PlantFAdb: a resource for exploring hundreds of plant fatty acid structures synthesized by thousands of plants and their phylogenetic relationships

Spatial omics for accelerating plant research and crop improvement

Plant cells communicate information to regulate developmental processes and respond to environmental stresses. This communication spans various 'omics' layers within a cell and operates through intricate regulatory networks. The emergence of spatial omics presents a promising approach to thoroughly analyze cells, allowing the combined analysis of diverse modalities either in parallel or on the same tissue section. Here, we provide an overview of recent advancements in spatial omics and delineate scientific discoveries in plant research enabled by these technologies. We delve into experimental and computational challenges and outline strategies to navigate these challenges for advancing breeding efforts. With ongoing insightful discoveries and improved accessibility, spatial omics stands on the brink of playing a crucial role in designing future crops.

Phylogenetic and biochemical drivers of plant species variation in organic compound hydrogen stable isotopes: novel mechanistic constraints

Significant variation in plant organic compound hydrogen stable isotope (δ2H) values among species from a single location suggests species biochemistry diversity as a key driver. However, the biochemical mechanisms and the biological relevance behind this species-specific δ2H variation remain unclear. We analyzed δ2H values of cellulose and n-alkanes across 179 eudicot species in a botanical garden sampled in 2019, and cellulose, n-alkanes, fatty acids and phytol δ2H values from 56 eudicot species sampled in 2020. We utilized the observed species variation in δ2H values to determine phylogenetic structure and mechanistic constraints for biochemical 2H-fractionation. A strong phylogenetic signal in lipid compound δ2H values implies that the drivers of species variation in lipid δ2H values are evolutionarily conserved. By contrast, species variation in cellulose δ2H values was not strongly linked to phylogeny. Generally low-explanatory power of relationships between δ2H values of different compounds (R2 < 0.26) implies nonubiquitous drivers of species variation in plant organic compound δ2H values. Historically, variable biochemical 2H-fractionation was often attributed to δ2H values of H incorporated from NADPH. Instead, the results from this study suggest that species variation in biochemical 2H-fractionation largely occurs independently within biosynthetic pathways. For lipids, these mechanisms appear strongly linked to evolutionary history.

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

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

Plant and algal lipidomes: Analysis, composition, and their societal significance

Plants and algae play a crucial role in the earth's ecosystems. Through photosynthesis they convert light energy into chemical energy, capture CO2 and produce oxygen and energy-rich organic compounds. Photosynthetic organisms are primary producers and synthesize the essential omega 3 and omega 6 fatty acids. They have also unique and highly diverse complex lipids, such as glycolipids, phospholipids, triglycerides, sphingolipids and phytosterols, with nutritional and health benefits. Plant and algal lipids are useful in food, feed, nutraceutical, cosmeceutical and pharmaceutical industries but also for green chemistry and bioenergy. The analysis of plant and algal lipidomes represents a significant challenge due to the intricate and diverse nature of their composition, as well as their plasticity under changing environmental conditions. Optimization of analytical tools is crucial for an in-depth exploration of the lipidome of plants and algae. This review highlights how lipidomics analytical tools can be used to establish a complete mapping of plant and algal lipidomes. Acquiring this knowledge will pave the way for the use of plants and algae as sources of tailored lipids for both industrial and environmental applications. This aligns with the main challenges for society, upholding the natural resources of our planet and respecting their limits.

Mapping of specialized metabolite terms onto a plant phylogeny using text mining and large language models

Plants produce a staggering array of chemicals that are the basis for organismal function and important human nutrients and medicines. However, it is poorly defined how these compounds evolved and are distributed across the plant kingdom, hindering a systematic view and understanding of plant chemical diversity. Recent advances in plant genome/transcriptome sequencing have provided a well-defined molecular phylogeny of plants, on which the presence of diverse natural products can be mapped to systematically determine their phylogenetic distribution. Here, we built a proof-of-concept workflow where previously reported diverse tyrosine-derived plant natural products were mapped onto the plant tree of life. Plant chemical-species associations were mined from literature, filtered, evaluated through manual inspection of over 2500 scientific articles, and mapped onto the plant phylogeny. The resulting "phylochemical" map confirmed several highly lineage-specific compound class distributions, such as betalain pigments and Amaryllidaceae alkaloids. The map also highlighted several lineages enriched in dopamine-derived compounds, including the orders Caryophyllales, Liliales, and Fabales. Additionally, the application of large language models, using our manually curated data as a ground truth set, showed that post-mining processing can largely be automated with a low false-positive rate, critical for generating a reliable phylochemical map. Although a high false-negative rate remains a challenge, our study demonstrates that combining text mining with language model-based processing can generate broader phylochemical maps, which will serve as a valuable community resource to uncover key evolutionary events that underlie plant chemical diversity and enable system-level views of nature's millions of years of chemical experimentation.

First draft reference genome and annotation of the alternative oil species Physaria fendleri

In the wake of increasing demand for renewable energy sources, plant-based sources including alternative oilseeds have come to the forefront of interest. Hydroxy fatty acids (HFAs), produced in a few oilseed species, are important chemical feed stocks for industrial applications. An integrated approach was taken to assemble the first draft genome of the alternative HFA producer Physaria fendleri (n = 6), an outcrossing species with high heterozygosity. Both de novo transcriptome assemblies and genome assemblies were produced with public and generated sequencing reads. Resulting intermediate assemblies were then scaffolded and patched with multiple data sources, followed by super-scaffolding onto a masked genome of Camelina laxa (n = 6). Despite a current lack of available resources for the physical mapping of genomic scaffolds of P. fendleri, topography of the genome with respect to repeat and gene content was preserved at the scaffold level and not significantly lost via super-scaffolding. Read representation, gene and genome completion statistics, and annotation results illustrated the creation of a functional draft genome and a tool for future research on alternative oil species.

