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Meng L, Zhou R, Liang L, Zang X, Lin J, Wang Q, Wang L, Wang W, Li Z, Ren P. 4-Coumarate-CoA ligase (4-CL) enhances flavonoid accumulation, lignin synthesis, and fruiting body formation in Ganoderma lucidum. Gene 2024; 899:148147. [PMID: 38191099 DOI: 10.1016/j.gene.2024.148147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
It is now understood that 4-Coumarate-CoA ligases (4-CL) are pivotal in bridging the phenylpropanoid metabolic pathway and the lignin biosynthesis pathway in plants. However, limited information on 4-CL genes and their functions in fungi is available. In this study, we cloned the 4-CL gene (Gl21040) from Ganoderma lucidum, which spans 2178 bp and consists of 10 exons and 9 introns. We also developed RNA interference and overexpression vectors for Gl21040 to investigate its roles in G. lucidum. Our findings indicated that in the Gl21040 interference transformants, 4-CL enzyme activities decreased by 31 %-57 %, flavonoids contents decreased by 10 %-22 %, lignin contents decreased by 20 %-36 % compared to the wild-type (WT) strain. Conversely, in the Gl21040 overexpression transformants, 4-CL enzyme activity increased by 108 %-143 %, flavonoids contents increased by 8 %-37 %, lignin contents improved by 15 %-17 % compared to the WT strain. Furthermore, primordia formation was delayed by approximately 10 days in the Gl21040-interferenced transformants but occurred 3 days earlier in the Gl21040-overexpressed transformants compared to the WT strain. These results underscored the involvement of the Gl21040 gene in flavonoid synthesis, lignin synthesis, and fruiting body formation in G. lucidum.
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Affiliation(s)
- Li Meng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Ruyue Zhou
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Lidan Liang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Xizhe Zang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Jialong Lin
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Qingji Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Li Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Wei Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China.
| | - Zhuang Li
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China.
| | - Pengfei Ren
- State Key Laboratory of Nutrient Use and Management, Shandong Academy of Agricultural Sciences, Jinan 250100, China; Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
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Sun X, Liu D, Zhao X. Transcription factors: switches for regulating growth and development in macrofungi. Appl Microbiol Biotechnol 2023; 107:6179-6191. [PMID: 37624406 DOI: 10.1007/s00253-023-12726-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Macrofungi (or mushrooms) act as an extraordinarily important part to human health due to their nutritional and/or medicinal value, but the detailed researches in growth and development mechanisms have yet to be explored further. Transcription factors (TFs) play indispensable roles in signal transduction and affect growth, development, and metabolism of macrofungi. In recent years, increasing research effort has been employed to probe the relationship between the development of macrofungi and TFs. Herein, the present review comprehensively summarized the functional TFs researched in macrofungi, including modulating mycelial growth, fructification, sclerotial formation, sexual reproduction, spore formation, and secondary metabolism. Meanwhile, the possible effect mechanisms of TFs on the growth and development of some macrofungi were also revealed. Specific examples of functional characterizations of TFs in macrofungi (such as Schizophyllum commune and Coprinopsis cinerea) were described to a better comprehension of regulatory effect. Future research prospects in the field of TFs of macrofungi are discussed. We illustrated the functional versatility of the TFs in macrofungi based on specific examples. A systematical realization of the interaction and possible mechanisms between TFs and macrofungi can supply possible solutions to regulate genetic characteristics, which supply novel insights into the regulation of growth, development and metabolism of macrofungi. KEY POINTS: • The functional TFs researched in macrofungi were summarized. • The possible effect mechanisms of TFs in macrofungal were described. • The multiple physiological functions of TFs in macrofungi were discussed.
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Affiliation(s)
- Xueyan Sun
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Dongmei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
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Liu G, Huang K, Ke J, Chen C, Bao GH, Wan X. Novel Camellia sinensis O-Methyltransferase Regulated by CsMADSL1 Specifically Methylates EGCG in Cultivar "GZMe4". JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6706-6716. [PMID: 37094255 DOI: 10.1021/acs.jafc.2c06031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Epigallocatechin-3-O-(4-O-methyl)gallate (EGCG4″Me) in Camellia sinensis possesses numerous beneficial biological activities. However, the germplasm rich in EGCG4″Me and the O-methyltransferase responsible for EGCG4″Me biosynthesis are poorly understood. Herein, the content of EGCG3″Me and EGCG4″Me in the shoots of 13 cultivars was analyzed to demonstrate that EGCG4″Me is characteristically accumulated in the "GZMe4" cultivar but not in the other 12 cultivars. A novel O-methyltransferase (CsOMTL1) was identified from "GZMe4" using RNA-Seq and correlation analysis. Using the recombinant enzyme, EGCG4″Me was synthesized in vitro. Overexpression of CsOMTL1 via Agrobacterium-mediated genetic transformation caused constitutive accumulation of EGCG4″Me in C. sinensis callus. Moreover, the transcription factor CsMADSL1 localized in the nucleus activated the transcription of CsOMTL1 and specifically interacted with its promoter. Hence, our study identified a novel O-methyltransferase that characteristically catalyzes the synthesis of EGCG4″Me and a positive regulator of EGCG4″Me synthesis in "GZMe4", which might provide a strategy for the breeding of a tea cultivar rich in EGCG4″Me.
