Using lipidomics for expanding the knowledge on lipid metabolism in plants

Unveiling resilience: coelomic fluid bacteria's impact on plant metabolism and abiotic stress tolerance

Earthworms' coelomic fluid (CF) has been discovered to possess properties that promote plant development. In particular, the earthworm's coelomic fluid-associated bacteria (CFB) are the primary factor influencing the plants' response. To investigate this, we used bacteria isolated from the CF and selected based on different plant growth-promoting traits, in a mesocosm ecosystem that includes plants. This experiment aimed to assess their impact on the metabolism of plants growing under abiotic stress environments (alkaline soil and nitrogen (N), phosphate (P), and potassium (K) deficit) and compare the lipid profiles of plants under the various treatments. We used seven different bacterial species isolated from the CF of Aporrectodea molleri and as a plant model Zea mays L. For the metabolomic analysis method, we used gas chromatography-mass spectrometry lipidomic. After observing the metabolomic profiles, we found that a few molecular pathways are involved in how plants react to bacterial biostimulants. The bacterial isolates belonging to Pantoea vagans, Pseudomonas aeruginosa, Bacillus paramycoides, and Bacillus thuringiensis have led to a significant increase in synthesizing several metabolites belonging to various chemical categories. Contrary to predictions, abiotic stress did not cause a drop in the composition and concentration of lipids in plants treated with the CFB, demonstrating the rigidity of the protective mechanisms. The statistical analysis based on the Pearson method revealed a positive significant correlation between plant growth parameters (length of the aerial part, surface of the leaves, and biomass) and some metabolites belonging to fatty acids, carboxylic acids, benzene derivatives, and alkanes. Moreover, the standard metabolic components of all treatments in much higher concentrations during bacterial treatments than the control treatment suggests that the bacteria have stimulated the overexpression of these metabolic components. According to these results, we could assume that plants treated with CFB exhibit an adaptability of abiotic stress defense mechanisms, which may be attributed to the upregulation of genes involved in lipid biosynthesis pathways.

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.

Metabolic and Antioxidant Responses of Different Control Methods to the Interaction of Sorghum sudangrass hybrids-Colletotrichum boninense

Colletotrichum boninense is the main pathogenic fungus causing leaf spot disease in Sorghum sudangrass hybrids, which seriously impairs its quality and yield. In order to find an efficient and green means of control, this study used the agar disk diffusion method to screen for a fungicide with the strongest inhibitory effect on C. boninense from among several bacteria, fungi, and chemicals. Then, the changes in the plant's antioxidant system and metabolic levels after treatment were used to compare the three means of control. The lowest inhibitory concentration of Zalfexam was 10 mg/mL, at which point C. boninense did not grow, and the inhibition rates of Bacillus velezensis (X7) and Trichoderma harzianum were 33.87-51.85% and 77.86-80.56%, respectively. Superoxide dismutase (SOD) and chitinase were up-regulated 2.43 and 1.24 folds in the Trichoderma harzianum group (M group) and SOD activity was up-regulated 2.2 folds in the Bacillus velezensis group (X7 group) compared to the control group (CK group). SOD, peroxidase (POD), and chitinase activities were elevated in the Zalfexam group (HX group). The differential metabolites in different treatment groups were mainly enriched in amino acid metabolism and production, flavonoid production, and lipid metabolism pathways. Compared with the diseased plants (ZB group), the M, X7, HX, and CK groups were co-enriched in the tryptophan metabolic pathway and glutamate-arginine metabolic pathway, and only the CK group showed a down-regulation of the metabolites in the two common pathways, while the metabolites of the common pathways were up-regulated in the M, X7, and HX groups. In addition, the salicylic acid-jasmonic acid pathway and ascorbic acid-glutathione, which were unique to the M group, played an important role in helping Sorghum sudangrass hybrids to acquire systemic resistance against stress. This study fills the gap in the control of Colletotrichum boninene, which causes leaf spot disease in Sorghum sudangrass hybrids. This paper represents the first reported case of biological control for leaf spot disease in Sorghum sudangrass hybrids and provides a reference for the control of leaf spot disease in Sorghum sudangrass hybrids as well as other crops infected with Colletotrichum boninense.

