Functional Characterization of Flax Fatty Acid Desaturase FAD2 and FAD3 Isoforms Expressed in Yeast Reveals a Broad Diversity in Activity

Expression of FAD and SAD Genes in Developing Seeds of Flax Varieties under Different Growth Conditions

Flax seed is one of the richest plant sources of linolenic acid (LIN) and also contains unsaturated linoleic acid (LIO) and oleic acid (OLE). Stearoyl-ACP desaturases (SADs) and fatty acid desaturases (FADs) play key roles in the synthesis of flax fatty acids (FAs). However, there is no holistic view of which genes from the SAD and FAD families and at which developmental stages have the highest expression levels in flax seeds, as well as the influence of genotype and growth conditions on the expression profiles of these genes. We sequenced flax seed transcriptomes at 3, 7, 14, 21, and 28 days after flowering (DAF) for ten flax varieties with different oil FA compositions grown under three temperature/watering conditions. The expression levels of 25 genes of the SAD, FAD2, and FAD3 families were evaluated. FAD3b, FAD3a, FAD2b-2, SAD3-1, SAD2-1, SAD2-2, SAD3-2, FAD2a-1, and FAD2a-2 had the highest expression levels, which changed significantly during seed development. These genes probably play a key role in FA synthesis in flax seeds. High temperature and insufficient watering shifted the maximum expression levels of FAD and SAD genes to earlier developmental stages, while the opposite trend was observed for low temperature and excessive watering. Differences in the FAD and SAD expression profiles under different growth conditions may affect the FA composition of linseed oil. Stop codons in the FAD3a gene, resulting in a reduced LIN content, decreased the level of FAD3a transcript. The obtained results provide new insights into the synthesis of linseed oil.

Comparison of nutritional quality of fourteen wild Linum species based on fatty acid composition, lipid health indices, and chemometric approaches unravelling their nutraceutical potential

Fatty acid profiles of 14 Linum species was determined by GC-MS analysis to study the nutritional quality of Linum species based on fatty acid composition, lipid health indices, and chemometric approaches. L. lewisii and L. marginale found to have the highest content of ALA i.e., 65.38 % and 62.79 %, respectively, L. tenuifolium recorded the highest linoleic acid content (69.69 %), while, L. catharticum recorded highest oleic acid (27.03 %). Health indices viz. polyunsaturated fatty acids/saturated fatty acids ratio, n-6/n-3 fatty acids ratio, atherogenicity, thrombogenicity, oxidability, oxidative stability, hypocholesterolemic/hypercholesterolemic fatty acids, and peroxidisability calculated based on the fatty acid composition revealed that all the linseed species except L. aristatum, L. tenuifolium and L. hudsoniodes have healthy fatty acid composition. L. lewisii clearly emerges as a promising species followed by L. bienne with great values across multiple indices, making them as a potential candidate for dietary or nutritional interests. The lipid profile of Linum species could be well distinguished by two principal components by Principal Component Analysis (PCA).

Key FAD2, FAD3, and SAD Genes Involved in the Fatty Acid Synthesis in Flax Identified Based on Genomic and Transcriptomic Data

FAD (fatty acid desaturase) and SAD (stearoyl-ACP desaturase) genes play key roles in the synthesis of fatty acids (FA) and determination of oil composition in flax (Linum usitatissimum L.). We searched for FAD and SAD genes in the most widely used flax genome of the variety CDC Bethune and three available long-read assembled flax genomes-YY5, 3896, and Atlant. We identified fifteen FAD2, six FAD3, and four SAD genes. Of all the identified genes, 24 were present in duplicated pairs. In most cases, two genes from a pair differed by a significant number of gene-specific SNPs (single nucleotide polymorphisms) or even InDels (insertions/deletions), except for FAD2a-1 and FAD2a-2, where only seven SNPs distinguished these genes. Errors were detected in the FAD2a-1, FAD2a-2, FAD3c-1, and FAD3d-2 sequences in the CDC Bethune genome assembly but not in the long-read genome assemblies. Expression analysis of the available transcriptomic data for different flax organs/tissues revealed that FAD2a-1, FAD2a-2, FAD3a, FAD3b, SAD3-1, and SAD3-2 were specifically expressed in embryos/seeds/capsules and could play a crucial role in the synthesis of FA in flax seeds. In contrast, FAD2b-1, FAD2b-2, SAD2-1, and SAD2-2 were highly expressed in all analyzed organs/tissues and could be involved in FA synthesis in whole flax plants. FAD2c-2, FAD2d-1, FAD3c-1, FAD3c-2, FAD3d-1, FAD3d-2, SAD3-1, and SAD3-2 showed differential expression under stress conditions-Fusarium oxysporum infection and drought. The obtained results are essential for research on molecular mechanisms of fatty acid synthesis, FAD and SAD editing, and marker-assisted and genomic selection for breeding flax varieties with a determined fatty acid composition of oil.

