Understanding the control of acyl flux through the lipid metabolic network of plant oil biosynthesis

Metabolomic and transcriptomic analysis of the synthesis process of unsaturated fatty acids in Korean pine seed kernels

Due to their rich unsaturated fatty acids, nuts of Korean pine are widely popular in the market. With growing public awareness about forest conservation and healthy eating, the primary focus of Korean pine forest management has gradually shifted from timber to nut production. The lack of understanding of the process of unsaturated fatty acid synthesis in Korean pine kernels and unclear identification of the critical period have hindered efforts to improve yield and genetic modification. This study, through metabolomic and transcriptomic analysis of five developmental stages of Korean pine kernels, identifies the critical period for the synthesis of unsaturated fatty acids, characterizes the gene expression spectrum, and identifies three gene co-expression modules highly correlated with unsaturated fatty acid synthesis. The findings not only provide new insights into the synthesis of oils in gymnosperm nuts but also offer valuable guidance for the cultivation and targeted improvement of high-quality Korean pine nut varieties.

Identification of novel candidate genes for regulating oil composition in soybean seeds under environmental stresses

Introduction

A key objective of soybean breeding programs is to enhance nutritional quality for human and animal consumption, with improved fatty acid (FA) composition for health benefits, and expand soybean use for industrial applications.

Methods

We conducted a metabolite genome-wide association study (mGWAS) to identify genomic regions associated with changes in FA composition and FA ratios in soybean seeds influenced by environmental factors. This mGWAS utilized 218 soybean plant introductions (PIs) grown in two field locations in Virginia over two years.

Results

The mGWAS revealed that 20 SNPs were significantly associated with 21 FA ratios, while additional suggestive SNPs were found for 36 FA ratios, highlighting potential quantitative trait loci linked to FA composition.

Discussion

Many of these SNPs are located near or within the genes related to phytohormone-mediated biotic and abiotic stress responses, suggesting the involvement of environmental factors in modulating FA composition in soybean seeds. Our findings provide novel insights into the genetic and environmental factors influencing FA composition in oilseeds. This research also lays the foundation for developing stable markers to develop soybean cultivars with tailored FA profiles for different practical applications under variable growth conditions.

BnLPAT2 gene regulates oil accumulation in Brassica napus by modulating linoleic and linolenic acid levels in seeds

Lysophosphatidate acyltransferase (LPAT) catalyzes the conversion of lysophosphatidic acid to phosphatidic acid, a key step in lipid biosynthesis. This study cloned four LPAT2 genes from Brassica napus: BnLPAT2-A04, A07, A09, and C08. Functional analysis using bioinformatics, qRT-PCR (Quantitative Reverse Transcription Polymerase Chain Reaction), CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9), overexpression, and transcriptome sequencing revealed that these genes encode proteins containing the conserved PLN02380 domain. BnLPAT2-A07/A09/C08 showed strong conservation with Arabidopsis AtLPAT2. Promoter analysis revealed multiple cis-elements related to stress, light, and phytohormone responses, with the BnLPAT2-A09/C08 promoters containing the most diverse cis-elements. Expression analysis showed that BnLPAT2-A07/C08 was highly expressed in various tissues, with BnLPAT2-A07 peaking during seed development. Overexpression of these genes increased seed oil content and the proportion of C18:2/C18:3 fatty acids, with BnLPAT2-A07 achieving an increase in oil content ranging from 4.46% to 6.44%. Gene knockout reduced oil content by 7.5% and affected fatty acid accumulation. Transcriptome sequencing analysis suggested that the BnLPAT2 genes promote the production of long-chain fatty acids, such as Linoleic acid (C18:2) and Linolenic acid (C18:3), through biological processes, including fatty acid biosynthesis, very long-chain fatty acid biosynthesis, and very long-chain fatty acid metabolism, thereby improving seed oil content. This study provides valuable insights into lipid metabolism and offers a theoretical foundation for improving oil content and fatty acid composition in B. napus.

Multi-Omics Analyses Offer Novel Insights into the Selection of Sugar and Lipid Metabolism During Maize Domestication and Improvement

Over thousands of years of domestication, maize has undergone significant environmental changes. Understanding the genetic and metabolic trace during maize evolution can better contribute to molecular breeding and nutrition quality improvement. This study examines the metabolic profiles and transcriptomes of maize kernels from teosinte, landrace, and maize accessions at 15 days post-pollination. Differentially accumulated metabolites were enriched in sugar and lipid metabolism pathways. The metabolic selection profile exhibited four distinct patterns: continuous increases, constant decrease, initial decline or stability followed by an increase, and initial growth or stability followed by a subsequent decline. Sugars and JA were positive selection while LPCs/LPEs were negative selection during evolution. The expression level of genes related to sugar accumulation was significantly higher in maize, contrasting with enhanced glycolysis and lipid metabolism activity in teosinte. The correlation network highlighted distinct hormonal regulation of sugar and lipid metabolism. We identified 27 candidate genes associated with sugar, lipid, and JA that have undergone strong selection by population genomic regions. The positive selection of the PLD may explain the negative selection of LPCs/LPEs due to substrate competition. These findings enhance our understanding of the evolutionary trajectory of primary metabolism in maize and provide valuable resources for breeding and improvement.

Triacylglycerol stability limits futile cycles and inhibition of carbon capture in oil-accumulating leaves

Engineering plant vegetative tissue to accumulate triacylglycerols (TAG, e.g. oil) can increase the amount of oil harvested per acre to levels that exceed current oilseed crops. Engineered tobacco (Nicotiana tabacum) lines that accumulate 15% to 30% oil of leaf dry weight resulted in starkly different metabolic phenotypes. In-depth analysis of the leaf lipid accumulation and 14CO2 tracking describe metabolic adaptations to the leaf oil engineering. An oil-for-membrane lipid tradeoff in the 15% oil line (referred to as HO) was surprisingly not further exacerbated when lipid production was enhanced to 30% (LEAFY COTYLEDON 2 (LEC2) line). The HO line exhibited a futile cycle that limited TAG yield through exchange with starch, altered carbon flux into various metabolite pools and end products, and suggested interference of the glyoxylate cycle with photorespiration that limited CO2 assimilation by 50%. In contrast, inclusion of the LEC2 transcription factor in tobacco improved TAG stability, alleviated the TAG-to-starch futile cycle, and recovered CO2 assimilation and plant growth comparable to wild type but with much higher lipid levels in leaves. Thus, the unstable production of storage reserves and futile cycling limit vegetative oil engineering approaches. The capacity to overcome futile cycles and maintain enhanced stable TAG levels in LEC2 demonstrated the importance of considering unanticipated metabolic adaptations while engineering vegetative oil crops.

Towards rational control of seed oil composition: dissecting cellular organization and flux control of lipid metabolism

Plant lipids represent a fascinating field of scientific study, in part due to a stark dichotomy in the limited fatty acid (FA) composition of cellular membrane lipids vs the huge diversity of FAs that can accumulate in triacylglycerols (TAGs), the main component of seed storage oils. With few exceptions, the strict chemical, structural, and biophysical roles imposed on membrane lipids since the dawn of life have constrained their FA composition to predominantly lengths of 16-18 carbons and containing 0-3 methylene-interrupted carbon-carbon double bonds in cis-configuration. However, over 450 "unusual" FA structures can be found in seed oils of different plants, and we are just beginning to understand the metabolic mechanisms required to produce and maintain this dichotomy. Here we review the current state of plant lipid research, specifically addressing the knowledge gaps in membrane and storage lipid synthesis from 3 angles: pathway fluxes including newly discovered TAG remodeling, key acyltransferase substrate selectivities, and the possible roles of "metabolons."

