Abnormal glycosphingolipid mannosylation triggers salicylic acid-mediated responses in Arabidopsis

Genetic Editing of Tomato Golgi-Localized Nucleotide Sugar Transporter 1.1 Promotes Immunity Against Phytophthora infestans

BACKGROUND

Functional alleles of host plant susceptibility genes (S genes) can exacerbate the severity of diseases by enhancing pathogen compatibility. Genetic editing of the targeted host S genes has demonstrated remarkable efficacy in conferring broad-spectrum resistance across multiple crop species. We have previously identified a Golgi-localized Nucleotide Sugar Transporter 1 homolog (SlGONST1.1) in the host plant Solanum lycopersicum as a susceptibility gene towards late blight caused by Phytophthora infestans.

METHODS

In this study, we performed a detailed characterization of tissue-specific and P. infestans-inducible expression patterns of this gene, and the subcellular localization of its encoded protein product.

RESULTS

Similar to phenotypes of two reported Slgonst1.1 edited lines, two newly generated genetically edited lines of SlGONST1.1 demonstrated enhanced resistance against P. infestans without obvious growth and developmental abnormality. Phytohormonal quantifications and reactive oxygen species measurements showed that an Slgonst1.1 line had lower constitutive abscisic acid contents and depleted reactive oxygen species burst induced by pathogen-associated molecular pattern. Further comparative transcriptomic analyses revealed that the expression of defense-related genes is disproportionally up-regulated in the Slgonst1.1 line.

CONCLUSIONS

In summary, our findings confirmed SlGONST1.1 as a functional host susceptibility gene towards late blight and shed light on the potential molecular mechanism underlying its function.

Identification of INOSITOL PHOSPHORYLCERAMIDE SYNTHASE 2 (IPCS2) as a new rate-limiting component in Arabidopsis pathogen entry control

INOSITOL PHOSPHORYLCERAMIDE SYNTHASE 2 (IPCS2) is involved in the biosynthesis of complex sphingolipids at the trans-Golgi network (TGN). Here, we demonstrate a role of IPCS2 in penetration resistance against non-adapted powdery mildew fungi. A novel ipcs2W205* mutant was recovered from a forward genetic screen for Arabidopsis plants with enhanced epidermal cell entry success of the non-adapted barley fungus Blumeria graminis f. sp. hordei (Bgh). A yeast complementation assay and a sphingolipidomic approach revealed that the ipcs2W205* mutant represents a knock-out and lacks IPCS2-specific enzymatic activity. Further mutant analyses suggested that IPCS2-derived glycosyl inositol phosphorylceramides (GIPCs) are required for cell entry control of non-adapted fungal intruders. Confocal laser scanning microscopy (CLSM) studies indicated that upon pathogen attack, IPCS2 remains at the TGN to produce GIPCs, while focal accumulation of the defense cargo PENETRATION 3 (PEN3) at Bgh penetration sites was reduced in the ipcs2W205* mutant background. Thus, we propose a model in which sorting events at the TGN are facilitated by complex sphingolipids, regulating polar secretion of PEN3 to host-pathogen contact sites to terminate fungal ingress.

Time-course dual RNA-seq analyses and gene identification during early stages of plant-Phytophthora infestans interactions

Late blight caused by Phytophthora infestans is a major threat to global potato and tomato production. Sustainable management of late blight requires the development of resistant crop cultivars. This process can be facilitated by high-throughput identification of functional genes involved in late blight pathogenesis. In this study, we generated a high-quality transcriptomic time-course dataset focusing on the initial 24 h of contact between P. infestans and 3 solanaceous plant species, tobacco (Nicotiana benthamiana), tomato (Solanum lycopersicum), and potato (Solanum tuberosum). Our results demonstrate species-specific transcriptional regulation in early stages of the infection. Transient silencing of putative RIBOSE-5-PHOSPHATE ISOMERASE and HMG-CoA REDUCTASE genes in N. benthamiana lowered plant resistance against P. infestans. Furthermore, heterologous expression of a putative tomato Golgi-localized nucleosugar transporter-encoding gene exacerbated P. infestans infection of N. benthamiana. In comparison, bioassays using transgenic tomato lines showed that the quantitative disease resistance genes were required but insufficient for late blight resistance; genetic knock-out of the susceptibility gene enhanced resistance. The same RNA-seq dataset was exploited to examine the transcriptional landscape of P. infestans and revealed host-specific gene expression patterns in the pathogen. This temporal transcriptomic diversity, in combination with genomic distribution features, identified the P. infestans IPI-B family GLYCINE-RICH PROTEINs as putative virulence factors that promoted disease severity or induced plant tissue necrosis when transiently expressed in N. benthamiana. These functional genes underline the effectiveness of functional gene-mining through a time-course dual RNA-seq approach and provide insight into the molecular interactions between solanaceous plants and P. infestans.

