Hezi Tenenboim

Biochimie 130 (2016) 91e96 Contents lists available at ScienceDirect Biochimie journal homepage: www.elsevier.com/locate/biochi Mini-review Using lipidomics for expanding the knowledge on lipid metabolism in plants Hezi Tenenboim a, 1, Asdrubal Burgos a, 1, Lothar Willmitzer a, Yariv Brotman b, * a b Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel a r t i c l e i n f o a b s t r a c t Article history: Received 19 April 2016 Accepted 6 June 2016 Available online 9 June 2016 Lipids are a crucial and diverse class of biomolecules. Their structural heterogeneity in plants is staggering, and many aspects of plant life are manifested and mediated by lipids. Recent advances in metabolomic and lipidomic technologies and analysis have immensely increased our knowledge of the plant lipidome, its biosynthesis, regulation, adaptation, remodeling, functions, roles, and interactions. Here we review the recent literature and trends in lipidomics, and discuss specific issues pertaining to lipidomic research in plants, and how lipidomics has helped elucidate key issues in plant cell biology, immunity, response to stress, evolution, crop enhancementdto name but a few. © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved. Keywords: Lipidomics Lipidome Fatty acid Omics integration 1. Introduction Lipids lie at the very definition of life. Membranes separate cells from each other, enclose organelles, and subdivide organelles into even smaller compartments. In this manner membranes generate a number of different environments within the cell in which different biochemical reactions occur. Aside from this important structural function, processes as fundamental for plants as photosynthesis or the electron transport chain in mitochondria occur in membranes; membranes in and of themselves therefore constitute an environment for biochemical reactions. Interestingly, separate environmentsdmultiple domains with specific roles and a particular lipid and protein compositiondexist within a membrane too. These domains are not static, can rather move through the surface of a membrane or blend into the membrane and later form again [1]. To add yet one more level of complexity, the lipid bilayer is not symmetrical: it contains different kinds of lipids on each of the leaflets, possibly due to the different conditions to which the membrane can be exposed on both sides [1]. This bilayer asymmetry, the domains within membranes, and indeed the entire membrane diversity existing in a single cell, are the product of an active lipid metabolism. Lipids forming the membranes of plant cells are constantly * Corresponding author. E-mail address:-(Y. Brotman). 1 These authors contributed equally to this work. being produced and degraded, portions of lipids can be recycled, and there is extensive trafficking between different organelles. Plant biochemists have been studying this fascinating nature of lipids for more than 30 years. Initially the main focus was to understand how lipids were synthesized and transformed. Radiolabeling studies indicated the sequence in which fatty acids were produced, incorporated into glycerolipids, and desaturated. In 1982, Roughan and Slack [2] systematized the evidence coming from those studies and pointed out a major conclusion: plant glycerolipids are produced by two discrete pathways, one taking place in the chloroplast (the prokaryotic pathway) and another one in the endoplasmic reticulum (ER; the eukaryotic pathway). The emergence of Arabidopsis thaliana, which possesses both pathways, as a genetic model, enabled the dissection of lipid-biosynthesis regulation. Mutagen screenings carried out on this species allowed to identify mutants for most fatty-acid desaturases and several other mutants with a drastic phenotype in lipid composition [3]. These studies revealed that most desaturation steps in plants occur once fatty acids are already bound to membrane lipids. Remarkably, the authors uncovered that the loss of a given function in either the chloroplast or the ER pathway would trigger compensation by the other pathway. At this point, however, most genes involved in these pathways remained unknown. In the 1990s, the molecular-biology boom allowed to characterize an important number of genes spread all across lipid metabolism. Map-based cloning allowed to find the genes coding for most desaturases found previously in mutagen screenings [4], and of other important http://dx.doi.org/10.1016/j.biochi-/© 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved. 92 H. Tenenboim et al. / Biochimie 130 (2016) 91e96 lipid biosynthetic genes. Particular progress was made on the galactolipid pathway [5]. The cloning of MGD1 and DGD1 sequences, the two main galactosylases in