Born of frustration: the emergence of Camelina sativa as a platform for lipid biotechnology

The emerging crop Camelina sativa (L.) Crantz (camelina) is a Brassicaceae oilseed with a rapidly growing reputation for the deployment of advanced lipid biotechnology and metabolic engineering. Camelina is recognized by agronomists for its traits, including yield, oil/protein content, drought tolerance, limited input requirements, plasticity, and resilience. Its utility as a platform for metabolic engineering was then quickly recognized, and biotechnologists have benefited from its short life cycle and facile genetic transformation, producing numerous transgenic interventions to modify seed lipid content and generate novel products. The desire to work with a plant that is both a model and crop has driven the expansion of research resources for camelina, including increased availability of genome and other -omics data sets. Collectively, the expansion of these resources has established camelina as an ideal plant to study the regulation of lipid metabolism and genetic improvement. Furthermore, the unique characteristics of camelina enables the design-build-test-learn cycle to be transitioned from the controlled environment to the field. Complex metabolic engineering to synthesize and accumulate high levels of novel fatty acids and modified oils in seeds can be deployed, tested, and undergo rounds of iteration in agronomically relevant environments. Engineered camelina oils are now increasingly being developed and used to sustainably supply improved nutrition, feed, biofuels, and fossil fuel replacements for high-value chemical products. In this review, we provide a summary of seed fatty acid synthesis and oil assembly in camelina, highlighting how discovery research in camelina supports the advance of metabolic engineering toward the predictive manipulation of metabolism to produce desirable bio-based products. Further examples of innovation in camelina seed lipid engineering and crop improvement are then provided, describing how technologies (e.g. genetic modification [GM], gene editing [GE], RNAi, alongside GM and GE stacking) can be applied to produce new products and denude undesirable traits. Focusing on the production of long chain polyunsaturated omega-3 fatty acids in camelina, we describe how lipid biotechnology can transition from discovery to a commercial prototype. The prospects to produce structured triacylglycerol with fatty acids in specified stereospecific positions are also discussed, alongside the future outlook for the agronomic uptake of camelina lipid biotechnology.

Dynamic Lipidomics and Transcriptome Profiling Reveals the Transcriptional Regulatory Mechanism Governing TAGs Formation in Seeds of Safflower

Safflower (Carthamus tinctorius L.) is a valuable oil crop due to its bioactive ingredients and high linoleic acid content, which contribute to its antioxidant properties and potential for preventing atherosclerosis. Current research on safflower focuses on understanding the biosynthesis of seed oil through omics strategies, yet there is a lack of comprehensive knowledge of the dynamic changes in lipids and the regulatory mechanisms during seed development. Here, we performed combined quantitative lipidomics profiles and transcriptomic analyses to characterize the lipid accumulation patterns of safflower seeds, investigate gene networks, and identify vital candidate genes and transcription factors (TFs) involved in triacylglycerol (TAGs) biosynthesis in safflower. A total of 417 lipid compounds and their corresponding coexpressed genes were categorized into seven distinct lipid metabolite vs gene modules. By integrating bioinformatic analyses, one TFs-genes transcriptional regulatory network for major lipid compounds was proposed, involving 10 hub transcription factors and 12 structure genes that participate in regulating the accumulation of triacylglycerols (TAGs) and fatty acids (FAs). Furthermore, the results of yeast one-hybrid assay suggested that CtAP2.1 and CtAP2.4, the homologous genes of AINTEGUMENTA-Like 5 and 6 (AIL5 and AIL6) in Arabidopsis thaliana, may play important roles in the TAGs biosynthesis in safflower seeds. Our findings provide insight into the regulatory network of lipid compounds in safflower seeds and offer potential gene resources for enhanced oil content through targeted crop breeding.

Two critical membranes: how does the chloroplast envelope affect plant acclimation properties?

Chloroplasts play a pivotal role in the metabolism of leaf mesophyll cells, functioning as a cellular hub that orchestrates molecular reactions in response to environmental stimuli. These organelles contain complex protein machinery for energy conversion and are indispensable for essential metabolic pathways. Proteins located within the chloroplast envelope membranes facilitate bidirectional communication with the cell and connect essential pathways, thereby influencing acclimation processes to challenging environmental conditions such as temperature fluctuations and light intensity changes. Despite their importance, a comprehensive overview of the impact of envelope-located proteins during acclimation to environmental changes is lacking. Understanding the role of these proteins in acclimation processes could provide insights into enhancing stress tolerance under increasingly challenging environments. This review highlights the significance of envelope-located proteins in plant acclimation.

Transcriptional engineering for value enhancement of oilseed crops: a forward perspective

Plant-derived oils provide 20%-35% of dietary calories and are a primary source of essential omega-6 (linoleic) and omega-3 (α-linolenic) fatty acids. While traditional breeding has significantly increased yields in key oilseed crops like soybean, sunflower, canola, peanut, and cottonseed, overall gains have plateaued over the past few decades. Oilseed crops also experience substantial yield losses in both prime and marginal agricultural areas due to biotic and abiotic stresses and shifting agro-climates. Recent genomic, transcriptomic, and metabolomics research has expanded our understanding of the genetic and physiological control of fatty acid biosynthesis and composition. Many oilseed species have inherent stress-combating mechanisms, including transcription factor regulation. Advances in genome editing tools like CRISPR/Cas9 offer precise genetic modifications, targeting transcription factors and binding sites to enhance desirable traits, such as the nutritional profile and chemical composition of fatty acids. This review explores the application of genome editing in oilseed improvement, covering recent progress, challenges, and future potential to boost yield and oil content. These advancements could play a transformative role in developing resilient, nutritious crop varieties essential for sustainable food security in a changing climate.

The first intron and promoter of Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 1 exert synergistic effects on pollen and embryo lipid accumulation

Accumulation of triacylglycerols (TAGs) is crucial during various stages of plant development. In Arabidopsis, two enzymes share overlapping functions to produce TAGs, namely acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) and phospholipid:diacylglycerol acyltransferase 1 (PDAT1). Loss of function of both genes in a dgat1-1/pdat1-2 double mutant is gametophyte lethal. However, the key regulatory elements controlling tissue-specific expression of either gene has not yet been identified. We transformed a dgat1-1/dgat1-1//PDAT1/pdat1-2 parent with transgenic constructs containing the Arabidopsis DGAT1 promoter fused to the AtDGAT1 open reading frame either with or without the first intron. Triple homozygous plants were obtained, however, in the absence of the DGAT1 first intron anthers fail to fill with pollen, seed yield is c. 10% of wild-type, seed oil content remains reduced (similar to dgat1-1/dgat1-1), and non-Mendelian segregation of the PDAT1/pdat1-2 locus occurs. Whereas plants expressing the AtDGAT1pro:AtDGAT1 transgene containing the first intron mostly recover phenotypes to wild-type. This study establishes that a combination of the promoter and first intron of AtDGAT1 provides the proper context for temporal and tissue-specific expression of AtDGAT1 in pollen. Furthermore, we discuss possible mechanisms of intron mediated regulation and how regulatory elements can be used as genetic tools to functionally replace TAG biosynthetic enzymes in Arabidopsis.

Increasing oil content in Brassica oilseed species

Brassica oilseed species are the third most important in the world, providing approximately 15 % of the total vegetable oils. Three species (Brassica rapa, B. juncea, B. napus) dominate with B. napus being the most common in Canada, China and Europe. Originally, B. napus was a crop producing seed with high erucic acid content, which still persists today, to some extent, and is used for industrial purposes. In contrast, cultivars which produce seed used for food and feed are low erucic acid cultivars which also have reduced glucosinolate content. Because of the limit to agricultural land, recent efforts have been made to increase productivity of oil crops, including Brassica oilseed species. In this article, we have detailed research in this regard. We have covered modern genetic, genomic and metabolic control analysis approaches to identifying potential targets for the manipulation of seed oil content. Details of work on the use of quantitative trait loci, genome-wide association and comparative functional genomics to highlight factors influencing seed oil accumulation are given and functional proteins which can affect this process are discussed. In summary, a wide variety of inputs are proving useful for the improvement of Brassica oilseed species, as major sources of global vegetable oil.

