Biochemical pathways in seed oil synthesis

Fat storage-inducing transmembrane (FIT or FITM) proteins are related to lipid phosphatase/phosphotransferase enzymes

Fat storage-inducing transmembrane (FIT or FITM) proteins have been implicated in the partitioning of triacylglycerol to lipid droplets and the budding of lipid droplets from the ER. At the molecular level, the sole relevant interaction is that FITMs directly bind to triacyglycerol and diacylglycerol, but how they function at the molecular level is not known. Saccharomyces cerevisiae has two FITM homologues: Scs3p and Yft2p. Scs3p was initially identified because deletion leads to inositol auxotrophy, with an unusual sensitivity to addition of choline. This strongly suggests a role for Scs3p in phospholipid biosynthesis. Looking at the FITM family as widely as possible, we found that FITMs are widespread throughout eukaryotes, indicating presence in the last eukaryotic common ancestor. Protein alignments also showed that FITM sequences contain the active site of lipid phosphatase/phosphotransferase (LPT) enzymes. This large family transfers phosphate-containing headgroups either between lipids or in exchange for water. We confirmed the prediction that FITMs are related to LPTs by showing that single amino-acid substitutions in the presumptive catalytic site prevented their ability to rescue growth of the mutants on low inositol/high choline media when over-expressed. The substitutions also prevented rescue of other phenotypes associated with loss of FITM in yeast, including mistargeting of Opi1p, defective ER morphology, and aberrant lipid droplet budding. These results suggest that Scs3p, Yft2p and FITMs in general are LPT enzymes involved in an as yet unknown critical step in phospholipid metabolism.

Using lipidomics to reveal details of lipid accumulation in developing seeds from oilseed rape (Brassica napus L.)

With dwindling available agricultural land, concurrent with increased demand for oil, there is much current interest in raising oil crop productivity. We have been addressing this issue by studying the regulation of oil accumulation in oilseed rape (Brassica napus L). As part of this research we have carried out a detailed lipidomic analysis of developing seeds.

The molecular species distribution in individual lipid classes revealed quite distinct patterns and showed where metabolic connections were important. As the seeds developed, the molecular species distributions changed, especially in the period of early (20 days after flowering, DAF) to mid phase (27DAF) of oil accumulation. The patterns of molecular species of diacylglycerol, phosphatidylcholine and acyl-CoAs were used to predict the possible relative contributions of diacylglycerol acyltransferase (DGAT) and phospholipid:diacylglycerol acyltransferase to triacylglycerol production. Our calculations suggest that DGAT may hold a more important role in influencing the molecular composition of TAG. Enzyme selectivity had an important influence on the final molecular species patterns.

Our data contribute significantly to our understanding of lipid accumulation in the world's third most important oil crop.

•

Lipidomic analysis of developing rapeseed seeds is reported

•

Results show distinct differences between lipid classes

•

Changes in molecular species distributions were found during development

•

The data were used to evaluate the contribution of different synthetic pathways

A reconfigured Kennedy pathway which promotes efficient accumulation of medium-chain fatty acids in leaf oils

Medium-chain fatty acids (MCFA, C6-14 fatty acids) are an ideal feedstock for biodiesel and broader oleochemicals. In recent decades, several studies have used transgenic engineering to produce MCFA in seeds oils, although these modifications result in unbalance membrane lipid profiles that impair oil yields and agronomic performance. Given the ability to engineer nonseed organs to produce oils, we have previously demonstrated that MCFA profiles can be produced in leaves, but this also results in unbalanced membrane lipid profiles and undesirable chlorosis and cell death. Here we demonstrate that the introduction of a diacylglycerol acyltransferase from oil palm, EgDGAT1, was necessary to channel nascent MCFA directly into leaf oils and therefore bypassing MCFA residing in membrane lipids. This pathway resulted in increased flux towards MCFA rich leaf oils, reduced MCFA in leaf membrane lipids and, crucially, the alleviation of chlorosis. Deep sequencing of African oil palm (Elaeis guineensis) and coconut palm (Cocos nucifera) generated candidate genes of interest, which were then tested for their ability to improve oil accumulation. Thioesterases were explored for the production of lauric acid (C12:0) and myristic (C14:0). The thioesterases from Umbellularia californica and Cinnamomum camphora produced a total of 52% C12:0 and 40% C14:0, respectively, in transient leaf assays. This study demonstrated that the introduction of a complete acyl-CoA-dependent pathway for the synthesis of MFCA-rich oils avoided disturbing membrane homoeostasis and cell death phenotypes. This study outlines a transgenic strategy for the engineering of biomass crops with high levels of MCFA rich leaf oils.

Analysis of the biosynthetic process of fatty acids in Thraustochytrium

Thraustochytrium is a marine protist producing a specific profile of nutritionally important fatty acids, including very long chain polyunsaturated fatty acids (VLCPUFAs) docosahexaenoic acid (DHA, 22:6n-3), even chain saturated fatty acids (SFAs) palmitic acid (16:0), and odd chain SFAs pentadecanoic acid (15:0). To study how these fatty acids are synthesized, a series of radiolabeled precursors were used to trace the biosynthetic process in vivo and in vitro. When Thraustochytrium was fed with long chain fatty acid intermediates such as [1-¹⁴C]-oleic acid, [1-¹⁴C]-linoleic acid and [1-¹⁴C]-α-linolenic acid, no VLCPUFAs were produced, indicating that the aerobic pathway for the biosynthesis of VLCPUFAs was not functional in Thraustochytrium. When fed with [1-¹⁴C]-acetic acid, both SFAs and VLCPUFAs were labeled, and when fed with [1-¹⁴C]-propionic acid, mainly SFAs were labeled. However, when fed with [1-¹⁴C]-acetic acid in the presence of cerulenin, a type I FAS inhibitor, only VLCPUFAs were labeled, and when fed with [1-¹⁴C]-propionic acid in the presence of cerulenin, neither SFAs nor VLCPUFAs were labeled. This result clearly indicates that the type I fatty acid synthase (FAS) in Thraustochytrium could use acetic acid and propionic acid as the primers to synthesize even chain and odd chain SFAs, respectively, and VLCPUFAs were synthesized by the PUFA synthase using acetic acid as the primer. In addition, radioactive acetic acid could label both phospholipids (PL) and triacylglycerols (TAG), and VLCPUFAs appeared first and were largely accumulated in PL, whereas TAG accumulated much more SFAs than VLCPUFAs. The in vitro assay with [1-¹⁴C]-malonyl-CoA in presence of cerulenin showed that the crude protein of Thraustochytrium produced only VLCPUFAs, not SFAs, further confirming the role of the PUFA synthase in the biosynthesis of VLCPUFAs. Collectively, these results have elucidated the biochemical mechanisms for the biosynthesis of all fatty acids in Thraustochytrium.

Genome of wild olive and the evolution of oil biosynthesis

Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics.

PrLPAAT4, a Putative Lysophosphatidic Acid Acyltransferase from Paeonia rockii, Plays an Important Role in Seed Fatty Acid Biosynthesis

Lysophosphatidic acid acyltransferases (LPAATs) are essential for the acylation of lysophosphatidic acid (LPA) and the synthesis of phosphatidic acid (PA), a key intermediate in the synthesis of membrane phospholipids and storage lipids. Here, a putative lysophosphatidic acid acyltransferase gene, designated PrLPAAT4, was isolated from seed unsaturated fatty acid (UFA)-rich P. rockii. The complete PrLPAAT4 cDNA contained a 1116-bp open reading frame (ORF), encoding a 42.9 kDa protein with 371 amino acid residues. Bioinformatic analysis indicates that PrLPAAT4 is a plasma membrane protein belonging to acyl-CoA:1-acylglycerol-sn-3-phosphate acyltranferases (AGPAT) family. PrLPAAT4 shared high sequence similarity with its homologs from Citrus clementina, Populus trichocarpa, Manihot esculenta, and Ricinus communis. In Arabidopsis, overexpression of PrLPAAT4 resulted in a significant increase in the content of oleic acid (OA) and total fatty acids (FAs) in seeds. AtDGAT1, AtGPAT9, and AtOleosin, involved in TAG assembly, were upregulated in PrLPAAT4-overexpressing lines. These results indicated that PrLPAAT4 functions may be as a positive regulator in seed FA biosynthesis.