Arabidopsis, allowed to reconstitute the plant galactolipid biosynthetic pathway in Escherichia coli [6]. The completion of the Arabidopsis genome sequencing [7] boosted the discovery of an unprecedented number of genes involved in lipid metabolism [8]. By querying the genome with known genes from other organisms it was often possible to find the Arabidopsis ortholog. It thus became possible to obtain a fairly complete picture of most genes involved in lipid synthesis. The pathways explored included not only membrane glycerolipidsdtraditionally the main focus of lipid biochemistrydbut also sphingolipids, the storage lipid triacylglycerol, cutin, waxes and suberin. Electronic databases have been created in order to contain the huge amount of generated data (for instance, in plants: [9]). The rise of high-throughput genomic, transcriptomic and metabolomic tools heralded the era of omics. Lipidomics, a field within metabolomics, aims to analyze simultaneously as many as possible lipid compounds in a given sampledand ideally, eventually, all of them. More than a decade after the first lipidomic study [10], we shall present recent key contributions of lipidomics to different aspects of plant lipid research (Fig. 1) and review developments and trends in the field. to direct infusion was developed employing liquidchromatographic (LC) separation prior to MS [13]. This reduced problems such as limited sensitivity of low-abundance species, and significantly improved the resolution for compounds with identical masses. Improved methods, often specifically developed for plant lipidomics, sprout continually: some address the general aspiration to detect as many lipid classes and species as accurately as possible and using as few analytical steps as possible [14]; while other focus on specialized topics, such as the spatial localization of lipids in plant tissues using lipidomics [15]. Biological significance is becoming more and more prominent in lipidomic studies, with mere “grocery” lists of lipids becoming a rarity. Even the authors of technical-advance reports make sure to apply their advance to reallife biology. Tarazona and co-workers [14], for instance, utilized their enhanced LC MS-based method to analyze lipid changes in cold- and drought-stressed plants, coming up with a record number of 393 species in 23 lipid classes and providing novel insights for the involvement of sphingolipids and sterols in these stresses. Indeed, several lipidomic endeavors were specifically dedicated to the two latter classes: sterols were catalogued and quantified comprehensively for the first time in plants only recently [16], and sphingolipids four years earlier [17]. 3. Beyond membranes 2. Modern lipidomics: the birth and rise of a new field Great technological strides have been achieved since the early days of lipid characterization. While the traditional method of choice, namely thin-layer chromatography (TLC) in conjunction with gas chromatography (GC), is still widely used, today's methods are truly highthroughput, and enable the analysis of lipids without prior degradation to their fatty-acid components. Welti and colleagues [10], in their formative lipidomic characterization of phospholipase D a's (PLDa) role in freezing tolerance, directly infused lipid extracts into a mass spectrometer (MS), a methodology that is still utilized nowadays ([11,12]). An alternative Aside from the important structural function of lipids, most prominently in membranes, plant lipidomic analysis has been used to research their other biological functions as well. When considering oil production in plants, for instance, a topic of current relevance that involves mainly the accumulation of triacylglycerols (TAGs), single-cell analysis enabled their direct in vivo profiling in green microalgae, sparing the need for extraction and providing real-time data [18]. A comprehensive systems approach comprising of global lipidomic and transcriptomic profiling was employed for the elucidation of oil-synthesis mechanisms in algae [19]. Industrial applications aside, lipid profiling is often exercised in nutritional research, where it is used, among others, to monitor the success of Fig. 1. A graphic summary of some of the topics discussed in this review, along with the relevant references. All icons taken from www.icons8.com. H. Tenenboim et al. / Biochimie 130 (2016) 91e96 genetic modifications. Much effort, for instance, is currently undertaken to increase the content of health-promoting u3 fatty acids in various crop and model plants [20]. Approaching the issue from a different angle, researchers profiled the fatty-acid composition in the exceptionally unsaturated-oily hickory nuts in order to learn how this plant achieves that; this