Putative rhamnogalacturonan-II glycosyltransferase identified through callus gene editing which bypasses embryo lethality

Rhamnogalacturonan II (RG-II) is a structurally complex and conserved domain of the pectin present in the primary cell walls of vascular plants. Borate cross-linking of RG-II is required for plants to grow and develop normally. Mutations that alter RG-II structure also affect cross-linking and are lethal or severely impair growth. Thus, few genes involved in RG-II synthesis have been identified. Here, we developed a method to generate viable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants in callus tissue via CRISPR/Cas9-mediated gene editing. We combined this with a candidate gene approach to characterize the male gametophyte defective 2 (MGP2) gene that encodes a putative family GT29 glycosyltransferase. Plants homozygous for this mutation do not survive. We showed that in the callus mutant cell walls, RG-II does not cross-link normally because it lacks 3-deoxy-D-manno-octulosonic acid (Kdo) and thus cannot form the α-L-Rhap-(1→5)-α-D-kdop-(1→sidechain). We suggest that MGP2 encodes an inverting RG-II CMP-β-Kdo transferase (RCKT1). Our discovery provides further insight into the role of sidechains in RG-II dimerization. Our method also provides a viable strategy for further identifying proteins involved in the biosynthesis of RG-II.

Comparative genome-wide analysis of circular RNAs in Brassica napus L.: target-site versus non-target-site resistance to herbicide stress

Circular RNAs (circRNAs), a class of non-coding RNA molecules, are recognized for their unique functions; however, their responses to herbicide stress in Brassica napus remain unclear. In this study, the role of circRNAs in response to herbicide treatment was investigated in two rapeseed cultivars: MH33, which confers non-target-site resistance (NTSR), and EM28, which exhibits target-site resistance (TSR). The genome-wide circRNA profiles of herbicide-stressed and non-stressed seedlings were analyzed. The findings indicate that NTSR seedlings exhibited a greater abundance of circRNAs, shorter lengths of circRNAs and their parent genes, and more diverse functions of parent genes compared with TSR seedlings. Compared to normal-growth plants, the herbicide-stressed group exhibited similar trends in the number of circRNAs, functions of parent genes, and differentially expressed circRNAs as observed in NTSR seedlings. In addition, a greater number of circRNAs that function as competing microRNA (miRNA) sponges were identified in the herbicide stress and NTSR groups compared to the normal-growth and TSR groups, respectively. The differentially expressed circRNAs were validated by qPCR. The differntially expressed circRNA-miRNA networks were predicted, and the mRNAs targeted by these miRNAs were annotated. Our results suggest that circRNAs play a crucial role in responding to herbicide stress, exhibiting distinct responses between NTSR and TSR in rapeseed. These findings offer valuable insights into the mechanisms underlying herbicide resistance in rapeseed.

The ascorbate biosynthesis pathway in plants is known, but there is a way to go with understanding control and functions

Ascorbate (vitamin C) is one of the most abundant primary metabolites in plants. Its complex chemistry enables it to function as an antioxidant, as a free radical scavenger, and as a reductant for iron and copper. Ascorbate biosynthesis occurs via the mannose/l-galactose pathway in green plants, and the evidence for this pathway being the major route is reviewed. Ascorbate accumulation is leaves is responsive to light, reflecting various roles in photoprotection. GDP-l-galactose phosphorylase (GGP) is the first dedicated step in the pathway and is important in controlling ascorbate synthesis. Its expression is determined by a combination of transcription and translation. Translation is controlled by an upstream open reading frame (uORF) which blocks translation of the main GGP-coding sequence, possibly in an ascorbate-dependent manner. GGP associates with a PAS-LOV protein, inhibiting its activity, and dissociation is induced by blue light. While low ascorbate mutants are susceptible to oxidative stress, they grow nearly normally. In contrast, mutants lacking ascorbate do not grow unless rescued by supplementation. Further research should investigate possible basal functions of ascorbate in severely deficient plants involving prevention of iron overoxidation in 2-oxoglutarate-dependent dioxygenases and iron mobilization during seed development and germination.

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.

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.

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.

Two nucleotide sugar transporters are important for cell wall integrity and full virulence of Magnaporthe oryzae

Cell wall polysaccharides play key roles in fungal development, virulence, and resistance to the plant immune system, and are synthesized from many nucleotide sugars in the endoplasmic reticulum (ER)-Golgi secretory system. Nucleotide sugar transporters (NSTs) are responsible for transporting cytosolic-derived nucleotide sugars to the ER lumen for processing, but their roles in plant-pathogenic fungi remain to be revealed. Here, we identified two important NSTs, NST1 and NST2, in the rice blast fungus Magnaporthe oryzae. Both NSTs were localized in the ER, which was consistent with a function in transporting nucleotide sugar for processing in the ER. Sugar transport property analysis suggested that NST1 is involved in transportation of mannose and glucose, while NST2 is only responsible for mannose transportation. Accordingly, deletion of NSTs resulted in a significant decrease in corresponding soluble saccharides abundance and defect in sugar utilization. Moreover, both NSTs played important roles in cell wall integrity, were involved in asexual development, and were required for full virulence. The NST mutants exhibited decreasing external glycoproteins and exposure of inner chitin, which resulted in activation of the host defence response. Altogether, our results revealed that two sugar transporters are required for fungal cell wall polysaccharides accumulation and full virulence of M. oryzae.

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.

