Modification of the fatty acid composition in Arabidopsis and maize seeds using a stearoyl-acyl carrier protein desaturase-1 (ZmSAD1) gene

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

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

The maize ATP-binding cassette (ABC) transporter ZmMRPA6 confers cold and salt stress tolerance in plants

KEY MESSAGE

ZmMRPA6 was cloned and characterized as the first ATP-binding cassette (ABC) transporter in maize to be proven to participate in cold and salt tolerance. Homologous genes AtABCC4 and AtABCC14 of ZmMRPA6 also responded to salt stress. ATP-binding cassette (ABC) proteins are major transmembrane transporters that play significant roles in plant development against various abiotic stresses. However, available information regarding stress-related ABC genes in maize is minimal. In this study, a maize ABC transporter gene, ZmMRPA6, was identified through genome-wide association analysis (GWAS) for cold tolerance in maize seeds germination and functionally characterized. During germination and seedling stages, the zmmrpa6 mutant exhibited enhanced resistance to cold or salt stress. Mutated of ZmMRPA6 did not affect the expression of downstream response genes related cold or salt response at the transcriptional level. Mass spectrometry analysis revealed that most of the differential proteins between zmmrpa6 and wild-type plants were involved in response to stress process including oxidative reduction, hydrolase activity, small molecule metabolism, and photosynthesis process. Meanwhile, the plants which lack the ZmMRPA6 homologous genes AtABCC4 or AtABCC14 were sensitive to salt stress in Arabidopsis. These results indicated that ZmMRPA6 and its homologous genes play a conserved role in cold and salt stress, and functional differentiation occurs in monocotyledonous and dicotyledonous plants. In summary, these findings dramatically improved our understanding of the function of ABC transporters resistance to abiotic stresses in plants.

Analysis of Delta(9) fatty acid desaturase gene family and their role in oleic acid accumulation in Carya cathayensis kernel

Carya cathayensis, commonly referred to as Chinese hickory, produces nuts that contain high-quality edible oils, particularly oleic acid (18:1). It is known that stearoyl-ACP desaturase (SAD) is the first key step converting stearic acid (C18:0, SA) to oleic acid (C18:1, OA) in the aminolevulinic acid (ALA) biosynthetic pathway and play an important role in OA accumulation. Thus far, there is little information about SAD gene family in C. cathayensis and the role of individual members in OA accumulation. This study searched the Chinese Hickory Genome Database and identified five members of SAD genes, designated as CcSADs, at the whole genome level through the comparison with the homologous genes from Arabidopsis. RNA-Seq analysis showed that CcSSI2-1, CcSSI2-2, and CcSAD6 were highly expressed in kernels. The expression pattern of CcSADs was significantly correlated with fatty acid accumulation during the kernel development. In addition, five full-length cDNAs encoding SADs were isolated from the developing kernel of C. cathayensis. CcSADs-green fluorescent protein (GFP) fusion construct was infiltrated into tobacco epidermal cells, and results indicated their chloroplast localization. The catalytic function of these CcSADs was further analyzed by heterologous expression in Saccharomyces cerevisiae, Nicotiana benthamiana, and walnut. Functional analysis demonstrated that all CcSADs had fatty acid desaturase activity to catalyze oleic acid biosynthesis. Some members of CcSADs also have strong substrate specificity for 16:0-ACP to synthesize palmitoleic acid (C16:1, PA). Our study documented SAD gene family in C. cathayensis and the role of CcSSI2-1, CcSSI2-2, and CcSAD6 in OA accumulation, which could be important for future improvement of OA content in this species via genetic manipulation.

