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Xia Y, Su Q, Li X, Yan S, Liu J, He C, Huang H, Jiang W, Pang Y. Two CYP93A enzymes play a dual role in isoflavonoid biosynthesis in Glycine max L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108073. [PMID: 37839274 DOI: 10.1016/j.plaphy.2023.108073] [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: 03/26/2023] [Revised: 09/08/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
Glycine max L. is rich in isoflavonoids with diverse biological activities. However, isoflavonoid biosynthetic pathway is not fully elucidated in soybean. In the present study, we investigated characteristics of all the thirteen CYP93 subfamily members, and found GmCYP93A1, GmCYP93A2, and GmCYP93A3 are closely clustered, preferentially expressed in roots, and highly inducible by elicitor. When expressed in yeast, GmCYP93A1 was active towards liquiritigenin, naringenin, and 3,9-dihydroxyptercarpan, GmCYP93A2 towards 3,9-dihydroxyptercarpan with strict substrate specificity, whereas GmCYP93A3 did not show any activity towards all the tested substrates. Both GmCYP93A1 and GmCYP93A2 could catalyze 3,9-dihydroxyptercarpan into daidzein and glycinol, with both hydroxylation and aryl migration activity. Site-directed mutagenesis assays revealed that mutation in Thr446 to Ser446 in heme-binding domain increased the enzyme activity of GmCYP93A1 towards 3,9-dihydroxyptercarpan, which highlights its key amino acid residues as shown with its molecular docking with 3,9-dihydroxyptercarpan and HEM. Overexpression of GmCYP93A1 and GmCYP93A2 in the soybean hairy roots reduced the content of daidzein, whereas knockdown of these two genes increased genistein content, indicating changes in expression level of GmCYP93A1 and GmCYP93A2 altered isoflavonoid flux in soybean. Our studies on the activity of GmCYP93A1 and GmCYP93A2 enriched diverse functions of CYP93 subfamily in soybean isoflavonoid pathway, which is valuable for further understanding and bioengineering of isoflavonoid pathway in soybean.
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Affiliation(s)
- Yaying Xia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qian Su
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xue Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Su Yan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jinyue Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Chunfeng He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Haijun Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Sahoo B, Nayak I, Parameswaran C, Kesawat MS, Sahoo KK, Subudhi HN, Balasubramaniasai C, Prabhukarthikeyan SR, Katara JL, Dash SK, Chung SM, Siddiqui MH, Alamri S, Samantaray S. A Comprehensive Genome-Wide Investigation of the Cytochrome 71 ( OsCYP71) Gene Family: Revealing the Impact of Promoter and Gene Variants (Ser33Leu) of OsCYP71P6 on Yield-Related Traits in Indica Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3035. [PMID: 37687282 PMCID: PMC10490456 DOI: 10.3390/plants12173035] [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: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. These genes were categorized into twelve distinct subfamilies, where members within the same subgroup exhibited comparable gene structures and conserved motifs. In addition, 105 OsCYP71 genes were distributed across 11 chromosomes, and 36 pairs of OsCYP71 involved in gene duplication events. Within the promoter region of OsCYP71, there exists an extensive array of cis-elements that are associated with light responsiveness, hormonal regulation, and stress-related signaling. Further, transcriptome profiling revealed that a majority of the genes exhibited responsiveness to hormones and were activated across diverse tissues and developmental stages in rice. The OsCYP71P6 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between OsCYP71P6 genetic variants and yield-related traits in rice varieties could provide novel insights for rice improvement. Through the utilization of linear regression models, a total of eight promoters were identified, and a specific gene variant (Ser33Leu) within OsCYP71P6 was found to be linked to spikelet fertility. Additionally, different alleles of the OsCYP71P6 gene identified through in/dels polymorphism in 131 rice varieties were validated for their allelic effects on yield-related traits. Furthermore, the single-plant yield, spikelet number, panicle length, panicle weight, and unfilled grain per panicle for the OsCYP71P6-1 promoter insertion variant were found to contribute 20.19%, 13.65%, 5.637%, 8.79%, and 36.86% more than the deletion variant, respectively. These findings establish a robust groundwork for delving deeper into the functions of OsCYP71-family genes across a range of biological processes. Moreover, these findings provide evidence that allelic variation in the promoter and amino acid substitution of Ser33Leu in the OsCYP71P6 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the OsCYP71P6 gene could be harnessed to amplify rice yields.
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Affiliation(s)
- Bijayalaxmi Sahoo
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
- Department of Botany, Ravenshaw University, Cuttack 753006, India;
| | - Itishree Nayak
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
- Department of Botany, Utkal University, Bhubaneswar 751004, India
| | - C. Parameswaran
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri University, Cuttack 754006, India
| | | | - H. N. Subudhi
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Cayalvizhi Balasubramaniasai
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | | | - Jawahar Lal Katara
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Sushanta Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Sang-Min Chung
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea;
| | - Manzer H. Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.H.S.); (S.A.)
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.H.S.); (S.A.)
| | - Sanghamitra Samantaray
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
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Li X, Wang L, Li W, Zhang X, Zhang Y, Dong S, Song X, Zhao J, Chen M, Yuan X. Genome-Wide Identification and Expression Profiling of Cytochrome P450 Monooxygenase Superfamily in Foxtail Millet. Int J Mol Sci 2023; 24:11053. [PMID: 37446233 DOI: 10.3390/ijms241311053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
The cytochrome P450 monooxygenases (CYP450) are the largest enzyme family in plant metabolism and widely involved in the biosynthesis of primary and secondary metabolites. Foxtail millet (Setaria italica (L.) P. Beauv) can respond to abiotic stress through a highly complex polygene regulatory network, in which the SiCYP450 family is also involved. Although the CYP450 superfamily has been systematically studied in a few species, the research on the CYP450 superfamily in foxtail millet has not been completed. In this study, three hundred and thirty-one SiCYP450 genes were identified in the foxtail millet genome by bioinformatics methods, which were divided into four groups, including forty-six subgroups. One hundred and sixteen genes were distributed in thirty-three tandem duplicated gene clusters. Chromosome mapping showed that SiCYP450 was distributed on seven chromosomes. In the SiCYP450 family of foxtail millet, 20 conserved motifs were identified. Cis-acting elements in the promoter region of SiCYP450 genes showed that hormone response elements were found in all SiCYP450 genes. Of the three hundred and thirty-one SiCYP450 genes, nine genes were colinear with the Arabidopsis thaliana genes. Two hundred SiCYP450 genes were colinear with the Setaria viridis genes, including two hundred and forty-five gene duplication events. The expression profiles of SiCYP450 genes in different organs and developmental stages showed that SiCYP450 was preferentially expressed in specific tissues, and many tissue-specific genes were identified, such as SiCYP75B6, SiCYP96A7, SiCYP71A55, SiCYP71A61, and SiCYP71A62 in the root, SiCYP78A1 and SiCYP94D9 in leaves, and SiCYP78A6 in the ear. The RT-PCR data showed that SiCYP450 could respond to abiotic stresses, ABA, and herbicides in foxtail millet. Among them, the expression levels of SiCYP709B4, SiCYP71A11, SiCYP71A14, SiCYP78A1, SiCYP94C3, and SiCYP94C4 were significantly increased under the treatment of mesotrione, florasulam, nicosulfuron, fluroxypyr, and sethoxydim, indicating that the same gene might respond to multiple herbicides. The results of this study will help reveal the biological functions of the SiCYP450 family in development regulation and stress response and provide a basis for molecular breeding of foxtail millet.
