An enhanced plant lipidomics method based on multiplexed liquid chromatography-mass spectrometry reveals additional insights into cold- and drought-induced membrane remodeling

Exploring lipid signaling in plant physiology: From cellular membranes to environmental adaptation

Lipids have evolved as versatile signaling molecules that regulate a variety of physiological processes in plants. Convincing evidence highlights their critical role as mediators in a wide range of plant processes required for survival, growth, development, and responses to environmental conditions such as water availability, temperature changes, salt, pests, and diseases. Understanding lipid signaling as a critical process has helped us expand our understanding of plant biology by explaining how plants sense and respond to environmental cues. Lipid signaling pathways constitute a complex network of lipids, enzymes, and receptors that coordinate important cellular responses and stressing plant biology's changing and adaptable traits. Plant lipid signaling involves a wide range of lipid classes, including phospholipids, sphingolipids, oxylipins, and sterols, each of which contributes differently to cellular communication and control. These lipids function not only as structural components, but also as bioactive molecules that transfer signals. The mechanisms entail the production of lipid mediators and their detection by particular receptors, which frequently trigger downstream cascades that affect gene expression, cellular functions, and overall plant growth. This review looks into lipid signaling in plant physiology, giving an in-depth look and emphasizing its critical function as a master regulator of vital activities.

MORN motif-containing protein OsMORN1 and OsMORN2 are crucial for rice pollen viability and cold tolerance

The pollen viability directly affects the pollination process and the ultimate grain yield of rice. Here, we identified that the MORN motif-containing proteins, OsMORN1 and OsMORN2, had a crucial role in maintaining pollen fertility. Compared with the wild type (WT), the pollen viability of the osmorn1 and osmorn2 mutants was reduced, and pollen germination was abnormal, resulting in significantly lower spikelet fertility, seed-setting rate, and grain yield per plant. Further investigation revealed that OsMORN1 was localized to the Golgi apparatus and lipid droplets. Lipids associated with pollen viability underwent alterations in osmorn mutants, such as the diacylglyceride (18:3_18:3) was 5.1-fold higher and digalactosyldiacylglycerol (18:2_18:2) was 5.2-fold lower in osmorn1, while the triacylglycerol (TG) (16:0_18:2_18:3) was 8.3-fold higher and TG (16:0_18:1_18:3) was 8.5-fold lower in osmorn2 than those in WT. Furthermore, the OsMORN1/2 was found to be associated with rice cold tolerance, as osmorn1 and osmorn2 mutants were more sensitive to chilling stress than WT. The mutants displayed increased hydrogen peroxide accumulation, reduced antioxidant enzyme activities, elevated malondialdehyde content, and a significantly decreased seedling survival rate. Lipidomics analysis revealed distinct alterations in lipids under low temperature, highlighting significant changes in TG (18:2_18:3_18:3) and TG (18:4_18:2_18:2) in osmorn1, TG (16:0_18:2_18:2) and PI (17:2_18:3) in osmorn2 compared to the WT. Therefore, it suggested that OsMORN1 and OsMORN2 regulate both pollen viability and cold tolerance through maintaining lipid homeostasis.

Integrating physiological and multi-omics methods to elucidate heat stress tolerance for sustainable rice production

Heat stress presents unique challenges compared to other environmental stressors, as predicting crop responses and understanding the mechanisms for heat tolerance are complex tasks. The escalating impact of devastating climate changes heightens the frequency and intensity of heat stresses, posing a noteworthy threat to global agricultural productivity, especially in rice-dependent regions of the developing world. Humidity has been demonstrated to negatively affect rice yields worldwide. Plants have evolved intricate biochemical adaptations, involving intricate interactions among genes, proteins, and metabolites, to counter diverse external signals and ensure their survival. Modern-omics technologies, encompassing transcriptomics, metabolomics, and proteomics, have revolutionized our comprehension of the intricate biochemical and cellular shifts that occur in stressed agricultural plants. Integrating these multi-omics approaches offers a comprehensive view of cellular responses to heat stress and other challenges, surpassing the insights gained from multi-omics analyses. This integration becomes vital in developing heat-tolerant crop varieties, which is crucial in the face of increasingly unpredictable weather patterns. To expedite the development of heat-resistant rice varieties, aiming at sustainability in terms of food production and food security globally, this review consolidates the latest peer-reviewed research highlighting the application of multi-omics strategies.

Transcriptome and metabolome analyses reveal the regulatory role of MdPYL9 in drought resistance in apple

BACKGROUND

The mechanisms by which the apple MdPYL9 gene mediates the response to drought stress remain unclear. Here, transcriptome and metabolome analyses of apple plants under drought were used to investigate the mechanisms by which MdPYL9 regulates the response to drought stress in apple. MdPYL9-overexpressed transgenic and non-transgenic apple histoculture seedlings were rooted, transplanted, and subjected to drought treatments to clarify the mechanisms underlying the responses of apples to drought stress through phenotypic observations, physiological and biochemical index measurements, and transcriptomic and metabolomic analyses.

RESULTS

Under drought stress treatment, transgenic plants were less affected by drought stress than non-transgenic plants. Decreases in the net photosynthetic rate, stomatal conductance, and transpiration rate of transgenic apple plants were less pronounced in transgenic plants than in non-transgenic plants, and increases in the intercellular CO2 concentration were less pronounced in transgenic plants than in non-transgenic plants. The relative electrical conductivity and content of malondialdehyde, superoxide anion, and hydrogen peroxide were significantly lower in transgenic plants than in non-transgenic plants, and the chlorophyll content and activities of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) were significantly higher in transgenic plants than in non-transgenic plants. The number of differentially expressed genes (DEGs) involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and the most significant and highly annotated DEGs in the transgenic plants were involved in the flavonoid biosynthesis pathway, and the most significant and highly annotated DEGs in control plants were involved in the phytohormone signal transduction pathway. The number of differentially accumulated metabolites involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and up-regulated metabolites were significantly enriched in apigenin-7-O-glucoside in transgenic plants and in abscisic acid in non-transgenic plants. In the flavonoid biosynthetic pathway, the expression of genes encoding chalcone synthase (CHS) and chalcone isomerase (CHI) was more significantly down-regulated in non-transgenic plants than in transgenic plants, and the expression of the gene encoding 4-coumarate-CoA ligase (4CL) was more significantly up-regulated in transgenic plants than in non-transgenic plants, which resulted in the significant up-regulation of apigenin-7-O-glucoside in transgenic plants.

CONCLUSIONS

The above results indicated that the over-expression of MdPYL9 increased the drought resistance of plants under drought stress by attenuating the down-regulation of the expression of genes encoding CHS and CHI and enhancing the up-regulated expression of the gene encoding 4CL, which enhanced the content of apigenin-7-O-glucoside.

Transcriptome Analysis and Metabolic Profiling Reveal the Key Regulatory Pathways in Drought Stress Responses and Recovery in Tomatoes

Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis-antenna proteins, nitrogen metabolism, plant-pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5'-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, the biosynthesis of secondary metabolites, the biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomatoes to enhance drought tolerance.

