the fruit spine formation. Our findings provide a valuable framework for dissecting the regulatory mechanism for the fruit spine development.

Promoter analysis and functional implications of the selenium binding protein (SBP) gene family in Arabidopsis thaliana

Selenium Βinding Protein (SBP, originally termed SBP56) was identified in mouse liver as a cytosolic protein that could bind radioactive selenium. SBPs are highly conserved proteins present in a wide array of species across all kingdoms and are likely to be involved in selenium metabolism. In Arabidopsis, the selenium binding protein (SBP) gene family comprises three genes (AtSBP1, AtSBP2 and AtSBP3). AtSBP1 and AtSBP2 are clustered in a head-to-tail arrangement on chromosome IV, while AtSBP3 is located on chromosome III. In this work, we studied the promoter activity of the Arabidopsis SBP genes, determined their tissue specificity and showed that they are differentially regulated by sodium selenite and sodium selenate. All three SBP genes are upregulated in response to externally applied selenium compounds and the antioxidant NAC selectively downregulates SBP2. Although the effect on SBP2 levels was the most prominent, in all cases, the concurrent exposure of plants to selenite and the antioxidant supressed the expression of the SBP genes. We provide evidence that (at least) SBP1 expression is tightly linked to detoxification processes related to oxidative stress, since it is downregulated in the presence of NAC in selenium-treated plants. Furthermore, our results suggest that SBP genes may participate in the mechanisms that sense redox imbalance.

Gibberellin Localization and Transport in Plants

Distribution patterns and finely-tuned concentration gradients of plant hormones govern plant growth and development. Gibberellin (GA) is a plant hormone regulating key processes in plants; many of them are of significant agricultural importance, such as seed germination, root and shoot elongation, flowering, and fruit patterning. Although studies have demonstrated that GA movement is essential for multiple developmental aspects, how GAs are transported throughout the plant and where exactly they accumulate remain largely unknown. Here, we summarize recent findings from studies of GA movement and localization, and discuss the importance of GA intermediates in long- and short-distance movement. We further review recently identified Arabidopsis GA transporters and highlight their complex specialization and robust functional redundancy in GA transport activity.

Essential Roles of Local Auxin Biosynthesis in Plant Development and in Adaptation to Environmental Changes

It has been a dominant dogma in plant biology that the self-organizing polar auxin transport system is necessary and sufficient to generate auxin maxima and minima that are essential for almost all aspects of plant growth and development. However, in the past few years, it has become clear that local auxin biosynthesis is required for a suite of developmental processes, including embryogenesis, endosperm development, root development, and floral initiation and patterning. Moreover, it was discovered that local auxin biosynthesis maintains optimal plant growth in response to environmental signals, including light, temperature, pathogens, and toxic metals. In this article, I discuss the recent progress in auxin biosynthesis research and the paradigm shift in recognizing the important roles of local auxin biosynthesis in plant biology.

Whole Root Transcriptomic Analysis Suggests a Role for Auxin Pathways in Resistance to Ralstonia solanacearum in Tomato

The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt and causes significant crop loss in the Solanaceae family. The pathogen first infects roots, which are a critical source of resistance in tomato (Solanum lycopersicum L.). Roots of both resistant and susceptible plants are colonized by the pathogen, yet rootstocks can provide significant levels of resistance. Currently, mechanisms of this 'root-mediated resistance' remain largely unknown. To identify the molecular basis of this resistance, we analyzed the genome-wide transcriptional response of roots of resistant 'Hawaii 7996' and susceptible 'West Virginia 700' (WV) tomatoes at multiple timepoints after inoculation with R. solanacearum. We found that defense pathways in roots of the resistant Hawaii 7996 are activated earlier and more strongly than roots of susceptible WV. Further, auxin signaling and transport pathways are suppressed in roots of the resistant variety. Functional analysis of an auxin transport mutant in tomato revealed a role for auxin pathways in bacterial wilt. Together, our results suggest that roots mediate resistance to R. solanacearum through genome-wide transcriptomic changes that result in strong activation of defense genes and alteration of auxin pathways.

