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Yu C, Liu G, Qin J, Wan X, Guo A, Wei H, Chen Y, Lian B, Zhong F, Zhang J. Genomic and transcriptomic studies on flavonoid biosynthesis in Lagerstroemia indica. BMC PLANT BIOLOGY 2024; 24:171. [PMID: 38443839 PMCID: PMC10913235 DOI: 10.1186/s12870-024-04776-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/29/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Lagerstroemia indica is a widely cultivated ornamental woody shrub/tree of the family Lythraceae that is used as a traditional medicinal plant in East Asia and Egypt. However, unlike other ornamental woody plants, its genome is not well-investigated, which hindered the discovery of the key genes that regulate important traits and the synthesis of bioactive compounds. RESULTS In this study, the genomic sequences of L. indica were determined using several next-generation sequencing technologies. Altogether, 324.01 Mb sequences were assembled and 98.21% (318.21 Mb) of them were placed in 24 pseudo-chromosomes. The heterozygosity, repeated sequences, and GC residues occupied 1.65%, 29.17%, and 38.64% of the genome, respectively. In addition, 28,811 protein-coding gene models, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs were identified. The intra- and interspecies synteny and Ks analysis revealed that L. indica exhibits a hexaploidy. The co-expression profiles of the genes involved in the phenylpropanoid (PA) and flavonoid/anthocyanin (ABGs) pathways with the R2R3 MYB genes (137 members) showed that ten R2R3 MYB genes positively regulate flavonoid/anthocyanin biosynthesis. The colors of flowers with white, purple (PB), and deep purplish pink (DPB) petals were found to be determined by the levels of delphinidin-based (Dp) derivatives. However, the substrate specificities of LiDFR and LiOMT probably resulted in the different compositions of flavonoid/anthocyanin. In L. indica, two LiTTG1s (LiTTG1-1 and LiTTG1-2) were found to be the homologs of AtTTG1 (WD40). LiTTG1-1 was found to repress anthocyanin biosynthesis using the tobacco transient transfection assay. CONCLUSIONS This study showed that the ancestor L. indica experienced genome triplication approximately 38.5 million years ago and that LiTTG1-1 represses anthocyanin biosynthesis. Furthermore, several genes such as LiDFR, LiOMTs, and R2R3 LiMYBs are related to anthocyanin biosynthesis. Further studies are required to clarify the mechanisms and alleles responsible for flower color development.
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Affiliation(s)
- Chunmei Yu
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Guoyuan Liu
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Jin Qin
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Xi Wan
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Anfang Guo
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Hui Wei
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Yanhong Chen
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Bolin Lian
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Fei Zhong
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Jian Zhang
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China.
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China.
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Li X, Luo X, Liu Z, Wang C, Lin A, Xiao K, Cao M, Fan J, Lian H, Xu P. FvDFR2 rather than FvDFR1 play key roles for anthocyanin synthesis in strawberry petioles. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111960. [PMID: 38103695 DOI: 10.1016/j.plantsci.2023.111960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
The accumulation of anthocyanins can be found in both the fruit and petioles of strawberries, but the fruit appears red while the petioles appear purple-red. Additionally, in the white-fruited diploid strawberries, the petioles can accumulate anthocyanins normally, suggesting a different synthesis pattern between the petioles and fruits. We screened the EMS mutagenized population of a red-fruited diploid strawberry 'Ruegen' and discovered a mutant which showed no anthocyanin accumulation in the petioles but normal accumulation in the fruit. Through BSA sequencing and allelic test, it was found that a mutation in FvDFR2 was responsible for this phenotype. Furthermore, the complex formed by the interaction between the petiole-specific FvMYB10L and FvTT8 only binds the promoter of FvDFR2 but not FvDFR1, resulting in the expression of only FvDFR2 in the petiole. FvDFR2 can catalyze the conversion of DHQ and eventually the formation of cyanidin and peonidin, giving the petiole a purplish-red color. In the fruit, however, both FvDFR1 and FvDFR2 can be expressed, which can mediate the synthesis of cyanidin and pelargonidin. Our study clearly reveals different regulation of FvDFR1 and FvDFR2 in mediating anthocyanin synthesis in petioles and fruits.
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Affiliation(s)
- Xinyu Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Luo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Chong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Anqi Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Kun Xiao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Minghao Cao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Department of Ecology, Lishui University, Lishui, China
| | - Junmiao Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongli Lian
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pengbo Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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Zhang F, Zeng T, Wu R. QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis. J Chem Inf Model 2023; 63:5018-5034. [PMID: 37556841 DOI: 10.1021/acs.jcim.3c00779] [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] [Indexed: 08/11/2023]
Abstract
Natural products and their derivatives are widely used across various industries, particularly pharmaceuticals. Modern engineered biosynthesis provides an alternative way of producing and meeting the growing need for diverse natural products. Natural enzymes, on the other hand, often exhibit unsatisfactory catalytic characteristics and necessitate further enzyme engineering modifications. QM/MM, as a powerful and extensively used computational tool in the field of enzyme catalysis, has been increasingly applied in rational enzyme engineering over the past decade. In this review, we summarize recent advances in QM/MM computational investigation on enzyme catalysis and enzyme engineering for natural product biosynthesis. The challenges and perspectives for future QM/MM applications aided enzyme engineering in natural product biosynthesis will also be discussed.
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Affiliation(s)
- Fan Zhang
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Tao Zeng
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
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Vainio J, Mattila S, Abdou SM, Sipari N, Teeri TH. Petunia dihydroflavonol 4-reductase is only a few amino acids away from producing orange pelargonidin-based anthocyanins. FRONTIERS IN PLANT SCIENCE 2023; 14:1227219. [PMID: 37645465 PMCID: PMC10461392 DOI: 10.3389/fpls.2023.1227219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Anthocyanins are responsible for the color spectrum of both ornamental and natural flowers. However, not all plant species produce all colors. For example, roses are not blue because they do not naturally possess a hydroxylase that opens the pathway for delphinidin and its derivatives. It is more intriguing why some plants do not carry orange or scarlet red flowers with anthocyanins based on pelargonidin, because the precursor for these anthocyanins should be available if anthocyanins are made at all. The key to this is the substrate specificity of dihydroflavonol 4-reductase (DFR), an enzyme located at the branch point between flavonols and anthocyanins. The most common example is petunia, which does not bear orange flowers unless the enzyme is complemented by biotechnology. We changed a few amino acids in the active site of the enzyme and showed that the mutated petunia DFR started to favor dihydrokaempferol, the precursor to orange pelargonidin, in vitro. When transferred to petunia, it produced an orange hue and dramatically more pelargonidin-based anthocyanins in the flowers.
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Affiliation(s)
- Jere Vainio
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Saku Mattila
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Sara M. Abdou
- Horticulture and Product Physiology Group, Wageningen University, Wageningen, Netherlands
| | - Nina Sipari
- Viikki Metabolomics Unit, University of Helsinki, Helsinki, Finland
| | - Teemu H. Teeri
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Viikki Metabolomics Unit, University of Helsinki, Helsinki, Finland
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Zheng H, Jiao J, Niu Q, Zhu N, Huang Y, Ke L, Tang S, Liu H, Sun Y. Cloning and functional analysis of GhDFR1, a key gene of flavonoid synthesis pathway in naturally colored cotton. Mol Biol Rep 2023; 50:4865-4873. [PMID: 37052804 DOI: 10.1007/s11033-023-08420-6] [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: 02/06/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND The naturally colored brown cotton fiber is the most widely used environmentally friendly textile material, which primarily contains proanthocyanidins and their derivatives. Many structural genes in the flavonoid synthesis pathway are known to improve the genetic resources of naturally colored cotton. Among them, DFR is a crucial late enzyme to synthesis both anthocyanins and proanthocyanidins in the plant flavonoid pathway. METHODS The protein sequences of GhDFRs were analyzed using bioinformatic tools. The expression levels of GhDFRs in various tissues and organs of upland cotton Zongxu1 (ZX1), were analyzed by quantitative real-time PCR, and the expression pattern of GhDFR1 during fiber development of white cotton and brown cotton was analyzed further. The function of GhDFR1 in NCC ZX1 was preliminarily analyzed by virus induced gene silencing (VIGS) technology. RESULTS Bioinformatic analysis revealed that GhDFRs sequences in upland cotton genome were extremely conserved. Furthermore, evolutionary tree analysis revealed that the functions of GhDFR1 and GhDFR2, and GhDFR3 and GhDFR4, presented different and shared some similarities. Our study showed GhDFR1 and GhDFR2 were specifically expressed in fibers, while GhDFR3 and GhDFR4 were specifically expressed in petals. GhDFR1 was exclusively expressed in brown cotton fiber at various stages of development and progressively increased with the growth of fiber, but the trend of expression in white cotton was quite the opposite. We silenced GhDFR1 expression in brown cotton fiber using VIGS technology, and observed the VIGS-interference plants. After reducing the expression level of GhDFR1, the period for significant GhDFR1 expression in the developing fibers changed, reducing the content of anthocyanins, and lightening the color of mature cotton fibers. CONCLUSION GhDFR1 was preferentially expressed in brown cotton during fiber development. The timing of GhDFR1 expression for flavonoid synthesis altered, resulting in anthocyanin contents reduced and the fiber color of the GhDFR1i lines lightened. These findings showed the role of GhDFR1 in fiber coloration of NCC and provided a new candidate for NCC genetic improvement.
