Genome-wide association study of drought tolerance traits in sugar beet germplasms at the seedling stage

Introduction: Sugar beets are an important crop for global sugar production. Intense drought and the increasing lack of water resources pose a great threat to sugar beet cultivation. It is a priority to investigate favourable germplasms and functional genes to improve the breeding of drought tolerant plants. Methods: Thus, in this study, 328 sugar beet germplasms were used in a genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers and candidate genes associated with drought tolerance. Results: The results showed that under drought stress (9% PEG-6000), there were 11 significantly associated loci on chromosomes 2, 3, 5, 7, and 9 from the 108946 SNPs filtered using a mixed linear model (MLM). Genome-wide association analysis combined with qRT-PCR identified 13 genes that were significantly differentially expressed in drought-tolerant extreme materials. Discussion: These candidate genes mainly exhibited functions such as regulating sugar metabolism, maintaining internal environmental stability and participating in photosystem repair. This study provides valuable information for exploring the molecular mechanisms of drought tolerance and improvement in sugar beet.

Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism

Plants typically orient their organs with respect to the Earth's gravity field by a dynamic process called gravitropism. To discover conserved genetic elements affecting seedling root gravitropism, we measured the process in a set of Zea mays (maize) recombinant inbred lines with machine vision and compared the results with those obtained in a similar study of Arabidopsis thaliana. Each of the several quantitative trait loci that we mapped in both species spanned many hundreds of genes, too many to test individually for causality. We reasoned that orthologous genes may be responsible for natural variation in monocot and dicot root gravitropism. If so, pairs of orthologous genes affecting gravitropism may be present within the maize and Arabidopsis QTL intervals. A reciprocal comparison of sequences within the QTL intervals identified seven pairs of such one-to-one orthologs. Analysis of knockout mutants demonstrated a role in gravitropism for four of the seven: CCT2 functions in phosphatidylcholine biosynthesis, ATG5 functions in membrane remodeling during autophagy, UGP2 produces the substrate for cellulose and callose polymer extension, and FAMA is a transcription factor. Automated phenotyping enabled this discovery of four naturally varying components of a conserved process (gravitropism) by making it feasible to conduct the same large-scale experiment in two species.

Lipidomics-Assisted GWAS (lGWAS) Approach for Improving High-Temperature Stress Tolerance of Crops

High-temperature stress (HT) over crop productivity is an important environmental factor demanding more attention as recent global warming trends are alarming and pose a potential threat to crop production. According to the Sixth IPCC report, future years will have longer warm seasons and frequent heat waves. Thus, the need arises to develop HT-tolerant genotypes that can be used to breed high-yielding crops. Several physiological, biochemical, and molecular alterations are orchestrated in providing HT tolerance to a genotype. One mechanism to counter HT is overcoming high-temperature-induced membrane superfluidity and structural disorganizations. Several HT lipidomic studies on different genotypes have indicated the potential involvement of membrane lipid remodelling in providing HT tolerance. Advances in high-throughput analytical techniques such as tandem mass spectrometry have paved the way for large-scale identification and quantification of the enormously diverse lipid molecules in a single run. Physiological trait-based breeding has been employed so far to identify and select HT tolerant genotypes but has several disadvantages, such as the genotype-phenotype gap affecting the efficiency of identifying the underlying genetic association. Tolerant genotypes maintain a high photosynthetic rate, stable membranes, and membrane-associated mechanisms. In this context, studying the HT-induced membrane lipid remodelling, resultant of several up-/down-regulations of genes and post-translational modifications, will aid in identifying potential lipid biomarkers for HT tolerance/susceptibility. The identified lipid biomarkers (LIPIDOTYPE) can thus be considered an intermediate phenotype, bridging the gap between genotype–phenotype (genotype–LIPIDOTYPE–phenotype). Recent works integrating metabolomics with quantitative genetic studies such as GWAS (mGWAS) have provided close associations between genotype, metabolites, and stress-tolerant phenotypes. This review has been sculpted to provide a potential workflow that combines MS-based lipidomics and the robust GWAS (lipidomics assisted GWAS-lGWAS) to identify membrane lipid remodelling related genes and associations which can be used to develop HS tolerant genotypes with enhanced membrane thermostability (MTS) and heat stable photosynthesis (HP).