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Affiliation(s)
- Guangjin Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Kelin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jiaping Ke
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Chenhui Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Guan-Hu Bao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
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Wu Y, Wu S, Shi Y, Jiang L, Yang J, Wang X, Zhu K, Zhang H, Zhang J. Integrated metabolite profiling and transcriptome analysis reveal candidate genes involved in the formation of yellow Nelumbo nucifera. Genomics 2022; 114:110513. [PMID: 36309147 DOI: 10.1016/j.ygeno.2022.110513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/17/2022] [Accepted: 10/22/2022] [Indexed: 01/15/2023]
Abstract
As a worldwide major ornamental flower and a edible plant, lotus (Nelumbo nucifera) is also used as medicine and tea beverage. Here, transcriptome and metabolites of yellow (MLQS) and white (YGB) lotus cultivars during five key flower coloration stages were profiled. 2014 differentially expressed genes were detected with 11 carotenoids in lotus were identified for the first time. Then, regulatory networks between and within functional modules was reconstructed, and the correlation between module-metabolites and gene-metabolites was conducted within 3 core modules. 18 candidate genes related to the formation of yellow flower were screened out and a gene regulatory model for the flower color difference between MLQS and YGB were speculated as follows: The substrate competition between F3'H and F3'5'H and substrate specificity of FLS, together with differential expression of CCD4a and CCD4b were contribute to the differences in flavonoids and carotenoids. Besides, UGT73C2, UGT91C1-2 and SGTase, and regulation of UGTs by transcription factors PLATZ, MADS, NAC031, and MYB308 may also play a role in the upstream regulation. The following verification results indicated that functional differences existed in the coding sequences of NnCCD4b and promoters of NnCCD4a of MLQS and YGB. In all, this study preliminarily reveals the mechanism of yellow flower coloration in lotus and provides new ideas for the study of complex ornamental characters of other plants.
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Affiliation(s)
- Yanyan Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Sihui Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Yan Shi
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Libo Jiang
- College of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong, China.
| | - Juxiang Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Xueqin Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Kaijie Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Hongyan Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Jie Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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Luo Q, Li N, Xu JW. A methyltransferase LaeA regulates ganoderic acid biosynthesis in Ganoderma lingzhi. Front Microbiol 2022; 13:1025983. [PMID: 36312944 PMCID: PMC9614229 DOI: 10.3389/fmicb.2022.1025983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/20/2022] [Indexed: 08/05/2023] Open
Abstract
The methyltransferase LaeA is a global regulator involved in the biosynthesis of secondary metabolites by ascomycete fungi. However, little is known of its regulatory role in basidiomycete fungi. In this study, the laeA gene was identified in the basidiomycete Ganoderma lingzhi and its function in regulating the biosynthesis of anti-tumor ganoderic acids was evaluated. A laeA deletion (ΔlaeA) Ganoderma strain exhibited significantly reduced concentration of ganoderic acids. qRT-PCR analysis further revealed that the transcription levels of genes involved in the biosynthesis of ganoderic acids were drastically lower in the ΔlaeA strain. Moreover, deletion of laeA resulted in decreased accumulation of intermediates and abundances of asexual spores in liquid static culture of G. lingzhi. In contrast, constitutive overexpression of laeA resulted in increased concentration of ganoderic acids. These results demonstrate an essential role of LaeA in the regulation of ganoderic acid biosynthesis in Ganoderma.