Molecular regulation of lipid metabolism in Suaeda salsa

Suaeda salsa is remarkable for its high oil content and abundant unsaturated fatty acids. In this study, the regulatory networks on fatty acid and lipid metabolism were constructed by combining the de novo transcriptome and lipidome data. Differentially expressed genes (DEGs) associated with lipids biosynthesis pathways were identified in the S. salsa transcriptome. DEGs involved in fatty acid and glycerolipids were generally up-regulated in leaf tissues. DEGs for TAG assembly were enriched in developing seeds, while DEGs in phospholipid metabolic pathways were enriched in root tissues. Polar lipids were extracted from S. salsa tissues and analyzed by lipidomics. The proportion of galactolipid MGDG was the highest in S. salsa leaves. The molar percentage of PG was high in the developing seeds, and the other main phospholipids had higher molar percentage in roots of S. salsa. The predominant C36:6 molecular species indicates that S. salsa is a typical 18:3 plant. The combined transcriptomic and lipidomic data revealed that different tissues of S. salsa were featured with DEGs associated with specific lipid metabolic pathways, therefore, represented unique lipid profiles. This study will be helpful on understanding lipid metabolism pathway and exploring the key genes involved in lipid synthesis in S. salsa.

Deuterium- and Alkyne-Based Bioorthogonal Raman Probes for In Situ Quantitative Metabolic Imaging of Lipids within Plants

Plants can rapidly respond to different stresses by activating multiple signaling and defense pathways. The ability to directly visualize and quantify these pathways in real time using bioorthogonal probes would have practical applications, including characterizing plant responses to both abiotic and biotic stress. Fluorescence-based labels are widely used for tagging of small biomolecules but are relatively bulky and with potential effects on their endogenous localization and metabolism. This work describes the use of deuterium- and alkyne-derived fatty acid Raman probes to visualize and track the real-time response of plants to abiotic stress within the roots. Relative quantification of the respective signals could be used to track their localization and overall real-time responses in their fatty acid pools due to drought and heat stress without labor-intensive isolation procedures. Their overall usability and low toxicity suggest that Raman probes have great untapped potential in the field of plant bioengineering.

Transcriptomics Reveals the Effect of Short-Term Freezing on the Signal Transduction and Metabolism of Grapevine

Low temperature is an important factor limiting plant growth. Most cultivars of Vitis vinifera L. are sensitive to low temperatures and are at risk of freezing injury or even plant death during winter. In this study, we analyzed the transcriptome of branches of dormant cv. Cabernet Sauvignon exposed to several low-temperature conditions to identify differentially expressed genes and determine their function based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)enrichment analyses. Our results indicated that exposure to subzero low temperatures resulted in damage to plant cell membranes and extravasation of intracellular electrolytes, and that this damage increased with decreasing temperature or increasing duration. The number of differential genes increased as the duration of stress increased, but most of the common differentially expressed genes reached their highest expression at 6 h of stress, indicating that 6 h may be a turning point for vines to tolerate extreme low temperatures. Several pathways play key roles in the response of Cabernet Sauvignon to low-temperature injury, namely: (1) the role of calcium/calmodulin-mediated signaling; (2) carbohydrate metabolism, including the hydrolysis of cell wall pectin and cellulose, decomposition of sucrose, synthesis of raffinose, and inhibition of glycolytic processes; (3) the synthesis of unsaturated fatty acids and metabolism of linolenic acid; and (4) the synthesis of secondary metabolites, especially flavonoids. In addition, pathogenesis-related protein may also play a role in plant cold resistance, but the mechanism is not yet clear. This study reveals possible pathways for the freezing response and leads to new insights into the molecular basis of the tolerance to low temperature in grapevine.

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.

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.

Genetic dissection of QTLs for oil content in four maize DH populations

Oil is one of the main components in maize kernels. Increasing the total oil content (TOC) is favorable to optimize feeding requirement by improving maize quality. To better understand the genetic basis of TOC, quantitative trait loci (QTL) in four double haploid (DH) populations were explored. TOC exhibited continuously and approximately normal distribution in the four populations. The moderate to high broad-sense heritability (67.00-86.60%) indicated that the majority of TOC variations are controlled by genetic factors. A total of 16 QTLs were identified across all chromosomes in a range of 3.49-30.84% in term of phenotypic variation explained. Among them, six QTLs were identified as the major QTLs that explained phenotypic variation larger than 10%. Especially, qOC-1-3 and qOC-2-3 on chromosome 9 were recognized as the largest effect QTLs with 30.84% and 21.74% of phenotypic variance, respectively. Seventeen well-known genes involved in fatty acid metabolic pathway located within QTL intervals. These QTLs will enhance our understanding of the genetic basis of TOC in maize and offer prospective routes to clone candidate genes regulating TOC for breeding program to cultivate maize varieties with the better grain quality.

