Cotyledon vascular pattern2-mediated inositol (1,4,5) triphosphate signal transduction is essential for closed venation patterns of Arabidopsis foliar organs

The low temperature response pathways for cold acclimation and vernalization are independent

Vernalization is the promotion of flowering in response to the prolonged cold of winter. To survive sub-zero winter temperatures, plants must first acclimate to low, non-freezing temperatures (cold acclimation). Induction of VERNALIZATION INSENSITIVE 3 (VIN3), the first gene in the vernalization pathway, is initiated within the same time frame as the induction of genes in the cold acclimation pathway raising the question of whether there are common elements in the signal transduction pathways that activate these two responses to cold. We show that none of the signalling components required for cold acclimation, including the 'master regulator'INDUCTION OF CBF EXPRESSION1 (ICE1) or HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 (HOS1), which has been described as a link between cold acclimation and vernalization, play a role in VIN3 induction. We also show that the hormone abscisic acid (ABA) does not modulate VIN3 induction, consistent with earlier reports that ABA signalling plays no role in the vernalization response. The cold acclimation pathway is activated at 12 °C, at which temperature there is no induction of VIN3 expression. Taken together, our data demonstrate that the responses to low temperatures leading to cold acclimation and vernalization are controlled by distinct signalling pathways.

Inositol polyphosphate 5-phosphatase7 regulates the production of reactive oxygen species and salt tolerance in Arabidopsis

Plants possess remarkable ability to adapt to adverse environmental conditions. The adaptation process involves the removal of many molecules from organelles, especially membranes, and replacing them with new ones. The process is mediated by an intracellular vesicle-trafficking system regulated by phosphatidylinositol (PtdIns) kinases and phosphatases. Although PtdIns comprise a fraction of membrane lipids, they function as major regulators of stress signaling. We analyzed the role of PtdIns 5-phosphatases (5PTases) in plant salt tolerance. The Arabidopsis (Arabidopsis thaliana) genome contains 15 At5PTases. We analyzed salt sensitivity in nine At5ptase mutants and identified one (At5ptase7) that showed increased sensitivity, which was improved by overexpression. At5ptase7 mutants demonstrated reduced production of reactive oxygen species (ROS). Supplementation of mutants with exogenous PtdIns dephosphorylated at the D5' position restored ROS production, while PtdIns(4,5)P(2), PtdIns(3,5)P(2), or PtdIns(3,4,5)P(3) were ineffective. Compromised salt tolerance was also observed in mutant NADPH Oxidase, in agreement with the low ROS production and salt sensitivity of PtdIns 3-kinase mutants and with the inhibition of NADPH oxidase activity in wild-type plants. Localization of green fluorescent protein-labeled At5PTase7 occurred in the plasma membrane and nucleus, places that coincided with ROS production. Analysis of salt-responsive gene expression showed that mutants failed to induce the RD29A and RD22 genes, which contain several ROS-dependent elements in their promoters. Inhibition of ROS production by diphenylene iodonium suppressed gene induction. In summary, our results show a nonredundant function of At5PTase7 in salt stress response by regulating ROS production and gene expression.

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.

Control of leaf and vein development by auxin

Leaves are the main photosynthetic organs of vascular plants and show considerable diversity in their geometries, ranging from simple spoon-like forms to complex shapes with individual leaflets, as in compound leaves. Leaf vascular tissues, which act as conduits of both nutrients and signaling information, are organized in networks of different architectures that usually mirror the surrounding leaf shape. Understanding the processes that endow leaves and vein networks with ordered and closely aligned shapes has captured the attention of biologists and mathematicians since antiquity. Recent work has suggested that the growth regulator auxin has a key role in both initiation and elaboration of final morphology of both leaves and vascular networks. A key feature of auxin action is the existence of feedback loops through which auxin regulates its own transport. These feedbacks may facilitate the iterative generation of basic modules that underlies morphogenesis of both leaves and vasculature.

FORKED1 encodes a PH domain protein that is required for PIN1 localization in developing leaf veins

The formation of Arabidopsis leaf veins is believed to require canalization of auxin into discrete and continuous cell files to generate a highly reproducible branched and reticulate pattern. During canalization, incipient veins become preferred routes for auxin transport through expression and asymmetric localization of the PINFORMED1 (PIN1) auxin efflux protein: PIN1 expression narrows from a group of cells to a single cell file, and localization of PIN1 protein becomes polarized to the cell membrane facing a previously formed vein. The shift in PIN1 localization is believed to require active vesicle cycling and be auxin-dependent, generating an autoregulatory loop. Previously, we have shown that fkd1 mutant leaves have an open vein pattern that lacks distal vein meeting. Here, we identify FKD1 as encoding a pleckstrin homology domain- and DUF828-containing protein. A fusion of the FKD1 promoter and the GUS reporter gene was expressed in vascular tissue throughout the plant, and its expression in incipient veins in leaves narrows in a manner similar to that of PIN1. FKD1 expression in roots and leaves can be altered by changes to auxin response and auxin transport. In the absence of FKD1, PIN1::GFP narrowing to incipient veins is delayed, and localization to the apical cell face is infrequent. The lack of apical PIN1 localization correlates with the failure of newly forming veins to connect distally with previously formed veins. Our data suggest that FKD1 influences PIN1 localization in an auxin-dependent manner, and we propose that it represents a key component of the auxin canalization pathway.

COE1, an LRR-RLK responsible for commissural vein pattern formation in rice

Leaf veins have a complex network pattern. Formation of this vein pattern has been widely studied as a model of tissue pattern formation in plants. To understand the molecular mechanism governing the vascular patterning process, we isolated the rice mutant, commissural vein excessive1 (coe1). The coe1 mutants had short commissural vein (CV) intervals and produced clustered CVs. Application of 1-N-naphthylphthalamic acid and brefeldin A decreased CV intervals, and application of 1-naphthaleneacetic acid increased CV intervals in wild-type rice; however, coe1 mutants were insensitive to these chemicals. COE1 encodes a leucine-rich repeat receptor-like kinase, whose amino acid sequence is similar to that of brassinosteroid-insensitive 1-associated receptor kinase 1 (BAK1), and which is localized at the plasma membrane. Because of the sequence similarity of COE1 to BAK1, we also examined the involvement of brassinosteroids in CV formation. Brassinolide, an active brassinosteroid, decreased the CV intervals of wild-type rice, and brassinazole, an inhibitor of brassinosteroid biosynthesis, increased the CV intervals of wild-type rice, but coe1 mutants showed insensitivity to these chemicals. These results suggest that auxin and brassinosteroids regulate CV intervals in opposite directions, and COE1 may regulate CV intervals downstream of auxin and brassinosteroid signals.

myo-Inositol-1-phosphate synthase is required for polar auxin transport and organ development

myo-Inositol-1-phosphate synthase is a conserved enzyme that catalyzes the first committed and rate-limiting step in inositol biosynthesis. Despite its wide occurrence in all eukaryotes, the role of myo-inositol-1-phosphate synthase and de novo inositol biosynthesis in cell signaling and organism development has been unclear. In this study, we isolated loss-of-function mutants in the Arabidopsis MIPS1 gene from different ecotypes. It was found that all null mips1 mutants are defective in embryogenesis, cotyledon venation patterning, root growth, and root cap development. The mutant roots are also agravitropic and have reduced basipetal auxin transport. mips1 mutants have significantly reduced levels of major phosphatidylinositols and exhibit much slower rates of endocytosis. Treatment with brefeldin A induces slower PIN2 protein aggregation in mips1, indicating altered PIN2 trafficking. Our results demonstrate that MIPS1 is critical for maintaining phosphatidylinositol levels and affects pattern formation in plants likely through regulation of auxin distribution.

