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Cabello-Hurtado F, El Amrani A. Phenanthrene-Induced Cytochrome P450 Genes and Phenanthrene Tolerance Associated with Arabidopsis thaliana CYP75B1 Gene. PLANTS (BASEL, SWITZERLAND) 2024; 13:1692. [PMID: 38931123 PMCID: PMC11207427 DOI: 10.3390/plants13121692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) form an important group of organic pollutants due to their distribution in the environment and their carcinogenic and/or mutagenic effects. In order to identify at the molecular level some of the players in the biodegradation and tolerance response to PAHs in plants, we have phenotyped 32 Arabidopsis thaliana T-DNA mutant lines corresponding to 16 cytochrome P450 (CYP) genes that showed to be differentially expressed under contrasted stress conditions induced by phenanthrene, a 3-ring PAH. This screening has allowed us to identify CYP75B1 (At5g07990) T-DNA mutants as the only ones being sensitive to phenanthrene-induced stress, supporting that CYP75B1 protein is necessary for PAH tolerance. CYP75B1 codes for a 3'flavonol hydroxylase. CYP75B1 gene was heterologously expressed on yeast in order to investigate whether it affects the A. thaliana response to phenanthrene by participating in its metabolization. Heterologously-produced CYP75B1 enzyme shows to be catalytically efficient against its physiological substrates (e.g., naringenin) but unable to metabolize phenanthrene or 9-phenanthrenol. In contrast, CYP75B1 seems rather involved in phenanthrene tolerance as a crucial element by regulating concentration of antioxidants through the production of 3'-hydroxylated flavonoids such as quercetin and cyanidin. In particular, we report a highly increased generation of reactive oxygen species (H2O2 and singlet oxygen) in cyp75b1 mutants compared to control plants in response to phenanthrene treatment. Overall, CYP75B1 shows to play an important role in the response to the deleterious effects of phenanthrene exposure and this is related to oxidative stress sensitivity rather than metabolization.
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2
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Karimzadegan V, Koirala M, Sobhanverdi S, Merindol N, Majhi BB, Gélinas SE, Timokhin VI, Ralph J, Dastmalchi M, Desgagné-Penix I. Characterization of cinnamate 4-hydroxylase (CYP73A) and p-coumaroyl 3'-hydroxylase (CYP98A) from Leucojum aestivum, a source of Amaryllidaceae alkaloids. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108612. [PMID: 38598867 DOI: 10.1016/j.plaphy.2024.108612] [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: 11/27/2023] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Biosynthesis of Amaryllidaceae alkaloids (AA) starts with the condensation of tyramine with 3,4-dihydroxybenzaldehyde. The latter derives from the phenylpropanoid pathway that involves modifications of trans-cinnamic acid, p-coumaric acid, caffeic acid, and possibly 4-hydroxybenzaldehyde, all potentially catalyzed by hydroxylase enzymes. Leveraging bioinformatics, molecular biology techniques, and cell biology tools, this research identifies and characterizes key enzymes from the phenylpropanoid pathway in Leucojum aestivum. Notably, we focused our work on trans-cinnamate 4-hydroxylase (LaeC4H) and p-coumaroyl shikimate/quinate 3'-hydroxylase (LaeC3'H), two key cytochrome P450 enzymes, and on the ascorbate peroxidase/4-coumarate 3-hydroxylase (LaeAPX/C3H). Although LaeAPX/C3H consumed p-coumaric acid, it did not result in the production of caffeic acid. Yeasts expressing LaeC4H converted trans-cinnamate to p-coumaric acid, whereas LaeC3'H catalyzed specifically the 3-hydroxylation of p-coumaroyl shikimate, rather than of free p-coumaric acid or 4-hydroxybenzaldehyde. In vivo assays conducted in planta in this study provided further evidence for the contribution of these enzymes to the phenylpropanoid pathway. Both enzymes demonstrated typical endoplasmic reticulum membrane localization in Nicotiana benthamiana adding spatial context to their functions. Tissue-specific gene expression analysis revealed roots as hotspots for phenylpropanoid-related transcripts and bulbs as hubs for AA biosynthetic genes, aligning with the highest AAs concentration. This investigation adds valuable insights into the phenylpropanoid pathway within Amaryllidaceae, laying the foundation for the development of sustainable production platforms for AAs and other bioactive compounds with diverse applications.
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Affiliation(s)
- Vahid Karimzadegan
- Department of Chemistry, Biochemistry and Physics, Université Du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Manoj Koirala
- Department of Chemistry, Biochemistry and Physics, Université Du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Sajjad Sobhanverdi
- Department of Chemistry, Biochemistry and Physics, Université Du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Natacha Merindol
- Department of Chemistry, Biochemistry and Physics, Université Du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Bharat Bhusan Majhi
- Department of Chemistry, Biochemistry and Physics, Université Du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Sarah-Eve Gélinas
- Department of Chemistry, Biochemistry and Physics, Université Du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Vitaliy I Timokhin
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, 53726, USA
| | - John Ralph
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, 53726, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Mehran Dastmalchi
- Department of Plant Science, McGill University, Montréal, Québec, Canada
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université Du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada.
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3
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Zhao Y, Chen Y, Gao M, Wang Y. Alcohol dehydrogenases regulated by a MYB44 transcription factor underlie Lauraceae citral biosynthesis. PLANT PHYSIOLOGY 2024; 194:1674-1691. [PMID: 37831423 DOI: 10.1093/plphys/kiad553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023]
Abstract
Lineage-specific terpenoids have arisen throughout the evolution of land plants and are believed to play a role in interactions between plants and the environment. Species-specific gene clusters in plants have provided insight on the evolution of secondary metabolism. Lauraceae is an ecologically important plant family whose members are also of considerable economic value given their monoterpene contents. However, the gene cluster responsible for the biosynthesis of monoterpenes remains yet to be elucidated. Here, a Lauraceae-specific citral biosynthetic gene cluster (CGC) was identified and investigated using a multifaceted approach that combined phylogenetic, collinearity, and biochemical analyses. The CGC comprises MYB44 as a regulator and 2 alcohol dehydrogenases (ADHs) as modifying enzymes, which derived from species-specific tandem and proximal duplication events. Activity and substrate divergence of the ADHs has resulted in the fruit of mountain pepper (Litsea cubeba), a core Lauraceae species, consisting of more than 80% citral. In addition, MYB44 negatively regulates citral biosynthesis by directly binding to the promoters of the ADH-encoding genes. The aggregation of citral biosynthetic pathways suggests that they may form the basis of important characteristics that enhance adaptability. The findings of this study provide insights into the evolution of and the regulatory mechanisms involved in plant terpene biosynthesis.
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Affiliation(s)
- Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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4
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Zhao L, Zhou W, He J, Li DZ, Li HT. Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant. eLife 2024; 12:RP89941. [PMID: 38353667 PMCID: PMC10942601 DOI: 10.7554/elife.89941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioecious Trichosanthes pilosa (Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - Wei Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - Jun He
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
- Kunming College of Life Science, University of Chinese Academy of SciencesKunmingChina
| | - Hong-Tao Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
- Kunming College of Life Science, University of Chinese Academy of SciencesKunmingChina
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5
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Wang J, Lian L, Qi J, Fang Y, Nyporko A, Yu Q, Bai L, Pan L. Metabolic resistance to acetolactate synthase inhibitors in Beckmannia syzigachne: identification of CYP81Q32 and its transcription regulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:317-334. [PMID: 37009643 DOI: 10.1111/tpj.16227] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/15/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
Frequent herbicide use selects for herbicide resistance in weeds. Cytochrome P450s are important detoxification enzymes responsible for herbicide resistance in plants. We identified and characterized a candidate P450 gene (BsCYP81Q32) from the problematic weed Beckmannia syzigachne to test whether it conferred metabolic resistance to the acetolactate synthase-inhibiting herbicides mesosulfuron-methyl, bispyribac-sodium, and pyriminobac-methyl. Transgenic rice overexpressing BsCYP81Q32 was resistant to the three herbicides. Equally, rice overexpressing the rice ortholog gene OsCYP81Q32 was more resistant to mesosulfuron-methyl. Conversely, an OsCYP81Q32 gene knockout generated using CRISPR/Cas9 enhanced mesosulfuron-methyl sensitivity in rice. Overexpression of the BsCYP81Q32 gene resulted in enhanced mesosulfuron-methyl metabolism in transgenic rice seedlings via O-demethylation. The major metabolite, demethylated mesosulfuron-methyl, was chemically synthesized and displayed reduced herbicidal effect in plants. Moreover, a transcription factor (BsTGAL6) was identified and shown to bind a key region in the BsCYP81Q32 promoter for gene activation. Inhibition of BsTGAL6 expression by salicylic acid treatment in B. syzigachne plants reduced BsCYP81Q32 expression and consequently changed the whole plant response to mesosulfuron-methyl. Sequence polymorphisms in an important region of the BsTGAL6 promoter may explain the higher expression of BsTGAL6 in resistant versus susceptible B. syzigachne plants. Collectively, the present study reveals the evolution of an herbicide-metabolizing and resistance-endowing P450 and its transcription regulation in an economically important weedy plant species.