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

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

Variety of Plant Oils: Species-Specific Lipid Biosynthesis

Plant oils represent a large group of neutral lipids with important applications in food, feed and oleochemical industries. Most plants accumulate oils in the form of triacylglycerol within seeds and their surrounding tissues, which comprises three fatty acids attached to a glycerol backbone. Different plant species accumulate unique fatty acids in their oils, serving a range of applications in pharmaceuticals and oleochemicals. To enable the production of these distinctive oils, select plant species have adapted specialized oil metabolism pathways, involving differential gene co-expression networks and structurally divergent enzymes/proteins. Here, we summarize some of the recent advances in our understanding of oil biosynthesis in plants. We compare expression patterns of oil metabolism genes from representative species, including Arabidopsis thaliana, Ricinus communis (castor bean), Linum usitatissimum L. (flax) and Elaeis guineensis (oil palm) to showcase the co-expression networks of relevant genes for acyl metabolism. We also review several divergent enzymes/proteins associated with key catalytic steps of unique oil accumulation, including fatty acid desaturases, diacylglycerol acyltransferases and oleosins, highlighting their structural features and preference toward unique lipid substrates. Lastly, we briefly discuss protein interactomes and substrate channeling for oil biosynthesis and the complex regulation of these processes.

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

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

EgMADS3 directly regulates EgLPAAT to mediate medium-chain fatty acids (MCFA) anabolism in the mesocarp of oil palm

KEY MESSAGE

EgMADS3, a pivotal transcription factor, positively regulates MCFA accumulation via binding to the EgLPAAT promoter, advancing lipid content in mesocarp of oil palm. Lipids function as the structural components of cell membranes, which serve as permeable barriers to the external environment of cells. The medium-chain fatty acid in the stored lipids of plants is an important renewable energy. Most research on MCFA production in plant lipid synthesis is based on biochemical methods, and the importance of transcriptional regulation in MCFA synthesis and its incorporation into TAGs needs further research. Oil palm is the most productive oil crop in the world and has the highest productivity among the main oil crops. In this study, the MADS transcription factor (EgMADS3) in the mesocarp of oil palm was characterized. Through the VIGS-virus induced gene silencing, it was determined that the potential target gene of EgMADS3 was related to the biosynthesis of medium-chain fatty acid (MCFA). Transient transformation in protoplasts and qRT-PCR analysis showed that EgMADS3 positively regulated the expression of EgLPAAT. The results of the yeast one-hybrid assays and EMSA indicated the interaction between EgMADS3 and EgLPAAT promoter. Through genetic transformation and fatty acid analysis, it is concluded that EgMADS3 directly regulates the mid-chain fatty acid synthesis pathway of the potential target gene EgLPAAT, thus promotes the accumulation of MCFA and improves the total lipid content. This study is innovative in the functional analysis of the MADS family transcription factor in the metabolism of medium-chain fatty acids (MCFA) of oil palm, provides a certain research basis for improving the metabolic pathway of chain fatty acids in oil palm, and improves the synthesis of MCFA in plants. Our results will provide a reference direction for further research on improving the oil quality through biotechnology of oil palm.

Imaging plant metabolism in situ

Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.

Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies

Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.

Can cardiolipins be used as a biomarker for arbuscular mycorrhizal fungi?

Specific biomarker molecules are increasingly being used for detection and quantification in plant and soil samples of arbuscular mycorrhizal (AM) fungi, an important and widespread microbial guild heavily implicated in transfers of nutrients and carbon between plants and soils and in the maintenance of soil physico-chemical properties. Yet, concerns have previously been raised as to the validity of a range of previously used approaches (e.g., microscopy, AM-specific fatty acids, sterols, glomalin-like molecules, ribosomal DNA sequences), justifying further research into novel biomarkers for AM fungal abundance and/or functioning. Here, we focused on complex polar lipids contained in pure biomass of Rhizophagus irregularis and in nonmycorrhizal and mycorrhizal roots of chicory (Cichorium intybus), leek (Allium porrum), and big bluestem (Andropogon gerardii). The lipids were analyzed by shotgun lipidomics using a high-resolution hybrid mass spectrometer. Size range between 1350 and 1550 Da was chosen for the detection of potential biomarkers among cardiolipins (1,3-bis(sn-3'-phosphatidyl)-sn-glycerols), a specific class of phospholipids. The analysis revealed a variety of molecular species, including cardiolipins containing one or two polyunsaturated fatty acids with 20 carbon atoms each, i.e., arachidonic and/or eicosapentaenoic acids, some of them apparently specific for the mycorrhizal samples. Although further verification using a greater variety of AM fungal species and samples from various soils/ecosystems/environmental conditions is needed, current results suggest the possibility to identify novel biochemical signatures specific for AM fungi within mycorrhizal roots. Whether they could be used for quantification of both root and soil colonization by the AM fungi merits further scrutiny.

Influence of Air Mass Source Regions on Signatures of Surface-Active Organic Molecules in Size Resolved Atmospheric Aerosol Particles

The physical and chemical properties of atmospheric aerosol particles depend on their sources and lifetime in the atmosphere. In coastal regions, sources may include influences from marine, continental, anthropogenic, and natural emissions. In this study, particles in ten diameter-size ranges were collected, and particle number size distributions were measured, at Skidaway Island, GA in May and June 2018. Based on air mass back trajectories and concentrations of major ions in the particles, the air mass source regions were identified as Marine Influenced, Mixed, and Continental Influenced. Organic molecules were extracted from the particles using solid-phase extraction and characterized using tensiometry and high-resolution mass spectrometry. The presence of surfactants was confirmed in the extracts through the observation of significant surface tension depressions. The organic formulas contained high hydrogen-to-carbon (H/C) and low oxygen-to-carbon (O/C) ratios, similar to surfactants and lipid-like molecules. In the Marine Influenced particles, the fraction of formulas identified as surfactant-like was negatively correlated with minimum surface tensions; as the surfactant fraction increased, the surface tension decreased. Analyses of fatty acid compounds demonstrated that organic compounds extracted from the Marine Influenced particles had the highest carbon numbers (18), compared to those of the Mixed (15) and Continental Influenced (9) particles. This suggests that the fatty acids in the Continental Influenced particles may have been more aged in the atmosphere and undergone fragmentation. This is one of the first studies to measure the chemical and physical properties of surfactants in size-resolved particles from different air mass source regions.