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Affiliation(s)
- Hongli Zheng
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- College of Textile Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Junye Jiao
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Qingqing Niu
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Ning Zhu
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yinshuai Huang
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Liping Ke
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Shouwu Tang
- China Colored-Cotton (Group) Co., Ltd., Ürümqi, 830011, Xinjiang, People's Republic of China
| | - Haifeng Liu
- China Colored-Cotton (Group) Co., Ltd., Ürümqi, 830011, Xinjiang, People's Republic of China.
| | - Yuqiang Sun
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
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Mikulic-Petkovsek M, Ivancic A, Gacnik S, Veberic R, Hudina M, Marinovic S, Molitor C, Halbwirth H. Biochemical Characterization of Black and Green Mutant Elderberry during Fruit Ripening. PLANTS (BASEL, SWITZERLAND) 2023; 12:504. [PMID: 36771589 PMCID: PMC9918921 DOI: 10.3390/plants12030504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/22/2022] [Accepted: 01/16/2023] [Indexed: 05/22/2023]
Abstract
The content of sugars, organic acids, phenolic compounds and selected enzyme activities in the anthocyanin pathway were analyzed in NIGRA (Sambucus nigra var. nigra-black fruits) and VIRIDIS (S. nigra var. viridis-green fruits) fruits over four stages of ripening. The share of glucose and fructose in green fruits was higher than in colored fruits, and the sugar content increased significantly until the third developmental stage. Ripe NIGRA berries had 47% flavonol glycosides, 34% anthocyanins, 3% hydroxycinnamic acids and 14% flavanols, whereas the major phenolic group in the VIRIDIS fruits, making up 88% of the total analyzed polyphenols, was flavonols. NIGRA fruits were rich in anthocyanins (6020 µg g-1 FW), showing strong activation of the late anthocyanin pathway (dihydroflavonol 4-reductase, anthocyanidin synthase). In both color types, phenylalanine ammonia lyase and chalcone synthase/chalcone isomerase activities were highest in the first stage and decreased during ripening. In VIRIDIS fruit, no anthocyanins and only one flavanol (procyanidin dimer) were found. This was most likely caused by a lack of induction of the late anthocyanin pathway in the last period of fruit ripening. The VIRIDIS genotype may be useful in studying the regulatory structures of anthocyanin biosynthesis and the contribution of distinct flavonoid classes to the health benefits of elderberries.
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Affiliation(s)
- Maja Mikulic-Petkovsek
- Chair for Fruit Growing, Viticulture and Vegetable Growing, Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Anton Ivancic
- 2 Chair for Genetics, Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, SI-2311 Hoce, Slovenia
| | - Sasa Gacnik
- Chair for Fruit Growing, Viticulture and Vegetable Growing, Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Robert Veberic
- Chair for Fruit Growing, Viticulture and Vegetable Growing, Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Metka Hudina
- Chair for Fruit Growing, Viticulture and Vegetable Growing, Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Silvija Marinovic
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Getreidemarkt 9, A-1060 Vienna, Austria
| | - Christian Molitor
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Getreidemarkt 9, A-1060 Vienna, Austria
| | - Heidi Halbwirth
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Getreidemarkt 9, A-1060 Vienna, Austria
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Aiguo Z, Ruiwen D, Cheng W, Cheng C, Dongmei W. Insights into the catalytic and regulatory mechanisms of dihydroflavonol 4-reductase, a key enzyme of anthocyanin synthesis in Zanthoxylum bungeanum. TREE PHYSIOLOGY 2023; 43:169-184. [PMID: 36054375 DOI: 10.1093/treephys/tpac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Accumulation of anthocyanins largely determines the fruit color, and dihydroflavonol 4-reductase (DFR) is a key enzyme involved in the formation of anthocyanins. However, the catalytic and regulatory mechanisms of DFR are unclear. In this study, the gene encoding DFR from Zanthoxylum bungeanum Maxim. was cloned and ZbDFR was analyzed in detail. The ZbDFR accepted dihydrokaempferol, dihydroquercetin and dihydromyricetin as substrates. Flavonols such as myricetin, quercetin and kaempferol significantly inhibited the activity of ZbDFR, while quercitrin and isoquercitrin slightly increased the activity. Quercetin was a competitive inhibitor at low concentrations, and it had a combined effect of competitive and noncompetitive inhibition at high concentrations, which was consistent with ZbDFR having two inhibitor binding sites. In addition, the content of different types of flavonoids in Z. bungeanum peel at green, semi-red and red stage was analyzed, and the in vivo results could be explained by the regulation of ZbDFR activity in vitro. Site-directed mutagenesis combined with enzyme activity experiments showed that Ser128, Tyr163, Phe164 and Lys167 are the key catalytic amino acid residues. The Ser128, Tyr163 and Lys167 were crucial for the hydrogen transfer reaction, and mutation of these amino acids resulted in the loss of all or most of the activity. Phe164 was found to be important for the regulation of ZbDFR by flavonols. Accordingly, ZbDFR is a node at which flavonoids regulate the synthesis of anthocyanins and proanthocyanins.
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Affiliation(s)
- Zhao Aiguo
- College of Forestry, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
- Key Laboratory of Exploitation and Utilization of Economic Plant Resources in Shaanxi Province, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Ding Ruiwen
- College of Forestry, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Wang Cheng
- College of Forestry, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
- Key Laboratory of Exploitation and Utilization of Economic Plant Resources in Shaanxi Province, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Chen Cheng
- College of Forestry, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
- Key Laboratory of Exploitation and Utilization of Economic Plant Resources in Shaanxi Province, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Wang Dongmei
- College of Forestry, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
- Key Laboratory of Exploitation and Utilization of Economic Plant Resources in Shaanxi Province, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
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Yu T, Han G, Luan Z, Zhu C, Zhao J, Sheng Y. Functional Analysis of Genes GlaDFR1 and GlaDFR2 Encoding Dihydroflavonol 4-Reductase (DFR) in Gentiana lutea L. Var. Aurantiaca (M. Laínz) M. Laínz. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1382604. [PMID: 35047628 PMCID: PMC8763498 DOI: 10.1155/2022/1382604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/17/2021] [Indexed: 11/29/2022]
Abstract
Anthocyanins are important pigments for flower color, determining the ornamental and economic values of horticultural plants. As a key enzyme in the biosynthesis of anthocyanidins, dihydroflavonol 4-reductase (DFR) catalyzes the reduction of dihydroflavonols to generate the precursors for anthocyanidins (i.e., leucoanthocyanidins) and anthocyanins. To investigate the functions of DFRs in plants, we cloned the GlaDFR1 and GlaDFR2 genes from the petals of Gentiana lutea var. aurantiaca and transformed both genes into Nicotiana tabacum by Agrobacterium-mediated leaf disc method. We further investigated the molecular and phenotypic characteristics of T1 generation transgenic tobacco plants selected based on the hygromycin resistance and verified by both PCR and semiquantitative real-time PCR analyses. The phenotypic segregation was observed in the flower color of the transgenic tobacco plants, showing petals darker than those in the wild-type (WT) plants. Results of high-performance liquid chromatography (HPLC) analysis showed that the contents of gentiocyanin derivatives were decreased in the petals of transgenic plants in comparison to those of WT plants. Ours results revealed the molecular functions of GlaDFR1 and GlaDFR2 in the formation of coloration, providing solid theoretical foundation and candidate genes for further genetic improvement in flower color of plants.
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Affiliation(s)
- Tingting Yu
- School of Life Sciences, Changchun Normal University, Changchun 130031, China
| | - Guojun Han
- School of Life Sciences, Changchun Normal University, Changchun 130031, China
| | - Zhihui Luan
- School of Life Sciences, Changchun Normal University, Changchun 130031, China
| | - Changfu Zhu
- School of Life Sciences, Changchun Normal University, Changchun 130031, China
| | - Jinghua Zhao
- School of Life Sciences, Changchun Normal University, Changchun 130031, China
| | - Yanmin Sheng
- School of Life Sciences, Changchun Normal University, Changchun 130031, China
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Diharce J, Bignon E, Fiorucci S, Antonczak S. Exploring Dihydroflavonol-4-Reductase Reactivity and Selectivity by QM/MM-MD Simulations. Chembiochem 2021; 23:e202100553. [PMID: 34859558 DOI: 10.1002/cbic.202100553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Flavonoids are secondary metabolites ubiquitously found in plants. Their antioxidant properties make them highly interesting natural compounds for use in pharmacology. Therefore, unravelling the mechanisms of flavonoid biosynthesis is an important challenge. Among all the enzymes involved in this biosynthetic pathway, dihydroflavonol-4-reductase (DFR) plays a key role in the production of anthocyanins and proanthocyanidins. Here, we provide new information on the mechanism of action of this enzyme by using QM/MM-MD simulations applied to both dihydroquercetin (DHQ) and dihydrokaempferol (DHK) substrates. The consideration of these very similar compounds shed light on the major role played by the enzyme on the stabilization of the transition state but also on the activation of the substrate before the reaction through near-attack conformer effects.
