Transcriptional regulation of fatty acid production in higher plants: Molecular bases and biotechnological outcomes

Exploring lipid signaling in plant physiology: From cellular membranes to environmental adaptation

Lipids have evolved as versatile signaling molecules that regulate a variety of physiological processes in plants. Convincing evidence highlights their critical role as mediators in a wide range of plant processes required for survival, growth, development, and responses to environmental conditions such as water availability, temperature changes, salt, pests, and diseases. Understanding lipid signaling as a critical process has helped us expand our understanding of plant biology by explaining how plants sense and respond to environmental cues. Lipid signaling pathways constitute a complex network of lipids, enzymes, and receptors that coordinate important cellular responses and stressing plant biology's changing and adaptable traits. Plant lipid signaling involves a wide range of lipid classes, including phospholipids, sphingolipids, oxylipins, and sterols, each of which contributes differently to cellular communication and control. These lipids function not only as structural components, but also as bioactive molecules that transfer signals. The mechanisms entail the production of lipid mediators and their detection by particular receptors, which frequently trigger downstream cascades that affect gene expression, cellular functions, and overall plant growth. This review looks into lipid signaling in plant physiology, giving an in-depth look and emphasizing its critical function as a master regulator of vital activities.

Genetic and Biotechnological Approaches to Improve Fruit Bioactive Content: A Focus on Eggplant and Tomato Anthocyanins

Anthocyanins are a large group of water-soluble flavonoid pigments. These specialized metabolites are ubiquitous in the plant kingdom and play an essential role not only in plant reproduction and dispersal but also in responses to biotic and abiotic stresses. Anthocyanins are recognized as important health-promoting and chronic-disease-preventing components in the human diet. Therefore, interest in developing food crops with improved levels and compositions of these important nutraceuticals is growing. This review focuses on work conducted to elucidate the genetic control of the anthocyanin pathway and modulate anthocyanin content in eggplant (Solanum melongena L.) and tomato (Solanum lycopersicum L.), two solanaceous fruit vegetables of worldwide relevance. While anthocyanin levels in eggplant fruit have always been an important quality trait, anthocyanin-based, purple-fruited tomato cultivars are currently a novelty. As detailed in this review, this difference in the anthocyanin content of the cultivated germplasm has largely influenced genetic studies as well as breeding and transgenic approaches to improve the anthocyanin content/profile of these two important solanaceous crops. The information provided should be of help to researchers and breeders in devising strategies to address the increasing consumer demand for nutraceutical foods.

Unveiling the molecular regulatory mechanisms underlying sucrose accumulation and oil reduction in peanut kernels through genetic mapping and transcriptome analysis

Sucrose content is a key factor for the flavor of edible peanut, which determines the sweet taste of fresh peanut and also attribute to pleasant flavor of roasted peanut. To explore the genetic mechanism of the sucrose content in peanut, an F2 population was created by crossing the sweet cultivar Zhonghuatian 1 (ZHT1) with Nanyangbaipi (NYBP). A genomic region spanning 28.26 kb on chromosome A06 was identified for the sucrose content through genetic mapping, elucidating 47.5% phenotypic variance explained. As the sucrose content had a significantly negative correlation with the oil content, this region was also found to be related to the oil content explaining 37.2% of phenotype variation. In this region, Arahy.42CAD1 was characterized as the most likely candidate gene through a comprehensive analysis. The nuclear localization of Arahy.42CAD1 suggests its potential involvement in the regulation of gene expression for sucrose and oil contents in peanut. Transcriptome analysis of the developing seeds in both parents revealed that genes involved in glycolysis and triacylglycerol biosynthesis pathways were not significantly down-regulated in ZHT1, indicating that the sucrose accumulation was not attributed to the suppression of triacylglycerol biosynthesis. Based on the WGCNA analysis, Arahy.42CAD1 was co-expressed with the genes involved in vesicle transport and oil body assembly, suggesting that the sucrose accumulation may be caused by disruptions in TAG transportation or storage mechanisms. These findings offer new insights into the molecular mechanisms governing sucrose accumulation in peanut, and also provide a potential gene target for enhancing peanut flavor.

Ectopic Expression of Perilla frutescens WRI1 Enhanced Storage Oil Accumulation in Nicotiana benthamiana Leaves

Vegetable oils are indispensable in human and animal diets and have been widely used for the production of detergents, lubricants, cosmetics, and biofuels. The seeds of an allotetraploid Perilla frutescens contain approximately 35 to 40% oils with high levels of polyunsaturated fatty acids (PUFAs). WRINKELD1 (WRI1) encoding an AP2/ERF-type transcription factor is known to upregulate the expression of genes involved in glycolysis and fatty acid biosynthesis and TAG assembly. In this study, two WRI1 isoforms, PfWRI1A, and PfWRI1B were isolated from Perilla and predominantly expressed in developing Perilla seeds. The fluorescent signals from PfWRI1A:eYFP and PfWRI1B:eYFP driven by the CaMV 35S promoter were detected in the nucleus of the Nicotiana benthamiana leaf epidermis. Ectopic expression of each of PfWRI1A and PfWRI1B increased the levels of TAG by approximately 2.9- and 2.7-fold in N. benthamiana leaves and particularly, the enhanced levels (mol%) of C18:2, and C18:3 in the TAGs were prominent with the concomitant reduction in the amounts of saturated fatty acids. The expression levels of NbPl-PKβ1, NbKAS1, and NbFATA, which were known to be target genes of WRI1, significantly increased in tobacco leaves overexpressing PfWRI1A or PfWRI1B. Therefore, newly characterized PfWRI1A and PfWRI1B can be potentially useful for the enhanced accumulation of storage oils with increased PUFAs in oilseed crops.

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.

Progress in understanding and improving oil content and quality in seeds

The world's population is projected to increase by two billion by 2050, resulting in food and energy insecurity. Oilseed crops have been identified as key to address these challenges: they produce and store lipids in the seeds as triacylglycerols that can serve as a source of food/feed, renewable fuels, and other industrially-relevant chemicals. Therefore, improving seed oil content and composition has generated immense interest. Research efforts aiming to unravel the regulatory pathways involved in fatty acid synthesis and to identify targets for metabolic engineering have made tremendous progress. This review provides a summary of the current knowledge of oil metabolism and discusses how photochemical activity and unconventional pathways can contribute to high carbon conversion efficiency in seeds. It also highlights the importance of ¹³C-metabolic flux analysis as a tool to gain insights on the pathways that regulate oil biosynthesis in seeds. Finally, a list of key genes and regulators that have been recently targeted to enhance seed oil production are reviewed and additional possible targets in the metabolic pathways are proposed to achieve desirable oil content and quality.