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Affiliation(s)
- Xiaorui Li
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Linlin Wang
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Weidong Li
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Xin Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Yujia Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Shuqi Dong
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Xi'e Song
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Juan Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Mingxun Chen
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiangyang Yuan
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
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Dong J, Jiang W, Gao P, Yang T, Zhang W, Huangfu M, Zhang J, Che D. Comparison of betalain compounds in two Beta vulgaris var. cicla and BvCYP76AD27 function identification in betalain biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107711. [PMID: 37116227 DOI: 10.1016/j.plaphy.2023.107711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/26/2023] [Accepted: 04/14/2023] [Indexed: 05/23/2023]
Abstract
Beta vulgaris var. cicla is an edible, ornamental and horticultural plant. However, the difference of components and contents of betalain in beets with different leaf color are not well understood. Here, the stress resistance and metabolites of two B. vulgaris var. cicla cultivars were determined. The differences in stress resistance between red leaf-colored chard (RC) and yellow leaf-colored chard (YC) were positively related to betacyanins (BC) and betaxathins (BX) content in the leaves. Furthermore, a total of 3615 distinct metabolites were identified by UPLC-QTOF-MS in two cultivars, including 70 alkaloids and their derivatives, 249 flavonoids, and 264 terpenoids. There were 17 metabolites attributed to betalain biosynthesis pathway, seven of nine BC were up-regulated, and eight BX showed no significant difference in RC compared with YC. The contents of celosianin II and betanin were the highest BC in RC, at approximately 84.38 and 19.97 times that of YC, respectively. The content of portulacaxanthin II was the highest BX in two beets. Additionally, the BvCYP450 genes were identified based on genome, and the members that might be involved in betalain biosynthesis were screened. BvCYP76AD27, a member of the BvCYP76AD subfamily, had a higher expression level in RC than YC under freezing, drought and shading stress. In yeast Saccharomyces cerevisiae, BvCYP76AD5 and BvCYP76AD27 only hydroxylated tyrosine to L-DOPA, which was transformed into portulacaxanthin II by 4,5-DOPA extradiol dioxygenase. The results contribute to illustrating the molecular mechanism of betalain biosynthesis and provide useful information for further investigation of beet chemistry and sufficient utilization of this species.
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Affiliation(s)
- Jie Dong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, 150030, China
| | - Wan Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, 150030, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, 150030, China
| | - Tao Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, 150030, China
| | - Wuhua Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, 150030, China
| | - Minge Huangfu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, 150030, China
| | - Jinzhu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, 150030, China.
| | - Daidi Che
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China; Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, 150030, China.
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Kurepa J, Shull TE, Smalle JA. Friends in Arms: Flavonoids and the Auxin/Cytokinin Balance in Terrestrialization. PLANTS (BASEL, SWITZERLAND) 2023; 12:517. [PMID: 36771601 PMCID: PMC9921348 DOI: 10.3390/plants12030517] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Land plants survive the challenges of new environments by evolving mechanisms that protect them from excess irradiation, nutrient deficiency, and temperature and water availability fluctuations. One such evolved mechanism is the regulation of the shoot/root growth ratio in response to water and nutrient availability by balancing the actions of the hormones auxin and cytokinin. Plant terrestrialization co-occurred with a dramatic expansion in secondary metabolism, particularly with the evolution and establishment of the flavonoid biosynthetic pathway. Flavonoid biosynthesis is responsive to a wide range of stresses, and the numerous synthesized flavonoid species offer two main evolutionary advantages to land plants. First, flavonoids are antioxidants and thus defend plants against those adverse conditions that lead to the overproduction of reactive oxygen species. Second, flavonoids aid in protecting plants against water and nutrient deficiency by modulating root development and establishing symbiotic relations with beneficial soil fungi and bacteria. Here, we review different aspects of the relationships between the auxin/cytokinin module and flavonoids. The current body of knowledge suggests that whereas both auxin and cytokinin regulate flavonoid biosynthesis, flavonoids act to fine-tune only auxin, which in turn regulates cytokinin action. This conclusion agrees with the established master regulatory function of auxin in controlling the shoot/root growth ratio.
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Tariq H, Asif S, Andleeb A, Hano C, Abbasi BH. Flavonoid Production: Current Trends in Plant Metabolic Engineering and De Novo Microbial Production. Metabolites 2023; 13:metabo13010124. [PMID: 36677049 PMCID: PMC9864322 DOI: 10.3390/metabo13010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/23/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Flavonoids are secondary metabolites that represent a heterogeneous family of plant polyphenolic compounds. Recent research has determined that the health benefits of fruits and vegetables, as well as the therapeutic potential of medicinal plants, are based on the presence of various bioactive natural products, including a high proportion of flavonoids. With current trends in plant metabolite research, flavonoids have become the center of attention due to their significant bioactivity associated with anti-cancer, antioxidant, anti-inflammatory, and anti-microbial activities. However, the use of traditional approaches, widely associated with the production of flavonoids, including plant extraction and chemical synthesis, has not been able to establish a scalable route for large-scale production on an industrial level. The renovation of biosynthetic pathways in plants and industrially significant microbes using advanced genetic engineering tools offers substantial promise for the exploration and scalable production of flavonoids. Recently, the co-culture engineering approach has emerged to prevail over the constraints and limitations of the conventional monoculture approach by harnessing the power of two or more strains of engineered microbes to reconstruct the target biosynthetic pathway. In this review, current perspectives on the biosynthesis and metabolic engineering of flavonoids in plants have been summarized. Special emphasis is placed on the most recent developments in the microbial production of major classes of flavonoids. Finally, we describe the recent achievements in genetic engineering for the combinatorial biosynthesis of flavonoids by reconstructing synthesis pathways in microorganisms via a co-culture strategy to obtain high amounts of specific bioactive compounds.
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Affiliation(s)
- Hasnat Tariq
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Saaim Asif
- Department of Biosciences, COMSATS University, Islamabad 45550, Pakistan
| | - Anisa Andleeb
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAE USC1328, Eure et Loir Campus, Université d’Orléans, 28000 Chartres, France
- Correspondence: (C.H.); (B.H.A.)
| | - Bilal Haider Abbasi
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Correspondence: (C.H.); (B.H.A.)