Modern mannan: a hemicellulose's journey

Hemicellulosic polysaccharides built of β-1,4-linked mannose units have been found throughout the plant kingdom and have numerous industrial applications. Here, I review recent advances in the biosynthesis and modification of plant β-mannans. These matrix polymers can associate with cellulose bundles to impact the mechanical properties of plant fibers or biocomposites. In certain algae, mannan microfibrils even replace cellulose as the dominant structural component of the cell wall. Conversely, patterned galactoglucomannan found in Arabidopsis thaliana seed mucilage significantly modulates cell wall architecture and abiotic stress tolerance despite its relatively low content. I also discuss the subcellular requirements for β-mannan biosynthesis, the increasing number of carbohydrate-active enzymes involved in this process, and the players that continue to be puzzling. I discuss how cellulose synthase-like enzymes elongate (gluco)mannans in orthogonal hosts and highlight the discoveries of plant enzymes that add specific galactosyl or acetyl decorations. Hydrolytic enzymes such as endo-β-1,4-mannanases have recently been involved in a wide range of biological contexts including seed germination, wood formation, heavy metal tolerance, and defense responses. Synthetic biology tools now provide faster tracks to modulate the increasingly-relevant mannan structures for improved plant traits and bioproducts.

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

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

Jasmonates modulate sphingolipid metabolism and accelerate cell death in the ceramide kinase mutant acd5

Sphingolipids are structural components of the lipid bilayer that acts as signaling molecules in many cellular processes, including cell death. Ceramides, key intermediates in sphingolipid metabolism, are phosphorylated by the ceramide kinase ACCELERATED CELL DEATH5 (ACD5). The loss of ACD5 function leads to ceramide accumulation and spontaneous cell death. Here, we report that the jasmonate (JA) pathway is activated in the Arabidopsis (Arabidopsis thaliana) acd5 mutant and that methyl JA treatment accelerates ceramide accumulation and cell death in acd5. Moreover, the double mutants of acd5 with jasmonate resistant1-1 and coronatine insensitive1-2 exhibited delayed cell death, suggesting that the JA pathway is involved in acd5-mediated cell death. Quantitative sphingolipid profiling of plants treated with methyl JA indicated that JAs influence sphingolipid metabolism by increasing the levels of ceramides and hydroxyceramides, but this pathway is dramatically attenuated by mutations affecting JA pathway proteins. Furthermore, we showed that JAs regulate the expression of genes encoding enzymes in ceramide metabolism. Together, our findings show that JAs accelerate cell death in acd5 mutants, possibly by modulating sphingolipid metabolism and increasing ceramide levels.

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.

The immune components ENHANCED DISEASE SUSCEPTIBILITY 1 and PHYTOALEXIN DEFICIENT 4 are required for cell death caused by overaccumulation of ceramides in Arabidopsis

Sphingolipids have key functions in plant membrane structure and signaling. Perturbations of plant sphingolipid metabolism often induce cell death and salicylic acid (SA) accumulation; SA accumulation, in turn, promotes sphingolipid metabolism and further cell death. However, the underlying molecular mechanisms remain unclear. Here, we show that the Arabidopsis thaliana lipase-like protein ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) and its partner PHYTOALEXIN DEFICIENT 4 (PAD4) participate in sphingolipid metabolism and associated cell death. The accelerated cell death 5 (acd5) mutants accumulate ceramides due to a defect in ceramide kinase and show spontaneous cell death. Loss of function of EDS1, PAD4 or SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2) in the acd5 background suppressed the acd5 cell death phenotype and prevented ceramide accumulation. Treatment with the SA analogue benzothiadiazole partially restored sphingolipid accumulation in the acd5 pad4 and acd5 eds1 double mutants, showing that the inhibitory effect of the pad4-1 and eds1-2 mutations on acd5-conferred sphingolipid accumulation partly depends on SA. Moreover, the pad4-1 and eds1-2 mutations substantially rescued the susceptibility of the acd5 mutant to Botrytis cinerea. Consistent with this, B. cinerea-induced ceramide accumulation requires PAD4 or EDS1. Finally, examination of plants overexpressing the ceramide synthase gene LAG1 HOMOLOGUE2 suggested that EDS1, PAD4 and SA are involved in long-chain ceramide metabolism and ceramide-associated cell death. Collectively, our observations reveal that EDS1 and PAD4 mediate ceramide (especially long-chain ceramide) metabolism and associated cell death, by SA-dependent and SA-independent pathways.

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.

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

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

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.

Dynamic membranes: the multiple roles of P4 and P5 ATPases

The lipid bilayer of biological membranes has a complex composition, including high chemical heterogeneity, the presence of nanodomains of specific lipids, and asymmetry with respect to lipid composition between the two membrane leaflets. In membrane trafficking, membrane vesicles constantly bud off from one membrane compartment and fuse with another, and both budding and fusion events have been proposed to require membrane lipid asymmetry. One mechanism for generating asymmetry in lipid bilayers involves the action of the P4 ATPase family of lipid flippases; these are biological pumps that use ATP as an energy source to flip lipids from one leaflet to the other. The model plant Arabidopsis (Arabidopsis thaliana) contains 12 P4 ATPases (AMINOPHOSPHOLIPID ATPASE1-12; ALA1-12), many of which are functionally redundant. Studies of P4 ATPase mutants have confirmed the essential physiological functions of these pumps and pleiotropic mutant phenotypes have been observed, as expected when genes required for basal cellular functions are disrupted. For instance, phenotypes associated with ala3 (dwarfism, pollen defects, sensitivity to pathogens and cold, and reduced polar cell growth) can be related to membrane trafficking problems. P5 ATPases are evolutionarily related to P4 ATPases, and may be the counterpart of P4 ATPases in the endoplasmic reticulum. The absence of P4 and P5 ATPases from prokaryotes and their ubiquitous presence in eukaryotes make these biological pumps a defining feature of eukaryotic cells. Here, we review recent advances in the field of plant P4 and P5 ATPases.

