Identification of a new polyphosphoinositide in plants, phosphatidylinositol 5-monophosphate (PtdIns5P), and its accumulation upon osmotic stress

Phosphoinositides in plant-pathogen interaction: trends and perspectives

Phosphoinositides are important regulatory membrane lipids, with a role in plant development and cellular function. Emerging evidence indicates that phosphoinositides play crucial roles in plant defence and are also utilized by pathogens for infection. In this review, we highlight the role of phosphoinositides in plant-pathogen interaction and the implication of this remarkable convergence in the battle against plant diseases.

Chlamydomonas proteases: classification, phylogeny, and molecular mechanisms

Proteases can regulate myriad biochemical pathways by digesting or processing target proteins. While up to 3% of eukaryotic genes encode proteases, only a tiny fraction of proteases are mechanistically understood. Furthermore, most of the current knowledge about proteases is derived from studies of a few model organisms, including Arabidopsis thaliana in the case of plants. Proteases in other plant model systems are largely unexplored territory, limiting our mechanistic comprehension of post-translational regulation in plants and hampering integrated understanding of how proteolysis evolved. We argue that the unicellular green alga Chlamydomonas reinhardtii has a number of technical and biological advantages for systematic studies of proteases, including reduced complexity of many protease families and ease of cell phenotyping. With this end in view, we share a genome-wide inventory of proteolytic enzymes in Chlamydomonas, compare the protease degradomes of Chlamydomonas and Arabidopsis, and consider the phylogenetic relatedness of Chlamydomonas proteases to major taxonomic groups. Finally, we summarize the current knowledge of the biochemical regulation and physiological roles of proteases in this algal model. We anticipate that our survey will promote and streamline future research on Chlamydomonas proteases, generating new insights into proteolytic mechanisms and the evolution of digestive and limited proteolysis.

Link between Lipid Second Messengers and Osmotic Stress in Plants

Plants are subject to different types of stress, which consequently affect their growth and development. They have developed mechanisms for recognizing and processing an extracellular signal. Second messengers are transient molecules that modulate the physiological responses in plant cells under stress conditions. In this sense, it has been shown in various plant models that membrane lipids are substrates for the generation of second lipid messengers such as phosphoinositide, phosphatidic acid, sphingolipids, and lysophospholipids. In recent years, research on lipid second messengers has been moving toward using genetic and molecular approaches to reveal the molecular setting in which these molecules act in response to osmotic stress. In this sense, these studies have established that second messengers can transiently recruit target proteins to the membrane and, therefore, affect protein conformation, activity, and gene expression. This review summarizes recent advances in responses related to the link between lipid second messengers and osmotic stress in plant cells.

Signalling Pinpointed to the Tip: The Complex Regulatory Network That Allows Pollen Tube Growth

Plants display a complex life cycle, alternating between haploid and diploid generations. During fertilisation, the haploid sperm cells are delivered to the female gametophyte by pollen tubes, specialised structures elongating by tip growth, which is based on an equilibrium between cell wall-reinforcing processes and turgor-driven expansion. One important factor of this equilibrium is the rate of pectin secretion mediated and regulated by factors including the exocyst complex and small G proteins. Critically important are also non-proteinaceous molecules comprising protons, calcium ions, reactive oxygen species (ROS), and signalling lipids. Among the latter, phosphatidylinositol 4,5-bisphosphate and the kinases involved in its formation have been assigned important functions. The negatively charged headgroup of this lipid serves as an interaction point at the apical plasma membrane for partners such as the exocyst complex, thereby polarising the cell and its secretion processes. Another important signalling lipid is phosphatidic acid (PA), that can either be formed by the combination of phospholipases C and diacylglycerol kinases or by phospholipases D. It further fine-tunes pollen tube growth, for example by regulating ROS formation. How the individual signalling cues are intertwined or how external guidance cues are integrated to facilitate directional growth remain open questions.

Guilt by Association: A Phenotype-Based View of the Plant Phosphoinositide Network

Eukaryotic membranes contain small amounts of phospholipids that have regulatory effects on the physiological functions of cells, tissues, and organs. Phosphoinositides (PIs)-the phosphorylated derivatives of phosphatidylinositol-are one example of such regulatory lipids. Although PIs were described in plants decades ago, their contribution to the regulation of physiological processes in plants is not well understood. In the past few years, evidence has emerged that PIs are essential for plant function and development. Recently reported phenotypes associated with the perturbation of different PIs suggest that some subgroups of PIs influence specific processes. Although the molecular targets of PI-dependent regulation in plants are largely unknown, the effects of perturbed PI metabolism can be used to propose regulatory modules that involve particular downstream targets of PI regulation. This review summarizes phenotypes associated with the perturbation of the plant PI network to categorize functions and suggest possible downstream targets of plant PI regulation.

PI5P and PI(3,5)P2: Minor, but Essential Phosphoinositides

In most eukaryotes, phosphoinositides (PIs) have crucial roles in multiple cellular functions. Although the cellular levels of phosphatidylinositol 5-phosphate (PI5P) and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P₂) are extremely low relative to some other PIs, emerging evidence demonstrates that both lipids are crucial for the endocytic pathway, intracellular signaling, and adaptation to stress. Mutations that causes defects in the biosynthesis of PI5P and PI(3,5)P₂ are linked to human diseases including neurodegenerative disorders. Here, we review recent findings on cellular roles of PI5P and PI(3,5)P₂, as well as the pathophysiological importance of these lipids.Key words: Phosphoinositides, Membrane trafficking, Endocytosis, Vacuoles/Lysosomes, Fab1/PIKfyve.