The phospho-base N-methyltransferases PMT1 and PMT2 produce phosphocholine for leaf growth in phosphorus-starved Arabidopsis

Phosphorus (P) is an essential nutrient for plants. Membrane lipid remodeling is an adaptive mechanism for P-starved plants that replaces membrane phospholipids with non-P galactolipids, presumably to retrieve scarce P sources and maintain membrane integrity. Whereas metabolic pathways to convert phospholipids to galactolipids are well-established, the mechanism by which phospholipid biosynthesis is involved in this process remains elusive. Here, we report that phospho-base N-methyltransferases 1 and 2 (PMT1 and PMT2), which convert phosphoethanolamine to phosphocholine (PCho), are transcriptionally induced by P starvation. Shoots of seedlings of pmt1 pmt2 double mutant showed defective growth upon P starvation; however, membrane lipid profiles were unaffected. We found that P-starved pmt1 pmt2 with defective leaf growth had reduced PCho content, and the growth defect was rescued by exogenous supplementation of PCho. We propose that PMT1 and PMT2 are induced by P starvation to produce PCho mainly for leaf growth maintenance, rather than for phosphatidylcholine biosynthesis, in membrane lipid remodeling.

The importance of Arabidopsis PHOSPHOLIPID N-METHYLTRANSFERASE in glycerolipid metabolism and plant growth

Phosphatidylcholine (PC) is a major class of phospholipids that are essential for post-embryonic growth in plants. In Arabidopsis, three copies of the phospho-base N-methyltransferase, PMT1, PMT2, and PMT3, are known to account for PC biosynthesis because the triple-knockout mutant is devoid of biosynthesis and shows lethality in post-embryonic but not embryonic growth. Arabidopsis also contains a distinct phospholipid N-methyltransferase (PLMT) that is homologous with yeast and animal PLMT that methylates phospholipids to produce PC. However, the knockout mutant of PLMT does not show morphological phenotypes or decreased PC content, so the role of PLMT remains unclear. Here, we show that PLMT is ubiquitously expressed in different organs and localized at the endoplasmic reticulum, where PC is produced. Overexpression of PLMT in planta increased the content of phospholipids including PC and affected vegetative but not reproductive growth. Although silique lengths were shorter, pollen remained viable and mature seeds were produced. Intriguingly, seed triacylglycerol content was increased with altered fatty acid composition. We conclude that PLMT might be a functional enzyme in PC biosynthesis and play an organ-specific role in developing seeds, where rapid accumulation of triacylglycerol dominates the entire glycerolipid metabolic flux.

Multiomic analyses of two sorghum cultivars reveals the change of membrane lipids in their responses to water deficit

Drought is one of the main abiotic stresses influencing crop production all over the world. Membranes are sensitive to drought stress and easy to be degraded and modified. Lipidome and transcriptome analyses were applied to analyze the responses of membrane lipids to drought stress in two sorghum (Sorghum bicolor (L.) Moench) cultivars, drought-sensitive cv. Hongyingzi and drought-tolerant cv. Kangsi. In total, 156 lipid compounds were identified and the contents of the predominant ones changed significantly under drought stress. Drought significantly decreased the unsaturation indices (UI) of digalactosyl-diacylglycerol (DGDG), monogalactosyl-diacylglycerol (MGDG), phosphatidylglycerol (PG) and phosphatidylcholine (PC) in both cultivars, except for insignificant changes of UI for DGDG in cv. Kangsi. Transcriptome sequencing analysis identified genes related to membrane lipid remodeling such as phospholipase D α1 (PLDα1), phospholipase D δ (PLDδ), and phospholipase A 2 (PLA2). By integrating transcriptome data and lipidome data, weighted gene co-expression network analysis (WGCNA) identified hub genes, transcription factors and the genes involved in lipid metabolism. Then, the protein and protein interaction (PPI) was analyzed using STRING and the possible candidate genes regulating membrane lipids under drought stress were obtained, including CCT2, CER1, DGK1, DGK5, EMB3174, KCS4, LCB2, PAH1, PLDP1, PKP-β1, and KCS11. The results from this study have the potential to accelerate the process to breed drought-tolerant sorghum lines.