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New dual functional CYP450 gene involves in isoflavone biosynthesis in Glycine max L. Synth Syst Biotechnol 2023; 8:157-167. [PMID: 36714060 PMCID: PMC9860299 DOI: 10.1016/j.synbio.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Glycine max L. accumulates a large amount of isoflavonoid compounds, which is beneficial for plant defense, plant-microbe symbiotic interactions, and human health. Several CYP450 subfamily genes are involved in the flavonoid biosynthetic pathway in plants. In the present study, we found 24 CYP82 subfamily genes were differentially expressed in various tissues of soybean, in Phytophthora sojae-infected soybean varieties and in soybean hairy roots treated with cell wall glucan elicitor. Six of them (GmCYP82A2, GmCYP82A3, GmCYP82A4, GmCYP82A23, GmCYP82C20 and GmCYP82D26) were co-expressed with other known isoflavonoid pathway genes in soybean. Their enzymatic activity in yeast feeding assays showed that only GmCYP82D26 was able to convert naringenin to daidzein with both aryl migration and dehydration function. When GmCYP82D26 was over-expressed in soybean hairy roots, the contents of the two major isoflavonoid aglycones in soybean (daidzein and genistein) were reduced, but total flavonoids were not affected. When GmCYP82D26 was suppressed by RNAi in the hairy roots, daidzein content was decreased but genistein content was increased, with unchanged total flavonoid content. GmCYP82D26 was found to be localized in the endoplasmic reticulum at subcellular level when transiently expressed in tobacco leaf epidermis. GmCYP82D26 gene was preferentially expressed in roots, with low expression level in other tissues in soybean. Homology modeling and molecular docking showed that GmCYP82D26 could form hydrogen bond with both HEM and naringenin at C5-OH and C4 carbonyl. All these results indicated that GmCYP82D26 possesses new and dual enzymatic activity, which bridges the two branches (daidzein and genistein branch) of isoflavonoid pathway in soybean.
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Singh G, Sharma S, Rawat S, Sharma RK. Plant Specialised Glycosides (PSGs): their biosynthetic enzymatic machinery, physiological functions and commercial potential. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1009-1028. [PMID: 36038144 DOI: 10.1071/fp21294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Plants, the primary producers of our planet, have evolved from simple aquatic life to very complex terrestrial habitat. This habitat transition coincides with evolution of enormous chemical diversity, collectively termed as 'Plant Specialised Metabolisms (PSMs)', to cope the environmental challenges. Plant glycosylation is an important process of metabolic diversification of PSMs to govern their in planta stability, solubility and inter/intra-cellular transport. Although, individual category of PSMs (terpenoids, phenylpropanoids, flavonoids, saponins, alkaloids, phytohormones, glucosinolates and cyanogenic glycosides) have been well studied; nevertheless, deeper insights of physiological functioning and genomic aspects of plant glycosylation/deglycosylation processes including enzymatic machinery (CYPs, GTs, and GHs) and regulatory elements are still elusive. Therefore, this review discussed the paradigm shift on genomic background of enzymatic machinery, transporters and regulatory mechanism of 'Plant Specialised Glycosides (PSGs)'. Current efforts also update the fundamental understanding about physiological, evolutionary and adaptive role of glycosylation/deglycosylation processes during the metabolic diversification of PSGs. Additionally, futuristic considerations and recommendations for employing integrated next-generation multi-omics (genomics, transcriptomics, proteomics and metabolomics), including gene/genome editing (CRISPR-Cas) approaches are also proposed to explore commercial potential of PSGs.
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Affiliation(s)
- Gopal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India; and Present address: Department of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Shikha Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
| | - Sandeep Rawat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Present address: G. B. Pant National Institute of Himalayan Environment and Sustainable Development, Sikkim Regional Centre, Pangthang, Gangtok 737101, Sikkim, India
| | - Ram Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
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Sajid M, Stone SR, Kaur P. Phylogenetic Analysis and Protein Modelling of Isoflavonoid Synthase Highlights Key Catalytic Sites towards Realising New Bioengineering Endeavours. Bioengineering (Basel) 2022; 9:bioengineering9110609. [PMID: 36354520 PMCID: PMC9687675 DOI: 10.3390/bioengineering9110609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 12/01/2022] Open
Abstract
Isoflavonoid synthase (IFS) is a critical enzyme for the biosynthesis of over 2400 isoflavonoids. Isoflavonoids are an important class of plant secondary metabolites that have a range of pharmaceutical and nutraceutical properties. With growing interest in isoflavonoids from both research and industrial perspectives, efforts are being forwarded to enhance isoflavonoid production in-planta and ex-planta; therefore, in-silico analysis and characterisation of available IFS protein sequences are needed. The present study is the first-ever attempt toward phylogenetic analysis and protein modelling of available IFS protein sequences. Phylogenetic analysis has shown that IFS amino acid sequences have 86.4% pairwise identity and 26.5% identical sites, and the sequences were grouped into six different clades. The presence of a β-hairpin and extra loop at catalytic sites of Trifolium pratense, Beta vulgaris and Medicago truncatula, respectively, compared with Glycyrrhiza echinata are critical structural differences that may affect catalytic function. Protein docking highlighted the preference of selected IFS for liquiritigenin compared with naringenin and has listed T. pratense as the most efficient candidate for heterologous biosynthesis of isoflavonoids. The in-silico characterisation of IFS represented in this study is vital in realising the new bioengineering endeavours and will help in the characterisation and selection of IFS candidate enzymes for heterologous biosynthesis of isoflavonoids.
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Wang Y, Durairaj J, Suárez Duran HG, van Velzen R, Flokova K, Liao C, Chojnacka A, MacFarlane S, Schranz ME, Medema MH, van Dijk ADJ, Dong L, Bouwmeester HJ. The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol. THE NEW PHYTOLOGIST 2022; 235:1884-1899. [PMID: 35612785 PMCID: PMC9542622 DOI: 10.1111/nph.18272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Strigolactones (SLs) are rhizosphere signalling molecules and phytohormones. The biosynthetic pathway of SLs in tomato has been partially elucidated, but the structural diversity in tomato SLs predicts that additional biosynthetic steps are required. Here, root RNA-seq data and co-expression analysis were used for SL biosynthetic gene discovery. This strategy resulted in a candidate gene list containing several cytochrome P450s. Heterologous expression in Nicotiana benthamiana and yeast showed that one of these, CYP712G1, can catalyse the double oxidation of orobanchol, resulting in the formation of three didehydro-orobanchol (DDH) isomers. Virus-induced gene silencing and heterologous expression in yeast showed that one of these DDH isomers is converted to solanacol, one of the most abundant SLs in tomato root exudate. Protein modelling and substrate docking analysis suggest that hydroxy-orbanchol is the likely intermediate in the conversion from orobanchol to the DDH isomers. Phylogenetic analysis demonstrated the occurrence of CYP712G1 homologues in the Eudicots only, which fits with the reports on DDH isomers in that clade. Protein modelling and orobanchol docking of the putative tobacco CYP712G1 homologue suggest that it can convert orobanchol to similar DDH isomers as tomato.