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Affiliation(s)
- Junzhi Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
- Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Lei Lian
- Guizhou University, Guiyang, 550025, China
| | - Jiale Qi
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Yuhang Fang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Alex Nyporko
- Taras Shevchenko National University of Kyiv, Kiev, 01033, Ukraine
| | - Qin Yu
- Australian Herbicide Resistance Initiative (AHRI), School of Agriculture and Environment, University of Western Australia, Perth, WA, 6009, Australia
| | - Lianyang Bai
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
- Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Guizhou University, Guiyang, 550025, China
| | - Lang Pan
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
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6
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Werck-Reichhart D. Promiscuity, a Driver of Plant Cytochrome P450 Evolution? Biomolecules 2023; 13:biom13020394. [PMID: 36830762 PMCID: PMC9953472 DOI: 10.3390/biom13020394] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Plant cytochrome P450 monooxygenases were long considered to be highly substrate-specific, regioselective and stereoselective enzymes, in this respect differing from their animal counterparts. The functional data that have recently accumulated clearly counter this initial dogma. Highly promiscuous P450 enzymes have now been reported, mainly in terpenoid pathways with functions in plant adaptation, but also some very versatile xenobiotic/herbicide metabolizers. An overlap and predictable interference between endogenous and herbicide metabolism are starting to emerge. Both substrate preference and permissiveness vary between plant P450 families, with high promiscuity seemingly favoring retention of gene duplicates and evolutionary blooms. Yet significant promiscuity can also be observed in the families under high negative selection and with essential functions, usually enhanced after gene duplication. The strategies so far implemented, to systematically explore P450 catalytic capacity, are described and discussed.
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Affiliation(s)
- Danièle Werck-Reichhart
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France
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7
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Liu X, Gong Q, Zhao C, Wang D, Ye X, Zheng G, Wang Y, Cao J, Sun C. Genome-wide analysis of cytochrome P450 genes in Citrus clementina and characterization of a CYP gene encoding flavonoid 3'-hydroxylase. HORTICULTURE RESEARCH 2023; 10:uhac283. [PMID: 36818367 PMCID: PMC9930397 DOI: 10.1093/hr/uhac283] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
Cytochrome P450s (CYPs) are the largest family of enzymes in plant and play multifarious roles in development and defense but the available information about the CYP superfamily in citrus is very limited. Here we provide a comprehensive genome-wide analysis of the CYP superfamily in Citrus clementina genome, identifying 301 CYP genes grouped into ten clans and 49 families. The characteristics of both gene structures and motif compositions strongly supported the reliability of the phylogenetic relationship. Duplication analysis indicated that tandem duplication was the major driving force of expansion for this superfamily. Promoter analysis revealed numerous cis-acting elements related to various responsiveness. RNA-seq data elucidated their expression patterns in citrus fruit peel both during development and in response to UV-B. Furthermore, we characterize a UV-B-induced CYP gene (Ciclev10019637m, designated CitF3'H) as a flavonoid 3'-hydroxylase for the first time. CitF3'H catalyzed numerous flavonoids and favored naringenin in yeast assays. Virus-induced silencing of CitF3'H in citrus seedlings significantly reduced the levels of 3'-hydroxylated flavonoids and their derivatives. These results together with the endoplasmic reticulum-localization of CitF3'H in plant suggest that this enzyme is responsible for the biosynthesis of 3'-hydroxylated flavonoids in citrus. Taken together, our findings provide extensive information about the CYP superfamily in citrus and contribute to further functional verification.
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Affiliation(s)
- Xiaojuan Liu
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
| | - Qin Gong
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
| | - Chenning Zhao
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
| | - Dengliang Wang
- Institute of Fruit Tree Research, Quzhou Academy of Agriculture and Forestry Acience, Quzhou, China
| | - Xianming Ye
- Research and Development Department, Zhejiang Jianong Fruit &Vegetable Co., Ltd, Quzhou, China
| | - Guixia Zheng
- Research and Development Department, Zhejiang Jianong Fruit &Vegetable Co., Ltd, Quzhou, China
| | - Yue Wang
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
| | - Jinping Cao
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
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8
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Smit SJ, Lichman BR. Plant biosynthetic gene clusters in the context of metabolic evolution. Nat Prod Rep 2022; 39:1465-1482. [PMID: 35441651 PMCID: PMC9298681 DOI: 10.1039/d2np00005a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 12/17/2022]
Abstract
Covering: up to 2022Plants produce a wide range of structurally and biosynthetically diverse natural products to interact with their environment. These specialised metabolites typically evolve in limited taxonomic groups presumably in response to specific selective pressures. With the increasing availability of sequencing data, it has become apparent that in many cases the genes encoding biosynthetic enzymes for specialised metabolic pathways are not randomly distributed on the genome. Instead they are physically linked in structures such as arrays, pairs and clusters. The exact function of these clusters is debated. In this review we take a broad view of gene arrangement in plant specialised metabolism, examining types of structures and variation. We discuss the evolution of biosynthetic gene clusters in the wider context of metabolism, populations and epigenetics. Finally, we synthesise our observations to propose a new hypothesis for biosynthetic gene cluster formation in plants.
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Affiliation(s)
- Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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9
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Zhou X, Liu Z. Unlocking plant metabolic diversity: A (pan)-genomic view. PLANT COMMUNICATIONS 2022; 3:100300. [PMID: 35529944 PMCID: PMC9073316 DOI: 10.1016/j.xplc.2022.100300] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 05/28/2023]
Abstract
Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life cycles. However, unlocking this metabolic diversity is significantly impeded by the size, complexity, and abundant repetitive elements of typical plant genomes. As genome sequencing becomes routine, we anticipate that links between metabolic diversity and genetic variation will be strengthened. In addition, an ever-increasing number of plant genomes have revealed that biosynthetic gene clusters are not only a hallmark of microbes and fungi; gene clusters for various classes of compounds have also been found in plants, and many are associated with important agronomic traits. We present recent examples of plant metabolic diversification that have been discovered through the exploration and exploitation of various genomic and pan-genomic data. We also draw attention to the fundamental genomic and pan-genomic basis of plant chemodiversity and discuss challenges and future perspectives for investigating metabolic diversity in the coming pan-genomics era.