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.

Biosynthesis and Transport of Nucleotide Sugars for Plant Hemicellulose

Hemicellulose is entangled with cellulose through hydrogen bonds and meanwhile acts as a bridge for the deposition of lignin monomer in the secondary wall. Therefore, hemicellulose plays a vital role in the utilization of cell wall biomass. Many advances in hemicellulose research have recently been made, and a large number of genes and their functions have been identified and verified. However, due to the diversity and complexity of hemicellulose, the biosynthesis and regulatory mechanisms are yet unknown. In this review, we summarized the types of plant hemicellulose, hemicellulose-specific nucleotide sugar substrates, key transporters, and biosynthesis pathways. This review will contribute to a better understanding of substrate-level regulation of hemicellulose synthesis.

Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots

BACKGROUND

The composition of biomass determines its suitability for different applications within a biorefinery system. The proportion of the major biomass fractions (sugar, cellulose, hemicellulose and lignin) may vary in different sugarcane genotypes and growth environments and different parts of the plant. This study investigated the composition of mature and immature internodes, roots and mature leaves of sugarcane.

RESULTS

Internodes were found to have a significantly larger alcohol-soluble component than leaves and roots. The primary difference between the immature and mature internodes was the ratio of soluble sugars. In mature tissues, sucrose content was significantly higher, whereas in immature internodal tissues there was lower sucrose and heightened concentrations of reducing sugars. Carbon (C) partitioning in leaf tissues was characterised by low levels of soluble components and high "other" and cell wall fractions. Root tissue had low ratios of soluble fractions relative to their cell wall contents, indicating a lack of storage of soluble carbon. There was no significant difference in the ratio of the major cell wall fractions between the major organ types. Characterisation of individual non-cellulosic monomers indicated leaf and root tissues had significantly higher arabinose and galactose fractions. Significantly larger proportions of syringyl lignin compounds and the hydroxycinnamic compound, p-coumaric acid were observed in mature internodal tissues compared to the other tissue types. Tissue-specific differences in composition were shown to greatly affect the recalcitrance of the cell wall to enzymatic saccharification.

CONCLUSIONS

Overall, this study displayed clear evidence of the differential partitioning of C throughout the sugarcane plant in specific organs. These organ-specific differences have major implications in their utility as a bioproduct feedstock. For example, the inclusion of trash (leaves) with the culms (internodes) may alter processing efficiency.

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.

Transcriptome profiling of raspberry (Rubus idaeus Var. Amira) in response to infection by tomato ringspot virus (ToRSV)

Raspberry (Rubus sp.) is a berries fruit with an ongoing agricultural and commercial interest due to its high contents of flavonoids and nutrients beneficial for human health. The growing demand for raspberries is facing great challenges associated mainly with the dispersal of diseases, which produces a decrease in productivity and fruit quality. A broad range of genomic resources is available for other Rosaceae species; however, genomic resources for species of the Rubus genus are still limited. Here, we characterize the transcriptome of the Rubus idaeus (Var. Amira) in order to 1) provide clues in the transcriptional changes of R. idaeus against tomato ringspot virus (ToRSV); and 2) generate genomic resources for this economically important species. We generate more than 200 million sequencing reads from two mRNA samples of raspberry, infected and not infected by ToRSV, using Illumina technology. After de novo assembly, we obtained 68,853 predicted protein-coding sequences of which 71.3% and 61.3% were annotated using Gene Ontology and Pfam databases, respectively. Moreover, we find 2,340 genes with differential expression between raspberries infected and not infected by ToRSV. Analysis of these genes shows functional enrichments of the oxidation-reduction process, cell wall biogenesis, terpene synthase activity, and lyase activity. These genes could be involved in the raspberry immune response through the interaction of different metabolic pathways; however, this statement needs further investigations. Up-regulation of genes encoding terpene synthases, multicopper oxidases, laccases, and beta-glucosidases might suggest that these enzymes appear to be the predominant transcriptome immune response of R. idaeus against ToRSV. Furthermore, we identify thousands of molecular markers (i.e., SSRs and SNPs), increasing considerably the genomic resources currently available for raspberries. This study is the first report on investigating the transcriptional changes of R. idaeus against ToRSV.

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.