The sterol methyltransferases SMT1, SMT2, and SMT3 influence Arabidopsis development through nonbrassinosteroid products

Plant sterols are structural components of cell membranes that provide rigidity, permeability, and regional identity to membranes. Sterols are also the precursors to the brassinosteroid signaling molecules. Evidence is accumulating that specific sterols have roles in pattern formation during development. COTYLEDON VASCULAR PATTERNING1 (CVP1) encodes C-24 STEROL METHYLTRANSFERASE2 (SMT2), one of three SMTs in Arabidopsis (Arabidopsis thaliana). SMT2 and SMT3, which also encodes a C-24 SMT, catalyze the reaction that distinguishes the synthesis of structural sterols from signaling brassinosteroid derivatives and are highly regulated. The deficiency of SMT2 in the cvp1 mutant results in moderate developmental defects, including aberrant cotyledon vein patterning, serrated floral organs, and reduced stature, but plants are viable, suggesting that SMT3 activity can substitute for the loss of SMT2. To test the distinct developmental roles of SMT2 and SMT3, we identified a transcript null smt3 mutant. Although smt3 single mutants appear wild type, cvp1 smt3 double mutants show enhanced defects relative to cvp1 mutants, such as discontinuous cotyledon vein pattern, and produce novel phenotypes, including defective root growth, loss of apical dominance, sterility, and homeotic floral transformations. These phenotypes are correlated with major alterations in the profiles of specific sterols but without significant alterations to brassinosteroid profiles. The alterations to sterol profiles in cvp1 mutants affect auxin response, demonstrated by weak auxin insensitivity, enhanced axr1 auxin resistance, ectopically expressed DR5:beta-glucuronidase in developing embryos, and defective response to auxin-inhibited PIN2-green fluorescent protein endocytosis. We discuss the developmental roles of sterols implied by these results.

The RON1/FRY1/SAL1 gene is required for leaf morphogenesis and venation patterning in Arabidopsis

To identify genes involved in vascular patterning in Arabidopsis (Arabidopsis thaliana), we screened for abnormal venation patterns in a large collection of leaf shape mutants isolated in our laboratory. The rotunda1-1 (ron1-1) mutant, initially isolated because of its rounded leaves, exhibited an open venation pattern, which resulted from an increased number of free-ending veins. We positionally cloned the RON1 gene and found it to be identical to FRY1/SAL1, which encodes an enzyme with inositol polyphosphate 1-phosphatase and 3' (2'),5'-bisphosphate nucleotidase activities and has not, to our knowledge, previously been related to venation patterning. The ron1-1 mutant and mutants affected in auxin homeostasis share perturbations in venation patterning, lateral root formation, root hair length, shoot branching, and apical dominance. These similarities prompted us to monitor the auxin response using a DR5-GUS auxin-responsive reporter transgene, the expression levels of which were increased in roots and reduced in leaves in the ron1-1 background. To gain insight into the function of RON1/FRY1/SAL1 during vascular development, we generated double mutants for genes involved in vein patterning and found that ron1 synergistically interacts with auxin resistant1 and hemivenata-1 but not with cotyledon vascular pattern1 (cvp1) and cvp2. These results suggest a role for inositol metabolism in the regulation of auxin responses. Microarray analysis of gene expression revealed that several hundred genes are misexpressed in ron1-1, which may explain the pleiotropic phenotype of this mutant. Metabolomic profiling of the ron1-1 mutant revealed changes in the levels of 38 metabolites, including myoinositol and indole-3-acetonitrile, a precursor of auxin.

The Arabidopsis thaliana Myo-inositol 1-phosphate synthase1 gene is required for Myo-inositol synthesis and suppression of cell death

l-myo-inositol 1-phosphate synthase (MIPS; EC 5.5.1.4) catalyzes the rate-limiting step in the synthesis of myo-inositol, a critical compound in the cell. Plants contain multiple MIPS genes, which encode highly similar enzymes. We characterized the expression patterns of the three MIPS genes in Arabidopsis thaliana and found that MIPS1 is expressed in most cell types and developmental stages, while MIPS2 and MIPS3 are mainly restricted to vascular or related tissues. MIPS1, but not MIPS2 or MIPS3, is required for seed development, for physiological responses to salt and abscisic acid, and to suppress cell death. Specifically, a loss in MIPS1 resulted in smaller plants with curly leaves and spontaneous production of lesions. The mips1 mutants have lower myo-inositol, ascorbic acid, and phosphatidylinositol levels, while basal levels of inositol (1,4,5)P(3) are not altered in mips1 mutants. Furthermore, mips1 mutants exhibited elevated levels of ceramides, sphingolipid precursors associated with cell death, and were complemented by a MIPS1-green fluorescent protein (GFP) fusion construct. MIPS1-, MIPS2-, and MIPS3-GFP each localized to the cytoplasm. Thus, MIPS1 has a significant impact on myo-inositol levels that is critical for maintaining levels of ascorbic acid, phosphatidylinositol, and ceramides that regulate growth, development, and cell death.

Increasing inositol (1,4,5)-trisphosphate metabolism affects drought tolerance, carbohydrate metabolism and phosphate-sensitive biomass increases in tomato

Inositol-(1,4,5)-trisphosphate (InsP(3)) is a second messenger in plants that increases in response to many stimuli. The metabolic consequences of this signalling pathway are not known. We reduced the basal level of InsP(3) in tomato (Solanum lycopersicum cv. Micro-Tom) by expressing the human type I inositol polyphosphate 5-phosphatase (InsP 5-ptase) gene. Transgenic lines producing InsP 5-ptase protein had between 15% and 30% of the basal InsP(3) level of control plants. This increased hydrolysis of InsP(3) caused dramatic increases in drought tolerance, vegetative biomass and lycopene and hexose concentrations in the fruits. Transcript profiling of root, leaf and fruit tissues identified a small group of genes, including a cell-wall invertase inhibitor gene, that were differentially regulated in all tissues of the InsP 5-ptase expressing plants. Significant differences were found in the amounts of carbohydrates and organic phosphate in these plants. Plants with increased hydrolysis of InsP(3) in the cytosol also showed increased net CO(2)-fixation and sucrose export into sink tissue and storage of hexoses in the source leaves. The increase in biomass was dependent on the supply of inorganic phosphate in the nutrient medium. Uptake and storage of phosphate was increased in the transgene expressing lines. This suggests that in tomato, increased flux through the inositol phosphate pathway uncoupled phosphate sensing from phosphate metabolism. Altering the second messenger, InsP(3), revealed multiple coordinated changes in development and metabolism in tomato that have potential for crop improvement.