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Affiliation(s)
- Xuan Zhou
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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SNORKEL Genes Relating to Flood Tolerance Were Pseudogenized in Normal Cultivated Rice. PLANTS 2022; 11:plants11030376. [PMID: 35161357 PMCID: PMC8840289 DOI: 10.3390/plants11030376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022]
Abstract
SNORKEL1 (SK1) and SNORKEL2 (SK2) are ethylene responsive factors that regulate the internode elongation of deepwater rice in response to submergence. We previously reported that normal cultivated rice lacks SK genes because the Chromosome 12 region containing SK genes was deleted from its genome. However, no study has analyzed how the genome defect occurred in that region by comparing normal cultivated rice and deepwater rice. In this study, comparison of the sequence of the end of Chromosome 12, which contains SK genes, between normal and deepwater rice showed that complicated genome changes such as insertions, deletions, inversions, substitutions, and translocation occurred frequently in this region. In addition to SK1 and SK2 of deepwater rice, gene prediction analysis identified four genes containing AP2/ERF domains in normal cultivated rice and six in deepwater rice; we called these genes SK-LIKE (SKL) genes. SKs and SKLs were present in close proximity to each other, and the SKLs in normal cultivated rice were in tandem. These predicted genes belong to the same AP2/ERF subfamily and were separated into four types: SK1, SK2, SKL3, and SKL4. Sequence comparison indicated that normal cultivated rice possesses a gene with high homology to SK2, which we named SKL1. However, none of the predicted SKLs except for SKL3s were expressed during submergence. Although SKL3s were expressed in both normal and deepwater rice, normal rice does not undergo internode elongation, suggesting that its expression does not contribute to internode elongation. Plants overexpressing SKL1, which showed the most homology to SK2, underwent internode elongation similar to plants overexpressing SK1 and SK2 under normal growth conditions. A yeast one-hybrid assay showed that the C-end of SKL1 has transcription activity, as do the C-ends of SK1 and SK2. Our results suggested that SKLs were derived via gene duplication, but were not expressed and pseudogenized in normal cultivated rice during sequence evolution.
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11
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Hansen CC, Nelson DR, Møller BL, Werck-Reichhart D. Plant cytochrome P450 plasticity and evolution. MOLECULAR PLANT 2021; 14:1244-1265. [PMID: 34216829 DOI: 10.1016/j.molp.2021.06.028] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/28/2021] [Accepted: 06/30/2021] [Indexed: 05/27/2023]
Abstract
The superfamily of cytochrome P450 (CYP) enzymes plays key roles in plant evolution and metabolic diversification. This review provides a status on the CYP landscape within green algae and land plants. The 11 conserved CYP clans known from vascular plants are all present in green algae and several green algae-specific clans are recognized. Clan 71, 72, and 85 remain the largest CYP clans and include many taxa-specific CYP (sub)families reflecting emergence of linage-specific pathways. Molecular features and dynamics of CYP plasticity and evolution are discussed and exemplified by selected biosynthetic pathways. High substrate promiscuity is commonly observed for CYPs from large families, favoring retention of gene duplicates and neofunctionalization, thus seeding acquisition of new functions. Elucidation of biosynthetic pathways producing metabolites with sporadic distribution across plant phylogeny reveals multiple examples of convergent evolution where CYPs have been independently recruited from the same or different CYP families, to adapt to similar environmental challenges or ecological niches. Sometimes only a single or a few mutations are required for functional interconversion. A compilation of functionally characterized plant CYPs is provided online through the Plant P450 Database (erda.dk/public/vgrid/PlantP450/).
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Affiliation(s)
- Cecilie Cetti Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Copenhagen, Denmark; VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark.
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Copenhagen, Denmark; VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
| | - Daniele Werck-Reichhart
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique (CNRS), University of Strasbourg, Strasbourg, France.
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12
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Kriegshauser L, Knosp S, Grienenberger E, Tatsumi K, Gütle DD, Sørensen I, Herrgott L, Zumsteg J, Rose JKC, Reski R, Werck-Reichhart D, Renault H. Function of the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE is evolutionarily conserved in embryophytes. THE PLANT CELL 2021; 33:1472-1491. [PMID: 33638637 PMCID: PMC8254490 DOI: 10.1093/plcell/koab044] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/31/2021] [Indexed: 05/04/2023]
Abstract
The plant phenylpropanoid pathway generates a major class of specialized metabolites and precursors of essential extracellular polymers that initially appeared upon plant terrestrialization. Despite its evolutionary significance, little is known about the complexity and function of this major metabolic pathway in extant bryophytes, which represent the non-vascular stage of embryophyte evolution. Here, we report that the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE (HCT) gene, which plays a critical function in the phenylpropanoid pathway during seed plant development, is functionally conserved in Physcomitrium patens (Physcomitrella), in the moss lineage of bryophytes. Phylogenetic analysis indicates that bona fide HCT function emerged in the progenitor of embryophytes. In vitro enzyme assays, moss phenolic pathway reconstitution in yeast and in planta gene inactivation coupled to targeted metabolic profiling, collectively indicate that P. patens HCT (PpHCT), similar to tracheophyte HCT orthologs, uses shikimate as a native acyl acceptor to produce a p-coumaroyl-5-O-shikimate intermediate. Phenotypic and metabolic analyses of loss-of-function mutants show that PpHCT is necessary for the production of caffeate derivatives, including previously reported caffeoyl-threonate esters, and for the formation of an intact cuticle. Deep conservation of HCT function in embryophytes is further suggested by the ability of HCT genes from P. patens and the liverwort Marchantia polymorpha to complement an Arabidopsis thaliana CRISPR/Cas9 hct mutant, and by the presence of phenolic esters of shikimate in representative species of the three bryophyte lineages.
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Affiliation(s)
- Lucie Kriegshauser
- Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Samuel Knosp
- Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Etienne Grienenberger
- Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Kanade Tatsumi
- Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Desirée D Gütle
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Iben Sørensen
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Laurence Herrgott
- Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Julie Zumsteg
- Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Danièle Werck-Reichhart
- Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Hugues Renault
- Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
- Author for correspondence:
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13
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Chen Y, Pan H, Hao S, Pan D, Wang G, Yu W. Evaluation of phenolic composition and antioxidant properties of different varieties of Chinese citrus. Food Chem 2021; 364:130413. [PMID: 34175629 DOI: 10.1016/j.foodchem.2021.130413] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/17/2021] [Accepted: 06/16/2021] [Indexed: 01/27/2023]
Abstract
Citrus peels have health-promoting effects and are a rich source of antioxidant substances. This study evaluated the compositions of phenolic compounds and antioxidant activities in the peels of 52 citrus varieties with consistent planting time and management. The highest levels of total phenols (72.95 ± 37.60 mg/g DW) and total flavonoids (71.43 ± 37.64 mg/g DW) were found in mandarin. The highest phenolic acid content (18.78 ± 0.38 mg/g DW), dominated by protocatechuic acid, was found in kumquat. The antioxidant potency composite index was 6.23-94.56, suggesting mandarin varieties HJ, TWPG, TTPG, AY28, BZH and TCJC had the highest antioxidant activity. Statistics analysis indicated phenolic compounds and antioxidant activity were positively correlated. Principal component analysis and hierarchical cluster analysis suggested a strong relationship between phenolic compound composition and genetic background. This study indicated significant differences in the biological properties of various types of citrus peels; which are valuable for future utilization and research of citrus peels.
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Affiliation(s)
- Yuan Chen
- Fujian Academy of Agricultural Sciences/Research Institute of Agri-engineering Technology, Fuzhou 350003, China; Fujian Academy of Agricultural Sciences, Fuzhou 350003, China.
| | - Heli Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian Engineering Research Center for Narcissus Breeding, Fuzhou 350003, China
| | - Shuxia Hao
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian Engineering Research Center for Narcissus Breeding, Fuzhou 350003, China
| | - Dongming Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian Engineering Research Center for Narcissus Breeding, Fuzhou 350003, China
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL 34946, USA.
| | - Wenquan Yu
- Fujian Academy of Agricultural Sciences, Fuzhou 350003, China.
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14
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Su W, Jing Y, Lin S, Yue Z, Yang X, Xu J, Wu J, Zhang Z, Xia R, Zhu J, An N, Chen H, Hong Y, Yuan Y, Long T, Zhang L, Jiang Y, Liu Z, Zhang H, Gao Y, Liu Y, Lin H, Wang H, Yant L, Lin S, Liu Z. Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. Proc Natl Acad Sci U S A 2021; 118:e2101767118. [PMID: 33986115 PMCID: PMC8157987 DOI: 10.1073/pnas.2101767118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole-genome duplication (WGD) plays important roles in plant evolution and function, yet little is known about how WGD underlies metabolic diversification of natural products that bear significant medicinal properties, especially in nonmodel trees. Here, we reveal how WGD laid the foundation for co-option and differentiation of medicinally important ursane triterpene pathway duplicates, generating distinct chemotypes between species and between developmental stages in the apple tribe. After generating chromosome-level assemblies of a widely cultivated loquat variety and Gillenia trifoliata, we define differentially evolved, duplicated gene pathways and date the WGD in the apple tribe at 13.5 to 27.1 Mya, much more recent than previously thought. We then functionally characterize contrasting metabolic pathways responsible for major triterpene biosynthesis in G. trifoliata and loquat, which pre- and postdate the Maleae WGD, respectively. Our work mechanistically details the metabolic diversity that arose post-WGD and provides insights into the genomic basis of medicinal properties of loquat, which has been used in both traditional and modern medicines.