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Affiliation(s)
- Qin Luo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Na Li
- Faculty of Science, Kunming University of Science and Technology, Kunming, China
| | - Jun-Wei Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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Meng L, Zhou R, Lin J, Zang X, Wang Q, Wang P, Wang L, Li Z, Wang W. Transcriptome and metabolome analyses reveal transcription factors regulating ganoderic acid biosynthesis in Ganoderma lucidum development. Front Microbiol 2022; 13:956421. [PMID: 35992655 PMCID: PMC9386254 DOI: 10.3389/fmicb.2022.956421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Ganoderma lucidum is an important medicinal fungus in Asian countries. Ganoderic acid (GA) is the major variety of bioactive and medicative components in G. lucidum. Biosynthesis of secondary metabolites is usually associated with cell differentiation and development. However, the mechanism underlying these phenomena remain unclear. Transcription factors play an essential regulatory role in the signal transduction pathway, owing to the fact that they represent the major link between signal transduction and expression of target genes. In the present study, we performed transcriptome and metabolome analyses to identify transcription factors involved in GA biosynthesis during development of G. lucidum. Transcriptome data revealed differentially expressed genes between mycelia and primordia, as well as between mycelia and the fruiting body. Results from gene ontology enrichment analysis and metabolome analyses suggested that GAs and flavonoids biosynthetic process significantly changed during fungal development. The analysis of predicted occurrences of DNA-binding domains revealed a set of 53 potential transcription factor families in G. lucidum. Notably, we found homeobox transcription factor and velvet family protein played important role in GA biosynthesis. Combined with previous studies, we provided a model diagram of transcription factors involved in GA biosynthesis during fruiting body formation. Collectively, these results are expected to enhance our understanding into the mechanisms underlying secondary metabolite biosynthesis and development in fungi.
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Integrated Transcriptomics and Nontargeted Metabolomics Analysis Reveal Key Metabolic Pathways in Ganoderma lucidum in Response to Ethylene. J Fungi (Basel) 2022; 8:jof8050456. [PMID: 35628712 PMCID: PMC9146657 DOI: 10.3390/jof8050456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 12/13/2022] Open
Abstract
Ganoderic acid (GA) is an important secondary metabolite of Ganoderma lucidum with a diverse array of pharmacological properties. In this study, we found that exogenous ethylene increased the production of endogenous ethylene and ganoderic acid in G. lucidum. However, the mechanism by which ethylene is regulated remains unclear. As a result, we performed a combined transcriptomics and nontargeted metabolomics analysis to evaluate the regulatory mechanism of ethylene. A total of 4070 differentially expressed genes (1835 up-regulated and 2235 down-regulated) and 378 differentially accumulated metabolites (289 up-regulated and 89 down-regulated) were identified in all groups. The transcriptomics and nontargeted metabolomics data revealed that genes involved in the tricarboxylic acid (TCA) cycle, polyamine metabolic pathway, acetyl-CoA carboxylase (ACC) pathway, and triterpenoid metabolism were up-regulated, whereas the metabolic intermediates involved in these metabolic pathways were down-regulated. These findings imply that ethylene potentially accelerates normal glucose metabolism, hence increasing the number of intermediates available for downstream biological processes, including polyamine metabolism, ethylene synthesis pathway, and ganoderic acid biosynthesis. The findings will contribute significantly to our understanding of secondary metabolites biosynthesis in fungi.
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Transcriptomic and Non-Targeted Metabolomic Analyses Reveal the Flavonoid Biosynthesis Pathway in Auricularia cornea. Molecules 2022; 27:molecules27072334. [PMID: 35408732 PMCID: PMC9000485 DOI: 10.3390/molecules27072334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
Flavonoids, which are abundant in plants, are recognized for their antioxidant and anticancer roles in clinical applications. However, little is known about the molecular basis of flavonoid biosynthesis in fungi. In this study, we found that inclusion of leachate of Korshinsk peashrub (Caragana korshinskii) in the fermentation medium increased the total flavonoid content of the edible fungus Auricularia cornea by 23.6% relative to that grown in a control medium. Combined transcriptomic and non-targeted metabolomic analysis of the flavonoid biosynthesis pathway in A. cornea illustrated that there are important metabolites in the phenylpropanoid, coumarin and isoflavonoid biosynthesis pathways. In addition, we found that certain homologous genes encode phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO) and chalcone isomerase (CHI) in these biosynthesis pathways. These results, in this study, provide a new line for studying the regulation of flavonoid production in edible fungi.
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Yang Y, Zhang Y, He J, Wu Q, Li Y, Li W, Zhou G, Kamol R, Yang X. Transcription factor GlbHLH regulates hyphal growth, stress resistance, and polysaccharide biosynthesis in Ganoderma lucidum. J Basic Microbiol 2021; 62:82-91. [PMID: 34927265 DOI: 10.1002/jobm.202100334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/18/2021] [Accepted: 10/31/2021] [Indexed: 11/12/2022]
Abstract
Basic helix-loop-helix (bHLH) transcription factors (TFs) participate in many physiological and cellular processes in eukaryotes. However, their functions remain unclear in the macro basidiomycete Ganoderma lucidum (G. lucidum). In this study, a gene encoding bHLH TF, GlbHLH, was identified in G. lucidum. The knockdown of GlbHLH by RNA interference reduced hyphal growth, hyphal branching, and resistant to osmotic, oxidative, and cell wall stress. The content of cell wall components β-1,3 glucan and chitin and the expression of their synthesis genes were decreased in the GlbHLH knockdown strains. The knockdown of GlbHLH led to an increase of intracellular reactive oxygen species by decreasing the enzyme activity and gene expression of antioxidant enzymes. Furthermore, the production of intracellular polysaccharides and extracellular polysaccharides was greatly decreased in the GlbHLH mutants. These results suggested that GlbHLH is involved in hyphal growth, stress response, and polysaccharide biosynthesis in G. lucidum.