Improving crop yield potential: Underlying biological processes and future prospects

The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant-derived products. In the coming years, plant-based research will be among the major drivers ensuring food security and the expansion of the bio-based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity.

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.

Molecular basis of the key regulator WRINKLED1 in plant oil biosynthesis

Vegetable oils are not only major components of human diet but also vital for industrial applications. WRINKLED1 (WRI1) is a pivotal transcription factor governing plant oil biosynthesis, but the underlying DNA-binding mechanism remains incompletely understood. Here, we resolved the structure of Arabidopsis WRI1 (AtWRI1) with its cognate double-stranded DNA (dsDNA), revealing two antiparallel β sheets in the tandem AP2 domains that intercalate into the adjacent major grooves of dsDNA to determine the sequence recognition specificity. We showed that AtWRI1 represented a previously unidentified structural fold and DNA-binding mode. Mutations of the key residues interacting with DNA element affected its binding affinity and oil biosynthesis when these variants were transiently expressed in tobacco leaves. Seed oil content was enhanced in stable transgenic wri1-1 expressing an AtWRI1 variant (W74R). Together, our findings offer a structural basis explaining WRI1 recognition and binding of DNA and suggest an alternative strategy to increase oil yield in crops through WRI1 bioengineering.

An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development

The transcription factor WRINKLED1 (WRI1) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase (FRK3) and of phosphoglucose isomerase (PGI1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.

BLISTER promotes seed maturation and fatty acid biosynthesis by interacting with WRINKLED1 to regulate chromatin dynamics in Arabidopsis

WRINKLED1 (WRI1) is an important transcription factor that regulates seed oil biosynthesis. However, how WRI1 regulates gene expression during this process remains poorly understood. Here, we found that BLISTER (BLI) is expressed in maturing Arabidopsis thaliana seeds and acts as an interacting partner of WRI1. bli mutant seeds showed delayed maturation, a wrinkled seed phenotype, and reduced oil content, similar to the phenotypes of wri1. In contrast, BLI overexpression resulted in enlarged seeds and increased oil content. Gene expression and genetic analyses revealed that BLI plays a role in promoting the expression of WRI1 targets involved in fatty acid biosynthesis and regulates seed maturation together with WRI1. BLI is recruited by WRI1 to the AW boxes in the promoters of fatty acid biosynthesis genes. BLI shows a mutually exclusive interaction with the Polycomb-group protein CURLY LEAF (CLF) or the chromatin remodeling factor SWITCH/SUCROSE NONFERMENTING 3B (SWI3B), which facilitates gene expression by modifying nucleosomal occupancy and histone modifications. Together, these data suggest that BLI promotes the expression of fatty acid biosynthesis genes by interacting with WRI1 to regulate chromatin dynamics, leading to increased fatty acid production. These findings provide insights into the roles of the WRI1-BLI-CLF-SWI3B module in mediating seed maturation and gene expression.

Genome-Wide Characterization of DGATs and Their Expression Diversity Analysis in Response to Abiotic Stresses in Brassica napus

Triacylglycerol (TAG) is the most important storage lipid for oil plant seeds. Diacylglycerol acyltransferases (DGATs) are a key group of rate-limiting enzymes in the pathway of TAG biosynthesis. In plants, there are three types of DGATs, namely, DGAT1, DGAT2 and DGAT3. Brassica napus, an allotetraploid plant, is one of the most important oil plants in the world. Previous studies of Brassica napus DGATs (BnaDGATs) have mainly focused on BnaDGAT1s. In this study, four DGAT1s, four DGAT2s and two DGAT3s were identified and cloned from B. napus ZS11. The analyses of sequence identity, chromosomal location and collinearity, phylogenetic tree, exon/intron gene structures, conserved domains and motifs, and transmembrane domain (TMD) revealed that BnaDGAT1, BnaDGAT2 and BnaDGAT3 were derived from three different ancestors and shared little similarity in gene and protein structures. Overexpressing BnaDGATs showed that only four BnaDGAT1s can restore TAG synthesis in yeast H1246 and promote the accumulation of fatty acids in yeast H1246 and INVSc1, suggesting that the three BnaDGAT subfamilies had greater differentiation in function. Transcriptional analysis showed that the expression levels of BnaDGAT1s, BnaDGAT2s and BnaDGAT3s were different during plant development and under different stresses. In addition, analysis of fatty acid contents in roots, stems and leaves under abiotic stresses revealed that P starvation can promote the accumulation of fatty acids, but no obvious relationship was shown between the accumulation of fatty acids with the expression of BnaDGATs under P starvation. This study provides an extensive evaluation of BnaDGATs and a useful foundation for dissecting the functions of BnaDGATs in biochemical and physiological processes.

The seed-specific transcription factor DPBF2 modulates the fatty acid composition in seeds

Triacylglycerol (TAG), an ester derived from glycerol and three fatty acids (FAs), is synthesized during seed development and controlled by transcriptional regulation. We examined the mechanism regulating the FA composition of developing Arabidopsis thaliana seeds. The seed-specific DC3 PROMOTER-BINDING FACTOR2 (DPBF2) transcription factor was upregulated by LEAFY COTYLEDON2 (LEC2). DPBF2 showed transcriptional activity in yeast and localized to the nucleus in Arabidopsis protoplast cells. The Arabidopsis dpbf2-1 homozygous T-DNA mutant and transgenic lines overexpressing of DPBF2 using a seed-specific phaseolin promoter in wild-type (WT) Arabidopsis and in dpbf2-1 showed similar FA composition profiles in their seeds. Their 18:2 and 20:1 FA contents were higher, but 18:1 and 18:3 contents were lower than that of WT. Transcript levels of FATTY ACID DESATURASE2 (FAD2), FAD3, LYSOPHOSPHATIDYLCHOLINE ACYLTRANSFERASE1 (LPCAT1), LPCAT2, PHOSPHATIDYLCHOLINE DIACYLGLYCEROL CHOLINEPHOSPHOTRANSFERASE (PDCT), and FATTY ACID ELONGASE 1 (FAE1) are increased in DPBF2-overexpressing seeds. Besides, PDCT and FAE1 were upregulated by DPBF2, LEC1-LIKE (L1L), and NUCLEAR FACTOR-YC2 (NF-YC2) transcriptional complex based on tobacco protoplast transcriptional activation assay. These results suggest that DPBF2 effectively modulates the expression of genes encoding FA desaturases, elongase, and acyl-editing enzymes for modifying the unsaturated FA composition in seeds.