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Affiliation(s)
- Wenbing Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yi Jing
- Research Cooperation Department, Beijing Genomics Institute Genomics, Shenzhen 518083, China
| | - Shoukai Lin
- Key laboratory of Loquat Germplasm Innovation and Utilization (Fujian Province), Putian University, Putian 351100, China
| | - Zhen Yue
- Research Cooperation Department, Beijing Genomics Institute Genomics, Shenzhen 518083, China
| | - Xianghui Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jiabao Xu
- Research Cooperation Department, Beijing Genomics Institute Genomics, Shenzhen 518083, China
| | - Jincheng Wu
- Key laboratory of Loquat Germplasm Innovation and Utilization (Fujian Province), Putian University, Putian 351100, China
| | - Zhike Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jiaojiao Zhu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ning An
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haixin Chen
- Research Cooperation Department, Beijing Genomics Institute Genomics, Shenzhen 518083, China
| | - Yanping Hong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ting Long
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ling Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yuanyuan Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zongli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hailan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yongshun Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yuexue Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hailan Lin
- Key laboratory of Loquat Germplasm Innovation and Utilization (Fujian Province), Putian University, Putian 351100, China
| | - Huicong Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Shunquan Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
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15
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Roumani M, Besseau S, Gagneul D, Robin C, Larbat R. Phenolamides in plants: an update on their function, regulation, and origin of their biosynthetic enzymes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2334-2355. [PMID: 33315095 DOI: 10.1093/jxb/eraa582] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Phenolamides represent a family of specialized metabolites, consisting of the association of hydroxycinnamic acid derivatives with aliphatic or aromatic amines. Since the discovery of the first phenolamide in the late 1940s, decades of phytochemical analyses have revealed a high structural diversity for this family and a wide distribution in the plant kingdom. The occurrence of structurally diverse phenolamides in almost all plant organs has led to early hypotheses on their involvement in floral initiation and fertility, as well as plant defense against biotic and abiotic stress. In the present work, we critically review the literature ascribing functional hypotheses to phenolamides and recent evidence on the control of their biosynthesis in response to biotic stress. We additionally provide a phylogenetic analysis of the numerous N-hydroxycinnamoyltransferases involved in the synthesis of phenolamides and discuss the potential role of other enzyme families in their diversification. The data presented suggest multiple evolutionary events that contributed to the extension of the taxonomic distribution and diversity of phenolamides.
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Affiliation(s)
- Marwa Roumani
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
| | - Sébastien Besseau
- EA 2106, Biomolécules et biotechnologies végétales (BBV), Université de Tours, Tours, France
| | - David Gagneul
- UMR 1158, BioEcoAgro, Université de Lille, INRAe, Université de Liège, UPJV, YNCREA, Université d'Artois, Université Littoral Côte d'Opale, Institut Charles Viollette (ICV), Lille, France
| | - Christophe Robin
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
| | - Romain Larbat
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
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16
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Zhang X, Tang N, Zhang H, Chen C, Li L, Dong C, Cheng Y. Comparative transcriptomic analysis of cantaloupe melon under cold storage with ozone treatment. Food Res Int 2021; 140:109993. [PMID: 33648227 DOI: 10.1016/j.foodres.2020.109993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 10/22/2022]
Abstract
Ozone treatment was found to delay the postharvest cantaloupe melon decay and improve its intrinsic quality during the cold storage. The transcriptomes of cantaloupe peel and pulp in response to ozone treatment were investigated to reveal the mechanisms using a high-throughput RNA sequencing approach. Results showed that 570 and 313 differentially expressed genes were identified in peel and pulp, respectively. According to these identified genes, the gene ontology and pathway enrichment analysis indicated that the ozone treatment could maintain the firmness of the cantaloupe by changing pectin metabolites and reduction of the ethylene production by regulating relevant genes especially in the peel. The total flavonoid content changes in peel and pulp related to the regulation of phenylalanine ammonia lyase, 4-coumarate-CoA ligase and P450 family genes which further leading to the inhibition of phenylalanine metabolic pathway in peel but promotion of secondary metabolism in pulp. The qRT-PCR results were in accordance with our RNA sequencing results which validated the conclusions. The present study for the first time reveals the mechanism of cantaloupe in response to ozone treatment at a transcriptome level which is of importance for cantaloupe storage.
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Affiliation(s)
- Xiaojun Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China
| | - Ning Tang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Huijie Zhang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Cunkun Chen
- National Engineering Technology Research Center for Preservation of Agriculture Products, Key Laboratory of Storage of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage of Agricultural Products, Tianjin 300384, China
| | - Li Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Chenghu Dong
- National Engineering Technology Research Center for Preservation of Agriculture Products, Key Laboratory of Storage of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage of Agricultural Products, Tianjin 300384, China
| | - Yongqiang Cheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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17
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Abdollahi F, Alebrahim MT, Ngov C, Lallemand E, Zheng Y, Villette C, Zumsteg J, André F, Navrot N, Werck-Reichhart D, Miesch L. Innate promiscuity of the CYP706 family of P450 enzymes provides a suitable context for the evolution of dinitroaniline resistance in weed. THE NEW PHYTOLOGIST 2021; 229:3253-3268. [PMID: 33253456 DOI: 10.1111/nph.17126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/24/2020] [Indexed: 05/24/2023]
Abstract
Increased metabolism is one of the main causes for evolution of herbicide resistance in weeds, a major challenge for sustainable food production. The molecular drivers of this evolution are poorly understood. We tested here the hypothesis that a suitable context for the emergence of herbicide resistance could be provided by plant enzymes with high innate promiscuity with regard to their natural substrates. A selection of yeast-expressed plant cytochrome P450 enzymes with well documented narrow to broad promiscuity when metabolizing natural substrates was tested for herbicide metabolism competence. The positive candidate was assayed for capacity to confer herbicide tolerance in Arabidopsis thaliana. Our data demonstrate that Arabidopsis thaliana CYP706A3, with the most promiscuous activity on monoterpenes and sesquiterpenes for flower defence, can also oxidize plant microtubule assembly inhibitors, dinitroanilines. Ectopic overexpression of CYP706A3 confers dinitroaniline resistance. We show, in addition, that the capacity to metabolize dinitroanilines is shared by other members of the CYP706 family from plants as diverse as eucalyptus and cedar. Supported by three-dimensional (3D) modelling of CYP706A3, the properties of enzyme active site and substrate access channel are discussed together with the shared physicochemical properties of the natural and exogenous substrates to explain herbicide metabolism.