An Autophagy-Related Kinase Is Essential for the Symbiotic Relationship between Phaseolus vulgaris and Both Rhizobia and Arbuscular Mycorrhizal Fungi

Eukaryotes contain three types of lipid kinases that belong to the phosphatidylinositol 3-kinase (PI3K) family. In plants and Saccharomyces cerevisiae, only PI3K class III family members have been identified. These enzymes regulate the innate immune response, intracellular trafficking, autophagy, and senescence. Here, we report that RNAi-mediated downregulation of common bean (Phaseolus vulgaris) PI3K severely impaired symbiosis in composite P. vulgaris plants with endosymbionts such as Rhizobium tropici and Rhizophagus irregularis Downregulation of Pv-PI3K was associated with a marked decrease in root hair growth and curling. Additionally, infection thread growth, root-nodule number, and symbiosome formation in root nodule cells were severely affected. Interestingly, root colonization by AM fungi and the formation of arbuscules were also abolished in PI3K loss-of-function plants. Furthermore, the transcript accumulation of genes encoding proteins known to interact with PI3K to form protein complexes involved in autophagy was drastically reduced in these transgenic roots. RNAi-mediated downregulation of one of these genes, Beclin1/Atg6, resulted in a similar phenotype as observed for transgenic roots in which Pv-PI3K had been downregulated. Our findings show that an autophagy-related process is crucial for the mutualistic interactions of P. vulgaris with beneficial microorganisms.

The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output

Phosphoinositides (PI) are important signaling molecules in the nucleus that influence gene expression. However, if and how nuclear PI directly affects the transcriptional machinery is not known. We report that the lipid kinase PIP4K2B regulates nuclear PI5P and the expression of myogenic genes during myoblast differentiation. A targeted screen for PI interactors identified the PHD finger of TAF3, a TATA box binding protein-associated factor with important roles in transcription regulation, pluripotency, and differentiation. We show that the PI interaction site is distinct from the known H3K4me3 binding region of TAF3 and that PI binding modulates association of TAF3 with H3K4me3 in vitro and with chromatin in vivo. Analysis of TAF3 mutants indicates that TAF3 transduces PIP4K2B-mediated alterations in PI into changes in specific gene transcription. Our study reveals TAF3 as a direct target of nuclear PI and further illustrates the importance of basal transcription components as signal transducers.

Plant phosphoinositides-complex networks controlling growth and adaptation

Plants differ in many ways from mammals or yeast. However, plants employ phosphoinositides for the regulation of essential cellular functions as do all other eukaryotes. In recent years the plant phosphoinositide system has been linked to the control of cell polarity. Phosphoinositides are also implicated in plant adaptive responses to changing environmental conditions. The current understanding is that plant phosphoinositides control membrane trafficking, ion channels and the cytoskeleton in similar ways as in other eukaryotic systems, but adapted to meet plant cellular requirements and with some plant-specific features. In addition, the formation of soluble inositol polyphosphates from phosphoinositides is important for the perception of important phytohormones, as the relevant receptor proteins contain such molecules as structural cofactors. Overall, the essential nature of phosphoinositides in plants has been established. Still, the complexity of the phosphoinositide networks in plant cells is only emerging and invites further study of its molecular details. This article is part of a special issue entitled Phosphoinositides.

Involvement of Phosphatidylinositol 3-kinase in the regulation of proline catabolism in Arabidopsis thaliana

Plant adaptation to abiotic stresses such as drought and salinity involves complex regulatory processes. Deciphering the signaling components that are involved in stress signal transduction and cellular responses is of importance to understand how plants cope with salt stress. Accumulation of osmolytes such as proline is considered to participate in the osmotic adjustment of plant cells to salinity. Proline accumulation results from a tight regulation between its biosynthesis and catabolism. Lipid signal components such as phospholipases C and D have previously been shown to be involved in the regulation of proline metabolism in Arabidopsis thaliana. In this study, we demonstrate that proline metabolism is also regulated by class-III Phosphatidylinositol 3-kinase (PI3K), VPS34, which catalyses the formation of phosphatidylinositol 3-phosphate (PI3P) from phosphatidylinositol. Using pharmacological and biochemical approaches, we show that the PI3K inhibitor, LY294002, affects PI3P levels in vivo and that it triggers a decrease in proline accumulation in response to salt treatment of A. thaliana seedlings. The lower proline accumulation is correlated with a lower transcript level of Pyrroline-5-carboxylate synthetase 1 (P5CS1) biosynthetic enzyme and higher transcript and protein levels of Proline dehydrogenase 1 (ProDH1), a key-enzyme in proline catabolism. We also found that the ProDH1 expression is induced in a pi3k-hemizygous mutant, further demonstrating that PI3K is involved in the regulation of proline catabolism through transcriptional regulation of ProDH1. A broader metabolomic analysis indicates that LY294002 also reduced other metabolites, such as hydrophobic and aromatic amino acids and sugars like raffinose.

Analysis of D3-,4-,5-phosphorylated phosphoinositides using HPLC

Detection of polyphosphoinositides (PPIs) is difficult due to their low chemical abundancy. This problem is further complicated by the fact that PPIs are present as various, distinct isomers, which are difficult, if not impossible, to separate by conventional thin layer chromatography (TLC) systems. PPIs in plants include PtdIns3P, PtdIns4P, PtdIns5P, PtdIns(3,5)P 2, and PtdIns(4,5)P 2. Here, a protocol is described analyzing plant PPIs using (32)P-orthophosphorus pre-labeled material. After extraction, lipids are deacylated and the resulting glycerophosphoinositol polyphosphates (GroPInsPs) separated by HPLC using a strong anion-exchange column and a shallow salt gradient. Alternatively, PPIs are first separated by TLC, the lipids reisolated, deacylated, and the GroPInsPs then separated by HPLC.

PtdIns5P: news and views of its appearance, disappearance and deeds

Accumulated evidence indicates that PtdIns5P, one of the seven phosphoinositides, found now to be constitutively present in yeast, plants and metazoa, serves as a signaling molecule to modulate pleiotropic cellular functions in both the nucleus and the cytoplasm. The enzymatic routes in biogenesis of basal PtdIns5P have remained incompletely understood. The role for candidate kinase PIKfyve that is principally involved in PtdIns(3,5)P2 production, has been questioned. In this review article we scrutinize the past obstacles that prevented the definitive implication of PIKfyve in PtdIns5P biosynthesis from PtdIns and focus on the recent pharmacological and genetic advancements that now make this conclusion well supported. We further summarize our current knowledge of the diverse stimuli modulating PtdIns5P levels, binding partners and regulated cellular process, with particular reference to the available mechanistic insights for the relevant signaling pathways.