was done in conjunction with transcriptomic profiling, in an example of omics integration for obtaining a comprehensive systemic picture [21]. Lipidomic analysis is not only able to detect known lipids, but also to identify novel ones. Even new lipid classes can be identified, as exemplified by Okazaki and colleagues [22], who used hydrophilic interaction chromatography (HILIC) in conjunction with MS/ MS to identify the novel lipid glucuronosyldiacylglycerol and to show that it accumulates as a protection mechanism upon phosphorus starvation. Four years earlier the same group used lipidomics in a supportive role; indeed, for every article that puts lipidomic discovery in the limelight, many more exist that focus rather on genetics, cell biology, or any other topic, and use lipidomics to show how the lipidome, or sometimes specific lipid classes, are affected by certain conditions. In the discussed case, the study deals with a novel lipid-biosynthetic gene, whereby it is shown that mutants are completely devoid of a whole lipid class, namely SQDG [23]. Lipidomic profiling helped to gain insights into the mechanisms through which the major Arabidopsis flowering inducer, FT, binds to phosphatidylcholine (PC), a lipid class that exhibits circadian oscillation, and that PC accumulation is correlated with flowering [24]. The authors showed that FT binds only to specific PC species, namely the ones that accumulate during the day. The result is that as day length changes throughout the year, PC levels change accordingly, and hence binding of FT and induction (or suppression) of flowering [24]. Indeed, several studies have utilized lipidomic analysis for the elucidation of developmentrelated questions. The same group reported a more general approach in the same year, whereby the lipidome and transcriptome of flowering-stage-synchronized Arabidopsis flowers were profiled, leading to a characterization of “distinct metabolic pathways stimulated at different stages of flower development” [25]. 4. Cell biology from a lipidomic point of view Lipid research does not only address lipids per se, but also lipidrelated organelles such as lipid droplets, large reservoirs for carbon storage with a plethora of other roles. Cai and colleagues [26] characterized a protein that regulates lipid-droplet formation in Arabidopsis and performed to this end lipidomic profiling of TAGs, the main storage lipid class. Lipid droplets and storage are also tightly related to autophagy, the self-degradation of cellular components that occurs when cells are stressed: as shown in animals, autophagy degrades stored lipids upon stress, and when autophagy is impaired, lipids accumulate [27]. The same was recently shown in plants, whereby autophagy-impaired mutants accumulated TAGs (as mediated by lipidomic profiling) upon carbon starvation [28]. A similar trend was found in a green-alga mutant impaired in cell division and autophagy, linking lipid composition, autophagy and cytokinesis [29]. But lipids are related to autophagy in an even more direct manner: phosphatidylethanolamine and phosphatidylinositol (PE and PI) are essential for autophagosome formation, by serving (PI) as an anchor for the PI3-kinase complex, an initial component of the autophagosome, and by being a major component of the autolysosome membrane (PE) [30]. In two other cellbiological efforts, the protein that exports fatty acids from their production site in the chloroplast to their processing site in the ER was discovered, whereupon lipidomic analysis was used to show impaired lipid synthesis when the transporter is absent [31]; and 93 the influence of lipid composition on the function of and protein localization in plasmodesmata, intracellular channels that facilitate communication between plant cells, was elucidated by means of lipidomic profiling of these isolated structures, a tour de force example of lipidomic analysis on specific parts of the cell [32]. In another remarkable example the utilization of nanomanipulators enabled the lipid profiling of a single lipid droplet [33]. Several techniques allow real-time as well as spatial lipidomic analysis. Raman spectroscopy [18] and matrix-assisted laser desorption ionization (MALDI-MS) [15,34] enable the analysis of single-cell organisms, and of cells within a tissue or a plant, respectively. The former allows for real-time analysis, whereby the effect of treatment or change in conditions on the lipidome can be immediately viewed, such as in the case of TAG production in algae [18]. MALDI-MS has been successfully used to measure the spatial distribution of lipids in cotton embryos [15] and in avocado mesocarp [34]. 