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Structure and content of the Web-based ALG database. Each box represents a different Web page. Arrows indicate links between pages. For each enzyme, there is a link to the corresponding Web page of the International Union of Biochemistry and Molecular Biology (http://www.chem.qmw.ac.uk/iubmb) when available. The International Union of Biochemistry and Molecular Biology Web pages have links to many other databases. TIGR and MIPS databases: see "Materials and Methods" for abbreviations and Web addresses.
Source publication
The genome of Arabidopsis has been searched for sequences of genes involved in acyl lipid metabolism. Over 600 encoded proteins have been identified, cataloged, and classified according to predicted function, subcellular location, and alternative splicing. At least one-third of these proteins were previously annotated as "unknown function" or with...
Contexts in source publication
Context 1
... identity and description of each gene and its encoded protein are given on the Web-based ver- sion of this survey (ALG database) as well as se- quences, literature references, and other information where available. The structure and the content of the database are summarized in Figure 2. ...
Context 2
... complete content of the Lipid Gene Catalog is available in the ALG database (http://www.plantbiology.msu.edu/lipids/genesurvey/index.htm). For a summary of the type of information contained in the catalog, see Figure 2. For a summary of the candidates, see Table I. been increased from 71 to 210, representing 600 genes, i.e. around 2.4% of the total number of predicted genes in Arabidopsis. ...
Citations
... In plants, two interconnected metabolic pathways-an acyl-CoA-dependent pathway and an acyl-CoA-independent pathway-lead to the export of processes for de novo fatty acid synthesis from plastids to the cytoplasm. The discovery and precise quantification of the expression of transcription factors and important genes associated with lipid metabolic pathways in soybean (Severin et al. 2010 ), Jatropha curcas (Costa et al. 2010 ), Arabidopsis (Beisson 2003 ), peanut (Gupta et al. 2016 ), and castor bean (Brown et al. 2012 ) have been made possible by high-quality RNA-seq data. Engineering plants to produce oilseed crops with higher yields and resilience to abiotic and biotic challenges make it possible to gather RNA-seq data and enhance plant transformation technology. ...
Oilseed crops are energy rich crops that are grown under energy deprived conditions. The demand for premium seed oils is increasing as the world’s population grows. The attack of pests and diseases reduces the production potential of these crops. The cost of controlling insect pests by synthetic chemical insecticides in agriculture annually is billions of dollars worldwide. The overuse of insecticides has many associated ill effects. To maintain the ecological balance of the environment, it is imperative to develop alternative pest management systems that aim for minimal pesticide use and the conservation of natural enemies. Resistance in host plants is one such alternative strategy. Since one of the main bottlenecks in realization of full yield potential of oilseed crops is attack of insect pests, a traditional and effective alternative crop protection method serves as the fundamental tool of integrated pest management. Future development of insect-resistant oilseed crop cultivars will depend on the adoption of technologies and breeding techniques such as genomic selection, high-throughput phenomics, gene editing, and landscape genomics as well as the continuous use of sources of resistance from crop germplasm.
... At the 20 DPA and 25 DPA, the grain weights of the six T3 transgenic lines were significantly higher than that of 2074B (Table 5). However, at the late developmental stages (30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45), most grain weights of the six T3 transgenic lines were significantly lower than that of in 2074B, which were mainly caused by the decreased moisture content at the late stages (Table 5). The oil content at the different stages of ovular developmental of the transgenic lines was measured using the Soxhlet extraction method. ...
... The storage oil in seeds mainly consists of TAG synthesized from glycerol-3-phosphate and fatty acids [34][35][36]. In higher plants, biosynthesis of fatty acids and lipids are well characterized in biochemical and molecular studies [37,38]. Fatty acid is de novo synthesized mainly from acetyl-CoA catalyzed in plastids by a series of enzymes, of which ACCase and the FAS multienzyme complex are the most critical enzymes. ...