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Affiliation(s)
- Fatemeh Abdollahi
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, 67084, France
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences & Natural Resources, University of Mohaghegh Ardabili, Ardabil, 56199-11367, Iran
- Equipe de Synthèse Organique et Phytochimie, Institut de Chimie, CNRS, Université de Strasbourg, Strasbourg, 67081, France
| | - Mohammad Taghi Alebrahim
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences & Natural Resources, University of Mohaghegh Ardabili, Ardabil, 56199-11367, Iran
| | - Chheng Ngov
- Equipe de Synthèse Organique et Phytochimie, Institut de Chimie, CNRS, Université de Strasbourg, Strasbourg, 67081, France
| | - Etienne Lallemand
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Yongxiang Zheng
- Equipe de Synthèse Organique et Phytochimie, Institut de Chimie, CNRS, Université de Strasbourg, Strasbourg, 67081, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, 67084, France
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, 67084, France
| | - François André
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Nicolas Navrot
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, 67084, France
| | - Danièle Werck-Reichhart
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, 67084, France
| | - Laurence Miesch
- Equipe de Synthèse Organique et Phytochimie, Institut de Chimie, CNRS, Université de Strasbourg, Strasbourg, 67081, France
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18
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Han H, Yu Q, Beffa R, González S, Maiwald F, Wang J, Powles SB. Cytochrome P450 CYP81A10v7 in Lolium rigidum confers metabolic resistance to herbicides across at least five modes of action. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:79-92. [PMID: 33098711 DOI: 10.1111/tpj.15040] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 05/23/2023]
Abstract
Rapid and widespread evolution of multiple herbicide resistance in global weed species endowed by increased capacity to metabolize (degrade) herbicides (metabolic resistance) is a great threat to herbicide sustainability and global food production. Metabolic resistance in the economically damaging crop weed species Lolium rigidum is well known but a molecular understanding has been lacking. We purified a metabolic resistant (R) subset from a field evolved R L. rigidum population. The R, the herbicide susceptible (S) and derived F2 populations were used for candidate herbicide resistance gene discovery by RNA sequencing. A P450 gene CYP81A10v7 was identified with higher expression in R vs. S plants. Transgenic rice overexpressing this Lolium CYP81A10v7 gene became highly resistant to acetyl-coenzyme A carboxylase- and acetolactate synthase-inhibiting herbicides (diclofop-methyl, tralkoxydim, chlorsulfuron) and moderately resistant to hydroxyphenylpyruvate dioxygenase-inhibiting herbicide (mesotrione), photosystem II-inhibiting herbicides (atrazine and chlorotoluron) and the tubulin-inhibiting herbicide trifluralin. This wide cross-resistance profile to many dissimilar herbicides in CYP81A10v7 transgenic rice generally reflects what is evident in the R L. rigidum. This report clearly showed that a single P450 gene in a cross-pollinated weed species L. rigidum confers resistance to herbicides of at least five modes of action across seven herbicide chemistries.
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Affiliation(s)
- Heping Han
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, 6009, Australia
| | - Qin Yu
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, 6009, Australia
| | - Roland Beffa
- Division Crop Science, Bayer AG, Weed Resistance Competence Center, Frankfurt am Main, 65926, Germany
| | - Susana González
- Division Crop Science, Bayer AG, Weed Resistance Competence Center, Frankfurt am Main, 65926, Germany
| | - Frank Maiwald
- Division CropScience, Computer Sciences, Bayer AG, Monheim, Monheim am Rhein, 40789, Germany
| | - Jian Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Stephen B Powles
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, 6009, Australia
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19
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Hu Y, Wu X, Jin G, Peng J, Leng R, Li L, Gui D, Fan C, Zhang C. Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications. FRONTIERS IN PLANT SCIENCE 2021; 12:772655. [PMID: 35058947 PMCID: PMC8764390 DOI: 10.3389/fpls.2021.772655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 05/21/2023]
Abstract
Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source of genetic variation. Thlaspi arvense, a close relative of the model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plant adaptation in extreme environments. However, how the retrotransposons affect the T. arvense genome evolution and adaptation is largely unknown. We report a high-quality chromosome-scale genome assembly of T. arvense with a scaffold N50 of 59.10 Mb. Long terminal repeat retrotransposons (LTR-RTs) account for 56.94% of the genome assembly, and the Gypsy superfamily is the most abundant TEs. The amplification of LTR-RTs in the last six million years primarily contributed to the genome size expansion in T. arvense. We identified 351 retrogenes and 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those retrogenes and genes flanked by LTRs have a higher percentage of significantly expanded orthogroups (SEOs), and these SEOs possess more recent tandem duplicated genes. All present results indicate that RNA-based gene duplication (retroduplication) accelerated the subsequent tandem duplication of homologous genes resulting in family expansions, and these expanded gene families were implicated in plant growth, development, and stress responses, which were one of the pivotal factors for T. arvense's adaptation to the harsh environment in the QTP regions. In conclusion, the high-quality assembly of the T. arvense genome provides insights into the retroduplication mediated mechanism of plant adaptation to extreme environments.
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Affiliation(s)
- Yanting Hu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaopei Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junchu Peng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Rong Leng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ling Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
- Chuanzhu Fan,
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Chengjun Zhang,
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20
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Kelly LJ, Plumb WJ, Carey DW, Mason ME, Cooper ED, Crowther W, Whittemore AT, Rossiter SJ, Koch JL, Buggs RJA. Convergent molecular evolution among ash species resistant to the emerald ash borer. Nat Ecol Evol 2020; 4:1116-1128. [PMID: 32451426 PMCID: PMC7610378 DOI: 10.1038/s41559-020-1209-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/16/2020] [Indexed: 11/08/2022]
Abstract
Recent studies show that molecular convergence plays an unexpectedly common role in the evolution of convergent phenotypes. We exploited this phenomenon to find candidate loci underlying resistance to the emerald ash borer (EAB, Agrilus planipennis), the United States' most costly invasive forest insect to date, within the pan-genome of ash trees (the genus Fraxinus). We show that EAB-resistant taxa occur within three independent phylogenetic lineages. In genomes from these resistant lineages, we detect 53 genes with evidence of convergent amino acid evolution. Gene-tree reconstruction indicates that, for 48 of these candidates, the convergent amino acids are more likely to have arisen via independent evolution than by another process such as hybridization or incomplete lineage sorting. Seven of the candidate genes have putative roles connected to the phenylpropanoid biosynthesis pathway and 17 relate to herbivore recognition, defence signalling or programmed cell death. Evidence for loss-of-function mutations among these candidates is more frequent in susceptible species than in resistant ones. Our results on evolutionary relationships, variability in resistance, and candidate genes for defence response within the ash genus could inform breeding for EAB resistance, facilitating ecological restoration in areas invaded by this beetle.
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Affiliation(s)
- Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Royal Botanic Gardens, Kew, Richmond, UK.
| | - William J Plumb
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Royal Botanic Gardens, Kew, Richmond, UK
- Forestry Development Department, Teagasc, Dublin, Republic of Ireland
| | - David W Carey
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Mary E Mason
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Endymion D Cooper
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - William Crowther
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Alan T Whittemore
- United States Department of Agriculture, Agricultural Research Service, US National Arboretum, Washington, DC, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jennifer L Koch
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Royal Botanic Gardens, Kew, Richmond, UK.
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21
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Liu Z, Suarez Duran HG, Harnvanichvech Y, Stephenson MJ, Schranz ME, Nelson D, Medema MH, Osbourn A. Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae. THE NEW PHYTOLOGIST 2020; 227:1109-1123. [PMID: 31769874 PMCID: PMC7383575 DOI: 10.1111/nph.16338] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/17/2019] [Indexed: 05/11/2023]
Abstract
Plants produce an array of specialized metabolites with important ecological functions. The mechanisms underpinning the evolution of new biosynthetic pathways are not well-understood. Here, we exploit available genome sequence resources to investigate triterpene biosynthesis across the Brassicaceae. Oxidosqualene cyclases (OSCs) catalyze the first committed step in triterpene biosynthesis. Systematic analysis of 13 sequenced Brassicaceae genomes was performed to identify all OSC genes. The genome neighbourhoods (GNs) around a total of 163 OSC genes were investigated to identify Pfam domains significantly enriched in these regions. All-vs-all comparisons of OSC neighbourhoods and phylogenomic analysis were used to investigate the sequence similarity and evolutionary relationships of the numerous candidate triterpene biosynthetic gene clusters (BGCs) observed. Functional analysis of three representative BGCs was carried out and their triterpene pathway products were elucidated. Our results indicate that plant genomes are remarkably plastic, and that dynamic GNs generate new biosynthetic pathways in different Brassicaceae lineages by shuffling the genes encoding a core palette of triterpene-diversifying enzymes, presumably in response to strong environmental selection pressure. These results illuminate a genomic basis for diversification of plant-specialized metabolism through natural combinatorics of enzyme families, which can be mimicked using synthetic biology to engineer diverse bioactive molecules.