Glycosyltransferase-Like RSE1 Negatively Regulates Leaf Senescence Through Salicylic Acid Signaling in Arabidopsis

Leaf senescence is a developmental process designed for nutrient recycling and relocation to maximize growth competence and reproductive capacity of plants. Thus, plants integrate developmental and environmental signals to precisely control senescence. To genetically dissect the complex regulatory mechanism underlying leaf senescence, we identified an early leaf senescence mutant, rse1. RSE1 encodes a putative glycosyltransferase. Loss-of-function mutations in RSE1 resulted in precocious leaf yellowing and up-regulation of senescence marker genes, indicating enhanced leaf senescence. Transcriptome analysis revealed that salicylic acid (SA) and defense signaling cascades were up-regulated in rse1 prior to the onset of leaf senescence. We found that SA accumulation was significantly increased in rse1. The rse1 phenotypes are dependent on SA-INDUCTION DEFICIENT 2 (SID2), supporting a role of SA in accelerated leaf senescence in rse1. Furthermore, RSE1 protein was localized to the cell wall, implying a possible link between the cell wall and RSE1 function. Together, we show that RSE1 negatively modulates leaf senescence through an SID2-dependent SA signaling pathway.

The Lipid Flippases ALA4 and ALA5 Play Critical Roles in Cell Expansion and Plant Growth

Aminophospholipid ATPases (ALAs) are lipid flippases involved in transporting specific lipids across membrane bilayers. Arabidopsis (Arabidopsis thaliana) contains 12 ALAs in five phylogenetic clusters, including four in cluster 3 (ALA4-ALA7). ALA4/5 and ALA6/7, are expressed primarily in vegetative tissues and pollen, respectively. Previously, a double knockout of ALA6/7 was shown to result in pollen fertility defects. Here we show that a double knockout of ALA4/5 results in dwarfism, characterized by reduced growth in rosettes (6.5-fold), roots (4.3-fold), bolts (4.5-fold), and hypocotyls (2-fold). Reduced cell size was observed for multiple vegetative cell types, suggesting a role for ALA4/5 in cellular expansion. Members of the third ALA cluster are at least partially interchangeable, as transgenes expressing ALA6 in vegetative tissues partially rescued ala4/5 mutant phenotypes, and expression of ALA4 transgenes in pollen fully rescued ala6/7 mutant fertility defects. ALA4-GFP displayed plasma membrane and endomembrane localization patterns when imaged in both guard cells and pollen. Lipid profiling revealed ala4/5 rosettes had perturbations in glycerolipid and sphingolipid content. Assays in yeast revealed that ALA5 can flip a variety of glycerolipids and the sphingolipid sphingomyelin across membranes. These results support a model whereby the flippase activity of ALA4 and ALA5 impacts the homeostasis of both glycerolipids and sphingolipids and is important for cellular expansion during vegetative growth.

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.

Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading

During phloem unloading, multiple cell-to-cell transport events move organic substances to the root meristem. Although the primary unloading event from the sieve elements to the phloem pole pericycle has been characterized to some extent, little is known about post-sieve element unloading. Here, we report a novel gene, PHLOEM UNLOADING MODULATOR (PLM), in the absence of which plasmodesmata-mediated symplastic transport through the phloem pole pericycle-endodermis interface is specifically enhanced. Increased unloading is attributable to a defect in the formation of the endoplasmic reticulum-plasma membrane tethers during plasmodesmal morphogenesis, resulting in the majority of pores lacking a visible cytoplasmic sleeve. PLM encodes a putative enzyme required for the biosynthesis of sphingolipids with very-long-chain fatty acid. Taken together, our results indicate that post-sieve element unloading involves sphingolipid metabolism, which affects plasmodesmal ultrastructure. They also raise the question of how and why plasmodesmata with no cytoplasmic sleeve facilitate molecular trafficking.

Characterization of a GDP-Fucose Transporter and a Fucosyltransferase Involved in the Fucosylation of Glycoproteins in the Diatom Phaeodactylum tricornutum

Although Phaeodactylum tricornutum is gaining importance in plant molecular farming for the production of high-value molecules such as monoclonal antibodies, little is currently known about key cell metabolism occurring in this diatom such as protein glycosylation. For example, incorporation of fucose residues in the glycans N-linked to protein in P. tricornutum is questionable. Indeed, such epitope has previously been found on N-glycans of endogenous glycoproteins in P. tricornutum. Meanwhile, the potential immunogenicity of the α(1,3)-fucose epitope present on plant-derived biopharmaceuticals is still a matter of debate. In this paper, we have studied molecular actors potentially involved in the fucosylation of the glycoproteins in P. tricornutum. Based on sequence similarities, we have identified a putative P. tricornutum GDP-L-fucose transporter and three fucosyltransferase (FuT) candidates. The putative P. tricornutum GDP-L-fucose transporter coding sequence was expressed in the Chinese Hamster Ovary (CHO)-gmt5 mutant lacking its endogenous GDP-L-fucose transporter activity. We show that the P. tricornutum transporter is able to rescue the fucosylation of proteins in this CHO-gmt5 mutant cell line, thus demonstrating the functional activity of the diatom transporter and its appropriate Golgi localization. In addition, we overexpressed one of the three FuT candidates, namely the FuT54599, in P. tricornutum and investigated its localization within Golgi stacks of the diatom. Our findings show that overexpression of the FuT54599 leads to a significant increase of the α(1,3)-fucosylation of the diatom endogenous glycoproteins.