Arabidopsis Leaf Chloroplasts Have a Specific Sphingolipidome

Sphingolipids are ubiquitous in eukaryotes and certain prokaryotes, where they serve as vital components of biological membranes and bioactive molecules. Chloroplasts have complex membrane structures that play crucial roles in photosynthesis, but their specific sphingolipidome remains unreported. In this study, we used liquid chromatography-mass spectrometry (LC-MS/MS) to analyze the sphingolipidome of purified Arabidopsis thaliana chloroplasts. We detected 92 chloroplast sphingolipids. The chloroplast sphingolipidome differed from total leaf (TL) samples, with a higher content of free long-chain bases and hydroxyceramides and a greater proportion of complex sphingolipids with 16C fatty acid (FA) forms. Notably, chloroplast glucosylceramides were predominantly the d18:1 h16:0 and t18:1 h16:0 forms rather than the 24C FA form found in TL and other cellular structures. Comparing the sphingolipidomes of different cellular structures underscores the inhomogeneity of the intracellular distribution of sphingolipids. This provides a robust reference for further elucidating the function of sphingolipids in plant cells.

High-Throughput Microbore LC-MS Lipidomics to Investigate APOE Phenotypes

Microflow liquid chromatography interfaced with mass spectrometry (μLC-MS/MS) is increasingly applied for high-throughput profiling of biological samples and has been proven to have an acceptable trade-off between sensitivity and reproducibility. However, lipidomics applications are scarce. We optimized a μLC-MS/MS system utilizing a 1 mm inner diameter × 100 mm column coupled to a triple quadrupole mass spectrometer to establish a sensitive, high-throughput, and robust single-shot lipidomics workflow. Compared to conventional lipidomics methods, we achieve a ∼4-fold increase in response, facilitating quantification of 351 lipid species from a single iPSC-derived cerebral organoid during a 15 min LC-MS analysis. Consecutively, we injected 303 samples over ∼75 h to prove the robustness and reproducibility of the microflow separation. As a proof of concept, μLC-MS/MS analysis of Alzheimer's disease patient-derived iPSC cerebral organoid reveals differential lipid metabolism depending on APOE phenotype (E3/3 vs E4/4). Microflow separation proves to be an environmentally friendly and cost-effective method as it reduces the consumption of harmful solvents. Also, the data demonstrate robust, in-depth, high-throughput performance to enable routine clinical or biomedical applications.

Uptake and Metabolic Conversion of Exogenous Phosphatidylcholines Depending on Their Acyl Chain Structure in Arabidopsis thaliana

Fungi and plants are not only capable of synthesizing the entire spectrum of lipids de novo but also possess a well-developed system that allows them to assimilate exogenous lipids. However, the role of structure in the ability of lipids to be absorbed and metabolized has not yet been characterized in detail. In the present work, targeted lipidomics of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs), in parallel with morphological phenotyping, allowed for the identification of differences in the effects of PC molecular species introduced into the growth medium, in particular, typical bacterial saturated (14:0/14:0, 16:0/16:0), monounsaturated (16:0/18:1), and typical for fungi and plants polyunsaturated (16:0/18:2, 18:2/18:2) species, on Arabidopsis thaliana. For comparison, the influence of an artificially synthesized (1,2-di-(3-(3-hexylcyclopentyl)-propanoate)-sn-glycero-3-phosphatidylcholine, which is close in structure to archaeal lipids, was studied. The phenotype deviations stimulated by exogenous lipids included changes in the length and morphology of both the roots and leaves of seedlings. According to lipidomics data, the main trends in response to exogenous lipid exposure were an increase in the proportion of endogenic 18:1/18:1 PC and 18:1_18:2 PC molecular species and a decrease in the relative content of species with C18:3, such as 18:3/18:3 PC and/or 16:0_18:3 PC, 16:1_18:3 PE. The obtained data indicate that exogenous lipid molecules affect plant morphology not only due to their physical properties, which are manifested during incorporation into the membrane, but also due to the participation of exogenous lipid molecules in the metabolism of plant cells. The results obtained open the way to the use of PCs of different structures as cellular regulators.

Divergent responses in desiccation experiments in two ecophysiologically different Zygnematophyceae

Water scarcity can be considered a major stressor on land, with desiccation being its most extreme form. Land plants have found two different solutions to this challenge: avoidance and tolerance. The closest algal relatives to land plants, the Zygnematophyceae, use the latter, and how this is realized is of great interest for our understanding of the conquest of land. Here, we worked with two representatives of the Zygnematophyceae, Zygnema circumcarinatum SAG 698-1b and Mesotaenium endlicherianum SAG 12.97, who differ in habitats and drought resilience. We challenged both algal species with severe desiccation in a laboratory setup until photosynthesis ceased, followed by a recovery period. We assessed their morphological, photophysiological, and transcriptomic responses. Our data pinpoint global differential gene expression patterns that speak of conserved responses, from calcium-mediated signaling to the adjustment of plastid biology, cell envelopes, and amino acid pathways, between Zygnematophyceae and land plants despite their strong ecophysiological divergence. The main difference between the two species appears to rest in a readjustment of the photobiology of Zygnema, while Mesotaenium experiences stress beyond a tipping point.

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses

The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.

Lipidomic Profiles of Lipid Biosynthesis in Oil Palm during Fruit Development

The fruit of the oil palm (Elaeis guineensis Jacq.) has fleshy mesocarpic tissue rich in lipids. This edible vegetable oil is economically and nutritionally significant across the world. The core concepts of oil biosynthesis in oil palms remain to be researched as the knowledge of oil biosynthesis in plants improves. In this study, we utilized a metabolite approach and mass spectral analysis to characterize metabolite changes and identify the sequences of protein accumulation during the physiological processes that regulate oil synthesis during oil palm fruit ripening. Here, we performed a comprehensive lipidomic data analysis in order to understand the role of lipid metabolism in oil biosynthesis mechanisms. The experimental materials were collected from the mesocarp of oil palm (Tenera) at 95 days (early accumulation of fatty acid, first stage), 125 days (rapid growth of fatty acid accumulation, second stage), and 185 days (stable period of fatty acid accumulation, third stage) after pollination. To gain a clear understanding of the lipid changes that occurred during the growth of the oil palm, the metabolome data were found using principal component analysis (PCA). Furthermore, the accumulations of diacylglycerols, ceramides, phosphatidylethanolamine, and phosphatidic acid varied between the developmental stages. Differentially expressed lipids were successfully identified and functionally classified using KEGG analysis. Proteins related to the metabolic pathway, glycerolipid metabolism, and glycerphospholipid metabolism were the most significantly changed proteins during fruit development. In this study, LC-MS analysis and evaluation of the lipid profile in different stages of oil palm were performed to gain insight into the regulatory mechanisms that enhance fruit quality and govern differences in lipid composition and biosynthesis.