Analyzing plant signaling phospholipids through 32Pi-labeling and TLC

Lipidomic analyses through LC-, GC-, and ESI-MS/MS can detect numerous lipid species based on headgroup and fatty acid compositions but usually miss the minor phospholipids involved in cell signaling because of their low chemical abundancy. Due to their high turnover, these signaling lipids are, however, readily picked up by labeling plant material with (32)P-orthophosphate and subsequent analysis of the lipid extracts by thin layer chromatography. Here, protocols are described for suspension-cultured tobacco BY-2 cells, young Arabidopsis seedlings, Vicia faba roots, and Arabidopsis leaf disks, which can easily be modified for other plant species and tissues.

Regulation of phosphatidylinositol-5-phosphate signaling by Pin1 determines sensitivity to oxidative stress

Oxidative signaling and oxidative stress contribute to aging, cancer, and diseases resulting from neurodegeneration. Pin1 is a proline isomerase that recognizes phosphorylated substrates and regulates the localization and conformation of its targets. Pin1(-/-) mice show phenotypes associated with premature aging, yet mouse embryonic fibroblasts (MEFs) from these mice are resistant to hydrogen peroxide (H(2)O(2))-induced cell death. We found that the abundance of phosphatidylinositol-5-phosphate (PtdIns5P) was increased in response to H(2)O(2), an effect that was enhanced in Pin1(-/-) MEFs. Reduction of H(2)O(2)-induced PtdIns5P compromised cell viability in response to oxidative stress, suggesting that PtdIns5P contributed to the enhanced cell viability of Pin1(-/-) MEFs exposed to oxidative stress. The increased PtdIns5P in the Pin1(-/-) MEFs stimulated the expression of genes involved in defense against oxidative stress and reduced the accumulation of reactive oxygen species. Pin1 and PtdIns5P 4-kinases (PIP4Ks), enzymes that phosphorylate and thereby reduce the amount of PtdIns5P, interacted in a manner dependent on the phosphorylation of PIP4K. Although reintroduction of Pin1 into the Pin1(-/-) MEFs reduced the amount of PtdIns5P produced in response to H(2)O(2), in vitro assays indicated that the isomerase activity of Pin1 inhibited PIP4K activity. Whether this isomerise-mediated inhibition of PIP4K occurs in cells remains an open question, but the data suggest that the regulation of PIP4K by Pin1 may be complex.

Divergent functions of the myotubularin (MTM) homologs AtMTM1 and AtMTM2 in Arabidopsis thaliana: evolution of the plant MTM family

Myotubularin and myotubularin-related proteins are evolutionarily conserved in eukaryotes. Defects in their function result in muscular dystrophy, neuronal diseases and leukemia in humans. In contrast to the animal lineage, where genes encoding both active and inactive myotubularins (phosphoinositide 3-phosphatases) have appeared and proliferated in the basal metazoan group, myotubularin genes are not found in the unicellular relatives of green plants. However, they are present in land plants encoding proteins highly similar to the active metazoan enzymes. Despite their remarkable structural conservation, plant and animal myotubularins have significantly diverged in their functions. While loss of myotubularin function causes severe disease phenotypes in humans it is not essential for the cellular homeostasis under normal conditions in Arabidopsis thaliana. Instead, myotubularin deficiency is associated with altered tolerance to dehydration stress. The two Arabidopsis genes AtMTM1 and AtMTM2 have originated from a segmental chromosomal duplication and encode catalytically active enzymes. However, only AtMTM1 is involved in elevating the cellular level of phosphatidylinositol 5-phosphate in response to dehydration stress, and the two myotubularins differentially affect the Arabidopsis dehydration stress-responding transcriptome. AtMTM1 and AtMTM2 display different localization patterns in the cell, consistent with the idea that they associate with different membranes to perform specific functions. A single amino acid mutation in AtMTM2 (L250W) results in a dramatic loss of subcellular localization. Mutations in this region are linked to disease conditions in humans.

Lipids of plant membrane rafts

Lipids tend to organize in mono or bilayer phases in a hydrophilic environment. While they have long been thought to be incapable of coherent lateral segregation, it is now clear that spontaneous assembly of these compounds can confer microdomain organization beyond spontaneous fluidity. Membrane raft microdomains have the ability to influence spatiotemporal organization of protein complexes, thereby allowing regulation of cellular processes. In this review, we aim at summarizing briefly: (i) the history of raft discovery in animals and plants, (ii) the main findings about structural and signalling plant lipids involved in raft segregation, (iii) imaging of plant membrane domains, and their biochemical purification through detergent-insoluble membranes, as well as the existing debate on the topic. We also discuss the potential involvement of rafts in the regulation of plant physiological processes, and further discuss the prospects of future research into plant membrane rafts.

Phosphatidylinositol 3-kinase plays a vital role in regulation of rice seed vigor via altering NADPH oxidase activity

Phosphatidylinositol 3-kinase (PI3K) has been reported to be important in normal plant growth and stress responses. In this study, it was verified that PI3K played a vital role in rice seed germination through regulating NADPH oxidase activity. Suppression of PI3K activity by inhibitors wortmannin or LY294002 could abate the reactive oxygen species (ROS) formation, which resulted in disturbance to the seed germination. And then, the signal cascades that PI3K promoted the ROS liberation was also evaluated. Diphenylene iodonium (DPI), an NADPH oxidase inhibitor, suppressed most of ROS generation in rice seed germination, which suggested that NADPH oxidase was the main source of ROS in this process. Pharmacological experiment and RT-PCR demonstrated that PI3K promoted the expression of Os rboh9. Moreover, functional analysis by native PAGE and the measurement of the 2, 3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazo-lium-5- carboxanilide (XTT) formazan concentration both showed that PI3K promoted the activity of NADPH oxidase. Furthermore, the western blot analysis of OsRac-1 demonstrated that the translocation of Rac-1 from cytoplasm to plasma membrane, which was known as a key factor in the assembly of NADPH oxidase, was suppressed by treatment with PI3K inhibitors, resulting in the decreased activity of NADPH oxidase. Taken together, these data favored the novel conclusion that PI3K regulated NADPH oxidase activity through modulating the recruitment of Rac-1 to plasma membrane and accelerated the process of rice seed germination.