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Affiliation(s)
- Julien Diharce
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France.,Université de Paris, INSERM, Biologie Intégrée du Globule Rouge, UMR_S1134, 75015, Paris, France.,Laboratoire d'Excellence GR-Ex, 75015, Paris, France
| | - Emmanuelle Bignon
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Serge Antonczak
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
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10
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Zhang F, Ma Z, Qiao Y, Wang Z, Chen W, Zheng S, Yu C, Song L, Lou H, Wu J. Transcriptome sequencing and metabolomics analyses provide insights into the flavonoid biosynthesis in Torreya grandis kernels. Food Chem 2021; 374:131558. [PMID: 34794838 DOI: 10.1016/j.foodchem.2021.131558] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/12/2022]
Abstract
The kernel of Torreya grandis (T. grandis) is a rare nut with a variety of bioactive compounds. Flavonoids are a very important class of bioactive compounds with high antioxidant activity in T. grandis kernels. However, the flavonoid compositions which mainly contribute to antioxidant capacity and the molecular basis of flavonoid biosynthesis in T. grandis remain unclear. Here, transcriptome sequencing and metabolomics analysis for kernels were performed. In total, 124 flavonoids were identified. Among them, 9 flavonoids were highly correlated with antioxidant activity. Furthermore, unigenes encoding CHS, DFR and ANS showed significant correlation with the 9 flavonoids. Transient overexpression of TgDFR1 in tobacco leaves resulted in increased antioxidant activity. Moreover, several transcription factors from MYB, bHLH and bZIP families were identified by co-expression assay, suggesting that they may regulate flavonoid biosynthesis. Our findings provide a molecular basis and new insights into the flavonoid biosynthesis in T. grandis kernels.
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Affiliation(s)
- Feicui Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Zhenmin Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Yan Qiao
- College of Agriculture and Forestry, Longdong University, Qingyang 745000, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Chenliang Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
| | - Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
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11
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Wen CH, Tsao NW, Wang SY, Chu FH. Color variation in young and senescent leaves of Formosan sweet gum (Liquidambar formosana) by the gene regulation of anthocyanidin biosynthesis. PHYSIOLOGIA PLANTARUM 2021; 172:1750-1763. [PMID: 33675234 DOI: 10.1111/ppl.13385] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/30/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
In certain plants, leaf coloration occurs in young and senescent leaves; however, it is unclear whether these two developmental stages are controlled by the same regulatory mechanisms. Formosan sweet gum (Liquidambar formosana Hance) is a subtropical deciduous tree species that possesses attractive autumnal leaf coloration. The color of young leaves is closer to purplish red, while senescent leaves are more orange-red to dark red. It was confirmed that delphinidin and cyanidin are the two anthocyanidins that contribute to the color of Formosan sweet gum leaves, and the content of different anthocyanins influences the appearance of color. To elucidate the regulation of anthocyanidin biosynthesis, recombinant DIHYDROFLAVONOL-4-REDUCTASEs (LfDFR1 and LfDFR2) (EC 1.1.1.234) were produced, and their substrate acceptability was investigated both in vitro and in planta. The functions of flavanones and dihydroflavonols modification by FLAVONOID 3' HYDROXYLASE (LfF3'H1) (EC 1.14.14.82) and FLAVONOID 3'5' HYDROXYLASE (LfF3'5'H) (EC 1.14.14.81) were verified using a transient overexpression experiment in Nicotiana benthamiana. The results showed that LfMYB5 induced LfF3'5'H and LfMYB123 induced both LfF3'H1 and LfDFR1 in spring when the leaves were expanding, whereas LfMYB113 induced LfF3'H1, LfDFR1, and LfDFR2 in late autumn to winter when the leaves were undergoing leaf senescence. In conclusion, the color variation of Formosan sweet gum in young and senescent leaves was attributed to the composition of anthocyanidins through the transcriptional regulation of LfF3'H1 and LfF3'5'H by LfMYB5, LfMYB113, and LfMYB123.
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Affiliation(s)
- Chi-Hsiang Wen
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Nai-Wen Tsao
- Department of Forestry, National Chung-Hsing University, Taichung, Taiwan
| | - Sheng-Yang Wang
- Department of Forestry, National Chung-Hsing University, Taichung, Taiwan
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
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12
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Qi Y, Wei H, Gu W, Shi W, Jiang L, Deng L, Liu X. Transcriptome profiling provides insights into the fruit color development of wild Lycium ruthenicum Murr. from Qinghai-Tibet Plateau. PROTOPLASMA 2021; 258:33-43. [PMID: 32886216 DOI: 10.1007/s00709-020-01542-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Lycium ruthenicum Murr. is an important ecological and economic species in the Qaidam Basin of Qinghai-Tibet Plateau. Its black fruits (BF) are rich in anthocyanins, which have health-promoting properties for humans and thus provide nutritional benefits for this plant. Although the fruit quality of natural white fruit (WF) is affected by the disappearance of pigmentation in phenotypes, this phenomenon provides an opportunity to unravel the complex color metabolic networks. In this study, anthocyanin profiling confirmed that WF was formed due to anthocyanin loss. Transcriptome analysis of BF and WF revealed 101,466 unigenes, 261 of which were identified as the putative homologs of color-related genes in other species. Genes encoding the enzymes involved in flavonoid biosynthesis were also identified systematically. The structural gene expression levels of chalcone synthase (CHS), chalcone isomerase (CHI), flavonoid 3'5'-hydroxylase (F3'5'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and anthocyanidin 3-O-glucosyltransferase (UFGT) were highly similar and significantly positively correlated with anthocyanin accumulation rate in BF. In particular, F3'5'H, UFGT, ANS, and DFR expression levels in BF were 2391, 119, 96, and 85 times higher than those in WF at S3 (35 days after anthesis), respectively. This result strongly suggests that the low expression of these genes in WF is responsible for the anthocyanin loss. Meanwhile, the expression patterns of the anthocyanin regulatory genes were also investigated by qRT-PCR. Mass sequencing data were obtained and annotated by deep sequencing and provided a platform for future function and molecular biological research on L. ruthenicum Murr.
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Affiliation(s)
- Yinyan Qi
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xining, 810016, Qinghai, China
| | - Haibin Wei
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xining, 810016, Qinghai, China
| | - Wenyi Gu
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xining, 810016, Qinghai, China
| | - Wenjun Shi
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xining, 810016, Qinghai, China
| | - Liling Jiang
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
| | - Lei Deng
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xining, 810016, Qinghai, China
| | - Xiaoli Liu
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China.
- Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xining, 810016, Qinghai, China.
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13
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Zhou Z, Ying Z, Wu Z, Yang Y, Fu S, Xu W, Yao L, Zeng A, Huang J, Lan S, Wang X, Liu Z. Anthocyanin Genes Involved in the Flower Coloration Mechanisms of Cymbidium kanran. FRONTIERS IN PLANT SCIENCE 2021; 12:737815. [PMID: 34712257 PMCID: PMC8545884 DOI: 10.3389/fpls.2021.737815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/07/2021] [Indexed: 05/13/2023]
Abstract
The Orchidaceae, otherwise known as orchids, is one of the largest plant families and is renowned for its spectacular flowers and ecological adaptations. Various polymorphisms of orchid flower colour can attract pollinators and be recognised as valuable horticultural ornamentals. As one of the longest historic cultured orchids, Cymbidium kanran has been domesticated for more than 2,500 years and is an ideal species to study coloration mechanisms because of plentiful variations in floral coloration and abundant traditional varieties. In this study, we used two distinct colour-type flowers of C. kanran as experimental materials to elucidate the mechanism of flower coloration. High-performance liquid chromatography (HPLC) analysis revealed that anthocyanins in purple-red-type flowers include three types of anthocyanidin aglycones, peonidin, malvidin, and cyanidin, whereas anthocyanins are lacking in white-type flowers. Through comparative transcriptome sequencing, 102 candidate genes were identified as putative homologues of colour-related genes. Based on comprehensive correlation analysis between colour-related compounds and gene expression profiles, four candidates from 102 captured genes showed a positive correlation with anthocyanidin biosynthesis. Furthermore, transient expression of CkCHS-1, CkDFR, and CkANS by particle bombardment confirmed that recovery of their expression completed the anthocyanin pathway and produced anthocyanin compounds in white-type flowers. Collectively, this study provided a comprehensive transcriptomic dataset for Cymbidium, which significantly facilitate our understanding of the molecular mechanisms of regulating floral pigment accumulation in orchids.