Wound-induced triacylglycerol biosynthesis is jasmonoy-l-isoleucin and abscisic acid independent

Triacylglycerol (TAG) plays a significant role during plant stress - it maintains lipid homeostasis. Upon wounding plants accumulate TAG, likely as a storage form of fatty acids (FAs) that originate from damaged membranes. This study asked if this process depends on the two phytohormones jasmonoyl-isoleucine (JA-Ile) and abscisic acid (ABA), which are involved in wound signalling. To analyse regulation of wound-induced TAG accumulation, we used mutants deficient in JA-Ile, with reduced ABA and the myb96 mutant, which is deficient in an ABA-dependent transcription factor. The expression of genes involved in TAG biosynthesis, and TAG content after wounding were analysed via LC-MS and GC-FID, plastidial lipid content in all mentioned mutant lines was also determined. The localization of newly synthesized TAG was investigated using lipid droplet staining. TAG accumulation upon wounding was confirmed as well as the fact that the newly synthesized TAG are mostly composed of polyunsaturated fatty acids. Nevertheless, all tested mutant lines were able to accumulate TAG similar to the WT. We observed differences in reduction of plastidial lipids - in WT plants this was higher than in mutant lines. Newly synthesized TAGs were stored in lipid droplets at and around the wounded area. Our results show that TAG accumulation upon wounding is not dependent on JA-Ile or ABA. The newly synthesized TAG species are composed of unsaturated fatty acids of membrane origin, and most likely serves as a transient energy store.

Transcriptome and metabolome analysis reveals key genes and secondary metabolites of Casuarina equisetifolia ssp. incana in response to drought stress

Casuarina equisetifolia is drought tolerant, salt tolerant, and able to grow in barren environments. It is often used to reduce wind damage, to prevent sand erosion, and to help establish plant communities in tropical and subtropical coastal zones. To determine the basis for its drought tolerance, we conducted transcriptomic and metabolic analyses of young branchlets under a non-drought treatment (D_0h) and 2-, 12-, and 24-h-long drought treatments (D_2h, D_12h, and D_24h). A total of 5033 and 8159 differentially expressed genes (DEGs) were identified in D_2h/D_0h and D_24h/D_0h. These DEGs were involved in plant hormone signal transduction, jasmonic acid (JA) biosynthesis, flavonoid biosynthesis, and phenylpropanoid biosynthesis. A total of 148 and 168 differentially accumulated metabolites (DAMs) were identified in D_12h/D_0h and D_24h/D_0h, which were mainly amino acids, phenolic acids, and flavonoids. In conclusion, C. equisetifolia responds to drought by regulating plant hormone signal transduction and the biosynthesis of JA, flavonoid, and phenylpropanoid. These results increase the understanding of drought tolerance in C. equisetifolia at both transcriptional and metabolic levels and provide new insights into coastal vegetation reconstruction and management.

Plastidic membrane lipids are oxidized by a lipoxygenase in Lobosphaera incisa

Green microalgae can accumulate neutral lipids, as part of a general lipid remodeling mechanism under stress such as nitrogen starvation. Lobosphaera incisa is of special interest because of its unique TAG acyl chain composition, especially 20:4 (n-6) can reach up to 21% of dry weight after nitrogen starvation. In order to identify factors that may influence the accumulation of polyunsaturated fatty acids (PUFAs), we identified recently a linoleate 13-lipoxygenase (LiLOX). It shares highest identity with plastidic enzymes from vascular plants and is induced upon nitrogen starvation. Here, we confirmed the localization of LiLOX in the stroma of plastids via transient expression in epithelial onion cells. In order to further characterize this enzyme, we focused on the identification of the endogenous substrate of LiLOX. In this regard, an ex vivo enzymatic assay, coupled with non-targeted analysis via mass spectrometry allowed the identification of MGDG, DGDG and PC as three substrate candidates, later confirmed via in vitro assays. Further investigation revealed that LiLOX has preferences towards the lipid class MGDG, which seems in agreement with its localization in the galactolipid rich plastid. Altogether, this study shows the first characterization of plastidic LOX from green algae, showing preference for MGDGs. However, lipidomics analysis did neither reveal an endogenous LiLOX product nor the final end product of MGDG oxidation. Nevertheless, the latter is a key to understanding the role of this enzyme and since its expression is highest during the degradation of the plastidic membrane, it is tempting to assume its involvement in this process.

Lipidomic analysis of moss species Bryum pseudotriquetrum and Physcomitrium patens under cold stress

Bryophytes, which lack lignin for protection, support themselves in harsh environments by producing various chemicals. In response to cold stress, lipids play a crucial role in cell adaptation and energy storage. Specifically, bryophytes survive at low temperatures by producing very long-chain polyunsaturated fatty acids (vl-PUFAs). The in-depth understanding of the lipid response to cold stress of bryophytes was studied by performing lipid profiling using ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS). Two moss species (Bryum pseudotriquetrum and Physcomitrium patens) cultivated at 23°C and at 10°C were included in this study. Relative quantitative lipid concentrations were compared and the potential lipid biomarkers were identified by multivariate statistical analysis in each species. In B. pseudotriquetrum, it was observed that the phospholipids and glycolipids increased under cold stress, while storage lipids decreased. The accumulation of the lipids with high unsaturation degrees mostly appears in phospholipids and glycolipids for both mosses. The results also indicate that two unusual lipid classes in plants, sulfonolipids and phosphatidylmethanol are biosynthesized by the bryophytes. This has not been seen previously and show that bryophytes have a very diverse chemistry and substantially different from other plant groups.

A high-throughput lipidomics and transcriptomic approach reveals novel compounds from sugarcane linked with promising therapeutic potential against COVID-19

Sugarcane (Saccharum ssp., Poaceae) provides enormous metabolites such as sugars, lipid, and other dietary metabolites to humans. Among them, lipids are important metabolites that perform various functions and have promising pharmacological value. However, in sugarcane, few studies are focusing on lipidomics and few lipid compounds were reported, and their pharmacological values are not explored yet. The transcriptomic and widely targeted lipidomics approach quantified 134 lipid compounds from the rind of six sugarcane genotypes. These lipid compounds include 57 fatty acids, 30 lysophosphatidylcholines, 23 glycerol esters, 21 lysophosphatidylethanolamines, 2 phosphatidylcholines, and 1 sphingolipid. Among them, 119 compounds were first time reported in sugarcane rind. Seventeen lipids compounds including 12 fatty acids, 2 glycerol lipids, LysoPC 16:0, LysoPE 16:0, and choline alfoscerate were abundantly found in the rind of sugarcane genotypes. From metabolic and transcriptomic results, we have developed a comprehensive lipid metabolic pathway and highlighted key genes that are differentially expressed in sugarcane. Several genes associated with α-linolenic acid and linoleic acid biosynthesis pathways were highly expressed in the rind of the ROC22 genotype. ROC22 has a high level of α-linolenic acid (an essential fatty acid) followed by ROC16. Moreover, we have explored pharmacological values of lipid compounds and found that the 2-linoleoylglycerol and gingerglycolipid C have strong binding interactions with 3CL^pro of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and these compounds can be utilized against SARS-CoV-2 as therapeutic agents. The transcriptome, metabolome, and bioinformatics analysis suggests that the sugarcane cultivars have a diversity of lipid compounds having promising therapeutic potential, and exploring the lipid metabolism will help to know more compounds that have promising cosmetic and pharmacological value.

Epigenetic marks for mitigating abiotic stresses in plants

Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.