Regulation of preprocambial cell state acquisition by auxin signaling in Arabidopsis leaves

The principles underlying the formation of veins in the leaf have long intrigued developmental biologists. In Arabidopsis leaves, files of anatomically inconspicuous subepidermal cells that will elongate into vein-forming procambial cells selectively activate ATHB8 gene expression. The biological role of ATHB8 in vein formation and the molecular events that culminate in acquisition of the ATHB8preprocambial cell state are unknown, but intertwined pathways of auxin transport and signal transduction have been implicated in defining paths of vascular strand differentiation. Here we show that ATHB8 is required to stabilize preprocambial cell specification against auxin transport perturbations, to restrict preprocambial cell state acquisition to narrow fields and to coordinate procambium formation within and between veins. We further show that ATHB8 expression at preprocambial stages is directly and positively controlled by the auxin-response transcription factor MONOPTEROS (MP) through an auxin-response element in the ATHB8promoter. We finally show that the consequences of loss of ATHB8function for vein formation are masked by MP activity. Our observations define, at the molecular level, patterning inputs of auxin signaling in vein formation.

The role of Arabidopsis 5PTase13 in root gravitropism through modulation of vesicle trafficking

Inositol polyphosphate 5-phosphatases (5PTases) are enzymes of phosphatidylinositol metabolism that affect various aspects of plant growth and development. Arabidopsis 5PTase13 regulates auxin homeostasis and hormone-related cotyledon vein development, and here we demonstrate that its knockout mutant 5pt13 has elevated sensitivity to gravistimulation in root gravitropic responses. The altered responses of 5pt13 mutants to 1-N-naphthylphthalamic acid (an auxin transport inhibitor) indicate that 5PTase13 might be involved in the regulation of auxin transport. Indeed, the auxin efflux carrier PIN2 is expressed more broadly under 5PTase13 deficiency, and observations of the internalization of the membrane-selective dye FM4-64 reveal altered vesicle trafficking in 5pt13 mutants. Compared with wild-type, 5pt13 mutant seedlings are less sensitive to the inhibition by brefeldin A of vesicle cycling, seedling growth, and the intracellular cycling of the PIN1 and PIN2 proteins. Further, auxin redistribution upon gravitropic stimulation is stimulated under 5PTase13 deficiency. These results suggest that 5PTase13 may modulate auxin transport by regulating vesicle trafficking and thereby play a role in root gravitropism.

CVP2- and CVL1-mediated phosphoinositide signaling as a regulator of the ARF GAP SFC/VAN3 in establishment of foliar vein patterns

In foliar organs of dicots, veins are arranged in a highly branched or reticulated pattern for efficient distribution of water, photosynthates and signaling molecules. Recent evidence suggests that the patterns rely in part on regulation of intracellular vesicle transport and cell polarity in selected cells during leaf development. The sorting of vesicle cargos to discrete cellular sites is regulated in yeast and animal cells by the binding of specific phosphoinositides (PIs). We report here that, in the plant Arabidopsis, specific PIs guide the vesicle traffic that is essential for polarized and continuous vein pattern formation. Mutations in SFC/VAN3, an ADP-ribosylation factor GTPase-activating protein (ARF GAP) with a PI-binding pleckstrin homology domain, result in discontinuous vein patterns. Plants with mutations in both CVP2 and CVL1, which encode inositol polyphosphate 5'-phosphatases that generate the specific PI ligand for the pleckstrin homology domain of SFC/VAN3, phosphatidylinositol-4-monophosphate (PI(4)P), have a discontinuous vein phenotype identical to that of sfc/van3 mutants. Single cvp2 or cvl1 mutants show weak and no discontinuous vein phenotypes, respectively, suggesting that they act redundantly. We propose that these two 5'-phosphatases regulate vein continuity and cell polarity by generating a specific PI ligand for SFC/VAN3.

Molecular characterization of ThIPK2, an inositol polyphosphate kinase gene homolog from Thellungiella halophila, and its heterologous expression to improve abiotic stress tolerance in Brassica napus

Inositol polyphosphate kinases play important roles in diverse cellular processes. In this study, the function of an inositol polyphosphate kinase gene homolog named ThIPK2 from a dicotyledonous halophyte Thellungiella halophila was investigated. The deduced translation product (ThIPK2) shares 85% identity with the Arabidopsis inositol polyphosphate kinase AtIPK2beta. Transient expression of ThIPK2-YFP fusion protein in tobacco (Nicotiana tabacum) protoplasts indicates that the protein is localized to the nucleus and plasma membrane, with a minor localization to the cytosol. Heterologous expression of ThIPK2 in ipk2Delta (also known as arg82Delta), a yeast mutant strain that lacks inositol polyphosphate multikinase (Ipk2) activity, rescued the mutant's salt-, osmotic- and temperature-sensitive growth defects. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed ubiquitous expression of ThIPK2 in various tissues, including roots, rosette leaves, cauline leaves, stem, flowers and siliques, and shoot ThIPK2 transcript was strongly induced by NaCl or mannitol in T. halophila as exhibited by real-time PCR analysis. Transgenic expression of ThIPK2 in Brassica napus led to significantly improved salt-, dehydration- and oxidative stress resistance. Furthermore, the transcripts of various stress responsive marker genes increased in ThIPK2 transgenic plants under salt stress condition. These results suggest that ThIPK2 is involved in plant stress responses, and for the first time demonstrate that ThIPK2 could be a useful candidate gene for improving drought and salt tolerance in important crop plants by genetic transformation.

Function and regulation of phospholipid signalling in plants

As an important metabolic pathway, phosphatidylinositol metabolism generates both constitutive and signalling molecules that are crucial for plant growth and development. Recent studies using genetic and molecular approaches reveal the important roles of phospholipid molecules and signalling in multiple processes of higher plants, including root growth, pollen and vascular development, hormone effects and cell responses to environmental stimuli plants. The present review summarizes the current progress in our understanding of the functional mechanism of phospholipid signalling, with an emphasis on the regulation of Ins(1,4,5)P3-Ca2+ oscillation, the second messenger molecule phosphatidic acid and the cytoskeleton.

Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants

ACAP-type ARF GTPase activating proteins (ARF-GAPs) regulate multiple cellular processes, including endocytosis, secretion, phagocytosis, cell adhesion and cell migration. However, the regulation of ACAP functions by other cellular proteins is poorly understood. We have reported previously that a plant ACAP, VAN3, plays a pivotal role in plant venation continuity. Here, we report on newly identified VAN3 regulators: the CVP2 (cotyledon vascular pattern 2) 5 PTase, which is considered to degrade IP(3) and also to produce PtdIns(4)P from PtdIns(4,5)P(2); and a PH domain-containing protein, VAB (VAN3 binding protein). Combinational mutations of both CVP2 and its closest homologue CVL1 (CVP2 like 1) phenocopied the strong allele of van3 mutants, showing severe vascular continuity. The phenotype of double mutants between van3, cvp2 and vab suggested that VAN3, CVP2 and VAB function in vascular pattern formation in the same pathway. Localization analysis revealed that both CVP2 and VAB colocalize with VAN3 in the trans-Golgi network (TGN), supporting their functions in the same pathway. The subcellular localization of VAN3 was dependent on its PH domain, and mislocalization of VAN3 was induced in cvp2 or vab mutants. These results suggest that CVP2 and VAB cooperatively regulate the subcellular localization of VAN3 through the interaction between its PH domain and phosphoinositides and/or inositol phosphates. In addition, PtdIns(4)P, to which VAN3 binds preferentially, enhanced the ARF-GAP activity of VAN3, whereas IP(3) inhibited it. These results suggest the existence of PtdIns(4)P and/or IP(3)-dependent subcellular targeting and regulation of VAN3 ACAP activity that governs plant vascular tissue continuity.