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Affiliation(s)
- Zhuang Zhou
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Zhen Ying
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Zhigang Wu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Yanping Yang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Shuangbin Fu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Wan Xu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Lijuan Yao
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Aiping Zeng
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Jian Huang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaole Wang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
- *Correspondence: Xiaole Wang
| | - Zhongjian Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
- Zhongjian Liu
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14
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Castillejo C, Waurich V, Wagner H, Ramos R, Oiza N, Muñoz P, Triviño JC, Caruana J, Liu Z, Cobo N, Hardigan MA, Knapp SJ, Vallarino JG, Osorio S, Martín-Pizarro C, Posé D, Toivainen T, Hytönen T, Oh Y, Barbey CR, Whitaker VM, Lee S, Olbricht K, Sánchez-Sevilla JF, Amaya I. Allelic Variation of MYB10 Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry ( Fragaria spp.) Fruit. THE PLANT CELL 2020; 32:3723-3749. [PMID: 33004617 PMCID: PMC7721342 DOI: 10.1105/tpc.20.00474] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/13/2020] [Accepted: 09/25/2020] [Indexed: 05/02/2023]
Abstract
The fruits of diploid and octoploid strawberry (Fragaria spp) show substantial natural variation in color due to distinct anthocyanin accumulation and distribution patterns. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 is the main activator in strawberry fruit. Here, we show that mutations in MYB10 cause most of the variation in anthocyanin accumulation and distribution observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F ×ananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function mutations in MYB10 were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses of octoploid Fragaria spp revealed that FaMYB10-2, one of three MYB10 homoeologs identified, regulates anthocyanin biosynthesis in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression. Our findings suggest that cis-regulatory elements in FaEnSpm-2 are responsible for enhanced MYB10-2 expression and anthocyanin biosynthesis in strawberry fruit flesh.
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Affiliation(s)
- Cristina Castillejo
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Veronika Waurich
- Hansabred GmbH & Co. KG, 01108 Dresden, Germany
- Institut für Botanik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Henning Wagner
- Hansabred GmbH & Co. KG, 01108 Dresden, Germany
- Institut für Botanik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Rubén Ramos
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Nicolás Oiza
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Pilar Muñoz
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | | | - Julie Caruana
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Nicolás Cobo
- Department of Plant Sciences, University of California, Davis, California 95616
- Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco 01145, Chile
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, California 95616
| | - José G Vallarino
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Sonia Osorio
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Carmen Martín-Pizarro
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - David Posé
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos 29071, Málaga, Spain
| | - Tuomas Toivainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00790, Finland
- National Institute of Agricultural Botany East Malling Research (NIAB EMR), Kent ME19 6BJ, United Kingdom
| | - Youngjae Oh
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Christopher R Barbey
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Vance M Whitaker
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Seonghee Lee
- Department of Horticultural Sciences, University of Florida, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | | | - José F Sánchez-Sevilla
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
| | - Iraida Amaya
- Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Málaga, 29140 Málaga, Spain
- Unidad Asociada de I + D + i IFAPA-Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IFAPA-IHSM) Biotecnología y Mejora en Fresa, Málaga 29071, Spain
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15
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Pott DM, Vallarino JG, Cruz-Rus E, Willmitzer L, Sánchez-Sevilla JF, Amaya I, Osorio S. Genetic analysis of phenylpropanoids and antioxidant capacity in strawberry fruit reveals mQTL hotspots and candidate genes. Sci Rep 2020; 10:20197. [PMID: 33214566 PMCID: PMC7677386 DOI: 10.1038/s41598-020-76946-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022] Open
Abstract
Phenylpropanoids are a large class of plant secondary metabolites, which play essential roles in human health mainly associated with their antioxidant activity. Strawberry (Fragaria × ananassa) is a rich source of phytonutrients, including phenylpropanoids, which have been shown to have beneficial effects on human health. In this study, using the F. × ananassa '232' × '1392' F1 segregating population, we analyzed the genetic control of individual phenylpropanoid metabolites, total polyphenol content (TPC) and antioxidant capacity (TEAC) in strawberry fruit over two seasons. We have identified a total of 7, 9, and 309 quantitative trait loci (QTL) for TPC, TEAC and for 77 polar secondary metabolites, respectively. Hotspots of stable QTL for health-related antioxidant compounds were detected on linkage groups LG IV-3, LG V-2 and V-4, and LG VI-1 and VI-2, where associated markers represent useful targets for marker-assisted selection of new varieties with increased levels of antioxidant secondary compounds. Moreover, differential expression of candidate genes for major and stable mQTLs was studied in fruits of contrasting lines in important flavonoids. Our results indicate that higher expression of FaF3'H, which encodes the flavonoid 3'-hydroxylase, is associated with increased content of these important flavonoids.
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Affiliation(s)
- Delphine M Pott
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain.,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
| | - José G Vallarino
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain.,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
| | - Eduardo Cruz-Rus
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain
| | - Lothar Willmitzer
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - José F Sánchez-Sevilla
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain
| | - Iraida Amaya
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain. .,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain.
| | - Sonia Osorio
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain. .,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.
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16
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Singh G, Singh V, Singh V. Genome-wide interologous interactome map (TeaGPIN) of Camellia sinensis. Genomics 2020; 113:553-564. [PMID: 33002625 DOI: 10.1016/j.ygeno.2020.09.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/15/2020] [Accepted: 09/22/2020] [Indexed: 11/27/2022]
Abstract
Tea, prepared from the young leaves of Camellia sinensis, is a non-alcoholic beverage globally consumed due to its antioxidant properties, strong taste and aroma. Although, the genomic data of this medicinally and commercially important plant is available, studies related to its sub-cellular interactomic maps are less explored. In this work, we propose a genome-wide interologous protein-protein interaction (PPI) network of tea, termed as TeaGPIN, consisting of 12,033 nodes and 216,107 interactions, developed using draft genome of tea and known PPIs exhaustively collected from 49 template plants. TeaGPIN interactions are prioritized using domain-domain interactions along with the interolog information. A high-confidence TeaGPIN consisting of 5983 nodes and 58,867 edges is reported and its interactions are further evaluated using protein co-localization similarities. Based on three network centralities (degree, betweenness and eigenvector), 1302 key proteins are reported in tea to have p-value <0.01 by comparing the TeaGPIN with 10,000 realizations of Erdős-Rényi and Barabási-Albert based corresponding random network models. Functional content of TeaGPIN is assessed using KEGG and GO annotations and its modular architecture is explored. Network based characterization is carried-out on the transcription factors, and proteins involved flavonoid biosynthesis and photosynthesis pathways to find novel candidates involved in various regulatory processes. We believe the proposed TeaGPIN will impart useful insights in understanding various mechanisms related to growth and development as well as defence against biotic and abiotic perturbations.
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Affiliation(s)
- Gagandeep Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India.
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17
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Pucker B, Reiher F, Schilbert HM. Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1103. [PMID: 32867203 PMCID: PMC7570183 DOI: 10.3390/plants9091103] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/11/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
The flavonoid biosynthesis is a well-characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions such as UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. Comprehensive sequence sets of flavonoid biosynthesis enzymes and knowledge about functionally relevant amino acids were collected. As a proof of concept, KIPEs was applied to investigate the flavonoid biosynthesis of the medicinal plant Croton tiglium on the basis of a transcriptome assembly. Enzyme candidates for all steps in the biosynthesis network were identified and matched to previous reports of corresponding metabolites in Croton species.
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Affiliation(s)
- Boas Pucker
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
- Department of Plant Sciences, Evolution and Diversity, University of Cambridge, Cambridge CB2 3EA, UK
| | - Franziska Reiher
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
| | - Hanna Marie Schilbert
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany; (B.P.); (F.R.)
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18
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Chen X, Liu W, Huang X, Fu H, Wang Q, Wang Y, Cao J. Arg-type dihydroflavonol 4-reductase genes from the fern Dryopteris erythrosora play important roles in the biosynthesis of anthocyanins. PLoS One 2020; 15:e0232090. [PMID: 32357153 PMCID: PMC7194404 DOI: 10.1371/journal.pone.0232090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022] Open
Abstract
Dihydroflavonol 4-reductase (DFR), a key enzyme involved in the biosynthesis of anthocyanins, has been cloned from various species. However, little research has been conducted on this enzyme in ferns, which occupy a unique evolutionary position. In this study, we isolated two novel DFR genes from the fern Dryopteris erythrosora. In vitro enzymatic analysis revealed that DeDFR1 and DeDFR2 enzymes can catalyze dihydrokaempferol and dihydroquercetin but cannot catalyze dihydromyricetin. Amino acid sequence analysis showed that DeDFR1 and DeDFR2 have an arginine at the same substrate-specificity-determining site as that in the ferns Salvinia cucullata and Azolla filiculoides. Thus, we speculate that the Arg-type DFR is a new DFR functional type. To further verify the substrate preferences of the Arg-type DFR, an amino acid substitution assay was conducted. When N133 was mutated to R133, Arabidopsis DFR protein completely lost its catalytic activity for dihydromyricetin, as observed for DeDFR1 and DeDFR2. Additionally, heterologous expression of DeDFR2 in the Arabidopsis tt3-1 mutant resulted in increasing anthocyanin accumulation. In summary, DeDFR1 and DeDFR2 are considered to be a new type of DFR with unique structures and functions. The discovery of the Arg-type DFR provides new insights into the anthocyanin biosynthesis pathway in ferns.