Sunflower WRINKLED1 Plays a Key Role in Transcriptional Regulation of Oil Biosynthesis

Sunflower (Helianthus annuus) is one of the most important oilseed crops worldwide. However, the transcriptional regulation underlying oil accumulation in sunflower is not fully understood. WRINKLED1 (WRI1) is an essential transcription factor governing oil accumulation in plant cells. Here, we identify and characterize a sunflower ortholog of WRI1 (HaWRI1), which is highly expressed in developing seeds. Transient production of HaWRI1 stimulated substantial oil accumulation in Nicotiana benthamiana leaves. Dual-luciferase reporter assay, electrophoretic mobility shift assay, fatty acid quantification, and gene expression analysis demonstrate that HaWRI1 acts as a pivotal transcription factor controlling the expression of genes involved in late glycolysis and fatty acid biosynthesis. HaWRI1 directly binds to the cis-element, AW-box, in the promoter of biotin carboxyl carrier protein isoform 2 (BCCP2). In addition, we characterize an 80 amino-acid C-terminal domain of HaWRI1 that is crucial for transactivation. Moreover, seed-specific overexpression of HaWRI1 in Arabidopsis plants leads to enhanced seed oil content as well as upregulation of the genes involved in fatty acid biosynthesis. Taken together, our work demonstrates that HaWRI1 plays a pivotal role in the transcriptional control of seed oil accumulation, providing a potential target for bioengineering sunflower oil yield improvement.

Elucidation of Triacylglycerol Overproduction in the C4 Bioenergy Crop Sorghum bicolor by Constraint-Based Analysis

Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C4 biomass crop Sorghum bicolor (iTJC1414) along with a minimal model for photosynthetic CO2 assimilation, sucrose and TAG biosynthesis in C3 plants. Extending iTJC1414 to a four-cell diel model we simulate C4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.

Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean

Soybean is a major source of edible protein and oil. Oil content is a quantitative trait that is significantly determined by genetic and environmental factors. Over the past 30 years, a large volume of soybean genetic, genomic, and transcriptomic data have been accumulated. Nevertheless, integrative analyses of such data remain scarce, in spite of their importance for crop improvement. We hypothesized that the co-occurrence of genomic regions for oil-related traits in different studies may reveal more stable regions encompassing important genetic determinants of oil content and quality in soybean. We integrated publicly available data, obtained with distinct techniques, to discover and prioritize candidate genes involved in oil biosynthesis and regulation in soybean. We detected key fatty acid biosynthesis genes (e.g., BCCP2 and ACCase, FADs, KAS family proteins) and several transcription factors, which are likely regulators of oil biosynthesis. In addition, we identified new candidates for seed oil accumulation and quality, such as Glyma.03G213300 and Glyma.19G160700, which encode a translocator protein homolog and a histone acetyltransferase, respectively. Further, oil and protein genomic hotspots are strongly associated with breeding and not with domestication, suggesting that soybean domestication prioritized other traits. The genes identified here are promising targets for breeding programs and for the development of soybean lines with increased oil content and quality.

Plant monounsaturated fatty acids: Diversity, biosynthesis, functions and uses

Monounsaturated fatty acids are straight-chain aliphatic monocarboxylic acids comprising a unique carbon‑carbon double bond, also termed unsaturation. More than 50 distinct molecular structures have been described in the plant kingdom, and more remain to be discovered. The evolution of land plants has apparently resulted in the convergent evolution of non-homologous enzymes catalyzing the dehydrogenation of saturated acyl chain substrates in a chemo-, regio- and stereoselective manner. Contrasted enzymatic characteristics and different subcellular localizations of these desaturases account for the diversity of existing fatty acid structures. Interestingly, the location and geometrical configuration of the unsaturation confer specific characteristics to these molecules found in a variety of membrane, storage, and surface lipids. An ongoing research effort aimed at exploring the links existing between fatty acid structures and their biological functions has already unraveled the importance of several monounsaturated fatty acids in various physiological and developmental contexts. What is more, the monounsaturated acyl chains found in the oils of seeds and fruits are widely and increasingly used in the food and chemical industries due to the physicochemical properties inherent in their structures. Breeders and plant biotechnologists therefore develop new crops with high monounsaturated contents for various agro-industrial purposes.

Analysis and Functional Verification of PoWRI1 Gene Associated with Oil Accumulation Process in Paeonia ostii

The plant transcription factor WRINKLED1 (WRI1), a member of AP2/EREBP, is involved in the regulation of glycolysis and the expression of genes related to the de novo synthesis of fatty acids in plastids. In this study, the key regulator of seed oil synthesis and accumulation transcription factor gene PoWRI1 was identified and cloned, having a complete open reading frame of 1269 bp and encoding 422 amino acids. Subcellular localization analysis showed that PoWRI1 is located at the nucleus. After the expression vector of PoWRI1 was constructed and transformed into wild-type Arabidopsis thaliana, it was found that the overexpression of PoWRI1 increased the expression level of downstream target genes such as BCCP2, KAS1, and PKP-β1. As a result, the seeds of transgenic plants became larger, the oil content increased significantly, and the unsaturated fatty acid content increased, which provide a scientific theoretical basis for the subsequent use of genetic engineering methods to improve the fatty acid composition and content of plant seeds.

Advances in production of high-value lipids by oleaginous yeasts

The global market for high-value fatty acids production, mainly omega-3/6, hydroxy fatty-acids, waxes and their derivatives, has seen strong development in the last decade. The reason for this growth was the increasing utilization of these lipids as significant ingredients for cosmetics, food and the oleochemical industries. The large demand for these compounds resulted in a greater scientific interest in research focused on alternative sources of oil production - among which microorganisms attracted the most attention. Microbial oil production offers the possibility to engineer the pathways and store lipids enriched with the desired fatty acids. Moreover, costly chemical steps are avoided and direct commercial use of these fatty acids is available. Among all microorganisms, the oleaginous yeasts have become the most promising hosts for lipid production - their efficient lipogenesis, ability to use various (often highly affordable) carbon sources, feasible large-scale cultivations and wide range of available genetic engineering tools turns them into powerful micro-factories. This review is an in-depth description of the recent developments in the engineering of the lipid biosynthetic pathway with oleaginous yeasts. The different classes of valuable lipid compounds with their derivatives are described and their importance for human health and industry is presented. The emphasis is also placed on the optimization of culture conditions in order to improve the yield and titer of these valuable compounds. Furthermore, the important economic aspects of the current microbial oil production are discussed.

Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds

Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism and facilitates the identification of new functional regions in oil crop genomes. The present study characterizes the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid-related genes and transcription factors in developing sunflower seeds. Two master transcriptional regulators identified in this analysis, VIV1 (homologous to Arabidopsis ABI3) and FUS3, cooperate in the regulation of WRINKLED 1, a transcriptional factor regulating glycolysis, and fatty acid synthesis in developing oilseeds.

Differential Activation of Partially Redundant Δ9 Stearoyl-ACP Desaturase Genes Is Critical for Omega-9 Monounsaturated Fatty Acid Biosynthesis During Seed Development in Arabidopsis

The spatiotemporal pattern of deposition, final amount, and relative abundance of oleic acid (cis-ω-9 C18:1) and its derivatives in the different lipid fractions of the seed of Arabidopsis (Arabidopsis thaliana) indicates that omega-9 monoenes are synthesized at high rates in this organ. Accordingly, we observed that four Δ9 stearoyl-ACP desaturase (SAD)-coding genes (FATTY ACID BIOSYNTHESIS2 [FAB2], ACYL-ACYL CARRIER PROTEIN5 [AAD5], AAD1, and AAD6) are transcriptionally induced in seeds. We established that the three most highly expressed ones are directly activated by the WRINKLED1 transcription factor. We characterized a collection of 30 simple, double, triple, and quadruple mutants affected in SAD-coding genes and thereby revealed the functions of these desaturases throughout seed development. Production of oleic acid by FAB2 and AAD5 appears to be critical at the onset of embryo morphogenesis. Double homozygous plants from crossing fab2 and aad5 could never be obtained, and further investigations revealed that the double mutation results in the arrest of embryo development before the globular stage. During later stages of seed development, these two SADs, together with AAD1, participate in the elaboration of the embryonic cuticle, a barrier essential for embryo-endosperm separation during the phase of invasive embryo growth through the endosperm. This study also demonstrates that the four desaturases redundantly contribute to storage lipid production during the maturation phase.

The function of the WRI1-TCP4 regulatory module in lipid biosynthesis

The plant-specific TCP transcription factors play pivotal roles in various processes of plant growth and development. However, little is known regarding the functions of TCPs in plant oil biosynthesis. Our recent work showed that TCP4 mediates oil production via interaction with WRINKLED1 (WRI1), an essential transcription factor governing plant fatty acid biosynthesis. Arabidopsis WRI1 (AtWRI1) physically interacts with multiple TCPs, including TCP4, TCP10, and TCP24. Transient co-expression of AtWRI1 with TCP4, but not TCP10 or TCP24, represses oil accumulation in Nicotiana benthamiana leaves. Increased TCP4 in transgenic plants overexpressing a miR319-resistant TCP4 (rTCP4) decreased the expression of AtWRI1 target genes. The tcp4 knockout mutant, the jaw-D mutant with significant reduction of TCP4 expression, and a tcp2 tcp4 tcp10 triple mutant, display increased seed oil contents compared to the wild-type Arabidopsis. The APETALA2 (AP2) transcription factor WRI1 is characterized by regulating fatty acid biosynthesis through cross-family interactions with multiple transcriptional, post-transcriptional, and post-translational regulators. The interacting regulator modules control the range of AtWRI1 transcriptional activity, allowing spatiotemporal modulation of lipid production. Interaction of TCP4 with AtWRI1, which results in a reduction of AtWRI1 activity, represents a newly discovered mechanism that enables the fine-tuning of plant oil biosynthesis.

An extreme-phenotype genome-wide association study identifies candidate cannabinoid pathway genes in Cannabis

Cannabis produces a class of isoprenylated resorcinyl polyketides known as cannabinoids, a subset of which are medically important and exclusive to this plant. The cannabinoid alkyl group is a critical structural feature that governs therapeutic activity. Genetic enhancement of the alkyl side-chain could lead to the development of novel chemical phenotypes (chemotypes) for pharmaceutical end-use. However, the genetic determinants underlying in planta variation of cannabinoid alkyl side-chain length remain uncharacterised. Using a diversity panel derived from the Ecofibre Cannabis germplasm collection, an extreme-phenotype genome-wide association study (XP-GWAS) was used to enrich for alkyl cannabinoid polymorphic regions. Resequencing of chemotypically extreme pools revealed a known cannabinoid synthesis pathway locus as well as a series of chemotype-associated genomic regions. One of these regions contained a candidate gene encoding a β-keto acyl carrier protein (ACP) reductase (BKR) putatively associated with polyketide fatty acid starter unit synthesis and alkyl side-chain length. Association analysis revealed twenty-two polymorphic variants spanning the length of this gene, including two nonsynonymous substitutions. The success of this first reported application of XP-GWAS for an obligate outcrossing and highly heterozygote plant genus suggests that this approach may have generic application for other plant species.

AtMYB92 enhances fatty acid synthesis and suberin deposition in leaves of Nicotiana benthamiana

Acyl lipids are important constituents of the plant cell. Depending on the cell type, requirements in acyl lipids vary greatly, implying a tight regulation of fatty acid and lipid metabolism. The discovery of the WRINKLED1 (WRI1) transcription factors, members of the AP2-EREBP (APETALA2-ethylene-responsive element binding protein) family, has emphasized the importance of transcriptional regulation for adapting the rate of acyl chain production to cell requirements. Here, we describe the identification of another activator of the fatty acid biosynthetic pathway, the Arabidopsis MYB92 transcription factor. This MYB and all the members of the subgroups S10 and S24 of MYB transcription factors can directly activate the promoter of BCCP2 that encodes a component of the fatty acid biosynthetic pathway. Two adjacent MYB cis-regulatory elements are essential for the binding and activation of the BCCP2 promoter by MYB92. Overexpression of MYB92 or WRI1 in Nicotiana benthamiana induces the expression of fatty acid biosynthetic genes but results in the accumulation of different types of acyl lipids. In the presence of WRI1, triacylglycerol biosynthetic enzymes coded by constitutively expressed genes efficiently channel the excess fatty acids toward reserve lipid accumulation. By contrast, MYB92 activates both fatty acid and suberin biosynthetic genes; hence, the remarkable increase in suberin monomers measured in leaves expressing MYB92. These results provide additional insight into the molecular mechanisms that control the biosynthesis of an important cell wall-associated acylglycerol polymer playing critical roles in plants.