Sergeeva L, Vreugdenhil D. Natural variation of hormone levels in Arabidopsis roots and correlations with complex root architecture

Studies on natural variation are an important tool to unravel the genetic basis of quantitative traits in plants. Despite the significant roles of phytohormones in plant development, including root architecture, hardly any studies have been done to investigate natural variation in endogenous hormone levels in plants. Therefore, in the present study a range of hormones were quantified in root extracts of thirteen Arabidopsis thaliana accessions using a ultra performance liquid chromatography triple quadrupole mass spectrometer. Root system architecture of the set of accessions was quantified, using a new parameter (mature root unit) for complex root systems, and correlated with the phytohormone data. Significant variations in phytohormone levels among the accessions were detected, but were remarkably small, namely less than three-fold difference between extremes. For cytokinins, relatively larger variations were found for ribosides and glucosides, as compared to the free bases. For root phenotyping, length-related traits-lateral root length and total root length-showed larger variations than lateral root number-related ones. For root architecture, antagonistic interactions between hormones, for example, indole-3-acetic acid to trans-zeatin were detected in correlation analysis. These findings provide conclusive evidence for the presence of natural variation in phytohormone levels in Arabidopsis roots, suggesting that quantitative genetic analyses are feasible.

Ectopic expression of SsPETE2, a plastocyanin from Suaeda salsa, improves plant tolerance to oxidative stress

Accumulating evidence indicates that plant plastocyanin is involved in copper homeostasis, yet the physiological relevance remains elusive. In this study, we found that a plastocyanin gene (SsPETE2) from euhalophyte Suaeda salsa possessed a novel antioxidant function, which was associated with the copper-chelating activity of SsPETE2. In S. salsa, expression of SsPETE2 increased in response to oxidative stress and ectopic expression of SsPETE2 in Arabidopsis enhanced the antioxidant ability of the transgenic plants. SsPETE2 bound Cu ion and alleviated formation of hydroxyl radicals in vitro. Accordingly, SsPETE2 expression lowered the free Cu content that was associated with reduced H₂O₂ level under oxidative stress. Arabidopsis pete1 and pete2 mutants showed ROS-sensitive phenotypes that could be restored by expression of SsPETE2 or AtPETEs. In addition, SsPETE2-expressing plants exhibited more potent tolerance to oxidative stress than plants overexpressing AtPETEs, likely owing to the stronger copper-binding activity of SsPETE2 than AtPETEs. Taken together, these results demonstrated that plant PETEs play a novel role in oxidative stress tolerance by regulating Cu homeostasis under stress conditions, and SsPETE2, as an efficient copper-chelating PETE, potentially could be used in crop genetic engineering.

Indole acetic acid overproduction transformants of the rhizobacterium Pseudomonas sp. UW4

The plant growth-promoting rhizobacterium Pseudomonas sp. UW4 was transformed to increase the biosynthesis of the auxin, indole-3-acetic acid (IAA). Four native IAA biosynthesis genes from strain UW4 were individually cloned into an expression vector and introduced back into the wild-type strain. Quantitative real-time polymerase chain reaction analysis revealed that the introduced genes ami, nit, nthAB and phe were all overexpressed in these transformants. A significant increase in the production of IAA was observed for all modified strains. Canola plants inoculated with the modified strains showed enhanced root elongation under gnotobiotic conditions. The growth rate and 1-aminocyclopropane-1-carboxylate deaminase activity of transformant strains was lower compared to the wild-type. The indoleacetic acid biosynthesis pathways and the role of this phytohormone in the mechanism of plant growth stimulation by Pseudomonas sp. UW4 is discussed.

Auxin Immunolocalization in Coffea canephora Tissues

Auxins are plant growth regulators that participate in a variety of biological mechanisms during the growth and development of plants. The most abundant natural auxin is indole-3-acetic acid (IAA). The physiological processes regulated by IAA depend on their temporal space accumulation in different tissues of a plant. This accumulation is regulated by its biosynthesis, conjugation, degradation, and transport. Therefore tools that allow us a qualitative and quantitative detection of IAA in plant tissues are very useful to understand the homeostasis of IAA during the life cycle of plants. In this protocol, the complete procedure for localization of IAA in different tissues of Coffea canephora is described using specific anti-IAA monoclonal antibodies.

A supramolecular hydrogel for spatial-temporal release of auxin to promote plant root growth

An auxin-based hydrogelator linked by a hydrolysable ester bond enabled spatial-temporal release of the plant hormone and significantly promoted root growth.

What Has Been Seen Cannot Be Unseen-Detecting Auxin In Vivo

Auxins mediate various processes that are involved in plant growth and development in response to specific environmental conditions. Its proper spatio-temporal distribution that is driven by polar auxin transport machinery plays a crucial role in the wide range of auxins physiological effects. Numbers of approaches have been developed to either directly or indirectly monitor auxin distribution in vivo in order to elucidate the basis of its precise regulation. Herein, we provide an updated list of valuable techniques used for monitoring auxins in plants, with their utilities and limitations. Because the spatial and temporal resolutions of the presented approaches are different, their combination may provide a comprehensive outcome of auxin distribution in diverse developmental processes.

