Direct infusion mass spectrometry of oxylipin-containing Arabidopsis membrane lipids reveals varied patterns in different stress responses

Lipid changes after leaf wounding in Arabidopsis thaliana: expanded lipidomic data form the basis for lipid co-occurrence analysis

A direct-infusion electrospray ionization triple-quadrupole mass spectrometry method with multiple reaction monitoring (MRM) was employed to measure 264 lipid analytes extracted from leaves of Arabidopsis thaliana subjected to mechanical wounding. The method provided precise measurements with an average coefficient of variation of 6.1%. Lipid classes analyzed comprised galactolipids and phospholipids (including monoacyl molecular species, molecular species with oxidized acyl chains, phosphatidic acids (PAs)), tri- and tetra-galactosyldiacylglycerols (TrGDGs and TeGDGs), head-group-acylated galactolipids, and head-group-acylated phosphatidylglycerol (acPG), sulfoquinovosyldiacylglycerols (SQDGs), sphingolipids, di- and tri-acylglycerols (DAGs and TAGs), and sterol derivatives. Of the 264 lipid analytes, 254 changed significantly in response to wounding. In general, levels of structural lipids decreased, whereas monoacyl molecular species, galactolipids and phosphatidylglycerols (PGs) with oxidized fatty acyl chains, PAs, TrGDGs, TeGDGs, TAGs, head-group-acylated galactolipids, acPG, and some sterol derivatives increased, many transiently. The observed changes are consistent with activation of lipid oxidizing, hydrolyzing, glycosylating, and acylating activities in the wounding response. Correlation analysis of the levels of lipid analytes across individual control and treated plants was used to construct a lipid dendrogram and to define clusters and sub-clusters of lipid analytes, each composed of a group of lipids which occurred in a coordinated manner. Current knowledge of metabolism supports the notion that observed sub-clusters comprise lipids generated by a common enzyme and/or metabolically downstream of a common enzyme. This work demonstrates that co-occurrence analysis, based on correlation of lipid levels among plants, is a powerful approach to defining lipids generated in vivo by a common enzymatic pathway.

A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches

Nitrogen (N), as an essential element in amino acids, nucleotides, and proteins, is a key factor in plant growth and development. Omics approaches such as metabolomics and transcriptomics have become a promising way to inspect complex network interactions in N metabolism and can be used for monitoring the uptake and regulation, translocation, and remobilization of N. In this review, the authors highlight recent progress in omics approaches, including transcript profiling using microarrays and deep sequencing, and show recent technical developments in metabolite profiling for N studies. Further, network analysis studies including network inference methods with correlations, information-theoretic measures, and a network concept to examine gene expression clusters in relation to N regulatory systems in plants are introduced, and integrating network inference methods and integrated networks using multiple omics data are discussed. Finally, this review summarizes recent omics application examples using metabolite and/or transcript profiling analysis to elucidate the regulation of N metabolism and signalling and the coordination of N and carbon metabolism in model plants (Arabidopsis and rice), crops (tomato, maize, and legumes), and trees (Populus).

Roles of lipids as signaling molecules and mitigators during stress response in plants

Lipids are the major constituents of biological membranes that can sense extracellular conditions. Lipid-mediated signaling occurs in response to various environmental stresses, such as temperature change, salinity, drought and pathogen attack. Lysophospholipid, fatty acid, phosphatidic acid, diacylglycerol, inositol phosphate, oxylipins, sphingolipid, and N-acylethanolamine have all been proposed to function as signaling lipids. Studies on these stress-inducible lipid species have demonstrated that each lipid class has specific biological relevance, biosynthetic mechanisms and signaling cascades, which activate defense reactions at the transcriptional level. In addition to their roles in signaling, lipids also function as stress mitigators to reduce the intensity of stressors. To mitigate particular stresses, enhanced syntheses of unique lipids that accumulate in trace quantities under normal growth conditions are often observed under stressed conditions. The accumulation of oligogalactolipids and glucuronosyldiacylglycerol has recently been found to mitigate freezing and nutrition-depletion stresses, respectively, during lipid remodeling. In addition, wax, cutin and suberin, which are not constituents of the lipid bilayer, but are components derived from lipids, contribute to the reduction of drought stress and tissue injury. These features indicate that lipid-mediated defenses against environmental stress contributes to plant survival.