Exogenous Proline Optimizes Osmotic Adjustment Substances and Active Oxygen Metabolism of Maize Embryo under Low-Temperature Stress and Metabolomic Analysis

Maize (Zea mays L.) is more sensitive to low-temperature stress in the early growth period. The study was to explore the response mechanism of proline to low-temperature stress during maize seed germination. Maize varieties Xinxin 2 (low-temperature insensitive) and Damin 3307 (low-temperature sensitive) were chosen as the test materials, setting the normal temperature for germination (22 °C/10 °C, 9d), low-temperature germination (4 °C/4 °C, 5d) and normal temperature recovery (22 °C/10 °C, 4d), combined with proline (15 mmol·L−1) soaking treatment, to study its effects on the osmotic regulation system and antioxidant protection system of maize embryos. Metabolomics analysis was carried out to initially reveal the basis of the metabolic regulation mechanism. The results showed that the activities of superoxide dismutase (SOD), peroxidase (POD), ascorbic acid peroxidase (APX) and glutathione reductase (GR) were induced to some extent under low-temperature stress. The activities of SOD, POD, APX and GR were further enhanced in the soaking seeds with proline. Proline treatment improved the activities of catalase (CAT), monodehydrated ascorbic acid reductase (MDHAR) and dehydroascorbic acid (DHAR), increased the contents of ascorbic acid (AsA) and glutathione (GSH) and decreased the contents of oxidized ascorbic acid (DHA) and reduced glutathione (GSSG) under low-temperature stress. The ratio of AsA/DHA and GSH/GSSG increased. The increase in antioxidant enzyme activity and the content of antioxidants can help to maintain the stability of the AsA-GSH cycle, and effectively reduce the production rate of superoxide anion (O2•−), hydrogen peroxide (H2O2) and malondialdehyde (MDA). Based on the UPLC-MS/MS detection platform and self-built database, 589 metabolites were detected in each treated maize embryo; 262 differential metabolites were obtained, including 32 organic acids, 28 amino acids, 20 nucleotides and their derivatives, 26 sugars and alcohols, 46 lipids, 51 alkaloids, 44 phenols and 15 other metabolites. Sixty-eight metabolic pathways involving different metabolites were obtained by KEGG enrichment analysis. The results showed that proline increased the accumulation of sorbitol, planteose, erythritose 4-phosphate, arabinose and other saccharides and alcohols in response to low-temperature stress, increased the content of osmoregulation substances under low-temperature stress. Proline also restored the TCA cycle by increasing the content of α-ketoglutarate and fumaric acid. Proline increased the contents of some amino acids (ornithine, proline, glycine, etc.), alkaloids (cocamidopropyl betaine, vanillylamine, 6-hydroxynicotinic acid, etc.), phenols (phenolic ayapin, chlorogenic acid, etc.) and vitamins (ascorbic acid, etc.) in the embryo under low-temperature stress. Combined with pathway enrichment analysis, proline could enhance the low-temperature stress resistance of germinated maize embryos by enhancing starch and sucrose metabolism, arginine and proline metabolism, biosynthesis of secondary metabolites, flavonoid biosynthesis and pentose phosphate pathway.

Characterization and expression analysis of the glycosyltransferase 64 familyin rice (Oryza sativa)

The glycosyltransferase 64 (GT64) family is widely conserved in many species, including animals and plants. The functions of GT64 family genes in animals have been well characterized in the biosynthesis of extracellular heparan sulfate, whereas two GT64 members in Arabidopsis thaliana are involved in the glycosylation of plasma membrane glycosylinositol phosphorylceramides (GIPCs). GIPCs are the main components of plant sphingolipids and serve as important signal molecules in various developmental processes and stress responses. Rice (Oryza sativa), a model monocot plant, contains four GT64 members in its genome. Using phylogenetic analysis, 73 GT64s from 19 plant species were divided into three main groups. Each group can be represented by the three members in Arabidopsis and show a trend of monocot-eudicot divergences. A promoter and genomic variation analysis of GT64s in rice showed that various stress-related regulatory elements exist in their promoters, and many sequence variations were found between the two main rice subspecies, japonica and indica. Additionally, the transmembrane domain and subcellular localization analyses revealed that these genes all encode membrane-bound glycosyltransferases and localize to the Golgi apparatus. Finally, expression analysis of the four GT64 genes in rice, as assessed by real-time quantitative PCR, showed that they have distinct tissue-specific expression patterns and respond to different hormone treatments or abiotic stresses. Our results indicated that this family of genes may play a role in different stress responses and hormone signaling pathways in rice, and therefore provides fundamental information for the further investigation of their function in rice.

Sphingolipids at Plasmodesmata: Structural Components and Functional Modulators

Plasmodesmata (PD) are plant-specific channels connecting adjacent cells to mediate intercellular communication of molecules essential for plant development and defense. The typical PD are organized by the close apposition of the plasma membrane (PM), the desmotubule derived from the endoplasmic reticulum (ER), and spoke-like elements linking the two membranes. The plasmodesmal PM (PD-PM) is characterized by the formation of unique microdomains enriched with sphingolipids, sterols, and specific proteins, identified by lipidomics and proteomics. These components modulate PD to adapt to the dynamic changes of developmental processes and environmental stimuli. In this review, we focus on highlighting the functions of sphingolipid species in plasmodesmata, including membrane microdomain organization, architecture transformation, callose deposition and permeability control, and signaling regulation. We also briefly discuss the difference between sphingolipids and sterols, and we propose potential unresolved questions that are of help for further understanding the correspondence between plasmodesmal structure and function.

Diversity in sphingolipid metabolism across land plants

Sphingolipids are essential metabolites found in all plant species. They are required for plasma membrane integrity, tolerance of and responses to biotic and abiotic stresses, and intracellular signalling. There is extensive diversity in the sphingolipid content of different plant species, and in the identities and roles of enzymes required for their processing. In this review, we survey results obtained from investigations of the classical genetic model Arabidopsis thaliana, from assorted dicots with less extensive genetic toolkits, from the model monocot Oryza sativa, and finally from the model bryophyte Physcomitrium patens. For each species or group, we first broadly summarize what is known about sphingolipid content. We then discuss the most insightful and puzzling features of modifications to the hydrophobic ceramides, and to the polar headgroups of complex sphingolipids. Altogether, these data can serve as a framework for our knowledge of sphingolipid metabolism across the plant kingdom. This chemical and metabolic heterogeneity underpins equally diverse functions. With greater availability of different tools for analytical measurements and genetic manipulation, our field is entering an exciting phase of expanding our knowledge of the biological functions of this persistently cryptic class of lipids.

Specific Changes in Arabidopsis thaliana Rosette Lipids during Freezing Can Be Associated with Freezing Tolerance

While the roles of a few specific lipids in plant freezing tolerance are understood, the effect of many plant lipids remains to be determined. Acclimation of plants to non-freezing cold before exposure to freezing temperatures improves the outcome of plants, compared to plants exposed to freezing without acclimation. Arabidopsis thaliana plants were subjected to one of three treatments: (1) "control", i.e., growth at 21 °C, (2) "non-acclimated", i.e., 3 days at 21 °C, 2 h at -8 °C, and 24 h recovery at 21 °C, and (3) "acclimated", i.e., 3 days at 4 °C, 2 h at -8 °C, and 24 h recovery at 21 °C. Plants were harvested at seven time points during the treatments, and lipid levels were measured by direct-infusion electrospray ionization tandem mass spectrometry. Ion leakage was measured at the same time points. To examine the function of lipid species in relation to freezing tolerance, the lipid levels in plants immediately following the freezing treatment were correlated with the outcome, i.e., ion leakage 24-h post-freezing. Based on the correlations, hypotheses about the functions of specific lipids were generated. Additionally, analysis of the lipid levels in plants with mutations in genes encoding patatin-like phospholipases, lipoxygenases, and 12-oxophytodienoic acid reductase 3 (opr3), under the same treatments as the wild-type plants, identified only the opr3-2 mutant as having major lipid compositional differences compared to wild-type plants.