Crosstalk Complexities between Auxin, Cytokinin, and Ethylene in Arabidopsis Root Development: From Experiments to Systems Modeling, and Back Again

Understanding how hormones and genes interact to coordinate plant growth in a changing environment is a major challenge in plant developmental biology. Auxin, cytokinin, and ethylene are three important hormones that regulate many aspects of plant development. This review critically evaluates the crosstalk between the three hormones in Arabidopsis root development. We integrate a variety of experimental data into a crosstalk network, which reveals multiple layers of complexity in auxin, cytokinin, and ethylene crosstalk. In particular, data integration reveals an additional, largely overlooked link between the ethylene and cytokinin pathways, which acts through a phosphorelay mechanism. This proposed link addresses outstanding questions on whether ethylene application promotes or inhibits receptor kinase activity of the ethylene receptors. Elucidating the complexity in auxin, cytokinin, and ethylene crosstalk requires a combined experimental and systems modeling approach. We evaluate important modeling efforts for establishing how crosstalk between auxin, cytokinin, and ethylene regulates patterning in root development. We discuss how a novel methodology that iteratively combines experiments with systems modeling analysis is essential for elucidating the complexity in crosstalk of auxin, cytokinin, and ethylene in root development. Finally, we discuss the future challenges from a combined experimental and modeling perspective.

Auxin Information Processing; Partners and Interactions beyond the Usual Suspects

Auxin plays a major role in a variety of processes involved in plant developmental patterning and its adaptation to environmental conditions. Therefore, an important question is how specificity in auxin signalling is achieved, that is, how a single signalling molecule can carry so many different types of information. In recent years, many studies on auxin specificity have been published, unravelling increasingly more details on differential auxin sensitivity, expression domains and downstream partners of the auxin receptors (transport inhibitor response 1 (TIR1) and other auxin signaling F-box proteins (AFB)), transcriptional repressors that are degraded in response to auxin (AUX/IAA) and downstream auxin response factors (ARF) that together constitute the plant’s major auxin response pathways. These data are critical to explain how, in the same cells, different auxin levels may trigger different responses, as well as how in different spatial or temporal contexts similar auxin signals converge to different responses. However, these insights do not yet answer more complex questions regarding auxin specificity. As an example, they leave open the question of how similar sized auxin changes at similar locations result in different responses depending on the duration and spatial extent of the fluctuation in auxin levels. Similarly, it leaves unanswered how, in the case of certain tropisms, small differences in signal strength at both sides of a plant organ are converted into an instructive auxin asymmetry that enables a robust tropic response. Finally, it does not explain how, in certain cases, substantially different auxin levels become translated into similar cellular responses, while in other cases similar auxin levels, even when combined with similar auxin response machinery, may trigger different responses. In this review, we illustrate how considering the regulatory networks and contexts in which auxin signalling takes place helps answer these types of fundamental questions.

Control of Endogenous Auxin Levels in Plant Root Development

In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.

Expression of Arabidopsis class 1 phytoglobin (AtPgb1) delays death and degradation of the root apical meristem during severe PEG-induced water deficit

Maintenance of a functional root is fundamental to plant survival in response to some abiotic stresses, such as water deficit. In this study, we found that overexpression of Arabidopsis class 1 phytoglobin (AtPgb1) alleviated the growth retardation of polyethylene glycol (PEG)-induced water stress by reducing programmed cell death (PCD) associated with protein folding in the endoplasmic reticulum (ER). This was in contrast to PEG-stressed roots down-regulating AtPgb1 that exhibited extensive PCD and reduced expression of several attenuators of ER stress, including BAX Inhibitor-1 (BI-1). The death program experienced by the suppression of AtPgb1 in stressed roots was mediated by reactive oxygen species (ROS) and ethylene. Suppression of ROS synthesis or ethylene perception reduced PCD and partially restored root growth. The PEG-induced cessation of root growth was preceded by structural changes in the root apical meristem (RAM), including the loss of cell and tissue specification, possibly as a result of alterations in PIN1- and PIN4-mediated auxin accumulation at the root pole. These events were attenuated by the overexpression of AtPgb1 and aggravated when AtPgb1 was suppressed. Specifically, suppression of AtPgb1 compromised the functionality of the WOX5-expressing quiescent cells (QCs), leading to the early and premature differentiation of the adjacent columella stem cells and to a rapid reduction in meristem size. The expression and localization of other root domain markers, such as SCARECROW (SCR), which demarks the endodermis and QCs, and WEREWOLF (WER), which specifies the lateral root cap, were also most affected in PEG-treated roots with suppressed AtPgb1. Collectively, the results demonstrate that AtPgb1 exercises a protective role in roots exposed to lethal levels of PEG, and suggest a novel function of this gene in ensuring meristem functionality through the retention of cell fate specification.

Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture

Shaping of root architecture is a quintessential developmental response that involves the concerted action of many different cell types, is highly dynamic, and underpins root plasticity. To determine to what extent the environmental regulation of lateral root development is a product of cell-type preferential activities, we tracked transcriptomic responses to two different treatments that both change root development in Arabidopsis thaliana at an unprecedented level of temporal detail. We found that individual transcripts are expressed with a very high degree of temporal and spatial specificity, yet biological processes are commonly regulated, in a mechanism we term response nonredundancy. Using causative gene network inference to compare the genes regulated in different cell types and during responses to nitrogen and a biotic interaction, we found that common transcriptional modules often regulate the same gene families but control different individual members of these families, specific to response and cell type. This reinforces that the activity of a gene cannot be defined simply as molecular function; rather, it is a consequence of spatial location, expression timing, and environmental responsiveness.

The MEDIATOR genes MED12 and MED13 control Arabidopsis root system configuration influencing sugar and auxin responses

Arabidopsis med12 and med13 mutants exhibit shoot and root phenotypes related to an altered auxin homeostasis. Sucrose supplementation reactivates both cell division and elongation in primary roots as well as auxin-responsive and stem cell niche gene expression in these mutants. An analysis of primary root growth of WT, med12, aux1-7 and med12 aux1 single and double mutants in response to sucrose and/or N-1-naphthylphthalamic acid (NPA) placed MED12 upstream of auxin transport for the sugar modulation of root growth. The MEDIATOR (MED) complex plays diverse functions in plant development, hormone signaling and biotic and abiotic stress tolerance through coordination of transcription. Here, we performed genetic, developmental, molecular and pharmacological analyses to characterize the role of MED12 and MED13 on the configuration of root architecture and its relationship with auxin and sugar responses. Arabidopsis med12 and med13 single mutants exhibit shoot and root phenotypes consistent with altered auxin homeostasis including altered primary root growth, lateral root development, and root hair elongation. MED12 and MED13 were required for activation of cell division and elongation in primary roots, as well as auxin-responsive and stem cell niche gene expression. Remarkably, most of these mutant phenotypes were rescued by supplying sucrose to the growth medium. The growth response of primary roots of WT, med12, aux1-7 and med12 aux1 single and double mutants to sucrose and application of auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) revealed the correlation of med12 phenotype with the activity of the auxin intake permease and suggests that MED12 acts upstream of AUX1 in the root growth response to sugar. These data provide compelling evidence that MEDIATOR links sugar sensing to auxin transport and distribution during root morphogenesis.

Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root

In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the Arabidopsis root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin's control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size.

mRNA Interactome Capture from Plant Protoplasts

RNA-binding proteins (RBPs) determine the fates of RNAs. They participate in all RNA biogenesis pathways and especially contribute to post-transcriptional gene regulation (PTGR) of messenger RNAs (mRNAs). In the past few years, a number of mRNA-bound proteomes from yeast and mammalian cell lines have been successfully isolated through the use of a novel method called "mRNA interactome capture," which allows for the identification of mRNA-binding proteins (mRBPs) directly from a physiological environment. The method is composed of in vivo ultraviolet (UV) crosslinking, pull-down and purification of messenger ribonucleoprotein complexes (mRNPs) by oligo(dT) beads, and the subsequent identification of the crosslinked proteins by mass spectrometry (MS). Very recently, by applying the same method, several plant mRNA-bound proteomes have been reported simultaneously from different Arabidopsis tissue sources: etiolated seedlings, leaf tissue, leaf mesophyll protoplasts, and cultured root cells. Here, we present the optimized mRNA interactome capture method for Arabidopsis thaliana leaf mesophyll protoplasts, a cell type that serves as a versatile tool for experiments that include various cellular assays. The conditions for optimal protein yield include the amount of starting tissue and the duration of UV irradiation. In the mRNA-bound proteome obtained from a medium-scale experiment (10⁷ cells), RBPs noted to have RNA-binding capacity were found to be overrepresented, and many novel RBPs were identified. The experiment can be scaled up (10⁹ cells), and the optimized method can be applied to other plant cell types and species to broadly isolate, catalog, and compare mRNA-bound proteomes in plants.