5. Abiotic stress and its effect on the lipidome The exposure of plants to different kinds of stress stars in numerous studies, and very often produces remarkable changes in lipid regulation, synthesis, degradation, relocalization or restructuring. Changes in temperature, for instance, result in changes in membrane lipid composition as an attempt to preserve the membrane's physical properties. As described above, many plant species possess a so-called prokaryotic and a eukaryotic pathway for glycerolipid biosynthesis. Lipidomic profiling, in conjunction with other methodsdamong them transcriptomic analysisdwas used to show that cold stress induces the prokaryotic pathway and suppresses the eukaryotic [35], although contrasting evidence exists too [36]. These studies showcase the value of lipidomics in distinguishing, for each given lipid, whether it derived from the prokaryotic or eukaryotic pathway. Cold stress, because of the obvious and immediate changes that it brings about in membrane lipids, is frequently used as an effector whose aftermath helps reveal the function of novel lipid-related genes. Another example of integration of transcriptomic data addresses a different kind of abiotic stress, namely hypoxia, which plants frequently meet when overwatered, flooded or otherwise submergence in water. Lipidomic profiling revealed that ceramides, a class of sphingolipids, accumulate as well as undergo unsaturation under hypoxic conditions [37]. The effect on the lipidome was also studied upon multiple stresses: glycerolipidomic profiling was performed on Arabidopsis plants exposed in a time course to eight combinations of light and temperature stress, whereupon important insights into lipid-class remodeling and fatty-acid saturation were gained, as well as new lipid species hitherto unobserved in this plant identified [38]. Using the same lipidomic data from this experiment, Szymanski and colleagues [39] added a transcriptomic layer, “revealing large-scale coordination between gene expression and changes in glycerolipid levels” [39]. Comprehensive systems approaches and omics data integration were employed in the elucidation of Arabidopsis [40] and Chlamydomonas [41,42] response to heat stress. Changes in lipid composition following heat stress were profiled in wheat as well [43,44]. The lipidomic response to wounding was analyzed too, followed by co-occurrence analysis, which contributes to sorting different lipids according to the enzymes and pathways that control them [12]. Nutrient starvation is another well-studied abiotic stress. Many nutrients affect lipid homeostasis, but the most prominent and well-studied one after carbon is phosphorus (P). Upon P starvation plant cells degrade phospholipids in order to utilize the P that is released. Phospholipids were shown, using lipidomic profiling, to be replaced with the nonphosphorous classes SQDG [45], DGDG 94 H. Tenenboim et al. / Biochimie 130 (2016) 91e96 [46,47], and TAG [48] upon P starvation. As described above, some lipids serve as protective agents upon P starvation [22]. Studies in Hakea plants adapted to grow in P-poor soils in Australia revealed the mechanisms by which they replace phospholipids with alternatives in order to increase photosynthetic P usage efficiency, and also showed that these plants do not always perform well upon increased P availability, indicating at the rigidity of the protective mechanisms [49]. 6. The lipids in the frontline: the lipidomics of biotic stress In comparison to the abiotic stresses detailed above, much fewer lipidomics studies have been conducted for biotic stress. Lipids under pathogen or herbivore attack are relevant in several respects: as components of mechanical barriers, as signaling molecules that participate in immunity cascades, as mediators of programmed cell death (PCD) associated with defense, and as antimicrobial or antifungal compounds. Lipidomic analysis contributed considerably to the unraveling of these roles. Lipid profiling of the Arabidopsis hypersensitive response (HR), a defense mechanism triggered by infection, addressed mechanisms of lipid peroxidation, which again occur upon infection and attack by reactive oxygen species [50]. Peroxidation of fatty acids produces oxylipins and jasmonates, signaling molecules prominent in plant immunity. Ceramide accumulation, as measured by sphingolipid profiling, was shown to modulate PCD in cells undergoing HR [51]. Oil bodies in the leaf were shown, in a novel type of plant defense, to produce a fattyacid phytoalexin, a diverse group of anti-pathogen compounds [52]. Profiling of waxes provided the composition of epidermal cuticle, the first line of defense against pathogens and herbivores [53]. But plant biotic interaction does not solely refer to relationships detrimental to the plant: the lipid lyso-phosphatidylcholine was shown, using various chromatographic and mass spectrometric techniques, to be a major signal in the arbuscular mycorrhizal symbiosis between plant roots and beneficial fungi [54]. 