Development of a High Oleic Cardoon Cell Culture Platform by SAD Overexpression and RNAi-Mediated FAD2.2 Silencing

The development of effective tools for the sustainable supply of phyto-ingredients and natural substances with reduced environmental footprints can help mitigate the dramatic scenario of climate change. Plant cell cultures-based biorefineries can be a technological advancement to face this challenge and offer a potentially unlimited availability of natural substances, in a standardized composition and devoid of the seasonal variability of cultivated plants. Monounsaturated (MUFA) fatty acids are attracting considerable attention as supplements for biodegradable plastics, bio-additives for the cosmetic industry, and bio-lubricants. Cardoon (Cynara cardunculus L. var. altilis) callus cultures accumulate fatty acids and polyphenols and are therefore suitable for large-scale production of biochemicals and valuable compounds, as well as biofuel precursors. With the aim of boosting their potential uses, we designed a biotechnological approach to increase oleic acid content through Agrobacterium tumefaciens-mediated metabolic engineering. Bioinformatic data mining in the C. cardunculus transcriptome allowed the selection and molecular characterization of SAD (stearic acid desaturase) and FAD2.2 (fatty acid desaturase) genes, coding for key enzymes in oleic and linoleic acid formation, as targets for metabolic engineering. A total of 22 and 27 fast-growing independent CcSAD overexpressing (OE) and CcFAD2.2 RNAi knocked out (KO) transgenic lines were obtained. Further characterization of five independent transgenic lines for each construct demonstrated that, successfully, SAD overexpression increased linoleic acid content, e.g., to 42.5%, of the relative fatty acid content, in the CcSADOE6 line compared with 30.4% in the wild type (WT), whereas FAD2.2 silencing reduced linoleic acid in favor of the accumulation of its precursor, oleic acid, e.g., to almost 57% of the relative fatty acid content in the CcFAD2.2KO2 line with respect to 17.7% in the WT. Moreover, CcSADOE6 and CcFAD2.2KO2 were also characterized by a significant increase in total polyphenolic content up to about 4.7 and 4.1 mg/g DW as compared with 2.7 mg/g DW in the WT, mainly due to the accumulation of dicaffeoyl quinic and feruloyl quinic acids. These results pose the basis for the effective creation of an engineered cardoon cells-based biorefinery accumulating high levels of valuable compounds from primary and specialized metabolism to meet the industrial demand for renewable and sustainable sources of innovative bioproducts.

Unraveling the metabolic effects of benzophenone-3 on the endosymbiotic dinoflagellate Cladocopium goreaui

As a well-known pseudo-persistent environmental pollutant, oxybenzone (BP-3) and its related organic ultraviolet (UV) filters have been verified to directly contribute to the increasing mortality rate of coral reefs. Previous studies have revealed the potential role of symbiotic Symbiodiniaceae in protecting corals from the toxic effects of UV filters. However, the detailed protection mechanism(s) have not been explained. Here, the impacts of BP-3 on the symbiotic Symbiodiniaceae Cladocopium goreaui were explored. C. goreaui cells exhibited distinct cell growth at different BP-3 doses, with increasing growth at the lower concentration (2 mg L^-1) and rapid death at a higher concentration (20 mg L^-1). Furthermore, C. goreaui cells showed a significant BP-3 uptake at the lower BP-3 concentration. BP-3 absorbing cells exhibited elevated photosynthetic efficiency, and decreased cellular carbon and nitrogen contents. Besides, the derivatives of BP-3 and aromatic amino acid metabolism highly responded to BP-3 absorption and biodegradation. Our physiological and metabolic results reveal that the symbiotic Symbiodiniaceae could resist the toxicity of a range of BP-3 through promoting cell division, photosynthesis, and reprogramming amino acid metabolism. This study provides novel insights into the influences of organic UV filters to coral reef ecosystems, which urgently needs increasing attention and management.

Full-length transcriptome analysis of pecan (Carya illinoinensis) kernels

Pecan is rich in bioactive components such as fatty acids (FAs) and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long-read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37,504 isoforms of 16,702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26,080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30,751, 81.99%) had functional annotations. A total of 15,465 alternative splicing (AS) events and 65,761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long noncoding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with FA and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. This study provides a full-length transcriptome data set of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.