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Affiliation(s)
- Xuefei Chen
- College of Life Science, East China Normal University, Shanghai, China
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Wenli Liu
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Xianyan Huang
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Huanhuan Fu
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Quanxi Wang
- College of Life Science, Shanghai Normal University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resource, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Youfang Wang
- College of Life Science, East China Normal University, Shanghai, China
| | - Jianguo Cao
- College of Life Science, Shanghai Normal University, Shanghai, China
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19
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Mei X, Zhou C, Zhang W, Rothenberg DO, Wan S, Zhang L. Comprehensive analysis of putative dihydroflavonol 4-reductase gene family in tea plant. PLoS One 2019; 14:e0227225. [PMID: 31877197 PMCID: PMC6932780 DOI: 10.1371/journal.pone.0227225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/13/2019] [Indexed: 11/19/2022] Open
Abstract
One identified dihydroflavonol 4-reductases (DFR) encoding gene (named as CsDFRa herein) and five putative DFRs (named as CsDFRb1, CsDFRb2, CsDFRb3, CsDFRc and CsDFRd) in tea (Camellia sinensis) have been widely discussed in recent papers concerning multi-omics data. However, except for CsDFRa, their function and biochemical characteristics are not clear. This study aims to compare all putative CsDFRs and preliminarily evaluate their function. We investigated the sequences of genes (coding and promoter regions) and predicted structures of proteins encoded, and determined the activities of heterologously expressed CsDFRs under various conditions. The results showed that the sequences of five putative CsDFRs were quite different from CsDFRa, and had lower expression levels as well. The five putative CsDFRs could not catalyze three dihydroflavonol substrates. The functional CsDFRa had the strongest affinity with dihydroquercetin, and performed best at pH around 7 and 35°C but was not stable at lower pHs or higher temperatures. Single amino acid mutation at position 141 modified the preference of CsDFRa for dihydroquercetin and dihydromyricetin, and also weakened its stability. These data suggest that only CsDFRa works in the pathway for generating anthocyanidins and catechins. This study provides new insights into the function of CsDFRs and may assist to develop new strategies to manipulate the composition of tea flavonoids in the future.
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Affiliation(s)
- Xin Mei
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Caibi Zhou
- College of Horticulture Science, South China Agricultural University, Guangzhou, Guangdong, China
- Department of Tea Science, Qiannan Normal University for Nationalities, Duyun, Guizhou, China
| | - Wenting Zhang
- College of Horticulture Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Dylan O’Neill Rothenberg
- College of Horticulture Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shihua Wan
- College of Horticulture Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lingyun Zhang
- College of Horticulture Science, South China Agricultural University, Guangzhou, Guangdong, China
- * E-mail:
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20
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Cloning and Functional Characterization of Dihydroflavonol 4-Reductase Gene Involved in Anthocyanidin Biosynthesis of Grape Hyacinth. Int J Mol Sci 2019; 20:ijms20194743. [PMID: 31554290 PMCID: PMC6801978 DOI: 10.3390/ijms20194743] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 11/21/2022] Open
Abstract
Grape hyacinth (Muscari spp.) is a popular ornamental plant with bulbous flowers noted for their rich blue color. Muscari species have been thought to accumulate delphinidin and cyanidin rather than pelargonidin-type anthocyanins because their dihydroflavonol 4-reductase (DFR) does not efficiently reduce dihydrokaempferol. In our study, we clone a novel DFR gene from blue flowers of Muscari. aucheri. Quantitative real-time PCR (qRT-PCR) and anthocyanin analysis showed that the expression pattern of MaDFR had strong correlations with the accumulation of delphinidin, relatively weak correlations with cyanidin, and no correations with pelargonidin. However, in vitro enzymatic analysis revealed that the MaDFR enzyme can reduce all the three types of dihydroflavonols (dihydrokaempferol, dihydroquercetin, and dihydromyricetin), although it most preferred dihydromyricetin as a substrate to produce leucodelphinidin, the precursor of blue-hued delphinidin. This indicated that there may be other functional genes responsible for the loss of red pelargonidin-based pigments in Muscari. To further verify the substrate-specific selection domains of MaDFR, an assay of amino acid substitutions was conducted. The activity of MaDFR was not affected whenever the N135 or E146 site was mutated. However, when both of them were mutated, the catalytic activity of MaDFR was lost completely. The results suggest that both the N135 and E146 sites are essential for the activity of MaDFR. Additionally, the heterologous expression of MaDFR in tobacco (Nicotiana tabacum) resulted in increasing anthocyanin accumulation, leading to a darker flower color, which suggested that MaDFR was involved in color development in flowers. In summary, MaDFR has a high preference for dihydromyricetin, and it could be a powerful candidate gene for genetic engineering for blue flower colour modification. Our results also make a valuable contribution to understanding the basis of color variation in the genus Muscari.
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21
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Transcriptional regulation of abscisic acid biosynthesis and signal transduction, and anthocyanin biosynthesis in 'Bluecrop' highbush blueberry fruit during ripening. PLoS One 2019; 14:e0220015. [PMID: 31318958 PMCID: PMC6638965 DOI: 10.1371/journal.pone.0220015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/05/2019] [Indexed: 11/19/2022] Open
Abstract
Highbush blueberry (Vaccinium corymbosum) fruit accumulate high levels of anthocyanins during ripening, which might be controlled by abscisic acid (ABA), a signal molecule in non-climacteric fruits. For an integrated view of the ripening process from ABA to anthocyanin biosynthesis, we analyzed the transcriptomes of ‘Bluecrop’ highbush blueberry fruit using RNA-Seq at three ripening stages, categorized based on fruit skin coloration: pale green at ca. 30 days after full bloom (DAFB), reddish purple at ca. 40 DAFB, and dark purple at ca. 50 DAFB. Mapping the trimmed reads against the reference sequences yielded 25,766 transcripts. Of these, 143 transcripts were annotated to encode five ABA biosynthesis enzymes, four ABA signal transduction regulators, four ABA-responsive transcription factors, and 12 anthocyanin biosynthesis enzymes. The analysis of differentially expressed genes between the ripening stages revealed that 11 transcripts, including those encoding nine-cis-epoxycarotenoid dioxygenase, SQUAMOSA-class MADS box transcription factor, and flavonoid 3′,5′-hydroxylase, were significantly up-regulated throughout the entire ripening stages. In fruit treated with 1 g L−1 ABA, at least nine transcripts of these 11 transcripts as well as one transcript encoding flavonoid 3′-hydroxylase were up-regulated, presumably promoting anthocyanin accumulation and fruit skin coloration. These results will provide fundamental information demonstrating that ABA biosynthesis and signal transduction, and anthocyanin biosynthesis are closely associated with anthocyanin accumulation and skin coloration in highbush blueberry fruit during ripening.
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Biochemical and Functional Characterization of Anthocyanidin Reductase (ANR) from Mangifera indica L. Molecules 2018; 23:molecules23112876. [PMID: 30400564 PMCID: PMC6278290 DOI: 10.3390/molecules23112876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/27/2018] [Accepted: 10/30/2018] [Indexed: 11/20/2022] Open
Abstract
Mango (Mangifera indica L.) is abundant in proanthocyanidins (PAs) that are important for human health and plant response to abiotic stresses. However, the molecular mechanisms involved in PA biosynthesis still need to be elucidated. Anthocyanidin reductase (ANR) catalyzes a key step in PA biosynthesis. In this study, three ANR cDNAs (MiANR1-1,1-2,1-3) were isolated from mango, and expressed in Escherichia coli. In vitro enzyme assay showed MiANR proteins convert cyanidin to their corresponding flavan-3-ols, such as (−)-catechin and (−)-epicatechin. Despite high amino acid similarity, the recombinant ANR proteins exhibited differences in enzyme kinetics and cosubstrate preference. MiANR1-2 and MiANR1-3 have the same optimum pH of 4.0 in citrate buffer, while the optimum pH for MiANR1-1 is pH 3.0 in phosphate buffer. MiANR1-1 does not use either NADPH or NADH as co-substrate while MiANR1-2/1-3 use only NADPH as co-substrate. MiANR1-2 has the highest Km and Vmax for cyanidin, followed by MiANR1-3 and MiANR1-1. The overexpression of MiANRs in ban mutant reconstructed the biosynthetic pathway of PAs in the seed coat. These data demonstrate MiANRs can form the ANR pathway, leading to the formation of two types of isomeric flavan-3-ols and PAs in mango.