Chios Mastic Gum: Chemical Profile and Pharmacological Properties in Inflammatory Bowel Disease: From the Past to the Future

Chios mastic gum, the product of the tree Pistacia lentiscus var. Chia, has been used for more than 2500 years in traditional Greek medicine for treating several diseases, thanks to the anti-inflammatory and antioxidant properties of its components. Despite the long-time use of mastic in gastroenterology and in particular in chronic-inflammation-associated diseases, to date, the literature lacks reviews regarding this topic. The aim of the present work is to summarize available data on the effects of P. lentiscus on inflammatory bowel disease. A comprehensive review of this topic could drive researchers to conduct future studies aimed at deeply investigating P. lentiscus effects and hypothesizing a mechanism of action. The present review, indeed, schematizes the possible bioactive components of mastic gum. Particular care is given to P. lentiscus var. Chia medicaments' and supplements' chemical compositions and their pharmacological action in inflammatory bowel disease.

Fatty Acid Profiles of Some Siberian Bryophytes and Prospects of Their Use in Chemotaxonomy

The composition of fatty acids (FAs) in gametophyte samples of 20 Siberian bryophyte species from four orders of mosses and four orders of liverworts collected in relatively cold months (April and/or October) was examined. FA profiles were obtained using gas chromatography. Thirty-seven FAs were found, from 12:0 to 26:0; they included mono-, polyunsaturated (PUFAs) and rare FAs, such as 22:5n-3 and two acetylenic FAs, 6a,9,12-18:3 and 6a,9,12,15-18:4 (dicranin). Acetylenic FAs were found in all examined species of the Bryales and Dicranales orders, dicranin being the predominant FA. The role of particular PUFAs in mosses and liverworts is discussed. Multivariate discriminant analysis (MDA) was performed to determine whether FAs can be used in the chemotaxonomy of bryophytes. Based on the MDA results, FA composition is related to the taxonomic status of species. Thus, several individual FAs were identified as chemotaxonomic markers at the level of bryophyte orders. These were 18:3n-3; 18:4n-3; 6a,9,12-18:3; 6a,9,12,15-18:4; 20:4n-3 and EPA in mosses and 16:3n-3; 16:2n-6; 18:2n-6; 18:3n-3 and EPA in liverworts. These findings indicate that further research into bryophyte FA profiles can shed light on phylogenetic relationships within this group of plants and the evolution of their metabolic pathways.

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

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

Unsaturated Fatty Acids and Their Immunomodulatory Properties

Oils are an essential part of the human diet and are primarily derived from plant (or sometimes fish) sources. Several of them exhibit anti-inflammatory properties. Specific diets, such as Mediterranean diet, that are high in ω-3 polyunsaturated fatty acids (PUFAs) and ω-9 monounsaturated fatty acids (MUFAs) have even been shown to exert an overall positive impact on human health. One of the most widely used supplements in the developed world is fish oil, which contains high amounts of PUFAs docosahexaenoic and eicosapentaenoic acid. This review is focused on the natural sources of various polyunsaturated and monounsaturated fatty acids in the human diet, and their role as precursor molecules in immune signaling pathways. Consideration is also given to their role in CNS immunity. Recent findings from clinical trials utilizing various fatty acids or diets high in specific fatty acids are reviewed, along with the mechanisms through which fatty acids exert their anti-inflammatory properties. An overall understanding of diversity of polyunsaturated fatty acids and their role in several molecular signaling pathways is useful in formulating diets that reduce inflammation and increase longevity.

Bioengineering of Soybean Oil and Its Impact on Agronomic Traits

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

Role of Thylakoid Lipids in Protochlorophyllide Oxidoreductase Activation: Allosteric Mechanism Elucidated by a Computational Study

Light-dependent protochlorophyllide oxidoreductase (LPOR) is a chlorophyll synthetase that catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) with indispensable roles in regulating photosynthesis processes. A recent study confirmed that thylakoid lipids (TL) were able to allosterically enhance modulator-induced LPOR activation. However, the allosteric modulation mechanism of LPOR by these compounds remains unclear. Herein, we integrated multiple computational approaches to explore the potential cavities in the Arabidopsis thaliana LPOR and an allosteric site around the helix-G region where high affinity for phosphatidyl glycerol (PG) was identified. Adopting accelerated molecular dynamics simulation for different LPOR states, we rigorously analyzed binary LPOR/PG and ternary LPOR/NADPH/PG complexes in terms of their dynamics, energetics, and attainable allosteric regulation. Our findings clarify the experimental observation of increased NADPH binding affinity for LPOR with PGs. Moreover, the simulations indicated that allosteric regulators targeting LPOR favor a mechanism involving lid opening upon binding to an allosteric hinge pocket mechanism. This understanding paves the way for designing novel LPOR activators and expanding the applications of LPOR.