Xylan in the Middle: Understanding Xylan Biosynthesis and Its Metabolic Dependencies Toward Improving Wood Fiber for Industrial Processing

Lignocellulosic biomass, encompassing cellulose, lignin and hemicellulose in plant secondary cell walls (SCWs), is the most abundant source of renewable materials on earth. Currently, fast-growing woody dicots such as Eucalyptus and Populus trees are major lignocellulosic (wood fiber) feedstocks for bioproducts such as pulp, paper, cellulose, textiles, bioplastics and other biomaterials. Processing wood for these products entails separating the biomass into its three main components as efficiently as possible without compromising yield. Glucuronoxylan (xylan), the main hemicellulose present in the SCWs of hardwood trees carries chemical modifications that are associated with SCW composition and ultrastructure, and affect the recalcitrance of woody biomass to industrial processing. In this review we highlight the importance of xylan properties for industrial wood fiber processing and how gaining a greater understanding of xylan biosynthesis, specifically xylan modification, could yield novel biotechnology approaches to reduce recalcitrance or introduce novel processing traits. Altering xylan modification patterns has recently become a focus of plant SCW studies due to early findings that altered modification patterns can yield beneficial biomass processing traits. Additionally, it has been noted that plants with altered xylan composition display metabolic differences linked to changes in precursor usage. We explore the possibility of using systems biology and systems genetics approaches to gain insight into the coordination of SCW formation with other interdependent biological processes. Acetyl-CoA, s-adenosylmethionine and nucleotide sugars are precursors needed for xylan modification, however, the pathways which produce metabolic pools during different stages of fiber cell wall formation still have to be identified and their co-regulation during SCW formation elucidated. The crucial dependence on precursor metabolism provides an opportunity to alter xylan modification patterns through metabolic engineering of one or more of these interdependent pathways. The complexity of xylan biosynthesis and modification is currently a stumbling point, but it may provide new avenues for woody biomass engineering that are not possible for other biopolymers.

Evolution of the Cell Wall Gene Families of Grasses

Grasses and related commelinid monocot species synthesize cell walls distinct in composition from other angiosperm species. With few exceptions, the genomes of all angiosperms contain the genes that encode the enzymes for synthesis of all cell-wall polysaccharide, phenylpropanoid, and protein constituents known in vascular plants. RNA-seq analysis of transcripts expressed during development of the upper and lower internodes of maize (Zea mays) stem captured the expression of cell-wall-related genes associated with primary or secondary wall formation. High levels of transcript abundances were not confined to genes associated with the distinct walls of grasses but also of those associated with xyloglucan and pectin synthesis. Combined with proteomics data to confirm that expressed genes are translated, we propose that the distinctive cell-wall composition of grasses results from sorting downstream from their sites of synthesis in the Golgi apparatus and hydrolysis of the uncharacteristic polysaccharides and not from differential expression of synthases of grass-specific polysaccharides.

A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction

BACKGROUND

Single guide RNA (sgRNA) selection is important for the efficiency of CRISPR/Cas9-mediated genome editing. However, in plants, the rules governing selection are not well established.

RESULTS

We developed a facile transient assay to screen sgRNA efficiency. We then used it to test top-performing bioinformatically predicted sgRNAs for two different Arabidopsis genes. In our assay, these sgRNAs had vastly different editing efficiencies, and these efficiencies were replicated in stably transformed Arabidopsis lines. One of the genes, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT), is an essential gene, required for lignin biosynthesis. Previously, HCT function has been studied using gene silencing. Here, to avoid the negative growth effects that are due to the loss of HCT activity in xylem vessels, we used a fiber-specific promoter to drive CAS9 expression. Two independent transgenic lines showed the expected lignin decrease. Successful editing was confirmed via the observation of mutations at the HCT target loci, as well as an approximately 90% decrease in HCT activity. Histochemical analysis and a normal growth phenotype support the fiber-specific knockout of HCT. For the targeting of the second gene, Golgi-localized nucleotide sugar transporter2 (GONST2), a highly efficient sgRNA drastically increased the rate of germline editing in T1 generation.

CONCLUSIONS

This screening method is widely applicable, and the selection and use of efficient sgRNAs will accelerate the process of expanding germplasm for both molecular breeding and research. In addition, this, to the best of our knowledge, is the first application of constrained genome editing to obtain chimeric plants of essential genes, thereby providing a dominant method to avoid lethal growth phenotypes.

Suppression of Arabidopsis GGLT1 affects growth by reducing the L-galactose content and borate cross-linking of rhamnogalacturonan-II

Boron is a micronutrient that is required for the normal growth and development of vascular plants, but its precise functions remain a subject of debate. One established role for boron is in the cell wall where it forms a diester cross-link between two monomers of the low-abundance pectic polysaccharide rhamnogalacturonan-II (RG-II). The inability of RG-II to properly assemble into a dimer results in the formation of cell walls with abnormal biochemical and biomechanical properties and has a severe impact on plant productivity. Here we describe the effects on RG-II structure and cross-linking and on the growth of plants in which the expression of a GDP-sugar transporter (GONST3/GGLT1) has been reduced. In the GGLT1-silenced plants the amount of L-galactose in side-chain A of RG-II is reduced by up to 50%. This leads to a reduction in the extent of RG-II cross-linking in the cell walls as well as a reduction in the stability of the dimer in the presence of calcium chelators. The silenced plants have a dwarf phenotype, which is rescued by growth in the presence of increased amounts of boric acid. Similar to the mur1 mutant, which also disrupts RG-II cross-linking, GGLT1-silenced plants display a loss of cell wall integrity under salt stress. We conclude that GGLT1 is probably the primary Golgi GDP-L-galactose transporter, and provides GDP-L-galactose for RG-II biosynthesis. We propose that the L-galactose residue is critical for RG-II dimerization and for the stability of the borate cross-link.

