Identification of a sphingolipid α-glucuronosyltransferase that is essential for pollen function in Arabidopsis

Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement

Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas.

Diverse INOSITOL PHOSPHORYLCERAMIDE SYNTHASE mutant alleles of Physcomitrium patens offer new insight into complex sphingolipid metabolism

Sphingolipids are widespread, abundant, and essential lipids in plants and in other eukaryotes. Glycosyl inositol phosphorylceramides (GIPCs) are the most abundant class of plant sphingolipids, and are enriched in the plasma membrane of plant cells. They have been difficult to study due to lethal or pleiotropic mutant phenotypes. To overcome this, we developed a CRISPR/Cas9-based method for generating multiple and varied knockdown and knockout populations of mutants in a given gene of interest in the model moss Physcomitrium patens. This system is uniquely convenient due to the predominantly haploid state of the Physcomitrium life cycle, and totipotency of Physcomitrium protoplasts used for transformation. We used this approach to target the INOSITOL PHOSPHORYLCERAMIDE SYNTHASE (IPCS) gene family, which catalyzes the first, committed step in the synthesis of GIPCs. We isolated knockout single mutants and knockdown higher-order mutants showing a spectrum of deficiencies in GIPC content. Remarkably, we also identified two mutant alleles accumulating inositol phosphorylceramides, the direct products of IPCS activity, and provide our best explanation for this unexpected phenotype. Our approach is broadly applicable for studying essential genes and gene families, and for obtaining unusual lesions within a gene of interest.

Glucosylceramides impact cellulose deposition and cellulose synthase complex motility in Arabidopsis

Cellulose is an abundant component of plant cell wall matrices, and this para-crystalline polysaccharide is synthesized at the plasma membrane by motile Cellulose Synthase Complexes (CSCs). However, the factors that control CSC activity and motility are not fully resolved. In a targeted chemical screen, we identified the alkylated nojirimycin analog N-Dodecyl Deoxynojirimycin (ND-DNJ) as a small molecule that severely impacts Arabidopsis seedling growth. Previous work suggests that ND-DNJ-related compounds inhibit the biosynthesis of glucosylceramides (GlcCers), a class of glycosphingolipid associated with plant membranes. Our work uncovered major changes in the sphingolipidome of plants treated with ND-DNJ, including reductions in GlcCer abundance and altered acyl chain length distributions. Crystalline cellulose content was also reduced in ND-DNJ-treated plants as well as plants treated with the known GlcCer biosynthesis inhibitor N-[2-hydroxy-1-(4-morpholinylmethyl)-2-phenyl ethyl]-decanamide (PDMP) or plants containing a genetic disruption in GLUCOSYLCERAMIDE SYNTHASE (GCS), the enzyme responsible for sphingolipid glucosylation that results in GlcCer synthesis. Live-cell imaging revealed that CSC speed distributions were reduced upon treatment with ND-DNJ or PDMP, further suggesting an important relationship between glycosylated sphingolipid composition and CSC motility across the plasma membrane. These results indicate that multiple interventions compromising GlcCer biosynthesis disrupt cellulose deposition and CSC motility, suggesting that GlcCers regulate cellulose biosynthesis in plants.

The function of sphingolipids in membrane trafficking and cell signaling in plants, in comparison with yeast and animal cells

Sphingolipids are essential membrane components involved in a wide range of cellular, developmental and signaling processes. Sphingolipids are so essential that knock-out mutation often leads to lethality. In recent years, conditional or weak allele mutants as well as the broadening of the pharmacological catalog allowed to decipher sphingolipid function more precisely in a less invasive way. This review intends to provide a discussion and point of view on the function of sphingolipids with a main focus on endomembrane trafficking, Golgi-mediated protein sorting, cell polarity, cell-to-cell communication and cell signaling at the plasma membrane. While our main angle is the plant field research, we will constantly refer to and compare with the advances made in the yeast and animal field. In this review, we will emphasize the role of sphingolipids not only as a membrane component, but also as a key player at a center of homeostatic regulatory networks involving direct or indirect interaction with other lipids, proteins and ion fluxes.

Arabidopsis TETRASPANIN8 mediates exosome secretion and glycosyl inositol phosphoceramide sorting and trafficking

Sphingolipids are components of plant membranes, and their heterogeneous distribution gives different membrane systems distinct properties. For example, glycosyl inositol phosphoceramides (GIPCs), 1 major type of sphingolipids, aggregate in the outer layer of the plasma membrane (PM), as well as in extracellular vesicles (EVs), including the small (30 to 100 nm) EVs termed exosomes. How these sphingolipids are sorted and trafficked is not clear. In this work, we report that Arabidopsis thaliana TETRASPANIN8 (TET8) acts as a sphingolipid carrier and thus regulates the export of GIPCs from the Golgi apparatus. TET8 recognized the coat protein complex I (COPI) subunit γ2-COPI and moved to its proper location in the PM; this recognition required the TET8 C-terminal tail. Deleting the C-terminal tail of TET8 largely restricted its roles in GIPC transport and endosomal trafficking. Further, we show that TET8 affects EV secretion in association with GIPCs. Thus, our findings shed light on GIPC transport and the molecular machinery involved in EV biogenesis.

The Golgi-localized transporter OsPML4 contributes to manganese homeostasis in rice

Manganese (Mn), an indispensable plant micronutrient, functions as a vital enzyme co-factor in numerous biochemical reactions. In rice, the Golgi-localized PHOTOSYNTHESIS-AFFECTED MUTANT 71-LIKE 3 (OsPML3), a member of the UNCHARACTERIZED PROTEIN FAMILY (UPF0016), plays a pivotal role in Mn homeostasis, particularly in rapidly developing tissues. This study focused on the functional characterization of another UPF0016 family member in rice, OsPML4, to elucidate its involvement in Mn homeostasis. OsPML4 had a 73% sequence identity with OsPML3 and exhibited expression in both shoots and roots, albeit at a lower transcriptional level than OsPML3. Furthermore, subcellular localization studies confirmed that OsPML4 localizes in the Golgi apparatus. Notably, heterologous expression of OsPML4 restored growth in the Mn uptake-deficient yeast strain Δsmf1 under Mn-limited conditions. Under Mn-deficient conditions, OsPML4 knockout exacerbated the decline in shoot dry weight and intensified necrosis in young leaves of OsPML3 knockout lines, which displayed stunted growth. The Mn concentration in OsPML3PML4 double knockout lines was lower than in wild-type (WT) and OsPML3 knockout lines. At the reproductive phase, OsPML3PML4 double knockout lines exhibited reduced fertility and grain yield compared to WT and OsPML3 knockout lines. Notably, reductions were observed in the deposition of cell wall polysaccharides and the content of Lea (Lewis A structure)-containing N-glycans in the young leaves of OsPML3PML4 double knockout lines, surpassing the reductions in WT and OsPML3 knockout lines. These findings underscore the significance of OsPML4 in Mn homeostasis in the Golgi apparatus, where it co-functions with OsPML3 to regulate cell wall polysaccharide deposition and late-stage Golgi N-glycosylation.