Green light for polyphosphoinositide signals in plants

Plant genomes lack homologues of the inositol 1,4,5-trisphosphate receptor and protein kinase C, which are important components of the canonical phospholipase C signalling system in animals. Instead, plants seem to utilize alternative downstream signalling molecules, that is, InsP(6) and phosphatidic acid. Inositol lipids may also function as second messengers themselves. By reversible phosphorylation of the inositol headgroup, five biologically active plant polyphosphoinositides can be detected. Protein targets interact with specific polyphosphoinositide isomers via selective lipid-binding domains, thereby altering their intracellular localization and/or enzymatic activity. Such lipid-binding domains have also been used to create GFP based-lipid biosensors to visualize PPIs dynamics in vivo. Here, we highlight some recent advances and ideas on PPIs' role in plant signalling.

The salt stress-induced LPA response in Chlamydomonas is produced via PLA₂ hydrolysis of DGK-generated phosphatidic acid

The unicellular green alga Chlamydomonas has frequently been used as a eukaryotic model system to study intracellular phospholipid signaling pathways in response to environmental stresses. Earlier, we found that hypersalinity induced a rapid increase in the putative lipid second messenger, phosphatidic acid (PA), which was suggested to be generated via activation of a phospholipase D (PLD) pathway and the combined action of a phospholipase C/diacylglycerol kinase (PLC/DGK) pathway. Lysophosphatidic acid (LPA) was also increased and was suggested to reflect a phospholipase A₂ (PLA₂) activity based on pharmacological evidence. The question of PA's and LPA's origin is, however, more complicated, especially as both function as precursors in the biosynthesis of phospho- and galactolipids. To address this complexity, a combination of fatty acid-molecular species analysis and in vivo ³²P-radiolabeling was performed. Evidence is provided that LPA is formed from a distinct pool of PA characterized by a high α-linolenic acid (18:3n-3) content. This molecular species was highly enriched in the polyphosphoinositide fraction, which is the substrate for PLC to form diacylglycerol. Together with differential ³²P-radiolabeling studies and earlier PLD-transphosphatidylation and PLA₂-inhibitor assays, the data were consistent with the hypothesis that the salt-induced LPA response is primarily generated through PLA₂-mediated hydrolysis of DGK-generated PA and that PLD or de novo synthesis [via endoplasmic reticulum - or plastid-localized routes] is not a major contributor.

The nucleophosmin-anaplastic lymphoma kinase oncogene interacts, activates, and uses the kinase PIKfyve to increase invasiveness

NPM-ALK is a chimeric tyrosine kinase detected in most anaplastic large cell lymphomas that results from the reciprocal translocation t(2,5)(p23;q35) that fuses the N-terminal domain of nucleophosmin (NPM) to the catalytic domain of the anaplastic lymphoma kinase (ALK) receptor. The constitutive activity of the kinase is responsible for its oncogenicity through the stimulation of several downstream signaling pathways, leading to cell proliferation, migration, and survival. We demonstrated previously that the high level of phosphatidylinositol 5-phosphate measured in NPM-ALK-expressing cells is controlled by the phosphoinositide kinase PIKfyve, a lipid kinase known for its role in vesicular trafficking. Here, we show that PIKfyve associates with NPM-ALK and that the interaction involves the 181-300 region of the oncogene. Moreover, we demonstrate that the tyrosine kinase activity of the oncogene controls PIKfyve lipid kinase activity but is dispensable for the formation of the complex. Silencing or inhibition of PIKfyve using siRNA or the PIKfyve inhibitor YM201636 have no effect on NPM-ALK-mediated proliferation and migration but strongly reduce invasive capacities of NPM-ALK-expressing cells and their capacity to degrade the extracellular matrix. Accordingly, immunofluorescence studies confirm a perturbation of matrix metalloproteinase 9 localization at the cell surface and defect in maturation. Altogether, these results suggest a role for PIKfyve in NPM-ALK-mediated invasion.

Phospholipidic signaling and vanillin production in response to salicylic acid and methyl jasmonate in Capsicum chinense J. cells

The phospholipidic signal transduction system involves generation of second messengers by hydrolysis or changes in phosphorylation state. Several studies have shown that the signaling pathway forms part of plant response to phytoregulators such as salicylic acid (SA) and methyl jasmonate (MJ), which have been widely used to stimulate secondary metabolite production in cell cultures. An evaluation was made of the effect of SA and MJ on phospholipidic signaling and capsaicinoid production in Capsicum chinense Jacq. suspension cells. Treatment with SA inhibited phospholipase C (PLC) (EC: 3.1.4.3) and phospholipase D (PLD) (EC: 3.1.4.4) activities in vitro, but increased lipid kinase activities in vitro at different SA concentrations. Treatment with MJ produced increases in PLC and PLD activities, while lipid kinase activities were variable and dose-dependent. The production of vanillin, a precursor of capsaicinoids, increased at specific SA or MJ doses. Preincubation with neomycin, a phospholipase inhibitor, before SA or MJ treatment inhibits increase in vanillin production which suggests that phospholipidic second messengers may participate in the observed increase in vanillin production.