Genome-Wide Identification and Expression Analysis of Fatty Acid Desaturase (FAD) Genes in Camelina sativa (L.) Crantz

Camelina sativa (L.) Crantz is an indispensable oilseed crop, and its seeds contain many unsaturated fatty acids. FAD (fatty acid desaturase) regulates the synthesis of unsaturated fatty acids. In this research, we performed CsFAD gene family analysis and identified 24 CsFAD genes in Camelina, which were unevenly distributed on 14 of the 19 total chromosomes. Phylogenetic analysis showed that CsFAD includes four subfamilies, supported by the conserved structures and motifs of CsFAD genes. In addition, we investigated the expression patterns of the FAD family in the different tissues of Camelina. We found that CsFAD family genes were all expressed in the stem, and CsFAD2-2 was highly expressed in the early stage of seed development. Moreover, during low temperature (4 °C) stress, we identified that the expression level of CsFAD2-2 significantly changed. By observing the transient expression of CsFAD2-2 in Arabidopsis protoplasts, we found that CsFAD2-2 was located on the nucleus. Through the detection and analysis of fatty acids, we prove that CsFAD2-2 is involved in the synthesis of linolenic acid (C18:3). In conclusion, we identified CsFAD2-2 through the phylogenetic analysis of the CsFAD gene family and further determined the fatty acid content to find that CsFAD2-2 is involved in fatty acid synthesis in Camelina.

Phosphatidylcholine:diacylglycerol cholinephosphotransferase's unique regulation of castor bean oil quality

Castor bean (Ricinus communis) seed oil (triacylglycerol [TAG]) is composed of ∼90% of the industrially important ricinoleoyl (12-hydroxy-9-octadecenoyl) groups. Here, phosphatidylcholine (PC):diacylglycerol (DAG) cholinephosphotransferase (PDCT) from castor bean was biochemically characterized and compared with camelina (Camelina sativa) PDCT. DAGs with ricinoleoyl groups were poorly used by Camelina PDCT, and their presence inhibited the utilization of DAG with "common" acyl groups. In contrast, castor PDCT utilized DAG with ricinoleoyl groups similarly to DAG with common acyl groups and showed a 10-fold selectivity for DAG with one ricinoleoyl group over DAG with two ricinoleoyl groups. Castor DAG acyltransferase2 specificities and selectivities toward different DAG and acyl-CoA species were assessed and shown to not acylate DAG without ricinoleoyl groups in the presence of ricinoleoyl-containing DAG. Eighty-five percent of the DAG species in microsomal membranes prepared from developing castor endosperm lacked ricinoleoyl groups. Most of these species were predicted to be derived from PC, which had been formed by PDCT in exchange with DAG with one ricinoleoyl group. A scheme of the function of PDCT in castor endosperm is proposed where one ricinoleoyl group from de novo-synthesized DAG is selectivity transferred to PC. Nonricinoleate DAG is formed and ricinoleoyl groups entering PC are re-used either in de novo synthesis of DAG with two ricinoleoyl groups or in direct synthesis of triricinoleoyl TAG by PDAT. The PC-derived DAG is not used in TAG synthesis but is proposed to serve as a substrate in membrane lipid biosynthesis during oil deposition.

Variation on a theme: the structures and biosynthesis of specialized fatty acid natural products in plants

Plants are able to construct lineage-specific natural products from a wide array of their core metabolic pathways. Considerable progress has been made toward documenting and understanding, for example, phenylpropanoid natural products derived from phosphoenolpyruvate via the shikimate pathway, terpenoid compounds built using isopentyl pyrophosphate, and alkaloids generated by the extensive modification of amino acids. By comparison, natural products derived from fatty acids have received little attention, except for unusual fatty acids in seed oils and jasmonate-like oxylipins. However, scattered but numerous reports show that plants are able to generate many structurally diverse compounds from fatty acids, including some with highly elaborate and unique structural features that have novel bioproduct functionalities. Furthermore, although recent work has shed light on multiple new fatty acid natural product biosynthesis pathways and products in diverse plant species, these discoveries have not been reviewed. The aims of this work, therefore, are to (i) review and systematize our current knowledge of the structures and biosynthesis of fatty acid-derived natural products that are not seed oils or jasmonate-type oxylipins, specifically, polyacetylenic, very-long-chain, and aromatic fatty acid-derived natural products, and (ii) suggest priorities for future investigative steps that will bring our knowledge of fatty acid-derived natural products closer to the levels of knowledge that we have attained for other phytochemical classes.

Separation of triacylglycerols containing positional isomers of hexadecenoic acids by enantiomeric liquid chromatography-mass spectrometry

Triacylglycerols (TAGs) containing positional isomers of hypogeic (Hy), palmitoleic (Po), and palmitvaccenic (Pv) acids from three microorganisms (top-fermenting brewer's yeast Saccharomyces cerevisiae, green alga Coccomyxa elongata, and arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis) were analyzed. Dozens of regioisomers and enantiomers of TAGs containing one, two or three hexadecenoic acids have been identified by means of reversed phase chromatography/mass spectrometry (RP-HPLC/MS). The regioisomers of TAGs containing two palmitic acids and any hexadecenoic acid were separated. Analysis of regioisomers of TAGs having one Pv residue showed that asymmetric molecular species such as PvPP or PPPv were dominant in Rhizophagus. TAGs were also analyzed on a chiral phase column and nine molecular species of TAGs containing two palmitic and any of three hexadecenoic acids were separated and identified. In the case of TAGs containing one palmitic and two hexadecenoic acids, the separation was successful only if the hexadecenoic acids were identical. Separation of TAGs containing three hexadecenoic acids was successful only if all three hexadecenoic acids were identical. Regardless of the type of TAG, it was found that TAGs in the AM fungus and containing palmitvaccenic acid bound at the sn-1 position of the glycerol backbone were dominant, suggesting similarity in the biosynthesis of the different TAGs. The covalent adduct chemical ionization method was used for identification of TAGs as adduct with (1-methyleneimino)-1-ethenyl ion, which reacted with double bond of the unsaturated fatty acid. Tandem MS thus makes it possible to identify TAGs containing various hexadecenoic acids.