Downregulation of the GhROD1 Gene Improves Cotton Fiber Fineness by Decreasing Acyl Pool Saturation, Stimulating Small Heat Shock Proteins (sHSPs), and Reducing H2O2 Production

Cotton fiber is one of the most important natural fiber sources in the world, and lipid metabolism plays a critical role in its development. However, the specific role of lipid molecules in fiber development and the impact of fatty acid alterations on fiber quality remain largely unknown. In this study, we demonstrate that the downregulation of GhROD1, a gene encoding phosphatidylcholine diacylglycerol cholinephosphotransferase (PDCT), results in an improvement of fiber fineness. We found that GhROD1 downregulation significantly increases the proportion of linoleic acid (18:2) in cotton fibers, which subsequently upregulates genes encoding small heat shock proteins (sHSPs). This, in turn, reduces H2O2 production, thus delaying secondary wall deposition and leading to finer fibers. Our findings reveal how alterations in linoleic acid influence cellulose synthesis and suggest a potential strategy to improve cotton fiber quality by regulating lipid metabolism pathways.

Comparative analysis of transcriptome in oil biosynthesis between seeds and non-seed tissues of Symplocos paniculata fruit

The Symplocos paniculata, a woody oil plant, has garnered attention for its oil-rich fruit, which exhibits potential for both oil production and ecological restoration endeavors, thereby presenting substantial developmental value. However, the comprehension of the distinctive oil biosynthesis and deposition strategies within the fruit's various compartments, coupled with the tissue-specific biosynthetic pathways yielding optimal fatty acid profiles, remains in its infancy. This investigation was designed to delineate the tissue specificity of oil biosynthetic disparities and to elucidate the molecular underpinnings within the fruit mesocarp and seeds of S. paniculata, employing lipidomic and transcriptomic analyses. The results revealed that oil biosynthesis within the fruit mesocarp commences approximately 40 days prior to that within the seeds, with a concomitant higher lipid content observed in the mesocarp, reaching 43% as opposed to 30% in the seeds. The fruit mesocarp was found to be enriched with palmitic acid (C16:0) and exhibited a harmonious ratio of saturated, monounsaturated, to polyunsaturated fatty acids (SFA: MUFA: PUFA=1:1:1), in stark contrast to the seed oil, which is predominantly composed of unsaturated fatty acids, accounting for 90% of its total FA content. Microstructural assessments have unveiled divergent oil deposition modalities; the fruit mesocarp oils are predominantly sequestered within oil cells (OC) and a spectrum of lipid droplets (LD), whereas the seeds predominantly harbor uniformly-sized LD. The expression patterns of pivotal genes implicated in oil biosynthesis were observed to be markedly contingent upon the tissue type and developmental stage. Notably, the light-responsive fatty acid synthase (FAS) gene demonstrated preferential transcription within the fruit mesocarp. In contrast, genes pivotal for carbon chain elongation, such as 3-ketoacyl-ACP synthase II (KASII) and fatty acyl-ACP thioesterase A (FATA), and desaturation, typified by Stearoyl-ACP desaturase (SAD) and Fatty Acid Desaturase (FAD), were noted to be more robustly transcribed within the seeds. Furthermore, isoenzyme gene families integral to the assembly of triacylglycerol (TAG), including long-chain acyl-CoA synthetases (LACSs), glycerol-3-phosphate acyltransferases (GPATs), and lysophosphatidic acid acyltransferases (LPATs), exhibited pronounced tissue specificity. This research endeavors to clarify the molecular regulatory mechanisms that oversee oil biosynthesis within both seed and non-seed tissues of oilseed-bearing plants with entire fruits. Collectively, these findings lay the groundwork and offer technical scaffolding for future targeted cultivation of woody oil plants, with the ultimate aim of augmenting fruit oil yield and refining FA compositions.

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/.

The enzyme encoded by Myrmecia incisa, a green microalga, phospholipase A2 gene preferentially hydrolyzes arachidonic acid at the sn-2 position of phosphatidylcholine

The enzyme phospholipase A2 (PLA2) plays a crucial role in acyl remodeling of phospholipids via the Lands' cycle, and consequently alters fatty acid compositions in triacylglycerol (TAG). In this study, a full-length cDNA sequence coding Myrmecia incisa phospholipase A2 (MiPLA2) was cloned using the technique of rapid amplification of cDNA ends. Comparison of the 1082-bp cDNA with its corresponding cloned DNA sequence revealed that MiPLA2 contained 3 introns. Mature MiPLA2 (mMiPLA2) had a conserved Ca2+-binding loop and a catalytic site motif that has been recognized in plant secretory PLA2 (sPLA2) proteins. Correspondingly, phylogenetic analysis illustrated that MiPLA2 was clustered within GroupXIA of plant sPLA2 proteins. To ascertain the function of MiPLA2, the cDNA coding for mMiPLA2 was subcloned into the vector pET-32a to facilitate the production of recombinant mMiPLA2 in Escherichia coli. Recombinant mMiPLA2 was purified and used for the in vitro enzyme reaction. Thin-layer chromatography profiles of the catalytic products generated by recombinant mMiPLA2 indicated a specificity for cleaving sn-2 acyl chains from phospholipids, thereby functionally characterizing MiPLA2. Although recombinant mMiPLA2 displayed a strong preference for phosphatidylethanolamine, it preferentially hydrolyzes arachidonic acid (ArA) at the sn-2 position of phosphatidylcholine. Results from the fused expression of p1300-sp-EGFP-mMiPLA2 illustrated that MiPLA2 was localized in the intercellular space of onion epidermis. Furthermore, the positive correlation between MiPLA2 transcription and free ArA levels were established. Consequently, the role of mMiPLA2 in the biosynthesis of ArA-rich TAG was elucidated. This study helps to understand how M. incisa preferentially uses ArA to synthesize TAG.

The Biosynthesis Pattern and Transcriptome Analysis of Sapindus saponaria Oil

The Sapindus saponaria (soapberry) kernel is rich in oil that has antibacterial, anti-inflammatory, and antioxidant properties, promotes cell proliferation, cell migration, and stimulates skin wound-healing effects. S. saponaria oil has excellent lubricating properties and is a high-quality raw material for biodiesel and premium lubricants, showing great potential in industrial and medical applications. Metabolite and transcriptome analysis revealed patterns of oil accumulation and composition and differentially expressed genes (DEGs) during seed development. Morphological observations of soapberry fruits at different developmental stages were conducted, and the oil content and fatty acid composition of the kernels were determined. Transcriptome sequencing was performed on kernels at 70, 100, and 130 days after flowering (DAF). The oil content of soapberry kernels was lowest at 60 DAF (5%) and peaked at 130 DAF (31%). Following soapberry fruit-ripening, the primary fatty acids in the kernels were C18:1 (oleic acid) and C18:3 (linolenic acid), accounting for an average proportion of 62% and 18%, respectively. The average contents of unsaturated fatty acids and saturated fatty acids in the kernel were 86% and 14%, respectively. Through the dynamic changes in fatty acid composition and DEGs analysis of soapberry kernels, FATA, KCR1, ECR, FAD2 and FAD3 were identified as candidate genes contributing to a high proportion of C18:1 and C18:3, while DGAT3 emerged as a key candidate gene for TAG biosynthesis. The combined analysis of transcriptome and metabolism unveiled the molecular mechanism of oil accumulation, leading to the creation of a metabolic pathway pattern diagram for oil biosynthesis in S. saponaria kernels. The study of soapberry fruit development, kernel oil accumulation, and the molecular mechanism of oil biosynthesis holds great significance in increasing oil yield and improving oil quality.

Membranes that make fat: roles of membrane lipids as acyl donors for triglyceride synthesis and organelle function

Triglycerides constitute an inert storage form for fatty acids deposited in lipid droplets and are mobilized to provide metabolic energy or membrane building blocks. The biosynthesis of triglycerides is highly conserved within eukaryotes and normally involves the sequential esterification of activated fatty acids with a glycerol backbone. Some eukaryotes, however, can also use cellular membrane lipids as direct fatty acid donors for triglyceride synthesis. The biological significance of a pathway that generates triglycerides at the expense of organelle membranes has remained elusive. Here we review current knowledge on how cells use membrane lipids as fatty acid donors for triglyceride synthesis and discuss the hypothesis that a primary function of this pathway is to regulate membrane lipid remodeling and organelle function.