At4g29530 is a phosphoethanolamine phosphatase homologous to PECP1 with a role in flowering time regulation

Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) are the most abundant phospholipids in membranes. The biosynthesis of phospholipids occurs mainly via the Kennedy pathway. Recent studies have shown that through this pathway, choline (Cho) moieties are synthesized through the methylation of phosphoethanolamine (PEtn) to phosphocholine (PCho) by phospho-base N-methyltransferase. In Arabidopsis thaliana, the phosphoethanolamine/phosphocholine phosphatase1 (PECP1) is described as an enzyme that regulates the synthesis of PCho by decreasing the PEtn level during phosphate starvation to avoid the energy-consuming methylation step. By homology search, we identified a gene (At4g29530) encoding a putative PECP1 homolog from Arabidopsis with a currently unknown biological function in planta. We found that At4g29530 is not induced by phosphate starvation, and is mainly expressed in leaves and flowers. The analysis of null mutants and overexpression lines revealed that PEtn, rather than PCho, is the substrate in vivo, as in PECP1. Hydrophilic interaction chromatography-coupled mass spectrometry analysis of head group metabolites shows an increased PEtn level and decreased ethanolamine level in null mutants. At4g29530 null mutants have an early flowering phenotype, which is corroborated by a higher PC/PE ratio. Furthermore, we found an increased PCho level. The choline level was not changed, so the results corroborate that the PEtn-dependent pathway is the main route for the generation of Cho moieties. We assume that the PEtn-hydrolyzing enzyme participates in fine-tuning the metabolic pathway, and helps prevent the energy-consuming biosynthesis of PCho through the methylation pathway.

Headgroup biosynthesis of phosphatidylcholine and phosphatidylethanolamine in seed plants

Phospholipid biosynthesis is crucial for plant growth and development. It involves attachment of fatty acids to a phospho-diacylglycerol backbone and modification of the phospho-group into an amino alcohol. The biochemistry and molecular biology of the former has been well established, but a number of enzymes responsible for the latter have only recently been cloned and functionally characterized in Arabidopsis and some other model plant species. The metabolism involving the polar head groups of phospholipids established by past biochemical studies can now be validated by available gene knockout models. Moreover, gene knockout studies have revealed emerging functions of phospholipids in regulating plant growth and development. This review aims to revisit the old questions of polar headgroup biosynthesis of plant phosphatidylcholine and phosphatidylethanolamine by giving an overview of recent advances in the field and beyond.

Identification and characterization of CTP:phosphocholine cytidylyltransferase CpCCT1 in the resurrection plant Craterostigma plantagineum

Phosphatidylcholine is a major phospholipid which is shown to be involved in stress adaptation. Phosphatidylcholine increased during dehydration in Craterostigma plantagineum, and therefore we characterized CTP:phosphocholine cytidylyltransferase (CpCCT1), a key regulatory enzyme for phosphatidylcholine synthesis in plants. The CpCCT1 gene from the resurrection plant C. plantagineum was cloned and the amino acid sequence was compared with homologs from other species including yeast and rat. CCT proteins have conserved catalytic and membrane-binding domains while the N-terminal and C-terminal domains have diverged. The tissue specific expression analysis indicated that CpCCT1 is expressed in all tested tissues and it is induced by dehydration and in response to 0.5 M NaCl solutions. In plants exposed to low temperature in the dark, the CpCCT1 transcript increased after 4 h at 4 °C. CpCCT1 expression also increased during mannitol and sorbitol treatments in a concentration dependent manner. Phytohormones such as abscisic acid and indole-3-acetic acid also trigged transcript accumulation. Comparisons of transcript and protein accumulations for different treatments (except for dehydration) suggest transcriptional and translational control mechanisms. Analysis of promoter activity and polysome occupancy suggest that CpCCT1 gene expression is mainly under translational regulation during dehydration.

Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual

PREMISE

Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Italy and Sweden provides an essential foundation for uncovering the genotype-phenotype-fitness map for an adaptive response to a key environmental stress.

METHODS

We examined the consequences of a naturally occurring loss-of-function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing-tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing the Italian CBF2 allele, and two contained deletions created using CRISPR-Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression before and after cold acclimation.

RESULTS

Freezing tolerance was lower in the Italian (11%) compared to the Swedish (72%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified 10 genes for which all CBF2 LOF lines, and the IT ecotype had similar patterns of reduced cold responsive expression compared to the SW ecotype.

CONCLUSIONS

We identified 10 genes that are at least partially regulated by CBF2 that may contribute to the differences in cold-acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.

Chloroplast Lipids and Their Biosynthesis

Chloroplasts contain high amounts of monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) and low levels of the anionic lipids sulfoquinovosyldiacylglycerol (SQDG), phosphatidylglycerol (PG), and glucuronosyldiacylglycerol (GlcADG). The mostly extraplastidial lipid phosphatidylcholine is found only in the outer envelope. Chloroplasts are the major site for fatty acid synthesis. In Arabidopsis, a certain proportion of glycerolipids is entirely synthesized in the chloroplast (prokaryotic lipids). Fatty acids are also exported to the endoplasmic reticulum and incorporated into lipids that are redistributed to the chloroplast (eukaryotic lipids). MGDG, DGDG, SQDG, and PG establish the thylakoid membranes and are integral constituents of the photosynthetic complexes. Phosphate deprivation induces phospholipid degradation accompanied by the increase in DGDG, SQDG, and GlcADG. During freezing and drought stress, envelope membranes are stabilized by the conversion of MGDG into oligogalactolipids. Senescence and chlorotic stress lead to lipid and chlorophyll degradation and the deposition of acyl and phytyl moieties as fatty acid phytyl esters.

A pair of phospho-base methyltransferases important for phosphatidylcholine biosynthesis in Arabidopsis

Phosphatidylcholine (PtdCho) is a predominant membrane lipid class in eukaryotes. Phospho-base N-methyltransferase (PMT) catalyzes a critical step in PtdCho biosynthesis. However, in Arabidopsis thaliana, the discovery of involvement of the specific PMT isoform in PtdCho biosynthesis remains elusive. Here, we show that PMT1 and PMT3 redundantly play an essential role in phosphocholine (PCho) biosynthesis, a prerequisite for PtdCho production. A pmt1 pmt3 double mutant was devoid of PCho, which affected PtdCho biosynthesis in vivo, showing severe growth defects in post-embryonic development. PMT1 and PMT3 were both highly expressed in the vasculature. The pmt1 pmt3 mutants had specifically affected leaf vein development and showed pale-green seedlings that were rescued by exogenous supplementation of PCho. We suggest that PMT1 and PMT3 are the primary enzymes for PCho biosynthesis and are involved in PtdCho biosynthesis and vascular development in Arabidopsis seedlings.

NMR-based metabolomic profiling of Peganum harmala L. reveals dynamic variations between different growth stages

Xerophytes play an active role in preventing soil denudation and desertification in arid and semi-arid areas. Peganum harmala L. (Zygophyllaceae family), a seasonally growing, poisonous and drought-tolerant plant, is widely distributed in the Xinjiang Uygur Autonomous Region and used as a traditional herbal medicine as well as, in winter, a fodder source. Previous research has focused on the pharmacological activity of isolated compounds and stress responses to growth environments. However, the metabolic profile of P. harmala and variations in its metabolites, including medicinally active and stress resistance components, have not been illustrated during different growth stages. Here, we collected plant samples in May, August, October and December. We determined the metabolic composition of methanol extracts using NMR spectroscopy, and comparisons of four growth stages were accomplished by applying statistical analysis. The results showed that vasicine, choline and sucrose were significantly elevated in samples harvested in May. Significantly higher amounts of betaine, lysine, 4-hydroxyisoleucine and proline were found in samples collected in August than in samples collected in other months, and the concentrations of phosphorylcholine, glucose, acetic acid and vasicinone were highest in December. The relationships between differential biomarkers and plant physiological states affected by diverse growth environmental factors were discussed. Our result deepened the understanding of metabolic mechanisms in plant development and confirmed the advantage of using NMR-based metabolomic treatments in quality evaluation when P. harmala is used for different purposes.