Divergent evolution of extreme production of variant plant monounsaturated fatty acids

The dietary and oleochemical value of vegetable oils is determined by their component fatty acids. Double bonds or “unsaturation” in fatty acids are critical for vegetable oil functionality. Seeds containing vegetable oils with extremely high levels of a single fatty acid have provided insights into enzyme-substrate recognition and metabolic plasticity and genes for biotechnological improvement of oilseeds. We report the discovery of species with seed oils containing >90% of an unusual monounsaturated fatty acid. We identified the variant enzyme that produces this fatty acid and elucidated its three-dimensional structure. We used this information to develop enzymes that produce nonnaturally occurring monounsaturated fatty acids and sourced genes from these species to engineer oilseeds and bacteria for modified fatty acid compositions.

Metabolic extremes provide opportunities to understand enzymatic and metabolic plasticity and biotechnological tools for novel biomaterial production. We discovered that seed oils of many Thunbergia species contain up to 92% of the unusual monounsaturated petroselinic acid (18:1Δ6), one of the highest reported levels for a single fatty acid in plants. Supporting the biosynthetic origin of petroselinic acid, we identified a Δ6-stearoyl-acyl carrier protein (18:0-ACP) desaturase from Thunbergia laurifolia, closely related to a previously identified Δ6-palmitoyl-ACP desaturase that produces sapienic acid (16:1Δ6)-rich oils in Thunbergia alata seeds. Guided by a T. laurifolia desaturase crystal structure obtained in this study, enzyme mutagenesis identified key amino acids for functional divergence of Δ6 desaturases from the archetypal Δ9-18:0-ACP desaturase and mutations that result in nonnative enzyme regiospecificity. Furthermore, we demonstrate the utility of the T. laurifolia desaturase for the production of unusual monounsaturated fatty acids in engineered plant and bacterial hosts. Through stepwise metabolic engineering, we provide evidence that divergent evolution of extreme petroselinic acid and sapienic acid production arises from biosynthetic and metabolic functional specialization and enhanced expression of specific enzymes to accommodate metabolism of atypical substrates.

Using interdisciplinary, phylogeny-guided approaches to understand the evolution of plant metabolism

To cope with relentless environmental pressures, plants produce an arsenal of structurally diverse chemicals, often called specialized metabolites. These lineage-specific compounds are derived from the simple building blocks made by ubiquitous core metabolic pathways. Although the structures of many specialized metabolites are known, the underlying metabolic pathways and the evolutionary events that have shaped the plant chemical diversity landscape are only beginning to be understood. However, with the advent of multi-omics data sets and the relative ease of studying pathways in previously intractable non-model species, plant specialized metabolic pathways are now being systematically identified. These large datasets also provide a foundation for comparative, phylogeny-guided studies of plant metabolism. Comparisons of metabolic traits and features like chemical abundances, enzyme activities, or gene sequences from phylogenetically diverse plants provide insights into how metabolic pathways evolved. This review highlights the power of studying evolution through the lens of comparative biochemistry, particularly how placing metabolism into a phylogenetic context can help a researcher identify the metabolic innovations enabling the evolution of structurally diverse plant metabolites.

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

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

Molecular Approaches Reduce Saturates and Eliminate trans Fats in Food Oils

Vegetable oils composed of triacylglycerols (TAG) are a major source of calories in human diets. However, the fatty acid compositions of these oils are not ideal for human nutrition and the needs of the food industry. Saturated fatty acids contribute to health problems, while polyunsaturated fatty acids (PUFA) can become rancid upon storage or processing. In this review, we first summarize the pathways of fatty acid metabolism and TAG synthesis and detail the problems with the oil compositions of major crops. Then we describe how transgenic expression of desaturases and downregulation of the plastid FatB thioesterase have provided the means to lower oil saturates. The traditional solution to PUFA rancidity uses industrial chemistry to reduce PUFA content by partial hydrogenation, but this results in the production of trans fats that are even more unhealthy than saturated fats. We detail the discoveries in the biochemistry and molecular genetics of oil synthesis that provided the knowledge and tools to lower oil PUFA content by blocking their synthesis during seed development. Finally, we describe the successes in breeding and biotechnology that are giving us new, high-oleic, low PUFA varieties of soybean, canola and other oilseed crops.

A multigene approach secures hydroxy fatty acid production in Arabidopsis

A central goal of green chemistry is to produce industrially useful fatty acids in oilseed crops. Although genes encoding suitable fatty acid-modifying enzymes are available from more than a dozen wild species, progress has been limited because expression of these enzymes in transgenic plants produces only low yields of the desired products. For example, fatty acid hydroxylase 12 (FAH12) from castor (Ricinus communis) produces only 17% hydroxy fatty acids (HFAs) when expressed in Arabidopsis (Arabidopsis thaliana), compared with 90% HFAs in castor seeds. The transgenic plants also have reduced oil content and seed vigor. Here, we review experiments that have provided for steady increased HFA accumulation and oil content. This research has led to exciting new discoveries of enzymes and regulatory processes in the pathways of both seed oil synthesis and lipid metabolism in other parts of the plant. Recent investigations have revealed that HFA-accumulating seeds are unable to rapidly mobilize HFA-containing triacylglycerol (TAG) storage lipid after germination to provide carbon and energy for seedling development, resulting in reduced seedling establishment. These findings present a new opportunity to investigate a different, key area of lipid metabolism-the pathways of TAG lipolysis and β-oxidation in germinating seedlings.

Regioselectivity mechanism of the Thunbergia alata Δ6-16:0-acyl carrier protein desaturase

Plant plastidial acyl-acyl carrier protein (ACP) desaturases are a soluble class of diiron-containing enzymes that are distinct from the diiron-containing integral membrane desaturases found in plants and other organisms. The archetype of this class is the stearoyl-ACP desaturase which converts stearoyl-ACP into oleoyl (18:1Δ9cis)-ACP. Several variants expressing distinct regioselectivity have been described including a Δ6-16:0-ACP desaturase from black-eyed Susan vine (Thunbergia alata). We solved a crystal structure of the T. alata desaturase at 2.05 Å resolution. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position C6 and C7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Δ6 desaturase to Δ9 regioselectivity. Additional modeling between ACP and the mutant variants confirmed the predicted regioselectivity. To validate the in-silico predictions, we synthesized two variants of the T. alata desaturase and analyzed their reaction products using gas chromatography-coupled mass spectrometry. Assay results confirmed that mutants designed to convert T. alata Δ6 to Δ9 selectivity exhibited the predicted changes. In complementary experiments, variants of the castor desaturase designed to convert Δ9 to Δ6 selectivity lost some of their Δ9 desaturation ability and gained the ability to desaturate at the Δ6 position. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.