Identification of triacylglycerol remodeling mechanism to synthesize unusual fatty acid containing oils

Typical plant membranes and storage lipids are comprised of five common fatty acids yet over 450 unusual fatty acids accumulate in seed oils of various plant species. Plant oils are important human and animal nutrients, while some unusual fatty acids such as hydroxylated fatty acids (HFA) are used in the chemical industry (lubricants, paints, polymers, cosmetics, etc.). Most unusual fatty acids are extracted from non-agronomic crops leading to high production costs. Attempts to engineer HFA into crops are unsuccessful due to bottlenecks in the overlapping pathways of oil and membrane lipid synthesis where HFA are not compatible. Physaria fendleri naturally overcomes these bottlenecks through a triacylglycerol (TAG) remodeling mechanism where HFA are incorporated into TAG after initial synthesis. TAG remodeling involves a unique TAG lipase and two diacylglycerol acyltransferases (DGAT) that are selective for different stereochemical and acyl-containing species of diacylglycerol within a synthesis, partial degradation, and resynthesis cycle. The TAG lipase interacts with DGAT1, localizes to the endoplasmic reticulum (with the DGATs) and to puncta around the lipid droplet, likely forming a TAG remodeling metabolon near the lipid droplet-ER junction. Each characterized DGAT and TAG lipase can increase HFA accumulation in engineered seed oils.

Overexpression of the Phosphatidylcholine:DiacylglycerolCholinephosphotransferase (PDCT) gene increases carbon flux toward triacylglycerol (TAG) synthesis in Camelinasativa seeds

Camelinasativa has considerable promise as a dedicated industrial oilseed crop. Its oil-based blends have been tested and approved as liquid transportation fuels. Previously, we utilized metabolomic and transcriptomic profiling approaches and identified metabolic bottlenecks that control oil production and accumulation in seeds. Accordingly, we selected candidate genes for the metabolic engineering of Camelina. Here we targeted the overexpression of Camelina PDCT gene, which encodes the phosphatidylcholine: diacylglycerol cholinephosphotransferase enzyme. PDCT is proposed as a gatekeeper responsible for the interconversions of diacylglycerol (DAG) and phosphatidylcholine (PC) pools and has the potential to increase the levels of TAG in seeds. To confirm whether increased CsPDCT activity in developing Camelina seeds would enhance carbon flux toward increased levels of TAG and alter oil composition, we overexpressed the CsPDCT gene under the control of the seed-specific phaseolin promoter. Camelina transgenics exhibited significant increases in seed yield (19-56%), seed oil content (9-13%), oil yields per plant (32-76%), and altered polyunsaturated fatty acid (PUFA) content compared to their parental wild-type (WT) plants. Results from [14C] acetate labeling of Camelina developing embryos expressing CsPDCT in culture indicated increased rates of radiolabeled fatty acid incorporation into glycerolipids (up to 64%, 59%, and 43% higher in TAG, DAG, and PC, respectively), relative to WT embryos. We conclude that overexpression of PDCT appears to be a positive strategy to achieve a synergistic effect on the flux through the TAG synthesis pathway, thereby further increasing oil yields in Camelina.

Targeted mutagenesis of flavonoid biosynthesis pathway genes reveals functional divergence in seed coat colour, oil content and fatty acid composition in Brassica napus L

Yellow-seed is widely accepted as a good-quality trait in Brassica crops. Previous studies have shown that the flavonoid biosynthesis pathway is essential for the development of seed colour, but its function in Brassica napus, an important oil crop, is poorly understood. To systematically explore the gene functions of the flavonoid biosynthesis pathway in rapeseed, several representative TRANSPARENT TESTA (TT) genes, including three structural genes (BnaTT7, BnaTT18, BnaTT10), two regulatory genes (BnaTT1, BnaTT2) and a transporter (BnaTT12), were selected for targeted mutation by CRISPR/Cas9 in the present study. Seed coat colour, lignin content, seed quality and yield-related traits were investigated in these Bnatt mutants together with Bnatt8 generated previously. These Bnatt mutants produced seeds with an elevated seed oil content and decreased pigment and lignin accumulation in the seed coat without any serious defects in the yield-related traits. In addition, the fatty acid (FA) composition was also altered to different degrees, i.e., decreased oleic acid and increased linoleic acid and α-linolenic acid, in all Bnatt mutants except Bnatt18. Furthermore, gene expression analysis revealed that most of BnaTT mutations resulted in the down-regulation of key genes related to flavonoid and lignin synthesis, and the up-regulation of key genes related to lipid synthesis and oil body formation, which may contribute to the phenotype. Collectively, our study generated valuable resources for breeding programs, and more importantly demonstrated the functional divergence and overlap of flavonoid biosynthesis pathway genes in seed coat colour, oil content and FA composition of rapeseed.

Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds

Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.

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

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

Genome-Wide Analysis of Glycerol-3-Phosphate Acyltransferase (GPAT) Family in Perilla frutescens and Functional Characterization of PfGPAT9 Crucial for Biosynthesis of Storage Oils Rich in High-Value Lipids

Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the first step in triacylglycerol (TAG) biosynthesis. However, GPAT members and their functions remain poorly understood in Perilla frutescens, a special edible-medicinal plant with its seed oil rich in polyunsaturated fatty acids (mostly α-linolenic acid, ALA). Here, 14 PfGPATs were identified from the P. frutescens genome and classified into three distinct groups according to their phylogenetic relationships. These 14 PfGPAT genes were distributed unevenly across 11 chromosomes. PfGPAT members within the same subfamily had highly conserved gene structures and four signature functional domains, despite considerable variations detected in these conserved motifs between groups. RNA-seq and RT-qPCR combined with dynamic analysis of oil and FA profiles during seed development indicated that PfGPAT9 may play a crucial role in the biosynthesis and accumulation of seed oil and PUFAs. Ex vivo enzymatic assay using the yeast expression system evidenced that PfGPAT9 had a strong GPAT enzyme activity crucial for TAG assembly and also a high substrate preference for oleic acid (OA, C18:1) and ALA (C18:3). Heterogeneous expression of PfGPAT9 significantly increased total oil and UFA (mostly C18:1 and C18:3) levels in both the seeds and leaves of the transgenic tobacco plants. Moreover, these transgenic tobacco lines exhibited no significant negative effect on other agronomic traits, including plant growth and seed germination rate, as well as other morphological and developmental properties. Collectively, our findings provide important insights into understanding PfGPAT functions, demonstrating that PfGPAT9 is the desirable target in metabolic engineering for increasing storage oil enriched with valuable FA profiles in oilseed crops.

Integrated lipidomic and transcriptomic analyses reveal the mechanism of lipid biosynthesis and accumulation during seed development in sesame

Sesame is one of the most important oilseed crops and attracts significant attention because of its huge nutritional capacity. However, the molecular mechanisms underlying oil accumulation in sesame remains poorly understood. In this study, lipidomic and transcriptomic analyses in different stages of sesame seed (Luzhi No.1, seed oil content 56%) development were performed to gain insight into the regulatory mechanisms that govern differences in lipid composition, content, biosynthesis, and transport. In total, 481 lipids, including fatty acids (FAs, 38 species), triacylglycerol (TAG, 127 species), ceramide (33 species), phosphatidic acid (20 species), and diacylglycerol (17 species), were detected in developing sesame seed using gas and liquid chromatography-mass spectrometry. Most FAs and other lipids accumulated 21-33 days after flowering. RNA-sequence profiling in developing seed highlighted the enhanced expression of genes involved in the biosynthesis and transport of FAs, TAGs, and membrane lipids, which was similar to that seen during lipid accumulation. Through the differential expression analysis of genes involved in lipid biosynthesis and metabolism during seed development, several candidate genes were found to affect the oil content and FA composition of sesame seed, including ACCase, FAD2, DGAT, G3PDH, PEPCase, WRI1 and WRI1-like genes. Our study reveals the patterns of lipid accumulation and biosynthesis-related gene expression and lays an important foundation for the further exploration of sesame seed lipid biosynthesis and accumulation.