Comprehensive widely targeted metabolomics to decipher the molecular mechanisms of Dioscorea opposita thunb. cv. Tiegun quality formation during harvest

Dioscorea opposita Thumb. cv. Tiegun is commonly consumed as both food and traditional Chinese medicine, which has a history of more than two thousand years. Harvest time directly affects its quality, but few studies have focused on metabolic changes during the harvesting process. Here, a comprehensive metabolomics approach was performed to determine the metabolic profiles during six harvest stages. Thirty eight metabolites with significant differences were determined as crucial participants. Related metabolic pathways including phenylalanine, tyrosine and tryptophan biosynthesis, stilbenoid, diarylheptanoid and gingerol biosynthesis, phenylpropanoid biosynthesis, flavonoid biosynthesis and tryptophan metabolism were the most active pathways during harvest. The results revealed that temperature has a significant impact on quality formation, which suggested that Dioscorea opposita thumb. cv. Tiegun harvested after frost had higher potential value of traditional Chinese medicine. This finding not only offered valuable guidance for yam production, but also provided essential information for assessing its quality.

Discovery of novel neutral glycosphingolipids in cereal crops: rapid profiling using reversed-phased HPLC-ESI-QqTOF with parallel reaction monitoring

This study explores the sphingolipid class of oligohexosylceramides (OHCs), a rarely studied group, in barley (Hordeum vulgare L.) through a new lipidomics approach. Profiling identified 45 OHCs in barley (Hordeum vulgare L.), elucidating their fatty acid (FA), long-chain base (LCB) and sugar residue compositions; and was accomplished by monophasic extraction followed by reverse-phased high performance liquid chromatography electrospray ionisation quadrupole-time-of-flight tandem mass spectrometry (HPLC-ESI-QqTOF-MS/MS) employing parallel reaction monitoring (PRM). Results revealed unknown ceramide species and highlighted distinctive FA and LCB compositions when compared to other sphingolipid classes. Structurally, the OHCs featured predominantly trihydroxy LCBs associated with hydroxylated FAs and oligohexosyl residues consisting of two-five glucose units in a linear 1 → 4 linkage. A survey found OHCs in tissues of major cereal crops while noting their absence in conventional dicot model plants. This study found salinity stress had only minor effects on the OHC profile in barley roots, leaving questions about their precise functions in plant biology unanswered.

Functions and interaction of plant lipid signalling under abiotic stresses

Lipids are the primary form of energy storage and a major component of plasma membranes, which form the interface between the cell and the extracellular environment. Several lipids - including phosphoinositide, phosphatidic acid, sphingolipids, lysophospholipids, oxylipins, and free fatty acids - also serve as substrates for the generation of signalling molecules. Abiotic stresses, such as drought and temperature stress, are known to affect plant growth. In addition, abiotic stresses can activate certain lipid-dependent signalling pathways that control the expression of stress-responsive genes and contribute to plant stress adaptation. Many studies have focused either on the enzymatic production and metabolism of lipids, or on the mechanisms of abiotic stress response. However, there is little information regarding the roles of plant lipids in plant responses to abiotic stress. In this review, we describe the metabolism of plant lipids and discuss their involvement in plant responses to abiotic stress. As such, this review provides crucial background for further research on the interactions between plant lipids and abiotic stress.

Characteristics and potential functional effects of long insertions in Asian butternuts

Background

Structural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly detected and studied in all but model species.

Results

We used whole-genome resequencing of paired reads from 80 Asian butternuts to detect long insertions and further analyse their characteristics and potential functional effects. By combining of mapping-based and de novo assembly-based methods, we obtained a multiple related species pangenome representing higher taxonomic groups. We obtained 89,312 distinct contigs totaling 147,773,999 base pair (bp) of new sequences, of which 347 were putative long insertions placed in the reference genome. Most of the putative long insertions appeared in multiple species; in contrast, only 62 putative long insertions appeared in one species, which may be involved in the response to the environment. 65 putative long insertions fell into 61 distinct protein-coding genes involved in plant development, and 105 putative long insertions fell into upstream of 106 distinct protein-coding genes involved in cellular respiration. 3,367 genes were annotated in 2,606 contigs. We propose PLAINS (https://github.com/CMB-BNU/PLAINS.git), a streamlined, comprehensive pipeline for the prediction and analysis of long insertions using whole-genome resequencing.

Conclusions

Our study lays down an important foundation for further whole-genome long insertion studies, allowing the investigation of their effects by experiments.