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.

Computational Assessment of Botrytis cinerea Lipase for Biofuel Production

The demand for ecofriendly green catalysts for biofuel synthesis is greatly increasing with the effects of fossil fuel depletion. Fungal lipases are abundantly used as biocatalysts for the synthesis of biofuel. The use of Botrytis cinerea lipase is an excellent approach for the conversion of agroindustrial residues into biofuel. In this study, phylogenetic analyses were carried out and the physicochemical properties of B. cinerea lipase were assessed. Furthermore, the protein structure of B. cinerea lipase was predicted and refined. Putative energy-rich phytolipid compounds were explored as a substrate for the synthesis of biofuel, owing to B. cinerea lipase catalysis. Approximately 161 plant-based fatty acids were docked with B. cinerea lipase in order to evaluate their binding affinities and interactions. Among the docked fatty acids, the top ten triglycerides having the lowest number of binding affinities with B. cinerea lipase were selected, and their interactions were assessed. The top three triglycerides having the greatest number of hydrogen bonds and hydrophobic interactions were selected for simulations of 20 ns. The docking and simulations revealed that docosahexaenoic acid, dicranin, and hexadeca-7,10,13-trienoic acid had stable bonding with the B. cinerea lipase. Therefore, B. cinerea lipase has the potential to be used for the transesterification of fatty acids into biofuels, whereas docosahexaenoic acid, dicranin, and hexadeca-7,10,13-trienoic acid can be used as substrates of B. cinerea lipase for biofuel synthesis.

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

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

Development of B. carinata with super-high erucic acid content through interspecific hybridization

KEY MESSAGE

Disomic alien chromosome addition Brassica carinata lines with super-high erucic acid content were developed through interspecific hybridization with B. juncea and characterized using molecular, cytological and biochemical techniques. Brassica carinata [A.] Braun (BBCC, 2n = 34) is a climate-resilient oilseed. Its seed oil is high in erucic acid (> 40%), rendering it well suited for the production of biofuel and other bio-based applications. To enhance the competitiveness of B. carinata with high erucic B. napus (HEAR), lines with super-high erucic acid content were developed through interspecific hybridization. To this end, a fad2B null allele from Brassica juncea (AABB, 2n = 36) was introgressed into B. carinata, resulting in a B. carinata fad2B mutant with erucic acid levels of over 50%. Subsequently, the FAE allele from B. rapa spp. yellow sarson (AA, 2n = 20) was transferred to the fad2B B. carinata line, yielding lines with erucic acid contents of up to 57.9%. Molecular analysis using the Brassica 90 K Illumina Infinium™ SNP genotyping array identified these lines as disomic alien chromosome addition lines, with two extra A08 chromosomes containing the BrFAE gene. The alien chromosomes from B. rapa were clearly distinguished by molecular cytogenetics in one of the addition lines. Analysis of microspore-derived offspring and hybrids from crosses with a CMS B. carinata line showed that the transfer rate of the A08 chromosome into male gametes was over 98%, resulting in almost completely stable transmission of an A08 chromosome copy into the progeny. The increase in erucic acid levels was accompanied by changes in the proportions of other fatty acids depending on the genetic changes that were introduced in the interspecific hybrids, providing valuable insights into erucic acid metabolism in Brassica.

Fatty Acids and their Derivatives as Renewable Platform Molecules for the Chemical Industry

Oils and fats of vegetable and animal origin remain an important renewable feedstock for the chemical industry. Their industrial use has increased during the last 10 years from 31 to 51 million tonnes annually. Remarkable achievements made in the field of oleochemistry in this timeframe are summarized herein, including the reduction of fatty esters to ethers, the selective oxidation and oxidative cleavage of C-C double bonds, the synthesis of alkyl-branched fatty compounds, the isomerizing hydroformylation and alkoxycarbonylation, and olefin metathesis. The use of oleochemicals for the synthesis of a great variety of polymeric materials has increased tremendously, too. In addition to lipases and phospholipases, other enzymes have found their way into biocatalytic oleochemistry. Important achievements have also generated new oil qualities in existing crop plants or by using microorganisms optimized by metabolic engineering.

Ectopic expression of cDNAs from larkspur (Consolida ajacis) for increased synthesis of gondoic acid (cis-11 eicosenoic acid) and its positional redistribution in seed triacylglycerol of Camelina sativa