Inositolphosphorylceramide synthases, OsIPCSs, regulate plant height in rice

Inositolphosphorylceramide synthase (IPCS) catalyses ceramides and phosphatidylinositol (PI) into inositolphosphorylceramide (IPC), which is involved in the regulation of plant growth and development. A total of three OsIPCS family genes have been identified in rice. However, most of their functions remain unknown. Here, the functions of OsIPCSs were analyzed by CRISPR/Cas9 technology, lipidomics analysis, and transcriptomics analysis. Single-gene mutation of OsIPCSs resulted in dwarf phenotype. Among them, the phenotype of osipcs3 mutant was more severe. Multi-gene mutation of OsIPCS genes led to more severe phenotypes, indicating the additive effects of OsIPCSs. We further determined that a significant decrease in epidermal cell elongation of internode in the mutants. There was a significant decrease in the content of IPC detected in the osipcs2/3 and osipcs1/2/3 mutants. The contents of glycosyl inositol phosphoryl ceramide (GIPC) were also decreased by 20% and 10% in osipcs2/3 and osipcs1/2/3, respectively. The results of RNA-seq showed that numerous DEGs found to be associated with cellular component organization, anatomical structure morphogenesis, and cell growth in the osipcs2, osipcs2/3, and osipcs1/2/3. Taken together, OsIPCSs may be involved in the regulation of plant height through affecting cell growth and sphingolipid metabolism in rice.

Overexpression of a GIPC glycosyltransferase gene, OsGMT1, suppresses plant immunity and delays heading time in rice

Glycosylinositol phosphorylceramides (GIPCs) are the major sphingolipids in the plant plasma membrane. In Arabidopsis, mutations of genes involved in the synthesis of GIPCs affect many physiological aspects of plants, including growth, pollen fertility, defense, and stress signaling. Loss of function of the GIPC MANNOSYL-TRANSFERASE1 (AtGMT1) results in GIPC misglycosylation and induces plant immune responses accompanied by a severely dwarfed phenotype, thus indicating that GIPCs play important roles in plant immunity. Here, we investigated the enzymatic activity and phenotypes of transgenic lines of OsGMT1, the ortholog of AtGMT1. Sphingolipidomic analysis indicated that OsGMT1 retained the enzymatic activity of GIPC hexose (Hex) glycosylation, but the knockout lines did not accumulate H₂O₂. In contrast, the OsGMT1 overexpression lines showed significant down-regulation of several defense-associated or cell wall synthesis-associated genes, and enhanced sensitivity to rice blast. Furthermore, we first demonstrated the sensitivity of rice cells to MoNLP1 protein through calcein AM release assays using rice protoplasts, thus legitimizing the presence of MoNLPs in rice blast fungus. In addition, yeast two-hybrid screens using OsGMT1 as bait revealed that OsGMT1 may regulate heading time through the OsHAP5C signaling pathway. Together, our findings suggested clear physiological functional differentiation of GMT1 orthologs between rice and Arabidopsis.

Nonspecific phospholipase C3 of radish has phospholipase D activity towards glycosylinositol phosphoceramide

Glycosylinositol phosphoceramide (GIPC) is a major sphingolipid in the plasma membranes of plants. Previously, we found an enzyme activity that produces phytoceramide 1-phosphate (PC1P) by hydrolysis of the D position of GIPC in cabbage and named this activity as GIPC-phospholipase D (PLD). Here, we purified GIPC-PLD by sequential chromatography from radish roots. Peptide mass fingerprinting analysis revealed that the potential candidate for GIPC-PLD protein was nonspecific phospholipase C3 (NPC3), which has not been characterized as a PLD. The recombinant NPC3 protein obtained by heterologous expression system in Escherichia coli produced PC1P from GIPC and showed essentially the same enzymatic properties as those we characterized as GIPC-PLD in cabbage, radish and Arabidopsis thaliana. From these results, we conclude that NPC3 is one of the enzymes that degrade GIPC.

Molecular Mechanisms of Plant Responses to Salt Stress

Saline-alkali soils pose an increasingly serious global threat to plant growth and productivity. Much progress has been made in elucidating how plants adapt to salt stress by modulating ion homeostasis. Understanding the molecular mechanisms that affect salt tolerance and devising strategies to develop/breed salt-resilient crops have been the primary goals of plant salt stress signaling research over the past few decades. In this review, we reflect on recent major advances in our understanding of the cellular and physiological mechanisms underlying plant responses to salt stress, especially those involving temporally and spatially defined changes in signal perception, decoding, and transduction in specific organelles or cells.

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.

Abiotic Stresses in Plants and Their Markers: A Practice View of Plant Stress Responses and Programmed Cell Death Mechanisms

Understanding how plants cope with stress and the intricate mechanisms thereby used to adapt and survive environmental imbalances comprise one of the most powerful tools for modern agriculture. Interdisciplinary studies suggest that knowledge in how plants perceive, transduce and respond to abiotic stresses are a meaningful way to design engineered crops since the manipulation of basic characteristics leads to physiological remodeling for plant adaption to different environments. Herein, we discussed the main pathways involved in stress-sensing, signal transduction and plant adaption, highlighting biochemical, physiological and genetic events involved in abiotic stress responses. Finally, we have proposed a list of practice markers for studying plant responses to multiple stresses, highlighting how plant molecular biology, phenotyping and genetic engineering interconnect for creating superior crops.

Detailed sphingolipid profile responded to salt stress in cotton root and the GhIPCS1 is involved in the regulation of plant salt tolerance

Sphingolipids are major structural components of membrane and active signaling molecules and play an important role in plant developmental processes and stress responses. As land salinization has increased globally, salinity has compromised the growth and productivity of crops such as cotton. Understanding the mechanisms of plant adaptation to salt stress is essential for breeding salt-tolerant crops. In this study, we explored the comprehensive metabolic profile of sphingolipids in cotton root under salt stress using lipidomics. 118 sphingolipid molecular species were identified, of which PhytoSph, PhytoCer, PhytoCer-OHFA, IPC, and GIPC were relatively high in content, and PhytoSph, PhytoCer, PhytoCer-OHFA, Phyto-GluCer, and IPC showed significant changes after salt stress, especially inositol phosphatidyl ceramide (IPC), which was significantly upregulated after salt treatment. Subsequently, we identified the genes encoding IPC synthase (IPCS), and ectopic expression of GhIPCS1 enhanced salt sensitivity in Arabidopsis, which might result from the disruption on the balance between various sphingolipid classes and/or molecular species. Overall, this study reveals key lipids and genes response to salt stress in cotton and provides a theoretical basis for the use of genetic engineering to improve cotton stress resistance.