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Affiliation(s)
- Yanting Wang
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| | - Janani Durairaj
- Bioinformatics GroupWageningen University6708PBWageningenthe Netherlands
| | | | - Robin van Velzen
- Biosystematics GroupWageningen University6708PBWageningenthe Netherlands
| | - Kristyna Flokova
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| | - Che‐Yang Liao
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht University3584 CHUtrechtthe Netherlands
| | - Aleksandra Chojnacka
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| | - Stuart MacFarlane
- Cell and Molecular Sciencesthe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - M. Eric Schranz
- Biosystematics GroupWageningen University6708PBWageningenthe Netherlands
| | - Marnix H. Medema
- Bioinformatics GroupWageningen University6708PBWageningenthe Netherlands
| | | | - Lemeng Dong
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| | - Harro J. Bouwmeester
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
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11
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McClean PE, Lee R, Howe K, Osborne C, Grimwood J, Levy S, Haugrud AP, Plott C, Robinson M, Skiba RM, Tanha T, Zamani M, Thannhauser TW, Glahn RP, Schmutz J, Osorno JM, Miklas PN. The Common Bean V Gene Encodes Flavonoid 3'5' Hydroxylase: A Major Mutational Target for Flavonoid Diversity in Angiosperms. FRONTIERS IN PLANT SCIENCE 2022; 13:869582. [PMID: 35432409 PMCID: PMC9009181 DOI: 10.3389/fpls.2022.869582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The classic V (violet, purple) gene of common bean (Phaseolus vulgaris) functions in a complex genetic network that controls seed coat and flower color and flavonoid content. V was cloned to understand its role in the network and the evolution of its orthologs in the Viridiplantae. V mapped genetically to a narrow interval on chromosome Pv06. A candidate gene was selected based on flavonoid analysis and confirmed by recombinational mapping. Protein and domain modeling determined V encodes flavonoid 3'5' hydroxylase (F3'5'H), a P450 enzyme required for the expression of dihydromyricetin-derived flavonoids in the flavonoid pathway. Eight recessive haplotypes, defined by mutations of key functional domains required for P450 activities, evolved independently in the two bean gene pools from a common ancestral gene. V homologs were identified in Viridiplantae orders by functional domain searches. A phylogenetic analysis determined F3'5'H first appeared in the Streptophyta and is present in only 41% of Angiosperm reference genomes. The evolutionarily related flavonoid pathway gene flavonoid 3' hydroxylase (F3'H) is found nearly universally in all Angiosperms. F3'H may be conserved because of its role in abiotic stress, while F3'5'H evolved as a major target gene for the evolution of flower and seed coat color in plants.
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Affiliation(s)
- Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Kevin Howe
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Caroline Osborne
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Shawn Levy
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Amanda Peters Haugrud
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Melanie Robinson
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Ryan M. Skiba
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Tabassum Tanha
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Mariam Zamani
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Theodore W. Thannhauser
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Raymond P. Glahn
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Juan M. Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip N. Miklas
- USDA-ARS, Grain Legumes Genetics and Physiology Research Unit, Prosser, WA, United States
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12
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Schumacher I, Menghini D, Ovinnikov S, Hauenstein M, Fankhauser N, Zipfel C, Hörtensteiner S, Aubry S. Evolution of chlorophyll degradation is associated with plant transition to land. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1473-1488. [PMID: 34931727 PMCID: PMC9306834 DOI: 10.1111/tpj.15645] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 05/27/2023]
Abstract
Chlorophyll, the central pigment of photosynthesis, is highly photo‐active and degraded enzymatically during leaf senescence. Merging comparative genomics and metabolomics, we evaluate the extent to which the chlorophyll detoxification pathway has evolved in Viridiplantae. We argue that cytosolic detoxification of phyllobilins in particular was a critical process to the green lineage’s transition to land.
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Affiliation(s)
- Isabel Schumacher
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Damian Menghini
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Serguei Ovinnikov
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Mareike Hauenstein
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Niklaus Fankhauser
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Cyril Zipfel
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Stefan Hörtensteiner
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Sylvain Aubry
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
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13
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Sun K, Fang H, Chen Y, Zhuang Z, Chen Q, Shan T, Khan MKR, Zhang J, Wang B. Genome-Wide Analysis of the Cytochrome P450 Gene Family Involved in Salt Tolerance in Gossypium hirsutum. FRONTIERS IN PLANT SCIENCE 2021; 12:685054. [PMID: 34925390 PMCID: PMC8674417 DOI: 10.3389/fpls.2021.685054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Plant cytochrome P450 (P450) participates in a wide range of biosynthetic reactions and targets a variety of biological molecules. These reactions lead to various fatty acid conjugates, plant hormones, secondary metabolites, lignin, and various defensive compounds. In our previous research, transcriptome analysis was performed on the salt-tolerant upland cotton "Tongyan No. 1." Many differentially expressed genes (DEGs) belong to the P450 family, and their domains occur widely in plants. In this current research, P450 genes were identified in Gossypium hirsutum with the aid of bioinformatics methods for investigating phylogenetic relations, gene structure, cis-elements, chromosomal localization, and collinearity within a genome. qRT-PCR was conducted to analyze P450 gene expression patterns under salt stress. The molecular weights of the 156 P450 genes were in the range of 5,949.6-245,576.3 Da, and the length of the encoded amino acids for all the identified P450 genes ranged from 51 to 2,144. P450 proteins are divided into four different subfamilies based on phylogenetic relationship, gene structure, and chromosomal localization of gene replication. The length of P450 genes in upland cotton differs greatly, ranging from 1,500 to 13,000 bp. The number of exons in the P450 family genes ranged from 1 to 9, while the number of introns ranged from 0 to 8, and there were similar trends within clusters. A total of 31 cis-acting elements were identified by analyzing 1,500 bp promoter sequences. Differences were found in cis-acting elements among genes. The consistency between qRT-PCR and previous transcriptome analysis of salt tolerance DEGs indicated that they were likely to be involved in the salt tolerance of cotton seedlings. Our results provide valuable information on the evolutionary relationships of genes and functional characteristics of the gene family, which is beneficial for further study of the cotton P450 gene family.