Phosphatidylinositol 5-phosphate links dehydration stress to the activity of ARABIDOPSIS TRITHORAX-LIKE factor ATX1

Background

Changes in gene expression enable organisms to respond to environmental stress. Levels of cellular lipid second messengers, such as the phosphoinositide PtdIns5P, change in response to a variety of stresses and can modulate the localization, conformation and activity of a number of intracellular proteins. The plant trithorax factor (ATX1) tri-methylates the lysine 4 residue of histone H3 (H3K4me3) at gene coding sequences, which positively correlates with gene transcription. Microarray analysis has identified a target gene (WRKY70) that is regulated by both ATX1 and by the exogenous addition of PtdIns5P in Arabidopsis. Interestingly, ATX1 contains a PtdIns5P interaction domain (PHD finger) and thus, phosphoinositide signaling, may link environmental stress to changes in gene transcription.

Principal Findings

Using the plant Arabidopsis as a model system, we demonstrate a link between PtdIns5P and the activity of the chromatin modifier ATX1 in response to dehydration stress. We show for the first time that dehydration leads to an increase in cellular PtdIns5P in Arabidopsis. The Arabidopsis homolog of myotubularin (AtMTM1) is capable of generating PtdIns5P and here, we show that AtMTM1 is essential for the induced increase in PtdIns5P upon dehydration. Furthermore, we demonstrate that the ATX1-dependent gene, WRKY70, is downregulated during dehydration and that lowered transcript levels are accompanied by a drastic reduction in H3K4me3 of its nucleosomes. We follow changes in WRKY70 nucleosomal K4 methylation as a model to study ATX1 activity at chromatin during dehydration stress. We found that during dehydration stress, the physical presence of ATX1 at the WRKY70 locus was diminished and that ATX1 depletion resulted from it being retained in the cytoplasm when PtdIns5P was elevated. The PHD of ATX1 and catalytically active AtMTM1 are required for the cytoplasmic localization of ATX1.

Conclusions/Significance

The novelty of the manuscript is in the discovery of a mechanistic link between a chromatin modifying activity (ATX1) and a lipid (PtdIns5P) synthesis in a signaling pathway that ultimately results in altered expression of ATX1 dependent genes downregulated in response to dehydration stress.

Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana

BACKGROUND

FYVE domains have emerged as membrane-targeting domains highly specific for phosphatidylinositol 3-phosphate (PtdIns(3)P). They are predominantly found in proteins involved in various trafficking pathways. Although FYVE domains may function as individual modules, dimers or in partnership with other proteins, structurally, all FYVE domains share a fold comprising two small characteristic double-stranded beta-sheets, and a C-terminal alpha-helix, which houses eight conserved Zn2+ ion-binding cysteines. To date, the structural, biochemical, and biophysical mechanisms for subcellular targeting of FYVE domains for proteins from various model organisms have been worked out but plant FYVE domains remain noticeably under-investigated.

RESULTS

We carried out an extensive examination of all Arabidopsis FYVE domains, including their identification, classification, molecular modeling and biophysical characterization using computational approaches. Our classification of fifteen Arabidopsis FYVE proteins at the outset reveals unique domain architectures for FYVE containing proteins, which are not paralleled in other organisms. Detailed sequence analysis and biophysical characterization of the structural models are used to predict membrane interaction mechanisms previously described for other FYVE domains and their subtle variations as well as novel mechanisms that seem to be specific to plants.

CONCLUSIONS

Our study contributes to the understanding of the molecular basis of FYVE-based membrane targeting in plants on a genomic scale. The results show that FYVE domain containing proteins in plants have evolved to incorporate significant differences from those in other organisms implying that they play a unique role in plant signaling pathways and/or play similar/parallel roles in signaling to other organisms but use different protein players/signaling mechanisms.

[Lipid signaling pathways in plants and their roles in response to water constraints]

Plants are sessile organisms that have developed the capacity to detect slight variations of their environment. They are able to perceive these environmental signals and to transduce them by signaling pathways in order to trigger adaptative responses. Lipid signaling elements play a central role in these pathways in plants. A key element is phosphatidic acid (PA), which can be produced by two pathways. In the first one, phospholipids are hydrolysed by phospholipase D (PLD) to release PA. In the second one, PA is produced through the activity of phospholipase C (PLC) to produce diacylglycerol (DAG) which is then phosphorylated by DAG kinase (DAGK). The amount of PA in the cell is regulated by PA kinase, which phosphorylates PA to produce diacylglycerolpyrophosphate (DGPP), considered as a second messenger as well. PLCs play a dual role in cell signaling by regulating the amount of intracellular Ca(2+), another essential second messenger. Phosphoinositides, such as PI3P, PI4P and PI(4,5)P(2), are substrates of PLCs and PLDs and are considered as second messengers also. In this review, we present recent data regarding the specific features of these lipid signaling pathways in plant compared with other eukaryotes.

Involvement of phospholipase C in the responses triggered by extracellular phosphatidylinositol 4-phosphate

Phosphatidylinositol 4-phosphate (PI4P) is a minor phospholipid signal molecule involved in diverse biological processes. It is also the main precursor of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P(2)], which is well described as the substrate of the phospholipase C (PLC)-diacylglycerol kinase (DGK) signalling pathway. Recently, we have demonstrated that PI4P plays a role as an extracellular signalling molecule involved in the activation of xylanase-induced defence responses in tomato cell suspensions. Here we make an approach to the possible mode of action of extracellular PI4P by analysing the involvement of PLC/DGK signalling pathway. We show that extracellular PI4P can be incorporated into tomato cells and further metabolized to PI, although its conversion to PI(4,5)P(2) could not be detected. In addition, treatment of tomato cells with the PLC inhibitor U73122 inhibited the oxidative burst triggered by PI4P treatment, suggesting the involvement of PLC in the induction of this response. Nevertheless, we demonstrate that PI4P treatment does not induce DGK activity. These results indicate that PLC but not DKG activation would be triggered by extracellular PI4P. In this sense, a possible mode of action of extracellular PI4P as a direct substrate of PLC to induce this signalling pathway is discussed.