Sphingolipid-Induced Programmed Cell Death is a Salicylic Acid and EDS1-Dependent Phenotype in Arabidopsis Fatty Acid Hydroxylase (Fah1, Fah2) and Ceramide Synthase (Loh2) Triple Mutants

Ceramides (Cers) and long-chain bases (LCBs) are plant sphingolipids involved in the induction of plant programmed cell death (PCD). The fatty acid hydroxylase mutant fah1 fah2 exhibits high Cer levels and moderately elevated LCB levels. Salicylic acid glucoside level is increased in this mutant, but no cell death can be detected by trypan blue staining. To determine the effect of Cers with different chain lengths, fah1 fah2 was crossed with ceramide synthase mutants longevity assurance gene one homologue1-3 (loh1, loh2 and loh3). Surprisingly, only triple mutants with loh2 show cell death detected by trypan blue staining under the selected conditions. Sphingolipid profiling revealed that the greatest differences between the triple mutant plants are in the LCB and LCB-phosphate (LCB-P) fraction. fah1 fah2 loh2 plants accumulate LCB d18:0, LCB t18:0 and LCB-P d18:0. Crossing fah1 fah2 loh2 with the salicylic acid (SA) synthesis mutant sid2-2 and with the SA signaling mutants enhanced disease susceptibility 1-2 (eds1-2) and phytoalexin deficient 4-1 (pad4-1) revealed that lesions are SA- and EDS1-dependent. These quadruple mutants also confirm that there may be a feedback loop between SA and sphingolipid metabolism as they accumulated less Cers and LCBs. In conclusion, PCD in fah1 fah2 loh2 is a SA- and EDS1-dependent phenotype, which is likely due to accumulation of LCBs.

Complex Changes in Membrane Lipids Associated with the Modification of Autophagy in Arabidopsis

Autophagy is a conserved mechanism among eukaryotes that degrades and recycles cytoplasmic components. Autophagy is known to influence the plant metabolome, including lipid content; however, its impact on the plant lipidome is not fully understood, and most studies have analyzed a single or few mutants defective in autophagy. To gain more insight into the effect of autophagy on lipid concentrations and composition, we quantitatively profiled glycerolipids from multiple Arabidopsis thaliana mutants altered in autophagy and compared them with wild-type seedlings under nitrogen replete (+N; normal growth) and nitrogen starvation (-N; autophagy inducing) conditions. Mutants include those in genes of the core autophagy pathway, together with other genes that have been reported to affect autophagy. Using Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry (MALDI-MS), we imaged the cellular distribution of specific lipids in situ and demonstrated that autophagy and nitrogen treatment did not affect their spatial distribution within Arabidopsis seedling leaves. We observed changes, both increases and decreases, in the relative amounts of different lipid species in the mutants compared to WT both in +N and -N conditions, although more changes were seen in -N conditions. The relative amounts of polyunsaturated and very long chain lipids were significantly reduced in autophagy-disrupted mutants compared to WT plants. Collectively, our results provide additional evidence that autophagy affects plant lipid content and that autophagy likely affects lipid properties such as chain length and unsaturation.

Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice

Drought differs from other natural disasters in several respects, largely because of the complexity of a crop's response to it and also because we have the least understanding of a crop's inductive mechanism for addressing drought tolerance among all abiotic stressors. Overall, the growth and productivity of crops at a global level is now thought to be an issue that is more severe and arises more frequently due to climatic change-induced drought stress. Among the major crops, rice is a frontline staple cereal crop of the developing world and is critical to sustaining populations on a daily basis. Worldwide, studies have reported a reduction in rice productivity over the years as a consequence of drought. Plants are evolutionarily primed to withstand a substantial number of environmental cues by undergoing a wide range of changes at the molecular level, involving gene, protein and metabolite interactions to protect the growing plant. Currently, an in-depth, precise and systemic understanding of fundamental biological and cellular mechanisms activated by crop plants during stress is accomplished by an umbrella of -omics technologies, such as transcriptomics, metabolomics and proteomics. This combination of multi-omics approaches provides a comprehensive understanding of cellular dynamics during drought or other stress conditions in comparison to a single -omics approach. Thus a greater need to utilize information (big-omics data) from various molecular pathways to develop drought-resilient crop varieties for cultivation in ever-changing climatic conditions. This review article is focused on assembling current peer-reviewed published knowledge on the use of multi-omics approaches toward expediting the development of drought-tolerant rice plants for sustainable rice production and realizing global food security.

Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants

Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.

The state of the art in plant lipidomics

Lipids are a group of compounds with diverse structures that perform several important functions in plants. To unravel and better understand their in vivo functions, plant biologists have been using various lipidomic technologies including liquid-chromatography (LC)-mass spectrometry (MS). However, there are still significant challenges in LC-MS based plant lipidomics, which need to be addressed. In this review, we provide an overview of the key developments in LC-MS based lipidomic approaches to detect and identify plant lipids with emphasis on areas that can be further improved. Given that the cellular lipidome is estimated to contain hundreds of thousands of lipids,^1,2 many of the lipid structures remain to be discovered. Furthermore, the plant lipidome is considered to be significantly more complex compared to that of mammals. Recent technical developments in mass spectrometry have made the detection of novel lipids possible; hence, approaches that can be used for plant lipid discovery are also discussed.

Nitric oxide alleviates chilling injury by regulating the metabolism of lipid and cell wall in cold-storage peach fruit

Peach fruit are prone to development of chilling injury during cold storage at around 0-7 °C. Nitric oxide (NO) has been proven to alleviate chilling injury, but the mechanism was still unclear. In this study, peach fruit were immersed in a NO donor (sodium nitroprusside, SNP) solution for 10 min, then stored at 0 °C. The SNP alleviated chilling injury, including decreasing the internal browning index, malondialdehyde content, electrolyte leakage, and lipoxygenase activity, and maintaining firmness. Furthermore, SNP maintenance of fruit firmness was associated with reduction of xyloglucan endotransglycosylase/hydrolase family member gene expression and decrease of cell wall hydrolase activity, especially the activities of polygalacturonase, xyloglucan endoglycosyl transferase, cellulase, and β-galactosidase. Meanwhile, SNP regulated the lipid metabolism by up-regulating the expression of genes encoding glycerol-3-phosphate acyltransferase, ketoacy-ACP synthase, phosphatidylinositol bisphosphate and long-chain acyl-CoA. Thus, the results of this study indicate that SNP alleviates chilling injury of post-harvest peach fruit by regulating cell wall and lipid metabolism.