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Affiliation(s)
- Kangtai Sun
- School of Life Sciences, Nantong University, Nantong, China
| | - Hui Fang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhimin Zhuang
- School of Life Sciences, Nantong University, Nantong, China
| | - Qi Chen
- School of Life Sciences, Nantong University, Nantong, China
| | - Tingyu Shan
- School of Life Sciences, Nantong University, Nantong, China
| | - Muhammad Kashif Riaz Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
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14
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De La Torre AR, Sekhwal MK, Neale DB. Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia. Genes (Basel) 2021; 12:1826. [PMID: 34828432 PMCID: PMC8621000 DOI: 10.3390/genes12111826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype-environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Manoj K. Sekhwal
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - David B. Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
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15
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Lam PY, Lui ACW, Wang L, Liu H, Umezawa T, Tobimatsu Y, Lo C. Tricin Biosynthesis and Bioengineering. FRONTIERS IN PLANT SCIENCE 2021; 12:733198. [PMID: 34512707 PMCID: PMC8426635 DOI: 10.3389/fpls.2021.733198] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/28/2021] [Indexed: 05/23/2023]
Abstract
Tricin (3',5'-dimethoxyflavone) is a specialized metabolite which not only confers stress tolerance and involves in defense responses in plants but also represents a promising nutraceutical. Tricin-type metabolites are widely present as soluble tricin O-glycosides and tricin-oligolignols in all grass species examined, but only show patchy occurrences in unrelated lineages in dicots. More strikingly, tricin is a lignin monomer in grasses and several other angiosperm species, representing one of the "non-monolignol" lignin monomers identified in nature. The unique biological functions of tricin especially as a lignin monomer have driven the identification and characterization of tricin biosynthetic enzymes in the past decade. This review summarizes the current understanding of tricin biosynthetic pathway in grasses and tricin-accumulating dicots. The characterized and potential enzymes involved in tricin biosynthesis are highlighted along with discussion on the debatable and uncharacterized steps. Finally, current developments of bioengineering on manipulating tricin biosynthesis toward the generation of functional food as well as modifications of lignin for improving biorefinery applications are summarized.
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Affiliation(s)
- Pui Ying Lam
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Andy C. W. Lui
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Lanxiang Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hongjia Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
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16
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Waseem M, Huang F, Wang Q, Aslam MM, Abbas F, Ahmad F, Ashraf U, Hassan W, Fiaz S, Ye X, Yu L, Ke Y. Identification, methylation profiling, and expression analysis of stress-responsive cytochrome P450 genes in rice under abiotic and phytohormones stresses. GM CROPS & FOOD 2021; 12:551-563. [PMID: 33877001 PMCID: PMC8820252 DOI: 10.1080/21645698.2021.1908813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cytochrome P450 (CYP) is a large and complex eukaryotic gene superfamily with enzymatic activities involved in several physiological and regulatory processes. As an objective, an in-silico genome-wide DNA methylation (5mC) analysis was performed in rice (Oryza sativa cv. Zhonghua11), and the epigenetic role of CYPs in two abiotic stresses was observed. Being a stable representative mark, DNA-methylation alters the gene expression under stressful environmental conditions. Rice plants under salinity and drought stresses were analyzed through MeDIP-chip hybridization, and 14 unique genes of the CYP family were identified in the rice genome with varying degrees of methylation. The gene structure, promoter sequences, and phylogenetic analysis were performed. Furthermore, the responses of CYPs to various abiotic stresses, including salinity, drought, and cold were revealed. Similarly, the expression profile of potential CYPs was also investigated under various phytohormone stresses, which revealed the potential involvement of CYPs to hormone regulations. Overall, the current study provides evidence for CYP's stress regulation and fundamental for further characterization and understanding their epigenetic roles in gene expression regulation and environmental stress regulation in higher plants.
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Affiliation(s)
- Muhammad Waseem
- College of Horticulture, South China Agricultural University, P.R. China
| | - Feiyan Huang
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Centre, Kunming University, Kunming China
| | - Qiyu Wang
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Centre, Kunming University, Kunming China
| | - Mehtab Muhammad Aslam
- College of Life Sciences, Joint International Research Laboratory of Water and 5 Nutrient in Cops, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Farhat Abbas
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou P.R. China
| | - Fiaz Ahmad
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing PR China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education Lahore, Punjab, Pakistan
| | - Waseem Hassan
- Institute of Environment and Sustainable Development in Agricultural, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Xianwen Ye
- Kunming Tobacco Corporation of Yunnan Province, Kunming China
| | - Lei Yu
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Centre, Kunming University, Kunming China
| | - Yanguo Ke
- College of Economics and Management, Kunming University, Kunming China
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17
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Transcriptomic Analyses Shed Light on Critical Genes Associated with Bibenzyl Biosynthesis in Dendrobium officinale. PLANTS 2021; 10:plants10040633. [PMID: 33810588 PMCID: PMC8065740 DOI: 10.3390/plants10040633] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 11/25/2022]
Abstract
The Dendrobium plants (members of the Orchidaceae family) are used as traditional Chinese medicinal herbs. Bibenzyl, one of the active compounds in Dendrobium officinale, occurs in low amounts among different tissues. However, market demands require a higher content of thes compounds to meet the threshold for drug production. There is, therefore, an immediate need to dissect the physiological and molecular mechanisms underlying how bibenzyl compounds are biosynthesized in D. officinale tissues. In this study, the accumulation of erianin and gigantol in tissues were studied as representative compounds of bibenzyl. Exogenous application of Methyl-Jasmonate (MeJA) promotes the biosynthesis of bibenzyl compounds; therefore, transcriptomic analyses were conducted between D. officinale-treated root tissues and a control. Our results show that the root tissues contained the highest content of bibenzyl (erianin and gigantol). We identified 1342 differentially expressed genes (DEGs) with 912 up-regulated and 430 down-regulated genes in our transcriptome dataset. Most of the identified DEGs are functionally involved in the JA signaling pathway and the biosynthesis of secondary metabolites. We also identified two candidate cytochrome P450 genes and nine other enzymatic genes functionally involved in bibenzyl biosynthesis. Our study provides insights on the identification of critical genes associated with bibenzyl biosynthesis and accumulation in Dendrobium plants, paving the way for future research on dissecting the physiological and molecular mechanisms of bibenzyl synthesis in plants as well as guide genetic engineering for the improvement of Dendrobium varieties through increasing bibenzyl content for drug production and industrialization.
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18
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Li DD, Ni R, Wang PP, Zhang XS, Wang PY, Zhu TT, Sun CJ, Liu CJ, Lou HX, Cheng AX. Molecular Basis for Chemical Evolution of Flavones to Flavonols and Anthocyanins in Land Plants. PLANT PHYSIOLOGY 2020; 184:1731-1743. [PMID: 33023939 PMCID: PMC7723094 DOI: 10.1104/pp.20.01185] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/26/2020] [Indexed: 05/20/2023]
Abstract
During the course of evolution of land plants, different classes of flavonoids, including flavonols and anthocyanins, sequentially emerged, facilitating adaptation to the harsh terrestrial environment. Flavanone 3β-hydroxylase (F3H), an enzyme functioning in flavonol and anthocyanin biosynthesis and a member of the 2-oxoglutarate-dependent dioxygenase (2-ODD) family, catalyzes the hydroxylation of (2S)-flavanones to dihydroflavonols, but its origin and evolution remain elusive. Here, we demonstrate that functional flavone synthase Is (FNS Is) are widely distributed in the primitive land plants liverworts and evolutionarily connected to seed plant F3Hs. We identified and characterized a set of 2-ODD enzymes from several liverwort species and plants in various evolutionary clades of the plant kingdom. The bifunctional enzyme FNS I/F2H emerged in liverworts, and FNS I/F3H evolved in Physcomitrium (Physcomitrella) patens and Selaginella moellendorffii, suggesting that they represent the functional transition forms between canonical FNS Is and F3Hs. The functional transition from FNS Is to F3Hs provides a molecular basis for the chemical evolution of flavones to flavonols and anthocyanins, which contributes to the acquisition of a broader spectrum of flavonoids in seed plants and facilitates their adaptation to the terrestrial ecosystem.