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Nitarska D, Stefanini C, Haselmair-Gosch C, Miosic S, Walliser B, Mikulic-Petkovsek M, Regos I, Slatnar A, Debener T, Terefe-Ayana D, Vilperte V, Hadersdorfer J, Stich K, Halbwirth H. The rare orange-red colored Euphorbia pulcherrima cultivar 'Harvest Orange' shows a nonsense mutation in a flavonoid 3'-hydroxylase allele expressed in the bracts. BMC PLANT BIOLOGY 2018; 18:216. [PMID: 30285622 PMCID: PMC6171185 DOI: 10.1186/s12870-018-1424-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 09/13/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND Commercially available poinsettia (Euphorbia pulcherrima) varieties prevalently accumulate cyanidin derivatives and show intense red coloration. Orange-red bract color is less common. We investigated four cultivars displaying four different red hues with respect to selected enzymes and genes of the anthocyanin pathway, putatively determining the color hue. RESULTS Red hues correlated with anthocyanin composition and concentration and showed common dark red coloration in cultivars 'Christmas Beauty' and 'Christmas Feeling' where cyanidin derivatives were prevalent. In contrast, orange-red bract color is based on the prevalent presence of pelargonidin derivatives that comprised 85% of the total anthocyanin content in cv. 'Premium Red' and 96% in cv. 'Harvest Orange' (synonym: 'Orange Spice'). cDNA clones of flavonoid 3'-hydroxylase (F3'H) and dihydroflavonol 4-reductase (DFR) were isolated from the four varieties, and functional activity and substrate specificity of the corresponding recombinant enzymes were studied. Kinetic studies demonstrated that poinsettia DFRs prefer dihydromyricetin and dihydroquercetin over dihydrokaempferol, and thus, favor the formation of cyanidin over pelargonidin. Whereas the F3'H cDNA clones of cultivars 'Christmas Beauty', 'Christmas Feeling', and 'Premium Red' encoded functionally active enzymes, the F3'H cDNA clone of cv. 'Harvest Orange' contained an insertion of 28 bases, which is partly a duplication of 20 bases found close to the insertion site. This causes a frameshift mutation with a premature stop codon after nucleotide 132 and, therefore, a non-functional enzyme. Heterozygosity of the F3'H was demonstrated in this cultivar, but only the mutated allele was expressed in the bracts. No correlation between F3'H-expression and the color hue could be observed in the four species. CONCLUSIONS Rare orange-red poinsettia hues caused by pelargonidin based anthocyanins can be achieved by different mechanisms. F3'H is a critical step in the establishment of orange red poinsettia color. Although poinsettia DFR shows a low substrate specificity for dihydrokaempferol, sufficient precursor for pelargonidin formation is available in planta, in the absence of F3'H activity.
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Affiliation(s)
- Daria Nitarska
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
| | - Carmen Stefanini
- Fruit Science, Technical University of Munich, 85354 Freising, Germany
| | - Christian Haselmair-Gosch
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
| | - Silvija Miosic
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
| | - Benjamin Walliser
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
| | - Maja Mikulic-Petkovsek
- Agronomy Department, Fruit, Wine and Vegetable Growing, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ionela Regos
- Fruit Science, Technical University of Munich, 85354 Freising, Germany
| | - Ana Slatnar
- Agronomy Department, Fruit, Wine and Vegetable Growing, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Diro Terefe-Ayana
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Vinicius Vilperte
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | | | - Karl Stich
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
| | - Heidi Halbwirth
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
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24
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Chen Q, Liu X, Hu Y, Sun B, Hu Y, Wang X, Tang H, Wang Y. Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus. Int J Genomics 2018; 2018:8084032. [PMID: 29805970 PMCID: PMC5901860 DOI: 10.1155/2018/8084032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 02/09/2018] [Accepted: 02/20/2018] [Indexed: 12/19/2022] Open
Abstract
The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. coreanus reads (125 bp in length) generated by RNA sequencing from fruits at three representative developmental stages. We also used the recently released draft genome of R. occidentalis to perform reference-guided assembly. We inferred a final 95,845-transcript reference for R. coreanus. Of these genetic resources, 66,597 (69.5%) were annotated. Based on these results, we carried out a comprehensive analysis of differentially expressed genes. Flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis pathways were significantly enriched throughout the ripening process. We identified 23 transcripts involved in the flavonoid biosynthesis pathway whose expression perfectly paralleled changes in the metabolites. Additionally, we identified 119 nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-coding genes, involved in pathogen resistance, of which 74 were in the completely conserved domain. These results provide, for the first time, genome-wide genetic information for understanding developmental regulation of R. coreanus fruits. They have the potential for use in breeding through functional genetic approaches in the near future.
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Affiliation(s)
- Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xunju Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yueyang Hu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yaodong Hu
- Science and Technology Management Division, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiaorong Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yan Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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25
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Haselmair-Gosch C, Miosic S, Nitarska D, Roth BL, Walliser B, Paltram R, Lucaciu RC, Eidenberger L, Rattei T, Olbricht K, Stich K, Halbwirth H. Great Cause-Small Effect: Undeclared Genetically Engineered Orange Petunias Harbor an Inefficient Dihydroflavonol 4-Reductase. FRONTIERS IN PLANT SCIENCE 2018; 9:149. [PMID: 29541079 PMCID: PMC5835687 DOI: 10.3389/fpls.2018.00149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/29/2018] [Indexed: 05/22/2023]
Abstract
A recall campaign for commercial, orange flowering petunia varieties in spring 2017 caused economic losses worldwide. The orange varieties were identified as undeclared genetically engineered (GE)-plants, harboring a maize dihydroflavonol 4-reductase (DFR, A1), which was used in former scientific transgenic breeding attempts to enable formation of orange pelargonidin derivatives from the precursor dihydrokaempferol (DHK) in petunia. How and when the A1 cDNA entered the commercial breeding process is unclear. We provide an in-depth analysis of three orange petunia varieties, released by breeders from three countries, with respect to their transgenic construct, transcriptomes, anthocyanin composition, and flavonoid metabolism at the level of selected enzymes and genes. The two possible sources of the A1 cDNA in the undeclared GE-petunia can be discriminated by PCR. A special version of the A1 gene, the A1 type 2 allele, is present, which includes, at the 3'-end, an additional 144 bp segment from the non-viral transposable Cin4-1 sequence, which does not add any functional advantage with respect to DFR activity. This unequivocally points at the first scientific GE-petunia from the 1980s as the A1 source, which is further underpinned e.g., by the presence of specific restriction sites, parts of the untranslated sequences, and the same arrangement of the building blocks of the transformation plasmid used. Surprisingly, however, the GE-petunia cannot be distinguished from native red and blue varieties by their ability to convert DHK in common in vitro enzyme assays, as DHK is an inadequate substrate for both the petunia and maize DFR. Recombinant maize DFR underpins the low DHK acceptance, and, thus, the strikingly limited suitability of the A1 protein for a transgenic approach for breeding pelargonidin-based flower color. The effect of single amino acid mutations on the substrate specificity of DFRs is demonstrated. Expression of the A1 gene is generally lower than the petunia DFR expression despite being under the control of the strong, constitutive p35S promoter. We show that a rare constellation in flavonoid metabolism-absence or strongly reduced activity of both flavonol synthase and B-ring hydroxylating enzymes-allows pelargonidin formation in the presence of DFRs with poor DHK acceptance.
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Affiliation(s)
- Christian Haselmair-Gosch
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Silvija Miosic
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Daria Nitarska
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Barbara L. Roth
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Benjamin Walliser
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Renate Paltram
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Rares C. Lucaciu
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Lukas Eidenberger
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Klaus Olbricht
- Thaer-Institute of Agricultural and Horticultural Sciences Humboldt University Berlin, Berlin, Germany
| | - Karl Stich
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Heidi Halbwirth
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- *Correspondence: Heidi Halbwirth
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26
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Zorenc Z, Veberic R, Slatnar A, Koron D, Miosic S, Chen MH, Haselmair-Gosch C, Halbwirth H, Mikulic-Petkovsek M. A wild 'albino' bilberry (Vaccinium myrtillus L.) from Slovenia shows three bottlenecks in the anthocyanin pathway and significant differences in the expression of several regulatory genes compared to the common blue berry type. PLoS One 2017; 12:e0190246. [PMID: 29272302 PMCID: PMC5741254 DOI: 10.1371/journal.pone.0190246] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/11/2017] [Indexed: 12/26/2022] Open
Abstract
Relative expressions of structural genes and a number of transcription factors of the anthocyanin pathway relevant in Vaccinium species, and related key enzyme activities were compared with the composition and content of metabolites in skins of ripe fruits of wild albino and blue bilberry (Vaccinium myrtillus) found in Slovenia. Compared to the common blue type, the albino variant had a 151-fold lower total anthocyanin and a 7-fold lower total phenolic content in their berry skin, which correlated with lower gene expression of flavonoid 3-O-glycosyltransferase (FGT; 33-fold), flavanone 3-hydroxylase (FHT; 18-fold), anthocyanidin synthase (ANS; 11-fold), chalcone synthase (CHS, 7.6-fold) and MYBPA1 transcription factor (22-fold). The expression of chalcone isomerase (CHI), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin reductase (LAR), anthocyanidin reductase (ANR) and MYBC2 transcription factor was reduced only by a factor of 1.5-2 in the albino berry skins, while MYBR3 and flavonoid 3',5'-hydroxylase (F3'5'H) were increased to a similar extent. Expression of the SQUAMOSA class transcription factor TDR4, in contrast, was independent of the color type and does therefore not seem to be correlated with anthocyanin formation in this variant. At the level of enzymes, significantly lower FHT and DFR activities, but not of phenylalanine ammonia-lyase (PAL) and CHS/CHI, were observed in the fruit skins of albino bilberries. A strong increase in relative hydroxycinnamic acid derivative concentrations indicates the presence of an additional bottleneck in the general phenylpropanoid pathway at a so far unknown step between PAL and CHS.