An Arabidopsis hydrophilic Ca2(+) -binding protein with a PEVK-rich domain, PCaP2, is associated with the plasma membrane and interacts with calmodulin and phosphatidylinositol phosphates

We found a new hydrophilic protein in Arabidopsis thaliana. Real-time PCR demonstrated that the protein was expressed in roots. Histochemical analysis of promoter-beta-glucuronidase fusions demonstrated its extensive expression in root hairs. The protein is rich in proline, glutamate, valine and lysine residues (PEVK-rich domain), and bound Ca(2+) even in the presence of Mg(2+) and K(+) when examined by the (45)Ca overlay assay. Treatment of seedlings with K(+), Mn(2+), Zn(2+), Na(+), ABA and gibberellic acid, and cold and drought stresses enhanced the transcription. Expression of the protein linked to green fluorescent protein in A. thaliana showed its plasma membrane localization and cell-specific expression in the epidermal cells including root hairs and the elongating pollen tubes. Therefore, we named the protein PCaP2 (plasma membrane-associated Ca(2+)-binding protein-2). The substitution of glycine at position 2 with alanine resulted in cytoplasmic localization of PCaP2. These results and the N-terminal characteristic motif suggest that PCaP2 is N-myristoylated at Gly2. We examined the capacity for binding to phosphatidylinositol phosphates (PtdInsPs), and found that PCaP2 interacts strongly with PtdIns(3,5)P(2), PtdIns(4,5)P(2) and PtdIns(3,4,5)P(3), and weakly with PtdIns(3,4)P(2). Furthermore, calmodulin was associated with PCaP2 in a Ca(2+)-dependent manner, and its association weakened the interaction of PCaP2 with PtdInsPs. These results indicate that PCaP2 is involved in intracellular signaling through interaction with PtdInsPs and calmodulin in growing root hairs. PCaP2 was previously reported as microtubule-associated protein-18. We discuss the physiological roles of PCaP2 in relation to microtubules in cells.

The Arabidopsis stem cell factor POLTERGEIST is membrane localized and phospholipid stimulated

Stem cell maintenance and differentiation are tightly regulated in multicellular organisms. In plants, proper control of the stem cell populations is critical for extensive postembryonic organogenesis. The Arabidopsis thaliana protein phosphatase type 2C proteins POLTERGEIST (POL) and PLL1 are essential for maintenance of both the root and shoot stem cells. Specifically, POL and PLL1 are required for proper specification of key asymmetric cell divisions during stem cell initiation and maintenance. POL and PLL1 are known to be integral components of the CLE/WOX signaling pathways, but the location and mechanisms by which POL and PLL1 are regulated within these pathways are unclear. Here, we show that POL and PLL1 are dual-acylated plasma membrane proteins whose membrane localization is required for proper function. Furthermore, this localization places POL and PLL1 in proximity of the upstream plasma membrane receptors that regulate their activity. Additionally, we find that POL and PLL1 directly bind to multiple lipids and that POL is catalytically activated by phosphatidylinositol (4) phosphate [PI(4)P] in vitro. Based on these results, we propose that the upstream receptors in the CLE/WOX signaling pathways may function to either limit PI(4)P availability or antagonize PI(4)P stimulation of POL/PLL1. Significantly, the findings presented here suggest that phospholipids play an important role in promoting stem cell specification.

The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and the response to drought

Plants respond to environmental stresses by altering transcription of genes involved in the response. The chromatin modifier ATX1 regulates expression of a large number of genes; consequently, factors that affect ATX1 activity would also influence expression from ATX1-regulated genes. Here, we demonstrate that dehydration is such a factor implicating ATX1 in the plant's response to drought. In addition, we report that a hitherto unknown Arabidopsis gene, At3g10550, encodes a phosphoinositide 3'-phosphatase related to the animal myotubularins (AtMTM1). Myotubularin activities in plants have not been described and herein, we identify an overlapping set of genes co-regulated by ATX1 and AtMTM under drought conditions. We propose that these shared genes represent the ultimate targets of partially overlapping branches of the pathways of the nuclear ATX1 and the cytoplasmic AtMTM1. Our analyses offer first genome-wide insights into the relationship of an epigenetic factor and a lipid phosphatase from the other end of a shared drought responding pathway in Arabidopsis.

Biochemical characterization of two wheat phosphoethanolamine N-methyltransferase isoforms with different sensitivities to inhibition by phosphatidic acid

In plants the triple methylation of phosphoethanolamine to phosphocholine catalyzed by phosphoethanolamine N-methyltransferase (PEAMT) is considered a rate-limiting step in the de novo synthesis of phosphatidylcholine. Besides being a major membrane phospholipid, phosphatidylcholine can be hydrolyzed into choline and phosphatidic acid. Phosphatidic acid is widely recognized as a second messenger in stress signaling, and choline can be oxidized within the chloroplast to yield the putative osmoprotectant glycine betaine. Here we describe the cloning and biochemical characterization of a second wheat PEAMT isoform that has a four times higher specific activity than the previously described WPEAMT/TaPEAMT1 enzyme and is less sensitive to product inhibition by S-adenosyl homocysteine, but more sensitive to inhibition by phosphocholine. Both enzymes follow a sequential random Bi Bi mechanism and show mixed-type product inhibition patterns with partial inhibition for TaPEAMT1 and a strong non-competitive component for TaPEAMT2. An induction of TaPEAMT protein expression and activity is observed after cold exposure, ahead of an increase in gene expression. Our results demonstrate direct repression of in vitro enzymatic activities by phosphatidic acid for both enzymes, with TaPEAMT1 being more sensitive than TaPEAMT2 in the physiological concentration range. Other lipid ligands identified in protein-lipid overlays are phosphoinositide mono- as well as some di-phosphates and cardiolipin. These results provide new insights into the complex regulatory circuits of phospholipid biosynthesis in plants and underline the importance of head group biosynthesis in adaptive stress responses.

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.

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."

Catalyst-Dependent Syntheses of Phosphatidylinositol-5 Phosphate-DiC8 and its Enantiomer

Peptide-based catalysts have been applied to the enantioselective syntheses of the title compounds, with this being the first report of the synthesis of an ent-PI5P analogue. The key steps in the synthesis involve asymmetric phosphorylation catalysis. Additional maneuvers were developed with a protecting groups scheme that enabled efficient, streamlined syntheses of these important mediators of biochemical events.