Changes in glycosyl inositol phosphoceramides during the cell cycle of the red alga Galdieria sulphuraria

Sphingolipids are significant component of plant-cell plasma membranes, as well as algal membranes, and mediate various biological processes. One of these processes is the change in lipid content during the cell cycle. This change is key to understanding cell viability and proliferation. There are relatively few papers describing highly glycosylated glycosyl inositol phosphorylceramide (GIPC) due to problems associated with the extractability of GIPCs and their analysis, especially in algae. After alkaline hydrolysis of total lipids from the red alga Galdieria sulphuraria, GIPCs were measured by high-resolution tandem mass spectrometry and fragmentation of precursor ions in an Orbitrap mass spectrometer in order to elucidate the structures of molecular species. Fragmentation experiments such as tandem mass spectrometry in the negative ion mode were performed to determine both the ceramide group and polar head structures. Measurement of mass spectra in the negative regime was possible because the phosphate group stabilizes negative molecular ions [M-H]^-. ANALYSIS: of GIPCs at various stages of the cell cycle provided information on their abundance. It was found that, depending on the phases of the cell cycle, in particular during division, the uptake of all three components of GIPC, i.e., long-chain amino alcohols, fatty acids, and polar heads, changes. Structural modifications of the polar headgroup significantly increased the number of molecular species. Analysis demonstrated a convex characteristic for molecular species with only one saccharide (hexose or hexuronic acid) as the polar head. For two carbohydrates, the course of Hex-HexA was linear, while for HexA-HexA it was concave. The same was true for GIPC with three and four monosaccharides.

Transport, functions, and interaction of calcium and manganese in plant organellar compartments

Calcium (Ca2+) and manganese (Mn2+) are essential elements for plants and have similar ionic radii and binding coordination. They are assigned specific functions within organelles, but share many transport mechanisms to cross organellar membranes. Despite their points of interaction, those elements are usually investigated and reviewed separately. This review takes them out of this isolation. It highlights our current mechanistic understanding and points to open questions of their functions, their transport, and their interplay in the endoplasmic reticulum (ER), vesicular compartments (Golgi apparatus, trans-Golgi network, pre-vacuolar compartment), vacuoles, chloroplasts, mitochondria, and peroxisomes. Complex processes demanding these cations, such as Mn2+-dependent glycosylation or systemic Ca2+ signaling, are covered in some detail if they have not been reviewed recently or if recent findings add to current models. The function of Ca2+ as signaling agent released from organelles into the cytosol and within the organelles themselves is a recurrent theme of this review, again keeping the interference by Mn2+ in mind. The involvement of organellar channels [e.g. glutamate receptor-likes (GLR), cyclic nucleotide-gated channels (CNGC), mitochondrial conductivity units (MCU), and two-pore channel1 (TPC1)], transporters (e.g. natural resistance-associated macrophage proteins (NRAMP), Ca2+ exchangers (CAX), metal tolerance proteins (MTP), and bivalent cation transporters (BICAT)], and pumps [autoinhibited Ca2+-ATPases (ACA) and ER Ca2+-ATPases (ECA)] in the import and export of organellar Ca2+ and Mn2+ is scrutinized, whereby current controversial issues are pointed out. Mechanisms in animals and yeast are taken into account where they may provide a blueprint for processes in plants, in particular, with respect to tunable molecular mechanisms of Ca2+ versus Mn2+ selectivity.

Abiotic stress responses in plants

Plants cannot move, so they must endure abiotic stresses such as drought, salinity and extreme temperatures. These stressors greatly limit the distribution of plants, alter their growth and development, and reduce crop productivity. Recent progress in our understanding of the molecular mechanisms underlying the responses of plants to abiotic stresses emphasizes their multilevel nature; multiple processes are involved, including sensing, signalling, transcription, transcript processing, translation and post-translational protein modifications. This improved knowledge can be used to boost crop productivity and agricultural sustainability through genetic, chemical and microbial approaches.

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.

Sphingolipids in foodstuff: Compositions, distribution, digestion, metabolism and health effects - A comprehensive review

Sphingolipids (SLs) are common in all eukaryotes, prokaryotes, and viruses, and played a vital role in human health. They are involved in physiological processes, including intracellular transport, cell division, and signal transduction. However, there are limited reviews on dietary effects on endogenous SLs metabolism and further on human health. Various dietary conditions, including the SLs-enriched diet, high-fat diet, and vitamins, can change the level of endogenous SLs metabolites and even affect human health. This review systematically summarizes the main known SLs in foods concerning their variety and contents, as well as their isolation and identification approaches. Moreover, the present review discusses the role of dietary (particularly SLs-enriched diet, high-fat diet, and vitamins) in endogenous SLs metabolism, highlighting how exogenous SLs are digested and absorbed. The role of SLs family in the pathogenesis of diseases, including cancers, neurological disorders, infectious and inflammatory diseases, and cardiovascular diseases, and in recently coronavirus disease-19 outbreak was also discussed. In the post-epidemic era, we believe that the concern for health and the need for plant-based products will increase. Therefore, a need for research on the absorption and metabolism pathway of SLs (especially plant-derived SLs) and their bioavailability is necessary. Moreover, the effects of storage treatment and processing on the content and composition of SLs in food are worth exploring. Further studies should also be conducted on the dose-response of SLs on human health to support the development of SLs supplements. More importantly, new approaches, such as, making SLs based hydrogels can effectively achieve sustained release and targeted therapies.

Sphingolipids mediate polar sorting of PIN2 through phosphoinositide consumption at the trans-Golgi network

The lipid composition of organelles acts as a landmark to define membrane identity and specify subcellular function. Phosphoinositides are anionic lipids acting in protein sorting and trafficking at the trans-Golgi network (TGN). In animal cells, sphingolipids control the turnover of phosphoinositides through lipid exchange mechanisms at endoplasmic reticulum/TGN contact sites. In this study, we discover a mechanism for how sphingolipids mediate phosphoinositide homeostasis at the TGN in plant cells. Using multiple approaches, we show that a reduction of the acyl-chain length of sphingolipids results in an increased level of phosphatidylinositol-4-phosphate (PtdIns(4)P or PI4P) at the TGN but not of other lipids usually coupled to PI4P during exchange mechanisms. We show that sphingolipids mediate Phospholipase C (PLC)-driven consumption of PI4P at the TGN rather than local PI4P synthesis and that this mechanism is involved in the polar sorting of the auxin efflux carrier PIN2 at the TGN. Together, our data identify a mode of action of sphingolipids in lipid interplay at the TGN during protein sorting.

Lipid composition impacts the function of cellular membranes. Here the authors show that a reduction in sphingolipid acyl-chain length promotes phosphoinositide consumption by phospholipase C at the Arabidopsis trans-Golgi network which in turn regulates sorting of the auxin efflux carrier PIN2.

Engineering the bilayer: Emerging genetic tool kits for mechanistic lipid biology

The structural diversity of lipids underpins the biophysical properties of cellular membranes, which vary across all scales of biological organization. Because lipid composition results from complex metabolic and transport pathways, its experimental control has been a major goal of mechanistic membrane biology. Here, we argue that in the wake of synthetic biology, similar metabolic engineering strategies can be applied to control the composition, physicochemical properties, and function of cell membranes. In one emerging area, titratable expression platforms allow for specific and genome-wide alterations in lipid biosynthetic genes, providing analog control over lipidome stoichiometry in membranes. Simultaneously, heterologous expression of biosynthetic genes and pathways has allowed for gain-of-function experiments with diverse lipids in non-native systems. Finally, we highlight future directions for tool development, including recently discovered lipid transport pathways to intracellular lipid pools. Further tool development providing synthetic control of membrane properties can allow biologists to untangle membrane lipid structure-associated functions.