7. Lipidomics in gene characterization Numerous genes involved in lipid biosynthesis, degradation, metabolism and regulation have been characterized over the years. Mutants of those genes almost invariably result in changes in lipid composition in the cell, whereupon lipidomic analysis is called to service. Many of those genes encode for enzymes that participate in the listed processes: lipid synthases, fatty-acid desaturases, lipases, acyltransferases, hydrolases, flippases and more. An ABHD-(a/b hydrolase domain)-protein, representing a class of lipases, was investigated in Arabidopsis. When absent, its lipid substrates accumulate and induce growth, resulting in faster-growing plants [55]. The flippase ALA10, the former a group of membrane-bound ATPase transporters that move lipids from one leaflet of the membrane to the other, and its control of FAD2/3, two fatty-acid desaturasesdenzymes turning single bonds into double bonds in fatty acids, were analyzed and shown to also affect chloroplast lipid composition [56]. PLA2, a phospholipasedenzymes separating fatty acids from glycerophospholipidsdwas analyzed in its contribution to the high production of an industrially valuable hydroxy fatty acid in castor plants [57]. Another phospholipase, PLC2, was revealed as the main enzyme in phosphoinositide (PI) biosynthesis, a major class of signal lipids [58]. Growth defects in PLC2 mutants underscored the fact that PIs are involved in growth and development [58], serving as an example of the many cellular deficiencies, alongside altered lipid composition, frequently observed in the studies listed here. Disruption of DGD1, a synthase converting monogalctosyldiacylglycerol into digalctosyldiacylglycerol, was shown to result in short plants and to induce oxylipin synthesis, including several jasmonate hormones. The latter, known to inhibit the cell cycle and cell expansion, caused lignification of the phloem cap, underlying the short-stem phenotype [59]. A family of desaturase-like proteins from Arabidopsis was characterized, whereby their disruption resulted in no visible phenotype but in dramatic changes, as mediated by lipidomic profiling, in the abundance of very-long-chain fatty acids and lipids containing them [60], an example of the power of omic approaches in defining non-visible deficiencies. Natural variation between different accessions, strains or cultivars of one species has been demonstrated numerous times in metabolomic research, but to a much lesser extent in the narrower realm of lipidomics. But there is no reason to believe that great differences in lipid composition do not exist. 289 inbred lines of maize were profiled in the frame of a genome-wide association study, leading to the identification of several candidate genes involved in lipid biology, as well as to the association of the lipidome with several agronomic traits [61]. Differences in lipidome remodeling in different accessions of Arabidopsis upon freezing treatment were analyzed, and indeed strong correlation was found between key lipid species and the freezing tolerance of specific accessions [62]. 8. Conclusion Lipidomics is emerging as an essential tool in plant science. Despite a deluge of studies in recent years, much remains unknown. Even in the most well-studied plant species, most genes annotated as lipid-related are yet to be functionally characterized. Among all the genes involved in lipid biology, biosynthetic genes require the most attention, since much information about other types of genes can be derived from them. But even outside the walls of lipid research, lipidomic analysis can refine our knowledge about genes studied and reported years ago, for example by demonstrating extensive lipid remodeling where no other phenotype is seen, but also by repeating earlier lipidomic studies while using improved technologies that will invariably expand the scope of detected species. Lipidomics data fared well within the trend of omics integration, and many studies already exist that employ a systems approach (Fig. 1). That said, there is still room for tighter integration, using sophisticated network algorithms, genome-wide association studies, and other methods increasingly seen in broader metabolomic studies. As the importance of lipid content in the food, fuel, and chemical industries is gradually being revealed, lipidomic analysis is now routinely employed not only in model organisms but also in crops and in ecologically, industrially and commercially important species. References [1] G. van Meer, D.R. Voelker, G.W. Feigenson, Membrane lipids: where they are and how they behave, Nat. Rev. Mol. Cell Biol. 9 -e124, http:// dx.doi.org/10.1038/nrm2330. [2] P.G. Roughan, C.R. Slack, Cellular organization of glycerolipid metabolism, Annu. Rev. Plant Physiol. 