Molecular Basis of Plant Oil Biosynthesis: Insights Gained From Studying the WRINKLED1 Transcription Factor

Most plant species generate and store triacylglycerol (TAG) in their seeds, serving as a core supply of carbon and energy to support seedling development. Plant seed oils have a wide variety of applications, from being essential for human diets to serving as industrial renewable feedstock. WRINKLED1 (WRI1) transcription factor plays a central role in the transcriptional regulation of plant fatty acid biosynthesis. Since the discovery of Arabidopsis WRI1 gene (AtWRI1) in 2004, the function of WRI1 in plant oil biosynthesis has been studied intensively. In recent years, the identification of WRI1 co-regulators and deeper investigations of the structural features and molecular functions of WRI1 have advanced our understanding of the mechanism of the transcriptional regulation of plant oil biosynthesis. These advances also help pave the way for novel approaches that will better utilize WRI1 for bioengineering oil production in crops.

Candidate genes-association study to identify loci related to oleic acid in Brassica napus using SNP markers and their heterologous expression in yeast

Brassica napus (rapeseed) serves as a main source of edible oil, and the oil's quality is mainly determined by the relative proportions of fatty acids. A high oleic acid concentration in B. napus oil increases its shelf life and oxidative stability. Therefore, attaining a high oleic acid concentration is necessary to enhance the nutritional quality of rapeseed oil. Here, an association study of candidate genes was conducted using a population of 324 genetically diverse rapeseed accessions, and several loci related to oleic acid content were identified. Furthermore, these loci were functionally characterized in Saccharomyces cerevisiae to assess their functions, and the promising candidate loci were validated using single nucleotide polymorphic markers in an independent inbred population. The results increased our understanding of fatty acid metabolism in B. napus. Moreover, these findings may assist in marker-based breeding efforts to improve the fatty acid composition and quality of B. napus oil.

A Versatile High Throughput Screening Platform for Plant Metabolic Engineering Highlights the Major Role of ABI3 in Lipid Metabolism Regulation

Traditional functional genetic studies in crops are time consuming, complicated and cannot be readily scaled up. The reason is that mutant or transformed crops need to be generated to study the effect of gene modifications on specific traits of interest. However, many crop species have a complex genome and a long generation time. As a result, it usually takes several months to over a year to obtain desired mutants or transgenic plants, which represents a significant bottleneck in the development of new crop varieties. To overcome this major issue, we are currently establishing a versatile plant genetic screening platform, amenable to high throughput screening in almost any crop species, with a unique workflow. This platform combines protoplast transformation and fluorescence activated cell sorting. Here we show that tobacco protoplasts can accumulate high levels of lipid if transiently transformed with genes involved in lipid biosynthesis and can be sorted based on lipid content. Hence, protoplasts can be used as a predictive tool for plant lipid engineering. Using this newly established strategy, we demonstrate the major role of ABI3 in plant lipid accumulation. We anticipate that this workflow can be applied to numerous highly valuable metabolic traits other than storage lipid accumulation. This new strategy represents a significant step toward screening complex genetic libraries, in a single experiment and in a matter of days, as opposed to years by conventional means.

Effect of Ethylene on Cell Wall and Lipid Metabolism during Alleviation of Postharvest Chilling Injury in Peach

Peach is prone to postharvest chilling injury (CI). Here it was found that exogenous ethylene alleviated CI, accompanied by an increased endogenous ethylene production. Ethylene treatment resulted in a moderately more rapid flesh softening as a result of stronger expression of genes encoding expansin and cell wall hydrolases, especially xylosidase and galactosidase. Ethylene treatment alleviated internal browning, accompanied by changes in expression of polyphenol oxidase, peroxidase and lipoxygenases. An enhanced content of phospholipids and glycerolipids and a reduced content of ceramide were observed in ethylene-treated fruit, and these were associated with up-regulation of lipid phosphate phosphatase, fatty acid alpha-hydroxylase, and golgi-localized nucleotide sugar transporter, as well as down-regulation of aminoalcohol phosphotransferases. Expression of two ethylene response factors (ERFs), ESE3 and ABR1, was highly correlated with that of genes involved in cell wall metabolism and lipid metabolism, respectively. Furthermore, the expression of these two ERFs was strongly regulated by ethylene treatment and the temperature changes during transfer of fruit into or out of cold storage. It is proposed that ERFs fulfill roles as crucial integrators between cell wall modifications and lipid metabolism involved in CI processes ameliorated by exogenous ethylene.

MaMYB4 Recruits Histone Deacetylase MaHDA2 and Modulates the Expression of ω-3 Fatty Acid Desaturase Genes during Cold Stress Response in Banana Fruit

Linoleic acid (LA; C18:2) and α-linolenic acid (ALA; C18:3) are two essential unsaturated fatty acids that play indispensable roles in maintaining membrane integrity in cold stress, and ω-3 fatty acid desaturases (FADs) are responsible for the transformation of LA into ALA. However, how this process is regulated at transcriptional and posttranscriptional levels remains largely unknown. In this study, an MYB transcription factor, MaMYB4, of a banana fruit was identified and found to target several ω-3 MaFADs, including MaFAD3-1, MaFAD3-3, MaFAD3-4 and MaFAD3-7, and repress their transcription. Intriguingly, the acetylation levels of histones H3 and H4 in the promoters of ω-3 MaFADs were elevated in response to cold stress, which was correlated with the enhancement in the transcription levels of ω-3 MaFADs and the ratio of ALA/LA. Moreover, a histone deacetylase MaHDA2 physically interacted with MaMYB4, thereby leading to the enhanced MaMYB4-mediated transcriptional repression of ω-3 MaFADs. Collectively, these data demonstrate that MaMYB4 might recruit MaHDA2 to repress the transcription of ω-3 MaFADs by affecting their acetylation levels, thus modulating fatty acid biosynthesis. Our findings provided new molecular insights into the regulatory mechanisms of fatty acid biosynthesis in cold stress in fruits.

FAX2 Mediates Fatty Acid Export from Plastids in Developing Arabidopsis Seeds

Vegetable oils are mainly stored in the form of triacylglycerol (TAG) in oilseeds. Fatty acids (FAs), one of the building blocks for TAG assembly, are synthesized in plastids and then exported to the endoplasmic reticulum for storage oil synthesis. A recent study demonstrated that the export of FAs from plastids was mediated by a FAX (FA export) family protein. However, the significance of FAs export from plastid during seed oil accumulation has not been investigated. In this study, we found that FAX2 was highly expressed in developing Arabidopsis seeds and the expression level was consistent with FAs synthesis activity. FAX2 mutant seeds showed an approximately 18% reduction of lipid levels compared with wild-type seeds. By contrast, overexpression of FAX2 enhanced seed lipid accumulation by up to 30%. The FAs export activity of FAX2 was confirmed by yeast mutant cell complementation analysis. Our results showed that FAX2 could interact with other proteins to facilitate FAs transport. Taken together, these results indicate that FAX2-mediated FA export from plastids is important for seed oil accumulation, and that FAX2 can be used as a target gene for increasing lipid production in oilseeds.