Plant monounsaturated fatty acids: Diversity, biosynthesis, functions and uses

Monounsaturated fatty acids are straight-chain aliphatic monocarboxylic acids comprising a unique carbon‑carbon double bond, also termed unsaturation. More than 50 distinct molecular structures have been described in the plant kingdom, and more remain to be discovered. The evolution of land plants has apparently resulted in the convergent evolution of non-homologous enzymes catalyzing the dehydrogenation of saturated acyl chain substrates in a chemo-, regio- and stereoselective manner. Contrasted enzymatic characteristics and different subcellular localizations of these desaturases account for the diversity of existing fatty acid structures. Interestingly, the location and geometrical configuration of the unsaturation confer specific characteristics to these molecules found in a variety of membrane, storage, and surface lipids. An ongoing research effort aimed at exploring the links existing between fatty acid structures and their biological functions has already unraveled the importance of several monounsaturated fatty acids in various physiological and developmental contexts. What is more, the monounsaturated acyl chains found in the oils of seeds and fruits are widely and increasingly used in the food and chemical industries due to the physicochemical properties inherent in their structures. Breeders and plant biotechnologists therefore develop new crops with high monounsaturated contents for various agro-industrial purposes.

Effects of extraction parameters on lipid profiling of mosses using UPLC-ESI-QTOF-MS and multivariate data analysis

INTRODUCTION

Non-target lipid profiling by using ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOF-MS) has been used extensively in the past decades in plant studies. However, the lipidomes of bryophytes have only been scarcely studied, although they are the second largest group in plant kingdom.

OBJECTIVES

We evaluated the effects of different cell disruption methods (no disruption, shake, ultrasound, and bead beating), and storage conditions (air-dried, freeze-dried, and fresh frozen) of five moss species (including Racomitrium lanuginosum B and D, Philonotis fontana, Sphagnum teres, and Hylocomium splendens).

METHODS

The lipid profiling results of each extraction parameter were analyzed by using multivariate data analysis including unsupervised principal component analysis and supervised orthogonal projections to latent structures discriminant analysis.

RESULTS

The results showed that extraction with bead beating resulted in the highest lipid content and the most detected features, but these were caused by the contamination from plastic tubes. Minor lipid metabolite changes were found in shaking and ultrasonication methods when compared with no disruption method. Significant amounts of phosphatidylcholine, diacylglyceryltrimethylhomoserine and their lyso lipids were observed in air-dried moss tissues, whereas diacylglycerol, triacylglycerol and ceramide were mostly exclusively detected when fresh frozen tissues were used for extraction.

CONCLUSION

We concluded that lipid extraction using fresh frozen samples with ultrasound assistance provide the most original lipid composition and gave a relatively high lipid content.

Sphingolipid metabolism, transport, and functions in plants: Recent progress and future perspectives

Sphingolipids, which comprise membrane systems together with other lipids, are ubiquitous in cellular organisms. They show a high degree of diversity across plant species and vary in their structures, properties, and functions. Benefiting from the development of lipidomic techniques, over 300 plant sphingolipids have been identified. Generally divided into free long-chain bases (LCBs), ceramides, glycosylceramides (GlcCers) and glycosyl inositol phosphoceramides (GIPCs), plant sphingolipids exhibit organized aggregation within lipid membranes to form raft domains with sterols. Accumulating evidence has revealed that sphingolipids obey certain trafficking and distribution rules and confer unique properties to membranes. Functional studies using sphingolipid biosynthetic mutants demonstrate that sphingolipids participate in plant developmental regulation, stimulus sensing, and stress responses. Here, we present an updated metabolism/degradation map and summarize the structures of plant sphingolipids, review recent progress in understanding the functions of sphingolipids in plant development and stress responses, and review sphingolipid distribution and trafficking in plant cells. We also highlight some important challenges and issues that we may face during the process of studying sphingolipids.

Comprehensive and High-Coverage Lipidomic Analysis of Oilseeds Based on Ultrahigh-Performance Liquid Chromatography Coupled with Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry

Oilseeds are an important source of dietary lipids, and a comprehensive analysis of oilseed lipids is of great significance to human health, while information about the global lipidomes in oilseeds was limited. Herein, an ultrahigh-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry method for comprehensive lipidomic profiling of oilseeds was established and applied. First, the lipid extraction efficiency and lipid coverage of four different lipid extraction methods were compared. The optimized methyl tert-butyl ether extraction method was superior to isopropanol, Bligh-Dyer, and Folch extraction methods, in terms of the operation simplicity, lipid coverage, and number of identified lipids. Then, global lipidomic analysis of soybean, sesame, peanut, and rapeseed was conducted. A total of 764 lipid molecules, including 260 triacylglycerols, 54 diacylglycerols, 313 glycerophospholipids, 36 saccharolipids, 35 ceramides, 30 free fatty acids, 21 fatty esters, and 15 sphingomyelins were identified and quantified. The compositions and contents of lipids significantly varied among different oilseeds. Our results provided a theoretical basis for the selection and breeding of varieties of oilseed as well as deep processing of oilseed for the edible oil industry.

Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress

Endoplasmic reticulum-plasma membrane contact sites (ER-PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER-PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER-PM tether that also functions in maintaining PM integrity. The ER-PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.

Sphingolipid long-chain base hydroxylation influences plant growth and callose deposition in Physcomitrium patens

Sphingolipids are enriched in microdomains in the plant plasma membrane (PM). Hydroxyl groups in the characteristic long-chain base (LCB) moiety might be essential for the interaction between sphingolipids and sterols during microdomain formation. Investigating LCB hydroxylase mutants in Physcomitrium patens might therefore reveal the role of certain plant sphingolipids in the formation of PM subdomains. Physcomitrium patens mutants for the LCB C-4 hydroxylase S4H were generated by homologous recombination. Plants were characterised by analysing their sphingolipid and steryl glycoside (SG) profiles and by investigating different gametophyte stages. s4h mutants lost the hydroxyl group at the C-4 position of their LCB moiety. Loss of this hydroxyl group caused global changes in the moss sphingolipidome and in SG composition. Changes in membrane lipid composition may trigger growth defects by interfering with the localisation of membrane-associated proteins that are crucial for growth processes such as signalling receptors or callose-modifying enzymes. Loss of LCB-C4 hydroxylation substantially changes the P. patens sphingolipidome and reveals a key role for S4H during development of nonvascular plants. Physcomitrium patens is a valuable model for studying the diversification of plant sphingolipids. The simple anatomy of P. patens facilitates visualisation of physiological processes in biological membranes.

Biosynthesis and Functions of Very-Long-Chain Fatty Acids in the Responses of Plants to Abiotic and Biotic Stresses

Very-long-chain fatty acids (i.e., fatty acids with more than 18 carbon atoms; VLCFA) are important molecules that play crucial physiological and structural roles in plants. VLCFA are specifically present in several membrane lipids and essential for membrane homeostasis. Their specific accumulation in the sphingolipids of the plasma membrane outer leaflet is of primordial importance for its correct functioning in intercellular communication. VLCFA are found in phospholipids, notably in phosphatidylserine and phosphatidylethanolamine, where they could play a role in membrane domain organization and interleaflet coupling. In epidermal cells, VLCFA are precursors of the cuticular waxes of the plant cuticle, which are of primary importance for many interactions of the plant with its surrounding environment. VLCFA are also major components of the root suberin barrier, which has been shown to be fundamental for nutrient homeostasis and plant adaptation to adverse conditions. Finally, some plants store VLCFA in the triacylglycerols of their seeds so that they later play a pivotal role in seed germination. In this review, taking advantage of the many studies conducted using Arabidopsis thaliana as a model, we present our current knowledge on the biosynthesis and regulation of VLCFA in plants, and on the various functions that VLCFA and their derivatives play in the interactions of plants with their abiotic and biotic environment.