Formation of oxidized phosphatidylinositol and 12-oxo-phytodienoic acid containing acylated phosphatidylglycerol during the hypersensitive response in Arabidopsis

Plant membranes are composed of a wide array of polar lipids. The functionality of these extends far beyond a pure structural role. Membrane lipids function as enzyme co-factors, establish organelle identity and as substrates for enzymes such as lipases and lipoxygenases. Enzymatic degradation or oxidation (enzymatic or non-enzymatic) of membrane lipids leads to the formation of a diverse group of bioactive compounds. Plant defense reactions provoked by pathogenic microorganisms are often associated with substantial modifications of the lipidome. In this study, we profiled changes in phospholipids during the hypersensitive response triggered by recognition of the bacterial effector protein AvrRpm1 in Arabidopsis thaliana. A simple and robust LC-MS based method for profiling plant lipids was designed to separate all the major species of glycerolipids extracted from Arabidopsis leaf tissue. The method efficiently separated several isobaric and near isobaric lipid species, which otherwise are difficult to quantify in direct infusion based profiling. In addition to the previously reported OPDA-containing galactolipids found to be induced during hypersensitive response in Arabidopsis, three OPDA-containing sulfoquinovosyl diacylglycerol species, one phosphatidylinositol species as well as two acylated OPDA-containing phosphatidylglycerol species were found to accumulate during the hypersensitive response in Arabidopsis. Our study confirms and extends on the notion that the hypersensitive response in Arabidopsis triggers a unique profile of Allene Oxide Synthase dependent oxidation of membrane lipids. Primary targets of this oxidation seem to be uncharged and anionic lipid species.

Head-group acylation of monogalactosyldiacylglycerol is a common stress response, and the acyl-galactose acyl composition varies with the plant species and applied stress

Formation of galactose-acylated monogalactosyldiacylglycerols has been shown to be induced by leaf homogenization, mechanical wounding, avirulent bacterial infection and thawing after snap-freezing. Here, lipidomic analysis using mass spectrometry showed that galactose-acylated monogalactosyldiacylglycerols, formed in wheat (Triticum aestivum) and tomato (Solanum lycopersicum) leaves upon wounding, have acyl-galactose profiles that differ from those of wounded Arabidopsis thaliana, indicating that different plant species accumulate different acyl-galactose components in response to the same stress. Additionally, the composition of the acyl-galactose component of Arabidopsis acMGDG (galactose-acylated monogalactosyldiacylglycerol) depends on the stress treatment. After sub-lethal freezing treatment, acMGDG contained mainly non-oxidized fatty acids esterified to galactose, whereas mostly oxidized fatty acids accumulated on galactose after wounding or bacterial infection. Compositional data are consistent with acMGDG being formed in vivo by transacylation with fatty acids from digalactosyldiacylglycerols. Oxophytodienoic acid, an oxidized fatty acid, was more concentrated on the galactosyl ring of acylated monogalactosyldiacylglycerols than in galactolipids in general. Also, oxidized fatty acid-containing acylated monogalactosyldiacylglycerols increased cumulatively when wounded Arabidopsis leaves were wounded again. These findings suggest that, in Arabidopsis, the pool of galactose-acylated monogalactosyldiacylglycerols may serve to sequester oxidized fatty acids during stress responses.