Recent advances in enhancement of oil content in oilseed crops

Plant oils are very valuable agricultural commodity. The manipulation of seed oil composition to deliver enhanced fatty acid compositions, which are appropriate for feed or fuel, has always been a main objective of metabolic engineers. The last two decennary have been noticeable by numerous significant events in genetic engineering for identification of different gene targets to improve oil yield in oilseed crops. Particularly, genetic engineering approaches have presented major breakthrough in elevating oil content in oilseed crops such as Brassica napus and soybean. Additionally, current research efforts to explore the possibilities to modify the genetic expression of key regulators of oil accumulation along with biochemical studies to elucidate lipid biosynthesis will establish protocols to develop transgenic oilseed crops along much improved oil content. In this review, we describe current distinct genetic engineering approaches investigated by researchers for ameliorating oil content and its nutritional quality. Moreover, we will also discuss some auspicious and innovative approaches and challenges for engineering oil content to yield oil at much higher rate in oilseed crops.

Complex Patterns of Cannabinoid Alkyl Side-Chain Inheritance in Cannabis

The cannabinoid alkyl side-chain represents an important pharmacophore, where genetic targeting of alkyl homologs has the potential to provide enhanced forms of Cannabis for biopharmaceutical manufacture. Delta(9)-tetrahydrocannabinolic acid (THCA) and cannabidiolic acid (CBDA) synthase genes govern dicyclic (CBDA) and tricyclic (THCA) cannabinoid composition. However, the inheritance of alkyl side-chain length has not been resolved, and few studies have investigated the contributions and interactions between cannabinoid synthesis pathway loci. To examine the inheritance of chemical phenotype (chemotype), THCAS and CBDAS genotypes were scored and alkyl cannabinoid segregation analysed in 210 F₂ progeny derived from a cross between two Cannabis chemotypes divergent for alkyl and cyclic cannabinoids. Inheritance patterns of F₂ progeny were non-Gaussian and deviated from Mendelian expectations. However, discrete alkyl cannabinoid segregation patterns consistent with digenic as well as epistatic modes of inheritance were observed among F₂ THCAS and CBDAS genotypes. These results suggest linkage between cannabinoid pathway loci and highlight the need for further detailed characterisation of cannabinoid inheritance to facilitate metabolic engineering of chemically elite germplasm.

WRINKLED1, a "Master Regulator" in Transcriptional Control of Plant Oil Biosynthesis

A majority of plant species generate and accumulate triacylglycerol (TAG) in their seeds, which is the main resource of carbon and energy supporting the process of seedling development. Plant seed oils have broad ranges of uses, being not only important for human diets but also renewable feedstock of industrial applications. The WRINKLED1 (WRI1) transcription factor is vital for the transcriptional control of plant oil biosynthetic pathways. Since the identification of the Arabidopsis WRI1 gene (AtWRI1) fifteen years ago, tremendous progress has been made in understanding the functions of WRI1 at multiple levels, ranging from the identification of AtWRI1 target genes to location of the AtWRI1 binding motif, and from discovery of intrinsic structural disorder in WRI1 to fine-tuning of WRI1 modulation by post-translational modifications and protein-protein interactions. The expanding knowledge on the functional understanding of the WRI1 regulatory mechanism not only provides a clearer picture of transcriptional regulation of plant oil biosynthetic pathway, but also helps generate new strategies to better utilize WRI1 for developing novel oil crops.

Microbial Lipid Alternatives to Plant Lipids

Lipids are in high demand in food production, nutritional supplements, detergents, lubricants, and biofuels. Different oil seeds produced from plants are conventionally extracted to yield lipids. With increasing population and reduced availability of cultivable land, conventional methods of producing lipids alone will not satisfy increasing demand. Lipids produced using different microbial sources are considered as sustainable alternative to plant derived lipids. Various microorganisms belonging to the genera of algae, bacteria, yeast, fungi, or marine-derived microorganisms such as thraustochytrids possess the ability to accumulate lipids in their cells. A variety of microbial production technologies are being used to cultivate these organisms under specific conditions using agricultural residues as carbon source to be cost competitive with plant derived lipids. Microbial oils, also known as single cell oils, have many advantages when compared with plant derived lipids, such as shorter life cycle, less labor required, season and climate independence, no use of arable land and ease of scale-up. In this chapter we compare the lipids derived from plants and different microorganisms. We also highlight various analytical techniques that are being used to characterize the lipids produced in oleaginous organisms and their applications in various processes.

Upregulated Lipid Biosynthesis at the Expense of Starch Production in Potato (Solanum tuberosum) Vegetative Tissues via Simultaneous Downregulation of ADP-Glucose Pyrophosphorylase and Sugar Dependent1 Expressions

Triacylglycerol is a major component of vegetable oil in seeds and fruits of many plants, but its production in vegetative tissues is rather limited. It would be intriguing and important to explore any possibility to expand current oil production platforms, for example from the plant vegetative tissues. By expressing a suite of transgenes involved in the triacylglycerol biosynthesis, we have previously observed substantial accumulation of triacylglycerol in tobacco (Nicotiana tabacum) leaf and potato (Solanum tuberosum) tuber. In this study, simultaneous RNA interference (RNAi) downregulation of ADP-glucose pyrophosphorylase (AGPase) and Sugar-dependent1 (SDP1), was able to increase the accumulation of triacylglycerol and other lipids in both wild type potato and the previously generated high oil potato line 69. Particularly, a 16-fold enhancement of triacylglycerol production was observed in the mature transgenic tubers derived from the wild type potato, and a two-fold increase in triacylglycerol was observed in the high oil potato line 69, accounting for about 7% of tuber dry weight, which is the highest triacylglycerol accumulation ever reported in potato. In addition to the alterations of lipid content and fatty acid composition, sugar accumulation, starch content of the RNAi potato lines in both tuber and leaf tissues were also substantially changed, as well as the tuber starch properties. Microscopic analysis further revealed variation of lipid droplet distribution and starch granule morphology in the mature transgenic tubers compared to their parent lines. This study reflects that the carbon partitioning between lipid and starch in both leaves and non-photosynthetic tuber tissues, respectively, are highly orchestrated in potato, and it is promising to convert low-energy starch to storage lipids via genetic manipulation of the carbon metabolism pathways.