The GDP-mannose transporter gene (DoGMT) from Dendrobium officinale is critical for mannan biosynthesis in plant growth and development

Dendrobium officinale is a precious traditional Chinese medicinal herb because it is abundant in mannose-containing polysaccharides (MCPs). GDP-mannose transporter (GMT), which translocates GDP-mannose into the Golgi lumen, is indispensable for the biosynthesis of MCPs. In this study, we found that the dominant polysaccharides in D. officinale were MCPs in a range of varieties and different physiological phases. After a positive correlation between the accumulation of mannose and the transcript levels of candidate GMT genes was found, three GMT genes (DoGMT1-3) were identified in D. officinale. DoGMT1, DoGMT2 and DoGMT3 exhibited the highest transcript level in stem that an organ for MCPs storage. All three DoGMT proteins were targeted to Golgi apparatus, and had a GDP binding domain (GXL/VNK) that was homologous to a specially characterized GMT protein GONST1 in Arabidopsis thaliana. Moreover, DoGMT1, DoGMT2 and DoGMT3 complemented a GDP-mannose transport-defective yeast mutant (vrg4-2), meanwhile they also demonstrated a higher GDP-mannose uptake activity. Therefore, we conclude that DoGMT1, DoGMT2 and DoGMT3 are able to transport GDP-mannose while the expression patterns of these genes correspond to the accumulation of MCPs in D. officinale. These findings support the importance of GMT genes from D. officinale in the biosynthesis of MCPs.

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.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014

This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.

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.

Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins

Necrosis and ethylene-inducing peptide 1-like (NLP) proteins constitute a superfamily of proteins produced by plant pathogenic bacteria, fungi, and oomycetes. Many NLPs are cytotoxins that facilitate microbial infection of eudicot, but not of monocot plants. Here, we report glycosylinositol phosphorylceramide (GIPC) sphingolipids as NLP toxin receptors. Plant mutants with altered GIPC composition were more resistant to NLP toxins. Binding studies and x-ray crystallography showed that NLPs form complexes with terminal monomeric hexose moieties of GIPCs that result in conformational changes within the toxin. Insensitivity to NLP cytolysins of monocot plants may be explained by the length of the GIPC head group and the architecture of the NLP sugar-binding site. We unveil early steps in NLP cytolysin action that determine plant clade-specific toxin selectivity.

Distribution of glycosylinositol phosphoceramide-specific phospholipase D activity in plants

Previously, we detected an unknown sphingophospholipid in cabbage leaves and identified it as phytoceramide-1-phosphate (PC1P). We also found an enzyme activity that produces PC1P by glycosylinositol phosphoceramide (GIPC)-specific hydrolysis in cabbage leaves. To characterize the GIPC-specific phospholipase D (GIPC-PLD) activity, we investigated distributions of GIPC-PLD activity in 25 tissues of 10 plants. In most plants, the GIPC-PLD activity was the highest in roots. Young leaves of cabbage and Welsh onion had higher activities than corresponding aged outer leaves. The GIPC-PLD activities in leaves, stems and roots of mung bean were higher in the sprouting stage than in more mature stages. We also examined the distribution of substrate GIPC and product PC1P and found that GIPC was ubiquitously distributed at 50–280 nmol/g (wet wt) in tissues of plants, whereas PC1P was detectable (3–60 nmol/g wet wt.) only in tissues showing considerable GIPC-PLD activity. These results suggest a possibility that GIPC-PLD activity is involved in plant growth.

CNGC2 Is a Ca2+ Influx Channel That Prevents Accumulation of Apoplastic Ca2+ in the Leaf

Ca²⁺ is absorbed by roots and transported upward through the xylem to the apoplastic space of the leaf, after which it is deposited into the leaf cell. In Arabidopsis (Arabidopsis thaliana), the tonoplast-localized Ca²⁺/H⁺ transporters CATION EXCHANGER1 (CAX1) and CAX3 sequester Ca²⁺ from the cytosol into the vacuole, but it is not known what transporter mediates the initial Ca²⁺ influx from the apoplast to the cytosol. Here, we report that Arabidopsis CYCLIC NUCLEOTIDE-GATED CHANNEL2 (CNGC2) encodes a protein with Ca²⁺ influx channel activity and is expressed in the leaf areas surrounding the free endings of minor veins, which is the primary site for Ca²⁺ unloading from the vasculature and influx into leaf cells. Under hydroponic growth conditions, with 0.1 mm Ca²⁺, both Arabidopsis cngc2 and cax1cax3 loss-of-function mutants grew normally. Increasing the Ca²⁺ concentration to 10 mm induced H₂O₂ accumulation, cell death, and leaf senescence and partially suppressed the hypersensitive response to avirulent pathogens in the mutants but not in the wild type. In vivo apoplastic Ca²⁺ overaccumulation was found in the leaves of cngc2 and cax1cax3 but not the wild type under the 10 mm Ca²⁺ condition, as monitored by Oregon Green BAPTA 488 5N, a low-affinity and membrane-impermeable Ca²⁺ probe. Our results indicate that CNGC2 likely has no direct roles in leaf development or the hypersensitive response but, instead, that CNGC2 could mediate Ca²⁺ influx into leaf cells. Finally, the in vivo extracellular Ca²⁺ imaging method developed in this study provides a new tool for investigating Ca²⁺ dynamics in plant cells.