Hormone interactions during vascular development

Vascular tissue in plants is unique due to its diverse and dynamic cellular patterns. Signals controlling vascular development have only recently started to emerge through biochemical, genetic, and genomic approaches in several organisms, such as Arabidopsis, Populus, and Zinnia. These signals include hormones (auxin, brassinosteroids, and cytokinins, in particular), other small regulatory molecules, their transporters, receptors, and various transcriptional regulators. In recent years it has become apparent that plant growth regulators rarely act alone, but rather their signaling pathways are interlocked in complex networks; for example, polar auxin transport (PAT) regulates vascular development during various stages and an emerging theme is its modulation by other growth regulators, depending on the developmental context. Also, several synergistic or antagonistic interactions between various growth regulators have been described. Furthermore, shoot-root interactions appear to be important for this signal integration.

VH1/BRL2 receptor-like kinase interacts with vascular-specific adaptor proteins VIT and VIK to influence leaf venation

VH1/BRL2 is a receptor-like kinase of the BRI1 family with a role in vascular development. In developing Arabidopsis leaves it is expressed first in ground cells and then becomes restricted to provascular and procambial cells as venation forms. We isolated proteins interacting with the activated (phosphorylated) cytoplasmic domain of VH1/BRL2, and found that most belong to three processes: proteasome activity, vesicle traffic and intracellular signal transduction. Two adaptor proteins are included that we named VIT [VH1-interacting tetratricopeptide repeat (TPR)-containing protein] and VIK (VH1-interacting kinase), which are co-expressed in the same cells as VH1/BRL2 at two distinct time points in vein differentiation. Mutation of either adaptor or of VH1 results in vein pattern defects and in alterations in response to auxin and brassinosteroids. We propose that these two adaptors facilitate the diversification and amplification of a ligand signal perceived by VH1/BRL2 in multiple downstream pathways affecting venation.

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

The functions of the plant body rely on interactions among distinct and nonequivalent cell types. The comparison of transcriptomes from different cell types should expose the transcriptional networks that underlie cellular attributes and contributions. Using laser microdissection and microarray profiling, we have produced a cell type transcriptome atlas that includes 40 cell types from rice (Oryza sativa) shoot, root and germinating seed at several developmental stages, providing patterns of cell specificity for individual genes and gene classes. Cell type comparisons uncovered previously unrecognized properties, including cell-specific promoter motifs and coexpressed cognate binding factor candidates, interaction partner candidates and hormone response centers. We inferred developmental regulatory hierarchies of gene expression in specific cell types by comparison of several stages within root, shoot and embryo.

Plant phospholipid signaling: "in a nutshell"

Since the discovery of the phosphoinositide/phospholipase C (PI/PLC) system in animal systems, we know that phospholipids are much more then just structural components of biological membranes. In the beginning, this idea was fairly straightforward. Receptor stimulation activates PLC, which hydrolyses phosphatidylinositol4,5-bisphosphate [PtdIns(4,5)P2] into two second messengers: inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DG). While InsP3 difuses into the cytosol and triggers the release of calcium from an internal store via ligand-gated calcium channels, DG remains in the membrane where it recruits and activates members of the PKC family. The increase in calcium, together with the change in phosphorylation status, (in)activates a variety of protein targets, leading to a massive reprogramming, allowing the cell to appropriately respond to the extracellular stimulus. Later, it became obvious that not just PLC, but a variety of other phospholipid-metabolizing enzymes were activated, including phospholipase A, phospholipase D, and PI 3-kinase. More recently, it has become apparent that PtdIns4P and PtdIns(4,5)P2 are not just signal precursors but can also function as signaling molecules themselves. While plants contain most of the components described above, and evidence for their role in cell signaling is progressively increasing, major differences between plants and the mammalian paradigms exist. Below, these are described "in a nutshell."

Interaction of the WD40 domain of a myoinositol polyphosphate 5-phosphatase with SnRK1 links inositol, sugar, and stress signaling

In plants, myoinositol signaling pathways have been associated with several stress, developmental, and physiological processes, but the regulation of these pathways is largely unknown. In our efforts to better understand myoinositol signaling pathways in plants, we have found that the WD40 repeat region of a myoinositol polyphosphate 5-phosphatase (5PTase13; At1g05630) interacts with the sucrose nonfermenting-1-related kinase (SnRK1.1) in the yeast two-hybrid system and in vitro. Plant SnRK1 proteins (also known as AKIN10/11) have been described as central integrators of sugar, metabolic, stress, and developmental signals. Using mutants defective in 5PTase13, we show that 5PTase13 can act as a regulator of SnRK1 activity and that regulation differs with different nutrient availability. Specifically, we show that under low-nutrient or -sugar conditions, 5PTase13 acts as a positive regulator of SnRK1 activity. In contrast, under severe starvation conditions, 5PTase13 acts as a negative regulator of SnRK1 activity. To delineate the regulatory interaction that occurs between 5PTase13 and SnRK1.1, we used a cell-free degradation assay and found that 5PTase13 is required to reduce the amount of SnRK1.1 targeted for proteasomal destruction under low-nutrient conditions. This regulation most likely involves a 5PTase13-SnRK1.1 interaction within the nucleus, as a 5PTase13:green fluorescent protein was localized to the nucleus. We also show that a loss of function in 5PTase13 leads to nutrient level-dependent reduction of root growth, along with abscisic acid (ABA) and sugar insensitivity. 5ptase13 mutants accumulate less inositol 1,4,5-trisphosphate in response to sugar stress and have alterations in ABA-regulated gene expression, both of which are consistent with the known role of inositol 1,4,5-trisphosphate in ABA-mediated signaling. We propose that by forming a protein complex with SnRK1.1 protein, 5PTase13 plays a regulatory role linking inositol, sugar, and stress signaling.

Cell differentiation in the longitudinal veins and formation of commissural veins in rice (Oryza sativa) and maize (Zea mays)

Vascular development is a central theme in plant science. However, little is known about the mechanism of vascular development in monocotyledons (compared with dicotyledons). Therefore, we investigated sequential processes of differentiation into various different vascular cells by carrying out detailed observations using serial sections of the bases of developing leaves of rice and maize. The developmental process of the longitudinal vascular bundles was divided into six stages in rice and five stages in maize. The initiation of differentiation into procambial progenitor cells forming the commissural vein arose in a circular layer cell that was adjacent to both a metaxylem vessel and one or a few phloem cells in stage V longitudinal vascular bundles. In most cases the differentiation of ground meristem cells into procambial progenitor cells extended in one direction, toward the next longitudinal vascular bundle, and subsequent periclinal divisions and further differentiation produced a vessel element, two companion cells and a sieve element to form a commissural vein. These results suggest the presence of an intercellular signal(s) that induces differentiation of the circular layer cell and the ground meristem cells into procambial progenitor cells, forming a commissural vein sequentially.

Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana

Leaf veins form a closed network that transports essential photosynthates, water and signaling molecules to the developing plant. The formation of the patterns of these networks during leaf ontogeny is an active subject of modeling and computer simulation. To investigate the vein patterning process, we performed screens for defects in juvenile leaf vein patterning in Arabidopsis thaliana lines subjected to mutagenesis via diepoxybutane, activation tagging or the Dissociation/Activator transposon. We identified over 40 vein pattern defective lines, providing a phenotypic resource for the testing of vein patterning models. In addition, we report the chromosomal linkage for 13 of these, eight of which were successfully cloned. We further describe the phenotypes of five of these mutants, which we call the defectively organized tributaries (dot) mutants, and their corresponding molecular identities. The diversity of the individual genes affected in this collection of pattern mutants suggests that vein pattern is highly sensitive to perturbations in many cellular processes. Despite this diversity of causes, the resulting pattern defects fall into a limited number of classes, including parallel, spurred, misaligned, open, midvein gap and irregularly spaced. These classes may represent sensitivities to cellular processes associated with the DOT genes. The ontogeny of common defective patterns should be accommodated into any robust model for the ontogeny and evolution of pattern.

A phosphatidylinositol phosphate-specific myo-inositol polyphosphate 5-phosphatase required for seedling growth

The phosphatidylinositol phosphate signaling pathway is involved in many crucial cellular functions. The myo-inositol polyphosphate 5-phosphatases (5PTases) (E.C. 3.1.3.56) comprise a large protein family that hydrolyze 5-phosphates from a variety of phosphatidylinositol phosphate and inositol phosphate substrates. We previously reported that the At5PTase11 enzyme (At1g47510), which is one of the smallest predicted 5PTases found in any organism, encodes an active 5PTase whose activity is restricted to tris- and bis-, but not mono-phosphorylated phosphatidylinositol phosphate substrates containing a 5-phosphate. This is in contrast to other unrestricted Arabidopsis 5PTases, which also hydrolyze tris- and bis inositol phosphate molecules. To further explore the function of At5PTase11, we have characterized two T-DNA mutants in the At5PTase11 gene, and have complemented this mutant. Seed from 5ptase11 mutants germinate slower than wildtype seed and mutant seedlings have decreased hypocotyl growth as compared to wildtype seedlings when grown in the dark. This phenotype is the opposite of the increased hypocotyl growth phenotype previously described for other 5ptase mutants defective in inositol phosphate-specific 5PTase enzymes. By labeling the endogenous myo-inositol pool in 5ptase11 mutants, we correlated these hypocotyl growth changes with a small increase in the 5PTase11 substrate, phosphatidylinositol (4,5) bisphosphate, and decreases in the potential products of 5PTase11, phosphatidylinositol (3) phosphate and phosphatidylinositol (4) phosphate. Surprisingly, we also found that dark-grown 5ptase11 mutants contain increases in inositol (1,4,5) trisphosphate and an inositol bisphosphate that is not a substrate for recombinant 5PTase11. We present a model for regulation of hypocotyl growth by specific molecules found in this pathway.

Auxin transport-dependent, stage-specific dynamics of leaf vein formation

For centuries, the formation of vein patterns in the leaf has intrigued biologists, mathematicians and philosophers. In leaf development, files of vein-forming procambial cells emerge from seemingly homogeneous subepidermal tissue through the selection of anatomically inconspicuous preprocambial cells. Although the molecular details underlying the orderly differentiation of veins in the leaf remain elusive, gradually restricted transport paths of the plant hormone auxin have long been implicated in defining sites of vein formation. Several recent advances now appear to converge on a more precise definition of the role of auxin flow at different stages of vascular development. The picture that emerges is that of vein formation as a self-organizing, reiterative, auxin transport-dependent process.

Enhancement of stress tolerance in transgenic tobacco plants constitutively expressing AtIpk2beta, an inositol polyphosphate 6-/3-kinase from Arabidopsis thaliana

Inositol phosphates (IPs) and their turnover products have been implicated to play important roles in stress signaling in eukaryotic cells. In higher plants genes encoding inositol polyphosphate kinases have been identified previously, but their physiological functions have not been fully resolved. Here we expressed Arabidopsis inositol polyphosphate 6-/3-kinase (AtIpk2beta) in two heterologous systems, i.e. the yeast Saccharomyces cerevisiae and in tobacco (Nicotiana tabacum), and tested the effect on abiotic stress tolerance. Expression of AtIpk2beta rescued the salt-, osmotic- and temperature-sensitive growth defects of a yeast mutant strain (arg82Delta) that lacks inositol polyphosphate multikinase activity encoded by the ARG82/IPK2 gene. Transgenic tobacco plants constitutively expressing AtIpk2beta under the control of the Cauliflower Mosaic Virus 35S promoter were generated and found to exhibit improved tolerance to diverse abiotic stresses when compared to wild type plants. Expression patterns of various stress responsive genes were enhanced, and the activities of anti-oxidative enzymes were elevated in transgenic plants, suggesting a possible involvement of AtIpk2beta in plant stress responses.

An inositol polyphosphate 5-phosphatase functions in PHOTOTROPIN1 signaling in Arabidopis by altering cytosolic Ca2+

Inositol polyphosphate 5-phosphatase (5PTase) is a key enzyme in the phosphatidylinositol metabolic pathway, which plays critical roles in a number of cellular processes in plants. Our previous work implicated the role of 5PTase13, which encodes a WD40-containing type II 5PTase, in hormone-mediated cotyledon vein development. Here, we show that 5PTase13 is also involved in blue light responses in Arabidopsis thaliana. Compared with that in darkness, the expression of 5PTase13 was suppressed by blue light irradiation, and disruption of the gene resulted in shortened hypocotyls and expanded cotyledons. Genetic analysis showed that 5PTase13 acted independently from CRYPTOCHROME1 and CONSTITUTIVE PHOTOMORPHOGENIC1 but interacted functionally with PHOTOTROPIN1 (PHOT1). The expression level of 5PTase13 was significantly enhanced in phot1 single or phot1 phot2 double mutants under blue light, and suppression of 5PTase13 expression rescued the elongated hypocotyls in the phot1 or phot1 phot2 mutants. Further analysis showed that the blue light-induced elevation of cytosolic Ca2+ was inhibited in the phot1 mutant but enhanced in the 5pt13 mutant, suggesting that 5PTase13 antagonizes PHOT1-mediated effects on calcium signaling under blue light.

Phytohormone collaboration: zooming in on auxin-brassinosteroid interactions

Similar to animal hormones, classic plant hormones are small organic molecules that regulate physiological and developmental processes. In development, this often involves the regulation of growth through the control of cell size or division. The plant hormones auxin and brassinosteroid modulate both cell expansion and proliferation and are known for their overlapping activities in physiological assays. Recent molecular genetic analyses in the model plant Arabidopsis suggest that this reflects interdependent and often synergistic action of the two hormone pathways. Such pathway interactions probably occur through the combinatorial regulation of common target genes by auxin- and brassinosteroid-controlled transcription factors. Moreover, auxin and brassinosteroid signaling and biosynthesis and auxin transport might be linked by an emerging upstream connection involving calcium-calmodulin and phosphoinositide signaling.