A β-ketoacyl-ACP-synthase II (KAS2) like enzyme and a lysophosphatidic acid acyltransferase (LPAT2) from Consolida ajacis catalyze gondoic acid biosynthesis and incorporation into the sn-2 position of seed TAG in engineered Camelina sativa. Gondoic acid (cis-11 eicosenoic acid, 20:1∆11) is the predominant very-long-chain fatty acid (VLCFA) in camelina (Camelina sativa) seed oil accounting for 12-15% of total triacylglycerol fatty acids. To explore the feasibility of engineering increased levels of this fatty acid in camelina seed, oils from a range of plant species were analyzed to identify those producing 20-Carbon (C20) fatty acids as the only VLCFAs in their seed oil. Seeds of Consolida and Delphinium species (Ranunculaceae) were found to contain moderate levels (0.2% to 25.5%) of C20 fatty acids without accompanying longer chain fatty acids. The C20 fatty acids were abundant in both sn-2 and sn-1/3 positions of seed TAG in Consolida, but were largely absent from the sn-2 position in Delphinium seed TAG. Through generation of a developing seed transcriptome, sequences were identified and cDNAs amplified from Consolida ajacis encoding a β-ketoacyl-ACP-synthase II like protein (CaKAS2B) that lacked a predicted chloroplast transit peptide, and two homologues of Arabidopsis thaliana lysophosphatidic acid acyltransferase 2 (CaLPAT2a and CaLPAT2b). Expression of CaKAS2B in conventional (WT) camelina and a line previously engineered for high seed oleic acid content (HO) resulted in increased seed VLCFA content. Total VLCFA levels were raised from 24 to 35% and from 7 to 23% in T3 seed from representative transformants in the WT and HO backgrounds, respectively. Gondoic acid was the predominant VLCFA in transformed HO lines with low endogenous cytoplasmic fatty acid elongation activity, suggesting limited capacity of CaKAS2B to elongate beyond C20. Expression in camelina of CaLPAT2b resulted in significantly increased C20-VLCFA esterification at the sn-2 position of seed TAG with VLCFA levels of 33.8% in this position in one transformed line compared to 0.3% at sn-2 in the corresponding control line. Only small changes in total seed VLCFA content were observed in transformed lines implying that increased VLCFA esterification capacity in camelina results in positional redistribution of VLCFAs but does not significantly enhance flux through the fatty acid elongation pathway. The full potential of CaKAS2B and CaLPAT2a for the engineering of high gondoic acid levels in camelina remains to be determined. Seed fatty acid composition of Consolida and Delphinium also provides information that may be of value in the systematics of the Ranunculaceae.

Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping

Camelina [Camelina sativa (L.) Crantz] is an oilseed crop in the Brassicaceae family that is currently being developed as a source of bioenergy and healthy fatty acids. To facilitate modern breeding efforts through marker-assisted selection and biotechnology, we evaluated genetic variation among a worldwide collection of 222 camelina accessions. We performed whole-genome resequencing to obtain single nucleotide polymorphism (SNP) markers and to analyze genomic diversity. We also conducted phenotypic field evaluations in two consecutive seasons for variations in key agronomic traits related to oilseed production such as seed size, oil content (OC), fatty acid composition, and flowering time. We determined the population structure of the camelina accessions using 161,301 SNPs. Further, we identified quantitative trait loci (QTL) and candidate genes controlling the above field-evaluated traits by genome-wide association studies (GWAS) complemented with linkage mapping using a recombinant inbred line (RIL) population. Characterization of the natural variation at the genome and phenotypic levels provides valuable resources to camelina genetic studies and crop improvement. The QTL and candidate genes should assist in breeding of advanced camelina varieties that can be integrated into the cropping systems for the production of high yield of oils of desired fatty acid composition.

Plant Lipid Databases

Along with the increase in knowledge on lipid metabolism during the last years, different lipid databases were established in a web-based system. This chapter presents an overview on plant lipid databases for simple and complex lipids focusing on nomenclature, structures as well as physical and chemical properties. Many databases provide information on methods and protocols for lipid isolation, fractionation, and analysis, including lipidomic procedures. References to the lipid literature are included in all databases. Additional data including mass spectra derived from GC-MS, LC-MS, and LC-MS/MS experiments are included in specialized lipid databases. An introduction is presented on how to use the most important lipid databases.

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

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

Molecular Control of Oil Metabolism in the Endosperm of Seeds

In angiosperm seeds, the endosperm develops to varying degrees and accumulates different types of storage compounds remobilized by the seedling during early post-germinative growth. Whereas the molecular mechanisms controlling the metabolism of starch and seed-storage proteins in the endosperm of cereal grains are relatively well characterized, the regulation of oil metabolism in the endosperm of developing and germinating oilseeds has received particular attention only more recently, thanks to the emergence and continuous improvement of analytical techniques allowing the evaluation, within a spatial context, of gene activity on one side, and lipid metabolism on the other side. These studies represent a fundamental step toward the elucidation of the molecular mechanisms governing oil metabolism in this particular tissue. In particular, they highlight the importance of endosperm-specific transcriptional controls for determining original oil compositions usually observed in this tissue. In the light of this research, the biological functions of oils stored in the endosperm of seeds then appear to be more diverse than simply constituting a source of carbon made available for the germinating seedling.

Transcriptome Analysis and Identification of Lipid Genes in Physaria lindheimeri, a Genetic Resource for Hydroxy Fatty Acids in Seed Oil

Hydroxy fatty acids (HFAs) have numerous industrial applications but are absent in most vegetable oils. Physaria lindheimeri accumulating 85% HFA in its seed oil makes it a valuable resource for engineering oilseed crops for HFA production. To discover lipid genes involved in HFA synthesis in P. lindheimeri, transcripts from developing seeds at various stages, as well as leaf and flower buds, were sequenced. Ninety-seven percent clean reads from 552,614,582 raw reads were assembled to 129,633 contigs (or transcripts) which represented 85,948 unique genes. Gene Ontology analysis indicated that 60% of the contigs matched proteins involved in biological process, cellular component or molecular function, while the remaining matched unknown proteins. We identified 42 P. lindheimeri genes involved in fatty acid and seed oil biosynthesis, and 39 of them shared 78-100% nucleotide identity with Arabidopsis orthologs. We manually annotated 16 key genes and 14 of them contained full-length protein sequences, indicating high coverage of clean reads to the assembled contigs. A detailed profiling of the 16 genes revealed various spatial and temporal expression patterns. The further comparison of their protein sequences uncovered amino acids conserved among HFA-producing species, but these varied among non-HFA-producing species. Our findings provide essential information for basic and applied research on HFA biosynthesis.