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Affiliation(s)
- Yingyin Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yifan Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiahao He
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yanzeng Li
- Henan Shijixiang Edible Mushroom Co., Ltd., Xuchang, China
| | - Weipeng Li
- Henan Shijixiang Edible Mushroom Co., Ltd., Xuchang, China
| | - Gaoli Zhou
- Henan Shijixiang Edible Mushroom Co., Ltd., Xuchang, China
| | - Rajabov Kamol
- Russia Green Manor Co., Ltd., Leningrad Oblas, Russia
| | - Xiaobing Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Ye Z, Yu J, Yan W, Zhang J, Yang D, Yao G, Liu Z, Wu Y, Hou X. Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera. HORTICULTURE RESEARCH 2021; 8:157. [PMID: 34193845 PMCID: PMC8245520 DOI: 10.1038/s41438-021-00591-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 05/12/2023]
Abstract
Camellia oleifera (C. oleifera) is one of the four major woody oil-bearing crops in the world and has relatively high ecological, economic, and medicinal value. Its seeds undergo a series of complex physiological and biochemical changes during ripening, which is mainly manifested as the accumulation and transformation of certain metabolites closely related to oil quality, especially flavonoids and fatty acids. To obtain new insights into the underlying molecular mechanisms, a parallel analysis of the transcriptome and proteome profiles of C. oleifera seeds at different maturity levels was conducted using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ) complemented with gas chromatography-mass spectrometry (GC-MS) data. A total of 16,530 transcripts and 1228 proteins were recognized with significant differential abundances in pairwise comparisons of samples at various developmental stages. Among these, 317 were coexpressed with a poor correlation, and most were involved in metabolic processes, including fatty acid metabolism, α-linolenic acid metabolism, and glutathione metabolism. In addition, the content of total flavonoids decreased gradually with seed maturity, and the levels of fatty acids generally peaked at the fat accumulation stage; these results basically agreed with the regulation patterns of genes or proteins in the corresponding pathways. The expression levels of proteins annotated as upstream candidates of phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) as well as their cognate transcripts were positively correlated with the variation in the flavonoid content, while shikimate O-hydroxycinnamoyltransferase (HCT)-encoding genes had the opposite pattern. The increase in the abundance of proteins and mRNAs corresponding to alcohol dehydrogenase (ADH) was associated with a reduction in linoleic acid synthesis. Using weighted gene coexpression network analysis (WGCNA), we further identified six unique modules related to flavonoid, oil, and fatty acid anabolism that contained hub genes or proteins similar to transcription factors (TFs), such as MADS intervening keratin-like and C-terminal (MIKC_MADS), type-B authentic response regulator (ARR-B), and basic helix-loop-helix (bHLH). Finally, based on the known metabolic pathways and WGCNA combined with the correlation analysis, five coexpressed transcripts and proteins composed of cinnamyl-alcohol dehydrogenases (CADs), caffeic acid 3-O-methyltransferase (COMT), flavonol synthase (FLS), and 4-coumarate: CoA ligase (4CL) were screened out. With this exploratory multiomics dataset, our results presented a dynamic picture regarding the maturation process of C. oleifera seeds on Hainan Island, not only revealing the temporal specific expression of key candidate genes and proteins but also providing a scientific basis for the genetic improvement of this tree species.
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Affiliation(s)
- Zhouchen Ye
- College of Horticulture, Hainan University, Haikou, China
| | - Jing Yu
- College of Horticulture, Hainan University, Haikou, China
| | - Wuping Yan
- College of Horticulture, Hainan University, Haikou, China
| | - Junfeng Zhang
- College of Horticulture, Hainan University, Haikou, China
| | - Dongmei Yang
- College of Horticulture, Hainan University, Haikou, China
| | - Guanglong Yao
- College of Horticulture, Hainan University, Haikou, China
| | - Zijin Liu
- College of Horticulture, Hainan University, Haikou, China
| | - Yougen Wu
- College of Horticulture, Hainan University, Haikou, China.
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Institute of Plasma Engineering, Nanjing, China.
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