Three carbon-chain extension genes associated with fatty acid synthesis in cotton, namely GhKAR, GhHAD, and GhENR, play important roles in oil accumulation in cotton seeds. In the present study, these three genes were cloned and characterized. The expression patterns of GhKAR, GhHAD and GhENR in the high seed oil content cultivars 10H1007, 10H1014, and 10H1041 differed somewhat compared with those of 2074B with low seed oil content at different stages of seed development. GhKAR showed all three cultivars showed higher transcript levels than that of 2074B at 10, 40 and 45 DPA. The expression pattern of GhHAD showed a lower transcript level than that of 2074B at both 10 and 30 DPA but higher transcript level than that of 2074B at 40 DPA. GhENR showed a lower transcript level than that of 2074B at both 15 and 30 DPA. The highest transcript levels of GhKAR and GhENR were detected at 15 DPA in 10H1007, 10H1014, and 10H1041 compared with 2074B. From 5 to 45 days post anthesis (DPA) cotton seed, the oil content accumulated continuously in the developing seed. Oil accumulation reached the peak at 40 DPA to 45 DPA and slightly decreased in mature seed. In addition, GhKAR and GhENR showed different expression patterns in fiber and ovule development processes, in which they showed high expression levels at 20 DPA during fiber elongation stage, but their expression level peaked at 15 DPA during ovule development processes. These two genes showed the lowest expression levels at the late seed maturation stage, while GhHAD showed peak at 10 DPA of fiber development. Compared to 2074B, the oil contents of GhKAR and GhENR overexpression lines increased 1.05~1.08 folds. These results indicated that GhHAD, GhENR and GhKAR were involved in both seed oil synthesis and fiber elongation with dual biological functions in cotton.
... According to the amino acid sequence and substrate preference, FAT is divided into two subfamilies, FATA and FATB [6,7]. In most plants, FATA encodes 18:1-ACP thioesterase, which has a relatively weak effect on C18:0-ACP [8][9][10] and determines the level of 18:1 output to the plastid. FATB tends to generate saturated acyl-ACP fatty acyl chains. ...
... As a result, saturated fatty acids were accumulated to the highest level at the same time point to provide sufficient substrates for the synthesis of unsaturated fatty acids. There are two genes encoding FATA and one gene encoding FATB in the Arabidopsis genome [9,34]. It was found that the total amount of saturated fatty acids in various tissues of the Arabidopsis fatb mutant decreased by 40%-50% compared with that of wild type, as a result of increased fatty acid turnover, leading to slow growth of seedlings [13]. ...
Fatty Acyl-ACP thioesterase (FAT) is a key enzyme controlling oil biosynthesis in plant seeds. FATs can be divided into two subfamilies, FATA and FATB according to their amino acid sequences and substrate specificity. The Upland cotton genome contains 20 GhFAT genes, amongst which 6 genes were of the GhFATA subfamily and 14 of the GhFATB subfamily. The 20 GhFAT genes are unevenly distributed on 14 chromosomes. The GhFATA genes have 5 or 7 exons and the GhFATB genes have 6 or 7 exons. All GhFAT proteins have the conserved Acyl-ACP_TE domain and PLN02370 super family, the typical characteristics of plant thioesterases. Analyses of the expression level of GhFATs and the compositions of fatty acid in 5–60 days-post-anthesis seeds showed that the ratio of saturated fatty acids to unsaturated fatty acids was consistent with the expression profile of GhFATB12, GhFATB3, and GhFATB10; the ratio of monounsaturated fatty acid to polyunsaturated fatty acids was consistent with the expression profile of GhFATA3. The oil contents of mature cottonseeds were positively correlated with the contents of palmitic acid and linolenic acid as well as seed vigor. These results provide essential information for further exploring the role(s) of the specific GhFATs in determining oil biosynthesis and cottonseed compositions.
... In the model plant Arabidopsis, significant progress has been made in understanding lipid biosynthesis, transport, and degradation. Many genes encoding enzymes involved in lipid metabolism have been characterized, and several transcription families such as B3, NFY-B, AP2/EREBP, and bZIP have been reported to regulate these structural genes to control seed oil accumulation (Beisson, 2003;Li-Beisson, 2013;Manan et al., 2017). Only a couple of studies on expression variation underlying oil accumulation of peanut seed are available for domesticated peanut, A. hypogaea (Wang et al., 2018;Zhang et al., 2021). ...