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Affiliation(s)
- Zhenhua Liu
- Department of Metabolic BiologyJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | | | - Yosapol Harnvanichvech
- Bioinformatics GroupWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Michael J. Stephenson
- Department of Metabolic BiologyJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - M. Eric Schranz
- Biosystematics GroupWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - David Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee858 Madison Avenue, Suite G01MemphisTN38163USA
| | - Marnix H. Medema
- Bioinformatics GroupWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Anne Osbourn
- Department of Metabolic BiologyJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
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22
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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23
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Rao MJ, Xu Y, Tang X, Huang Y, Liu J, Deng X, Xu Q. CsCYT75B1, a Citrus CYTOCHROME P450 Gene, Is Involved in Accumulation of Antioxidant Flavonoids and Induces Drought Tolerance in Transgenic Arabidopsis. Antioxidants (Basel) 2020; 9:E161. [PMID: 32079281 PMCID: PMC7070963 DOI: 10.3390/antiox9020161] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/05/2020] [Accepted: 02/14/2020] [Indexed: 01/19/2023] Open
Abstract
CYTOCHROME P450s genes are a large gene family in the plant kingdom. Our earlier transcriptome data revealed that a CYTOCHROME P450 gene of Citrus sinensis (CsCYT75B1) was associated with flavonoid metabolism and was highly induced after drought stress. Here, we characterized the function of CsCYT75B1 in drought tolerance by overexpressing it in Arabidopsis thaliana. Our results demonstrated that the overexpression of the CsCYT75B1 gene significantly enhanced the total flavonoid contents with increased antioxidant activity in transgenic Arabidopsis. The gene expression results showed that several genes that are responsible for the biosynthesis of antioxidant flavonoids were induced by 2-12 fold in transgenic Arabidopsis lines. After 14 days of drought stress, all transgenic lines displayed an enhanced tolerance to drought stress along with accumulating antioxidant flavonoids with lower superoxide radicals and reactive oxygen species (ROS) than wild type plants. In addition, drought-stressed transgenic lines possessed higher antioxidant enzymatic activities than wild type transgenic lines. Moreover, the stressed transgenic lines had significantly lower levels of electrolytic leakage than wild type transgenic lines. These results demonstrate that the CsCYT75B1 gene of sweet orange functions in the metabolism of antioxidant flavonoid and contributes to drought tolerance by elevating ROS scavenging activities.
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Affiliation(s)
| | | | | | | | | | | | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, China; (M.J.R.); (Y.X.); (X.T.); (Y.H.); (J.L.); (X.D.)
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24
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Levsh O, Pluskal T, Carballo V, Mitchell AJ, Weng JK. Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants. J Biol Chem 2019; 294:15193-15205. [PMID: 31481469 PMCID: PMC6802498 DOI: 10.1074/jbc.ra119.010454] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/24/2019] [Indexed: 11/06/2022] Open
Abstract
As a means to maintain their sessile lifestyle amid challenging environments, plants produce an enormous diversity of compounds as chemical defenses against biotic and abiotic insults. The underpinning metabolic pathways that support the biosynthesis of these specialized chemicals in divergent plant species provide a rich arena for understanding the molecular evolution of complex metabolic traits. Rosmarinic acid (RA) is a phenolic natural product first discovered in plants of the mint family (Lamiaceae) and is recognized for its wide range of medicinal properties and potential applications in human dietary and medical interventions. Interestingly, the RA chemotype is present sporadically in multiple taxa of flowering plants as well as some hornworts and ferns, prompting the question whether its biosynthesis arose independently across different lineages. Here we report the elucidation of the RA biosynthetic pathway in Phacelia campanularia (desert bells). This species represents the borage family (Boraginaceae), an RA-producing family closely related to the Lamiaceae within the Lamiids clade. Using a multi-omics approach in combination with functional characterization of candidate genes both in vitro and in vivo, we found that RA biosynthesis in P. campanularia involves specific activities of a BAHD acyltransferase and two cytochrome P450 hydroxylases. Further phylogenetic and comparative structure-function analyses of the P. campanularia RA biosynthetic enzymes clearly indicate that RA biosynthesis has evolved independently at least twice in the Lamiids, an exemplary case of chemotypic convergence through disparate evolutionary trajectories.
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Affiliation(s)
- Olesya Levsh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Valentina Carballo
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Andrew J Mitchell
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Jing-Ke Weng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
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25
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Alber AV, Renault H, Basilio-Lopes A, Bassard JE, Liu Z, Ullmann P, Lesot A, Bihel F, Schmitt M, Werck-Reichhart D, Ehlting J. Evolution of coumaroyl conjugate 3-hydroxylases in land plants: lignin biosynthesis and defense. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:924-936. [PMID: 31038800 DOI: 10.1111/tpj.14373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/03/2019] [Accepted: 04/17/2019] [Indexed: 05/16/2023]
Abstract
Multiple adaptations were necessary when plants conquered the land. Among them were soluble phenylpropanoids related to plant protection and lignin necessary for upright growth and long-distance water transport. Cytochrome P450 monooxygenase 98 (CYP98) catalyzes a rate-limiting step in phenylpropanoid biosynthesis. Phylogenetic reconstructions suggest that a single copy of CYP98 founded each major land plant lineage (bryophytes, lycophytes, monilophytes, gymnosperms and angiosperms), and was maintained as a single copy in all lineages but the angiosperms. In angiosperms, a series of independent gene duplications and losses occurred. Biochemical assays in four angiosperm species tested showed that 4-coumaroyl-shikimate, a known intermediate in lignin biosynthesis, was the preferred substrate of one member in each species, while independent duplicates in Populus trichocarpa and Amborella trichopoda each showed broad substrate ranges, accepting numerous 4-coumaroyl-esters and -amines, and were thus capable of producing a wide range of hydroxycinnamoyl conjugates. The gymnosperm CYP98 from Pinus taeda showed a broad substrate range, but preferred 4-coumaroyl-shikimate as its best substrate. In contrast, CYP98s from the lycophyte Selaginella moellendorffii and the fern Pteris vittata converted 4-coumaroyl-shikimate poorly in vitro, but were able to use alternative substrates, in particular 4-coumaroyl-anthranilate. Thus, caffeoyl-shikimate appears unlikely to be an intermediate in monolignol biosynthesis in non-seed vascular plants, including ferns. The best substrate for CYP98A34 from the moss Physcomitrella patens was also 4-coumaroyl-anthranilate, while 4-coumaroyl-shikimate was converted to lower extents. Despite having in vitro activity with 4-coumaroyl-shikimate, CYP98A34 was unable to complement the Arabidopsis thaliana cyp98a3 loss-of-function phenotype, suggesting distinct properties also in vivo.