Cleome, a genus closely related to Arabidopsis, contains species spanning a developmental progression from C(3) to C(4) photosynthesis

C(4) photosynthesis involves alterations to leaf development, cell biology and biochemistry. Different lineages of C(4) plants use varying mechanisms to generate the C(4) pathway. Although the biochemistry of C(4) photosynthesis was described around 20 years ago, the phylogenetic distance between Arabidopsis and the traditional C(4) models has not facilitated the transfer of knowledge from Arabidopsis research to understanding C(4) systems. We show that Cleome, a genus closely related to Arabidopsis, contains species spanning a developmental progression from C(3) to C(4) photosynthesis. The majority of species we assessed are C(3) plants but have increased venation in leaves. Three C(3) species have both increased venation and enlarged bundle sheath cells, and there is also a tendency to accumulate proteins and transcripts needed for C(4) photosynthesis. Cleome gynandra shows all the characteristics needed for efficient C(4) photosynthesis, including alterations to leaf biochemistry, cell biology and development, and belongs to the NAD-dependent malic enzyme subtype. Combined with its phylogenetic proximity to Arabidopsis, the developmental progression from C(3) to C(4) photosynthesis within the genus provides a potentially excellent new model to increase our understanding of C(4) photosynthesis, and provide insights into its evolution.

Arabidopsis nucleolin affects plant development and patterning

Nucleolin is a major nucleolar protein implicated in many aspects of ribosomal biogenesis, including early events such as processing of the large 35S preribosomal RNA. We found that the Arabidopsis (Arabidopsis thaliana) parallel1 (parl1) mutant, originally identified by its aberrant leaf venation, corresponds to the Arabidopsis nucleolin gene. parl1 mutants display parallel leaf venation, aberrant localization of the provascular marker Athb8:beta-glucuronidase, the auxin-sensitive reporter DR5:beta-glucuronidase, and auxin-dependent growth defects. PARL1 is highly similar to the yeast (Saccharomyces cerevisiae) nucleolin NUCLEAR SIGNAL RECOGNITION 1 (NSR1) multifunctional protein; the Arabidopsis PARL1 gene can rescue growth defects of yeast nsr1 null mutants. This suggests that PARL1 protein may have roles similar to those of the yeast nucleolin in nuclear signal recognition, ribosomal processing, and ribosomal subunit accumulation. Based on the range of auxin-related defects in parl1 mutants, we propose that auxin-dependent organ growth and patterning is highly sensitive to the efficiency of nucleolin-dependent ribosomal processing.

Components of the Arabidopsis mRNA decapping complex are required for early seedling development

To understand the mechanisms controlling vein patterning in Arabidopsis thaliana, we analyzed two phenotypically similar mutants, varicose (vcs) and trident (tdt). We had previously identified VCS, and recently, human VCS was shown to function in mRNA decapping. Here, we report that TDT encodes the mRNA-decapping enzyme. VCS and TDT function together in small cytoplasmic foci that appear to be processing bodies. To understand the developmental requirements for mRNA decapping, we characterized the vcs and tdt phenotypes. These mutants were small and chlorotic, with severe defects in shoot apical meristem formation and cotyledon vein patterning. Many capped mRNAs accumulated in tdt and vcs mutants, but surprisingly, some mRNAs were specifically depleted. In addition, loss of decapping arrested the decay of some mRNAs, while others showed either modest or no decay defects, suggesting that mRNAs may show specificity for particular decay pathways (3' to 5' and 5' to 3'). Furthermore, the severe block to postembryonic development in vcs and tdt and the accompanying accumulation of embryonic mRNAs indicate that decapping is important for the embryo-to-seedling developmental transition.

Inositol polyphosphate 5-phosphatases 1 and 2 are required for regulating seedling growth

Signals can be perceived and amplified at the cell membrane by receptors coupled to the production of a variety of second messengers, including myoinositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)]. The myoinositol polyphosphate 5-phosphatases (5PTases; EC 3.1.3.56) comprise a large protein family that hydrolyzes 5-phosphates from a variety of myoinositol phosphate (InsP) and phosphoinositide phosphate (PtdInsP) substrates. Arabidopsis thaliana has 15 genes encoding 5PTases. Biochemical analyses of a subgroup of 5PTase enzymes suggest that these enzymes have both overlapping and unique substrate preferences. Ectopic expression of these genes in transgenic plants can reduce Ins(1,4,5)P(3) levels and alter abscisic acid (ABA) signaling. To further explore the function of 5PTases in signaling, we have identified and characterized T-DNA insertional mutants for 5PTase1 and 5PTase2 and produced a double mutant. When grown in the dark, the seeds from these mutants germinate faster than wild-type seeds and the mutant seedlings have longer hypocotyls than wild-type seedlings. Seeds from these mutant lines also demonstrate an increase in sensitivity to ABA. These changes in early seedling growth are accompanied by mass increases in Ins(1,4,5)P(3), but not by changes in endogenous ABA content. By labeling the endogenous myoinositol pool in 5ptase1 and 5ptase2 mutants, we detected increases in Ins(1,4,5)P(3) and a decrease in PtdIns, PtdIns(4)P, and phosphatidylinositol (4,5) bisphosphate. Taken together, these data indicate that the At5PTase1 and At5PTase2 genes have nonredundant roles in hydrolyzing inositol second-messenger substrates and that regulation of Ins(1,4,5)P(3) levels is important during germination and early seedling development.

How canalization can make loops: A new model of reticulated leaf vascular pattern formation

Formation of the vascular system in plant leaves can be explained by the canalization hypothesis which states that veins are formed in an initially homogeneous field by a self-organizing process between the plant hormone auxin and auxin carrier proteins. Previous models of canalization can generate vein patterns with branching but fail to generate vein patterns with closed loops. However, closed vein loops are commonly observed in plant leaves and are important in making them robust to herbivore attacks and physical damage. Here we propose a new model which generates a vein system with closed loops. We postulate that the "flux bifurcator" level is enhanced in cells with a high auxin flux and that it causes reallocation of auxin carriers toward neighbouring cells also having a high bifurcator level. This causes the auxin flux to bifurcate, allowing vein tips to attach to other veins creating vein loops. We explore several alternative functional forms for the flux bifurcator affecting the reallocation of efflux carriers and examine parameter dependence of the resulting vein pattern.

Down-regulation of the 26S proteasome subunit RPN9 inhibits viral systemic transport and alters plant vascular development

Plant viruses utilize the vascular system for systemic movement. The plant vascular network also transports water, photosynthates, and signaling molecules and is essential for plant growth. However, the molecular mechanisms governing vascular development and patterning are still largely unknown. From viral transport suppressor screening using virus-induced gene silencing, we identified a 26S proteasome subunit, RPN9, which is required for broad-spectrum viral systemic transport. Silencing of RPN9 in Nicotiana benthamiana inhibits systemic spread of two taxonomically distinct viruses, Tobacco mosaic virus and Turnip mosaic virus. The 26S proteasome is a highly conserved eukaryotic protease complex controlling many fundamental biochemical processes, but the functions of many 26S proteasome regulatory subunits, especially in plants, are still poorly understood. We demonstrate that the inhibition of viral systemic transport after RPN9 silencing is largely due to alterations in the vascular tissue. RPN9-silenced plants display extra leaf vein formation with increased xylem and decreased phloem. We further illustrate that RPN9 functions at least in part through regulation of auxin transport and brassinosteroid signaling, two processes that are crucial for vascular formation. We propose that RPN9 regulates vascular formation by targeting a subset of regulatory proteins for degradation. The brassinosteroid-signaling protein BZR1 is one of the targets.