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Affiliation(s)
- Zala Zorenc
- Department of Agronomy, Chair for Fruit, Wine and Vegetable Growing, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Robert Veberic
- Department of Agronomy, Chair for Fruit, Wine and Vegetable Growing, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ana Slatnar
- Department of Agronomy, Chair for Fruit, Wine and Vegetable Growing, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Darinka Koron
- Department of Fruit Growing, Viticulture and Oenology, Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Silvija Miosic
- Institute of Chemical, Environmental and Biological Engineering, Technische Universität Wien, Vienna, Austria
| | - Ming-Hui Chen
- Institute of Chemical, Environmental and Biological Engineering, Technische Universität Wien, Vienna, Austria
| | - Christian Haselmair-Gosch
- Institute of Chemical, Environmental and Biological Engineering, Technische Universität Wien, Vienna, Austria
| | - Heidi Halbwirth
- Institute of Chemical, Environmental and Biological Engineering, Technische Universität Wien, Vienna, Austria
| | - Maja Mikulic-Petkovsek
- Department of Agronomy, Chair for Fruit, Wine and Vegetable Growing, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Katsu K, Suzuki R, Tsuchiya W, Inagaki N, Yamazaki T, Hisano T, Yasui Y, Komori T, Koshio M, Kubota S, Walker AR, Furukawa K, Matsui K. A new buckwheat dihydroflavonol 4-reductase (DFR), with a unique substrate binding structure, has altered substrate specificity. BMC PLANT BIOLOGY 2017; 17:239. [PMID: 29228897 PMCID: PMC5725924 DOI: 10.1186/s12870-017-1200-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 12/01/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND Dihydroflavonol 4-reductase (DFR) is the key enzyme committed to anthocyanin and proanthocyanidin biosynthesis in the flavonoid biosynthetic pathway. DFR proteins can catalyse mainly the three substrates (dihydrokaempferol, dihydroquercetin, and dihydromyricetin), and show different substrate preferences. Although relationships between the substrate preference and amino acids in the region responsible for substrate specificity have been investigated in several plant species, the molecular basis of the substrate preference of DFR is not yet fully understood. RESULTS By using degenerate primers in a PCR, we isolated two cDNA clones that encoded DFR in buckwheat (Fagopyrum esculentum). Based on sequence similarity, one cDNA clone (FeDFR1a) was identical to the FeDFR in DNA databases (DDBJ/Gen Bank/EMBL). The other cDNA clone, FeDFR2, had a similar sequence to FeDFR1a, but a different exon-intron structure. Linkage analysis in an F2 segregating population showed that the two loci were linked. Unlike common DFR proteins in other plant species, FeDFR2 contained a valine instead of the typical asparagine at the third position and an extra glycine between sites 6 and 7 in the region that determines substrate specificity, and showed less activity against dihydrokaempferol than did FeDFR1a with an asparagine at the third position. Our 3D model suggested that the third residue and its neighbouring residues contribute to substrate specificity. FeDFR1a was expressed in all organs that we investigated, whereas FeDFR2 was preferentially expressed in roots and seeds. CONCLUSIONS We isolated two buckwheat cDNA clones of DFR genes. FeDFR2 has unique structural and functional features that differ from those of previously reported DFRs in other plants. The 3D model suggested that not only the amino acid at the third position but also its neighbouring residues that are involved in the formation of the substrate-binding pocket play important roles in determining substrate preferences. The unique characteristics of FeDFR2 would provide a useful tool for future studies on the substrate specificity and organ-specific expression of DFRs.
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Affiliation(s)
- Kenjiro Katsu
- National Agriculture and Food Research Organization (NARO), Kyushu Okinawa Agricultural Research Center, Suya 2421, Koshi, Kumamoto, 861-1192 Japan
| | - Rintaro Suzuki
- NARO, Advanced Analysis Center, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602 Japan
| | - Wataru Tsuchiya
- NARO, Advanced Analysis Center, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602 Japan
| | - Noritoshi Inagaki
- NARO, Advanced Analysis Center, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602 Japan
| | - Toshimasa Yamazaki
- NARO, Advanced Analysis Center, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602 Japan
| | - Tomomi Hisano
- National Agriculture and Food Research Organization (NARO), Kyushu Okinawa Agricultural Research Center, Suya 2421, Koshi, Kumamoto, 861-1192 Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Yoshida-honmachi, Sakyou-ku, Kyoto, 606-8501 Japan
| | - Toshiyuki Komori
- Laboratory of Glycobiology, Department of Bioengineering, Nagaoka University, Kamitomioka 1603-1, Nagaoka, Niigata, 940-2188 Japan
| | - Motoyuki Koshio
- Laboratory of Glycobiology, Department of Bioengineering, Nagaoka University, Kamitomioka 1603-1, Nagaoka, Niigata, 940-2188 Japan
| | - Seiji Kubota
- Laboratory of Glycobiology, Department of Bioengineering, Nagaoka University, Kamitomioka 1603-1, Nagaoka, Niigata, 940-2188 Japan
| | - Amanda R. Walker
- CSIRO Agriculture & Food, Wine Innovation West, Hartley Grove, Urrbrae, SA 5064 Australia
| | - Kiyoshi Furukawa
- Laboratory of Glycobiology, Department of Bioengineering, Nagaoka University, Kamitomioka 1603-1, Nagaoka, Niigata, 940-2188 Japan
| | - Katsuhiro Matsui
- National Agriculture and Food Research Organization (NARO), Kyushu Okinawa Agricultural Research Center, Suya 2421, Koshi, Kumamoto, 861-1192 Japan
- Present address: NARO, Institute of Crop Science, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518 Japan
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28
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Zhuang Y, Tripp EA. The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). DNA Res 2017; 24:179-192. [PMID: 28431014 PMCID: PMC5397612 DOI: 10.1093/dnares/dsw054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/13/2022] Open
Abstract
The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3'5'H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3'H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.
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Affiliation(s)
- Yongbin Zhuang
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA
- Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309, USA
| | - Erin A. Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA
- Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309, USA
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29
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Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes. Sci Rep 2017; 7:45113. [PMID: 28327625 PMCID: PMC5361166 DOI: 10.1038/srep45113] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/17/2017] [Indexed: 01/22/2023] Open
Abstract
Strawberry fruits (Fragaria vesca) are valued for their sweet fruity flavor, juicy texture, and characteristic red color caused by anthocyanin pigments. To gain a deeper insight into the regulation of anthocyanin biosynthesis, we performed comparative metabolite profiling and transcriptome analyses of one red-fruited and two natural white-fruited strawberry varieties in two tissues and three ripening stages. Developing fruit of the three genotypes showed a distinctive pattern of polyphenol accumulation already in green receptacle and achenes. Global analysis of the transcriptomes revealed that the ripening process in the white-fruited varieties is already affected at an early developmental stage. Key polyphenol genes showed considerably lower transcript levels in the receptacle and achenes of both white genotypes, compared to the red genotype. The expression of the anthocyanidin glucosyltransferase gene and a glutathione S-transferase, putatively involved in the vacuolar transport of the anthocyanins, seemed to be critical for anthocyanin formation. A bHLH transcription factor is among the differentially expressed genes as well. Furthermore, genes associated with flavor formation and fruit softening appear to be coordinately regulated and seem to interact with the polyphenol biosynthesis pathway. This study provides new information about polyphenol biosynthesis regulators in strawberry, and reveals genes unknown to affect anthocyanin formation.