Influence of Root Diameter and Soil Depth on the Xylem Anatomy of Fine- to Medium-Sized Roots of Mature Beech Trees in the Top- and Subsoil

Despite their importance for water uptake and transport, the xylem anatomical and hydraulic properties of tree roots have only rarely been studied in the field. We measured mean vessel diameter (D), vessel density (VD), relative vessel lumen area (lumen area per xylem area) and derived potential hydraulic conductivity (Kp) in the xylem of 197 fine- to medium-diameter roots (1-10 mm) in the topsoil and subsoil (0-200 cm) of a mature European beech forest on sandy soil for examining the influence of root diameter and soil depth on xylem anatomical and derived hydraulic traits. All anatomical and functional traits showed strong dependence on root diameter and thus root age but no significant relation to soil depth. Averaged over topsoil and deep soil and variable flow path lengths in the roots, D increased linearly with root diameter from ∼50 μm in the smallest diameter class (1-2 mm) to ∼70 μm in 6-7 mm roots (corresponding to a mean root age of ∼12 years), but remained invariant in roots >7 mm. D never exceeded ∼82 μm in the 1-10 mm roots, probably in order to control the risk of frost- or drought-induced cavitation. This pattern was overlain by a high variability in xylem anatomy among similar-sized roots with Kp showing a higher variance component within than between root diameter classes. With 8% of the roots exceeding average Kp in their diameter class by 50-700%, we obtained evidence of the existence of 'high-conductivity roots' indicating functional differentiation among similar-sized roots. We conclude that the hydraulic properties of small to medium diameter roots of beech are mainly determined by root age, rendering root diameter a suitable predictor of hydraulic functioning, while soil depth - without referring to path length - had a negligible effect.

Zooming In on Plant Hormone Analysis: Tissue- and Cell-Specific Approaches

Plant hormones are a group of naturally occurring, low-abundance organic compounds that influence physiological processes in plants. Our knowledge of the distribution profiles of phytohormones in plant organs, tissues, and cells is still incomplete, but advances in mass spectrometry have enabled significant progress in tissue- and cell-type-specific analyses of phytohormones over the last decade. Mass spectrometry is able to simultaneously identify and quantify hormones and their related substances. Biosensors, on the other hand, offer continuous monitoring; can visualize local distributions and real-time quantification; and, in the case of genetically encoded biosensors, are noninvasive. Thus, biosensors offer additional, complementary technologies for determining temporal and spatial changes in phytohormone concentrations. In this review, we focus on recent advances in mass spectrometry-based quantification, describe monitoring systems based on biosensors, and discuss validations of the various methods before looking ahead at future developments for both approaches.

Shoot stem cell specification in roots by the WUSCHEL transcription factor

The WUSCHEL homeobox transcription factor is required to specify stem-cell identity at the shoot apical meristem and its ectopic expression is sufficient to induce de novo shoot meristem formation. Yet, the manner by which WUS promotes stem-cell fate is not yet fully understood. In the present research we address this question by inducing WUS function outside of its domain. We show that activation of WUS function in the root inhibits the responses to exogenous auxin and suppresses the initiation and growth of lateral roots. Using time lapse movies to follow the cell-cycle marker CYCB1;1::GFP, we also show that activation of WUS function suppresses cell division and cell elongation. In addition, activation of WUS represses the auxin-induced expression of the PLETHORA1 root identity gene and promotes shoot fate. Shoot apical meristem formation requires a high cytokinin-to-auxin ratio. Our findings provide evidence for the manner by which WUS specifies stem-cell identity: by affecting auxin responses, by reducing the cell mitotic activity and by repressing other developmental pathways. At the meristem, the stem-cells which are characterized by low division rate are surrounded by the highly proliferative meristematic cells. Our results also provide a model for WUS establishing the differential mitotic rates between two cell populations at the minute structure of the meristem.