Linum usitatissimum AccD Enhances Seed Fatty Acid Accumulation and Tolerance to Environmental Stresses during Seed Germination in Arabidopsis thaliana

Flax (Linum usitatissimum L.), as an important oil-producing crop, is widely distributed throughout the world, and its seeds are rich in polyunsaturated fatty acids (FAs). Previous studies have revealed that Arabidopsis thaliana ACETYL-CoA CARBOXYLASE (AtACCase) is vital for FA biosynthesis. However, the functions of L. usitatissimum AccD (LuAccD) on FA accumulation and seed germination remain unclear. In the present study, we cloned the LuAccD coding sequence from the flax cultivar 'Longya 10', identified conserved protein domains, and performed a phylogenetic analysis to elucidate its relationship with homologs from a range of plant species. Ectopic expression of LuAccD in A. thaliana wild-type background enhanced seed FA accumulation without altering seed morphological characteristics, including seed size, 1000-seed weight, and seed coat color. Consistently, the expression of key genes involved in FA biosynthesis was greatly up-regulated in the developing seeds of LuAccD overexpression lines. Additionally, we demonstrated that LuAccD acts as a positive regulator of salt and mannitol tolerance during seed germination in A. thaliana. These results provide important insights into the functions of LuAccD, which facilitates the oil quantity and abiotic stress tolerance of oil-producing crops through genetic manipulation.

Linum usitatissimum ABI3 enhances the accumulation of seed storage reserves and tolerance to environmental stresses during seed germination and seedling establishment in Arabidopsis thaliana

Flax (Linum usitatissimum) is an important oil crop in arid and semi-arid regions of North and Northwest China, and its seeds are rich in nutritious storage reserves, such as polyunsaturated fatty acids (FAs) and proteins. However, the regulatory networks that control the accumulation of seed storage reserves in flax are still largely unknown. In this study, we found that LuABI3-1 and LuABI3-2 homologs from the flax cultivar 'Longya 10' play important roles in regulating the accumulation of seed storage reserves in Arabidopsis thaliana. The results of subcellular localization and transcriptional activity assays showed that both LuABI3-1 and LuABI3-2 function as transcription factors. Overexpression of either LuABI3-1 or LuABI3-2 resulted in the significant increase in the contents of total seed FAs and storage proteins, but did not alter other key agronomic traits in A. thaliana. Accordingly, the expression of key genes involved in the biosynthesis of FAs and storage proteins was also greatly up-regulated in the developing seeds of LuABI3-1-overexpression lines. Additionally, both LuABI3-1 and LuABI3-2 enhanced the tolerance to the high salt and mannitol stresses during seed germination and seedling establishment in A. thaliana. These results increase our understanding of the LuABI3 regulatory functions and provide promising targets for genetic manipulation of L. usitatissimum to innovate the germplasm resources and cultivate high yield and quality varieties.

A Histoplasma capsulatum Lipid Metabolic Map Identifies Antifungal Targets

Lipids play a fundamental role in fungal cell biology, being essential cell membrane components and major targets of antifungal drugs. A deeper knowledge of lipid metabolism is key for developing new drugs and a better understanding of fungal pathogenesis. Here, we built a comprehensive map of the Histoplasma capsulatum lipid metabolic pathway by incorporating proteomic and lipidomic analyses. We performed genetic complementation and overexpression of H. capsulatum genes in Saccharomyces cerevisiae to validate reactions identified in the map and to determine enzymes responsible for catalyzing orphan reactions. The map led to the identification of both the fatty acid desaturation and the sphingolipid biosynthesis pathways as targets for drug development. We found that the sphingolipid biosynthesis inhibitor myriocin, the fatty acid desaturase inhibitor thiocarlide, and the fatty acid analog 10-thiastearic acid inhibit H. capsulatum growth in nanomolar to low-micromolar concentrations. These compounds also reduced the intracellular infection in an alveolar macrophage cell line. Overall, this lipid metabolic map revealed pathways that can be targeted for drug development.