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30
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Jin X, Huang H, Wang L, Sun Y, Dai S. Transcriptomics and Metabolite Analysis Reveals the Molecular Mechanism of Anthocyanin Biosynthesis Branch Pathway in Different Senecio cruentus Cultivars. FRONTIERS IN PLANT SCIENCE 2016; 7:1307. [PMID: 27656188 PMCID: PMC5012328 DOI: 10.3389/fpls.2016.01307] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/15/2016] [Indexed: 05/23/2023]
Abstract
The cyanidin (Cy), pelargonidin (Pg), and delphinidin (Dp) pathways are the three major branching anthocyanin biosynthesis pathways that regulate flavonoid metabolic flux and are responsible for red, orange, and blue flower colors, respectively. Different species have evolved to develop multiple regulation mechanisms that form the branched pathways. In the current study, five Senecio cruentus cultivars with different colors were investigated. We found that the white and yellow cultivars do not accumulate anthocyanin and that the blue, pink, and carmine cultivars mainly accumulate Dp, Pg, and Cy in differing densities. Subsequent transcriptome analysis determined that there were 43 unigenes encoding anthocyanin biosynthesis genes in the blue cultivar. We also combined chemical and transcriptomic analyses to investigate the major metabolic pathways that are related to the observed differences in flower pigmentation in the series of S. cruentus. The results showed that mutations of the ScbHLH17 and ScCHI1/2 coding regions abolish anthocyanin formation in the white and the yellow cultivars; the competition of the ScF3'H1, ScF3'5'H, and ScDFR1/2 genes for naringenin determines the differences in branching metabolic flux of the Cy, Dp, and Pg pathways. Our findings provide new insights into the regulation of anthocyanin branching and also supplement gene resources (including ScF3'5 'H, ScF3'H, and ScDFRs) for flower color modification of ornamentals.
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Affiliation(s)
- Xuehua Jin
- College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
- Faculty of Architecture and City Planning, Kunming University of Science and TechnologyKunming, China
| | - He Huang
- College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Lu Wang
- College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Yi Sun
- College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Silan Dai
- College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
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31
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Berman J, Sheng Y, Gómez Gómez L, Veiga T, Ni X, Farré G, Capell T, Guitián J, Guitián P, Sandmann G, Christou P, Zhu C. Red Anthocyanins and Yellow Carotenoids Form the Color of Orange-Flower Gentian (Gentiana lutea L. var. aurantiaca). PLoS One 2016; 11:e0162410. [PMID: 27589396 PMCID: PMC5010251 DOI: 10.1371/journal.pone.0162410] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/22/2016] [Indexed: 01/07/2023] Open
Abstract
Flower color is an important characteristic that determines the commercial value of ornamental plants. Gentian flowers occur in a limited range of colors because this species is not widely cultivated as a cut flower. Gentiana lutea L. var. aurantiaca (abbr, aurantiaca) is characterized by its orange flowers, but the specific pigments responsible for this coloration are unknown. We therefore investigated the carotenoid and flavonoid composition of petals during flower development in the orange-flowered gentian variety of aurantiaca and the yellow-flowered variety of G. lutea L. var. lutea (abbr, lutea). We observed minor varietal differences in the concentration of carotenoids at the early and final stages, but only aurantiaca petals accumulated pelargonidin glycosides, whereas these compounds were not found in lutea petals. We cloned and sequenced the anthocyanin biosynthetic gene fragments from petals, and analyzed the expression of these genes in the petals of both varieties to determine the molecular mechanisms responsible for the differences in petal color. Comparisons of deduced amino acid sequences encoded by the isolated anthocyanin cDNA fragments indicated that chalcone synthase (CHS), chalcone isomerase (CHI), anthocyanidin synthase 1 (ANS1) and ANS2 are identical in both aurantiaca and lutea varieties whereas minor amino acid differences of the deduced flavonone 3-hydroxylase (F3H) and dihydroflavonol 4-reductase (DFR) between both varieties were observed. The aurantiaca petals expressed substantially higher levels of transcripts representing CHS, F3H, DFR, ANS and UDP-glucose:flavonoid-3-O-glucosyltransferase genes, compared to lutea petals. Pelargonidin glycoside synthesis in aurantiaca petals therefore appears to reflect the higher steady-state levels of pelargonidin synthesis transcripts. Moreover, possible changes in the substrate specificity of DFR enzymes may represent additional mechanisms for producing red pelargonidin glycosides in petals of aurantiaca. Our report describing the exclusive accumulation of pelargonidin glycosides in aurantiaca petals may facilitate the modification of gentian flower color by the production of red anthocyanins.
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Affiliation(s)
- Judit Berman
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
| | - Yanmin Sheng
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Lourdes Gómez Gómez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Albacete, Spain
| | - Tania Veiga
- Departamento de Botánica, Universidad de Santiago de Compostela, Galicia, Spain
| | - Xiuzhen Ni
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Gemma Farré
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
| | - Teresa Capell
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
| | - Javier Guitián
- Departamento de Botánica, Universidad de Santiago de Compostela, Galicia, Spain
| | - Pablo Guitián
- Departamento de Botánica, Universidad de Santiago de Compostela, Galicia, Spain
| | - Gerhard Sandmann
- Biosynthesis Group, Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Paul Christou
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain
| | - Changfu Zhu
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
- School of Life Sciences, Changchun Normal University, Changchun, China
- * E-mail:
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32
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Functional Characterization of a Dihydroflavanol 4-Reductase from the Fiber of Upland Cotton (Gossypium hirsutum). Molecules 2016; 21:32. [PMID: 26821011 PMCID: PMC6273761 DOI: 10.3390/molecules21020032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/10/2015] [Accepted: 12/21/2015] [Indexed: 11/16/2022] Open
Abstract
Dihydroflavanol 4-reductase (DFR) is a key later enzyme involved in two polyphenols' (anthocyanins and proanthocyanidins (PAs)) biosynthesis, however it is not characterized in cotton yet. In present reports, a DFR cDNA homolog (designated as GhDFR1) was cloned from developing fibers of upland cotton. Silencing GhDFR1 in cotton by virus-induced gene silencing led to significant decrease in accumulation of anthocyanins and PAs. More interestingly, based on LC-MS analysis, two PA monomers, (-)-epicatachin and (-)-epigallocatachin, remarkably decreased in content in fibers of GhDFR1-silenced plants, but two new monomers, (-)-catachin and (-)-gallocatachin were present compared to the control plants infected with empty vector. The ectopic expression of GhDFR1 in an Arabidopsis TT3 mutant allowed for reconstruction of PAs biosynthesis pathway and led to accumulation of PAs in seed coat. Taken together, these data demonstrate that GhDFR1 contributes to the biosynthesis of anthocyanins and PAs in cotton.
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33
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Zhang Y, Li W, Dou Y, Zhang J, Jiang G, Miao L, Han G, Liu Y, Li H, Zhang Z. Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca. PLoS One 2015; 10:e0144356. [PMID: 26636322 PMCID: PMC4670188 DOI: 10.1371/journal.pone.0144356] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 11/17/2015] [Indexed: 11/22/2022] Open
Abstract
Fragaria vesca (2n = 2x = 14), the woodland strawberry, is a perennial herbaceous plant with a small sequenced genome (240 Mb). It is commonly used as a genetic model plant for the Fragaria genus and the Rosaceae family. Fruit skin color is one of the most important traits for both the commercial and esthetic value of strawberry. Anthocyanins are the most prominent pigments in strawberry that bring red, pink, white, and yellow hues to the fruits in which they accumulate. In this study, we conducted a de novo assembly of the fruit transcriptome of woodland strawberry and compared the gene expression profiles with yellow (Yellow Wonder, YW) and red (Ruegen, RG) fruits. De novo assembly yielded 75,426 unigenes, 21.3% of which were longer than 1,000 bp. Among the high-quality unique sequences, 45,387 (60.2%) had at least one significant match to an existing gene model. A total of 595 genes, representing 0.79% of total unigenes, were differentially expressed in YW and RG. Among them, 224 genes were up-regulated and 371 genes were down-regulated in the fruit of YW. Particularly, some flavonoid biosynthetic pathway genes, including C4H, CHS, CHI, F3H, DFR and ANS, as well as some transcription factors (TFs), including MYB (putative MYB86 and MYB39), WDR and MADS, were down-regulated in YW fruit, concurrent with a reduction in anthocyanin accumulation in the yellow pigment phenotype, whereas a putative transcription repressor MYB1R was up-regulated in YW fruit. The altered expression levels of the genes encoding flavonoid biosynthetic enzymes and TFs were confirmed by quantitative RT-PCR. Our study provides important insights into the molecular mechanisms underlying the yellow pigment phenotype in F. vesca.
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Affiliation(s)
- Yuchao Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 139 Shiqiao Road, Hangzhou 310021, China
| | - Weijia Li
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China
| | - Yujuan Dou
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China
- Institute of Soil and Water Conservation of Liaoning Province, Chaoyang 122000, China
| | - Junxiang Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China
| | - Guihua Jiang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 139 Shiqiao Road, Hangzhou 310021, China
| | - Lixiang Miao
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 139 Shiqiao Road, Hangzhou 310021, China
| | - Guofen Han
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China
| | - Yuexue Liu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China
| | - He Li
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China
| | - Zhihong Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China
- * E-mail:
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