The utility of metabolomics as a tool to inform maize biology

With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).

Gene atlas of iron-containing proteins in Arabidopsis thaliana

Iron (Fe) is an essential element for the development and physiology of plants, owing to its presence in numerous proteins involved in central biological processes. Here, we established an exhaustive, manually curated inventory of genes encoding Fe-containing proteins in Arabidopsis thaliana, and summarized their subcellular localization, spatiotemporal expression and evolutionary age. We have currently identified 1068 genes encoding potential Fe-containing proteins, including 204 iron-sulfur (Fe-S) proteins, 446 haem proteins and 330 non-Fe-S/non-haem Fe proteins (updates of this atlas are available at https://conf.arabidopsis.org/display/COM/Atlas+of+Fe+containing+proteins). A fourth class, containing 88 genes for which iron binding is uncertain, is indexed as 'unclear'. The proteins are distributed in diverse subcellular compartments with strong differences per category. Interestingly, analysis of the gene age index showed that most genes were acquired early in plant evolutionary history and have progressively gained regulatory elements, to support the complex organ-specific and development-specific functions necessitated by the emergence of terrestrial plants. With this gene atlas, we provide a valuable and updateable tool for the research community that supports the characterization of the molecular actors and mechanisms important for Fe metabolism in plants. This will also help in selecting relevant targets for breeding or biotechnological approaches aiming at Fe biofortification in crops.

Identification of Key Genes Involved in Embryo Development and Differential Oil Accumulation in Two Contrasting Maize Genotypes

Maize is an important oil seed crop and a major food crop in different parts of the world. Since maize has relatively lower seed oil content as compared to other oil crops, efforts are continuing to improve its oil content percentage. In this study, we analyzed two contrasting maize genotypes with differential oil accumulation percentages. High oil-content (HOC) maize had 11% oil content while low oil-content (LOC) maize had significantly lower oil content (5.4%). Transmission electron microscopy revealed a higher accumulation of oil bodies in the HOC maize embryo as compared to LOC maize. Comparative RNA-sequencing analysis at different developmental stages of the seed embryos identified 739 genes that are constantly differentially expressed (DEGs) at all the six developmental stages from 15 days after pollination (DAP) to 40 DAP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified fatty acid metabolism and fatty acid biosynthesis as the most enriched biological pathways contributed by these DEGs. Notably, transcriptional changes are more intense at the early stages of embryo development as compared to later stages. In addition, pathways related to oil biosynthesis and their corresponding genes were more enriched at 30 DAP, which seems to be the key stage for oil accumulation. The study also identified 33 key DEGs involved in fatty acid and triacylglycerols biosynthesis, most of which were up-regulated in HOC, that may shape the differential oil contents in the two contrasting maize. Notably, we discovered that both acyl-CoA-dependent and acyl-CoA-independent processes are essential for the high oil accumulation in maize embryo.

Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition of Theobroma cacao L. Beans

The main ingredients of chocolate are usually cocoa powder, cocoa butter, and sugar. Both the powder and the butter are extracted from the beans of the cacao tree (Theobroma cacao L.). The cocoa butter represents the fat in the beans and possesses a unique fatty acid profile that results in chocolate's characteristic texture and mouthfeel. Here, we used a linkage mapping population and phenotypic data of 3,292 samples from 420 progeny which led to the identification of 27 quantitative trait loci (QTLs) for fatty acid composition and six QTLs for fat content. Progeny showed extensive variation in fat levels and composition, with the level of palmitic acid negatively correlated to the sum of stearic acid, oleic acid, and linoleic acid. A major QTL explaining 24% of the relative level of palmitic acid was mapped to the distal end of chromosome 4, and those higher levels of palmitic acid were associated with the presence of a haplotype from the "TSH 1188" parent in the progeny. Within this region of chromosome 4 is the Thecc1EG017405 gene, an orthologue and isoform of the stearoyl-acyl carrier protein (ACP) desaturase (SAD) gene in plants, which is involved in fatty acid biosynthesis. Besides allelic differences, we also show that climate factors can change the fatty acid composition in the beans, including a significant positive correlation between higher temperatures and the higher level of palmitic acid. Moreover, we found a significant pollen donor effect from the variety "SIAL 70" which was associated with decreased palmitic acid levels.