TheHVE/CAND1gene is required for the early patterning of leaf venation inArabidopsis

The hemivenata-1 (hve-1) recessive allele was isolated in a search for natural variations in the leaf venation pattern of Arabidopsis thaliana, where it was seen to cause extremely simple venation in vegetative leaves and cotyledons, increased shoot branching, and reduced root waving and fertility, traits that are reminiscent of some mutants deficient in auxin signaling. Reduced sensitivity to exogenous auxin was found in the hve-1 mutant, which otherwise displayed a wild-type response to auxin transport inhibitors. The HVE gene was positionally cloned and found to encode a CAND1 protein. The hve-1 mutation caused mis-splicing of the transcripts of the HVE/CAND1 gene and a vein phenotype indistinguishable from that of hve-2 and hve-3,two putatively null T-DNA alleles. Inflorescence size and fertility were more affected by hve-2 and hve-3, suggesting that hve-1is hypomorphic. The simple venation pattern of hve plants seems to arise from an early patterning defect. We found that HVE/CAND1 binds to CULLIN1, and that the venation patterns of axr1 and hvemutants are similar, which suggest that ubiquitin-mediated auxin signaling is required for venation patterning in laminar organs, the only exception being cauline leaves. Our analyses of double mutant and transgenic plants indicated that auxin transport and perception act independently to pattern leaf veins,and that the HVE/CAND1 gene acts upstream of ATHB-8 at least in higher order veins, in a pathway that involves AXR1, but not LOP1, PIN1, CVP1 or CVP2.

SCARFACE encodes an ARF-GAP that is required for normal auxin efflux and vein patterning in Arabidopsis

To identify molecular mechanisms controlling vein patterns, we analyzed scarface (sfc) mutants. sfc cotyledon and leaf veins are largely fragmented, unlike the interconnected networks in wild-type plants. SFC encodes an ADP ribosylation factor GTPase activating protein (ARF-GAP), a class with well-established roles in vesicle trafficking regulation. Quadruple mutants of SCF and three homologs (ARF-GAP DOMAIN1, 2, and 4) showed a modestly enhanced vascular phenotype. Genetic interactions between sfc and pinoid and between sfc and gnom suggest a possible function for SFC in trafficking of auxin efflux regulators. Genetic analyses also revealed interaction with cotyledon vascular pattern2, suggesting that lipid-based signals may underlie some SFC ARF-GAP functions. To assess possible roles for SFC in auxin transport, we analyzed sfc roots, which showed exaggerated responses to exogenous auxin and higher auxin transport capacity. To determine whether PIN1 intracellular trafficking was affected, we analyzed PIN1:green fluorescent protein (GFP) dynamics using confocal microscopy in sfc roots. We found normal PIN1:GFP localization at the apical membrane of root cells, but treatment with brefeldin A resulted in PIN1 accumulating in smaller and more numerous compartments than in the wild type. These data suggest that SFC is required for normal intracellular transport of PIN1 from the plasma membrane to the endosome.

A universal role for inositol 1,4,5-trisphosphate-mediated signaling in plant gravitropism

Inositol 1,4,5-trisphosphate (InsP3) has been implicated in the early signaling events of plants linking gravity sensing to the initiation of the gravitropic response. However, at present, the contribution of the phosphoinositide signaling pathway in plant gravitropism is not well understood. To delineate the role of InsP3 in plant gravitropism, we generated Arabidopsis (Arabidopsis thaliana) plants constitutively expressing the human type I inositol polyphosphate 5-phosphatase (InsP 5-ptase), an enzyme that specifically hydrolyzes InsP3. The transgenic plants show no significant differences in growth and life cycle compared to wild-type plants, although basal InsP3 levels are reduced by greater than 90% compared to wild-type plants. With gravistimulation, InsP3 levels in inflorescence stems of transgenic plants show no detectable change, whereas in wild-type plant inflorescences, InsP3 levels increase approximately 3-fold within the first 5 to 15 min of gravistimulation, preceding visible bending. Furthermore, gravitropic bending of the roots, hypocotyls, and inflorescence stems of the InsP 5-ptase transgenic plants is reduced by approximately 30% compared with the wild type. Additionally, the cold memory response of the transgenic plants is attenuated, indicating that InsP3 contributes to gravisignaling in the cold. The transgenic roots were shown to have altered calcium sensitivity in controlling gravitropic response, a reduction in basipetal indole-3-acetic acid transport, and a delay in the asymmetric auxin-induced beta-glucuronidase expression with gravistimulation as compared to the controls. The compromised gravitropic response in all the major axes of growth in the transgenic Arabidopsis plants reveals a universal role for InsP3 in the gravity signal transduction cascade of plants.

Vascular development: the long and winding road

Vascular development involves the specification of distinct meristematic cells that proliferate and then differentiate into two separate multicellular tissues: xylem and phloem. Organ-specific patterning, which requires the co-ordination of vascular development with organogenesis, introduces another layer of complexity to the development of vascular tissues. Because vascular tissues develop internally, analyses of their development are technically challenging. Nevertheless, the combined use of genetic and genomic approaches has provided significant insight into the mechanisms of vascular development. Notable highlights include the identification of class III HD-ZIP genes as regulators of both (pro)cambial activity and vascular tissue specification, the characterization of vesicle-trafficking components (SCARFACE [SFC]/VAN3) as being necessary for axial vein pattern, the genetic characterization of xylogen, and the identification of transcription factors and hormone signals that regulate vascular cell identity.

At5PTase13 modulates cotyledon vein development through regulating auxin homeostasis

Phosphatidylinositol signaling pathway and the relevant metabolites are known to be critical to the modulation of different aspects of plant growth, development, and stress responses. Inositol polyphosphate 5-phosphatase is a key enzyme involved in phosphatidylinositol metabolism and is encoded by an At5PTase gene family in Arabidopsis thaliana. A previous study shows that At5PTase11 mediates cotyledon vascular development probably through the regulation of intracellular calcium levels. In this study, we provide evidence that At5PTase13 modulates the development of cotyledon veins through its regulation of auxin homeostasis. A T-DNA insertional knockout mutant, At5pt13-1, showed a defect in development of the cotyledon vein, which was rescued completely by exogenous auxin and in part by brassinolide, a steroid hormone. Furthermore, the mutant had reduced auxin content and altered auxin accumulation in seedlings revealed by the DR5:beta-glucuronidase fusion construct in seedlings. In addition, microarray analysis shows that the transcription of key genes responsible for auxin biosynthesis and transport was altered in At5pt13-1. The At5pt13-1 mutant was also less sensitive to auxin inhibition of root elongation. These results suggest that At5PTase13 regulates the homeostasis of auxin, a key hormone controlling vascular development in plants.