The effects of clearcut harvesting on moss chloroplast lipidome and adaptation to light stress during boreal forest regeneration

Moss plays an important role in boreal forest ecosystems as an understory bryophyte species. Clearcut harvesting is a common boreal forest regeneration method that can expose understory vegetation to abiotic stressors impeding their recovery following post-harvest conditions. Very little is known concerning how moss remodel their chloroplast lipidome to enhance photosynthetic performance for successful acclimation to light and water stress during boreal forest regeneration following clearcut harvesting. The chloroplast lipidome and photosynthetic performance of Sphagnum sp. and three feathermoss species (Pleurozium schreberi, Hylocomium splendens, and Ptilium crista-castrensis) from a boreal black spruce (Picea mariana) forest were assessed using liquid chromatography-mass spectrometry (LC-MS), photospectrometry, and light response curves. We observed an overall increase in monogalactosyldiacylglycerol (MGDG) and sulfoquinovosyldiacylglycerol (SQDG) and decrease in digalactosyldiacylglycerol (DGDG) and phosphatidylglycerol (PG). In addition, unsaturation of the chloroplast lipidome occurred concomitant with photoprotection by carotenoid pigments to enhance the efficiency and photosynthetic capacity in moss exposed to light and water stress following clearcut harvesting. This appears to be a successful acclimation strategy used by moss to circumvent light stress during boreal forest regeneration following clearcut harvesting. These findings could be of significance in the development of boreal forest management strategies following resource harvesting.

Lipidomics analysis unravels changes from flavor precursors in different processing treatments of purple-leaf tea

BACKGROUND

Lipids are one of the most important bioactive compounds, affecting the character and quality of tea. However, the contribution of lipids to tea productions is still elusive. Here, we systematically identified the lipid profiles of green, oolong, and black teas in purple-leaf tea (Jinmingzao, JMZ) and green-leaf tea (Huangdan, HD), respectively.

RESULTS

The lipids analysis showed regular accumulation in tea products with different manufacturing processes, among which the fatty acids, glycerolipids, glycerophospholipids, and sphingolipids contribute to the quality characteristics of tea products, including typical fatty acyl (FA), monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerols (DGDG), and phosphatidylcholine (PC). Compared tea materials with products, levels of fatty acids were up-regulated, while glycerolipids and glycerophospholipids were down-regulated in tea products. FA 18:3, FA 16:0, MGDG 36:6, DGDG 36:6, PC 34:3, and PC 36:6 were the negative contributors to green tea flavor formation of purple-leaf tea. The pathway analysis of significant lipids in materials and products of purple-leaf tea were enriched linolenic acid metabolism pathway and glycerolipid metabolism.

CONCLUSION

This study provides insights into the lipid metabolism profiles of different tea leaf colors, and found that fatty acids are essential precursors of black tea flavor formation. © 2021 Society of Chemical Industry.

Patatin-like phospholipase A-induced alterations in lipid metabolism and jasmonic acid production affect the heat tolerance of Gracilariopsis lemaneiformis

High temperatures seriously limit the growth and productivity of Gracilariopsis lemaneiformis. By hydrolyzing glycerolipids into lysophospholipids (LPs) and free fatty acids (FFAs), patatin-like phospholipase A (pPLA) plays an important role in stress responses. GlpPLA expression was up-regulated under heat stress, however, the regulation of pPLA in heat tolerance of G. lemaneiformis is unknown. In this study, G. lemaneiformis under heat stress was treated with bromoenololide (BEL), a chemical inhibitor of pPLA, to evaluate the cellular function of pPLA in this species. When pPLA was inhibited through BEL treatment, the sensitivity of G. lemaneiformis to heat stress increased and the biomass and maximum and effective quantum yield of photosystem II decreased. Moreover, BEL treatment resulted in a significant decrease in many lipid molecular species, all of which are mainly composed of 16C, 18C, and 20C fatty acids. Consistently, FFA levels and LPs contents in G. lemaneiformis under BEL treatment showed a significant decrease. The first step in the synthesis of jasmonic acid (JA) is the lipoxygenase (LOX)-mediated oxygenation of linolenic acid (C18:3). BEL treatment decreased JA and C18:3 accumulation and markedly downregulated the expression of GILOX under heat stress. Together, these results indicate that pPLA is closely related to the growth of G. lemaneiformis under heat stress, and pPLA is involved in the lipid metabolism and JA biosynthesis of G. lemaneiformis in response to heat stress. This research broadens the understanding of the heat stress adaptation mechanism of G. lemaneiformis.

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.

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.

Metabolomics Intervention Towards Better Understanding of Plant Traits

The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).

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.

Towards model-driven characterization and manipulation of plant lipid metabolism

Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.