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.

Phosphatidylinositol kinases as regulators of GA-stimulated alpha-amylase secretion in barley (Hordeum vulgare)

Phosphorylated derivatives of phosphatidylinositol, in association with phosphatidylinositol 3-kinase (PI3 kinase, EC 2.7.1.137) and phosphatidylinositol 4-kinase (PI4 kinase, EC 2.7.1.67), play a key role in regulation of fundamental cell processes. We present evidence for a relationship between alpha-amylase (EC 3.2.1.1) secretion regulated by GA and levels of phosphatidylinositol 3-phosphate and phosphatidylinositol 4-phosphate (PtdIns(4)P) in barley (Hordeum vulgare). Microsomal membranes were incubated in the presence of [gamma-(32)P]ATP, and radiolabeled membrane lipids were extracted and separated by TLC using a boric acid system. Treatment of aleurone layers with GA for short or long periods of time increased PI4 kinase activity. To evaluate the effect of PtdIns(4)P levels on GA signaling, we used phenylarsine oxide (PAO), an inhibitor of PI4 kinase activity. PAO reversibly reduced the alpha-amylase secretion and protoplast cell vacuolation in a dose-dependent manner. Wortmannin showed a similar inhibitory effect on alpha-amylase secretion and PI4 kinase activity. GA evoked only a long-term increase in PI3 kinase activity, which was also affected by PAO. The effect of PAO was suppressed by the reducing agent 2,3-dimercapto-1-propanol (BAL), leading to restoration of secretion, vacuolation and PI4 kinase activity. In contrast, the effect of PAO on PI3 kinase activity was not abolished by BAL, suggesting that PI3 kinase is not involved in the secretion process. Likewise, the compound LY294002 inhibited PI3 kinase but had no effect on the secretion process. These findings indicate that PI4 kinase acts as a positive regulator of early GA signaling in aleurone.

Nitric oxide triggers phosphatidic acid accumulation via phospholipase D during auxin-induced adventitious root formation in cucumber

Auxin and nitric oxide (NO) play fundamental roles throughout plant life. NO is a second messenger in auxin signal transduction leading to root developmental processes. The mechanisms triggered by auxin and NO that direct adventitious root (AR) formation are beginning to be unraveled. The goal of this work was to study phospholipid (PL) signaling during the auxin- and NO-induced AR formation in cucumber (Cucumis sativus) explants. Explants were labeled with 32P-inorganic phosphate and treated with the auxins indole-3-acetic acid or 1-naphthylacetic acid, or the NO donor S-nitroso N-acetyl penicillamine, in the presence or absence of the specific NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide. PLs were separated by thin-layer chromatography and quantified. We report that the signaling PLs phosphatidic acid (PA), phosphatidylinositol phosphate, and phosphatidylinositol bisphosphate accumulated within 1 min after auxin or NO treatment. Both auxin and NO evoked similar and transient time course responses, since signaling PLs returned to control levels after 20 or 30 min of treatment. The results indicate that auxin relies on NO in inducing PA, phosphatidylinositol phosphate, and phosphatidylinositol bisphosphate accumulation. Furthermore, we demonstrate that auxin and NO trigger PA formation via phospholipase D (PLD) activity. Explants treated for 10 min with auxin or NO displayed a 200% increase in AR number compared with control explants. In addition, PLD activity was required for the auxin- and NO-induced AR formation. Finally, exogenously applied PA increased up to 300% the number of ARs. Altogether, our data support the idea that PLD-derived PA is an early signaling event during AR formation induced by auxin and NO in cucumber explants.

The Arabidopsis Phosphatidylinositol Phosphate 5-Kinase PIP5K3 is a key regulator of root hair tip growth

Phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] functions as a site-specific signal on membranes to promote cytoskeletal reorganization and membrane trafficking. Localization of PtdIns(4,5)P2 to apices of growing root hairs and pollen tubes suggests that it plays an important role in tip growth. However, its regulation and mode of action remain unclear. We found that Arabidopsis thaliana PIP5K3 (for Phosphatidylinositol Phosphate 5-Kinase 3) encodes a phosphatidylinositol 4-phosphate 5-kinase, a key enzyme producing PtdIns(4,5)P2, that is preferentially expressed in growing root hairs. T-DNA insertion mutations that substantially reduced the expression of PIP5K3 caused significantly shorter root hairs than in the wild type. By contrast, overexpression caused longer root hairs and multiple protruding sites on a single trichoblast. A yellow fluorescent protein (YFP) fusion of PIP5K3, driven by the PIP5K3 promoter, complemented the short-root-hair phenotype. PIP5K3-YFP localized to the plasma membrane and cytoplasmic space of elongating root hair apices, to growing root hair bulges, and, notably, to sites about to form root hair bulges. The signal was greatest in rapidly growing root hairs and quickly disappeared when elongation ceased. These results provide evidence that PIP5K3 is involved in localizing PtdIns(4,5)P2 to the elongating root hair apex and is a key regulator of the machinery that initiates and promotes root hair tip growth.

Nuclear PtdIns5P as a transducer of stress signaling: an in vivo role for PIP4Kbeta

Inhibitor of growth protein-2 (ING2) is a nuclear adaptor protein that can regulate p53 and histone acetylation in response to cellular stress and contains a PHD (plant homeodomain) finger that can interact with phosphatidylinositol-5-phosphate (PtdIns5P). However, whether or how nuclear PtdIns5P levels are regulated in response to cellular stress or whether ING2 can sense these changes has not been demonstrated. We show that UV irradiation increases nuclear PtdIns5P levels via inhibition of the activity of the beta isoform of PtdIns5P 4-kinase (PIP4Kbeta), an enzyme that can phosphorylate and remove PtdIns5P. Inhibition of PIP4Kbeta activity occurs through the direct phosphorylation of PIP4Kbeta at Ser326 by the p38 stress-activated protein kinase. Finally, we show that changes in nuclear PtdIns5P are translated into changes in the association of ING2 with chromatin. Our data define a pathway connecting cellular stressors with changes in nuclear PtdIns5P levels and the regulation of PHD motif-containing proteins.