Introduction
The wild allotetraploid peanut Arachis monticola contains a higher oil content than the cultivated allotetraploid Arachis hypogaea. Besides the fact that increasing oil content is the most important peanut breeding objective, a proper understanding of its molecular mechanism controlling oil accumulation is still lacking.
Methods
We investigated this aspect by performing comparative transcriptomics from developing seeds between three wild and five cultivated peanut varieties.
Results
The analyses not only showed species-specific grouping transcriptional profiles but also detected two gene clusters with divergent expression patterns between two species enriched in lipid metabolism. Further analysis revealed that expression alteration of lipid metabolic genes with co-expressed transcription factors in wild peanut led to enhanced activity of oil biogenesis and retarded the rate of lipid degradation. In addition, bisulfite sequencing was conducted to characterize the variation of DNA methylation between wild allotetraploid (245, WH 10025) and cultivated allotetraploid (Z16, Zhh 7720) genotypes. CG and CHG context methylation was found to antagonistically correlate with gene expression during seed development. Differentially methylated region analysis and transgenic assay further illustrated that variations of DNA methylation between wild and cultivated peanuts could affect the oil content via altering the expression of peroxisomal acyl transporter protein (Araip.H6S1B).
Discussion
From the results, we deduced that DNA methylation may negatively regulate lipid metabolic genes and transcription factors to subtly affect oil accumulation divergence between wild and cultivated peanuts. Our work provided the first glimpse on the regulatory mechanism of gene expression altering for oil accumulation in wild peanut and gene resources for future breeding applications.
... The oil metabolism genes of sesame were identified by performing homology searches against Arabidopsis genes that are involved in fatty acid (FA) and triacylglycerol (TAG) biosynthesis. 66,67 The expression levels of each gene in the seeds were evaluated using the Fragments per Kilobase per Million (FPKM) values calculated by Cufflinks v2.2.1. 68 Genes with an FPKM value > 0.5 were considered to be expressed in the seeds. ...
Sesame (Sesamum indicum L.) is an important oilseed crop that produces abundant seed oil and has a pleasant flavor and high nutritional value. To date, several Illumina-based genome assemblies corresponding to different sesame genotypes have been published and widely used in genetic and genomic studies of sesame. However, these assemblies consistently showed low continuity with numerous gaps. Here, we reported a high-quality, reference-level sesame genome assembly by integrating PacBio high-fidelity sequencing and Hi-C technology. Our updated sesame assembly was 309.35 Mb in size with a high chromosome anchoring rate (97.54%) and contig N50 size (13.48 Mb), which were better than previously published genomes. We identified 163.38 Mb repetitive elements and 24,345 high-confidence protein-coding genes in the updated sesame assembly. Comparative genomic analysis showed that sesame shared an ancient whole-genome duplication event with two Lamiales species. A total of 2,782 genes were tandemly duplicated. We also identified several genes that were likely involved in fatty acid and triacylglycerol biosynthesis. Our improved sesame assembly and annotation will facilitate future genetic studies and genomics-assisted breeding of sesame.
... Concerning specificity and sensitivity, oligonucleotide-based microarrays are superior to cDNA-based microarrays. Drosophila, Saccharomyces cerevisiae, and Arabidopsis have been extensively studied utilizing DNA microarrays for gene expression profiling (White et al. 1999;Beisson et al. 2003;Marzancola et al. 2016). ...
DNA microarrays are a powerful technology that has great implications in plant sciences, biomedical sciences, veterinary, and pharmacological research. It can deal with large numbers of samples for the detection of microbes, clinical diagnosis, gene expression analysis, host–pathogen interactions, food safety testing, and environmental monitoring. Detecting and quantifying the microbial populations in microbial ecology are difficult due to practical difficulties. Conventional procedures such as dilution plating and biochemical assays are ineffective in identifying bacteria and yeasts at the species level and in identifying multiple species simultaneously. These techniques are also imprecise, time-consuming, and unable to identify unculturable species. This chapter focuses on the review of applications of DNA microarrays for identifying the plant pathogens, fungi, viruses, bacteria, mycoplasma-like organisms, and nematodes. In this chapter, we discuss the gene expression profiling of pathogens and their host plants, new virulent and resistance genes discovery, regulation of gene networks, and physiological pathways under biotic stresses. The supremacy of microarray technology has unraveled the unprecedented knowledge about plant pathogens and their interactions with the host plants, creating new research avenues in the field of molecular plant pathology.KeywordsGenomicscDNAMicroarray chipProbesPathogen identification
... At high-temperature regimes, an increased oleic acid level can improve the oil stability and produce scarcer uninvited compounds [30,31]. Both FAE1 (fatty acid elongase1) and FAD2 (fatty acid desturase2) are essential enzymes for the fatty acid biosynthesis pathway [29,32]. FAE1, a critical gene in erucic acid biosynthesis, catalyzes the first condensation step in the elongation route of extremely long-chain fatty acid production and FAD2 regulates the percentage of polyunsaturated fatty acids in seed oil. ...