Oil body biogenesis and biotechnology in legume seeds

The seeds of many legume species including soybean, Pongamia pinnata and the model legume Medicago truncatula store considerable oil, apart from protein, in their cotyledons. However, as a group, legume storage strategies are quite variable and provide opportunities for better understanding of carbon partitioning into different storage products. Legumes with their ability to fix nitrogen can also increase the sustainability of agricultural systems. This review integrates the cell biology, biochemistry and molecular biology of oil body biogenesis before considering biotechnology strategies to enhance oil body biosynthesis. Cellular aspects of packaging triacylglycerol (TAG) into oil bodies are emphasized. Enhancing seed oil content has successfully focused on the up-regulation of the TAG biosynthesis pathways using overexpression of enzymes such as diacylglycerol acyltransferase1 and transcription factors such as WRINKLE1 and LEAFY COTYLEDON1. While these strategies are central, decreasing carbon flow into other storage products and maximizing the packaging of oil bodies into the cytoplasm are other strategies that need further examination. Overall there is much potential for integrating carbon partitioning, up-regulation of fatty acid and TAG synthesis and oil body packaging, for enhancing oil levels. In addition to the potential for integrated strategies to improving oil yields, the capacity to modify fatty acid composition and use of oil bodies as platforms for the production of recombinant proteins in seed of transgenic legumes provide other opportunities for legume biotechnology.

Review: Metabolic engineering of unusual lipids in the synthetic biology era

The plant kingdom produces a variety of fatty acid structures, many of which possess functional groups useful for industrial applications. The species that produce these unusual fatty acids are often not suitable for large scale commercial production. The ability to create genetically modified plants, together with emerging synthetic biology approaches, offers the potential to develop alternative oil seed crops capable of producing high levels of modified lipids. In some cases, by combining genes from different species, non-natural lipids with a targeted structure can be conceived. However, the expression of the biosynthetic enzymes responsible for the synthesis of unusual fatty acids typically results in poor accumulation of the desired product. An improved understanding of fatty acid flux from synthesis to storage revealed that specialized enzymes are needed to traffic unusual fatty acids. Co-expression of some of these additional enzymes has incrementally increased the levels of unusual fatty acids in transgenic seeds. Understanding how the introduced pathways interact with the endogenous pathways will be important for further enhancing the levels of unusual fatty acids in transgenic plants. Eliminating endogenous activities, as well as segregating the different pathways, represent strategies to further increase accumulation of unusual lipids.

Unravelling a stearidonic acid-rich triacylglycerol biosynthetic pathway in the developing seeds of Buglossoides arvensis: A transcriptomic landscape

Buglossoides arvensis is an emerging oilseed crop that is rich in stearidonic acid (SDA) and has several potential applications in human health and nutrition. The molecular basis of SDA biosynthesis in this plant remains unknown due to lack of genomic information. To unravel key genes involved in SDA-rich triacylglycerol (TAG) biosynthesis, we performed transcriptome sequencing of pooled mRNA from five different developmental stages of B. arvensis seeds using Illumina NextSeq platform. De novo transcriptome assembly generated 102,888 clustered transcripts from 39.83 million high-quality reads. Of these, 62.1% and 55.54% of transcripts were functionally annotated using Uniprot-Viridiplantae and KOG databases, respectively. A total of 10,021 SSR-containing sequences were identified using the MISA tool. Deep mining of transcriptome assembly using in silico tools led to the identification of genes involved in fatty acid and TAG biosynthesis. Expression profiling of 17 key transcripts involved in fatty acid desaturation and TAG biosynthesis showed expression patterns specific to the development stage that positively correlated with polyunsaturated fatty acid accumulation in the developing seeds. This first comprehensive transcriptome analysis provides the basis for future research on understanding molecular mechanisms of SDA-rich TAG accumulation in B. arvensis and aids in biotechnological production of SDA in other oilseed crops.

Diet of Arbuscular Mycorrhizal Fungi: Bread and Butter?

Most plants entertain mutualistic interactions known as arbuscular mycorrhiza (AM) with soil fungi (Glomeromycota) which provide them with mineral nutrients in exchange for reduced carbon from the plant. Mycorrhizal roots represent strong carbon sinks in which hexoses are transferred from the plant host to the fungus. However, most of the carbon in AM fungi is stored in the form of lipids. The absence of the type I fatty acid synthase (FAS-I) complex from the AM fungal model species Rhizophagus irregularis suggests that lipids may also have a role in nutrition of the fungal partner. This hypothesis is supported by the concerted induction of host genes involved in lipid metabolism. We explore the possible roles of lipids in the light of recent literature on AM symbiosis.

Characterisation of phospholipid: diacylglycerol acyltransferases (PDATs) from Camelina sativa and their roles in stress responses

As an important oilseed worldwide, Camelina sativa is being increasingly explored for its use in production of food, feed, biofuel and industrial chemicals. However, detailed mechanisms of camelina oil biosynthesis and accumulation, particularly in vegetative tissues, are understood to a very small extent. Here, we present genome-wide identification, cloning and functional analysis of phospholipid diacylglycerol acyltransferase (PDAT) in C. sativa, which catalyses the final acylation step in triacylglycerol (TAG) biosynthesis by transferring a fatty acyl moiety from a phospholipid to diacylglycerol (DAG). We identified five genes (namely CsPDAT1-A, B, and C and CsPDAT2-A and B) encoding PDATs from the camelina genome. CsPDAT1-A is mainly expressed in seeds, whereas CsPDAT1-C preferentially accumulates in flower and leaf tissues. High expression of CsPDAT2-A and CsPDAT2-B was detected in stem and root tissues, respectively. Cold stress induced upregulation of CsPDAT1-A and CsPDAT1-C expression by 3.5- and 2.5-fold, respectively, compared to the control. Salt stress led to an increase in CsPDAT2-B transcripts by 5.1-fold. Drought treatment resulted in an enhancement of CsPDAT2-A mRNAs by twofold and a reduction of CsPDAT2-B expression. Osmotic stress upregulated the expression of CsPDAT1-C by 3.3-fold. Furthermore, the cDNA clones of these CsPDAT genes were isolated for transient expression in tobacco leaves. All five genes showed PDAT enzymatic activity and substantially increased TAG accumulation in the leaves, with CsPDAT1-A showing a higher preference for ɑ-linolenic acid (18:3 ω-3). Overall, this study demonstrated that different members of CsPDAT family contribute to TAG synthesis in different tissues. More importantly, they are involved in different types of stress responses in camelina seedlings, providing new evidence of their roles in oil biosynthesis and regulation in camelina vegetative tissue. The identified CsPDATs may have practical applications in increasing oil accumulation and enhancing stress tolerance in other plants as well.

Summary: Five CsPDAT family members were identified from Camelina sativa and they contribute to TAG synthesis in different tissues and various stress responses, offering new targets for lipid metabolic engineering.