The maize leaf lipidome shows multilevel genetic control and high predictive value for agronomic traits

Although the plant lipidome show an enormous level of structural and functional diversity, our knowledge about its genetic control and its connection to whole-plant phenotypes is very limited. Here, we profiled 563 lipid species with UPLC-FT-MS in 289 field-grown inbred lines genotyped with 56,110 SNPs. Genome-wide association study identified 174 associations for 76 lipids explaining up to 31.4% of the genetic variance (P-value 8.4 × 10(-18)). Candidate genes were found for lipid synthesis, breakdown, transfer, and protection against peroxidation. The detected SNP-lipid associations could be grouped into associations with 1) individual lipids, 2) lipids from one biochemical class, and 3) lipids from several classes, suggesting a multilevel genetic control architecture. We further found a strong connection between the lipidome and agronomic traits in field-evaluated hybrid progeny. A cross-validated prediction model yielded correlations of up to 0.78 suggesting that the lipidome accurately predicts agronomic traits relevant in hybrid maize breeding.

Quantification of selected endogenous hydroxy-oxylipins from tropical marine macroalgae

The present study investigated the contents of hydroxy-oxylipins hydroxyoctadecadienoic acids (HODEs), hydroxyoctadecatrienoic acids (HOTrEs), and hydroxyeicosatetraenoic acids (HETEs) in 40 macroalgae belonging to the Chlorophyceae, Rhodophyceae and, Phaeophyceae. The hydroxy-oxylipin content was low and ranged from 0.14 ± 0.012 ng/g (Codium dwarkense) to 8,161.9 ± 253 ng/g (Chaetomorpha linum) among the Chlorophyceae, 345.4 ± 56.8 ng/g (Scytosiphon lomentaria) to 2,574.5 ± 155.5 ng/g (Stoechospermum marginatum) among the Phaeophyceae, and 19.4 ± 2.2 ng/g (Laurencia cruciata) to 1,753.1 ± 268.2 ng/g in Gracilaria corticata v. folifera) among the Rhodophyceae on fresh weight basis (p ≤ 0.01). The concentrations of C18-oxylipins were greater than C20-oxylipins in all the investigated macroalgae, except forUlva linza, Codium sursum, Dictyopteris deliculata, S. marginatum, Sargassum tenerrimum, Gracilaria spp. (except G. textorii), Rhodymenia sonderi, and Odonthalia veravalensis.The macroalgal species rich in HODEs, HOTrEs, and HETEs were segregated using principal component analysis. The red macroalgae showed the highest contents of HETEs, followed by brown and green macroalgae in consistent with their PUFA profiles. The relative contents of isomeric forms of oxylipins displayed the species-specific positional selectivity of lipoxygenase (LOX) enzyme in macroalgae. All the species exhibited 13-LOX specificity for linoleic acid analogous of higher plants, while 21 out of 40 species showed 9-LOX selectivity for the oxygenation of α-linolenic acid. No trend was observed for the oxygenation of arachidonic acid in macroalgae, except for in the Halymeniales, Ceramiales (except L. cruciata), and Corallinales. This study infers that LOX products, octadecanoids and eicosanoids, described in macroalgal taxa were similar to those of higher plants and mammals, respectively, and thus can be utilized as an alternative source of chemically synthesized oxylipin analogues in therapeutics, cosmetics, and nutritional oil supplements.

A lipidomic approach to identify cold-induced changes in Arabidopsis membrane lipid composition

Lipidomic analysis using electrospray ionization triple quadrupole mass spectrometry can be employed to monitor lipid changes that occur during cold and freezing stress of plants. Here we describe the analysis of Arabidopsis thaliana polar glycerolipids with normal and oxidized acyl chains, sampled during cold and freezing treatments. Mass spectral data are processed using the online capabilities of LipidomeDB Data Calculation Environment.