Lipid transport required to make lipids of photosynthetic membranes

Photosynthetic membranes provide much of the usable energy for life on earth. To produce photosynthetic membrane lipids, multiple transport steps are required, including fatty acid export from the chloroplast stroma to the endoplasmic reticulum, and lipid transport from the endoplasmic reticulum to the chloroplast envelope membranes. Transport of hydrophobic molecules through aqueous space is energetically unfavorable and must be catalyzed by dedicated enzymes, frequently on specialized membrane structures. Here, we review photosynthetic membrane lipid transport to the chloroplast in the context of photosynthetic membrane lipid synthesis. We independently consider the identity of transported lipids, the proteinaceous transport components, and membrane structures which may allow efficient transport. Recent advances in lipid transport of chloroplasts, bacteria, and other systems strongly suggest that lipid transport is achieved by multiple mechanisms which include membrane contact sites with specialized protein machinery. This machinery is likely to include the TGD1, 2, 3 complex with the TGD5 and TGD4/LPTD1 systems, and may also include a number of proteins with domains similar to other membrane contact site lipid-binding proteins. Importantly, the likelihood of membrane contact sites does not preclude lipid transport by other mechanisms including vectorial acylation and vesicle transport. Substantial progress is needed to fully understand all photosynthetic membrane lipid transport processes and how they are integrated.

Can the world's favorite fruit, tomato, provide an effective biosynthetic chassis for high-value metabolites?

Tomato has a relatively short growth cycle (fruit ready to pick within 65-85 days from planting) and a relatively high yield (the average for globe tomatoes is 3-9 kg fruit per plant rising to as much as 40 kg fruit per plant). Tomatoes also produce large amounts of important primary and secondary metabolites which can serve as intermediates or substrates for producing valuable new compounds. As a model crop, tomato already has a broad range of tools and resources available for biotechnological applications, either increased nutrients for health-promoting biofortified foods or as a production system for high-value compounds. These advantages make tomato an excellent chassis for the production of important metabolites. We summarize recent achievements in metabolic engineering of tomato and suggest new candidate metabolites which could be targets for metabolic engineering. We offer a scheme for how to establish tomato as a chassis for industrial-scale production of high-value metabolites.

Seeds as oil factories

Studying seed oil metabolism. The seeds of higher plants represent valuable factories capable of converting photosynthetically derived sugars into a variety of storage compounds, including oils. Oils are the most energy-dense plant reserves and fatty acids composing these oils represent an excellent nutritional source. They supply humans with much of the calories and essential fatty acids required in their diet. These oils are then increasingly being utilized as renewable alternatives to petroleum for the chemical industry and for biofuels. Plant oils therefore represent a highly valuable agricultural commodity, the demand for which is increasing rapidly. Knowledge regarding seed oil production is extensively exploited in the frame of breeding programs and approaches of metabolic engineering for oilseed crop improvement. Complementary aspects of this research include (1) the study of carbon metabolism responsible for the conversion of photosynthetically derived sugars into precursors for fatty acid biosynthesis, (2) the identification and characterization of the enzymatic actors allowing the production of the wide set of fatty acid structures found in seed oils, and (3) the investigation of the complex biosynthetic pathways leading to the production of storage lipids (waxes, triacylglycerols). In this review, we outline the most recent developments in our understanding of the underlying biochemical and molecular mechanisms of seed oil production, focusing on fatty acids and oils that can have a significant impact on the emerging bioeconomy.

WRINKLED1 transcription factor: How much do we know about its regulatory mechanism?

Many plant species produce and build up triacylglycerol (TAG) in their seeds as a main resource to provide carbon and energy during seedling development. Plant seed oils are important not only for human diets but also as renewable feedstock of industrial uses. WRINKLED1 (WRI1), an APETALA2 (AP2) transcription factor, plays an essential role in the transcriptional regulation of TAG biosynthesis as WRI1 regulates the expression of key genes in the glycolytic and fatty acid biosynthetic pathways. Recent work has identified intrinsic structural disorder in WRI1 that may affect the stability of the protein. Furthermore, WRI1 activity is modulated by post-translational modifications and interacting partners. These progresses shed light on regulatory functions of WRI1 at the molecular levels, paving new paths to the use of WRI1 for bioengineering of TAG in plants.

Transcriptomic analysis of Perilla frutescens seed to insight into the biosynthesis and metabolic of unsaturated fatty acids

Background

Perilla frutescens is well known for its high α-linolenic acid (ALA) accumulation in seeds and medicinal values as well as a source of edible and general-purpose oils. However, the regulatory mechanisms of the biosynthesis of fatty acid in its seeds remain poorly understood due to the lacking of sequenced genome. For better understanding the regulation of lipid metabolism and further increase its oil content or modify oil composition, time-course transcriptome and lipid composition analyses were performed.

Results

Analysis of fatty acid content and composition showed that the α-linolenic acid and oleic acid accumulated rapidly from 5 DAF to 15 DAF and then kept relatively stable. However, the amount of palmitic acid and linoleic acid decreased quickly from 5 DAF to 15DAF. No significant variation of stearic acid content was observed from 5 DAF to 25DAF. Our transcriptome data analyses revealed that 110,176 unigenes were generated from six seed libraries at 5, 10, 20 DAF. Of these, 53 (31 up, 22 down) and 653 (259 up, 394 down) genes showed temporal and differentially expression during the seed development in 5 DAF vs 10 DAF, 20 vs 10 DAF, respectively. The differentially expressed genes were annotated and found to be involved in distinct functional categories and metabolic pathways. Deep mining of transcriptome data led to the identification of key genes involved in fatty acid and triacylglycerol biosynthesis and metabolism. Thirty seven members of transcription factor family AP2, B3 and NFYB putatively involved in oil synthesis and deposition were differentially expressed during seed development. The results of qRT-PCR for selected genes showed a strong positive correlation with the expression abundance measured in RNA-seq analysis.

Conclusions

The present study provides valuable genomic resources for characterizing Perilla seed gene expression at the transcriptional level and will extend our understanding of the complex molecular and cellular events of oil biosynthesis and accumulation in oilseed crops.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4595-z) contains supplementary material, which is available to authorized users.