Tailoring the composition of novel wax esters in the seeds of transgenic Camelina sativa through systematic metabolic engineering

The functional characterization of wax biosynthetic enzymes in transgenic plants has opened the possibility of producing tailored wax esters (WEs) in the seeds of a suitable host crop. In this study, in addition to systematically evaluating a panel of WE biosynthetic activities, we have also modulated the acyl-CoA substrate pool, through the co-expression of acyl-ACP thioesterases, to direct the accumulation of medium-chain fatty acids. Using this combinatorial approach, we determined the additive contribution of both the varied acyl-CoA pool and biosynthetic enzyme substrate specificity to the accumulation of non-native WEs in the seeds of transgenic Camelina plants. A total of fourteen constructs were prepared containing selected FAR and WS genes in combination with an acyl-ACP thioesterase. All enzyme combinations led to the successful production of wax esters, of differing compositions. The impact of acyl-CoA thioesterase expression on wax ester accumulation varied depending on the substrate specificity of the WS. Hence, co-expression of acyl-ACP thioesterases with Marinobacter hydrocarbonoclasticus WS and Marinobacter aquaeolei FAR resulted in the production of WEs with reduced chain lengths, whereas the co-expression of the same acyl-ACP thioesterases in combination with Mus musculus WS and M. aquaeolei FAR had little impact on the overall final wax composition. This was despite substantial remodelling of the acyl-CoA pool, suggesting that these substrates were not efficiently incorporated into WEs. These results indicate that modification of the substrate pool requires careful selection of the WS and FAR activities for the successful high accumulation of these novel wax ester species in Camelina seeds.

Transcriptome Analysis of Genes Involved in Lipid Biosynthesis in the Developing Embryo of Pecan (Carya illinoinensis)

Pecan (Carya illinoinensis) is an important woody tree species because of the high content of healthy oil in its nut. Thus far, the pathways and key genes related to oil biosynthesis in developing pecan seeds remain largely unclear. Our analyses revealed that mature pecan embryo accumulated more than 80% oil, in which 90% was unsaturated fatty acids with abundant oleic acid. RNA sequencing generated 84,643 unigenes in three cDNA libraries prepared from pecan embryos collected at 105, 120, and 165 days after flowering (DAF). We identified 153 unigenes associated with lipid biosynthesis, including 107 unigenes for fatty acid biosynthesis, 34 for triacylglycerol biosynthesis, 7 for oil bodies, and 5 for transcription factors involved in oil synthesis. The genes associated with fatty acid synthesis were the most abundantly expressed genes at 120 DAF. Additionally, the biosynthesis of oil began to increase while crude fat contents increased from 16.61 to 74.45% (165 DAF). We identified four SAD, two FAD2, one FAD6, two FAD7, and two FAD8 unigenes responsible for unsaturated fatty acid biosynthesis. However, FAD3 homologues were not detected. Consequently, we inferred that the linolenic acid in developing pecan embryos is generated by FAD7 and FAD8 in plastids rather than FAD3 in endoplasmic reticula. During pecan embryo development, different unigenes are expressed for plastidial and cytosolic glycolysis. Plastidial glycolysis is more relevant to lipid synthesis than cytosolic glycolysis. The 18 most important genes associated with lipid biosynthesis were evaluated in five stages of developing embryos using quantitative PCR (qPCR). The qPCR data were well consistent with their expression in transcriptomic analyses. Our data would be important for the metabolic engineering of pecans to increase oil contents and modify fatty acid composition.

Functional photosystem I maintains proper energy balance during nitrogen depletion in Chlamydomonas reinhardtii, promoting triacylglycerol accumulation

BACKGROUND

Nutrient deprivation causes significant stress to the unicellular microalga, Chlamydomonas reinhardtii, which responds by significantly altering its metabolic program. Following N deprivation, the accumulation of starch and triacylglycerols (TAGs) is significantly altered following massive reprogramming of cellular metabolism. One protein that was found to change dramatically and early to this stress was TAB2, a photosystem I (PSI) translation initiation factor, whose transcript and protein levels increased significantly after only 30 min of N deprivation. A detailed physiological and omics-based analysis of an insertional mutant of Chlamydomonas with reduced TAB2 function was conducted to determine what role the functional PSI plays in regulating the cellular response to N deprivation.

RESULTS

The tab2 mutant displayed increased acetate assimilation and elevated starch levels during the first 6 h of N deprivation, followed by a shift toward altered amino acid synthesis, reduced TAG content and altered fatty acid profiles. These results suggested a central role for PSI in controlling cellular metabolism and its implication in regulation of lipid/starch partitioning. Time course analyses of the tab2 mutant versus wild type under N-deprived versus N replete conditions revealed changes in the ATP/NADPH ratio and suggested that TAG biosynthesis may be associated with maintaining the redox state of the cell during N deprivation. The loss of ability to accumulate TAG in the tab2 mutant co-occurred with an up-regulation of photo-protective mechanisms, suggesting that the synthesis of TAG in the wild type occurs not only as a temporal energy sink, but also as a protective electron sink.

CONCLUSIONS

By exploiting the tab2 mutation in the cells of C. reinhardtii cultured under autotrophic, mixotrophic, and heterotrophic conditions during nitrogen replete growth and for the first 8 days of nitrogen deprivation, we showed that TAG accumulation and lipid/starch partitioning are dynamically regulated by alterations in PSI function, which concomitantly alters the immediate ATP/NADPH demand. This occurs even without removal of nitrogen from the medium, but sufficient external carbon must nevertheless be available. Efforts to increase lipid accumulation in algae such as Chlamydomonas need to consider carefully how the energy balance of the cell is involved in or affected by such efforts and that numerous layers of metabolic and genetic regulatory control are likely to interfere with such efforts to control oil biosynthesis. Such knowledge will enable synthetic biology approaches to alter the response to the N depletion stress, leading to rewiring of the regulatory networks so that lipid accumulation could be turned on in the absence of N deprivation, allowing for the development of algal production strains with highly enhanced lipid accumulation profiles.

An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype

Mutagenesis is a useful tool in many crop species to induce heritable genetic variability for trait improvement and gene discovery. In this study, forward screening of a soybean fast neutron (FN) mutant population identified an individual that produced seed with nearly twice the amount of sucrose (8.1% on dry matter basis) and less than half the amount of oil (8.5% on dry matter basis) as compared to wild type. Bulked segregant analysis (BSA), comparative genomic hybridization, and genome resequencing were used to associate the seed composition phenotype with a reciprocal translocation between chromosomes 8 and 13. In a backcross population, the translocation perfectly cosegregated with the seed composition phenotype and exhibited non-Mendelian segregation patterns. We hypothesize that the translocation is responsible for the altered seed composition by disrupting a β-ketoacyl-[acyl carrier protein] synthase 1 (KASI) ortholog. KASI is a core fatty acid synthesis enzyme that is involved in the conversion of sucrose into oil in developing seeds. This finding may lead to new research directions for developing soybean cultivars with modified carbohydrate and oil seed composition.