Plasma membranes as heat stress sensors: from lipid-controlled molecular switches to therapeutic applications

The classic heat shock (stress) response (HSR) was originally attributed to protein denaturation. However, heat shock protein (Hsp) induction occurs in many circumstances where no protein denaturation is observed. Recently considerable evidence has been accumulated to the favor of the "Membrane Sensor Hypothesis" which predicts that the level of Hsps can be changed as a result of alterations to the plasma membrane. This is especially pertinent to mild heat shock, such as occurs in fever. In this condition the sensitivity of many transient receptor potential (TRP) channels is particularly notable. Small temperature stresses can modulate TRP gating significantly and this is influenced by lipids. In addition, stress hormones often modify plasma membrane structure and function and thus initiate a cascade of events, which may affect HSR. The major transactivator heat shock factor-1 integrates the signals originating from the plasma membrane and orchestrates the expression of individual heat shock genes. We describe how these observations can be tested at the molecular level, for example, with the use of membrane perturbers and through computational calculations. An important fact which now starts to be addressed is that membranes are not homogeneous nor do all cells react identically. Lipidomics and cell profiling are beginning to address the above two points. Finally, we observe that a deregulated HSR is found in a large number of important diseases where more detailed knowledge of the molecular mechanisms involved may offer timely opportunities for clinical interventions and new, innovative drug treatments. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.

Glycerolipids in photosynthesis: composition, synthesis and trafficking

Glycerolipids constituting the matrix of photosynthetic membranes, from cyanobacteria to chloroplasts of eukaryotic cells, comprise monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sulfoquinovosyldiacylglycerol and phosphatidylglycerol. This review covers our current knowledge on the structural and functional features of these lipids in various cellular models, from prokaryotes to eukaryotes. Their relative proportions in thylakoid membranes result from highly regulated and compartmentalized metabolic pathways, with a cooperation, in the case of eukaryotes, of non-plastidic compartments. This review also focuses on the role of each of these thylakoid glycerolipids in stabilizing protein complexes of the photosynthetic machinery, which might be one of the reasons for their fascinating conservation in the course of evolution. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components.

Metabolic survey of defense responses to a compatible hemibiotroph, Phytophthora parasitica var. nicotianae, in ethylene signaling-impaired tobacco

Reactive oxygen species (ROS) and ethylene play an important role in determining the resistance or susceptibility of plants to pathogen attack. A previous study of the response of tobacco cultivar ( Nicotiana tabacum L. cv. Wisconsin 38) to a compatible hemibiotroph, Phytophthora parasitica var. nicotianae (Ppn) showed that biphasic bursts of ROS and ethylene are positively associated with disease severity. The levels of ethylene and ROS might influence the susceptibility of plants to pathogens, with changing levels of metabolite related to disease resistance or susceptibility. In this study, to obtain more detailed information on the interaction of ROS and ethylene signaling related to resistance and/or susceptibility of plants to pathogen, Ppn-induced metabolic profiles from wild type (WT) and ethylene signaling-impaired transgenic plants that expressed Ein3 antisense (Ein3-AS) were compared using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS). Nonredundant mass ions (576 in ESI+ mode and 336 in ESI- mode) were selected, and 56 mass ions were identified on the basis of their accurate mass ions and MS/MS spectra. Two-way hierarchical clustering analysis of the selected mass ions revealed that nicotine and phenylpropanoid-polyamine conjugates, such as caffeoyl-dihydrocaffeoyl-spermidine, dicaffeoyl-spermidine, caffeoyl-feruloyl-spermidine, and two bis(dihydrocaffeoyl)-spermine isomers, and their intermediates, such as arginine and putrecine, were present at lower levels in Ein3-AS transgenic plants during Ppn interaction than in WT, whereas galactolipid and oxidized free fatty acid levels were higher in Ein3-AS transgenic plants. Taken together, these results reveal a function for ethylene signaling in tobacco defense responses during Ppn interaction.