RNA-seq data reveals a coordinated regulation mechanism of multigenes involved in the high accumulation of palmitoleic acid and oil in sea buckthorn berry pulp

BACKGROUND

Sea buckthorn is a woody oil crop in which palmitoleic acid (C16:1n7, an omega-7 fatty acid (FA)) contributes approximately 40% of the total FA content in berry pulp (non-seed tissue). However, the molecular mechanisms contributing to the high accumulation of C16:1n7 in developing sea buckthorn berry pulp (SBP) remain poorly understood.

RESULTS

We identified 1737 unigenes associated with lipid metabolism through RNA-sequencing analysis of the four developmental stages of berry pulp in two sea buckthorn lines, 'Za56' and 'TF2-36'; 139 differentially expressed genes were detected between the different berry pulp developmental stages in the two lines. Analyses of the FA composition showed that the C16:1n7 contents were significantly higher in line 'Za56' than in line 'TF2-36' in the mid-late developmental stages of SBP. Additionally, qRT-PCR analyses of 15 genes involved in FA and triacylglycerol (TAG) biosynthesis in both lines revealed that delta9-ACP-desaturase (ACP-Δ9D) competed with 3-ketoacyl-ACP-synthase II (KASII) for the substrate C16:0-ACP and that ACP-Δ9D and delta9-CoA-desaturase (CoA-Δ9D) gene expression positively correlated with C16:1n7 content; KASII and fatty acid elongation 1 (FAE1) gene expression positively correlated with C18:0 content in developing SBP. Specifically, the abundance of ACP-Δ9D and CoA-Δ9D transcripts in line 'Za56', which had a higher C16:1n7 content than line 'TF2-36', suggests that these two genes play an important role in C16:1n7 biosynthesis. Furthermore, the high expressions of the glycerol-3-phosphate dehydrogenase (GPD1) gene and the WRINKLED1 (WRI1) transcription factor contributed to increased biosynthesis of TAG precursor and FAs, respectively, in the early developmental stages of SBP, and the high expression of the diacylglycerol O-acyltransferase 1 (DGAT1) gene increased TAG assembly in the later developmental stages of SBP. Overall, we concluded that increased ACP-Δ9D and CoA-Δ9D levels coupled with decreased KASII and FAE1 activity is a critical event for high C16:1n7 accumulation and that the coordinated high expression of WRI1, GPD1, and DGAT1 genes resulted in high oil accumulation in SBP.

CONCLUSION

Our results provide a scientific basis for understanding the mechanism of high C16:1n7 accumulation in berry pulp (non-seed tissue) and are valuable to the genetic breeding programme for achieving a high quality and yield of SBP oil.

Enhancing freezing tolerance of Brassica napus L. by overexpression of a stearoyl-acyl carrier protein desaturase gene (SAD) from Sapium sebiferum (L.) Roxb

Sapium sebiferum (L.) Roxb. is an important woody oil tree and traditional herbal medicine in China. Stearoyl-acyl carrier protein desaturase (SAD) is a dehydrogenase enzyme that plays a key role in the transformation of saturated fatty acids into unsaturated fatty acids in oil; these fatty acids greatly influence the freezing tolerance of plants. However, it remains unclear whether freezing tolerance can be regulated by the expression level of SsSAD in S. sebiferum L. Our research indicated that SsSAD expression in S. sebiferum L. increased under freezing stress. To further confirm this result, we constructed a pEGAD-SsSAD vector and transformed it into B. napus L. W10 by Agrobacterium tumefaciens-mediated transformation. Transgenic plants that overexpressed the SsSAD gene exhibited significantly higher linoleic (18:2) and linolenic acid (18:3) content and advanced freezing tolerance. These results suggest that SsSAD overexpression in B. napus L. can increase the content of polyunsaturated fatty acids (PUFAs) such as linoleic (18:2) and linolenic acid (18:3), which are likely pivotal in improving freezing tolerance in B. napus L. plants. Thus, SsSAD overexpression could be useful in the production of freeze-tolerant varieties of B. napus L.