Glycosylation of inositol phosphorylceramide sphingolipids is required for normal growth and reproduction in Arabidopsis

Sphingolipids are a major component of plant plasma membranes and endomembranes, and mediate a diverse range of biological processes. Study of the highly glycosylated glycosyl inositol phosphorylceramide (GIPC) sphingolipids has been slow as a result of challenges associated with the extractability of GIPCs, and their functions in the plant remain poorly characterized. We recently discovered an Arabidopsis GIPC glucuronosyltransferase, INOSITOL PHOSPHORYLCERAMIDE GLUCURONOSYLTRANSFERASE 1 (IPUT1), which is the first enzyme in the GIPC glycosylation pathway. Plants homozygous for the iput1 loss-of-function mutation were unobtainable, and so the developmental effects of reduced GIPC glucuronosylation could not be analyzed in planta. Using a pollen-specific rescue construct, we have here isolated homozygous iput1 mutants. The iput1 mutants show severe dwarfism, compromised pollen tube guidance, and constitutive activation of salicyclic acid-mediated defense pathways. The mutants also possess reduced GIPCs, increased ceramides, and an increased incorporation of short-chain fatty acids and dihydroxylated bases into inositol phosphorylceramides and GIPCs. The assignment of a direct role for GIPC glycan head groups in the impaired processes in iput1 mutants is complicated by the vast compensatory changes in the sphingolipidome; however, our results reveal that the glycosylation steps of GIPC biosynthesis are important regulated components of sphingolipid metabolism. This study corroborates previously suggested roles for GIPC glycans in plant growth and defense, suggests important roles for them in reproduction and demonstrates that the entire sphingolipidome is sensitive to their status.

Knocking Down the Expression of GMPase Gene OsVTC1-1 Decreases Salt Tolerance of Rice at Seedling and Reproductive Stages

Salinity is a severe environmental stress that greatly impairs production of crops worldwide. Previous studies have shown that GMPase plays an important role in tolerance of plants to salt stress at vegetative stage. However, the function of GMPase in plant responses to salt stress at reproductive stage remains unclear. Studies have shown that heterologous expression of rice GMPase OsVTC1-1 enhanced salt tolerance of tobacco seedlings, but the native role of OsVTC1-1 in salt stress tolerance of rice is unknown. To illustrate the native function of GMPase in response of rice to salt stress, OsVTC1-1 expression was suppressed using RNAi-mediated gene silencing. Suppressing OsVTC1-1 expression obviously decreased salt tolerance of rice varieties at vegetative stage. Intriguingly, grain yield of OsVTC1-1 RNAi rice was also significantly reduced under salt stress, indicating that OsVTC1-1 plays an important role in salt tolerance of rice at both seedling and reproductive stages. OsVTC1-1 RNAi rice accumulated more ROS under salt stress, and supplying exogenous ascorbic acid restored salt tolerance of OsVTC1-1 RNAi lines, suggesting that OsVTC1-1 is involved in salt tolerance of rice through the biosynthesis regulation of ascorbic acid. Altogether, results of present study showed that rice GMPase gene OsVTC1-1 plays a critical role in salt tolerance of rice at both vegetative and reproductive stages through AsA scavenging of excess ROS.

Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis

Glycosylinositol phosphorylceramides (GIPCs) are a class of glycosylated sphingolipids found in plants, fungi, and protozoa. These lipids are abundant in the plant plasma membrane, forming ∼25% of total plasma membrane lipids. Little is known about the function of the glycosylated headgroup, but two recent studies have indicated that they play a key role in plant signaling and defense. Here, we show that a member of glycosyltransferase family 64, previously named ECTOPICALLY PARTING CELLS1, is likely a Golgi-localized GIPC-specific mannosyl-transferase, which we renamed GIPC MANNOSYL-TRANSFERASE1 (GMT1). Sphingolipid analysis revealed that the Arabidopsis thaliana gmt1 mutant almost completely lacks mannose-carrying GIPCs. Heterologous expression of GMT1 in Saccharomyces cerevisiae and tobacco (Nicotiana tabacum) cv Bright Yellow 2 resulted in the production of non-native mannosylated GIPCs. gmt1 displays a severe dwarfed phenotype and a constitutive hypersensitive response characterized by elevated salicylic acid and hydrogen peroxide levels, similar to that we previously reported for the Golgi-localized, GIPC-specific, GDP-Man transporter GONST1 (Mortimer et al., 2013). Unexpectedly, we show that gmt1 cell walls have a reduction in cellulose content, although other matrix polysaccharides are unchanged.