Plant Phospholipid Diversity: Emerging Functions in Metabolism and Protein-Lipid Interactions

Phospholipids are essential components of biological membranes and signal transduction cascades in plants. In recent years, plant phospholipid research was greatly advanced by the characterization of numerous mutants affected in phospholipid biosynthesis and the discovery of a number of functionally important phospholipid-binding proteins. It is now accepted that most phospholipids to some extent have regulatory functions, including those that serve as constituents of biological membranes. Phospholipids are more than an inert end product of lipid biosynthesis. This review article summarizes recent advances on phospholipid biosynthesis with a particular focus on polar head group synthesis, followed by a short overview on protein-phospholipid interactions as an emerging regulatory mechanism of phospholipid function in arabidopsis (Arabidopsis thaliana).

A Transcription Factor γMYB1 Binds to the P1BS cis-Element and Activates PLA2-γ Expression with its Co-Activator γMYB2

Phospholipase A2(PLA2) hydrolyzes phospholipid molecules to produce two products that are both precursors of second messengers of signaling pathways and signaling molecules per se.Arabidopsis thaliana PLA2 paralogs (-β,-γ and -δ) play critical roles during pollen development, pollen germination and tube growth. In this study, analysis of the PLA2-γ promoter using a deletion series revealed that the promoter region -153 to -1 is crucial for its pollen specificity. Using a yeast one-hybrid screening assay with the PLA2-γ promoter and an Arabidopsis transcription factor (TF)-only library, we isolated two novel MYB-like TFs belonging to the MYB-CC family, denoted here as γMYB1 and γMYB2. By electrophoretic mobility shift assay, we found that these two TFs bind directly to the P1BS (phosphate starvation response 1-binding sequence)cis-element of the PLA2-γ promoter. γMYB1 alone functioned as a transcriptional activator for PLA2-γ expression, whereas γMYB2 directly interacted with γMYB1 and enhanced its activation. Overexpression of γMYB1 in the mature pollen grain led to increased expression of not only the PLA2-γ gene but also of several genes whose promoters contain the P1BS cis-element and which are involved in the Pi starvation response, phospholipid biosynthesis and sugar synthesis. Based on these results, we suggest that the TF γMYB1 binds to the P1BS cis-element, activates the expression of PLA2-γ with the assistance of its co-activator, γMYB2, and regulates the expression of several target genes involved in many plant metabolic reactions.

C1 Metabolism Inhibition and Nitrogen Deprivation Trigger Triacylglycerol Accumulation in Arabidopsis thaliana Cell Cultures and Highlight a Role of NPC in Phosphatidylcholine-to-Triacylglycerol Pathway

Triacylglycerol (TAG) accumulation often occurs in growth limiting conditions such as nutrient deprivations. We analyzed and compared the lipid contents of Arabidopsis cells grown under two conditions that inhibited growth as a way to study interactions between membrane and storage lipids. In order to inhibit C1 metabolism, the first condition utilized methotrexate (MTX), a drug that inhibits methyl transfer reactions and potentially reduces Pi-choline synthesis, the polar head of phosphatidylcholine (PC). MTX-treated cells displayed a 10- to 15-fold increase in TAG compared to that found in control cells. This corresponded to a net increase of lipids as the total amount of membrane glycerolipids was minimally affected. Under this condition, PC homeostasis appeared tightly regulated and not strictly dependent on the rate of Pi-choline synthesis. The second condition we investigated involved nitrogen deprivation. Here, we observed a 40-fold increase of TAG. In these cells, the overall lipid content remained unchanged, but membrane lipids decreased by a factor of two suggesting a reduction of the membrane network and a rerouting of membrane lipids to storage lipids. Under all conditions, fatty acid (FA) analyses showed that the FA composition of TAG was comparable to that in PC, but different from that in acyl-CoA, suggesting that TAG accumulation involved PC-derived DAG moieties. In agreement, analyses by qPCR of genes coding for TAG synthesis showed a strong increase of non-specific phospholipase C (NPC) expressions, and experiments using labeled (fluorescent) PC indicated higher rates of PC-to-TAG conversion under both situations. These results highlight a role for NPC in plant cell oil production.