33 (1982) 97e132, http://dx.doi.org/10.1146/ annurev.pp-. [3] C. Somerville, J. Browse, Plant lipids: metabolism, mutants, and membranes, Science (80-. ) 252 (1991) 80e87, http://dx.doi.org/10.1126/ science-. [4] J.G. Wallis, J. Browse, Mutants of Arabidopsis reveal many roles for membrane lipids, Prog. Lipid Res. 41 -e278. € rmann, C. Benning, Galactolipids rule in seed plants, Trends Plant Sci. 7 [5] P. Do -e118. €rmann, I. Balbo, C. Benning, Arabidopsis galactolipid biosynthesis and [6] P. Do lipid trafficking mediated by DGD1, Science (80-. ) 284 -e2184. [7] Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature 408 -e815, http:// dx.doi.org/10.1038/-. [8] J.G. Wallis, J. Browse, Lipid biochemists salute the genome, Plant J. 61 (2010) H. Tenenboim et al. / Biochimie 130 (2016) 91e96 1092e1106, http://dx.doi.org/10.1111/j-X-.x. [9] Y. Li-Beisson, B. Shorrosh, F. Beisson, M.X. Andersson, V. Arondel, P.D. Bates, et al., Acyl-lipid metabolism, Arab. Book 11 (2013) e0161, http://dx.doi.org/ 10.1199/tab.0161. [10] R. Welti, W. Li, M. Li, Y. Sang, H. Biesiada, H.-E. Zhou, et al., Profiling membrane lipids in plant stress responses. Role of phospholipase D alpha in freezing-induced lipid changes in Arabidopsis, J. Biol. Chem. 277 -e32002, http://dx.doi.org/10.1074/jbc.M-. € rmann, et al., [11] F. Gasulla, K. vom Dorp, I. Dombrink, U. Z€ ahringer, N. Gisch, P. Do The role of lipid metabolism in the acquisition of desiccation tolerance in Craterostigma plantagineum: a comparative approach, Plant J. 75 -e741, http://dx.doi.org/10.1111/tpj.12241. [12] H.S. Vu, S. Shiva, M.R. Roth, P. Tamura, L. Zheng, M. Li, et al., Lipid changes after leaf wounding in Arabidopsis thaliana: expanded lipidomic data form the basis for lipid co-occurrence analysis, Plant J. 80 -e743, http:// dx.doi.org/10.1111/tpj.12659. [13] J. Hummel, S. Segu, Y. Li, S. Irgang, J. Jueppner, P. Giavalisco, Ultra performance liquid Chromatography and high resolution mass spectrometry for the analysis of plant lipids, Front. Plant Sci. 2 (2011) 54, http://dx.doi.org/10.3389/ fpls-. [14] P. Tarazona, K. Feussner, I. Feussner, An enhanced plant lipidomics method based on multiplexed liquid chromatography-mass spectrometry reveals additional insights into cold- and drought-induced membrane remodeling, Plant J. 84 -e633, http://dx.doi.org/10.1111/tpj.13013. [15] P.J. Horn, A.R. Korte, P.B. Neogi, E. Love, J. Fuchs, K. Strupat, et al., Spatial mapping of lipids at cellular resolution in embryos of cotton, Plant Cell. 24 -e636, http://dx.doi.org/10.1105/tpc-. € rmann, Quantification of sterol [16] V. Wewer, I. Dombrink, K. vom Dorp, P. Do lipids in plants by quadrupole time-of-flight mass spectrometry, J. Lipid Res. 52 -e1054, http://dx.doi.org/10.1194/jlr.D013987. [17] J.E. Markham, J.G. Jaworski, Rapid measurement of sphingolipids fromArabidopsis thaliana by reversed-phase high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry, Rapid Commun, Mass Spectrom. 21 -e1314, http://dx.doi.org/10.1002/ rcm.2962. [18] H. Wu, J.V. Volponi, A.E. Oliver, A.N. Parikh, B.A. Simmons, S. Singh, In vivo lipidomics using single-cell Raman spectroscopy, Proc. Natl. Acad. Sci. U. S. A. 108 -e3814, http://dx.doi.org/10.1073/pnas-. [19] J. Li, D. Han, D. Wang, K. Ning, J. Jia, L. Wei, et al., Choreography of transcriptomes and lipidomes of nannochloropsis reveals the mechanisms of oil synthesis in microalgae, Plant Cell 26 -e1665, http://dx.doi.org/ 10.1105/tpc-. [20] X.-R. Zhou, D.L. Callahan, P. Shrestha, Q. Liu, J.R. Petrie, S.P. Singh, Lipidomic analysis of Arabidopsis seed genetically engineered to contain DHA, Front. Plant Sci. 5 -, http://dx.doi.org/10.3389/fpls-. [21] J. Huang, T. Zhang, Q. Zhang, M. Chen, Z. Wang, B. Zheng, et al., The mechanism of high contents of oil and oleic acid revealed by transcriptomic and lipidomic analysis during embryogenesis in Carya cathayensis Sarg, BMC Genomics 17 -, http://dx.doi.org/10.1186/s-. [22] Y. Okazaki, H. Otsuki, T. Narisawa, M. Kobayashi, S. Sawai, Y. Kamide, et al., A new class of plant lipid is essential for protection against phosphorus depletion, Nat. Commun. 4 -, http://dx.doi.org/10.1038/ ncomms2512. [23] Y. Okazaki, M. Shimojima, Y. Sawada, K. Toyooka, T. Narisawa, K. Mochida, et al., A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis, Plant Cell 21 -e909, http://dx.doi.org/10.1105/tpc-. s, K. Kanehara, Y. Liu, P. Do € rmann, G. Coupland, Ara[24] Y. Nakamura, F. Andre bidopsis florigen FT binds to diurnally oscillating phospholipids that accelerate flowering, Nat. Commun. 