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Affiliation(s)
- Dan-Dan Li
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Rong Ni
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Ping-Ping Wang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Xiao-Shuang Zhang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Piao-Yi Wang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Ting-Ting Zhu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Chun-Jing Sun
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
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19
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Sielemann K, Hafner A, Pucker B. The reuse of public datasets in the life sciences: potential risks and rewards. PeerJ 2020; 8:e9954. [PMID: 33024631 PMCID: PMC7518187 DOI: 10.7717/peerj.9954] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
The 'big data' revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define 'successful reuse' as the use of previously published data to enable novel scientific findings. By using selected examples of successful reuse from different disciplines, we illustrate the enormous potential of the practice, while acknowledging the respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of this practice as a norm has the potential to benefit all stakeholders in the life sciences.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany
| | - Alenka Hafner
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Current Affiliation: Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, United States of America
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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20
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Chen Y, Klinkhamer PGL, Memelink J, Vrieling K. Diversity and evolution of cytochrome P450s of Jacobaea vulgaris and Jacobaea aquatica. BMC PLANT BIOLOGY 2020; 20:342. [PMID: 32689941 PMCID: PMC7372880 DOI: 10.1186/s12870-020-02532-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Collectively, plants produce a huge variety of secondary metabolites (SMs) which are involved in the adaptation of plants to biotic and abiotic stresses. The most characteristic feature of SMs is their striking inter- and intraspecific chemical diversity. Cytochrome P450 monooxygenases (CYPs) often play an important role in the biosynthesis of SMs and thus in the evolution of chemical diversity. Here we studied the diversity and evolution of CYPs of two Jacobaea species which contain a characteristic group of SMs namely the pyrrolizidine alkaloids (PAs). RESULTS We retrieved CYPs from RNA-seq data of J. vulgaris and J. aquatica, resulting in 221 and 157 full-length CYP genes, respectively. The analyses of conserved motifs confirmed that Jacobaea CYP proteins share conserved motifs including the heme-binding signature, the PERF motif, the K-helix and the I-helix. KEGG annotation revealed that the CYPs assigned as being SM metabolic pathway genes were all from the CYP71 clan but no CYPs were assigned as being involved in alkaloid pathways. Phylogenetic analyses of full-length CYPs were conducted for the six largest CYP families of Jacobaea (CYP71, CYP76, CYP706, CYP82, CYP93 and CYP72) and were compared with CYPs of two other members of the Asteraceae, Helianthus annuus and Lactuca sativa, and with Arabidopsis thaliana. The phylogenetic trees showed strong lineage specific diversification of CYPs, implying that the evolution of CYPs has been very fast even within the Asteraceae family. Only in the closely related species J. vulgaris and J. aquatica, CYPs were found often in pairs, confirming a close relationship in the evolutionary history. CONCLUSIONS This study discovered 378 full-length CYPs in Jacobaea species, which can be used for future exploration of their functions, including possible involvement in PA biosynthesis and PA diversity.
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Affiliation(s)
- Yangan Chen
- Plant Ecology and Phytochemistry, Institute of Biology, Leiden University, Sylviusweg 72, P. O. Box 9505, 2300 RA, Leiden, The Netherlands
- Plant Cell Physiology, Institute of Biology, Leiden University, Sylviusweg 72, P. O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Peter G L Klinkhamer
- Plant Ecology and Phytochemistry, Institute of Biology, Leiden University, Sylviusweg 72, P. O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Johan Memelink
- Plant Cell Physiology, Institute of Biology, Leiden University, Sylviusweg 72, P. O. Box 9505, 2300 RA, Leiden, The Netherlands.
| | - Klaas Vrieling
- Plant Ecology and Phytochemistry, Institute of Biology, Leiden University, Sylviusweg 72, P. O. Box 9505, 2300 RA, Leiden, The Netherlands.
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21
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Sanchez-Muñoz R, Perez-Mata E, Almagro L, Cusido RM, Bonfill M, Palazon J, Moyano E. A Novel Hydroxylation Step in the Taxane Biosynthetic Pathway: A New Approach to Paclitaxel Production by Synthetic Biology. Front Bioeng Biotechnol 2020; 8:410. [PMID: 32528936 PMCID: PMC7247824 DOI: 10.3389/fbioe.2020.00410] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/14/2020] [Indexed: 11/13/2022] Open
Abstract
Engineered plant cell lines have the potential to achieve enhanced metabolite production rates, providing a high-yielding source of compounds of interest. Improving the production of taxanes, pharmacologically valuable secondary metabolites of Taxus spp., is hindered by an incomplete knowledge of the taxane biosynthetic pathway. Of the five unknown steps, three are thought to involve cytochrome P450-like hydroxylases. In the current work, after an in-depth in silico characterization of four candidate enzymes proposed in a previous cDNA-AFLP assay, TB506 was selected as a candidate for the hydroxylation of the taxane side chain. A docking assay indicated TB506 is active after the attachment of the side chain based on its affinity to the ligand 3'N-dehydroxydebenzoyltaxol. Finally, the involvement of TB506 in the last hydroxylation step of the paclitaxel biosynthetic pathway was confirmed by functional assays. The identification of this hydroxylase will contribute to the development of alternative sustainable paclitaxel production systems using synthetic biology techniques.
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Affiliation(s)
- Raul Sanchez-Muñoz
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Edgar Perez-Mata
- Secció de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, Barcelona, Spain
| | - Lorena Almagro
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Rosa M. Cusido
- Secció de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, Barcelona, Spain
| | - Mercedes Bonfill
- Secció de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, Barcelona, Spain
| | - Javier Palazon
- Secció de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, Barcelona, Spain
| | - Elisabeth Moyano
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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22
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Suzuki H, Fukushima EO, Shimizu Y, Seki H, Fujisawa Y, Ishimoto M, Osakabe K, Osakabe Y, Muranaka T. Lotus japonicus Triterpenoid Profile and Characterization of the CYP716A51 and LjCYP93E1 Genes Involved in Their Biosynthesis In Planta. PLANT & CELL PHYSIOLOGY 2019; 60:2496-2509. [PMID: 31418782 DOI: 10.1093/pcp/pcz145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 07/12/2019] [Indexed: 05/23/2023]
Abstract
Lotus japonicus is an important model legume plant in several fields of research, such as secondary (specialized) metabolism and symbiotic nodulation. This plant accumulates triterpenoids; however, less information regarding its composition, content and biosynthesis is available compared with Medicago truncatula and Glycine max. In this study, we analyzed the triterpenoid content and composition of L. japonicus. Lotus japonicus accumulated C-28-oxidized triterpenoids (ursolic, betulinic and oleanolic acids) and soyasapogenols (soyasapogenol B, A and E) in a tissue-dependent manner. We identified an oxidosqualene cyclase (OSC) and two cytochrome P450 enzymes (P450s) involved in triterpenoid biosynthesis using a yeast heterologous expression system. OSC9 was the first enzyme derived from L. japonicus that showed α-amyrin (a precursor of ursolic acid)-producing activity. CYP716A51 showed triterpenoid C-28 oxidation activity. LjCYP93E1 converted β-amyrin into 24-hydroxy-β-amyrin, a metabolic intermediate of soyasapogenols. The involvement of the identified genes in triterpenoid biosynthesis in L. japonicus plants was evaluated by quantitative real-time PCR analysis. Furthermore, gene loss-of-function analysis of CYP716A51 and LjCYP93E1 was conducted. The cyp716a51-mutant L. japonicus hairy roots generated by the genome-editing technique produced no C-28 oxidized triterpenoids. Likewise, the complete abolition of soyasapogenols and soyasaponin I was observed in mutant plants harboring Lotus retrotransposon 1 (LORE1) in LjCYP93E1. These results indicate that the activities of these P450 enzymes are essential for triterpenoid biosynthesis in L. japonicus. This study increases our understanding of triterpenoid biosynthesis in leguminous plants and provides information that will facilitate further studies of the physiological functions of triterpenoids using L. japonicus.