Identification of Early Nuclear Target Genes of Plastidial Redox Signals that Trigger the Long-Term Response of Arabidopsis to Light Quality Shifts

Natural illumination conditions are highly variable and because of their sessile life style, plants are forced to acclimate to them at the cellular and molecular level. Changes in light intensity or quality induce changes in the reduction/oxidation (redox) state of the photosynthetic electron chain that acts as a trigger for compensatory acclimation responses comprising functional and structural adjustments of photosynthesis and metabolism. Such responses include redox-controlled changes in plant gene expression in the nucleus and organelles. Here we describe a strategy for the identification of early redox-regulated genes (ERGs) in the nucleus of the model organism Arabidopsis thaliana that respond significantly 30 or 60 min after the generation of a reduction signal in the photosynthetic electron transport chain. By comparing the response of wild-type plants with that of the acclimation mutant stn7, we could specifically identify ERGs. The results reveal a significant impact of chloroplast redox signals on distinct nuclear gene groups including genes for the mitochondrial electron transport chain, tetrapyrrole biosynthesis, carbohydrate metabolism, and signaling lipid synthesis. These expression profiles are clearly different from those observed in response to the reduction of photosynthetic electron transport by high light treatments. Thus, the ERGs identified are unique to redox imbalances in photosynthetic electron transport and were then used for analyzing potential redox-responsive cis-elements, trans-factors, and chromosomal regulatory hot spots. The data identify a novel redox-responsive element and indicate extensive redox control at transcriptional and chromosomal levels that point to an unprecedented impact of redox signals on epigenetic processes.

CTP:phosphocholine cytidylyltransferase: Function, regulation, and structure of an amphitropic enzyme required for membrane biogenesis

CTP:phosphocholine cytidylyltransferase (CCT) catalyzes a rate-limiting and regulated step in the CDP-choline pathway for the synthesis of phosphatidylcholine (PC) and PC-derived lipids. Control of CCT activity is multi-layered, and includes direct regulation by reversible membrane binding involving a built-in lipid compositional sensor. Thus CCT contributes to phospholipid compositional homeostasis. CCT also modifies the curvature of its target membrane. Knowledge of CCT structure and regulation of its catalytic function are relatively advanced compared to many lipid metabolic enzymes, and are reviewed in detail. Recently the genetic origins of two human developmental and lipogenesis disorders have been traced to mutations in the gene for CCTα.

PHOSPHATIDIC ACID PHOSPHOHYDROLASE Regulates Phosphatidylcholine Biosynthesis in Arabidopsis by Phosphatidic Acid-Mediated Activation of CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE Activity

Regulation of membrane lipid biosynthesis is critical for cell function. We previously reported that disruption of PHOSPHATIDIC ACID PHOSPHOHYDROLASE1 (PAH1) and PAH2 stimulates net phosphatidylcholine (PC) biosynthesis and proliferation of the endoplasmic reticulum (ER) in Arabidopsis thaliana. Here, we show that this response is caused specifically by a reduction in the catalytic activity of the protein and positively correlates with an accumulation of its substrate, phosphatidic acid (PA). The accumulation of PC in pah1 pah2 is suppressed by disruption of CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE1 (CCT1), which encodes a key enzyme in the nucleotide pathway for PC biosynthesis. The activity of recombinant CCT1 is stimulated by lipid vesicles containing PA. Truncation of CCT1, to remove the predicted C-terminal amphipathic lipid binding domain, produced a constitutively active enzyme. Overexpression of native CCT1 in Arabidopsis has no significant effect on PC biosynthesis or ER morphology, but overexpression of the truncated constitutively active version largely replicates the pah1 pah2 phenotype. Our data establish that membrane homeostasis is regulated by lipid composition in Arabidopsis and reveal a mechanism through which the abundance of PA, mediated by PAH activity, modulates CCT activity to govern PC content.