Characterization of genes encoding ω-6 desaturase PoFAD2 and PoFAD6, and ω-3 desaturase PoFAD3 for ALA accumulation in developing seeds of oil crop Paeonia ostii var. lishizhenii

Paeonia ostii var. lishizhenii has emerged as a valuable oil-producing crop with splendid characteristic of high α-linolenic acid (C18:3, ALA) content in its seed oil for healthy food supplement, but the molecular mechanism for seed ALA accumulation remains enigmatic. In our previous report, a PoSAD gene encoding stearoyl-ACP desaturase had been cloned and functional charactered for the first desaturation procedure involved in ALA biosynthesis pathway in P. ostii var. lishizhenii endosperms, while other participants have not been identified to date. In this study, full-length cDNAs of PoFAD2 (1489 bp), PoFAD6 (1638 bp), and PoFAD3 (1709 bp) were isolated based on our recent transcriptome sequencing data. Bioinformatic analyses revealed that the PoFADs were closest to their counterparts from Paeoniaceae species P. ludlowii, P. rockii, and P. suffruticosa in phylogenetic tree, which shared highly conserved histidine boxes (HXXXH, HXXHH, and HXXHH), exhibiting typical characters of membrane-bound desaturases in higher plants. Additionally, the PoFAD2 and PoFAD3 were specifically expressed and highly associated with LA and ALA accumulation in developing endosperms, whereas PoFAD6 expression has no significantly difference during whole seed developing stages. The catalytic function of these PoFADs were further analyzed by heterologous expression in Saccharomyces cerevisiae and Arabidopsis thaliana. The results showed that PoFAD2 and PoFAD6 could catalyze linoleic acid (C18:2) synthesis, while PoFAD3 had ability to produce ALA. This study functional identified three PoFAD genes, which indicates their critical roles in ALA biosynthesis pathway in P. ostii var. lishizhenii, and is of great theoretical and practical meaning on breeding and cultivating new tree peony varieties to promote human health and nutrition supplement.

Linum usitatissimum FAD2A and FAD3A enhance seed polyunsaturated fatty acid accumulation and seedling cold tolerance in Arabidopsis thaliana

Flax (Linum usitatissimum) seed oil is rich in polyunsaturated fatty acids (PUFAs), particularly linolenic acid, which is converted from linoleic acid. Studies have indicated that the biosynthesis of linoleic acid and linolenic acid is controlled by FAD2 and FAD3, respectively. However, the functional distinctions of different LuFAD2 and LuFAD3 copies from L. usitatissimum in governing the biosynthesis of linoleic acid or linolenic acid, respectively, remain unclear. In this study, five LuFAD2 and three LuFAD3 cDNAs were cloned from the L. usitatissimum cultivar 'Longya 10', and GC-MS results demonstrated that LuFAD2A and LuFAD3A play predominant roles in the accumulation of linoleic acid and linolenic acid, respectively. Their simultaneous overexpression in Arabidopsis thaliana seeds led to a significant increase in fatty acid contents, especially PUFAs. Additionally, LuFAD2A and LuFAD3A promoted the biosynthesis of jasmonic acid by increasing the levels of linolenic acid, which, in turn, enhanced plant cold tolerance. When the amount of linolenic acid is not sufficient, plants adapt to low temperature via the accumulation of anthocyanins. These findings provide insights into the higher accumulation of PUFAs in L. usitatissimum seeds, and provide potential targets for improving oil quality of other oil-producing crops through molecular manipulation.