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Affiliation(s)
- Annette V Alber
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, Strasbourg, France
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada
| | - Hugues Renault
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, Strasbourg, France
| | | | - Jean-Etienne Bassard
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, Strasbourg, France
| | - Zhenhua Liu
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, Strasbourg, France
| | - Pascaline Ullmann
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, Strasbourg, France
| | - Agnès Lesot
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, Strasbourg, France
| | - Frédéric Bihel
- Laboratoire d'Innovation Thérapeutique, UMR CNRS 7200, Illkirch, France
| | - Martine Schmitt
- Laboratoire d'Innovation Thérapeutique, UMR CNRS 7200, Illkirch, France
| | | | - Jürgen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada
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26
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Teng L, Fan X, Nelson DR, Han W, Zhang X, Xu D, Renault H, Markov GV, Ye N. Diversity and evolution of cytochromes P450 in stramenopiles. PLANTA 2019; 249:647-661. [PMID: 30341489 DOI: 10.1007/s00425-018-3028-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
MAIN CONCLUSION Comparative genomic analysis of cytochromes P450 revealed high diversification and dynamic changes in stramenopiles, associated with transcriptional responsiveness to various environmental stimuli. Comparative genomic and molecular evolution approaches were used to characterize cytochromes P450 (P450) diversity in stramenopiles. Phylogenetic analysis pointed to a high diversity of P450 in stramenopiles and identified three major clans. The CYP51 and CYP97 clans were present in brown algae, diatoms and Nannochloropsis gaditana, whereas the CYP5014 clan mainly includes oomycetes. Gene gain and loss patterns revealed that six CYP families-CYP51, CYP97, CYP5160, CYP5021, CYP5022, and CYP5165-predated the split of brown algae and diatoms. After they diverged, diatoms gained more CYP families, especially in the cold-adapted species Fragilariopsis cylindrus, in which eight new CYP families were found. Selection analysis revealed that the expanded CYP51 family in the brown alga Cladosiphon okamuranus exhibited a more relaxed selection constraint compared with those of other brown algae and diatoms. Our RNA-seq data further evidenced that most of P450s in Saccharina japonica are highly expressed in large sporophytes, which could potentially promote the large kelp formation in this developmental stage. A survey of Ectocarpus siliculosus and diatom transcriptomes showed that many P450s are responsive to stress, nutrient limitation or light quality, suggesting pivotal roles in detoxification or metabolic processes under adverse environmental conditions. The information provided in this study will be helpful in designing functional experiments and interpreting P450 roles in this particular lineage.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave. Suite G01, Memphis, 38163, TN, USA
| | - Wentao Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Hugues Renault
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 67084, Strasbourg, France
| | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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27
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Deshmukh AB, Datir SS, Bhonde Y, Kelkar N, Samdani P, Tamhane VA. De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway. PHYTOCHEMISTRY 2018; 156:201-213. [PMID: 30317159 DOI: 10.1016/j.phytochem.2018.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 09/25/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
Oroxylum indicum (L.) Kurz is a medicinally important and rare tree species of the family Bignoniaceae. It is rich in flavonoid content and its mature roots are extensively used in Ayurvedic formulations. O. indicum specific flavonoids like oroxylin B, prunetin and oroxindin possess antibacterial, antiproliferative, antioxidant and anticancerous properties, signifying its importance in modern medicine. In the present study, de novo transcriptome analysis of O. indicum root was performed to elucidate the genes involved in flavonoid metabolism. A total of 24,625,398 high quality reads were assembled into 121,286 transcripts with N50 value 1783. The BLASTx search of 81,002 clustered transcripts against Viridiplantae Uniprot database led to annotation of 46,517 transcripts. Furthermore, Gene ontology (GO) revealed that 34,231 transcripts mapped to 3049 GO terms and KEGG analysis demonstrated that 4570 transcripts plausibly involved in 132 biosynthetic pathways. The transcriptome data indicated that cinnamyl-alcohol dehydrogenase (OinCAD) was abundant in phenylpropanoid pathway genes while; naringenin chalcone synthase (OinCHS), flavone synthase (OinFNS) and flavonoid 3', 5'-methyltransferase (OinF35 MT) were abundant in flavonoid, isoflavonoid, flavone and flavonol biosynthesis pathways, respectively. Transcription factor analysis demonstrated the abundance of MYB, bHLH and WD40 transcription factor families, which regulate the flavonoid biosynthesis. Flavonoid pathway genes displayed differential expression in young and old roots of O. indicum. The transcriptome led to the identification of 31 diverse full length Cytochrome P450 (CYP450) genes which may be involved in biosynthesis of specialized metabolites and flavonoids like baicalein and baicalin. Thus, the information obtained in this study will be a valuable tool for identifying genes and developing system biology approaches for in vitro synthesis of specialized O. indicum metabolites.
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Affiliation(s)
- Aaditi B Deshmukh
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Sagar S Datir
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India
| | - Yogesh Bhonde
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Natasha Kelkar
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Pawan Samdani
- Eumentis Cloud, Office, 310, Amenity Building, Rose Icon, Pimple Saudagar, Pune, 411027, India
| | - Vaijayanti A Tamhane
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India.
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28
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Renault H, Werck-Reichhart D, Weng JK. Harnessing lignin evolution for biotechnological applications. Curr Opin Biotechnol 2018; 56:105-111. [PMID: 30439673 DOI: 10.1016/j.copbio.2018.10.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Abstract
Lignin evolved concomitantly with the rise of vascular plants on planet earth ∼450 million years ago. Several iterations of exploiting ancestral phenylpropanoid metabolism for biopolymers occurred prior to lignin that facilitated early plants' adaptation to terrestrial environments. The first true lignin was constructed via oxidative coupling of a number of simple phenylpropanoid alcohols to form a sturdy polymer that supports long-distance water transport. This invention has directly contributed to the dominance of vascular plants in the Earth's flora, and has had a profound impact on the establishment of the rich terrestrial ecosystems as we know them today. Within vascular plants, new lignin traits continued to emerge with expanded biological functions pertinent to host fitness under complex environmental niches. Understanding the chemical and biochemical basis for lignin's evolution in diverse plants therefore offers new opportunities and tools for engineering desirable lignin traits in crops with economic significance.
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Affiliation(s)
- Hugues Renault
- Institute of Plant Molecular Biology, CNRS UPR 2357, University of Strasbourg, F-67000 Strasbourg, France.
| | - Danièle Werck-Reichhart
- Institute of Plant Molecular Biology, CNRS UPR 2357, University of Strasbourg, F-67000 Strasbourg, France.
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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29
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Ilc T, Arista G, Tavares R, Navrot N, Duchêne E, Velt A, Choulet F, Paux E, Fischer M, Nelson DR, Hugueney P, Werck-Reichhart D, Rustenholz C. Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome. PLoS One 2018; 13:e0199902. [PMID: 29953551 PMCID: PMC6023221 DOI: 10.1371/journal.pone.0199902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/15/2018] [Indexed: 12/26/2022] Open
Abstract
Cytochromes P450 are enzymes that participate in a wide range of functions in plants, from hormonal signaling and biosynthesis of structural polymers, to defense or communication with other organisms. They represent one of the largest gene/protein families in the plant kingdom. The manual annotation of cytochrome P450 genes in the genome of Vitis vinifera PN40024 revealed 579 P450 sequences, including 279 complete genes. Most of the P450 sequences in grapevine genome are organized in physical clusters, resulting from tandem or segmental duplications. Although most of these clusters are small (2 to 35, median = 3), some P450 families, such as CYP76 and CYP82, underwent multiple duplications and form large clusters of homologous sequences. Analysis of gene expression revealed highly specific expression patterns, which are often the same within the genes in large physical clusters. Some of these genes are induced upon biotic stress, which points to their role in plant defense, whereas others are specifically activated during grape berry ripening and might be responsible for the production of berry-specific metabolites, such as aroma compounds. Our work provides an exhaustive and robust annotation including clear identification, structural organization, evolutionary dynamics and expression patterns for the grapevine cytochrome P450 families, paving the way to efficient functional characterization of genes involved in grapevine defense pathways and aroma biosynthesis.
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Affiliation(s)
- Tina Ilc
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Gautier Arista
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon 1, Lyon, France
| | - Nicolas Navrot
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Eric Duchêne
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Amandine Velt
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Frédéric Choulet
- Laboratoire Structure et Evolution du Génome du Blé, Institut National de la Recherche Agronomique, Université Blaise Pascal, Clermont-Ferrand, France
| | - Etienne Paux
- Laboratoire Structure et Evolution du Génome du Blé, Institut National de la Recherche Agronomique, Université Blaise Pascal, Clermont-Ferrand, France
| | - Marc Fischer
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | | | - Danièle Werck-Reichhart
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Camille Rustenholz
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
- * E-mail:
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30
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Cerbin S, Jiang N. Duplication of host genes by transposable elements. Curr Opin Genet Dev 2018; 49:63-69. [PMID: 29571044 DOI: 10.1016/j.gde.2018.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/12/2022]
Abstract
The availability of large amounts of genomic and transcriptome sequences have allowed systematic surveys about the host gene sequences that have been duplicated by transposable elements. It is now clear that all super-families of transposons are capable of duplicating genes or gene fragments, and such incidents have been detected in a wide spectrum of organisms. Emerging evidence suggests that a considerable portion of them function as coding or non-coding sequences, driving innovations at molecular and phenotypic levels. Interestingly, the duplication events not only have to occur in the reproductive tissues to become heritable, but the duplicated copies are also preferentially expressed in those tissues. As a result, reproductive tissues may serve as the 'incubator' for genes generated by transposable elements.