Next-Generation Plant Metabolic Engineering, Inspired by an Ancient Chinese Irrigation System

Specialized secondary metabolites serve not only to protect plants against abiotic and biotic challenges, but have also been used extensively by humans to combat diseases. Due to the great importance of medicinal plants for health, we need to find new and sustainable ways to improve the production of the specialized metabolites. In addition to direct extraction, recent progress in metabolic engineering of plants offers an alternative supply option. We argue that metabolic engineering for producing the secondary metabolites in plants may have distinct advantages over microbial production platforms, and thus propose new approaches of plant metabolic engineering, which are inspired by an ancient Chinese irrigation system. Metabolic engineering strategies work at three levels: introducing biosynthetic genes, using transcription factors, and improving metabolic flux including increasing the supply of precursors, energy, and reducing power. In addition, recent progress in biotechnology contributes markedly to better engineering, such as the use of specific promoters and the deletion of competing branch pathways. We propose that next-generation plant metabolic engineering will improve current engineering strategies, for the purpose of producing valuable metabolites in plants on industrial scales.

Medicine is not health care, food is health care: plant metabolic engineering, diet and human health

Contents 699 I. 699 II. 700 III. 700 IV. 706 V. 707 VI. 714 714 References 714 SUMMARY: Plants make substantial contributions to our health through our diets, providing macronutrients for energy and growth as well as essential vitamins and phytonutrients that protect us from chronic diseases. Imbalances in our food can lead to deficiency diseases or obesity and associated metabolic disorders, increased risk of cardiovascular diseases and cancer. Nutritional security is now a global challenge which can be addressed, at least in part, through plant metabolic engineering for nutritional improvement of foods that are accessible to and eaten by many. We review the progress that has been made in nutritional enhancement of foods, both improvements through breeding and through biotechnology and the engineering principles on which increased phytonutrient levels are based. We also consider the evidence, where available, that such foods do enhance health and protect against chronic diseases.

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.

Step changes in leaf oil accumulation via iterative metabolic engineering

Synthesis and accumulation of plant oils in the entire vegetative biomass offers the potential to deliver yields surpassing those of oilseed crops. However, current levels still fall well short of those typically found in oilseeds. Here we show how transcriptome and biochemical analyses pointed to a futile cycle in a previously established Nicotiana tabacum line, accumulating up to 15% (dry weight) of the storage lipid triacylglycerol in leaf tissue. To overcome this metabolic bottleneck, we either silenced the SDP1 lipase or overexpressed the Arabidopsis thaliana LEC2 transcription factor in this transgenic background. Both strategies independently resulted in the accumulation of 30-33% triacylglycerol in leaf tissues. Our results demonstrate that the combined optimization of de novo fatty acid biosynthesis, storage lipid assembly and lipid turnover in leaf tissue results in a major overhaul of the plant central carbon allocation and lipid metabolism. The resulting further step changes in oil accumulation in the entire plant biomass offers the possibility of delivering yields that outperform current oilseed crops.

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.

14-3-3 protein mediates plant seed oil biosynthesis through interaction with AtWRI1

Plant 14-3-3 proteins are phosphopeptide-binding proteins, belonging to a large family of proteins involved in numerous physiological processes including primary metabolism, although knowledge about the function of 14-3-3s in plant lipid metabolism is sparse. WRINKLED1 (WRI1) is a key transcription factor that governs plant oil biosynthesis. At present, AtWRI1-interacting partners remain largely unknown. Here, we show that 14-3-3 proteins are able to interact with AtWRI1, both in yeast and plant cells. Transient co-expression of 14-3-3- and AtWRI1-encoding cDNAs led to increased oil biosynthesis in Nicotiana benthamiana leaves. Stable transgenic plants overproducing a 14-3-3 protein also displayed increased seed oil content. Co-production of a 14-3-3 protein with AtWRI1 enhanced the transcriptional activity of AtWRI1. The 14-3-3 protein was found to increase the stability of AtWRI1. A possible 14-3-3 binding motif was identified in one of the two AP2 domains of AtWRI1, which was also found to be critical for the interaction of AtWRI1 with an E3 ligase linker protein. Thus, we hypothesize a regulatory mechanism by which the binding of 14-3-3 to AtWRI1 interferes with the interaction of AtWRI1 and the E3 ligase, thereby protecting AtWRI1 from degradation. Taken together, our studies identified AtWRI1 as a client of 14-3-3 proteins and provide insights into a role of 14-3-3 in mediating plant oil biosynthesis.

Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds

Increasing yield and quality of seed storage compounds in a sustainable way is a key challenge for our societies. Genome-wide analyses conducted in both monocot and dicot angiosperms emphasized drastic transcriptional switches that occur during seed development. In Arabidopsis thaliana, a reference species, genetic and molecular analyses have demonstrated the key role of LAFL (LEC1, ABI3, FUS3, and LEC2) transcription factors (TFs), in controlling gene expression programs essential to accomplish seed maturation and the accumulation of storage compounds. Here, we summarize recent progress obtained in the characterization of these LAFL proteins, their regulation, partners and target genes. Moreover, we illustrate how these evolutionary conserved TFs can be used to engineer new crops with altered seed compositions and point out the current limitations. Last, we discuss about the interest of investigating further the environmental and epigenetic regulation of this network for the coming years.

Gene coexpression network analysis of oil biosynthesis in an interspecific backcross of oil palm

Global demand for vegetable oils is increasing at a dramatic rate, while our understanding of the regulation of oil biosynthesis in plants remains limited. To gain insights into the mechanisms that govern oil synthesis and fatty acid (FA) composition in the oil palm fruit, we used a multilevel approach combining gene coexpression analysis, quantification of allele-specific expression and joint multivariate analysis of transcriptomic and lipid data, in an interspecific backcross population between the African oil palm, Elaeis guineensis, and the American oil palm, Elaeis oleifera, which display contrasting oil contents and FA compositions. The gene coexpression network produced revealed tight transcriptional coordination of fatty acid synthesis (FAS) in the plastid with sugar sensing, plastidial glycolysis, transient starch storage and carbon recapture pathways. It also revealed a concerted regulation, along with FAS, of both the transfer of nascent FA to the endoplasmic reticulum, where triacylglycerol assembly occurs, and of the production of glycerol-3-phosphate, which provides the backbone of triacylglycerols. Plastid biogenesis and auxin transport were the two other biological processes most tightly connected to FAS in the network. In addition to WRINKLED1, a transcription factor (TF) known to activate FAS genes, two novel TFs, termed NF-YB-1 and ZFP-1, were found at the core of the FAS module. The saturated FA content of palm oil appeared to vary above all in relation to the level of transcripts of the gene coding for β-ketoacyl-acyl carrier protein synthase II. Our findings should facilitate the development of breeding and engineering strategies in this and other oil crops.