Mass Spectrometry-Based Profiling of Plant Sphingolipids from Typical and Aberrant Metabolism

Mass spectrometry has increasingly been used as a tool to complement studies of sphingolipid metabolism and biological functions in plants and other eukaryotes. Mass spectrometry is now essential for comprehensive sphingolipid analytical profiling because of the huge diversity of sphingolipid classes and molecular species in eukaryotes, particularly in plants. This structural diversity arises from large differences in polar head group glycosylation as well as carbon-chain lengths of fatty acids and desaturation and hydroxylation patterns of fatty acids and long-chain bases that together comprise the ceramide hydrophobic backbone of glycosphingolipids. The standard methods for liquid chromatography-mass spectrometry (LC-MS)-based analyses of Arabidopsis thaliana leaf sphingolipids profile >200 molecular species of four sphingolipid classes and free long-chain bases and their phosphorylated forms. While these methods have proven valuable for A. thaliana based sphingolipid research, we have recently adapted them for use with ultraperformance liquid chromatography separations of molecular species and to profile aberrant sphingolipid forms in pollen, transgenic lines, and mutants. This chapter provides updates to standard methods for LC-MS profiling of A. thaliana sphingolipids to expand the utility of mass spectrometry for plant sphingolipid research.

Plasma and vacuolar membrane sphingolipidomes: composition and insights on the role of main molecular species

Lipid structures affect membrane biophysical properties such as thickness, stability, permeability, curvature, fluidity, asymmetry, and interdigitation, contributing to membrane function. Sphingolipids are abundant in plant endomembranes and plasma membranes (PMs) and comprise four classes: ceramides, hydroxyceramides, glucosylceramides, and glycosylinositolphosphoceramides (GIPCs). They constitute an array of chemical structures whose distribution in plant membranes is unknown. With the aim of describing the hydrophobic portion of sphingolipids, 18 preparations from microsomal (MIC), vacuolar (VM), PM, and detergent-resistant membranes (DRM) were isolated from Arabidopsis (Arabidopsis thaliana) leaves. Sphingolipid species, encompassing pairing of long-chain bases and fatty acids, were identified and quantified in these membranes. Sphingolipid concentrations were compared using univariate and multivariate analysis to assess sphingolipid diversity, abundance, and predominance across membranes. The four sphingolipid classes were present at different levels in each membrane: VM was enriched in glucosylceramides, hydroxyceramides, and GIPCs; PM in GIPCs, in agreement with their key role in signal recognition and sensing; and DRM in GIPCs, as reported by their function in nanodomain formation. While a total of 84 sphingolipid species was identified in MIC, VM, PM, and DRM, only 34 were selectively distributed in the four membrane types. Conversely, every membrane contained a different number of predominant species (11 in VM, 6 in PM, and 17 in DRM). This study reveals that MIC, VM, PM, and DRM contain the same set of sphingolipid species but every membrane source contains its own specific assortment based on the proportion of sphingolipid classes and on the predominance of individual species.

Nonspecific phospholipase C4 hydrolyzes phosphosphingolipids and sustains plant root growth during phosphate deficiency

Phosphate is a vital macronutrient for plant growth, and its availability in soil is critical for agricultural sustainability and productivity. A substantial amount of cellular phosphate is used to synthesize phospholipids for cell membranes. Here, we identify a key enzyme, nonspecific phospholipase C4 (NPC4) that is involved in phosphosphingolipid hydrolysis and remodeling in Arabidopsis during phosphate starvation. The level of glycosylinositolphosphorylceramide (GIPC), the most abundant sphingolipid in Arabidopsis thaliana, decreased upon phosphate starvation. NPC4 was highly induced by phosphate deficiency, and NPC4 knockouts in Arabidopsis decreased the loss of GIPC and impeded root growth during phosphate starvation. Enzymatic analysis showed that NPC4 hydrolyzed GIPC and displayed a higher activity toward GIPC as a substrate than toward the common glycerophospholipid phosphatidylcholine. NPC4 was associated with the plasma membrane lipid rafts in which GIPC is highly enriched. These results indicate that NPC4 uses GIPC as a substrate in planta and the NPC4-mediated sphingolipid remodeling plays a positive role in root growth in Arabidopsis response to phosphate deficiency.

Reprogramming sphingolipid glycosylation is required for endosymbiont persistence in Medicago truncatula

Plant endosymbiosis relies on the development of specialized membranes that encapsulate the endosymbiont and facilitate nutrient exchange. However, the identity and function of lipids within these membrane interfaces is largely unknown. Here, we identify GLUCOSAMINE INOSITOL PHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) as a sphingolipid glycosyltransferase highly expressed in Medicago truncatula root nodules and roots colonized by arbuscular mycorrhizal (AM) fungi and further demonstrate that this enzyme functions in the synthesis of N-acetyl-glucosamine-decorated glycosyl inositol phosphoryl ceramides (GIPCs) in planta. MtGINT1 expression was developmentally regulated in symbiotic tissues associated with the development of symbiosome and periarbuscular membranes. RNAi silencing of MtGINT1 did not affect overall root growth but strongly impaired nodulation and AM symbiosis, resulting in the senescence of symbiosomes and arbuscules. Our results indicate that, although M. truncatula root sphingolipidome predominantly consists of hexose-decorated GIPCs, local reprogramming of GIPC glycosylation by MtGINT1 is required for the persistence of endosymbionts within the plant cell.

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.

The Arabidopsis thaliana nucleotide sugar transporter GONST2 is a functional homolog of GONST1

Glycosylinositolphosphorylceramides (GIPCs) are the predominant lipid in the outer leaflet of the plasma membrane. Characterized GIPC glycosylation mutants have severe or lethal plant phenotypes. However, the function of the glycosylation is unclear. Previously, we characterized Arabidopsis thaliana GONST1 and showed that it was a nucleotide sugar transporter which provides GDP-mannose for GIPC glycosylation. gonst1 has a severe growth phenotype, as well as a constitutive defense response. Here, we characterize a mutant in GONST1's closest homolog, GONST2. The gonst2-1 allele has a minor change to GIPC headgroup glycosylation. Like other reported GIPC glycosylation mutants, gonst1-1gonst2-1 has reduced cellulose, a cell wall polymer that is synthesized at the plasma membrane. The gonst2-1 allele has increased resistance to a biotrophic pathogen Golovinomyces orontii but not the necrotrophic pathogen Botrytis cinerea. Expression of GONST2 under the GONST1 promoter can rescue the gonst1 phenotype, indicating that GONST2 has a similar function to GONST1 in providing GDP-D-Man for GIPC mannosylation.