Role of plant peroxisomes in the production of jasmonic acid-based signals

Jasmonates are a family of oxylipins derived from linolenic acid that control plant responses to biotic and abiotic stress factors and also regulate plant growth and development. Jasmonic acid (JA) is synthesized through the octadecanoid pathway that involves the translocation of lipid intermediates from the chloroplast membranes to the cytoplasm and later on into peroxisomes. The peroxisomal steps of the pathway involve the reduction of cis-(+)-12-oxophytodienoic acid (12-OPDA) and dinor-OPDA, which are the final products of the choroplastic phase of the biosynthetic pathway acting on 18:3 and 16:3 fatty acids, respectively. Further shortening of the carbon side-chain by successive rounds of β-oxidation reactions are required to complete JA biosynthesis. After peroxisomal reactions are completed, (+)-7-iso-JA is synthesized and then transported to the cytoplasm where is conjugated to the amino acid isoleucine to form the bioactive form of the hormone (+)-7-iso-JA-Ile (JA-Ile). Further regulatory activity of JA-Ile triggering gene activation in the jasmonate-dependent signaling cascades is exerted through a process mediated by the perception via the E3 ubiquitin ligase COI1 and further ligand-activated interaction with the family of JAZ repressor proteins. Upon interaction, JAZ are ubiquitinated and degraded by the proteasome, thus releasing transcription factors such as MYC2 from repression and allowing the activation of JA-responsive genes.

Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana

Freezing injury is a major factor limiting the geographical distribution of plant species and the growth and yield of crop plants. Plants from temperate climates are able to increase their freezing tolerance during exposure to low but non-freezing temperatures in a process termed cold acclimation. Damage to cellular membranes is the major cause of freezing injury in plants, and membrane lipid composition is strongly modified during cold acclimation. Forward and reverse genetic approaches have been used to probe the role of specific lipid-modifying enzymes in the freezing tolerance of plants. In the present paper we describe an alternative ecological genomics approach that relies on the natural genetic variation within a species. Arabidopsis thaliana has a wide geographical range throughout the Northern Hemisphere with significant natural variation in freezing tolerance that was used for a comparative analysis of the lipidomes of 15 Arabidopsis accessions using ultra-performance liquid chromatography coupled to Fourier-transform mass spectrometry, allowing the detection of 180 lipid species. After 14 days of cold acclimation at 4°C the plants from most accessions had accumulated massive amounts of storage lipids, with most of the changes in long-chain unsaturated triacylglycerides, while the total amount of membrane lipids was only slightly changed. Nevertheless, major changes in the relative amounts of different membrane lipids were also evident. The relative abundance of several lipid species was highly correlated with the freezing tolerance of the accessions, allowing the identification of possible marker lipids for plant freezing tolerance.

Lipid profiling of the Arabidopsis hypersensitive response reveals specific lipid peroxidation and fragmentation processes: biogenesis of pimelic and azelaic acid

Lipid peroxidation (LPO) is induced by a variety of abiotic and biotic stresses. Although LPO is involved in diverse signaling processes, little is known about the oxidation mechanisms and major lipid targets. A systematic lipidomics analysis of LPO in the interaction of Arabidopsis (Arabidopsis thaliana) with Pseudomonas syringae revealed that LPO is predominantly confined to plastid lipids comprising galactolipid and triacylglyceride species and precedes programmed cell death. Singlet oxygen was identified as the major cause of lipid oxidation under basal conditions, while a 13-lipoxygenase (LOX2) and free radical-catalyzed lipid oxidation substantially contribute to the increase upon pathogen infection. Analysis of lox2 mutants revealed that LOX2 is essential for enzymatic membrane peroxidation but not for the pathogen-induced free jasmonate production. Despite massive oxidative modification of plastid lipids, levels of nonoxidized lipids dramatically increased after infection. Pathogen infection also induced an accumulation of fragmented lipids. Analysis of mutants defective in 9-lipoxygenases and LOX2 showed that galactolipid fragmentation is independent of LOXs. We provide strong in vivo evidence for a free radical-catalyzed galactolipid fragmentation mechanism responsible for the formation of the essential biotin precursor pimelic acid as well as of azelaic acid, which was previously postulated to prime the immune response of Arabidopsis. Our results suggest that azelaic acid is a general marker for LPO rather than a general immune signal. The proposed fragmentation mechanism rationalizes the pathogen-induced radical amplification and formation of electrophile signals such as phytoprostanes, malondialdehyde, and hexenal in plastids.