Exploring the Lipidome: Current Lipid Extraction Techniques for Mass Spectrometry Analysis

In recent years, high-throughput lipid profiling has contributed to understand the biological, physiological and pathological roles of lipids in living organisms. Across all kingdoms of life, important cell and systemic processes are mediated by lipids including compartmentalization, signaling and energy homeostasis. Despite important advances in liquid chromatography and mass spectrometry, sample extraction procedures remain a bottleneck in lipidomic studies, since the wide structural diversity of lipids imposes a constrain in the type and amount of lipids extracted. Differences in extraction yield across lipid classes can induce a bias on down-stream analysis and outcomes. This review aims to summarize current lipid extraction techniques used for untargeted and targeted studies based on mass spectrometry. Considerations, applications, and limitations of these techniques are discussed when used to extract lipids in complex biological matrices, such as tissues, biofluids, foods, and microorganisms.

Lipidomics reveals associations between rice quality traits

INTRODUCTION

Lipids are a diverse group of macromolecules that occur in rice grains and are known to impact rice grain properties. Identifying the relationships between specific lipids and traits of quality is important to improve varietal selection for high quality rice.

OBJECTIVES

Using untargeted lipidomics, this study aims to understand the role of lipids on different traits of quality by identifying the genotypic effect of lipids and their impact on traits of cooking and eating quality of a rice mapping population.

METHODS

Lipids from milled rice grains of three sets of rice samples were screened by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) in the positive ionisation mode. Lipid features were putatively identified using analytical standards and online databases. Multivariate statistics were carried out to identify the lipid profile of varieties across three experiments. Correlation analysis was carried out between lipid features and 12 quality traits across a rice mapping population that segregates for grain physical and texture-associated traits.

RESULTS

Thousands of features in rice grain lipids were detected, and were grouped into six categories-fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids and prenol lipids. A strong genotypic basis for the lipid profile was observed among the four varieties grown under five nitrogen treatments. Clear differentiation in lipid profiles between waxy and non-waxy rice was observed. Strong correlations were observed for putative lipids that form the amylose-lipid complex and with amylose content and viscosity parameters.

CONCLUSIONS

This study demonstrates the strength of untargeted lipidomics in putatively determining features that differentiate varieties from each other, and reveals the role of specific lipids on the physical and textural quality of rice.

Insights Into Oxidized Lipid Modification in Barley Roots as an Adaptation Mechanism to Salinity Stress

Lipidomics is an emerging technology, which aims at the global characterization and quantification of lipids within biological matrices including biofluids, cells, whole organs and tissues. The changes in individual lipid molecular species in stress treated plant species and different cultivars can indicate the functions of genes affecting lipid metabolism or lipid signaling. Mass spectrometry-based lipid profiling has been used to track the changes of lipid levels and related metabolites in response to salinity stress. We have developed a comprehensive lipidomics platform for the identification and direct qualification and/or quantification of individual lipid species, including oxidized lipids, which enables a more systematic investigation of peroxidation of individual lipid species in barley roots under salinity stress. This new lipidomics approach has improved with an advantage of analyzing the composition of acyl chains at the molecular level, which facilitates to profile precisely the 18:3-containing diacyl-glycerophosphates and allowed individual comparison of lipids across varieties. Our findings revealed a general decrease in most of the galactolipids in plastid membranes, and an increase of glycerophospholipids and acylated steryl glycosides, which indicate that plastidial and extraplastidial membranes in barley roots ubiquitously tend to form a hexagonal II (HII) phase under salinity stress. In addition, salt-tolerant and salt-sensitive cultivars showed contrasting changes in the levels of oxidized membrane lipids. These results support the hypothesis that salt-induced oxidative damage to membrane lipids can be used as an indication of salt stress tolerance in barley.

Highest accumulated microalgal lipids (polar and non-polar) for biodiesel production with advanced wastewater treatment: Role of lipidomics

Microalgal lipids consist of non-polar and polar lipids. Triacyleglyceride (TAG), a non-polar lipid, is convertible to biodiesel, whereas glycolipids and phospholipids are polar and not convertible to biodiesel owing to their high degree of unsaturation (polyunsaturated fatty acids), which makes the production process insufficient and expensive. In this review, microalgal species that contain the highest lipid content (≥40%) in the literature till 2019 are highlighted. The differentiation between non-polar and polar lipids and the limitations in the conversion of polar lipids to biodiesel are reported. The basic and advanced factors contributing to the accumulation of lipids convertible to biodiesel is discussed. Microalgal species including Scenedesmus obliquus, Ourococcus multisporus, Chlamydomonas pitschmannii, Micractinium reisseri, and Botryococcus braunii with high lipid content are potential candidates for biomass/biodiesel production and nutrient removal from wastewater. Application of lipidomics and transcriptomics to manipulate the lipid associated gene acetyl-CoA synthetase in microalgae improves the accumulative lipid content.

