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Bu M, Fan W, Li R, He B, Cui P. Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies. Metabolites 2023; 13:1170. [PMID: 38132852 PMCID: PMC10744971 DOI: 10.3390/metabo13121170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
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.
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Affiliation(s)
- Mengjia Bu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruonan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bing He
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Cui
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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Yin X, Guo X, Hu L, Li S, Chen Y, Wang J, Wang RRC, Fan C, Hu Z. Genome-Wide Characterization of DGATs and Their Expression Diversity Analysis in Response to Abiotic Stresses in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2022; 11:1156. [PMID: 35567157 PMCID: PMC9104862 DOI: 10.3390/plants11091156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Triacylglycerol (TAG) is the most important storage lipid for oil plant seeds. Diacylglycerol acyltransferases (DGATs) are a key group of rate-limiting enzymes in the pathway of TAG biosynthesis. In plants, there are three types of DGATs, namely, DGAT1, DGAT2 and DGAT3. Brassica napus, an allotetraploid plant, is one of the most important oil plants in the world. Previous studies of Brassica napus DGATs (BnaDGATs) have mainly focused on BnaDGAT1s. In this study, four DGAT1s, four DGAT2s and two DGAT3s were identified and cloned from B. napus ZS11. The analyses of sequence identity, chromosomal location and collinearity, phylogenetic tree, exon/intron gene structures, conserved domains and motifs, and transmembrane domain (TMD) revealed that BnaDGAT1, BnaDGAT2 and BnaDGAT3 were derived from three different ancestors and shared little similarity in gene and protein structures. Overexpressing BnaDGATs showed that only four BnaDGAT1s can restore TAG synthesis in yeast H1246 and promote the accumulation of fatty acids in yeast H1246 and INVSc1, suggesting that the three BnaDGAT subfamilies had greater differentiation in function. Transcriptional analysis showed that the expression levels of BnaDGAT1s, BnaDGAT2s and BnaDGAT3s were different during plant development and under different stresses. In addition, analysis of fatty acid contents in roots, stems and leaves under abiotic stresses revealed that P starvation can promote the accumulation of fatty acids, but no obvious relationship was shown between the accumulation of fatty acids with the expression of BnaDGATs under P starvation. This study provides an extensive evaluation of BnaDGATs and a useful foundation for dissecting the functions of BnaDGATs in biochemical and physiological processes.
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Affiliation(s)
- Xiangzhen Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Y.); (X.G.); (L.H.); (S.L.); (Y.C.)
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xupeng Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Y.); (X.G.); (L.H.); (S.L.); (Y.C.)
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lizong Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Y.); (X.G.); (L.H.); (S.L.); (Y.C.)
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- College of Biology and Agriculture, Zhoukou Normal University, Zhoukou 466001, China
| | - Shuangshuang Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Y.); (X.G.); (L.H.); (S.L.); (Y.C.)
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhong Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Y.); (X.G.); (L.H.); (S.L.); (Y.C.)
| | - Jingqiao Wang
- Institute of Economical Crops, Yunnan Agricultural Academy, Kunming 650205, China;
| | - Richard R.-C. Wang
- United States Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA;
| | - Chengming Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Y.); (X.G.); (L.H.); (S.L.); (Y.C.)
| | - Zanmin Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; (X.Y.); (X.G.); (L.H.); (S.L.); (Y.C.)
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Ma R, Huang B, Huang Z, Zhang Z. Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo ( Phyllostachys edulis (Carrière) J. Houz). PeerJ 2021; 9:e11780. [PMID: 34327057 PMCID: PMC8310622 DOI: 10.7717/peerj.11780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 12/16/2022] Open
Abstract
Background The YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo. Methods In the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments. Results Based on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress.
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Affiliation(s)
- Ruifang Ma
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Hangzhou, Lin'an, China.,School of Forestry and Biotechnology, ZhejiangA&F University, Zhejiang, Lin'an, China
| | - Bin Huang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Hangzhou, Lin'an, China.,School of Forestry and Biotechnology, ZhejiangA&F University, Zhejiang, Lin'an, China
| | - Zhinuo Huang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Hangzhou, Lin'an, China.,School of Forestry and Biotechnology, ZhejiangA&F University, Zhejiang, Lin'an, China
| | - Zhijun Zhang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Hangzhou, Lin'an, China.,School of Forestry and Biotechnology, ZhejiangA&F University, Zhejiang, Lin'an, China
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Yang Z, Wang K, Aziz U, Zhao C, Zhang M. Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat ( Avena sativa L.). PLANT METHODS 2020; 16:138. [PMID: 33072174 PMCID: PMC7560290 DOI: 10.1186/s13007-020-00679-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids. RESULTS In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for "all samples", "shoots and roots of seedlings", "developing seeds" and "developing endosperms" were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets. CONCLUSIONS Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.
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Affiliation(s)
- Zheng Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Usman Aziz
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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