Cocoa butter-like lipid production ability of non-oleaginous and oleaginous yeasts under nitrogen-limited culture conditions

Cocoa butter (CB) extracted from cocoa beans is the main raw material for chocolate production. However, growing chocolate demands and limited CB production has resulted in a shortage of CB supply. CB is mainly composed of three different kinds of triacylglycerols (TAGs), POP (C16:0–C18:1–C16:0), POS (C16:0–C18:1–C18:0), and SOS (C18:0–C18:1–C18:0). The storage lipids of yeasts, mainly TAGs, also contain relative high-level of C16 and C18 fatty acids and might be used as CB-like lipids (CBL). In this study, we cultivated six different yeasts, including one non-oleaginous yeast strain, Saccharomyces cerevisiae CEN.PK113-7D, and five oleaginous yeast strains, Trichosporon oleaginosus DSM11815, Rhodotorula graminis DSM 27356, Lipomyces starkeyi DSM 70296, Rhodosporidium toruloides DSM 70398, and Yarrowia lipolytica CBS 6124, in nitrogen-limited medium and compared their CBL production ability. Under the same growth conditions, we found that TAGs were the main lipids in all six yeasts and that T. oleaginosus can produce more TAGs than the other five yeasts. Less than 3% of the total TAGs were identified as potential SOS in the six yeasts. However, T. oleaginosus produced 27.8% potential POP and POS at levels of 378 mg TAGs/g dry cell weight, hinting that this yeast may have potential as a CBL production host after further metabolic engineering in future.

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as industrial materials. Gene expression profiles are powerful tools for investigating metabolic regulation in plant cells. Therefore, detailed, accurate gene expression profiles during seed development are required for crop breeding. Acquiring highly purified RNA is essential for producing these profiles. Efficient methods are needed to isolate highly purified RNA from seeds. Here, we describe a method for isolating RNA from seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method enables highly purified RNA to be obtained from seeds without the use of phenol, chloroform, or additional processes for RNA purification. This method is applicable to Arabidopsis, rapeseed, and soybean seeds. Our method will be useful for monitoring the expression patterns of low level transcripts in developing and mature seeds.

Identification of target genes and processes involved in erucic acid accumulation during seed development in the biodiesel feedstock Pennycress (Thlaspi arvense L.)

We studied erucic acid accumulation in the biodiesel feedstock Pennycress (Thlaspi arvense L.) as a first step towards the development of a sustainable strategy for biofuel production in the EU territory. To that end, two inbred Pennycress lines of European origin, "NASC" and "French," were cultivated in a controlled chamber and in experimental field plots, and their growth, seed production and seed oil characteristics analyzed. Differences in some agronomical traits like vernalization (winter-French versus spring-NASC), flowering time (delayed in the French line) and seed production (higher in the French line) were detected. Both lines showed a high amount (35-39%) of erucic acid (22:1^Δ13) in their seed oil. Biochemical characterization of the Pennycress seed oil indicated that TAG was the major reservoir of 22:1^Δ13. Incorporation of 22:1^Δ13 to TAG occurred very early during seed maturation, concomitant with a decrease of desaturase activity. This change in the acyl fluxes towards elongation was controlled by different genes at different levels. TaFAE1 gene, encoding the fatty acid elongase, seemed to be controlled at the transcriptional level with high expression at the early stages of seed development. On the contrary, the TaFAD2 gene that encodes the Δ12 fatty acid desaturase or TaDGAT1 that catalyzes TAG biosynthesis were controlled post-transcriptionally. TaWRI1, the master regulator of seed-oil biosynthesis, showed also high expression at the early stages of seed development. Our data identified genes and processes that might improve the biotechnological manipulation of Pennycress seeds for high-quality biodiesel production.

Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel

BACKGROUND

Lindera glauca fruit with high quality and quantity of oil has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of carbon flux and energy source for oil biosynthesis in developing fruits is still unknown. To better develop fruit oils of L. glauca as woody biodiesel, a combination of two different sequencing platforms (454 and Illumina) and qRT-PCR analysis was used to define a minimal reference transcriptome of developing L. glauca fruits, and to construct carbon and energy metabolic model for regulation of carbon partitioning and energy supply for FA biosynthesis and oil accumulation.

RESULTS

We first analyzed the dynamic patterns of growth tendency, oil content, FA compositions, biodiesel properties, and the contents of ATP and pyridine nucleotide of L. glauca fruits from seven different developing stages. Comprehensive characterization of transcriptome of the developing L. glauca fruit was performed using a combination of two different next-generation sequencing platforms, of which three representative fruit samples (50, 125, and 150 DAF) and one mixed sample from seven developing stages were selected for Illumina and 454 sequencing, respectively. The unigenes separately obtained from long and short reads (201, and 259, respectively, in total) were reconciled using TGICL software, resulting in a total of 60,031 unigenes (mean length = 1061.95 bp) to describe a transcriptome for developing L. glauca fruits. Notably, 198 genes were annotated for photosynthesis, sucrose cleavage, carbon allocation, metabolite transport, acetyl-CoA formation, oil synthesis, and energy metabolism, among which some specific transporters, transcription factors, and enzymes were identified to be implicated in carbon partitioning and energy source for oil synthesis by an integrated analysis of transcriptomic sequencing and qRT-PCR. Importantly, the carbon and energy metabolic model was well established for oil biosynthesis of developing L. glauca fruits, which could help to reveal the molecular regulatory mechanism of the increased oil production in developing fruits.

CONCLUSIONS

This study presents for the first time the application of an integrated two different sequencing analyses (Illumina and 454) and qRT-PCR detection to define a minimal reference transcriptome for developing L. glauca fruits, and to elucidate the molecular regulatory mechanism of carbon flux control and energy provision for oil synthesis. Our results will provide a valuable resource for future fundamental and applied research on the woody biodiesel plants.

Cloning, Characterization, and Expression Analysis of a Gene Encoding a Putative Lysophosphatidic Acid Acyltransferase from Seeds of Paeonia rockii

Tree peony (Paeonia section Moutan DC.) is an excellent woody oil crop, and the cloning and functional analysis of genes related to fatty acid (FA) metabolism from this organism has not been reported. Lysophosphatidic acid acyltransferase (LPAAT), which converts lysophosphatidic acid (LPA) to phosphatidic acid (PA), catalyzes the addition of fatty acyl moieties to the sn-2 position of the LPA glycerol backbone in triacylglycerol (TAG) biosynthesis. This project reports a putative lysophosphatidic acid acyltransferase gene PrLPAAT1 isolated from Paeonia rockii. Our data indicated that PrLPAAT1 has 1047 nucleotides and encodes a putative 38.8 kDa protein with 348 amino acid residues. Bioinformatic analysis demonstrated that PrLPAAT1 contains two transmembrane domains (TMDs). Subcellular localization analysis confirmed that PrLPAAT1 is a plasma membrane protein. Phylogenetic analysis revealed that PrLPAAT1 shared 74.3 and 65.5% amino acid sequence identities with the LPAAT1 sequences from columbine and grape, respectively. PrLPAAT1 belongs to AGPAT family, and may have acyltransferase activity. PrLPAAT1 was ubiquitously expressed in diverse tissues, and PrLPAAT1 expression was higher in the flower and developing seed. PrLPAAT1 is probably an important component in the FA accumulation process, especially during the early stages of seed development. PrLPAAT1 overexpression using a seed-specific promoter increased total FA content and the main FA accumulation in Arabidopsis transgenic plants.