The proof is in the bulb: glycerol influences key stages of lily development

A bulb is a whole plant condensed into an underground organ. A geophyte's bulb comprises both food reserves and important developmental history that may affect its whole growth. In Easter lily (Lilium longiflorum), bulb size is associated with the plant's flowering pathway - vernalization or photoperiod - and also affects sprouting, flower quality and abortion rate. The aim of this study was to investigate the reasons for the major physiological differences between large and small bulbs. Lily bulbs start their development from secondary meristems along the stem, with large bulbs being heavier and bear more scales than small ones. Peeling the outer scales of a large bulb converts its physiological responses into those of a small bulb, implying that the physiological discrepancies in plants developing from large or small bulbs are mediated by factors inherent to the bulb. We therefore performed broad analyses of the metabolite composition in the scales of bulbs subjected to temperature regimes affecting further plant development. We found a striking association between the level of glycerol, a primary metabolite mostly synthesized in the outer scales, and a delay in sprouting and flowering time, and reduction in abortion rate. Exogenous glycerol application to the bulbs before planting corroborated these results. Moreover, transcriptome analyses showed that flowering-promoting gene expression was downregulated in the bulb after glycerol treatment, while potential flowering inhibitor as well as a dormancy-related gene expressions were upregulated. Based on these studies, we postulate that glycerol is a major factor influencing both vegetative and reproductive development in lily.

A chemical genetic screen reveals that iminosugar inhibitors of plant glucosylceramide synthase inhibit root growth in Arabidopsis and cereals

Iminosugars are carbohydrate mimics that are useful as molecular probes to dissect metabolism in plants. To analyse the effects of iminosugar derivatives on germination and seedling growth, we screened a library of 390 N-substituted iminosugar analogues against Arabidopsis and the small cereal Eragrostis tef (Tef). The most potent compound identified in both systems, N-5-(adamantane-1-yl-ethoxy)pentyl- L-ido-deoxynojirimycin (L-ido-AEP-DNJ), inhibited root growth in agar plate assays by 92% and 96% in Arabidopsis and Tef respectively, at 10 µM concentration. Phenocopying the effect of L-ido-AEP-DNJ with the commercial inhibitor (PDMP) implicated glucosylceramide synthase as the target responsible for root growth inhibition. L-ido-AEP-DNJ was twenty-fold more potent than PDMP. Liquid chromatography-mass spectrometry (LC-MS) analysis of ceramide:glucosylceramide ratios in inhibitor-treated Arabidopsis seedlings showed a decrease in the relative quantity of the latter, confirming that glucosylceramide synthesis is perturbed in inhibitor-treated plants. Bioinformatic analysis of glucosylceramide synthase indicates gene conservation across higher plants. Previous T-DNA insertional inactivation of glucosylceramide synthase in Arabidopsis caused seedling lethality, indicating a role in growth and development. The compounds identified herein represent chemical alternatives that can overcome issues caused by genetic intervention. These inhibitors offer the potential to dissect the roles of glucosylceramides in polyploid crop species.

Functional Metabolomics—A Useful Tool to Characterize Stress-Induced Metabolome Alterations Opening New Avenues towards Tailoring Food Crop Quality

The breeding of stress-tolerant cultivated plants that would allow for a reduction in harvest losses and undesirable decrease in quality attributes requires a new quality of knowledge on molecular markers associated with relevant agronomic traits, on quantitative metabolic responses of plants to stress challenges, and on the mechanisms controlling the biosynthesis of these molecules. By combining metabolomics with genomics, transcriptomics and proteomics datasets a more comprehensive knowledge of the composition of crop plants used for food or animal feed is possible. In order to optimize crop trait developments, to enhance crop yields and quality, as well as to guarantee nutritional and health factors that provide the possibility to create functional food or feedstuffs, knowledge about the plants’ metabolome is crucial. Next to classical metabolomics studies, this review focuses on several metabolomics-based working techniques, such as sensomics, lipidomics, hormonomics and phytometabolomics, which were used to characterize metabolome alterations during abiotic and biotic stress in order to find resistant food crops with a preferred quality or at least to produce functional food crops.