A Pipeline towards the Biochemical Characterization of the Arabidopsis GT14 Family

Glycosyltransferases (GTs) catalyze the synthesis of glycosidic linkages and are essential in the biosynthesis of glycans, glycoconjugates (glycolipids and glycoproteins), and glycosides. Plant genomes generally encode many more GTs than animal genomes due to the synthesis of a cell wall and a wide variety of glycosylated secondary metabolites. The Arabidopsis thaliana genome is predicted to encode over 573 GTs that are currently classified into 42 diverse families. The biochemical functions of most of these GTs are still unknown. In this study, we updated the JBEI Arabidopsis GT clone collection by cloning an additional 105 GT cDNAs, 508 in total (89%), into Gateway-compatible vectors for downstream characterization. We further established a functional analysis pipeline using transient expression in tobacco (Nicotiana benthamiana) followed by enzymatic assays, fractionation of enzymatic products by reversed-phase HPLC (RP-HPLC) and characterization by mass spectrometry (MS). Using the GT14 family as an exemplar, we outline a strategy for identifying effective substrates of GT enzymes. By addition of UDP-GlcA as donor and the synthetic acceptors galactose-nitrobenzodiazole (Gal-NBD), β-1,6-galactotetraose (β-1,6-Gal₄) and β-1,3-galactopentose (β-1,3-Gal₅) to microsomes expressing individual GT14 enzymes, we verified the β-glucuronosyltransferase (GlcAT) activity of three members of this family (AtGlcAT14A, B, and E). In addition, a new family member (AT4G27480, 248) was shown to possess significantly higher activity than other GT14 enzymes. Our data indicate a likely role in arabinogalactan-protein (AGP) biosynthesis for these GT14 members. Together, the updated Arabidopsis GT clone collection and the biochemical analysis pipeline present an efficient means to identify and characterize novel GT catalytic activities.

Protein kinases in plant responses to drought, salt, and cold stress

Protein kinases are major players in various signal transduction pathways. Understanding the molecular mechanisms behind plant responses to biotic and abiotic stresses has become critical for developing and breeding climate-resilient crops. In this review, we summarize recent progress on understanding plant drought, salt, and cold stress responses, with a focus on signal perception and transduction by different protein kinases, especially sucrose nonfermenting1 (SNF1)-related protein kinases (SnRKs), mitogen-activated protein kinase (MAPK) cascades, calcium-dependent protein kinases (CDPKs/CPKs), and receptor-like kinases (RLKs). We also discuss future challenges in these research fields.

Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants

Sphingolipids are a vital component of plant cellular endomembranes and carry out multiple functional and regulatory roles. Different sphingolipid species confer rigidity to the membrane structure, facilitate trafficking of secretory proteins, and initiate programmed cell death. Although the regulation of the sphingolipid pathway is yet to be uncovered, increasing evidence has pointed to orosomucoid proteins (ORMs) playing a major regulatory role and potentially interacting with a number of components in the pathway, including both enzymes and sphingolipids. However, experimental exploration of new regulatory interactions is time consuming and often infeasible. In this work, a computational approach was taken to address this challenge. A metabolic network of the sphingolipid pathway in plants was reconstructed. The steady-state rates of reactions in the network were then determined through measurements of growth and cellular composition of the different sphingolipids in Arabidopsis seedlings. The Ensemble modeling framework was modified to accurately account for activation mechanisms and subsequently used to generate sets of kinetic parameters that converge to the measured steady-state fluxes in a thermodynamically consistent manner. In addition, the framework was appended with an additional module to automate screening the parameters and to output models consistent with previously reported network responses to different perturbations. By analyzing the network's response in the presence of different combinations of regulatory mechanisms, the model captured the experimentally observed repressive effect of ORMs on serine palmitoyltransferase (SPT). Furthermore, predictions point to a second regulatory role of ORM proteins, namely as an activator of class II (or LOH1 and LOH3) ceramide synthases. This activating role was found to be modulated by the concentration of free ceramides, where an accumulation of these sphingolipid species dampened the activating effect of ORMs on ceramide synthase. The predictions pave the way for future guided experiments and have implications in engineering crops with higher biotic stress tolerance.

A comprehensive comparison of four methods for extracting lipids from Arabidopsis tissues

BACKGROUND

The plant lipidome is highly complex, and the composition of lipids in different tissues as well as their specific functions in plant development, growth and stress responses have yet to be fully elucidated. To do this, efficient lipid extraction protocols which deliver target compounds in solution at concentrations adequate for subsequent detection, quantitation and analysis through spectroscopic methods are required. To date, numerous methods are used to extract lipids from plant tissues. However, a comprehensive analysis of the efficiency and reproducibility of these methods to extract multiple lipid classes from diverse tissues of a plant has not been undertaken.

RESULTS

In this study, we report the comparison of four different lipid extraction procedures in order to determine the most effective lipid extraction protocol to extract lipids from different tissues of the model plant Arabidopsis thaliana.

CONCLUSION

While particular methods were best suited to extract different lipid classes from diverse Arabidopsis tissues, overall a single-step extraction method with a 24 h extraction period, which uses a mixture of chloroform, isopropanol, methanol and water, was the most efficient, reproducible and the least labor-intensive to extract a broad range of lipids for untargeted lipidomic analysis of Arabidopsis tissues. This method extracted a broad range of lipids from leaves, stems, siliques, roots, seeds, seedlings and flowers of Arabidopsis. In addition, appropriate methods for targeted lipid analysis of specific lipids from particular Arabidopsis tissues were also identified.

Sphingolipids in plants: a guidebook on their function in membrane architecture, cellular processes, and environmental or developmental responses

Sphingolipids are fundamental lipids involved in various cellular, developmental and stress-response processes. As such, they orchestrate not only vital molecular mechanisms of living cells but also act in diseases, thus qualifying as potential pharmaceutical targets. Sphingolipids are universal to eukaryotes and are also present in some prokaryotes. Some sphingolipid structures are conserved between animals, plants and fungi, whereas others are found only in plants and fungi. In plants, the structural diversity of sphingolipids, as well as their downstream effectors and molecular and cellular mechanisms of action, are of tremendous interest to both basic and applied researchers, as about half of all small molecules in clinical use originate from plants. Here, we review recent advances towards a better understanding of the biosynthesis of sphingolipids, the diversity in their structures as well as their functional roles in membrane architecture, cellular processes such as membrane trafficking and cell polarity, and cell responses to environmental or developmental signals.

Bringing rafts to life: Lessons learned from lipid organization across diverse biological membranes

The ability of lipids to drive lateral organization is a remarkable feature of membranes and has been hypothesized to underlie the architecture of cells. Models for lipid rafts and related domains were originally based on the mammalian plasma membrane, but the nature of heterogeneity in this system is still not fully resolved. However, the concept of lipid-driven organization has been highly influential across biology, and has led to discoveries in organisms that feature a diversity of lipid chemistries and physiological needs. Here we review several emerging and instructive cases of membrane organization in non-mammalian systems. In bacteria, several types of membrane domains that act in metabolism and signaling have been elucidated. These widen our view of what constitutes a raft, but also introduce new questions about the relationship between organization and function. In yeast, observable membrane organization is found in both the plasma membrane and the vacuole. The latter serves as the best example of classic membrane phase partitioning in a living system to date, suggesting that internal organelles are important membranes to investigate across eukaryotes. Finally, we highlight plants as powerful model systems for complex membrane interactions in multicellular organisms. Plant membranes are organized by unique glycosphingolipids, supporting the importance of carbohydrate interactions in organizing lateral domains. These examples demonstrate that membrane organization is a potentially universal phenonenon in biology and argue for the continued broadening of lipid physical chemistry research into a wide range of systems.