A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana

The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base. A minimal model of the gene regulatory network that underlies cell-fate specification and patterning at the root stem cell niche was proposed before. In this study, we update and couple such network with both the auxin and cytokinin hormone signaling pathways to address how they collectively give rise to attractors that correspond to the genetic and hormonal activity profiles that are characteristic of different cell types along A. thaliana root apical meristem. We used a Boolean model of the genetic-hormonal regulatory network to integrate known and predicted regulatory interactions into alternative models. Our analyses show that, after adding some putative missing interactions, the model includes the necessary and sufficient components and regulatory interactions to recover attractors characteristic of the root cell types, including the auxin and cytokinin activity profiles that correlate with different cellular behaviors along the root apical meristem. Furthermore, the model predicts the existence of activity configurations that could correspond to the transition domain. The model also provides a possible explanation for apparently paradoxical cellular behaviors in the root meristem. For example, how auxin may induce and at the same time inhibit WOX5 expression. According to the model proposed here the hormonal regulation of WOX5 might depend on the cell type. Our results illustrate how non-linear multi-stable qualitative network models can aid at understanding how transcriptional regulators and hormonal signaling pathways are dynamically coupled and may underlie both the acquisition of cell fate and the emergence of hormonal activity profiles that arise during complex organ development.

Model of polar auxin transport coupled to mechanical forces retrieves robust morphogenesis along the Arabidopsis root

Stem cells are identical in many scales, they share the same molecular composition, DNA, genes, and genetic networks, yet they should acquire different properties to form a functional tissue. Therefore, they must interact and get some external information from their environment, either spatial (dynamical fields) or temporal (lineage). In this paper we test to what extent coupled chemical and physical fields can underlie the cell's positional information during development. We choose the root apical meristem of Arabidopsis thaliana to model the emergence of cellular patterns. We built a model to study the dynamics and interactions between the cell divisions, the local auxin concentration, and physical elastic fields. Our model recovers important aspects of the self-organized and resilient behavior of the observed cellular patterns in the Arabidopsis root, in particular, the reverse fountain pattern observed in the auxin transport, the PIN-FORMED (protein family of auxin transporters) polarization pattern and the accumulation of auxin near the region of maximum curvature in a bent root. Our model may be extended to predict altered cellular patterns that are expected under various applied auxin treatments or modified physical growth conditions.

A recovery principle provides insight into auxin pattern control in the Arabidopsis root

Regulated auxin patterning provides a key mechanism for controlling root growth and development. We have developed a data-driven mechanistic model using realistic root geometry and formulated a principle to theoretically investigate quantitative auxin pattern recovery following auxin transport perturbation. This principle reveals that auxin patterning is potentially controlled by multiple combinations of interlinked levels and localisation of influx and efflux carriers. We demonstrate that (1) when efflux carriers maintain polarity but change levels, maintaining the same auxin pattern requires non-uniform and polar distribution of influx carriers; (2) the emergence of the same auxin pattern, from different levels of influx carriers with the same nonpolar localisation, requires simultaneous modulation of efflux carrier level and polarity; and (3) multiple patterns of influx and efflux carriers for maintaining an auxin pattern do not have spatially proportional correlation. This reveals that auxin pattern formation requires coordination between influx and efflux carriers. We further show that the model makes various predictions that can be experimentally validated.

Sirtinol, a Sir2 protein inhibitor, affects stem cell maintenance and root development in Arabidopsis thaliana by modulating auxin-cytokinin signaling components

In Arabidopsis thaliana, besides several key transcription factors and chromatin modifiers, phytohormones auxin and cytokinin play pivotal role in shoot and root meristem maintenance, and lateral root (LR) development. Sirtinol, a chemical inhibitor of Sir2 proteins, is known to promote some auxin induced phenotypes in Arabidopsis. However, its effect on plant stem cell maintenance or organ formation remained unaddressed. Here we show that sirtinol affects meristem maintenance by altering the expression of key stem cell regulators, cell division and differentiation by modulating both auxin and cytokinin signaling in Arabidopsis thaliana. The expression of shoot stem cell niche related genes WUSCHEL (WUS) and CLAVATA3 (CLV3) was upregulated, whereas SHOOT MERISTEMLESS (STM) was downregulated in sirtinol treated seedlings. The expression level and domain of key root stem cell regulators PLETHORA (PLTs) and WUS-Related Homeobox 5 (WOX5) were altered in sirtinol treated roots. Sirtinol affects LR development by disturbing proper auxin transport and maxima formation, similar to 2,4-dichlorophenoxyacetic acid (2,4-D). Sirtinol also affects LR formation by altering cytokinin biosynthesis and signaling genes in roots. Therefore, sirtinol affects shoot and root growth, meristem maintenance and LR development by altering the expression of cytokinin-auxin signaling components, and regulators of stem cells, meristems, and LRs.