... FAE1, a critical gene in erucic acid biosynthesis, catalyzes the first condensation step in the elongation route of extremely long-chain fatty acid production and FAD2 regulates the percentage of polyunsaturated fatty acids in seed oil. Gene FAD2 catalyzes the first step in the conversion of oleic acid to linoleic acid in the production of polyunsaturated fatty acids [29,32,33]. ...
Codon usage bias (CUB) phenomenon varies with the species and even within the genes of the same species, where few codons are preferred more frequently than their other synonymous codons. It also categorizes the differences between species. Nucleotide compositional analysis reveals the molecular mechanisms of genes and the evolutionary relationship of a gene in dissimilar plant species. In the present study, three orthologous sequences of each FAE1 (FAE1.1, FAE1.2, and FAE1.3) and FAD2 (FAD2.1, FAD2.2, and FAD2.3) genes, from six Brassica species were accessed using the GenBank database. Further, CUB-related parameters such as nucleotide composition (AT and GC content), relative synonymous codon usage (RSCU), the effective number of codons (ENC), frequency of optimal codons (Fop), relative codon usage bias (RCBS), neutrality plot (GC12 vs. GC3), parity rule-2 [(A3/(A3 + T3) vs. (G3/(G3 + C3)], and correspondence analysis (COA) were analyzed to compare codon bias in U's triangle Brassica species. The FAE1 genes were AT-biased and FAD2 genes were GC-biased across the studied Brassica species. RSCU values indicated that both the genes had moderate codon usage frequency for selected amino acids. The evolutionary study confirmed that codon usage preference is similar within the species grouped into the same cluster for FAE1; however, B. nigra performed differently for FAD2.2 orthologue. The high ENC value, low Fop, and RSCU value highlighted that FAE1 and FAD2 genes had a low level of gene expression and moderate preference for codon usage across the Brassicas. In addition, neutrality plot, parity rule, and correspondence analysis revealed that natural selection pressure had significantly contributed to CUB for FAE1 genes, whereas mutation and selection pressure occurred for FAD2 genes. This study would help to decode codon optimization, improve the level of expression of exogenous genes, and transgenic engineering to increase fatty acid profiling for the betterment of seed oil in Brassica species.
... FATA2 plays an important function in chain termination within de novo synthesis of fatty acid and is also essential for plant viability 49 . Long-chain acyl-CoA synthetases (LACSs) synthesize long-chain acyl-CoAs from free fatty acids in plant cells. ...
Milk thistle is an oil and medicinal crop known as an alternative oil crop with a high level of unsaturated fatty acids, which makes it a favorable edible oil for use in food production. To evaluate the importance of Milk thistle lipids in drought tolerance, an experiment was performed in field conditions under three different water deficit levels (Field capacity (FC), 70% FC and 40% FC). After harvesting seeds of the plant, their oily and methanolic extracts were isolated, and subsequently, types and amounts of lipids were measured using GC–MS. Genes and enzymes engaged in biosynthesizing of these lipids were identified and their expression in Arabidopsis was investigated under similar conditions. The results showed that content of almost all measured lipids of milk thistle decreased under severe drought stress, but genes (belonged to Arabidopsis), which were involved in their biosynthetic pathway showed different expression patterns. Genes biosynthesizing lipids, which had significant amounts were selected and their gene and metabolic network were established. Two networks were correlated, and for each pathway, their lipids and respective biosynthesizing genes were grouped together. Four up-regulated genes including PXG3, LOX2, CYP710A1, PAL and 4 down-regulated genes including FATA2, CYP86A1, LACS3, PLA2-ALPHA were selected. The expression of these eight genes in milk thistle was similar to Arabidopsis under drought stress. Thus, PXG3, PAL, LOX2 and CYP86A1 genes that increased expression were selected for protein analysis. Due to the lack of protein structure of these genes in the milk thistle, modeling homology was performed for them. The results of molecular docking showed that the four proteins CYP86A1, LOX2, PAL and PXG3 bind to ligands HEM, 11O, ACT and LIG, respectively. HEM ligand was involved in production of secondary metabolites and dehydration tolerance, and HEM binding site remained conserved in various plants. CA ligands were involved in synthesis of cuticles and waxes. Overall, this study confirmed the importance of lipids in drought stress tolerance in milk thistle.