A Comprehensive Targeted Metabolomics Assay for Crop Plant Sample Analysis

Metabolomics plays an important role in various fields from health to agriculture. However, the comprehensive quantitative metabolomic analysis of plants and plant metabolites has not been widely performed. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based plant metabolomics offers the sensitivity and breadth of coverage for both phenotyping and disease diagnosis of plants. Here, we report a high-coverage and quantitative MS-based assay for plant metabolite analysis. The assay detects and quantifies 206 primary and secondary plant metabolites, including many key plant hormones. In total, it measures 28 amino acids and derivatives, 27 organic acids, 20 biogenic amines and derivatives, 40 acylcarnitines, 90 phospholipids and C-6 sugars. All the analysis methods in this assay are based on LC-MS/MS techniques using both positive and negative-mode multiple reaction monitoring (MRM). The recovery rates of spiked plant samples at three different concentration levels (low, medium and high) ranged from 80% to 120%, with satisfactory precision values of less than 20%. This targeted plant metabolomic assay has been successfully applied to the analysis of large numbers of pine and spruce needle samples, canola root samples, as well as cannabis samples. Moreover, the assay was specifically developed in a 96-well plate format, which enables automated, high-throughput sample analysis. This assay has already been used to analyze over 1500 crop plant samples in less than two months.

Membrane dynamics during individual and combined abiotic stresses in plants and tools to study the same

The plasma membrane (PM) is possibly the most diverse biological membrane of plant cells; it separates and guards the cell against its external environment. It has an extremely complex structure comprising a mosaic of lipids and proteins. The PM lipids are responsible for maintaining fluidity, permeability and integrity of the membrane and also influence the functioning of membrane proteins. However, the PM is the primary target of environmental stress, which affects its composition, conformation and properties, thereby disturbing the cellular homeostasis. Maintenance of integrity and fluidity of the PM is a prerequisite for ensuring the survival of plants during adverse environmental conditions. The ability of plants to remodel membrane lipid and protein composition plays a crucial role in adaptation towards varying abiotic environmental cues, including high or low temperature, drought, salinity and heavy metals stress. The dynamic changes in lipid composition affect the functioning of membrane transporters and ultimately regulate the physical properties of the membrane. Plant membrane-transport systems play a significant role in stress adaptation by cooperating with the membrane lipidome to maintain the membrane integrity under stressful conditions. The present review provides a holistic view of stress responses and adaptations in plants, especially the changes in the lipidome and proteome of PM under individual or combined abiotic stresses, which cause alterations in the activity of membrane transporters and modifies the fluidity of the PM. The tools to study the varying lipidome and proteome of the PM are also discussed.

Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation

The plant plasma membrane (PM) is an essential barrier between the cell and the external environment, controlling signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols, and phospholipids. The glycosyl inositol phosphoryl ceramides (GIPCs), representing up to 40% of total sphingolipids, are assumed to be almost exclusively in the outer leaflet of the PM. However, their biological role and properties are poorly defined. In this study, we investigated the role of GIPCs in membrane organization. Because GIPCs are not commercially available, we developed a protocol to extract and isolate GIPC-enriched fractions from eudicots (cauliflower and tobacco) and monocots (leek and rice). Lipidomic analysis confirmed the presence of trihydroxylated long chain bases and 2-hydroxylated very long-chain fatty acids up to 26 carbon atoms. The glycan head groups of the GIPCs from monocots and dicots were analyzed by gas chromatograph-mass spectrometry, revealing different sugar moieties. Multiple biophysics tools, namely Langmuir monolayer, ζ-Potential, light scattering, neutron reflectivity, solid state 2H-NMR, and molecular modeling, were used to investigate the physical properties of the GIPCs, as well as their interaction with free and conjugated phytosterols. We showed that GIPCs increase the thickness and electronegativity of model membranes, interact differentially with the different phytosterols species, and regulate the gel-to-fluid phase transition during temperature variations. These results unveil the multiple roles played by GIPCs in the plant PM.

Effect of Intermittent Warming on the Quality and Lipid Metabolism of Blueberry (Vaccinium corymbosum L., cv. Duke) Fruit

The change of lipid metabolism is a key point of blueberry fruit after refrigeration. This study was conducted to evaluate the effects of intermittent warming (IW) of "DuKe" blueberry fruit on its shelf life at 20 ± 0.5°C following 30 days of refrigeration. IW-treated fruit showed higher contents of phosphatidylcholine, linoleic acid, and oleic acid but lower contents of phosphatidic acid and palmitic acid compared to controls. Protective effects on the cell membrane were also reflected as inhibition of the activity of phospholipase D and lipoxygenase. The blueberry fruit showed a lower decay and pitting incidence with higher firmness than control. Interestingly, IW increased C-repeat binding transcription factor gene expression, which can induce the expression of genes related to hypothermia tolerance in plant cells at low temperature. These results indicate that IW can prevent damage to the membrane lipids, which occurs by senescence at a low temperature of blueberry fruit.

Convergence of sphingolipid desaturation across over 500 million years of plant evolution

For plants, acclimation to low temperatures is fundamental to survival. This process involves the modification of lipids to maintain membrane fluidity. We previously identified a new cold-induced putative desaturase in Physcomitrium (Physcomitrella) patens. Lipid profiles of null mutants of this gene lack sphingolipids containing monounsaturated C24 fatty acids, classifying the new protein as sphingolipid fatty acid denaturase (PpSFD). PpSFD mutants showed a cold-sensitive phenotype as well as higher susceptibility to the oomycete Pythium, assigning functions in stress tolerance for PpSFD. Ectopic expression of PpSFD in the Atads2.1 (acyl coenzyme A desaturase-like 2) Arabidopsis thaliana mutant functionally complemented its cold-sensitive phenotype. While these two enzymes catalyse a similar reaction, their evolutionary origin is clearly different since AtADS2 is a methyl-end desaturase whereas PpSFD is a cytochrome b₅ fusion desaturase. Altogether, we suggest that adjustment of membrane fluidity evolved independently in mosses and seed plants, which diverged more than 500 million years ago.

Targeted Analysis of the Plant Lipidome by UPLC-NanoESI-MS/MS

The plant lipidome is highly complex and changes dynamically under the influence of various biotic and abiotic stresses. Targeted analyses based on mass spectrometry enable the detection and characterization of the plant lipidome. It can be analyzed in plant tissues of different developmental stages and from isolated cellular organelles and membranes. Here, we describe a sensitive method to establish the relative abundance of molecular lipid species belonging to three lipid categories: glycerolipids, sphingolipids, and sterol lipids. The method is based on a monophasic lipid extraction and includes the derivatization of a few rare and low-abundant lipid classes. The molecular lipid species are resolved by lipid class-specific reverse-phase liquid chromatography and detected by nanoelectrospray ionization coupled with tandem mass spectrometry. The triple quadrupole analyzer is used for detection with multiple reaction monitoring (MRM). Mass transition lists are constructed based on the knowledge of organism-specific lipid building blocks. They are initially determined by classical lipid analytical methods and then used for combinative assembly of all possible lipid structures. The targeted analysis enables detailed and comprehensive profiling of the entire lipid content and composition of plants.