A potential pathway for flippase-facilitated glucosylceramide catabolism in plants

The Aminophospholipid ATPase (ALA) family of plant lipid flippases is involved in the selective transport of lipids across membrane bilayers. Recently, we demonstrated that double mutants lacking both ALA4 and -5 are severely dwarfed. Dwarfism in ala4/5 mutants was accompanied by cellular elongation defects and various lipidomic perturbations, including a 1.4-fold increase in the accumulation of glucosylceramides (GlcCers) relative to total sphingolipid content. Here, we present a potential model for flippase-facilitated GlcCer catabolism in plants, where a combination of ALA flippases transport GlcCers to cytosolic membrane surfaces where they are degraded by Glucosylceramidases (GCDs). GCDs remove the glucose headgroup from GlcCers to produce a ceramide (Cer) backbone, which can be further degraded to sphingoid bases (Sphs, e.g, phytosphingosine) and fatty acids (FAs). In the absence of GlcCer-transporting flippases, GlcCers are proposed to accumulate on extracytoplasmic (i.e., apoplastic) or lumenal membrane surfaces. As GlcCers are potential precursors for Sph production, impaired GlcCer catabolism might also result in the decreased production of the secondary messenger Sph-1-phosphate (Sph-1-P, e.g., phytosphingosine-1-P), a regulator of cell turgor. Importantly, we postulate that either GlcCer accumulation or reduced Sph-1-P signaling might contribute to the growth reductions observed in ala4/5 mutants. Similar catabolic pathways have been proposed for humans and yeast, suggesting flippase-facilitated GlcCer catabolism is conserved across eukaryotes.

Synthesis and Function of Complex Sphingolipid Glycosylation

Glycosylinositol phosphorylceramides (GIPCs) constitute an important class of plasma-membrane lipids in plants. The complex glycan headgroups of GIPCs vary between plant species and tissues. Recent studies have shown that the structure of the glycan headgroup is important for plant development, abiotic stress tolerance, and interactions with pathogenic and symbiotic microorganisms.

How Plants Sense and Respond to Stressful Environments

Plants are exposed to an ever-changing environment to which they have to adjust accordingly. Their response is tightly regulated by complex signaling pathways that all start with stimulus perception. Here, we give an overview of the latest developments in the perception of various abiotic stresses, including drought, salinity, flooding, and temperature stress. We discuss whether proposed perception mechanisms are true sensors, which is well established for some abiotic factors but not yet fully elucidated for others. In addition, we review the downstream cellular responses, many of which are shared by various stresses but result in stress-specific physiological and developmental output. New sensing mechanisms have been identified, including heat sensing by the photoreceptor phytochrome B, salt sensing by glycosylinositol phosphorylceramide sphingolipids, and drought sensing by the specific calcium influx channel OSCA1. The simultaneous occurrence of multiple stress conditions shows characteristic downstream signaling signatures that were previously considered general signaling responses. The integration of sensing of multiple stress conditions and subsequent signaling responses is a promising venue for future research to improve the understanding of plant abiotic stress perception.

A xylan glucuronosyltransferase gene exhibits pleiotropic effects on cellular composition and leaf development in rice

Leaf chlorophyll content is an important physiological indicator of plant growth, metabolism and nutritional status, and it is highly correlated with leaf nitrogen content and photosynthesis. In this study, we report the cloning and identification of a xylan glucuronosyltransferase gene (OsGUX1) that affects relative chlorophyll content in rice leaf. Using a set of chromosomal segment substitution lines derived from a cross of wild rice accession ACC10 and indica variety Zhenshan 97 (ZS97), we identified numerous quantitative trait loci for relative chlorophyll content. One major locus of them for relative chlorophyll content was mapped to a 10.3-kb region that contains OsGUX1. The allele OsGUX1^AC from ACC10 significantly decreases nitrogen content and chlorophyll content of leaf compared with OsGUX1^ZS from ZS97. The overexpression of OsGUX1 reduced chlorophyll content, and the suppression of this gene increased chlorophyll content of rice leaf. OsGUX1 is located in Golgi apparatus, and highly expressed in seedling leaf and the tissues in which primary cell wall synthesis occurring. Our experimental data indicate that OsGUX1 is responsible for addition of glucuronic acid residues onto xylan and participates in accumulation of cellulose and hemicellulose in the cell wall deposition, thus thickening the primary cell wall of mesophyll cells, which might lead to reduced chlorophyll content in rice leaf. These findings provide insights into the association of cell wall components with leaf nitrogen content in rice.

Sphingolipids: towards an integrated view of metabolism during the plant stress response

Plants exist in an environment of changing abiotic and biotic stresses. They have developed a complex set of strategies to respond to these stresses and over recent years it has become clear that sphingolipids are a key player in these responses. Sphingolipids are not universally present in all three domains of life. Many bacteria and archaea do not produce sphingolipids but they are ubiquitous in eukaryotes and have been intensively studied in yeast and mammals. During the last decade there has been a steadily increasing interest in plant sphingolipids. Plant sphingolipids exhibit structural differences when compared with their mammalian counterparts and it is now clear that they perform some unique functions. Sphingolipids are recognised as critical components of the plant plasma membrane and endomembrane system. Besides being important structural elements of plant membranes, their particular structure contributes to the fluidity and biophysical order. Sphingolipids are also involved in multiple cellular and regulatory processes including vesicle trafficking, plant development and defence. This review will focus on our current knowledge as to the function of sphingolipids during plant stress responses, not only as structural components of biological membranes, but also as signalling mediators.

Plant-Unique cis/trans Isomerism of Long-Chain Base Unsaturation is Selectively Required for Aluminum Tolerance Resulting from Glucosylceramide-Dependent Plasma Membrane Fluidity

Cis/trans isomerism of the Δ8 unsaturation of long-chain base (LCB) is found only in plant sphingolipids. This unique geometry is generated by sphingolipid LCB Δ8 desaturase SLD which produces both isomers at various ratios, resulting in diverse cis/trans ratios in plants. However, the biological significance of this isomeric diversity remains controversial. Here, we show that the plant-specific cis unsaturation of LCB selectively contributes to glucosylceramide (GlcCer)-dependent tolerance to aluminum toxicity. We established three transgenic rice lines with altered LCB unsaturation profiles. Overexpression of SLD from rice (OsSLD-OX), which preferentially exhibits cis-activity, or Arabidopsis (AtSLD-OX), showing preference for trans-activity, facilitated Δ8 unsaturation in different manners: a slight increase of cis-unsaturated glycosylinositolphosphoceramide (GIPC) in OsSLD-OX, and a drastic increase of trans-unsaturated GlcCer and GIPC in AtSLD-OX. Disruption of LCB Δ4 desaturase (des) significantly decreased the content of GlcCer. Fluorescence imaging analysis revealed that OsSLD-OX and AtSLD-OX showed increased plasma membrane fluidity, whereas des had less fluidity, demonstrating that the isomers universally contributed to increasing membrane fluidity. However, the results of a hydroponic assay showed decreased aluminum tolerance in AtSLD-OX and des compared to OsSLD-OX and the control plants, which did not correlate with membrane fluidity. These results suggest that cis-unsaturated GlcCer, not GIPC, selectively serves to maintain the membrane fluidity specifically associated with aluminum tolerance.