Functional characterization and expression profile of microsomal FAD2 and FAD3 genes involved in linoleic and α-linolenic acid production in Leucas cephalotes

The genus Leucas belongs to Lamiaceae, and has attained more attention due to the presence of unusual allenic fatty acids called laballenic and phlomic acid in majority of its species. This genus has been known since traditional medicinal times and has numerous economical, nutritional, and industrial properties. So far genetic, molecular and biochemical analyses of lipid metabolism and fatty acid biosynthetic pathway in Leucas has not been reported. The objective of this study is to identify, isolate, analyze expression profiles, and functionally characterize the membrane-associated desaturases responsible for unsaturated fatty acid accumulation in Leucas cephalotes. Full-length LcFAD2 and LcFAD3 cDNAs were isolated and expressed in Saccharomyces cerevisiae BY4741 for functional characterization. Substrate feeding assay using S. cerevisiae confirmed that the LcFAD2 enzyme catalyzes desaturation of both palmitoleic (16:1∆⁹) and oleic (18:1∆⁹) acids to form palmitolinoleic (16:2∆^9,12) and linoleic (18:2∆^9,12) acids respectively. As a contrast, the heterologous activity of LcFAD2 enzyme in S. cerevisiae led to the synthesis of palmitolinoleic (16:2∆^9,12) acid, an unusual fatty acid that is not found naturally in Leucas cephalotes. While the LcFAD3 enzyme catalyzed linoleic acid (18:2∆^9,12) into α-linolenic acid (18:3∆^9,12,15). Furthermore, transcript abundance of LcFAD2 and LcFAD3 cDNAs were estimated from various plant parts such as roots, shoots, leaves, petals and developing seeds. Our results have shown that the differential transcriptional activity of LcFAD2 and LcFAD3 desaturase genes differs significantly in developing seeds, petals, leaves, stems, and roots of L. cephalotes. Furthermore, for the industrial production of these essential fatty acids, namely, linoleic and α-linolenic acid, FAD2 and FAD3 enzyme activity could be exploited from this upcoming significant oil plant, Leucas cephalotes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01016-z.

Identification and characterization of Pseudozyma antarctica Δ12 fatty acid desaturase and its utilization for the production of polyunsaturated fatty acids

Fatty acid desaturases, especially Δ12 fatty acid desaturases, are key enzymes for the production of unsaturated fatty acids in oleaginous yeasts. In this study, we identified and characterized a gene encoding Δ12 fatty acid desaturase of Pseudozyma antarctica named PaFAD2. Almost all oleic acid (C18:1) was converted to linoleic acid by the heterologous expression of the PaFAD2 gene in Saccharomyces cerevisiae and Lipomyces starkeyi oleaginous yeast. Notably, PaFad2 converted not only oleic acid to linoleic acid, but also palmitoleic acid (C16:1) to 9,12-hexadecadienoic acid (C16:2). These results indicated that the PaFAD2 gene was very useful for the production of polyunsaturated fatty acids in yeast, including oleaginous yeast.

Identification and functional characterization of Buglossoides arvensis microsomal fatty acid desaturation pathway genes involved in polyunsaturated fatty acid synthesis in seeds

Buglossoides arvensis seed oil is the richest natural source of stearidonic acid (SDA), an ω-3 fatty acid with nutraceutical potential superior to α-linolenic acid (ALA). The molecular basis of polyunsaturated fatty acid synthesis in B. arvensis is unknown. Here, we describe the identification of B. arvensis fatty acid desaturase2 (BaFAD2), fatty acid desaturase3 (BaFAD3), and Delta-6-desaturase (BaD6D-1 and BaD6D-2) genes by mining the transcriptome of developing seeds and their functional characterization by heterologous expression in Saccharomyces cerevisiae. In silico analysis of their encoded protein sequences showed conserved histidine-boxes and signature motifs essential for desaturase activity. Expression profiling of these genes showed higher transcript abundance in reproductive tissues than in vegetative tissues, and their expression varied with temperature stress treatments. Yeast expressing BaFAD2 was found to desaturate both oleic acid and palmitoleic acid into linoleic acid (LA) and hexadecadienoic acid, respectively. Fatty acid supplementation studies in yeast expressing BaFAD3 and BaD6D-1 genes revealed that the encoded enzyme activities of BaFAD3 efficiently converted LA to ALA, and BaD6D-1 converted LA to γ-linolenic acid and ALA to SDA, but with an apparent preference to LA. BaD6D-2 did not show the encoded enzyme activity and is not a functional D6D. Our results provide an insight into SDA biosynthesis in B. arvensis and expand the repository of fatty acid desaturase targets available for biotechnological production of SDA in traditional oilseed crops.