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Affiliation(s)
- Stefan Cerbin
- Department of Horticulture, 1066 Bogue Street, Michigan State University, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, 1066 Bogue Street, Michigan State University, East Lansing, MI 48824, USA.
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31
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Renault H, De Marothy M, Jonasson G, Lara P, Nelson DR, Nilsson I, André F, von Heijne G, Werck-Reichhart D. Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants. Mol Biol Evol 2018; 34:2041-2056. [PMID: 28505373 PMCID: PMC5850782 DOI: 10.1093/molbev/msx160] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Evolution of the phenolic metabolism was critical for the transition of plants from water to land. A cytochrome P450, CYP73, with cinnamate 4-hydroxylase (C4H) activity, catalyzes the first plant-specific and rate-limiting step in this pathway. The CYP73 gene is absent from green algae, and first detected in bryophytes. A CYP73 duplication occurred in the ancestor of seed plants and was retained in Taxaceae and most angiosperms. In spite of a clear divergence in primary sequence, both paralogs can fulfill comparable cinnamate hydroxylase roles both in vitro and in vivo. One of them seems dedicated to the biosynthesis of lignin precursors. Its N-terminus forms a single membrane spanning helix and its properties and length are highly constrained. The second is characterized by an elongated and variable N-terminus, reminiscent of ancestral CYP73s. Using as proxies the Brachypodium distachyon proteins, we show that the elongation of the N-terminus does not result in an altered subcellular localization, but in a distinct membrane topology. Insertion in the membrane of endoplasmic reticulum via a double-spanning open hairpin structure allows reorientation to the lumen of the catalytic domain of the protein. In agreement with participation to a different functional unit and supramolecular organization, the protein displays modified heme proximal surface. These data suggest the evolution of divergent C4H enzymes feeding different branches of the phenolic network in seed plants. It shows that specialization required for retention of gene duplicates may result from altered protein topology rather than change in enzyme activity.
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Affiliation(s)
- Hugues Renault
- Centre National de la Recherche Scientifique, Institute of Plant Molecular Biology, University of Strasbourg, Strasbourg, France
| | - Minttu De Marothy
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Gabriella Jonasson
- Institute for Integrative Biology of the Cell (I2BC), DRF/Joliot/SB2SM, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Patricia Lara
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN
| | - IngMarie Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - François André
- Institute for Integrative Biology of the Cell (I2BC), DRF/Joliot/SB2SM, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Danièle Werck-Reichhart
- Centre National de la Recherche Scientifique, Institute of Plant Molecular Biology, University of Strasbourg, Strasbourg, France
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32
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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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33
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Casola C, Betrán E. The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses? Genome Biol Evol 2017; 9:1351-1373. [PMID: 28605529 PMCID: PMC5470649 DOI: 10.1093/gbe/evx081] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 02/07/2023] Open
Abstract
Gene duplication is a major driver of organismal evolution. Gene retroposition is a mechanism of gene duplication whereby a gene's transcript is used as a template to generate retroposed gene copies, or retrocopies. Intriguingly, the formation of retrocopies depends upon the enzymatic machinery encoded by retrotransposable elements, genomic parasites occurring in the majority of eukaryotes. Most retrocopies are depleted of the regulatory regions found upstream of their parental genes; therefore, they were initially considered transcriptionally incompetent gene copies, or retropseudogenes. However, examples of functional retrocopies, or retrogenes, have accumulated since the 1980s. Here, we review what we have learned about retrocopies in animals, plants and other eukaryotic organisms, with a particular emphasis on comparative and population genomic analyses complemented with transcriptomic datasets. In addition, these data have provided information about the dynamics of the different "life cycle" stages of retrocopies (i.e., polymorphic retrocopy number variants, fixed retropseudogenes and retrogenes) and have provided key insights into the retroduplication mechanisms, the patterns and evolutionary forces at work during the fixation process and the biological function of retrogenes. Functional genomic and transcriptomic data have also revealed that many retropseudogenes are transcriptionally active and a biological role has been experimentally determined for many. Finally, we have learned that not only non-long terminal repeat retroelements but also long terminal repeat retroelements play a role in the emergence of retrocopies across eukaryotes. This body of work has shown that mRNA-mediated duplication represents a widespread phenomenon that produces an array of new genes that contribute to organismal diversity and adaptation.
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Affiliation(s)
- Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University, TX
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, TX
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34
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Protein-Coding Genes' Retrocopies and Their Functions. Viruses 2017; 9:v9040080. [PMID: 28406439 PMCID: PMC5408686 DOI: 10.3390/v9040080] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of “relaxed” selection and remain “dormant” because they are lacking regulatory regions; however, many become functional. In the course of evolution, they may undergo subfunctionalization, neofunctionalization, or replace their progenitors. Functional retrocopies (retrogenes) can encode proteins, novel or similar to those encoded by their progenitors, can be used as alternative exons or create chimeric transcripts, and can also be involved in transcriptional interference and participate in the epigenetic regulation of parental gene expression. They can also act in trans as natural antisense transcripts, microRNA (miRNA) sponges, or a source of various small RNAs. Moreover, many retrocopies of protein-coding genes are linked to human diseases, especially various types of cancer.
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35
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Renault H, Alber A, Horst NA, Basilio Lopes A, Fich EA, Kriegshauser L, Wiedemann G, Ullmann P, Herrgott L, Erhardt M, Pineau E, Ehlting J, Schmitt M, Rose JKC, Reski R, Werck-Reichhart D. A phenol-enriched cuticle is ancestral to lignin evolution in land plants. Nat Commun 2017; 8:14713. [PMID: 28270693 PMCID: PMC5344971 DOI: 10.1038/ncomms14713] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/24/2017] [Indexed: 12/22/2022] Open
Abstract
Lignin, one of the most abundant biopolymers on Earth, derives from the plant phenolic metabolism. It appeared upon terrestrialization and is thought critical for plant colonization of land. Early diverging land plants do not form lignin, but already have elements of its biosynthetic machinery. Here we delete in a moss the P450 oxygenase that defines the entry point in angiosperm lignin metabolism, and find that its pre-lignin pathway is essential for development. This pathway does not involve biochemical regulation via shikimate coupling, but instead is coupled with ascorbate catabolism, and controls the synthesis of the moss cuticle, which prevents desiccation and organ fusion. These cuticles share common features with lignin, cutin and suberin, and may represent the extant representative of a common ancestor. Our results demonstrate a critical role for the ancestral phenolic metabolism in moss erect growth and cuticle permeability, consistent with importance in plant adaptation to terrestrial conditions. The phenolic polymer lignin is thought to have contributed to adaptation of early land plants to terrestrial environments. Here Renault et al. show that moss, which does not produce lignin, contains an ancestral phenolic metabolism pathway that produces a phenol-enriched cuticle and prevents desiccation.
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Affiliation(s)
- Hugues Renault
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France.,Faculty of Biology, Chair of Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany.,University of Strasbourg Institute for Advanced Study, 5 allée du Général Rouvillois, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany
| | - Annette Alber
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France.,Department of Biology &Centre for Forest Biology, University of Victoria, British Columbia, Canada V8P 5C2
| | - Nelly A Horst
- Faculty of Biology, Chair of Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Alexandra Basilio Lopes
- Laboratoire d'Innovation Thérapeutique, UMR CNRS 7200, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
| | - Eric A Fich
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Lucie Kriegshauser
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Gertrud Wiedemann
- Faculty of Biology, Chair of Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Pascaline Ullmann
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Laurence Herrgott
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Mathieu Erhardt
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Emmanuelle Pineau
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Jürgen Ehlting
- Department of Biology &Centre for Forest Biology, University of Victoria, British Columbia, Canada V8P 5C2
| | - Martine Schmitt
- Laboratoire d'Innovation Thérapeutique, UMR CNRS 7200, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Ralf Reski
- Faculty of Biology, Chair of Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany.,University of Strasbourg Institute for Advanced Study, 5 allée du Général Rouvillois, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Danièle Werck-Reichhart
- University of Strasbourg, Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67000 Strasbourg, France.,University of Strasbourg Institute for Advanced Study, 5 allée du Général Rouvillois, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany
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