Membrane Lipid Remodeling in Response to Salinity

Salinity is one of the most decisive environmental factors threatening the productivity of crop plants. Understanding the mechanisms of plant salt tolerance is critical to be able to maintain or improve crop yield under these adverse environmental conditions. Plant membranes act as biological barriers, protecting the contents of cells and organelles from biotic and abiotic stress, including salt stress. Alterations in membrane lipids in response to salinity have been observed in a number of plant species including both halophytes and glycophytes. Changes in membrane lipids can directly affect the properties of membrane proteins and activity of signaling molecules, adjusting the fluidity and permeability of membranes, and activating signal transduction pathways. In this review, we compile evidence on the salt stress responses of the major membrane lipids from different plant tissues, varieties, and species. The role of membrane lipids as signaling molecules in response to salinity is also discussed. Advances in mass spectrometry (MS)-based techniques have largely expanded our knowledge of salt-induced changes in lipids, however only a handful studies have investigated the underlying mechanisms of membrane lipidome regulation. This review provides a comprehensive overview of the recent works that have been carried out on lipid remodeling of plant membranes under salt treatment. Challenges and future perspectives in understanding the mechanisms of salt-induced changes to lipid metabolisms are proposed.

Plant cell-surface GIPC sphingolipids sense salt to trigger Ca2+ influx

Salinity is detrimental to plant growth, crop production and food security worldwide. Excess salt triggers increases in cytosolic Ca²⁺ concentration, which activate Ca²⁺-binding proteins and upregulate the Na⁺/H⁺ antiporter in order to remove Na⁺. Salt-induced increases in Ca²⁺ have long been thought to be involved in the detection of salt stress, but the molecular components of the sensing machinery remain unknown. Here, using Ca²⁺-imaging-based forward genetic screens, we isolated the Arabidopsis thaliana mutant monocation-induced [Ca^2+]_i increases 1 (moca1), and identified MOCA1 as a glucuronosyltransferase for glycosyl inositol phosphorylceramide (GIPC) sphingolipids in the plasma membrane. MOCA1 is required for salt-induced depolarization of the cell-surface potential, Ca²⁺ spikes and waves, Na⁺/H⁺ antiporter activation, and regulation of growth. Na⁺ binds to GIPCs to gate Ca²⁺ influx channels. This salt-sensing mechanism might imply that plasma-membrane lipids are involved in adaption to various environmental salt levels, and could be used to improve salt resistance in crops.

The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity

Resistance to 157 different herbicides and 88% of known sites of action has been observed, with many weeds resistant to two or more modes. Coupled with tighter environmental regulation, this demonstrates the need to identify new modes of action and novel herbicides. The plant sphingolipid biosynthetic enzyme, inositol phosphorylceramide synthase (IPCS), has been identified as a novel, putative herbicide target. The non-mammalian nature of this enzyme offers the potential of discovering plant specific inhibitory compounds with minimal impact on animals and humans, perhaps leading to the development of new non-toxic herbicides. The best characterised and most highly expressed isoform of the enzyme in the model-dicot Arabidopsis, AtIPCS2, was formatted into a yeast-based assay which was then utilized to screen a proprietary library of over 11,000 compounds provided by Bayer AG. Hits from this screen were validated in a secondary in vitro enzyme assay. These studies led to the identification of a potent inhibitor that showed selectivity for AtIPCS2 over the yeast orthologue, and activity against Arabidopsis seedlings. This work highlighted the use of a yeast-based screening assay to discover herbicidal compounds and the status of the plant IPCS as a novel herbicidal target.

Modulation of sphingolipid long-chain base composition and gene expression during early olive-fruit development, and putative role of brassinosteroid

Sphingolipids are abundant membrane components and signalling molecules in various aspects of plant development. However, the role of sphingolipids in early fleshy-fruit growth has rarely been investigated. In this study, we first investigated the temporal changes in sphingolipid long-chain base (LCB) content, composition, and gene expression that occurred during flower opening and early fruit development in olive (Olea europaea L. cv Picual). Moreover, the interaction between sphingolipid and the plant hormone, brassinosteroid (BR), during the early fruit development was also explored. For this, BR levels were manipulated through the application of exogenous BRs (24-epibrassinolide, EBR) or a BR biosynthesis inhibitor (brassinazole, Brz) and their effects on early fruit development, sphingolipid LCB content, and gene expression were examined in olive fruit at 14 days post-anthesis (DPA). We here show that sphingolipid with C-4 hydroxylation and Δ8 desaturation with a preference for (E)-isomer formation are quantitatively the most important sphingolipids in olive reproductive organs. In this work, the total LCB amount significantly decreased at the anthesis stage, but olive sphingosine-1-phosphate lyase (OeSPL) gene was expressed exclusively in flower and upregulated during the anthesis, revealing an association with the d18:1(8E) accumulation. However, the LCB content increased in parallel with the upregulation of the expression of genes for key sphingolipid biosynthetic and LCB modification enzymes during early fruit development in olive. Likewise, we found that EBR exogenously applied to olive trees significantly stimulated the fruit growth rate whereas Brz inhibited fruit growth rate after 7 and 14 days of treatment. In addition, this inhibitory effect could be counteracted by the application of EBR. The promotion of early fruit growth was accompanied by the down-regulation of sphingolipid LCB content and gene expression in olive fruit, whereas Brz application raised levels of sphingolipid LCB content and gene expression in olive fruit after 7 and 14 days of treatment. Thus, our data indicate that endogenous sphingolipid LCB and gene-expression levels are intricately controlled during early fruit development and also suggest a possible link between BR, the sphingolipid content/gene expression, and early fruit development in olive.

Plant lipids: Key players of plasma membrane organization and function

The plasma membrane (PM) is the biological membrane that separates the interior of all cells from the outside. The PM is constituted of a huge diversity of proteins and lipids. In this review, we will update the diversity of molecular species of lipids found in plant PM. We will further discuss how lipids govern global properties of the plant PM, explaining that plant lipids are unevenly distributed and are able to organize PM in domains. From that observation, it emerges a complex picture showing a spatial and multiscale segregation of PM components. Finally, we will discuss how lipids are key players in the function of PM in plants, with a particular focus on plant-microbe interaction, transport and hormone signaling, abiotic stress responses, plasmodesmata function. The last chapter is dedicated to the methods that the plant membrane biology community needs to develop to get a comprehensive understanding of membrane organization in plants.