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Affiliation(s)
- Hayato Suzuki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
| | - Ery Odette Fukushima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
- Universidad Regional Amaz�nica IKIAM, Km 7 Via Muyuna, Napo, Tena, Ecuador
| | - Yuko Shimizu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
| | - Hikaru Seki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
| | - Yukiko Fujisawa
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Masao Ishimoto
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Keishi Osakabe
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Yuriko Osakabe
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
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23
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Bannoud F, Ellison S, Paolinelli M, Horejsi T, Senalik D, Fanzone M, Iorizzo M, Simon PW, Cavagnaro PF. Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2485-2507. [PMID: 31144001 DOI: 10.1007/s00122-019-03366-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/17/2019] [Indexed: 05/08/2023]
Abstract
Inheritance, QTL mapping, phylogenetic, and transcriptome (RNA-Seq) analyses provide insight into the genetic control underlying carrot root and leaf tissue-specific anthocyanin pigmentation and identify candidate genes for root phloem pigmentation. Purple carrots can accumulate large quantities of anthocyanins in their root tissues, as well as in other plant parts. This work investigated the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root phloem and xylem, and in leaf petioles. Inheritance of anthocyanin pigmentation in these three tissues was first studied in segregating F2 and F4 populations, followed by QTL mapping of phloem and xylem anthocyanin pigments (independently) onto two genotyping by sequencing-based linkage maps, to reveal two regions in chromosome 3, namely P1 and P3, controlling pigmentation in these three tissues. Both P1 and P3 condition pigmentation in the phloem, with P3 also conditioning pigmentation in the xylem and petioles. By means of linkage mapping, phylogenetic analysis, and comparative transcriptome (RNA-Seq) analysis among carrot roots with differing purple pigmentation phenotypes, we identified candidate genes conditioning pigmentation in the phloem, the main tissue influencing total anthocyanin levels in the root. Among them, a MYB transcription factor, DcMYB7, and two cytochrome CYP450 genes with putative flavone synthase activity were identified as candidates regulating both the presence/absence of pigmentation and the concentration of anthocyanins in the root phloem. Concomitant expression patterns of DcMYB7 and eight anthocyanin structural genes were found, suggesting that DcMYB7 regulates transcription levels in the latter. Another MYB, DcMYB6, was upregulated in specific purple-rooted samples, suggesting a genotype-specific regulatory activity for this gene. These data contribute to the understanding of anthocyanin regulation in the carrot root at a tissue-specific level and maybe instrumental for improving carrot nutritional value.
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Affiliation(s)
- Florencia Bannoud
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
| | - Shelby Ellison
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
| | - Marcos Paolinelli
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria INTA EEA Mendoza, San Martin 3853, Luján de Cuyo, 5507, Mendoza, Argentina
| | - Thomas Horejsi
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
| | - Douglas Senalik
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA
| | - Martín Fanzone
- Instituto Nacional de Tecnología Agropecuaria INTA EEA Mendoza, San Martin 3853, Luján de Cuyo, 5507, Mendoza, Argentina
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA
| | - Philipp W Simon
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA.
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1590, USA.
| | - Pablo F Cavagnaro
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina.
- Instituto de Horticultura, Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza, Argentina.
- Instituto Nacional de Tecnología Agropecuaria (INTA) - E.E.A. La Consulta, Ex Ruta 40 km 96, La Consulta, 5567, San Carlos, Mendoza, Argentina.
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24
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The auxin response factor gene family in allopolyploid Brassica napus. PLoS One 2019; 14:e0214885. [PMID: 30958842 PMCID: PMC6453480 DOI: 10.1371/journal.pone.0214885] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/21/2019] [Indexed: 12/20/2022] Open
Abstract
Auxin response factor (ARF) is a member of the plant-specific B3 DNA binding superfamily. Here, we report the results of a comprehensive analysis of ARF genes in allotetraploid Brassica napus (2n = 38, AACC). Sixty-seven ARF genes were identified in B. napus (BnARFs) and divided into four subfamilies (I–IV). Sixty-one BnARFs were distributed on all chromosomes except C02; the remaining were on Ann and Cnn. The full length of the BnARF proteins was highly conserved especially within each subfamily with all members sharing the N-terminal DNA binding domain (DBD) and the middle region (MR), and most contained the C-terminal dimerization domain (PBI). Twenty-one members had a glutamine-rich MR that may be an activator and the remaining were repressors. Accordingly, the intron patterns are highly conserved in each subfamily or clade, especially in DBD and PBI domains. Several members in subfamily III are potential targets for miR167. Many putative cis-elements involved in phytohormones, light signaling responses, and biotic and abiotic stress were identified in BnARF promoters, implying their possible roles. Most ARF proteins are likely to interact with auxin/indole-3-acetic acid (Aux/IAA) -related proteins, and members from different subfamilies generally shared many common interaction proteins. Whole genome-wide duplication (WGD) by hybridization between Brassica rapa and Brassica oleracea and segmental duplication led to gene expansion. Gene loss following WGD is biased with the An-subgenome retaining more ancestral genes than the Cn-subgenome. BnARFs have wide expression profiles across vegetative and reproductive organs during different developmental stages. No obvious expression bias was observed between An- and Cn-subgenomes. Most synteny-pair genes had similar expression patterns, indicating their functional redundancy. BnARFs were sensitive to exogenous IAA and 6-BA treatments especially subfamily III. The present study provides insights into the distribution, phylogeny, and evolution of ARF gene family.