WRINKLED1 Positively Regulates Oil Biosynthesis in Carya cathayensis

Hickory (Carya cathayensis Sarg.) is a kind of important woody oil tree species, and its nut has high nutritional value. Previous gene coexpression analysis showed that WRINKLED1 (WRI1) may be a core regulator during embryo oil accumulation in hickory. However, its specific regulatory mechanism on hickory oil biosynthesis has not been investigated. Herein, two hickory orthologs of WRI1 (CcWRI1A and CcWRI1B) containing two AP2 domains with AW-box binding sites and three intrinsically disordered regions (IDRs) but lacking the PEST motif in the C-terminus were characterized. They are nucleus-located and have self-activated ability. The expression of these two genes was tissue-specific and relatively high in the developing embryo. Notably, CcWRI1A and CcWRI1B can restore the low oil content, shrinkage phenotype, composition of fatty acid, and expression of oil biosynthesis pathway genes of Arabidopsis wri1-1 mutant seeds. Additionally, CcWRI1A/B were shown to modulate the expression of some fatty acid biosynthesis genes in the transient expression system of nonseed tissues. Transcriptional activation analysis further indicated that CcWRI1s directly activated the expression of SUCROSE SYNTHASE2 (SUS2), PYRUVATE KINASE β SUBUNIT 1 (PKP-β1), and BIOTIN CARBOXYL CARRIER PROTEIN2 (BCCP2) involved in oil biosynthesis. These results suggest that CcWRI1s can promote oil synthesis by upregulating some late glycolysis- and fatty acid biosynthesis-related genes. This work reveals the positive function of CcWRI1s in oil accumulation and provides a potential target for improving plant oil by bioengineering technology.

Metabolic Control Analysis of triacylglycerol accumulation in oilseed rape

The increasing global demand for vegetable oils will only be met if there are significant improvements in the productivity of the major oil crops, such as oilseed rape. Metabolic engineering offers the prospect of further gains in yield beyond that already achieved by breeding and selection but requires guidance as to the changes that need to be made. Metabolic Control Analysis, through measurement and estimation of flux control coefficients, can indicate which enzymes have the most influence on a desired flux. Some experiments have previously reported flux control coefficients for oil accumulation in the seeds of oilseed rape, and others have measured control coefficient distributions for multi-enzyme segments of oil synthesis in seed embryo metabolism measured in vitro. In addition, other reported manipulations of oil accumulation contain results that are exploited further here to calculate previously unknown flux control coefficients. These results are then assembled within a framework that allows an integrated interpretation of the controls on oil accumulation from the assimilation of CO₂ to deposition of oil in the seed. The analysis shows that the control is distributed to an extent that the gains from amplifying any single target are necessarily limited, but there are candidates for joint amplification that are likely to act synergistically to produce much more significant gains.

High triacylglycerol turnover is required for efficient opening of stomata during heat stress in Arabidopsis

Heat stress triggers the accumulation of triacylglycerols in Arabidopsis leaves, which increases basal thermotolerance. However, how triacylglycerol synthesis is linked to thermotolerance remains unclear and the mechanisms involved remain to be elucidated. It has been shown that triacylglycerol and starch degradation are required to provide energy for stomatal opening induced by blue light at dawn. To investigate whether triacylglycerol turnover is involved in heat-induced stomatal opening during the day, we performed feeding experiments with labeled fatty acids. Heat stress strongly induced both triacylglycerol synthesis and degradation to channel fatty acids destined for peroxisomal ß-oxidation through the triacylglycerol pool. Analysis of mutants defective in triacylglycerol synthesis or peroxisomal fatty acid uptake revealed that triacylglycerol turnover and fatty acid catabolism are required for heat-induced stomatal opening in illuminated leaves. We show that triacylglycerol turnover is continuous (1.2 mol% per min) in illuminated leaves even at 22°C. The ß-oxidation of triacylglycerol-derived fatty acids generates C₂ carbon units that are channeled into the tricarboxylic acid pathway in the light. In addition, carbohydrate catabolism is required to provide oxaloacetate as an acceptor for peroxisomal acetyl-CoA and maintain the tricarboxylic acid pathway for energy and amino acid production during the day.

Assessing the biotechnological potential of cotton type-1 and type-2 diacylglycerol acyltransferases in transgenic systems

The chemical and physical properties of vegetable oils are largely dictated by the ratios of 4-6 common fatty acids contained within each oil. However, examples of plant species that accumulate from trace amounts to >90% of certain unusual fatty acids in seed triacylglycerols have been reported. Many of the general enzymatic reactions that drive both common and unusual fatty acid biosynthesis and accumulation in stored lipids are known, but which isozymes have evolved to specifically fill this role and how they coordinate in vivo is still poorly understood. Cotton (Gossypium sp.) is the very rare example of a commodity oilseed that produces biologically relevant amounts of unusual fatty acids in its seeds and other organs. In this case, unusual cyclopropyl fatty acids (named after the cyclopropane and cyclopropene moieties within the fatty acids) are found in membrane and storage glycerolipids (e.g. seed oils). Such fatty acids are useful in the synthesis of lubricants, coatings, and other types of valuable industrial feedstocks. To characterize the role of cotton acyltransferases in cyclopropyl fatty acid accumulation for bioengineering applications, we cloned and characterized type-1 and type-2 diacylglycerol acyltransferases from cotton and compared their biochemical properties to that of litchi (Litchi chinensis), another cyclopropyl fatty acid-producing plant. The results presented from transgenic microbes and plants indicate both cotton DGAT1 and DGAT2 isozymes efficiently utilize cyclopropyl fatty acid-containing substrates, which helps to alleviate biosynthetic bottlenecks and enhances total cyclopropyl fatty acid accumulation in the seed oil.

Recent progress in molecular genetics and omics-driven research in seed biology

Elucidating the mechanisms that control seed development, metabolism, and physiology is a fundamental issue in biology. Michel Caboche had long been a catalyst for seed biology research in France up until his untimely passing away last year. To honour his memory, we have updated a review written under his coordination in 2010 entitled "Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research". This review encompassed different molecular aspects of seed development, reserve accumulation, dormancy and germination, that are studied in the lab created by M. Caboche. We have extended the scope of this review to highlight original experimental approaches implemented in the field over the past decade such as omics approaches aimed at investigating the control of gene expression, protein modifications, primary and specialized metabolites at the tissue or even cellular level, as well as seed biodiversity and the impact of the environment on seed quality.

Characterization and functional analysis of AhGPAT9 gene involved in lipid synthesis in peanut (Arachis hypogaea L.)

GPAT enzymes (glycerol-3-phosphate 1-O-acyltransferase, EC 2.3.1.15) catalyze the initial and rate-limiting step of plant glycerolipid biosynthesis for membrane homeostasis and lipid accumulation, yet little research has been done on peanuts. By reverse genetics and bioinformatics analyses, we have characterized an AhGPAT9 isozyme, of which the homologous product is isolated from cultivated peanut. QRT-PCR assay revealed a spatio-temporal expression pattern that the transcripts of AhGPAT9 accumulating in various peanut tissues are highly expressed during seed development, followed by leaves. Green fluorescent protein tagging of AhGPAT9 confirmed its subcellular accumulation in the endoplasmic reticulum. Compared with the wild type control, overexpressed AhGPAT9 delayed the bolting stage of transgenic Arabidopsis, reduced the number of siliques, and increased the seed weight as well as seed area, suggesting the possibility of participating in plant growth and development. Meanwhile, the mean seed oil content from five overexpression lines increased by about 18.73%. The two lines with the largest increases in seed oil content showed a decrease in palmitic acid (C16:0) and eicosenic acid (C20:1) by 17.35% and 8.33%, respectively, and an increase in linolenic acid (C18:3) and eicosatrienoic acid (C20:3) by 14.91% and 15.94%, respectively. In addition, overexpressed AhGPAT9 had no significant effect on leaf lipid content of transgenic plants. Taken together, these results suggest that AhGPAT9 is critical for the biosynthesis of storage lipids, which contributes to the goal of modifying peanut seeds for improved oil content and fatty acid composition.