Oil Biosynthesis in Underground Oil-Rich Storage Vegetative Tissue: Comparison of Cyperus esculentus Tuber with Oil Seeds and Fruits

Cyperus esculentus is unique in that it can accumulate rich oil in its tubers. However, the underlying mechanism of tuber oil biosynthesis is still unclear. Our transcriptional analyses of the pathways from pyruvate production up to triacylglycerol (TAG) accumulation in tubers revealed many distinct species-specific lipid expression patterns from oil seeds and fruits, indicating that in C. esculentus tuber: (i) carbon flux from sucrose toward plastid pyruvate could be produced mostly through the cytosolic glycolytic pathway; (ii) acetyl-CoA synthetase might be an important contributor to acetyl-CoA formation for plastid fatty acid biosynthesis; (iii) the expression pattern for stearoyl-ACP desaturase was associated with high oleic acid composition; (iv) it was most likely that endoplasmic reticulum (ER)-associated acyl-CoA synthetase played a significant role in the export of fatty acids between the plastid and ER; (v) lipid phosphate phosphatase (LPP)-δ was most probably related to the formation of the diacylglycerol (DAG) pool in the Kennedy pathway; and (vi) diacylglyceroltransacylase 2 (DGAT2) and phospholipid:diacylglycerolacyltransferase 1 (PDAT1) might play crucial roles in tuber oil biosynthesis. In contrast to oil-rich fruits, there existed many oleosins, caleosins and steroleosins with very high transcripts in tubers. Surprisingly, only a single ortholog of WRINKLED1 (WRI1)-like transcription factor was identified and it was poorly expressed during tuber development. Our study not only provides insights into lipid metabolism in tuber tissues, but also broadens our understanding of TAG synthesis in oil plants. Such knowledge is of significance in exploiting this oil-rich species and manipulating other non-seed tissues to enhance storage oil production.

Histone acetyltransferase general control non-repressed protein 5 (GCN5) affects the fatty acid composition of Arabidopsis thaliana seeds by acetylating fatty acid desaturase3 (FAD3)

Seed oils are important natural resources used in the processing and preparation of food. Histone modifications represent key epigenetic mechanisms that regulate gene expression, plant growth and development. However, histone modification events during fatty acid (FA) biosynthesis are not well understood. Here, we demonstrate that a mutation of the histone acetyltransferase GCN5 can decrease the ratio of α-linolenic acid (ALA) to linoleic acid (LA) in seed oil. Using RNA-Seq and ChIP assays, we identified FAD3, LACS2, LPP3 and PLAIIIβ as the targets of GCN5. Notably, the GCN5-dependent H3K9/14 acetylation of FAD3 determined the expression levels of FAD3 in Arabidopsis thaliana seeds, and the ratio of ALA/LA in the gcn5 mutant was rescued to the wild-type levels through the overexpression of FAD3. The results of this study indicated that GCN5 modulated FA biosynthesis by affecting the acetylation levels of FAD3. We provide evidence that histone acetylation is involved in FA biosynthesis in Arabidopsis seeds and might contribute to the optimization of the nutritional structure of edible oils through epigenetic engineering.

Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit

BACKGROUND

Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages.

RESULTS

The transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant putative transcripts with a mean length of 592.91 bp and N50 length of 785 bp, respectively. Based on the functional annotation through Basic Local Alignment Search Tool (BLAST) with public protein database, the key enzymes involved in lipid metabolism were identified, and a schematic diagram of the pathway and temporal expression patterns of lipid metabolism was established. About 13,939 differentially expressed unigenes (DEGs) were screened out using differentially expressed sequencing (DESeq) method. The transcriptional regulatory patterns of the identified enzymes were highly related to the dynamic oil accumulation along with the fruit development of S. paniculata. In addition, quantitative real-time PCR (qRT-PCR) of six vital genes was significantly correlated with DESeq data.

CONCLUSIONS

The transcriptome sequences obtained and deposited in NCBI would enrich the public database and provide an unprecedented resource for the discovery of the genes associated with lipid metabolism pathway in S. paniculata. Results in this study will lay the foundation for exploring transcriptional regulatory profiles, elucidating molecular regulatory mechanisms, and accelerating genetic engineering process to improve the yield and quality of seed oil of S. paniculata.

FUSCA3 activates triacylglycerol accumulation in Arabidopsis seedlings and tobacco BY2 cells

Triacylglycerol (TAG) is the main storage lipid in plant seeds and the major form of plant oil used for food and, increasingly, for industrial and biofuel applications. Several transcription factors, including FUSCA3 (At3 g26790, FUS3), are associated with embryo maturation and oil biosynthesis in seeds. However, the ability of FUS3 to increase TAG biosynthesis in other tissues has not been quantitatively examined. Here, we evaluated the ability of FUS3 to activate TAG accumulation in non-seed tissues. Overexpression of FUS3 driven by an estradiol-inducible promoter increased oil contents in Arabidopsis seedlings up to 6% of dry weight; more than 50-fold over controls. Eicosenoic acid, a characteristic fatty acid of Arabidopsis seed oil, accumulated to over 20% of fatty acids in cotyledons and leaves. These large increases depended on added sucrose, although without sucrose TAG increased three- to four-fold. Inducing the expression of FUS3 in tobacco BY2 cells also increased TAG accumulation, and co-expression of FUS3 and diacylglycerol acyltransferase 1 (DGAT1) further increased TAG levels to 4% of dry weight. BY2 cell growth was not altered by FUS3 expression, although Arabidopsis seedling development was impaired, consistent with the ability of FUS3 to induce embryo characteristics in non-seed tissues. Microarrays of Arabidopsis seedlings revealed that FUS3 overexpression increased the expression of a higher proportion of genes involved in TAG biosynthesis than genes involved in fatty acid biosynthesis or other lipid pathways. Together these results provide additional insights into FUS3 functions in TAG metabolism and suggest complementary strategies for engineering vegetative oil accumulation.

Comparative Transcriptomic Analysis of Two Brassica napus Near-Isogenic Lines Reveals a Network of Genes That Influences Seed Oil Accumulation

Rapeseed (Brassica napus) is an important oil seed crop, providing more than 13% of the world's supply of edible oils. An in-depth knowledge of the gene network involved in biosynthesis and accumulation of seed oil is critical for the improvement of B. napus. Using available genomic and transcriptomic resources, we identified 1,750 acyl-lipid metabolism (ALM) genes that are distributed over 19 chromosomes in the B. napus genome. B. rapa and B. oleracea, two diploid progenitors of B. napus, contributed almost equally to the ALM genes. Genome collinearity analysis demonstrated that the majority of the ALM genes have arisen due to genome duplication or segmental duplication events. In addition, we profiled the expression patterns of the ALM genes in four different developmental stages. Furthermore, we developed two B. napus near isogenic lines (NILs). The high oil NIL, YC13-559, accumulates significantly higher (∼10%) seed oil compared to the other, YC13-554. Comparative gene expression analysis revealed upregulation of lipid biosynthesis-related regulatory genes in YC13-559, including SHOOTMERISTEMLESS, LEAFY COTYLEDON 1 (LEC1), LEC2, FUSCA3, ABSCISIC ACID INSENSITIVE 3 (ABI3), ABI4, ABI5, and WRINKLED1, as well as structural genes, such as ACETYL-CoA CARBOXYLASE, ACYL-CoA DIACYLGLYCEROL ACYLTRANSFERASE, and LONG-CHAIN ACYL-CoA SYNTHETASES. We observed that several genes related to the phytohormones, gibberellins, jasmonate, and indole acetic acid, were differentially expressed in the NILs. Our findings provide a broad account of the numbers, distribution, and expression profiles of acyl-lipid metabolism genes, as well as gene networks that potentially control oil accumulation in B. napus seeds. The upregulation of key regulatory and structural genes related to lipid biosynthesis likely plays a major role for the increased seed oil in YC13-559.