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25
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Yonekura-Sakakibara K, Higashi Y, Nakabayashi R. The Origin and Evolution of Plant Flavonoid Metabolism. FRONTIERS IN PLANT SCIENCE 2019; 10:943. [PMID: 31428108 PMCID: PMC6688129 DOI: 10.3389/fpls.2019.00943] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/08/2019] [Indexed: 05/18/2023]
Abstract
During their evolution, plants have acquired the ability to produce a huge variety of compounds. Unlike the specialized metabolites that accumulate in limited numbers of species, flavonoids are widely distributed in the plant kingdom. Therefore, a detailed analysis of flavonoid metabolism in genomics and metabolomics is an ideal way to investigate how plants have developed their unique metabolic pathways during the process of evolution. More comprehensive and precise metabolite profiling integrated with genomic information are helpful to emerge unexpected gene functions and/or pathways. The distribution of flavonoids and their biosynthetic genes in the plant kingdom suggests that flavonoid biosynthetic pathways evolved through a series of steps. The enzymes that form the flavonoid scaffold structures probably first appeared by recruitment of enzymes from primary metabolic pathways, and later, enzymes that belong to superfamilies such as 2-oxoglutarate-dependent dioxygenase, cytochrome P450, and short-chain dehydrogenase/reductase modified and varied the structures. It is widely accepted that the first two enzymes in flavonoid biosynthesis, chalcone synthase, and chalcone isomerase, were derived from common ancestors with enzymes in lipid metabolism. Later enzymes acquired their function by gene duplication and the subsequent acquisition of new functions. In this review, we describe the recent progress in metabolomics technologies for flavonoids and the evolution of flavonoid skeleton biosynthetic enzymes to understand the complicate evolutionary traits of flavonoid metabolism in plant kingdom.
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26
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Liu X, He Z, Yin Y, Xu X, Wu W, Li L. Transcriptome sequencing and analysis during seed growth and development in Euryale ferox Salisb. BMC Genomics 2018; 19:343. [PMID: 29743016 PMCID: PMC5944168 DOI: 10.1186/s12864-018-4707-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 04/22/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Euryale ferox Salisb., an annual aquatic plant, is the only species in the genus Euryale in the Nymphaeaceae. Seeds of E. ferox are a nutritious food and also used in traditional Chinese medicine (Qian Shi in Mandarin). The molecular events that occurred during seed development in E. ferox have not yet been characterized. In this study, we performed transcriptomic analysis of four developmental stages (T1, T2, T3, and T4) in E. ferox seeds with three biological replicates per developmental stage to understand the physiological and biochemical processes during E. ferox seeds development. RESULTS 313,844,425 clean reads were assembled into 160,107 transcripts and 85,006 unigenes with N50 lengths of 2052 bp and 1399 bp, respectively. The unigenes were annotated using five public databases (NR, COG, Swiss-Prot, KEGG, and GO). In the KEGG database, all of the unigenes were assigned to 127 pathways, of which phenylpropanoid biosynthesis was associated with the synthesis of secondary metabolites during E. ferox seed growth and development. Phenylalanine ammonia-lyase (PAL) as the first key enzyme catalyzed the conversion of phenylalanine to trans-cinnamic acid, then was related to the synthesis of flavonoids, lignins and alkaloid. The expression of PAL1 reached its peak at T3 stage, followed by a slight decrease at T4 stage. Cytochrome P450 (P450), encoded by CYP84A1 (which also called ferulate-5-hydroxylase (F5H) in Arabidopsis), was mainly involved in the biosynthesis of lignins. CONCLUSIONS Our study provides a transcriptomic analysis to better understand the morphological changes and the accumulation of medicinal components during E. ferox seed development. The increasing expression of PAL and P450 encoded genes in phenylpropanoid biosynthesis may promote the maturation of E. ferox seed including size, color, hardness and accumulation of medicinal components.
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Affiliation(s)
- Xian Liu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Yulai Yin
- Suzhou Vegetable Research Institute, 188 Xitang Road, Suzhou, Jiangsu Province 215008 People’s Republic of China
| | - Xu Xu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Weiwen Wu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Liangjun Li
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
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27
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Albert NW, Thrimawithana AH, McGhie TK, Clayton WA, Deroles SC, Schwinn KE, Bowman JL, Jordan BR, Davies KM. Genetic analysis of the liverwort Marchantia polymorpha reveals that R2R3MYB activation of flavonoid production in response to abiotic stress is an ancient character in land plants. THE NEW PHYTOLOGIST 2018; 218:554-566. [PMID: 29363139 DOI: 10.1111/nph.15002] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/19/2017] [Indexed: 05/21/2023]
Abstract
The flavonoid pathway is hypothesized to have evolved during land colonization by plants c. 450 Myr ago for protection against abiotic stresses. In angiosperms, R2R3MYB transcription factors are key for environmental regulation of flavonoid production. However, angiosperm R2R3MYB gene families are larger than those of basal plants, and it is not known whether the regulatory system is conserved across land plants. We examined whether R2R3MYBs regulate the flavonoid pathway in liverworts, one of the earliest diverging land plant lineages. We characterized MpMyb14 from the liverwort Marchantia polymorpha using genetic mutagenesis, transgenic overexpression, gene promoter analysis, and transcriptomic and chemical analysis. MpMyb14 is phylogenetically basal to characterized angiosperm R2R3MYB flavonoid regulators. Mpmyb14 knockout lines lost all red pigmentation from the flavonoid riccionidin A, whereas overexpression conferred production of large amounts of flavones and riccionidin A, activation of associated biosynthetic genes, and constitutive red pigmentation. MpMyb14 expression and flavonoid pigmentation were induced by light- and nutrient-deprivation stress in M. polymorpha as for anthocyanins in angiosperms. MpMyb14 regulates stress-induced flavonoid production in M. polymorpha, and is essential for red pigmentation. This suggests that R2R3MYB regulated flavonoid production is a conserved character across land plants which arose early during land colonization.
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Affiliation(s)
- Nick W Albert
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
| | - Amali H Thrimawithana
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Tony K McGhie
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
| | - William A Clayton
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, 7647, New Zealand
| | - Simon C Deroles
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Brian R Jordan
- Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, 7647, New Zealand
| | - Kevin M Davies
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
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28
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Liu F, Chen JR, Tang YH, Chang HT, Yuan YM, Guo Q. Isolation and characterization of cinnamate 4-hydroxylase gene from cultivated ramie ( Boehmeria nivea). BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2017.1418675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Fang Liu
- College of Agriculture, Ramie Institute, Hunan Agricultural University, Changsha, PR China
- Laboratory of Economic Animal and Plant Quality Control and Application, College of Biological and Environmental Engineering, Changsha University, Changsha, PR China
| | - Jian-Rong Chen
- Laboratory of Economic Animal and Plant Quality Control and Application, College of Biological and Environmental Engineering, Changsha University, Changsha, PR China
| | - Ying-Hong Tang
- College of Agriculture, Ramie Institute, Hunan Agricultural University, Changsha, PR China
| | - Hong-Tao Chang
- College of Agriculture, Ramie Institute, Hunan Agricultural University, Changsha, PR China
| | - You-Mei Yuan
- College of Agriculture, Ramie Institute, Hunan Agricultural University, Changsha, PR China
| | - Qingquan Guo
- College of Agriculture, Ramie Institute, Hunan Agricultural University, Changsha, PR China
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