The metabolic (under)groundwork of the lily bulb toward sprouting

Large bulbs of Lilium longiflorum have an obligatory cold requirement to flower. Bulb cooling is widely used to induce and accelerate flowering. However, in-depth investigations of the effect of bulb cooling on major landmarks of plant development are lacking. It has been demonstrated that low temperature induces carbohydrate degradation, yet integrative studies on metabolic changes occurring in the bulb are not available. We detected that cold exposure mainly hastened bulb sprouting, rather than floral transition or blooming. Metabolite profiling of cooled and non-cooled bulbs was carried out, revealing cold-induced accumulation of soluble sugars, lipids and specific amino acids, and a significant reduction in tricarboxylic acid (TCA)-cycle elements. We observed that metabolic pathways located in the cytosol - including glycolysis, lipid synthesis and part of the gamma-Aminobutyric acid (GABA) shunt - were enhanced by cold exposure, while mitochondrial metabolism - namely the TCA cycle - was reduced by cold. We suggest a physiological model accounting for this metabolic discrepancy.

Melatonin-Stimulated Triacylglycerol Breakdown and Energy Turnover under Salinity Stress Contributes to the Maintenance of Plasma Membrane H+-ATPase Activity and K+/Na+ Homeostasis in Sweet Potato

Melatonin (MT) is a multifunctional molecule in animals and plants and is involved in defense against salinity stress in various plant species. In this study, MT pretreatment was simultaneously applied to the roots and leaves of sweet potato seedlings [Ipomoea batatas (L.) Lam.], which is an important food and industry crop worldwide, followed by treatment of 150 mM NaCl. The roles of MT in mediating K+/Na+ homeostasis and lipid metabolism in salinized sweet potato were investigated. Exogenous MT enhanced the resistance to NaCl and improved K+/Na+ homeostasis in sweet potato seedlings as indicated by the low reduced K+ content in tissues and low accumulation of Na+ content in the shoot. Electrophysiological experiments revealed that exogenous MT significantly suppressed NaCl-induced K+ efflux in sweet potato roots and mesophyll tissues. Further experiments showed that MT enhanced the plasma membrane (PM) H+-ATPase activity and intracellular adenosine triphosphate (ATP) level in the roots and leaves of salinized sweet potato. Lipidomic profiling revealed that exogenous MT completely prevented salt-induced triacylglycerol (TAG) accumulation in the leaves. In addition, MT upregulated the expression of genes related to TAG breakdown, fatty acid (FA) β-oxidation, and energy turnover. Chemical inhibition of the β-oxidation pathway led to drastic accumulation of lipid droplets in the vegetative tissues of NaCl-stressed sweet potato and simultaneously disrupted the MT-stimulated energy state, PM H+-ATPase activity, and K+/Na+ homeostasis. Results revealed that exogenous MT stimulated TAG breakdown, FA β-oxidation, and energy turnover under salinity conditions, thereby contributing to the maintenance of PM H+-ATPase activity and K+/Na+ homeostasis in sweet potato.

Lipidomic Analysis: From Archaea to Mammals

Lipids are among the most important organic compounds found in all living cells, from primitive archaebacteria to flowering plants or mammalian cells. They form part of cell walls and constitute cell storage material. Their biosynthesis and metabolism play key roles in faraway topics such as biofuel production (third-generation biofuels produced by microorganisms, e.g. algae) and human diseases such as adrenoleukodystrophy, Zellweger syndrome, or Refsum disease. Current lipidomic analysis requires fast and accurate processing of samples and especially their characterization. Because the number of possible lipids and, more specifically, molecular species of lipids is of the order of hundreds to thousands, it is necessary to process huge amounts of data in a short time. There are two basic approaches to lipidomic analysis: shotgun and liquid chromatography-mass spectometry. Both methods have their pros and cons. This review deals with lipidomics not according to the type of ionization or the lipid classes analyzed but according to the types of samples (organisms) under study. Thus, it is divided into lipidomic analysis of archaebacteria, bacteria, yeast, fungi, algae, plants, and animals.

Metabolomics for Plant Improvement: Status and Prospects

Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.

Plant lipidomics at the crossroads: From technology to biology driven science

The identification and quantification of lipids from plant tissues have become commonplace and many researchers now incorporate lipidomics approaches into their experimental studies. Plant lipidomics research continues to involve technological developments such as those in mass spectrometry imaging, but in large part, lipidomics approaches have matured to the point of being accessible to the novice. Here we review some important considerations for those planning to apply plant lipidomics to their biological questions, and offer suggestions for appropriate tools and practices. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.