Endoplasmic reticulum retention signaling and transmembrane channel proteins predicted for oilseed ω3 fatty acid desaturase 3 (FAD3) genes

Oilseed crop oils contain a variety of unsaturated fatty acids that are synthesized and regulated by fatty acid desaturases (FADs). In this study, 14 FAD3 (ω3 desaturase) protein sequences from oilseeds are analyzed and presented through the application of several computational tools. The results indicated a close relationship between Brassica napus and Camelina sativa, as well as between Salvia hispanica and Perilla frutescens FAD3s, due to a high similarity in codon preferences in codon usage clusters and the phylogenetic tree. The cis-acting element results reveal that the seed-specific promoter region of BnFAD3 contains the critical conserved boxes such as HSE and ABRE, which are involved in responsiveness to heat stress and abscisic acid. The presence of the aforementioned conserved boxes may increase cold acclimation as well as tolerance to drought and high salinity. Omega(ω)3 desaturases contain a Skn-1 motif which is a cis-acting regulatory element required involved in endosperm development. In oilseed FAD3s, leucine is the most repeated amino acid in FAD3 proteins. The study conveyed that B. napus, Camelina sativa, Linum usitatissimum, Vernicia fordii, Gossypium hirsutum, S. hispanica, Cannabis sativa, and P. frutescens have retention signal KXKXX/XKXX at their c-terminus sites, which is one of the most important characteristics of FADs. Additionally, it was found that BnFAD3 is a transmembrane protein that can convert ω6 to ω3 fatty acids and may simultaneously act as a potassium ion channel in the ER.

A transferase interactome that may facilitate channeling of polyunsaturated fatty acid moieties from phosphatidylcholine to triacylglycerol

Polyunsaturated fatty acids (PUFAs) such as α-linolenic acid (ALA, 18:3Δ^{9 cis ,12 cis ,15 cis} ) have high nutritional and industrial values. In oilseed crops, PUFAs are synthesized on phosphatidylcholine (PC) and accumulated in triacylglycerol (TAG). Therefore, exploring the mechanisms that route PC-derived PUFA to TAG is essential for understanding and improving PUFA production. The seed oil of flax (Linum usitatissimum) is enriched in ALA, and this plant has many lipid biosynthetic enzymes that prefer ALA-containing substrates. In this study, using membrane yeast two-hybrid and bimolecular fluorescence complementation assays, we probed recombinant flax transferase enzymes, previously shown to contribute to PUFA enrichment of TAG, for physical interactions with each other under in vivo conditions. We found that diacylglycerol acyltransferases, which catalyze the final reaction in acyl-CoA-dependent TAG biosynthesis, interact with the acyl-editing enzymes phosphatidylcholine: diacylglycerol cholinephosphotransferase, and lysophosphatidylcholine acyltransferase. Physical interactions among the acyl-editing enzymes were also identified. These findings reveal the presence of an assembly of interacting transferases that may facilitate the channeling of PUFA from PC to TAG in flax and possibly also in other oleaginous plants that produce seeds enriched in PC-modified fatty acids.

The Evolution and Biocatalysis of FAD2 Indicate Its Correlation to the Content of Seed Oil in Plants

Unsaturated fatty acids are the main components of vegetable oils. Fatty acid desaturase 2 (FAD2) catalyzes oleic acid (OA) into linoleic acid (LA) transformations, which are essential to the profile of FAs in seeds. To further understand the roles of FAD2s in the synthesis of oil, the evolution and biocatalysis of FAD2s were comprehensively analyzed. The evolution history of the FAD2 gene family showed that most of the FAD2 genes formed monophyletic clades except in eudicots. The FAD2 genes in some eudicots diverged into constitutive and seed-specific expression clades. Notably, the biocatalysis of seed-specific or -abundant expression FAD2s in soybean, perilla, rice, and spruce revealed that their catalytic activity was strongly correlated with the total oil content of their seeds in nature. Additionally, it was found that I and Y in site 143 of GmaFAD2-1 were strictly conserved in the seed-specific and constitutive expression clades of Fabaceae, respectively. Furthermore, the site-directed mutation demonstrated that I and Y are vital to improving and reducing the activity of GmaFAD2s. Therefore, the results indicate that the activity of FAD2s in seeds might be a reference to the total oil content of seeds, and site 143 might have been specifically evolved to be required for the activity of FAD2s in some expression-diverged eudicots, especially in legumes.