Evaluation of oil accumulation and biodiesel property of Lindera glauca fruits among different germplasms and revelation of high oil producing mechanism for developing biodiesel

BACKGROUND

Lindera glauca with rich resource and fruit oil has emerged as novel source of biodiesel in China, but different germplasms show a variation for fruit oil content and FA profile. To develop L. glauca fruit oils as biodiesel, a concurrent exploration of oil content, FA composition, biodiesel yield, fuel property and prediction model construction was conducted on the fruits from 8 plus germplasms to select superior genotype for ideal biodiesel production. Another vital focus was to highlight mechanism that govern the differences in oil content and FA profile of different germplasms. The cross-accessions comparisons associated with oil-synthesized gene transcriptional level and oil accumulative amount led to the identification of potential determinants (enzymes, transporters or transcription factors) and regulatory mechanisms responsible for high-quality oil accumulation.

RESULTS

To select superior germplasm and unravel regulatory mechanism of high oil production for developing L. glauca fruit oils as biodiesel, 8 plus trees (accession LG01/02/03/04/05/06/07/08) with high-yield fruits were selected to evaluate the differences in oil content, FA profile, biodiesel yield and fuel property, and to construct fuel property prediction model, revealing a variation in the levels of fruit oil (45.12-60.95%), monounsaturated FA (52.43-78.46%) and polyunsaturated FA (17.69-38.73%), and biodiesel yield (80.12-98.71%) across different accessions. Of note, LG06 had a maximum yield of oil (60.95%) and biodiesel (98.71%), and ideal proportions of C18:1 (77.89%), C18:2 (14.16%) and C18:3 (1.55%), indicating that fruit oils from accession LG06 was the most suitable for high-quality biodiesel production. To highlight molecular mechanism that govern such differences in oil content and FA composition of different accessions, the quantitative relationship between oil-synthesized gene transcription and oil accumulative amount were conducted on different accessions to identify some vital determinants (enzymes, transporters or transcription factors) with a model of carbon metabolic regulatory for high-quality oil accumulation by an integrated analysis of our recent transcriptome data and qRT-PCR detection. Our findings may present strategies for developing L. glauca fruit oils as biodiesel feedstock and engineering its oil accumulation.

CONCLUSIONS

This is the first report on the cross-accessions evaluations of L. glauca fruit oils to determine ideal accession for producing ideal biodiesel, and the associations of oil accumulative amount with oil-synthesized gene transcription was performed to identify some crucial determinants (enzymes, transporters or transcription factors) with metabolic regulation model established for governing high oil production. Our finding may provide molecular basis for new strategies of developing biodiesel resource and engineering oil accumulation.

Bioengineering of Soybean Oil and Its Impact on Agronomic Traits

Soybean is a major oil crop and is also a dominant source of nutritional protein. The 20% seed oil content (SOC) of soybean is much lower than that in most oil crops and the fatty acid composition of its native oil cannot meet the specifications for some applications in the food and industrial sectors. Considerable effort has been expended on soybean bioengineering to tailor fatty acid profiles and improve SOC. Although significant advancements have been made, such as the creation of high-oleic acid soybean oil and high-SOC soybean, those genetic modifications have some negative impacts on soybean production, for instance, impaired germination or low protein content. In this review, we focus on recent advances in the bioengineering of soybean oil and its effects on agronomic traits.

Improved fatty acid composition of field cress (Lepidium campestre) by CRISPR/Cas9-mediated genome editing

The wild species field cress (Lepidium campestre) has the potential to become a novel cover and oilseed crop for the Nordic climate. Its seed oil is however currently unsuitable for most food, feed, and industrial applications, due to the high contents of polyunsaturated fatty acids (PUFAs) and erucic acid (C22:1). As the biosynthesis of these undesirable fatty acids is controlled by a few well-known major dominant genes, knockout of these genes using CRISPR/Cas9 would thus be more effective in improving the seed oil quality. In order to increase the level of the desirable oleic acid (C18:1), and reduce the contents of PUFAs and C22:1, we targeted three important genes FATTY ACID ELONGASE1 (FAE1), FATTY ACID DESATURASE2 (FAD2), and REDUCED OLEATE DESATURASE1 (ROD1) using a protoplast-based CRISPR/Cas9 gene knockout system. By knocking out FAE1, we obtained a mutated line with almost no C22:1, but an increase in C18:1 to 30% compared with 13% in the wild type. Knocking out ROD1 resulted in an increase of C18:1 to 23%, and a moderate, but significant, reduction of PUFAs. Knockout of FAD2, in combination with heterozygous FAE1fae1 genotype, resulted in mutated lines with up to 66% C18:1, very low contents of PUFAs, and a significant reduction of C22:1. Our results clearly show the potential of CRISPR/Cas9 for rapid trait improvement of field cress which would speed up its domestication process. The mutated lines produced in this study can be used for further breeding to develop field cress into a viable crop.

A lipidomics platform to analyze the fatty acid compositions of non-polar and polar lipid molecular species from plant tissues: Examples from developing seeds and seedlings of pennycress (Thlaspi arvense)

The lipidome comprises the total content of molecular species of each lipid class, and is measured using the analytical techniques of lipidomics. Many liquid chromatography-mass spectrometry (LC-MS) methods have previously been described to characterize the lipidome. However, many lipidomic approaches may not fully uncover the subtleties of lipid molecular species, such as the full fatty acid (FA) composition of certain lipid classes. Here, we describe a stepwise targeted lipidomics approach to characterize the polar and non-polar lipid classes using complementary LC-MS methods. Our "polar" method measures 260 molecular species across 12 polar lipid classes, and is performed using hydrophilic interaction chromatography (HILIC) on a NH2 column to separate lipid classes by their headgroup. Our "non-polar" method measures 254 molecular species across three non-polar lipid classes, separating molecular species on their FA characteristics by reverse phase (RP) chromatography on a C30 column. Five different extraction methods were compared, with an MTBE-based extraction chosen for the final lipidomics workflow. A state-of-the-art strategy to determine and relatively quantify the FA composition of triacylglycerols is also described. This lipidomics workflow was applied to developing, mature, and germinated pennycress seeds/seedlings and found unexpected changes among several lipid molecular species. During development, diacylglycerols predominantly contained long chain length FAs, which contrasted with the very long chain FAs of triacylglycerols in mature seeds. Potential metabolic explanations are discussed. The lack of very long chain fatty acids in diacylglycerols of germinating seeds may indicate very long chain FAs, such as erucic acid, are preferentially channeled into beta-oxidation for energy production.

Using transcriptomic and metabolomic data to investigate the molecular mechanisms that determine protein and oil contents during seed development in soybean

Soybean [Glycine max (L.) Merri.] is one of the most valuable global crops. And vegetable soybean, as a special type of soybean, provides rich nutrition in people's life. In order to investigate the gene expression networks and molecular regulatory mechanisms that regulate soybean seed oil and protein contents during seed development, we performed transcriptomic and metabolomic analyses of soybean seeds during development in two soybean varieties that differ in protein and oil contents. We identified a total of 41,036 genes and 392 metabolites, of which 12,712 DEGs and 315 DAMs were identified. Analysis of KEGG enrichment demonstrated that DEGs were primarily enriched in phenylpropanoid biosynthesis, glycerolipid metabolism, carbon metabolism, plant hormone signal transduction, linoleic acid metabolism, and the biosynthesis of amino acids and secondary metabolites. K-means analysis divided the DEGs into 12 distinct clusters. We identified candidate gene sets that regulate the biosynthesis of protein and oil in soybean seeds, and present potential regulatory patterns that high seed-protein varieties may be more sensitive to desiccation, show earlier photomorphogenesis and delayed leaf senescence, and thus accumulate higher protein contents than high-oil varieties.

Transcriptional regulation of oil biosynthesis in seed plants: Current understanding, applications, and perspectives

Plants produce and accumulate triacylglycerol (TAG) in their seeds as an energy reservoir to support the processes of seed germination and seedling development. Plant seed oils are vital not only for the human diet but also as renewable feedstocks for industrial use. TAG biosynthesis consists of two major steps: de novo fatty acid biosynthesis in the plastids and TAG assembly in the endoplasmic reticulum. The latest advances in unraveling transcriptional regulation have shed light on the molecular mechanisms of plant oil biosynthesis. We summarize recent progress in understanding the regulatory mechanisms of well-characterized and newly discovered transcription factors and other types of regulators that control plant fatty acid biosynthesis. The emerging picture shows that plant oil biosynthesis responds to developmental and environmental cues that stimulate a network of interacting transcriptional activators and repressors, which in turn fine-tune the spatiotemporal regulation of the pathway genes.