Oxo-phytodienoic acid (OPDA) is formed on fatty acids esterified to galactolipids after tissue disruption in Arabidopsis thaliana

Biotic and abiotic stress induces the formation of galactolipids esterified with the phytohormones 12-oxo-phytodienoic acid (OPDA) and dinor-oxo-phytodienoic acid (dnOPDA) in Arabidopsis thaliana. The biosynthetic pathways of free (dn)OPDA is well described, but it is unclear how they are incorporated into galactolipids. We herein show that (dn)OPDA containing lipids are formed rapidly after disruption of cellular integrity in leaf tissue. Five minutes after freeze-thawing, 60-70% of the trienoic acids esterified to chloroplast galactolipids are converted to (dn)OPDA. Stable isotope labeling with (18)O-water provides strong evidence for that the fatty acids remain attached to galactolipids during the enzymatic conversion to (dn)OPDA.

Analysis of plant galactolipids by reversed-phase high-performance liquid chromatography/mass spectrometry with accurate mass measurement

The composition of plant membrane lipids was investigated by reversed-phase high performance liquid chromatography mass spectrometry with accurate mass measurement. The data dependent methods for the analysis of monogalactosyldiacylglycerols (MGDGs) and digalactosyldiacylglycerols (DGDGs) have been developed. The optimised chromatographic systems were based on a 2.0 mm i.d. Nucleosil C18 column with methanol/water (MGDGs) or acetonitrile/methanol/water (DGDGs) gradients. The galactolipids were ionised by electrospray operated in the positive ion mode and identified based on their MS/MS spectra. High resolution spectra with accurate masses were found to be essential for correct interpretation of the MS data. The elution order of non-oxidised MGDGs and DGDGs followed the equivalent carbon numbers. The methods were applied for detailed characterisation of the MGDGs and DGDGs in the leaves of Arabidopsis thaliana and Melissa officinalis.

Oxylipin Signaling: A Distinct Role for the Jasmonic Acid Precursor cis-(+)-12-Oxo-Phytodienoic Acid (cis-OPDA)

Oxylipins are lipid-derived compounds, many of which act as signals in the plant response to biotic and abiotic stress. They include the phytohormone jasmonic acid (JA) and related jasmonate metabolites cis-(+)-12-oxo-phytodienoic acid (cis-OPDA), methyl jasmonate, and jasmonoyl-L-isoleucine (JA-Ile). Besides the defense response, jasmonates are involved in plant growth and development and regulate a range of processes including glandular trichome development, reproduction, root growth, and senescence. cis-OPDA is known to possess a signaling role distinct from JA-Ile. The non-enzymatically derived phytoprostanes are structurally similar to cis-OPDA and induce a common set of genes that are not responsive to JA in Arabidopsis thaliana. A novel role for cis-OPDA in seed germination regulation has recently been uncovered based on evidence from double mutants and feeding experiments showing that cis-OPDA interacts with abscisic acid (ABA), inhibits seed germination, and increases ABA INSENSITIVE5 (ABI5) protein abundance. Large amounts of cis-OPDA are esterified to galactolipids in A. thaliana and the resulting compounds, known as Arabidopsides, are thought to act as a rapidly available source of cis-OPDA.

Arabidopsis thaliana membrane lipid molecular species and their mass spectral analysis

Herein, current approaches to electrospray ionization mass spectrometry-based analyses of membrane lipid molecular species found in Arabidopsis thaliana are summarized. Additionally, the identities of over 500 reported membrane lipid molecular species are assembled.