UPLC-QTof-MSE Metabolomics Reveals Changes in Leaf Primary and Secondary Metabolism of Hop (Humulus lupulus L.) Plants under Drought Stress

The hop (Humulus lupulus L.) is an important specialty crop used in beer production. Untargeted UPLC-QTof-MS^E metabolomics was used to determine metabolite changes in the leaves of hop plants under varying degrees of drought stress. Principal component analysis revealed that drought treatments produced qualitatively distinct changes in the overall chemical composition of three out of four genotypes tested (i.e., Cascade, Sultana, and a wild var. neomexicanus accession but not Aurora), although differences among treatments were smaller than differences among genotypes. A total of 14 compounds consistently increased or decreased in response to drought stress, and this effect was generally progressive as the severity of drought increased. A total of 10 of these marker compounds were tentatively identified as follows: five glycerolipids, glutaric acid, pheophorbide A, abscisic acid, roseoside, and dihydromyricetin. Some of the observed metabolite changes likely occur across all plants under drought conditions, while others may be specific to hops or to the type of drought treatments performed.

The roles of chloroplast membrane lipids in abiotic stress responses

Plant chloroplasts have complex membrane systems. Among these, thylakoids serve as the sites for photosynthesis and photosynthesis-related adaptation. In addition to the photosynthetic membrane complexes and associated molecules, lipids in the thylakoid membranes, are predominantly composed of MGDG (monogalactosyldiacylglycerol), DGDG (digalactosyldiacylglycerol), SQDG (sulfoquinovosyldiacylglycerol) and PG (phosphatidylglycerol), play essential roles in shaping the thylakoid architecture, electron transfer, and photoregulation. In this review, we discuss the effect of abiotic stress on chloroplast structure, the changes in membrane lipid composition, and the degree of unsaturation of fatty acids. Advanced understanding of the mechanisms regulating chloroplast membrane lipids and unsaturated fatty acids in response to abiotic stresses is indispensable for improving plant resistance and may inform the strategies of crop breeding.

A Lipidomic Analysis of Leaves of Esca-Affected Grapevine Suggests a Role for Galactolipids in the Defense Response and Appearance of Foliar Symptoms

Both qualitative and quantitative changes occur in the lipid composition of Vitis vinifera L. tissues, which may compromise the defense response against Esca complex disease, a widespread and damaging trunk disease. In this study, a lipidomic analysis of grapevine leaves is conducted to assess how lipid membrane remodeling relates to the emergence and progression of Esca foliar symptoms. In total, 208 molecular species (including lipids, four hormones, and some other compounds of the metabolism of lipids) were detected. Lipid species were readily assigned to the classes fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterols, and prenol lipids. Using different clustering analyses, distinct metabolic pathways stimulated at different stages of disease development were characterized. These analyses revealed consistent changes in the abundance of 13 galactolipids and two diacylglycerolipids. Overall, the observations indicated an increment in the levels of these lipid species in leaves of asymptomatic vines and a progressive drop with increasing foliar symptom severity in symptomatic vines. Five fatty acids also appear to exert a central role in the etiopathogenesis of Esca complex disease because of their accumulation in leaves of asymptomatic vines, namely, heptadecanoic, linoleic, γ-linolenic, arachidonic, and stearic acids. Symptomatic leaves were characterized by high levels of all lipid classes, except for galactolipids, lyso-galactolipids, and compounds relevant to the biosynthesis of chlorophylls and carotenoids, that exhibited decreased levels. The data also suggested a jasmonic acid-associated signaling mechanism activation upon the invasion of woods by Esca-associated fungi, compared with abscisic and salicylic acids. Further research is required for validation of these results with additional molecular analyses using more vine cultivars.

Liquid Chromatography-Mass Spectrometry (LC-MS)-Based Analysis for Lipophilic Compound Profiling in Plants

Lipids are fascinating due to their chemical diversity, which is especially vast in the plant kingdom thanks to the high plasticity of the plant biosynthetic machinery. Lipidomic studies aim to simultaneously analyze a large number of lipid compounds of diverse classes in a given sample. The method presented here uses liquid chromatography-mass spectrometry (LC-MS)-based lipidomic profiling in a relatively fast, robust, and high-throughput manner for high-coverage quantification and annotation of lipophilic compounds. Protocols cover sample preparation, LC-MS-based measurement, and data extraction and annotation. An extensive lipid library for triacylglycerols, galactolipids, and phospholipids is provided. The extended profiling described here could be used in a range of applications and is suitable for integration with other omic datasets. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Sample preparation and metabolite extraction Basic Protocol 2: Liquid chromatography-mass spectrometry (LC-MS) analysis Basic Protocol 3: Data extraction, annotation, and quantification.

The dynamics and role of sphingolipids in eukaryotic organisms upon thermal adaptation

All living beings have an optimal temperature for growth and survival. With the advancement of global warming, the search for understanding adaptive processes to climate changes has gained prominence. In this context, all living beings monitor the external temperature and develop adaptive responses to thermal variations. These responses ultimately change the functioning of the cell and affect the most diverse structures and processes. One of the first structures to detect thermal variations is the plasma membrane, whose constitution allows triggering of intracellular signals that assist in the response to temperature stress. Although studies on this topic have been conducted, the underlying mechanisms of recognizing thermal changes and modifying cellular functioning to adapt to this condition are not fully understood. Recently, many reports have indicated the participation of sphingolipids (SLs), major components of the plasma membrane, in the regulation of the thermal stress response. SLs can structurally reinforce the membrane or/and send signals intracellularly to control numerous cellular processes, such as apoptosis, cytoskeleton polarization, cell cycle arresting and fungal virulence. In this review, we discuss how SLs synthesis changes during both heat and cold stresses, focusing on fungi, plants, animals and human cells. The role of lysophospholipids is also discussed.

An improved extraction method enables the comprehensive analysis of lipids, proteins, metabolites and phytohormones from a single sample of leaf tissue under water-deficit stress

Phytohormones play essential roles in the regulation of growth and development in plants. Plant hormone profiling is therefore essential to understand developmental processes and the adaptation of plants to biotic and/or abiotic stresses. Interestingly, commonly used hormone extraction and profiling methods do not adequately resolve other molecular entities, such as polar metabolites, lipids, starch and proteins, which would be required to comprehensively describe the continuing biological processes at a systematic level. In this article we introduce an updated version of a previously published liquid:liquid metabolite extraction protocol, which not only allows for the profiling of primary and secondary metabolites, lipids, starch and proteins, but also enables the quantitative analysis of the major plant hormone classes, including abscisic acid, auxins, cytokinins, jasmonates and salicylates, from a single sample aliquot. The optimization of the method, which uses the introduction of acidified water, enabling the complete purification of major plant hormones into the organic (methyl-tert-butyl-ether) phase, eliminated the need for solid-phase extraction for sample clean-up, and therefore reduces both sampling time and cost. As a proof-of-concept analysis, Arabidopsis thaliana plants were subjected to water-deficit stress, which were then profiled for hormonal, metabolic, lipidomic and proteomic changes. Surprisingly, we determined not only previously described molecular changes but also significant changes regarding the breakdown of specific galactolipids, followed by the substantial accumulation of unsaturated fatty-acid derivatives and diverse jasmonates in the course of adaptation to water-deficit stress.