Fatty acid export (FAX) proteins contribute to oil production in the green microalga Chlamydomonas reinhardtii

In algae and land plants, transport of fatty acids (FAs) from their site of synthesis in the plastid stroma to the endoplasmic reticulum (ER) for assembly into acyl lipids is crucial for cellular lipid homeostasis, including the biosynthesis of triacylglycerol (TAG) for energy storage. In the unicellular green alga Chlamydomonas reinhardtii, understanding and engineering of these processes is of particular interest for microalga-based biofuel and biomaterial production. Whereas in the model plant Arabidopsis thaliana, FAX (fatty acid export) proteins have been associated with a function in plastid FA-export and hence TAG synthesis in the ER, the knowledge on the function and subcellular localization of this protein family in Chlamydomonas is still scarce. Among the four FAX proteins encoded in the Chlamydomonas genome, we found Cr-FAX1 and Cr-FAX5 to be involved in TAG production by functioning in chloroplast and ER membranes, respectively. By in situ immunolocalization, we show that Cr-FAX1 inserts into the chloroplast envelope, while Cr-FAX5 is located in ER membranes. Severe reduction of Cr-FAX1 or Cr-FAX5 proteins by an artificial microRNA approach results in a strong decrease of the TAG content in the mutant strains. Further, overexpression of chloroplast Cr-FAX1, but not of ER-intrinsic Cr-FAX5, doubled the content of TAG in Chlamydomonas cells. We therefore propose that Cr-FAX1 in chloroplast envelopes and Cr-FAX5 in ER membranes represent a basic set of FAX proteins to ensure shuttling of FAs from chloroplasts to the ER and are crucial for oil production in Chlamydomonas.

Carbon supply and water status regulate fatty acid and triacylglycerol biosynthesis at transcriptional level in the olive mesocarp

The relative contribution of carbon sources generated from leaves and fruits photosynthesis for triacylglycerol biosynthesis in the olive mesocarp and their interaction with water stress was investigated. With this aim, altered carbon source treatments were combined with different irrigation conditions. A higher decrease in mesocarp oil content was observed in fruits under girdled and defoliated shoot treatment compared to darkened fruit conditions, indicating that both leaf and fruit photosynthesis participate in carbon supply for oil biosynthesis being leaves the main source. The carbon supply and water status affected oil synthesis in the mesocarp, regulating the expression of DGAT and PDAT genes and implicating DGAT1-1, DGAT2, PDAT1-1, and PDAT1-2 as the principal genes responsible for triacylglycerol biosynthesis. A major role was indicated for DGAT2 and PDAT1-2 in well-watered conditions. Moreover, polyunsaturated fatty acid content together with FAD2-1, FAD2-2 and FAD7-1 expression levels were augmented in response to modified carbon supply in the olive mesocarp. Furthermore, water stress caused an increase in DGAT1-1, DGAT1-2, PDAT1-1, and FAD2-5 gene transcript levels. Overall, these data indicate that oil content and fatty acid composition in olive fruit mesocarp are regulated by carbon supply and water status, affecting the transcription of key genes in both metabolic pathways.

Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control

Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.

Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism

Soybean oil is one of the most consumed vegetable oils worldwide. Genetic improvement of its concentration in seeds has been historically pursued due to its direct association with its market value. Engineering attempts aiming to increase soybean seed oil presented different degrees of success that varied with the genetic design and the specific variety considered. Understanding the embryo's responses to the genetic modifications introduced, is a critical step to successful approaches. In this work, the metabolic and transcriptional responses to AtWRI1 and AtDGAT1 expression in soybean seeds were evaluated. AtWRI1 is a master regulator of fatty acid (FA) biosynthesis, and AtDGAT1 encodes an enzyme catalysing the final and rate-limiting step of triacylglycerides biosynthesis. The events expressing these genes in the embryo did not show an increase in total FA content, but they responded with changes in the oil and carbohydrate composition. Transcriptomic studies revealed a down-regulation of genes putatively encoding for oil body packaging proteins, and a strong induction of genes annotated as lipases and FA biosynthesis inhibitors. Novel putative AtWRI1 targets, presenting an AW-box in the upstream region of the genes, were identified by comparison with an event that harbours only AtWRI1. Lastly, targeted metabolomics analysis showed that carbon from sugar phosphates could be used for FA competing pathways, such as starch and cell wall polysaccharides, contributing to the restriction in oil accumulation. These results allowed the identification of key cellular processes that need to be considered to break the embryo's natural restriction to uncontrolled seed lipid increase.

Enhanced production of hydroxy fatty acids in Arabidopsis seed through modification of multiple gene expression

BACKGROUND

Castor (Ricinus communis L.) seeds contain unusual fatty acid, hydroxy fatty acid (HFA) used as a chemical feedstock for numerous industrial products. Castor cultivation is limited by the potent toxin ricin in its seeds and other poor agronomic traits, so it is advantageous to develop a suitable HFA-producing crop. Significant research efforts have been made to produce HFA in model Arabidopsis, but the level of HFA produced in transgenic Arabidopsis is much less than the level found in castor seeds which produce 90% HFA in seed oil.

RESULTS

We designed a transformation construct that allowed co-expression of five essential castor genes (named pCam5) involved in HFA biosynthesis, including an oleate [Formula: see text] 12-hydroxylase (FAH12), diacylglycerol (DAG) acyltransferase 2 (DGAT2), phospholipid: DAG acyltransferase 1-2 (PDAT1-2), phosphatidylcholine (PC): DAG cholinephosphotransferase (PDCT) and Lyso-PC acyltransferase (LPCAT). Transgenic Arabidopsis pCam5 lines produced HFA counting for 25% in seed oil. By knocking out Arabidopsis Fatty acid elongase 1 (AtFAE1) in pCam5 using CRISPR/Cas9 technology, the resulted pCam5-atfae1 lines produced over 31% of HFA. Astonishingly, the pCam5-atfae1 line increased seed size, weight, and total oil per seed exceeding wild type by 40%. Seed germination, seedling growth and seed mucilage content of pCam5-atfae1 lines were not affected by the genetic modification.

CONCLUSIONS

Our results provide not only insights for future research uncovering mechanisms of HFA synthesis in seed, but also metabolic engineering strategies for generating safe HFA-producing crops.

Suppression of Physaria fendleri SDP1 Increased Seed Oil and Hydroxy Fatty Acid Content While Maintaining Oil Biosynthesis Through Triacylglycerol Remodeling

Physaria fendleri is a burgeoning oilseed crop that accumulates the hydroxy fatty acid (HFA), lesquerolic acid, and can be a non-toxic alternative crop to castor for production of industrially valuable HFA. Recently, P. fendleri was proposed to utilize a unique seed oil biosynthetic pathway coined "triacylglycerol (TAG) remodeling" that utilizes a TAG lipase to remove common fatty acids from TAG allowing the subsequent incorporation of HFA after initial TAG synthesis, yet the lipase involved is unknown. SUGAR DEPENDENT 1 (SDP1) has been characterized as the dominant TAG lipase involved in TAG turnover during oilseed maturation and germination. Here, we characterized the role of a putative PfeSDP1 in both TAG turnover and TAG remodeling. In vitro assays confirmed that PfeSDP1 is a TAG lipase and demonstrated a preference for HFA-containing TAG species. Seed-specific RNAi knockdown of PfeSDP1 resulted in a 12%-16% increase in seed weight and 14%-19% increase in total seed oil content with no major effect on seedling establishment. The increase in total oil content was primarily due to ~4.7% to ~14.8% increase in TAG molecular species containing two HFA (2HFA-TAG), and when combined with a smaller decrease in 1HFA-TAG content the proportion of total HFA in seed lipids increased 4%-6%. The results are consistent with PfeSDP1 involved in TAG turnover but not TAG remodeling to produce 2HFA-TAG. Interestingly, the concomitant reduction of 1HFA-TAG in PfeSDP1 knockdown lines suggests PfeSDP1 may have a role in reverse TAG remodeling during seed maturation that produces 1HFA-TAG from 2HFA-TAG. Overall, our results provide a novel strategy to enhance the total amount of industrially valuable lesquerolic acid in P. fendleri seeds.