Arabidopsis GPAT9 contributes to synthesis of intracellular glycerolipids but not surface lipids

GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE (GPAT) genes encode enzymes involved in glycerolipid biosynthesis in plants. Ten GPAT homologues have been identified in Arabidopsis. GPATs 4-8 have been shown to be involved in the production of extracellular lipid barrier polyesters. Recently, GPAT9 was reported to be essential for triacylglycerol (TAG) biosynthesis in developing Arabidopsis seeds. The enzymatic properties and possible functions of GPAT9 in surface lipid, polar lipid and TAG biosynthesis in non-seed organs, however, have not been investigated. Here we show that Arabidopsis GPAT9 exhibits sn-1 acyltransferase activity with high specificity for acyl-coenzyme A, thus providing further evidence that this GPAT is involved in storage lipid biosynthesis. We also confirm a role for GPAT9 in seed oil biosynthesis and further demonstrate that GPAT9 contributes to the biosynthesis of both polar lipids and TAG in developing leaves, as well as lipid droplet production in developing pollen grains. Conversely, alteration of constitutive GPAT9 expression had no obvious effects on surface lipid biosynthesis. Taken together, these studies expand our understanding of GPAT9 function to include modulation of several different intracellular glycerolipid pools in plant cells.

Synthetic redesign of plant lipid metabolism

Plant seed lipid metabolism is an area of intensive research, including many examples of transgenic events in which oil composition has been modified. In the selected examples described in this review, progress towards the predictive manipulation of metabolism and the reconstitution of desired traits in a non-native host is considered. The advantages of a particular oilseed crop, Camelina sativa, as a flexible and utilitarian chassis for advanced metabolic engineering and applied synthetic biology are considered, as are the issues that still represent gaps in our ability to predictably alter plant lipid biosynthesis. Opportunities to deliver useful bio-based products via transgenic plants are described, some of which represent the most complex genetic engineering in plants to date. Future prospects are considered, with a focus on the desire to transition to more (computationally) directed manipulations of metabolism.

Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens

Background

Perilla (Perilla frutescens (L.) var frutescens) produces high levels of α-linolenic acid (ALA), a ω-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cDNAs from developing seeds and leaves for understanding the mechanism underlying ALA and seed TAG biosynthesis.

Results

Perilla cultivar Dayudeulkkae contains 66.0 and 56.2 % ALA in seeds and leaves, respectively. Using Illumina HiSeq 2000, we have generated a total of 392 megabases of raw sequences from four mRNA samples of seeds at different developmental stages and one mature leaf sample of Dayudeulkkae. De novo assembly of these sequences revealed 54,079 unique transcripts, of which 32,237 belong to previously annotated genes. Among the annotated genes, 66.5 % (21,429 out of 32,237) showed highest sequences homology with the genes from Mimulus guttatus, a species placed under the same Lamiales order as perilla. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome and identified 540 unique perilla genes involved in all known pathways of acyl-lipid metabolism. We characterized the expression profiles of 43 genes involved in FA and TAG synthesis using quantitative PCR. Key genes were identified through sequence and gene expression analyses.

Conclusions

This work is the first report on building transcriptomes from perilla seeds. The work also provides the first comprehensive expression profiles for genes involved in seed oil biosynthesis. Bioinformatic analysis indicated that our sequence collection represented a major transcriptomic resource for perilla that added valuable genetic information in order Lamiales. Our results provide critical information not only for studies of the mechanisms involved in ALA synthesis, but also for biotechnological production of ALA in other oilseeds.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2805-0) contains supplementary material, which is available to authorized users.

Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens

BACKGROUND

Perilla (Perilla frutescens (L.) var frutescens) produces high levels of α-linolenic acid (ALA), a ω-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cDNAs from developing seeds and leaves for understanding the mechanism underlying ALA and seed TAG biosynthesis.

RESULTS

Perilla cultivar Dayudeulkkae contains 66.0 and 56.2 % ALA in seeds and leaves, respectively. Using Illumina HiSeq 2000, we have generated a total of 392 megabases of raw sequences from four mRNA samples of seeds at different developmental stages and one mature leaf sample of Dayudeulkkae. De novo assembly of these sequences revealed 54,079 unique transcripts, of which 32,237 belong to previously annotated genes. Among the annotated genes, 66.5 % (21,429 out of 32,237) showed highest sequences homology with the genes from Mimulus guttatus, a species placed under the same Lamiales order as perilla. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome and identified 540 unique perilla genes involved in all known pathways of acyl-lipid metabolism. We characterized the expression profiles of 43 genes involved in FA and TAG synthesis using quantitative PCR. Key genes were identified through sequence and gene expression analyses.

CONCLUSIONS

This work is the first report on building transcriptomes from perilla seeds. The work also provides the first comprehensive expression profiles for genes involved in seed oil biosynthesis. Bioinformatic analysis indicated that our sequence collection represented a major transcriptomic resource for perilla that added valuable genetic information in order Lamiales. Our results provide critical information not only for studies of the mechanisms involved in ALA synthesis, but also for biotechnological production of ALA in other oilseeds.

Vegetable Oil: Nutritional and Industrial Perspective

Oils of plant origin have been predominantly used for food-based applications. Plant oils not only represent a non-polluting renewable resource but also provide a wide diversity in fatty acids (FAs) composition with diverse applications. Besides being edible, they are now increasingly being used in industrial applications such as paints, lubricants, soaps, biofuels etc. In addition, plants can be engineered to produce fatty acids which are nutritionally beneficial to human health. Thus these oils have potential to 1) substitute ever increasing demand of non –renewable petroleum sources for industrial application and 2) also spare the marine life by providing an alternative source to nutritionally and medically important long chain polyunsaturated fatty acids or ‘Fish oil’. The biochemical pathways producing storage oils in plants have been extensively characterized, but the factors regulating fatty acid synthesis and controlling total oil content in oilseed crops are still poorly understood. Thus understanding of plant lipid metabolism is fundamental to its manipulation and increased production. This review on oils discusses fatty acids of nutritional and industrial importance, and approaches for achieving future designer vegetable oil for both edible and non-edible uses. The review will discuss the success and bottlenecks in efficient production of novel FAs in non-native plants using genetic engineering as a tool.

Extension of oil biosynthesis during the mid-phase of seed development enhances oil content in Arabidopsis seeds

Regulation of oil biosynthesis in plant seeds has been extensively studied, and biotechnological approaches have been designed to increase seed oil content. Oil and protein synthesis is negatively correlated in seeds, but the mechanisms controlling interactions between these two pathways are unknown. Here, we identify the molecular mechanism controlling oil and protein content in seeds. We utilized transgenic Arabidopsis thaliana plants overexpressing WRINKLED1 (WRI1), a master transcription factor regulating seed oil biosynthesis, and knockout mutants of major seed storage proteins. Oil and protein biosynthesis in wild-type plants was sequentially activated during early and late seed development, respectively. The negative correlation between oil and protein contents in seeds arises from competition between the pathways. Extension of WRI1 expression during mid-phase of seed development significantly enhanced seed oil content. This study demonstrates that temporal activation of genes involved in oil or storage protein biosynthesis determines the oil/protein ratio in Arabidopsis seeds. These results provide novel insights into potential breeding strategies to generate crops with high oil contents in seeds.

Identification of multiple lipid genes with modifications in expression and sequence associated with the evolution of hydroxy fatty acid accumulation in Physaria fendleri

Two Brassicaceae species, Physaria fendleri and Camelina sativa, are genetically very closely related to each other and to Arabidopsis thaliana. Physaria fendleri seeds contain over 50% hydroxy fatty acids (HFAs), while Camelina sativa and Arabidopsis do not accumulate HFAs. To better understand how plants evolved new biochemical pathways with the capacity to accumulate high levels of unusual fatty acids, transcript expression and protein sequences of developing seeds of Physaria fendleri, wild-type Camelina sativa, and Camelina sativa expressing a castor bean (Ricinus communis) hydroxylase were analyzed. A number of potential evolutionary adaptations within lipid metabolism that probably enhance HFA production and accumulation in Physaria fendleri, and, in their absence, limit accumulation in transgenic tissues were revealed. These adaptations occurred in at least 20 genes within several lipid pathways from the onset of fatty acid synthesis and its regulation to the assembly of triacylglycerols. Lipid genes of Physaria fendleri appear to have co-evolved through modulation of transcriptional abundances and alterations within protein sequences. Only a handful of genes showed evidence for sequence adaptation through gene duplication. Collectively, these evolutionary changes probably occurred to minimize deleterious effects of high HFA amounts and/or to enhance accumulation for physiological advantage. These results shed light on the evolution of pathways for novel fatty acid production in seeds, help explain some of the current limitations to accumulation of HFAs in transgenic plants, and may provide improved strategies for future engineering of their production.