Visualization of PtdIns3P dynamics in living plant cells

To investigate PtdIns3P localization and function in plants, a fluorescent PtdIns3P-specific biosensor (YFP-2xFYVE) was created. On lipid dot blots it bound specifically and with high affinity to PtdIns3P. Transient expression in cowpea protoplasts labelled vacuolar membranes and highly motile structures undergoing fusion and fission. Stable expression in tobacco BY-2 cells labelled similar motile structures, but labelled vacuolar membranes hardly at all. YFP-2xFYVE fluorescence strongly co-localized with the pre-vacuolar marker AtRABF2b, partially co-localized with the endosomal tracer FM4-64, but showed no overlap with the Golgi marker STtmd-CFP. Treatment of cells with wortmannin, a PI3 kinase inhibitor, caused the YFP-2xFYVE fluorescence to redistribute into the cytosol and nucleus within 15 min. BY-2 cells expressing YFP-2xFYVE contained twice as much PtdIns3P as YFP-transformed cells, but this had no effect on cell-growth or stress-induced phospholipid signalling responses. Upon treatment with wortmannin, PtdIns3P levels were reduced by approximately 40% within 15 min in both cell lines. Stable expression of YFP-2xFYVE in Arabidopsis plants labelled different subcellular structures in root compared with shoot tissues. In addition labelling the motile structures common to all cells, YFP-2xFYVE strongly labelled the vacuolar membrane in leaf epidermal and guard cells, suggesting that cell differentiation alters the distribution of PtdIns3P. In dividing BY-2 cells, YFP-2xFYVE-labelled vesicles surrounded the newly formed cell plate, suggesting a role for PtdIns3P in cytokinesis. Together, these data show that YFP-2xFYVE may be used as a biosensor to specifically visualize PtdIns3P in living plant cells.

Isolation of a novel nodulin: a molecular marker of osmotic stress in Glycine max/Bradyrhizobium japonicum nodule

Symbiotic N(2) fixation of legume crops is highly sensitive to drought, which results in a dramatic drop of N accumulation and yield. The symbiosis between soybean (Glycine max) and Bradyrhizobium japonicum, because of its extreme sensitivity to drought, was chosen as a model to analyse the response to drought stress at a molecular level. The mRNA differential display technique was performed to isolate cDNA markers differentially expressed in well-watered [100% of N(2) fixation capacity (NFC)] and drought-stressed nodules (40% NFC). One gene noted, G93, appeared strongly down-regulated by drought and fully recovered after rehydration. In situ hybridization showed that G93 transcripts were localized in N(2)-fixing cells of mature nodules, indicating that G93 could be considered as a late nodulin. However, G93 expression was not directly correlated to N(2) fixation but mainly responded to osmotic stress. Other stresses that lead to decrease of N(2) fixation did not affect G93 expression. Sequence analyses showed that G93 presented a strong homology with two soybean expressed sequence tags (ESTs) and with the ZR1 protein of Medicago sativa. Putative roles of this nodulin in adaptation of soybean nodule to osmotic stress are proposed.

Lipid content in higher plants under osmotic stress

In this work, we performed investigations on the lipid content of higher plants (spinach) under hyperosmotic stress, by means of thin layer chromatography (TLC) and mass spectrometry. In particular, the experiments have been performed at different plant organization levels: whole leaves, freshly prepared protoplast suspension and mesophyll cells obtained by reformation of the cell wall from protoplast suspension. The results obtained showed that hyperosmotic stress induces changes in the phospholipid content depending on the different plant organization levels studied. All phospholipids showed an increment of their content in stressed whole leaves. In particular, phosphatidylglycerol (PG) redoubles its content by 1 h of osmotic shock. Different responses to hyperosmotic stress were reported for the other systems. In the case of protoplasts, an increment of PG, phosphatidylcholine (PC) and phosphatidylinositol (PI) together with biphosphatidylglycerol (BPG) and phosphatidylethanolamine (PE) content decreasing were observed in stressed sample. For PG, identified as PG (34:4) by elecrospray ionization mass spectrometry, the increment was of about 30%. In the case of cells, conversely, a decrease of PG content under osmotic stress was recorded. The results suggest an important role of phospholipids, in particular of PG, in the osmotic stress response.

Phosphoinositide 5-phosphate and phosphoinositide 4-phosphate trigger distinct specific responses of Arabidopsis genes: genome-wide expression analyses

Phosphoinositide phosphates, PtdInsP, are important components of the cell lipid pool that can function as messengers in diverse cellular processes. Lack of information on downstream targets, however, has impeded our understanding of the potential of lipid-signaling to influence gene activity. Our goals here were to identify genes that altered expression in the presence of two isomeric monophosphate lipid messengers (Phosphoinositide 5-Phosphate, PtdIns(5)P, and Phosphoinositide 4-Phosphate, PtdIns(4)P) and to establish whether the two lipids influence distinct or overlapping gene-sets. Our results indicated that PtdIns(5)P and PtdIns(4)P affected genes within shared gene-families but that each messenger influenced the expression of different members within the same family. These results suggested that PtdIns(5)P and PtdIns(4)P participate in separate pathways that, ultimately, may control gene expression. The pathways may have points of convergence but may also counteract each other's effects. A significant fraction ( approximately 40%) of the PtdIns(5)P-stimulated genes belong to various families of wall-modifying genes. Wall-modifying activities are recognized as factors affecting cell extension and plant growth. Elevated PtdIns(5)P concentration influenced stem growth and the effects were different from those triggered by PtdIns(4)P. The data allow insights into plants' response to two related PtdInsP at whole-plant/genome-wide levels and demonstrate that PtdIns(5)P-and PtdIns(4)P-involving mechanisms are distinct, selective and specific.