Phloem and xylem specification: pieces of the puzzle emerge

The plant vascular system is composed of two tissue types, xylem and phloem, which originate from the vascular meristem, the procambium. Recently, several regulatory mechanisms that control the specification of these two tissue types have been uncovered. These include the asymmetric patterning of xylem and phloem in the vascular bundle by the class III HD-ZIP and KANADI genes, the tissue-type-specific control of vascular cell proliferation by brassinosteroids and class III HD-ZIP genes, the regulation of vascular tissue identity by the MYB-like transcription factor APL, and inductive signalling during xylem differentiation by xylogen. These findings define an emerging developmental framework for the control of vascular tissue specification.

Multiple regulatory elements contribute to the vascular-specific expression of the rice HD-Zip gene Oshox1 in Arabidopsis

The primary vascular tissues of plants differentiate from a single precursor tissue, the procambium. The role of upstream regulatory sequences in the transcriptional control of early vascular-specific gene expression is largely unknown. The onset of expression of the rice homeodomain-leucine zipper (HD-Zip) gene Oshox1 marks procambial cells that have acquired their distinctive anatomical features but do not yet display any overt signs of terminal vascular differentiation. The expression pattern of Oshox1 in rice appears to be mainly controlled by the activity of the 1.6 kb upstream promoter region. Here, we show that the Oshox1 promoter directs vascular, auxin- and sucrose-responsive reporter gene expression in Arabidopsis plants in a fashion comparable with that in rice. This is the case not only during normal development but also upon experimental manipulation, suggesting that the cis-acting regulatory elements that are instrumental in Oshox1 expression pattern are conserved between rice and Arabidopsis. Finally, through analysis of reporter gene expression profiles conferred by progressive 5' deletions of the Oshox1 promoter in transgenic Arabidopsis, we have identified upstream regulatory regions required for auxin and sucrose inducibility, and for cell type-, tissue- and organ-specific aspects of Oshox1 expression. Our study suggests that Oshox1 embryonic vascular expression is mainly achieved through suppression of expression in non-vascular tissues.

Mutations in the Arabidopsis phosphoinositide phosphatase gene SAC9 lead to overaccumulation of PtdIns(4,5)P2 and constitutive expression of the stress-response pathway

Phosphoinositides (PIs) are signaling molecules that regulate cellular events including vesicle targeting and interactions between membrane and cytoskeleton. Phosphatidylinositol (PtdIns)(4,5)P(2) is one of the best characterized PIs; studies in which PtdIns(4,5)P(2) localization or concentration is altered lead to defects in the actin cytoskeleton and exocytosis. PtdIns(4,5)P(2) and its derivative Ins(1,4,5)P(3) accumulate in salt, cold, and osmotically stressed plants. PtdIns(4,5)P(2) signaling is terminated through the action of inositol polyphosphate phosphatases and PI phosphatases including supressor of actin mutation (SAC) domain phosphatases. In some cases, these phosphatases also act on Ins(1,4,5)P(3). We have characterized the Arabidopsis (Arabidopsis thaliana) sac9 mutants. The SAC9 protein is different from other SAC domain proteins in several ways including the presence of a WW protein interaction domain within the SAC domain. The rice (Oryza sativa) and Arabidopsis SAC9 protein sequences are similar, but no apparent homologs are found in nonplant genomes. High-performance liquid chromatography studies show that unstressed sac9 mutants accumulate elevated levels of PtdIns(4,5)P(2) and Ins(1,4,5)P(3) as compared to wild-type plants. The sac9 mutants have characteristics of a constitutive stress response, including dwarfism, closed stomata, and anthocyanin accumulation, and they overexpress stress-induced genes and overaccumulate reactive-oxygen species. These results suggest that the SAC9 phosphatase is involved in modulating phosphoinsitide signals during the stress response.

The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl

The growth of secondary xylem and phloem depends on the division of cells in the vascular cambium and results in an increase in the diameter of the root and stem. Very little is known about the genetic mechanisms that control cambial activity and the differentiation of secondary xylem and phloem cell types. To begin to identify new genes required for vascular cell differentiation and function, we performed genome-wide expression profiling of xylem and phloem-cambium isolated from the root-hypocotyl of Arabidopsis (Arabidopsis thaliana). Gene expression in the remaining nonvascular tissue was also profiled. From these transcript profiles, we assembled three sets of genes with expression significantly biased toward xylem, phloem-cambium, or nonvascular tissue. We also assembled three two-tissue sets of genes with expression significantly biased toward xylem/phloem-cambium, xylem/nonvascular, or phloem-cambium/nonvascular tissues. Localizations predicted by transcript profiles were supported by results from promoter-reporter and reverse transcription-polymerase chain reaction experiments with nine xylem- or phloem-cambium-biased genes. An analysis of the members of the phloem-cambium gene set suggested that some genes involved in regulating primary meristems are also regulators of the cambium. Secondary phloem was implicated in the synthesis of auxin, glucosinolates, cytokinin, and gibberellic acid. Transcript profiles also supported the importance of class III HD ZIP and KANADI transcription factors as regulators of radial patterning during secondary growth, and identified several members of the G2-like, NAC, AP2, MADS, and MYB transcription factor families that may play roles as regulators of xylem or phloem cell differentiation and activity.

FRAGILE FIBER3, an Arabidopsis gene encoding a type II inositol polyphosphate 5-phosphatase, is required for secondary wall synthesis and actin organization in fiber cells

Type II inositol polyphosphate 5-phosphatases (5PTases) in yeast and animals have been known to regulate the level of phosphoinositides and thereby influence various cellular activities, such as vesicle trafficking and actin organization. In plants, little is known about the phosphatases involved in hydrolysis of phosphoinositides, and roles of type II 5PTases in plant cellular functions have not yet been characterized. In this study, we demonstrate that the FRAGILE FIBER3 (FRA3) gene of Arabidopsis thaliana, which encodes a type II 5PTase, plays an essential role in the secondary wall synthesis in fiber cells and xylem vessels. The fra3 mutations caused a dramatic reduction in secondary wall thickness and a concomitant decrease in stem strength. These phenotypes were associated with an alteration in actin organization in fiber cells. Consistent with the defective fiber and vessel phenotypes, the FRA3 gene was found to be highly expressed in fiber cells and vascular tissues in stems. The FRA3 protein is composed of two domains, an N-terminal localized WD-repeat domain and a C-terminal localized 5PTase catalytic domain. In vitro activity assay demonstrated that recombinant FRA3 exhibited phosphatase activity toward PtdIns(4,5)P2, PtdIns(3,4,5)P3, and Ins(1,4,5)P3, with the highest substrate affinity toward PtdIns(4,5)P2. The fra3 missense mutation, which caused an amino acid substitution in the conserved motif II of the 5PTase catalytic domain, completely abolished the FRA3 phosphatase activity. Moreover, the endogenous levels of PtdIns(4,5)2 and Ins(1,4,5)P3 were found to be elevated in fra3 stems. Together, our findings suggest that the FRA3 type II 5PTase is involved in phosphoinositide metabolism and influences secondary wall synthesis and actin organization.