Triacylglycerol Metabolism, Function, and Accumulation in Plant Vegetative Tissues

Oils in the form of triacylglycerols are the most abundant energy-dense storage compounds in eukaryotes, and their metabolism plays a key role in cellular energy balance, lipid homeostasis, growth, and maintenance. Plants accumulate oils primarily in seeds and fruits. Plant oils are used for food and feed and, increasingly, as feedstocks for biodiesel and industrial chemicals. Although plant vegetative tissues do not accumulate significant levels of triacylglycerols, they possess a high capacity for their synthesis, storage, and metabolism. The development of plants that accumulate oil in vegetative tissues presents an opportunity for expanded production of triacylglycerols as a renewable and sustainable bioenergy source. Here, we review recent progress in the understanding of triacylglycerol synthesis, turnover, storage, and function in leaves and discuss emerging genetic engineering strategies targeted at enhancing triacylglycerol accumulation in biomass crops. Such plants could potentially be modified to produce oleochemical feedstocks or nutraceuticals.

Expression of Castor LPAT2 Enhances Ricinoleic Acid Content at the sn-2 Position of Triacylglycerols in Lesquerella Seed

Lesquerella is a potential industrial oilseed crop that makes hydroxy fatty acid (HFA). Unlike castor its seeds are not poisonous but accumulate lesquerolic acid mostly at the sn-1 and sn-3 positions of triacylglycerol (TAG), whereas castor contains ricinoleic acid (18:1OH) at all three positions. To investigate whether lesquerella can be engineered to accumulate HFAs in the sn-2 position, multiple transgenic lines were made that express castor lysophosphatidic acid acyltransferase 2 (RcLPAT2) in the seed. RcLPAT2 increased 18:1OH at the sn-2 position of TAGs from 2% to 14%–17%, which resulted in an increase of tri-HFA-TAGs from 5% to 13%–14%. Our result is the first example of using a LPAT to increase ricinoleic acid at the sn-2 position of seed TAG. This work provides insights to the mechanism of HFA-containing TAG assembly in lesquerella and directs future research to optimize this plant for HFA production.

Triacylglycerol biosynthesis in developing Ribes nigrum and Ribes rubrum seeds from gene expression to oil composition

Oils with sufficient contents of fatty acids, which can be metabolized into precursors of anti-inflammatory eicosanoids, have potential health effects. Ribes sp. seed oil is rich in α-linolenic, γ-linolenic and stearidonic acids belonging to this fatty acid group. Only a few previous studies exist on Ribes sp. gene expression. We followed the seed oil biosynthesis of four Ribes nigrum and two Ribes rubrum cultivars at different developmental stages over 2 years in Southern and Northern Finland with a 686 km latitudinal difference. The species and the developmental stage were the most important factors causing differences in gene expression levels and oil composition. Differences between cultivars were detected in some cases, but year and location had only small effects. However, expression of the gene encoding Δ(9)-desaturase in R. nigrum was affected by location. Triacylglycerol biosynthesis in Ribes sp. was distinctly buffered and typically followed a certain path, regardless of growth environment.

Acylcarnitines participate in developmental processes associated to lipid metabolism in plants

Plant acylcarnitines are present during anabolic processes of lipid metabolism. Their low contents relatively to the corresponding acyl-CoAs suggest that they are associated to specific pools of activated fatty acids. The non-proteinaceous amino acid carnitine exists in plants either as a free form or esterified to fatty acids. To clarify the biological significance of acylcarnitines in plant lipid metabolism, we have analyzed their content in plant extracts using an optimized tandem mass spectrometry coupled to liquid chromatography method. We have studied different developmental processes (post-germination, organogenesis, embryogenesis) targeted for their high requirement for lipid metabolism. The modulation of the acylcarnitine content was compared to that of the lipid composition and lipid biosynthetic gene expression level in the analyzed materials. Arabidopsis mutants were also studied based on their alteration in de novo fatty acid partitioning between the prokaryotic and eukaryotic pathways of lipid biosynthesis. We show that acylcarnitines cannot specifically be associated to triacylglycerol catabolism but that they are also associated to anabolic pathways of lipid metabolism. They are present during membrane and storage lipid biosynthesis processes. A great divergence in the relative contents of acylcarnitines as compared to the corresponding acyl-CoAs suggests that acylcarnitines are associated to very specific process(es) of lipid metabolism. The nature of their involvement as the transport form of activated fatty acids or in connection with the management of acyl-CoA pools is discussed. Also, the occurrence of medium-chain entities suggests that acylcarnitines are associated with additional lipid processes such as protein acylation for instance. This work strengthens the understanding of the role of acylcarnitines in plant lipid metabolism, probably in the management of specific acyl-CoA pools.

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

Plant oil biosynthesis involves a complex metabolic network with multiple subcellular compartments, parallel pathways, cycles, and pathways that have a dual function to produce essential membrane lipids and triacylglycerol. Modern molecular biology techniques provide tools to alter plant oil compositions through bioengineering, however with few exceptions the final composition of triacylglycerol cannot be predicted. One reason for limited success in oilseed bioengineering is the inadequate understanding of how to control the flux of fatty acids through various fatty acid modification, and triacylglycerol assembly pathways of the lipid metabolic network. This review focuses on the mechanisms of acyl flux through the lipid metabolic network, and highlights where uncertainty resides in our understanding of seed oil biosynthesis. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.

Analysis of triacylglycerol accumulation under nitrogen deprivation in the red alga Cyanidioschyzon merolae

Triacylglycerol (TAG) produced by microalgae is a potential source of biofuel. Although various metabolic pathways in TAG synthesis have been identified in land plants, the pathway of TAG synthesis in microalgae remains to be clarified. The unicellular rhodophyte Cyanidioschyzon merolae has unique properties as a producer of biofuel because of easy culture and feasibility of genetic engineering. Additionally, it is useful in the investigation of the pathway of TAG synthesis, because all of the nuclear, mitochondrial and plastid genomes have been completely sequenced. We found that this alga accumulated TAG under nitrogen deprivation. Curiously, the amount and composition of plastid membrane lipids did not change significantly, whereas the amount of endoplasmic reticulum (ER) lipids increased with considerable changes in fatty acid composition. The nitrogen deprivation did not decrease photosynthetic oxygen evolution per chlorophyll significantly, while phycobilisomes were degraded preferentially. These results suggest that the synthesis of fatty acids is maintained in the plastid, which is used for the synthesis of TAG in the ER. The accumulated TAG contained mainly 18 : 2(9,12) at the C-2 position, which could be derived from phosphatidylcholine, which also contains this acid at the C-2 position.