Different acyl-CoA:diacylglycerol acyltransferases vary widely in function, and a targeted amino acid substitution enhances oil accumulation

Triacylglycerols (TAGs) are the major component of plant storage lipids such as oils. Acyl-CoA:diacylglycerol acyltransferase (DGAT) catalyzes the final step of the Kennedy pathway, and is mainly responsible for plant oil accumulation. We previously found that the activity of Vernonia DGAT1 was distinctively higher than that of Arabidopsis and soybean DGAT1 in a yeast microsome assay. In this study, the DGAT1 cDNAs of Arabidopsis, Vernonia, soybean, and castor bean were introduced into Arabidopsis. All Vernonia DGAT1-expressing lines showed a significantly higher oil content (49% mean increase compared with the wild-type) followed by soybean and castor bean. Most Arabidopsis DGAT1-overexpressing lines did not show a significant increase. In addition to these four DGAT1 genes, sunflower, Jatropha, and sesame DGAT1 genes were introduced into a TAG biosynthesis-defective yeast mutant. In the yeast expression culture, DGAT1s from Arabidopsis, castor bean, and soybean only slightly increased the TAG content; however, DGAT1s from Vernonia, sunflower, Jatropha, and sesame increased TAG content >10-fold more than the former three DGAT1s. Three amino acid residues were characteristically common in the latter four DGAT1s. Using soybean DGAT1, these amino acid substitutions were created by site-directed mutagenesis and substantially increased the TAG content.

Overexpression of phospholipid: diacylglycerol acyltransferase in Brassica napus results in changes in lipid metabolism and oil accumulation

The regulation of lipid metabolism in oil seeds is still not fully understood and increasing our knowledge in this regard is of great economic, as well as intellectual, importance. Oilseed rape (Brassica napus) is a major global oil crop where increases in triacylglycerol (TAG) accumulation have been achieved by overexpression of relevant biosynthetic enzymes. In this study, we expressed Arabidopsis phospholipid: diacylglycerol acyltransferase (PDAT1), one of the two major TAG-forming plant enzymes in B. napus DH12075 to evaluate its effect on lipid metabolism in developing seeds and to estimate its flux control coefficient. Despite several-fold increase in PDAT activity, seeds of three independently generated PDAT transgenic events showed a small but consistent decrease in seed oil content and had altered fatty acid composition of phosphoglycerides and TAG, towards less unsaturation. Mass spectrometry imaging of seed sections confirmed the shift in lipid compositions and indicated that PDAT overexpression altered the distinct heterogeneous distributions of phosphatidylcholine (PC) molecular species. Similar, but less pronounced, changes in TAG molecular species distributions were observed. Our data indicate that PDAT exerts a small, negative, flux control on TAG biosynthesis and could have under-appreciated effects in fine-tuning of B. napus seed lipid composition in a tissue-specific manner. This has important implications for efforts to increase oil accumulation in similar crops.

Transgenic manipulation of triacylglycerol biosynthetic enzymes in B. napus alters lipid-associated gene expression and lipid metabolism

Oilseed rape (Brassica napus) is an important crop that is cultivated for the oil (mainly triacylglycerol; TAG) it produces in its seeds. TAG synthesis is controlled mainly by key enzymes in the Kennedy pathway, such as glycerol 3-phosphate acyltransferase (GPAT), lysophosphatidate acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT) but can also be produced from phosphoglycerides such as phosphatidylcholine (PC) by the activity of the enzyme phospholipid: diacylglycerol acyltransferase (PDAT). To evaluate the potential for these enzymes to alter oil yields or composition, we analysed transgenic B. napus lines which overexpressed GPAT, LPAT or PDAT using heterologous transgenes from Arabidopsis and Nasturtium and examined lipid profiles and changes in gene expression in these lines compared to WT. Distinct changes in PC and TAG abundance and spatial distribution in embryonic tissues were observed in some of the transgenic lines, together with altered expression of genes involved generally in acyl-lipid metabolism. Overall our results show that up-regulation of these key enzymes differentially affects lipid composition and distribution as well as lipid-associated gene expression, providing important information which could be used to improve crop properties by metabolic engineering.

Autophagy Improves ARA-Rich TAG Accumulation in Mortierella alpina by Regulating Resource Allocation

The present study was designed to explore the possibility of improving lipid production in oleaginous filamentous fungus Mortierella alpina based on an autophagy regulation strategy. According to multiomics information, vacuolate-centered macroautophagy was identified as the main type of autophagy in M. alpina under nitrogen-limited conditions. Mutation of autophagy-related gene MAatg8 led to impaired fatty acid synthesis, while overexpression of both MAatg8 and phosphatidylserine decarboxylases (MApsd2) showed promoting effects on fatty acid synthesis. MAatg8 overexpression strain with external supply of ethanolamine significantly increased arachidonic acid (ARA)-rich triacylglycerol (TAG) and biomass synthesis in M. alpina, and the final fatty acid content increased by approximately 110% compared with that in the wild-type strain. Metabolomics and lipidomics analyses revealed that cell autophagy enhanced the recycling of preformed carbon, nitrogen, and lipid in mycelium, and the released carbon skeleton and energy were contributed to the accumulation of TAG in M. alpina. This study suggests that regulation of autophagy-related MAatg8-phosphatidylethanolamine (MAatg8-PE) conjugation system could be a promising strategy for attaining higher lipid production and biomass growth. The mechanism of autophagy in regulating nitrogen limitation-induced lipid accumulation elucidated in this study provides a reference for development of autophagy-based strategies for improving nutrient use efficiency and high value-added lipid production by oleaginous microorganism.

IMPORTANCE Studies have indicated that functional oil accumulation occurs in oleaginous microorganisms under nitrogen limitation. However, until now, large-scale application of nitrogen-deficiency strategies was limited by low biomass. Therefore, the identification of the critical nodes of nitrogen deficiency-induced lipid accumulation is urgently needed to further guide functional oil production. The significance of our research is in uncovering the function of cell autophagy in the ARA-rich TAG accumulation of oleaginous fungus M. alpina and demonstrating the feasibility of improving lipid production based on an autophagy regulation strategy at the molecular and omics levels. Our study proves that regulation of cell autophagy through the MAatg8-PE conjugation system-related gene overexpression or exogenous supply of ethanolamine would be an efficient strategy to increase and maintain biomass productivity when high TAG content is obtained under nitrogen deficiency, which could be useful for the development of new strategies that will achieve more biomass and maximal lipid productivity.

Triacylglycerol remodeling in Physaria fendleri indicates oil accumulation is dynamic and not a metabolic endpoint

Oilseed plants accumulate triacylglycerol (TAG) up to 80% of seed weight with the TAG fatty acid composition determining its nutritional value or use in the biofuel or chemical industries. Two major pathways for production of diacylglycerol (DAG), the immediate precursor to TAG, have been identified in plants: de novo DAG synthesis and conversion of the membrane lipid phosphatidylcholine (PC) to DAG, with each pathway producing distinct TAG compositions. However, neither pathway fits with previous biochemical and transcriptomic results from developing Physaria fendleri seeds for accumulation of TAG containing >60% lesquerolic acid (an unusual 20 carbon hydroxylated fatty acid), which accumulates at only the sn-1 and sn-3 positions of TAG. Isotopic tracing of developing P. fendleri seed lipid metabolism identified that PC-derived DAG is utilized to initially produce TAG with only one lesquerolic acid. Subsequently a nonhydroxylated fatty acid is removed from TAG (transiently reproducing DAG) and a second lesquerolic acid is incorporated. Thus, a dynamic TAG remodeling process involving anabolic and catabolic reactions controls the final TAG fatty acid composition. Reinterpretation of P. fendleri transcriptomic data identified potential genes involved in TAG remodeling that could provide a new approach for oilseed engineering by altering oil fatty acid composition after initial TAG synthesis; and the comparison of current results to that of related Brassicaceae species in the literature suggests the possibility of TAG remodeling involved in incorporation of very long-chain fatty acids into the TAG sn-1 position in various plants.