A Golgi UDP-GlcNAc transporter delivers substrates for N-linked glycans and sphingolipids

Glycosylation requires activated glycosyl donors in the form of nucleotide sugars to drive processes such as post-translational protein modifications and glycolipid and polysaccharide biosynthesis. Most of these reactions occur in the Golgi, requiring cytosolic-derived nucleotide sugars, which need to be actively transferred into the Golgi lumen by nucleotide sugar transporters. We identified a Golgi-localized nucleotide sugar transporter from Arabidopsis thaliana with affinity for UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) and assigned it UDP-GlcNAc transporter 1 (UGNT1). Profiles of N-glycopeptides revealed that plants carrying the ugnt1 loss-of-function allele are virtually devoid of complex and hybrid N-glycans. Instead, the N-glycopeptide population from these alleles exhibited high-mannose structures, representing structures prior to the addition of the first GlcNAc in the Golgi. Concomitantly, sphingolipid profiling revealed that the biosynthesis of GlcNAc-containing glycosyl inositol phosphorylceramides (GIPCs) is also reliant on this transporter. By contrast, plants carrying the loss-of-function alleles affecting ROCK1, which has been reported to transport UDP-GlcNAc and UDP-N-acetylgalactosamine, exhibit no changes in N-glycan or GIPC profiles. Our findings reveal that plants contain a single UDP-GlcNAc transporter that delivers an essential substrate for the maturation of N-glycans and the GIPC class of sphingolipids.

GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) Is a GlcNAc-Containing Glycosylinositol Phosphorylceramide Glycosyltransferase

Glycosylinositol phosphorylceramides (GIPCs), which have a ceramide core linked to a glycan headgroup of varying structures, are the major sphingolipids in the plant plasma membrane. Recently, we identified the major biosynthetic genes for GIPC glycosylation in Arabidopsis (Arabidopsis thaliana) and demonstrated that the glycan headgroup is essential for plant viability. However, the function of GIPCs and the significance of their structural variation are poorly understood. Here, we characterized the Arabidopsis glycosyltransferase GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) and showed that it is responsible for the glycosylation of a subgroup of GIPCs found in seeds and pollen that contain GlcNAc and GlcN [collectively GlcN(Ac)]. In Arabidopsis gint1 plants, loss of the GlcN(Ac) GIPCs did not affect vegetative growth, although seed germination was less sensitive to abiotic stress than in wild-type plants. However, in rice, where GlcN(Ac) containing GIPCs are the major GIPC subgroup in vegetative tissue, loss of GINT1 was seedling lethal. Furthermore, we could produce, de novo, "rice-like" GlcN(Ac) GIPCs in Arabidopsis leaves, which allowed us to test the function of different sugars in the GIPC headgroup. This study describes a monocot GIPC biosynthetic enzyme and shows that its Arabidopsis homolog has the same biochemical function. We also identify a possible role for GIPCs in maintaining cell-cell adhesion.

Screening Arabidopsis thaliana mutants for low sensitivity to manganese identifies novel alleles of NRAMP1 and PGSIP6

Manganese (Mn) is an essential micronutrient; however, few genes required for growth under low-Mn conditions have been identified. In this study, we isolated Arabidopsis thaliana mutants sensitive to low-Mn conditions from ethyl methanesulfonate-mutagenized seeds. Among them, we identified the causal genes of two mutants. One mutant (35-34) exhibited a short root phenotype and low Mn concentration in the shoots. The other mutant (30-11) exhibited a small shoot phenotype with Mn concentrations similar to the control. Genetic mapping, allelism tests, and gene complementation tests identified the causal genes as At1g80830 (NRAMP1) for 35-34 and At5g18480 (PGSIP6) for 30-11. NRAMP1 was previously reported to be essential for Mn uptake under low-Mn conditions, thus validating our screening method. PGSIP6 encodes inositol phosphorylceramide glucuronosyltransferase, which is involved in glycosyl inositol phosphorylceramide sphingolipid glycosylation. PGSIP6-green fluorescent protein was localized to the Golgi apparatus, which is consistent with its function in the glycosylation of sphingolipids. Our screening identified a novel gene required for low-Mn tolerance, and we also provide new insights towards understanding the physiological function of PGSIP6.

Sphingolipid Distribution, Content and Gene Expression during Olive-Fruit Development and Ripening

Plant sphingolipids are involved in the building of the matrix of cell membranes and in signaling pathways of physiological processes and environmental responses. However, information regarding their role in fruit development and ripening, a plant-specific process, is unknown. The present study seeks to determine whether and, if so, how sphingolipids are involved in fleshy-fruit development and ripening in an oil-crop species such as olive (Olea europaea L. cv. Picual). Here, in the plasma-membranes of live protoplasts, we used fluorescence to examine various specific lipophilic stains in sphingolipid-enriched regions and investigated the composition of the sphingolipid long-chain bases (LCBs) as well as the expression patterns of sphingolipid-related genes, OeSPT, OeSPHK, OeACER, and OeGlcCerase, during olive-fruit development and ripening. The results demonstrate increased sphingolipid content and vesicle trafficking in olive-fruit protoplasts at the onset of ripening. Moreover, the concentration of LCB [t18:1(8Z), t18:1 (8E), t18:0, d18:2 (4E/8Z), d18:2 (4E/8E), d18:1(4E), and 1,4-anhydro-t18:1(8E)] increases during fruit development to reach a maximum at the onset of ripening, although these molecular species decreased during fruit ripening. On the other hand, OeSPT, OeSPHK, and OeGlcCerase were expressed differentially during fruit development and ripening, whereas OeACER gene expression was detected only at the fully ripe stage. The results provide novel data about sphingolipid distribution, content, and biosynthesis/turnover gene transcripts during fleshy-fruit ripening, indicating that all are highly regulated in a developmental manner.

A Plastid-Localized Pentatricopeptide Repeat Protein is Required for Both Pollen Development and Plant Growth in Rice

Several mitochondrial-targeted pentatricopeptide repeat (PPR) proteins involved in pollen development have been reported to be fertility restorer (Rf) proteins. However, the roles of plastid-localized PPR proteins in plant male reproduction are poorly defined. Here, we described a plastid-localized PPR-SMR protein, OsPPR676, which is required for plant growth and pollen development in rice. In this study, OsPPR676 was confirmed to be an interacted protein with Osj10gBTF3, β-subunit of nascent polypeptide-associated complex (β-NAC), by bimolecular fluorescence complementation assays, indicating that both proteins are probably involved in the same regulatory pathway of pollen development. Compared with other chloroplast-rich tissues, OsPPR676 was only weakly expressed in anther, but in the Mei and YM stages of pollen development, its expression was relatively strong in the tapetum. Disruption of OsPPR676 resulted in growth retardation of plants and partial sterility of pollens. Phenotypic analysis of different osppr676 mutant lines implied that the SMR domain was not essential for the function of OsPPR676. We further demonstrated that OsPPR676 is essential for production of plastid atpB subunit, and then plays crucial roles in biosynthesis of fatty acids, carbohydrates, and other organic matters via affecting activity of ATP synthase.