Chia Seed (Salvia hispanica L.) as a Source of Proteins and Bioactive Peptides with Health Benefits: A Review

The consumption of chia seed (Salvia hispanica L.) has increased in recent years due its high content of omega-3 fatty acids and dietary fiber. This seed also has a high concentration of proteins and essential amino acids, becoming a promising source of bioactive peptides. The objective of this review was to identify the composition and the beneficial effects of chia seeds (S. hispanica L.), their proteins, peptides, and their potential impact on human health. The UniProt database was used to identify the chia proteins and their amino acid sequences. The BIOPEP database was used to analyze the peptides's bioactive potential. A total of 20 proteins were cataloged in chia seed, 12 of those were involved in the regular metabolic processes of the plant cells. However, eight proteins were specifically related to production and storage of plant lipids, thus explaining the high concentration of lipids in chia seeds (around 30%), especially omega-3 fatty acids (around 20%). The analyses of amino acid sequences showed peptides with bioactive potential, including dipeptidyl peptidase-IV inhibitors, angiotensin-converting enzyme inhibitors, and antioxidant capacity. These results correlated with the main health benefits of whole chia seed in humans such as antioxidant capacity, and hypotensive, hypoglycemic, and anticholesterolemic effects. Such relation can be associated with chia protein and peptide compositions and therefore needs further investigation in vitro and in vivo.

Comparative Transcriptome Analysis Reveals an Efficient Mechanism of α-Linolenic Acid in Tree Peony Seeds

Tree peony (Paeonia section Moutan DC.) species are woody oil crops with high unsaturated fatty acid content, including α-linolenic acid (ALA/18:3; >40% of the total fatty acid). Comparative transcriptome analyses were carried out to uncover the underlying mechanisms responsible for high and low ALA content in the developing seeds of P. rockii and P. lutea, respectively. Expression analysis of acyl lipid metabolism genes revealed upregulation of select genes involved in plastidial fatty acid synthesis, acyl editing, desaturation, and triacylglycerol assembly in seeds of P. rockii relative to P. lutea. Also, in association with ALA content in seeds, transcript levels for fatty acid desaturases (SAD, FAD2, and FAD3), which encode enzymes necessary for polyunsaturated fatty acid synthesis, were higher in P. rockii compared to P. lutea. Furthermore, the overexpression of PrFAD2 and PrFAD3 in Arabidopsis increased linoleic and ALA content, respectively, and modulated the final ratio 18:2/18:3 in the seed oil. In conclusion, we identified the key steps and validated the necessary desaturases that contribute to efficient ALA synthesis in a woody oil crop. Together, these results will aid to increase essential fatty acid content in seeds of tree peonies and other crops of agronomic interest.

Identification and characterization of Δ12 and Δ12/Δ15 bifunctional fatty acid desaturases in the oleaginous yeast Lipomyces starkeyi

Fatty acid desaturases play vital roles in the synthesis of unsaturated fatty acids. In this study, Δ12 and Δ12/Δ15 fatty acid desaturases of the oleaginous yeast Lipomyces starkeyi, termed LsFad2 and LsFad3, respectively, were identified and characterized. Saccharomyces cerevisiae expressing LsFAD2 converted oleic acid (C18:1) to linoleic acid (C18:2), while a strain of LsFAD3-expressing S. cerevisiae converted oleic acid to linoleic acid, and linoleic acid to α-linolenic acid (C18:3), indicating that LsFad2 and LsFad3 were Δ12 and bifunctional Δ12/Δ15 fatty acid desaturases, respectively. The overexpression of LsFAD2 in L. starkeyi caused an accumulation of linoleic acid and a reduction in oleic acid levels. In contrast, overexpression of LsFAD3 induced the production of α-linolenic acid. Deletion of LsFAD2 and LsFAD3 induced the accumulation of oleic acid and linoleic acid, respectively. Our findings are significant for the commercial production of polyunsaturated fatty acids, such as ω-3 polyunsaturated fatty acids, in L. starkeyi.

Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.)

BACKGROUND

Alternative splicing (AS) represents a mechanism widely used by eukaryotes for the post-transcriptional regulation of genes. The detailed exploration of AS in peanut has not been documented.