Abiotic factors influence plant storage lipid accumulation and composition

The demand for plant-derived oils has increased substantially over the last decade, and is sure to keep growing. While there has been a surge in research efforts to produce plants with improved oil content and quality, in most cases the enhancements have been small. To add further complexity to this situation, substantial differences in seed oil traits among years and field locations have indicated that plant lipid biosynthesis is also influenced to a large extent by multiple environmental factors such as temperature, drought, light availability and soil nutrients. On the molecular and biochemical levels, the expression and/or activities of fatty acid desaturases, as well as diacylglycerol acyltransferase 1, have been found to be affected by abiotic factors, suggesting that they play a role in the lipid content and compositional changes seen under abiotic stress conditions. Unfortunately, while only a very small number of strategies have been developed as of yet to minimize these environmental effects on the production of storage lipids, it is clear that this feat will be of the utmost importance for developing superior oil crops with the capability to perform in a consistent manner in field conditions in the future.

Fatty Acid and Lipid Transport in Plant Cells

Fatty acids (FAs) and lipids are essential - not only as membrane constituents but also for growth and development. In plants and algae, FAs are synthesized in plastids and to a large extent transported to the endoplasmic reticulum for modification and lipid assembly. Subsequently, lipophilic compounds are distributed within the cell, and thus are transported across most membrane systems. Membrane-intrinsic transporters and proteins for cellular FA/lipid transfer therefore represent key components for delivery and dissemination. In addition to highlighting their role in lipid homeostasis and plant performance, different transport mechanisms for land plants and green algae - in the model systems Arabidopsis thaliana, Chlamydomonas reinhardtii - are compared, thereby providing a current perspective on protein-mediated FA and lipid trafficking in photosynthetic cells.

Enhancement of α-linolenic acid content in transgenic tobacco seeds by targeting a plastidial ω-3 fatty acid desaturase (fad7) gene of Sesamum indicum to ER

KEY MESSAGE

Expression of sesame plastidial FAD7 desaturase modified with the endoplasmic reticulum targeting and retention signals, enhances the α-linolenic acid accumulation in seeds of Nicotiana tabacum. In plants, plastidial ω-3 fatty acid desaturase-7 (FAD7) catalyzes the formation of C16 and C18 trienoic fatty acids using organellar glycerolipids and participate in the membrane lipid formation. The plastidial ω-3 desaturases (FAD7) share high sequence homology with the microsomal ω-3 desaturases (FAD3) at the amino acid level except the N-terminal organelle transit peptide. In the present study, the predicted N-terminal plastidial signal peptide of fad7 gene was replaced by the endoplasmic reticulum signal peptide and an endoplasmic reticulum retention signal was placed at the C-terminal. The expression of the modified sesame ω-3 desaturase increases the α-linolenic acid content in the range of 4.78-6.77 % in the seeds of transgenic tobacco plants with concomitant decrease in linoleic acid content. The results suggested the potential of the engineered plastidial ω-3 desaturase from sesame to influence the profile of α-linolenic acid in tobacco plant by shifting the carbon flux from linoleic acid, and thus it can be used in suitable genetic engineering strategy to increase the α-linolenic acid content in sesame and other vegetable oils.

Microalgae as a Source for VLC-PUFA Production

Microalgae present a huge and still insufficiently tapped resource of very long-chain omega-3 and omega-6 polyunsaturated fatty acids (VLC-PUFA) for human nutrition and medicinal applications. This chapter describes the diversity of unicellular eukaryotic microalgae in respect to VLC-PUFA biosynthesis. Then, we outline the major biosynthetic pathways mediating the formation of VLC-PUFA by sequential desaturation and elongation of C18-PUFA acyl groups. We address the aspects of spatial localization of those pathways and elaborate on the role for VLC-PUFA in microalgal cells. Recent progress in microalgal genetic transformation and molecular engineering has opened the way to increased production efficiencies for VLC-PUFA. The perspectives of photobiotechnology and metabolic engineering of microalgae for altered or enhanced VLC-PUFA production are also discussed.

Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus

Fatty acids and their composition in seeds determine oil value for nutritional or industrial purposes and also affect seed germination as well as seedling establishment. To better understand the genetic basis of seed fatty acid biosynthesis in oilseed rape (Brassica napus L.) we applied a genome-wide association study, using 91,205 single nucleotide polymorphisms (SNPs) characterized across a mapping population with high-resolution skim genotyping by sequencing (SkimGBS). We identified a cluster of loci on chromosome A05 associated with oleic and linoleic seed fatty acids. The delineated genomic region contained orthologs of the Arabidopsis thaliana genes known to play a role in regulation of seed fatty acid biosynthesis such as Fatty acyl-ACP thioesterase B (FATB) and Fatty Acid Desaturase (FAD5). This approach allowed us to identify potential functional genes regulating fatty acid composition in this important oil producing crop and demonstrates that this approach can be used as a powerful tool for dissecting complex traits for B. napus improvement programs.

Construction of Global Acyl Lipid Metabolic Map by Comparative Genomics and Subcellular Localization Analysis in the Red Alga Cyanidioschyzon merolae

Pathways of lipid metabolism have been established in land plants, such as Arabidopsis thaliana, but the information on exact pathways is still under study in microalgae. In contrast with Chlamydomonas reinhardtii, which is currently studied extensively, the pathway information in red algae is still in the state in which enzymes and pathways are estimated by analogy with the knowledge in plants. Here we attempt to construct the entire acyl lipid metabolic pathways in a model red alga, Cyanidioschyzon merolae, as an initial basis for future genetic and biochemical studies, by exploiting comparative genomics and localization analysis. First, the data of whole genome clustering by Gclust were used to identify 121 acyl lipid-related enzymes. Then, the localization of 113 of these enzymes was analyzed by GFP-based techniques. We found that most of the predictions on the subcellular localization by existing tools gave erroneous results, probably because these tools had been tuned for plants or green algae. The experimental data in the present study as well as the data reported before in our laboratory will constitute a good training set for tuning these tools. The lipid metabolic map thus constructed show that the lipid metabolic pathways in the red alga are essentially similar to those in A. thaliana, except that the number of enzymes catalyzing individual reactions is quite limited. The absence of fatty acid desaturation to produce oleic and linoleic acids within the plastid, however, highlights the central importance of desaturation and acyl editing in the endoplasmic reticulum, for the synthesis of plastid lipids as well as other cellular lipids. Additionally, some notable characteristics of lipid metabolism in C. merolae were found. For example, phosphatidylcholine is synthesized by the methylation of phosphatidylethanolamine as in yeasts. It is possible that a single 3-ketoacyl-acyl carrier protein synthase is involved in the condensation reactions of fatty acid synthesis in the plastid. We will also discuss on the redundant β-oxidation enzymes, which are characteristic to red algae.

De novo Assembly and Characterization of the Fruit Transcriptome of Idesia polycarpa Reveals Candidate Genes for Lipid Biosynthesis

Idesia polycarpa, is a valuable oilseed-producing tree of the Flacourtiaceae family that has the potential to fulfill edible oil production and is also a possible biofuel feedstock. The fruit is unique in that it contains both saturated and unsaturated lipids present in pericarp and seed, respectively. However, triglyceride synthesis and storage in tissues outside of the seeds has been poorly studied in previous researches. To gain insight into the unique properties of I. polycarpa fruit lipid synthesis, biochemical, and transcriptomic approaches were used to compare the lipid accumulation between pericarp and seed of the fruit. Lipid accumulation rates, final lipid content and composition were significantly different between two tissues. Furthermore, we described the annotated transcriptome assembly and differential gene expression analysis generated from the pericarp and seed tissues. The data allowed the identification of distinct candidate genes and reconstruction of lipid pathways, which may explain the differences of oil synthesis between the two tissues. The results may be useful for engineering alternative pathways for lipid production in non-seed or vegetative tissues.