... PA is produced and metabolized through complex pathways, of which the cytidinediphosphate diacylglycerol synthase (CDS) catalyzes PA to cytidine diphosphate diacylglycerol (CDP-DAG), the important branch point intermediate of glycerolipid biosynthesis of prokaryotic and eukaryotic organisms [15]. There are five CDS isoforms in Arabidopsis thaliana [15,16], among them CDS1, CDS2 and CDS3 genes probably encode extraplastidial isoforms and have similar enzymatic properties [15,17]. CDS1 and CDS2 present redundant functions and knockout of both genes leads to suppressed growth, smaller cotyledons and shorter hypocotyls, and death~2 weeks after germination. ...
Embryonic development is a key developmental event in plant sexual reproduction; however, regulatory networks of plant early embryonic development, particularly the effects and functional mechanisms of phospholipid molecules are still unknown due to the limitation of sample collection and analysis. We innovatively applied the microspore-derived in vitro embryogenesis of Brassica napus and revealed the dynamics of phospholipid molecules, especially phosphatidic acid (PA, an important second messenger that plays an important role in plant growth, development, and stress responses), at different embryonic developmental stages by using a lipidomics approach. Further analysis of Arabidopsis mutants deficiency of CDS1 and CDS2 (cytidinediphosphate diacylglycerol synthase, key protein in PA metabolism) revealed the delayed embryonic development from the proembryo stage, indicating the crucial effect of CDS and PA metabolism in early embryonic development. Decreased auxin level and disturbed polar localization of auxin efflux carrier PIN1 implicate that CDS-mediated PA metabolism may regulate early embryogenesis through modulating auxin transport and distribution. These results demonstrate the dynamics and importance of phospholipid molecules during embryo development, and provide informative clues to elucidate the regulatory network of embryogenesis.
... In Arabidopsis thaliana, 71 putative LTPs with highly divergent sequences have been identified (Beisson et al., 2003). Further, Silverstein et al. (2007) identified 276 members of the LTP gene family with varied expression patterns in different tissues and under different stimuli in Arabidopsis (Jose-Estanyol et al., 2004;Zimmermann et al., 2004). ...
Drought is a major abiotic stress that causes severely crop yield loss worldwide. Lipid transfer proteins (LTPs) play an essential role during plant growth and cell signaling transduction associated with stress responses. However, the regulatory circuits involved in drought stress remain largely unresolved. Here, we reported that a nonspecific lipid transfer protein, namely GhLTP4, positively modulated drought stress tolerance in cotton. GhLTP4 (synonym Pfs6, GenBank: ABO42261) was preferentially expressed in fiber cells, while, it was also strongly induced by phytohormone abscisic acid (ABA) and drought stress treatments. Compared with wild type, over- and down-expression of GhLTP4 in cotton led to the increased and decreased drought tolerance, respectively. Overexpression of GhLTP4 remarkably increased lipid components and the accumulation of culticular waxes in transgenic cotton leaves under normal condition. Under drought stress, GhLTP4-overexpressing transgenic cotton exhibited the remodeled lipid profiles, more ABA contents, and the improved tricarboxylic acid cycle process. Taken together, we reveal the function and underlying mechanisms of GhLTP4 in regulating cotton drought tolerance and create valuable genetic accessions for cotton drought-tolerant breeding.