RESULTS

The strand-specific RNA-Seq technique was exploited to characterize the distribution of AS in the four samples of peanut (FH1-seed1, FH1-seed2, FH1-root and FH1-leaf). AS was detected as affecting around 37.2% of the full set of multi-exon genes. Some of these genes experienced AS throughout the plant, while in the case of others, the effect was organ-specific. Overall, AS was more frequent in the seed than in either the root or leaf. The predominant form of AS was intron retention, and AS in transcription start site and transcription terminal site were commonly identified in all the four samples. It is interesting that in genes affected by AS, the majority experienced only a single type of event. Not all of the in silico predicted transcripts appeared to be translated, implying that these are either degraded or sequestered away from the translation machinery. With respect to genes involved in fatty acid metabolism, about 61.6% were shown to experience AS.

CONCLUSION

Our report contributes significantly in AS analysis of peanut genes in general, and these results have not been mentioned before. The specific functions of different AS forms need further investigation.

Omega-3 fatty acid desaturase gene family from two ω-3 sources, Salvia hispanica and Perilla frutescens: Cloning, characterization and expression

Omega-3 fatty acid desaturase (ω-3 FAD, D15D) is a key enzyme for α-linolenic acid (ALA) biosynthesis. Both chia (Salvia hispanica) and perilla (Perilla frutescens) contain high levels of ALA in seeds. In this study, the ω-3 FAD gene family was systematically and comparatively cloned from chia and perilla. Perilla FAD3, FAD7, FAD8 and chia FAD7 are encoded by single-copy (but heterozygous) genes, while chia FAD3 is encoded by 2 distinct genes. Only 1 chia FAD8 sequence was isolated. In these genes, there are 1 to 6 transcription start sites, 1 to 8 poly(A) tailing sites, and 7 introns. The 5'UTRs of PfFAD8a/b contain 1 to 2 purine-stretches and 2 pyrimidine-stretches. An alternative splice variant of ShFAD7a/b comprises a 5'UTR intron. Their encoded proteins harbor an FA_desaturase conserved domain together with 4 trans-membrane helices and 3 histidine boxes. Phylogenetic analysis validated their identity of dicot microsomal or plastidial ω-3 FAD proteins, and revealed some important evolutionary features of plant ω-3 FAD genes such as convergent evolution across different phylums, single-copy status in algae, and duplication events in certain taxa. The qRT-PCR assay showed that the ω-3 FAD genes of two species were expressed at different levels in various organs, and they also responded to multiple stress treatments. The functionality of the ShFAD3 and PfFAD3 enzymes was confirmed by yeast expression. The systemic molecular and functional features of the ω-3 FAD gene family from chia and perilla revealed in this study will facilitate their use in future studies on genetic improvement of ALA traits in oilseed crops.

A mitochondrial proteomics view of complex I deficiency in Candida albicans

Proteomic analyses were carried out on isolated mitochondrial samples of C. albicans from gene-deleted mutants (nuo1Δ, nuo2Δ and goa1Δ) as well as the parental strain in order to better understand the contribution of these three fungal-specific mitochondrial ETC complex I (CI) subunits to cellular activities. Herein, we identify 2333 putative proteins from four strains, in which a total of 663 proteins (28.5%) are putatively located in mitochondria. Comparison of protein abundances between mutants and the parental strain reveal 146 differentially-expressed proteins, of which 78 are decreased and 68 are increased in at least one mutant. The common changes across the three mutants include the down-regulation of nuclear-encoded CI subunit proteins as well as phospholipid, ergosterol and cell wall mannan synthesis, and up-regulated proteins in CIV and the alternative oxidase (AOX2). As for gene-specific functions, we find that NUO1 participates in nucleotide synthesis and ribosomal biogenesis; NUO2 is involved in vesicle trafficking; and GOA1 appears to regulate membrane transporter proteins, ROS removal, and substrates trafficking between peroxisomes and mitochondria. The proteomic view of general as well as mutant-specific proteins further extends our understanding of the functional roles of non-mammalian CI-specific subunit proteins in cell processes. Particularly intriguing is the confirmation of a regulatory role for GOA1 on ETC function, a protein found almost exclusively in Candida species.