Exploratory Study of Fatty Acid Profile in Two Filmy Ferns with Contrasting Desiccation Tolerance Reveal the Production of Very Long Chain Polyunsaturated Omega-3 Fatty Acids

Lipids are fundamental components of cell membranes and play a significant role in their integrity and fluidity. Alteration in lipid composition of membranes has been reported to be a major response to abiotic environmental stresses. This work was focused on the characterization of frond lipid composition and membrane integrity during a desiccation–rehydration cycle of two filmy fern species with contrasting desiccation tolerance: Hymenophyllum caudiculatum (less tolerant) and Hymenophyllum plicatum (more tolerant). The relative water content decreased without differences between species when both filmy ferns were subjected to desiccation. However, H. plicatum reached a higher relative water content than H. caudiculatum after rehydration. Fatty acids profiles showed the presence of a very long chain polyunsaturated fatty acid during the desiccation–rehydration cycle, with eicosatrienoic acid being the most abundant. Additionally, propidium iodide permeation staining and confocal microscopy demonstrated that, following the desiccation–rehydration cycle, H. plicatum exhibited a greater membrane integrity than H. caudiculatum. The lack of some very long chain fatty acids such as C22:1n9 and C24:1n9 in this species contrasting with H. plicatum may be associated with its lower membrane stability during the desiccation–rehydration cycle. This report provides the first insight into the fatty acid composition and dynamics of the membrane integrity of filmy ferns during a desiccation–rehydration cycle. This could potentially play a role in determining the different levels of desiccation tolerance and microhabitat preferences exhibited by Hymenophyllaceae species.

Pattern recognition based on machine learning identifies oil adulteration and edible oil mixtures

Previous studies have shown that each edible oil type has its own characteristic fatty acid profile; however, no method has yet been described allowing the identification of oil types simply based on this characteristic. Moreover, the fatty acid profile of a specific oil type can be mimicked by a mixture of 2 or more oil types. This has led to fraudulent oil adulteration and intentional mislabeling of edible oils threatening food safety and endangering public health. Here, we present a machine learning method to uncover fatty acid patterns discriminative for ten different plant oil types and their intra-variability. We also describe a supervised end-to-end learning method that can be generalized to oil composition of any given mixtures. Trained on a large number of simulated oil mixtures, independent test dataset validation demonstrates that the model has a 50^th percentile absolute error between 1.4–1.8% and a 90^th percentile error of 4–5.4% for any 3-way mixtures of the ten oil types. The deep learning model can also be further refined with on-line training. Because oil-producing plants have diverse geographical origins and hence slightly varying fatty acid profiles, an online-training method provides also a way to capture useful knowledge presently unavailable. Our method allows the ability to control product quality, determining the fair price of purchased oils and in-turn allowing health-conscious consumers the future of accurate labeling.

Fraudulent adulteration of edible oils is based on the fact that their characteristic fatty acid profile can be mimicked with mixtures of other oil types. Here, the authors use a deep learning method to uncover fatty acid patterns discriminative for ten different plant oil types and to discern composition of mixtures.

Biotechnology tools and applications for development of oilseed crops with healthy vegetable oils

Vegetable oils, consisting principally of triacylglycerols (TAG), are major sources of calories and essential fatty acids in the human diet. The fatty acid composition of TAG is a primary determinant of the nutritional quality and health-promoting properties of vegetable oils. TAG fatty acid composition also affects the functionality and properties of vegetable oils in food applications and in food processing and preparation. Vegetable oils with improved nutritional and functional properties have been developed for oilseed crops by selection and breeding of fatty acid biosynthetic mutants. These efforts have been effective at generating vegetable oils with altered relative amounts of saturated and unsaturated fatty acids in seed TAG, but are constrained by insufficient genetic diversity for producing oils with "healthy" fatty acids that are not typically found in major oilseeds. The development and application of biotechnological tools have instead enabled the generation of oilseeds that produce novel fatty acid compositions with improved nutritional value by the introduction of genes from alternative sources, including plants, bacteria, and fungi. These tools have also allowed the generation of desired oil compositions that have proven difficult to obtain by breeding without compromised performance in selected oilseed crops. Here, we review biotechnological tools for increasing crop genetic diversity and their application for commercial or proof-of-principal development of oilseeds with expanded utility for food and feed applications and higher value nutritional and nutraceutical markets.

A predicted transmembrane region in plant diacylglycerol acyltransferase 2 regulates specificity toward very-long-chain acyl-CoAs

Triacylglycerols are the main constituent of seed oil. The specific fatty acid composition of this oil is strongly impacted by the substrate specificities of acyltransferases involved in lipid synthesis, such as the integral membrane enzyme diacylglycerol acyltransferase (DGAT). Two forms of DGAT, DGAT1 and DGAT2, are thought to contribute to the formation of seed oil, and previous characterizations of various DGAT2 enzymes indicate that these often are associated with the incorporation of unusual fatty acids. However, the basis of DGAT2's acyl-donor specificity is not known because of the inherent challenges of predicting structural features of integral membrane enzymes. The recent characterization of DGAT2 enzymes from Brassica napus reveals that DGAT2 enzymes with similar amino acid sequences exhibit starkly contrasting acyl-donor specificities. Here we have designed and biochemically tested a range of chimeric enzymes, substituting parts of these B. napus DGAT2 enzymes with each other, allowing us to pinpoint a region that dramatically affects the specificity toward 22:1-CoA. It may thus be possible to redesign the acyl-donor specificity of DGAT2 enzymes, potentially altering the fatty acid composition of seed oil. Further, the characterization of a DGAT2 chimera between Arabidopsis and B. napus demonstrates that the specificity regulated by this region is transferrable across species. The identified region contains two predicted transmembrane helices that appear to reoccur in a wide range of plant DGAT2 orthologues, suggesting that it is a general feature of plant DGAT2 enzymes.

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity and recruitment of primary metabolic enzymes and examples of genomic clustering of pathway genes. Solanaceae glandular trichomes produce defensive acylsugars, with sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals insights into the dynamics behind gene cluster evolution and cell-type specific metabolite diversity.