5 (2014), http://dx.doi.org/10.1038/ ncomms4553. [25] Y. Nakamura, N.Z.W. Teo, G. Shui, C.H.L. Chua, W.-F. Cheong, S. Parameswaran, et al., Transcriptomic and lipidomic profiles of glycerolipids during Arabidopsis flower development, New Phytol. 203 -e322, http:// dx.doi.org/10.1111/nph.12774. [26] Y. Cai, J.M. Goodman, M. Pyc, R.T. Mullen, J.M. Dyer, K.D. Chapman, Arabidopsis SEIPIN proteins modulate triacylglycerol accumulation and influence lipid droplet proliferation, Plant Cell 27 -e2636, http://dx.doi.org/ 10.1105/tpc-. [27] R. Singh, S. Kaushik, Y. Wang, Y. Xiang, I. Novak, M. Komatsu, et al., Autophagy regulates lipid metabolism, Nature 458 -e1135, http://dx.doi.org/ 10.1038/nature07976. [28] T. Avin-Wittenberg, K. Bajdzienko, G. Wittenberg, S. Alseekh, T. Tohge, R. Bock, et al., Global analysis of the role of autophagy in cellular metabolism and energy homeostasis in Arabidopsis seedlings under carbon starvation, Plant Cell 27 -e322, http://dx.doi.org/10.1105/tpc-. [29] H. Tenenboim, J. Smirnova, L. Willmitzer, M. Steup, Y. Brotman, VMP1deficient Chlamydomonas exhibits severely aberrant cell morphology and disrupted cytokinesis, BMC Plant Biol. 14 -, http://dx.doi.org/ 10.1186/-. [30] F. Li, R.D. Vierstra, Autophagy: a multifaceted intracellular system for bulk and selective recycling, Trends Plant Sci. 17 -e537, http://dx.doi.org/ 10.1016/j.tplants-. [31] N. Li, I.L. Gügel, P. Giavalisco, V. Zeisler, L. Schreiber, J. Soll, et al., FAX1, a novel membrane protein mediating plastid fatty acid export, PLoS Biol. 13 (2015) 95 e-, http://dx.doi.org/10.1371/journal.pbio-. € rmann, et al., [32] M.S. Grison, L. Brocard, L. Fouillen, W. Nicolas, V. Wewer, P. Do Specific membrane lipid composition is important for plasmodesmata function in Arabidopsis, Plant Cell 27 -e1250, http://dx.doi.org/ 10.1105/tpc-. [33] P.J. Horn, N.R. Ledbetter, C.N. James, W.D. Hoffman, C.R. Case, G.F. Verbeck, et al., Visualization of lipid droplet composition by direct organelle mass spectrometry, J. Biol. Chem. 286 -e3306, http://dx.doi.org/10.1074/ jbc.M-. [34] P.J. Horn, C.N. James, S.K. Gidda, A. Kilaru, J.M. Dyer, R.T. Mullen, et al., Identification of a new class of lipid droplet-associated proteins in plants, Plant Physiol. 162 -e1936, http://dx.doi.org/10.1104/pp-. [35] Q. Li, Q. Zheng, W. Shen, D. Cram, D.B. Fowler, Y. Wei, et al., Understanding the biochemical basis of temperature-induced lipid pathway adjustments in plants, Plant Cell 27 (2015) 86e103, http://dx.doi.org/10.1105/ tpc-. [36] M. Chen, J.J. Thelen, ACYL-LIPID DESATURASE2 is required for chilling and freezing tolerance in Arabidopsis, Plant Cell 25 -e1444, http:// dx.doi.org/10.1105/tpc-. [37] L.-J. Xie, Q.-F. Chen, M.-X. Chen, L.-J. Yu, L. Huang, L. Chen, et al., Unsaturation of very-long-chain ceramides protects plant from hypoxia-induced damages by modulating ethylene signaling in Arabidopsis, PLoS Genet. 11 (2015) e-, http://dx.doi.org/10.1371/journal.pgen-. [38] A. Burgos, J. Szymanski, B. Seiwert, T. Degenkolbe, M.A. Hannah, P. Giavalisco, et al., Analysis of short-term changes in the Arabidopsis thaliana glycerolipidome in response to temperature and light, Plant J. 66 -e668, http://dx.doi.org/10.1111/j-X-.x. Cuadros-Inostroza, Linking gene [39] J. Szymanski, Y. Brotman, L. Willmitzer, A. expression and membrane lipid composition of Arabidopsis, Plant Cell 26 -e928, http://dx.doi.org/10.1105/tpc-. [40] Y. Higashi, Y. Okazaki, F. Myouga, K. Shinozaki, K. Saito, D.A. Los, et al., Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana, Sci. Rep. 5 -, http://dx.doi.org/10.1038/srep10533. [41] D. Hemme, D. Veyel, T. Mühlhaus, F. Sommer, J. Jüppner, A.-K. Unger, et al., Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii, Plant Cell 26 -e4297, http://dx.doi.org/10.1105/tpc-. geret, M. Schulz-Raffelt, H.M. Nguyen, P. Auroy, F. Beisson, G. Peltier, et [42] B. Le al., Lipidomic and transcriptomic analyses of Chlamydomonas reinhardtii under heat stress unveil a direct route for the conversion of membrane lipids into storage lipids, Plant. Cell Environ. 39 -e847, http://dx.doi.org/ 10.1111/pce.12656. [43] S. Narayanan, P.J. Tamura, M.R. Roth, P.V. Prasad, R. Welti, Wheat leaf lipids during heat stress: I. High day and night temperatures result in major lipid alterations, Plant. Cell Environ. 39 -e803. [44] S. Narayanan, P.V.V. Prasad, R. Welti, Wheat leaf lipids during heat stress: II. Lipids experiencing coordinated metabolism are detected by analysis of lipid co-occurrence, Plant. Cell Environ. 