Arabidopsis florigen FT binds to diurnally oscillating phospholipids that accelerate flowering

Arabidopsis FT protein is a component of florigen, which transmits photoperiodic flowering signals from leaf companion cells to the shoot apex. Here, we show that FT specifically binds phosphatidylcholine (PC) in vitro. A transgenic approach to increase PC levels in vivo in the shoot meristem accelerates flowering whereas reduced PC levels delay flowering, demonstrating that PC levels are correlated with flowering time. The early flowering is related to FT activity, because expression of FT-effector genes is increased in these plants. Simultaneous increase of FT and PC in the shoot apical meristem further stimulates flowering, whereas a loss of FT function leads to an attenuation of the effect of increased PC. Specific molecular species of PC oscillate diurnally, and night-dominant species are not the preferred ligands of FT. Elevating night-dominant species during the day delays flowering. We suggest that FT binds to diurnally changing molecular species of PC to promote flowering.

Daytime flowering in Arabidopsis is stimulated by the secreted protein FT. Nakamura et al. show that FT binds the lipid phosphatidylcholine (PC) in vitro, and that in plants, different PC species predominate during day and night, with daytime species stimulating flowering in a manner that is partially dependent on FT.

Acyl-lipid metabolism

Acyl lipids in Arabidopsis and all other plants have a myriad of diverse functions. These include providing the core diffusion barrier of the membranes that separates cells and subcellular organelles. This function alone involves more than 10 membrane lipid classes, including the phospholipids, galactolipids, and sphingolipids, and within each class the variations in acyl chain composition expand the number of structures to several hundred possible molecular species. Acyl lipids in the form of triacylglycerol account for 35% of the weight of Arabidopsis seeds and represent their major form of carbon and energy storage. A layer of cutin and cuticular waxes that restricts the loss of water and provides protection from invasions by pathogens and other stresses covers the entire aerial surface of Arabidopsis. Similar functions are provided by suberin and its associated waxes that are localized in roots, seed coats, and abscission zones and are produced in response to wounding. This chapter focuses on the metabolic pathways that are associated with the biosynthesis and degradation of the acyl lipids mentioned above. These pathways, enzymes, and genes are also presented in detail in an associated website (ARALIP: http://aralip.plantbiology.msu.edu/). Protocols and methods used for analysis of Arabidopsis lipids are provided. Finally, a detailed summary of the composition of Arabidopsis lipids is provided in three figures and 15 tables.

Comparative deep transcriptional profiling of four developing oilseeds

Transcriptome analysis based on deep expressed sequence tag (EST) sequencing allows quantitative comparisons of gene expression across multiple species. Using pyrosequencing, we generated over 7 million ESTs from four stages of developing seeds of Ricinus communis, Brassica napus, Euonymus alatus and Tropaeolum majus, which differ in their storage tissue for oil, their ability to photosynthesize and in the structure and content of their triacylglycerols (TAG). The larger number of ESTs in these 16 datasets provided reliable estimates of the expression of acyltransferases and other enzymes expressed at low levels. Analysis of EST levels from these oilseeds revealed both conserved and distinct species-specific expression patterns for genes involved in the synthesis of glycerolipids and their precursors. Independent of the species and tissue type, ESTs for core fatty acid synthesis enzymes maintained a conserved stoichiometry and a strong correlation in temporal profiles throughout seed development. However, ESTs associated with non-plastid enzymes of oil biosynthesis displayed dissimilar temporal patterns indicative of different regulation. The EST levels for several genes potentially involved in accumulation of unusual TAG structures were distinct. Comparison of expression of members from multi-gene families allowed the identification of specific isoforms with conserved function in oil biosynthesis. In all four oilseeds, ESTs for Rubisco were present, suggesting its possible role in carbon metabolism, irrespective of light availability. Together, these data provide a resource for use in comparative and functional genomics of diverse oilseeds. Expression data for more than 350 genes encoding enzymes and proteins involved in lipid metabolism are available at the 'ARALIP' website (http://aralip.plantbiology.msu.edu/).