SIGNIFICANCE

Fungal mitochondria are critical for fungal pathogenesis. The absence of any of the three fungal specific CI subunits in mitochondria causes an avirulence phenotype of C. albicans in a murine model of invasive disease. As model yeast (Saccharomyces cerevisiae) lacks a CI and is rarely a pathogen of humans, C. albicans is a better choice for establishing a link between mitochondrial CI and pathogenesis. Apart from the general effects of CI mutants on respiration, previous phenotyping of these mutants were quite similar to each other or to CI conservative subunit. By comparison to transcriptional data, the proteomic data obtained in this study indicate that biosynthetic events in each mutant such as cell wall and cell membrane phospholipids and ergosterol are generally decreased in both transcriptomal and translational levels. However, in the case of mitochondrial function, glycolysis/gluconeogenesis, and ROS scavengers, often gene changes are opposite that of proteomic data in mutants. We hypothesize that the loss of energy production in mutants is compensated by increases in protein levels of glycolysis, gluconeogenesis, and anti-ROS scavengers that at least extend mutant survival.

Structural organization of fatty acid desaturase loci in linseed lines with contrasting linolenic acid contents

Flax (Linum usitatissimum L.), the richest crop source of omega-3 fatty acids (FAs), is a diploid plant with an estimated genome size of ~370 Mb and is well suited for studying genomic organization of agronomically important traits. In this study, 12 bacterial artificial chromosome clones harbouring the six FA desaturase loci sad1, sad2, fad2a, fad2b, fad3a and fad3b from the conventional variety CDC Bethune and the high linolenic acid line M5791 were sequenced, analysed and compared to determine the structural organization of these loci and to gain insights into the genetic mechanisms underlying FA composition in flax. With one gene every 3.2-4.6 kb, the desaturase loci have a higher gene density than the genome's average of one gene per 7.8-8.2 kb. The gene order and orientation across the two genotypes were generally conserved with the exception of the sad1 locus that was predicted to have additional genes in CDC Bethune. High sequence conservation in both genic and intergenic regions of the sad and fad2b loci contrasted with the significant level of variation of the fad2a and fad3 loci, with SNPs being the most frequently observed mutation type. The fad2a locus had 297 SNPs and 36 indels over ~95 kb contrasting with the fad2b locus that had a mere seven SNPs and four indels in ~110 kb. Annotation of the gene-rich loci revealed other genes of known role in lipid or carbohydrate metabolic/catabolic pathways. The organization of the fad2b locus was particularly complex with seven copies of the fad2b gene in both genotypes. The presence of Gypsy, Copia, MITE, Mutator, hAT and other novel repeat elements at the desaturase loci was similar to that of the whole genome. This structural genomic analysis provided some insights into the genomic organization and composition of the main desaturase loci of linseed and of their complex evolution through both tandem and whole genome duplications.

Differential Contribution of Endoplasmic Reticulum and Chloroplast ω-3 Fatty Acid Desaturase Genes to the Linolenic Acid Content of Olive (Olea europaea) Fruit

Linolenic acid is a polyunsaturated fatty acid present in plant lipids, which plays key roles in plant metabolism as a structural component of storage and membrane lipids, and as a precursor of signaling molecules. The synthesis of linolenic acid is catalyzed by two different ω-3 fatty acid desaturases, which correspond to microsomal- (FAD3) and chloroplast- (FAD7 and FAD8) localized enzymes. We have investigated the specific contribution of each enzyme to the linolenic acid content in olive fruit. With that aim, we isolated two different cDNA clones encoding two ω-3 fatty acid desaturases from olive (Olea europaea cv. Picual). Sequence analysis indicates that they code for microsomal (OepFAD3B) and chloroplast (OepFAD7-2) ω-3 fatty acid desaturase enzymes, different from the previously characterized OekFAD3A and OekFAD7-1 genes. Functional expression in yeast of the corresponding OepFAD3A and OepFAD3B cDNAs confirmed that they encode microsomal ω-3 fatty acid desaturases. The linolenic acid content and transcript levels of olive FAD3 and FAD7 genes were measured in different tissues of Picual and Arbequina cultivars, including mesocarp and seed during development and ripening of olive fruit. Gene expression and lipid analysis indicate that FAD3A is the gene mainly responsible for the linolenic acid present in the seed, while FAD7-1 and FAD7-2 contribute mostly to the linolenic acid present in the mesocarp and, therefore, in the olive oil. These results also indicate the relevance of lipid trafficking between the endoplasmic reticulum and chloroplast in determining the linolenic acid content of membrane and storage lipids in oil-accumulating photosynthetic tissues.