39 -e617, http://dx.doi.org/ 10.1111/pce.12648. [45] B. Essigmann, S. Güler, R.A. Narang, D. Linke, C. Benning, Phosphate availability affects the thylakoid lipid composition and the expression of SQD1, a gene required for sulfolipid biosynthesis in Arabidopsis thaliana, Proc. Natl. Acad. Sci. U. S. A. 95 -e1955. http://www.ncbi.nlm.nih.gov/ pubmed/-. accessed-. €rtel, P. Dormann, C. Benning, DGD1-independent biosynthesis of [46] H. Ha extraplastidic galactolipids after phosphate deprivation in Arabidopsis, Proc. Natl. Acad. Sci. U. S. A. 97 -e10654, http://dx.doi.org/10.1073/ pnas-. [47] M. Li, R. Welti, X. Wang, Quantitative profiling of Arabidopsis polar glycerolipids in response to phosphorus starvation. Roles of phospholipases D zeta1 and D zeta2 in phosphatidylcholine hydrolysis and digalactosyldiacylglycerol accumulation in phosphorus-starved plants, Plant Physiol. 142 -e761, http://dx.doi.org/10.1104/pp-. [48] B.D. Pant, A. Burgos, P. Pant, A. Cuadros-Inostroza, L. Willmitzer, W.R. Scheible, The transcription factor PHR1 regulates lipid remodeling and triacylglycerol accumulation in Arabidopsis thaliana during phosphorus starvation, J. Exp. Bot. 66 -e1918, http://dx.doi.org/10.1093/jxb/ eru535. [49] T. Kuppusamy, P. Giavalisco, S. Arvidsson, R. Sulpice, M. Stitt, P.M. Finnegan, et al., Lipid biosynthesis and protein concentration respond uniquely to phosphate supply during leaf development in highly phosphorus-efficient Hakea prostrata, Plant Physiol. 166 -e1911, http://dx.doi.org/10.1104/ pp-. [50] M. Zoeller, N. Stingl, M. Krischke, A. Fekete, F. Waller, S. Berger, et al., Lipid profiling of the Arabidopsis hypersensitive response reveals specific lipid peroxidation and fragmentation processes: biogenesis of pimelic and azelaic acid, Plant Physiol. 160 -e378, http://dx.doi.org/10.1104/ pp-. [51] W. Wang, X. Yang, S. Tangchaiburana, R. Ndeh, J.E. Markham, Y. Tsegaye, et al., An inositolphosphorylceramide synthase is involved in regulation of plant programmed cell death associated with defense in Arabidopsis, Plant Cell 20 -e3179, http://dx.doi.org/10.1105/tpc-. [52] T.L. Shimada, Y. Takano, T. Shimada, M. Fujiwara, Y. Fukao, M. Mori, et al., Leaf oil body functions as a subcellular factory for the production of a phytoalexin in Arabidopsis, Plant Physiol. 164 -e118, http://dx.doi.org/10.1104/ 96 H. Tenenboim et al. / Biochimie 130 (2016) 91e96 pp-. [53] M.C. Suh, A.L. Samuels, R. Jetter, L. Kunst, M. Pollard, J. Ohlrogge, et al., Cuticular lipid composition, surface structure, and gene expression in Arabidopsis stem epidermis, Plant Physiol. 139 -e1665, http:// dx.doi.org/10.1104/pp-. [54] D. Drissner, G. Kunze, N. Callewaert, P. Gehrig, M. Tamasloukht, T. Boller, et al., Lyso-phosphatidylcholine is a signal in the arbuscular mycorrhizal symbiosis, Science 318 (2007), 80. [55] A. Vijayakumar, P. Vijayaraj, A.K. Vijayakumar, R. Rajasekharan, The Arabidopsis ABHD11 mutant accumulates polar lipids in leaves as a consequence of absent acylhydrolase activity, Plant Physiol. 170 -e193, http:// dx.doi.org/10.1104/pp-. re, M. Michaud, E. Dubots, Y. Yamaryo-Botte , et [56] C. Botella, E. Sautron, L. Boudie al., ALA10, a phospholipid flippase, controls FAD2/FAD3 desaturation of phosphatidylcholine in the ER, and affects chloroplast lipid composition in Arabidopsis thaliana, Plant Physiol. 170 -e1314, http://dx.doi.org/ 10.1104/PP-. [57] S. Bayon, G. Chen, R.J. Weselake, J. Browse, A small phospholipase A 2 -a from castor catalyzes the removal of hydroxy fatty acids from phosphatidylcholine in transgenic Arabidopsis seeds, Plant Physiol. 167 -e1270, http:// dx.doi.org/10.1104/pp-. [58] K. Kanehara, C.-Y. Yu, Y. Cho, W.-F. Cheong, F. Torta, G. Shui, et al., Arabidopsis AtPLC2 is a primary phosphoinositide-specific phospholipase C in phosphoinositide metabolism and the endoplasmic reticulum stress response, PLoS Genet. 11 (2015) e-, http://dx.doi.org/10.1371/journal.pgen-. [59] Y.-T. Lin, L.-J. Chen, C. Herrfurth, I. Feussner, H. Li, Reduced digalactosyldiacylglycerol synthesis in Arabidopsis leads to oxylipin overproduction and phloem cap lignification, Plant Cell 28 (2015), http://dx.doi.org/10.1105/ tpc-. TPC2015e01002eRA. [60] M.A. Smith, M. Dauk, H. Ramadan, H. Yang, L.E. Seamons, R.P. Haslam, et al., Involvement of Arabidopsis ACYL-COENZYME A DESATURASE-LIKE2 (At2g31360) in the biosynthesis of the very-long-chain monounsaturated fatty acid components of membrane lipids, Plant Physiol. 161 (2013) 81e96, http://dx.doi.org/10.1104/pp-. ret, A.E. Melchinger, L. Willmitzer, The [61] C. Riedelsheimer, Y. Brotman, M. Me maize leaf lipidome shows multilevel genetic control and high predictive value for agronomic traits, Sci. Rep. 3 (2013) 67e84, http://dx.doi.org/ 10.1038/srep02479. [62] T. Degenkolbe, P. Giavalisco, E. Zuther, B. Seiwert, D.K. Hincha, L. Willmitzer, Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana, Plant J. 72 -e982, http:// dx.doi.org/10.1111/tpj.12007.