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Swamidatta SH, Lichman BR. Beyond co-expression: pathway discovery for plant pharmaceuticals. Curr Opin Biotechnol 2024; 88:103147. [PMID: 38833915 DOI: 10.1016/j.copbio.2024.103147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Plant natural products have been an important source of medicinal molecules since ancient times. To gain access to the whole diversity of these molecules for pharmaceutical applications, it is important to understand their biosynthetic origins. Whilst co-expression is a reliable tool for identifying gene candidates, a variety of complementary methods can aid in screening or refining candidate selection. Here, we review recently employed plant biosynthetic pathway discovery approaches, and highlight future directions in the field.
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Affiliation(s)
- Sandesh H Swamidatta
- 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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2
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Liu J, Yin X, Kou C, Thimmappa R, Hua X, Xue Z. Classification, biosynthesis, and biological functions of triterpene esters in plants. PLANT COMMUNICATIONS 2024; 5:100845. [PMID: 38356259 PMCID: PMC11009366 DOI: 10.1016/j.xplc.2024.100845] [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: 11/29/2023] [Revised: 01/12/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Triterpene esters comprise a class of secondary metabolites that are synthesized by decorating triterpene skeletons with a series of oxidation, glycosylation, and acylation modifications. Many triterpene esters with important bioactivities have been isolated and identified, including those with applications in the pesticide, pharmaceutical, and cosmetic industries. They also play essential roles in plant defense against pests, diseases, physical damage (as part of the cuticle), and regulation of root microorganisms. However, there has been no recent summary of the biosynthetic pathways and biological functions of plant triterpene esters. Here, we classify triterpene esters into five categories based on their skeletons and find that C-3 oxidation may have a significant effect on triterpenoid acylation. Fatty acid and aromatic moieties are common ligands present in triterpene esters. We further analyze triterpene ester synthesis-related acyltransferases (TEsACTs) in the triterpene biosynthetic pathway. Using an evolutionary classification of BAHD acyltransferases (BAHD-ATs) and serine carboxypeptidase-like acyltransferases (SCPL-ATs) in Arabidopsis thaliana and Oryza sativa, we classify 18 TEsACTs with identified functions from 11 species. All the triterpene-skeleton-related TEsACTs belong to BAHD-AT clades IIIa and I, and the only identified TEsACT from the SCPL-AT family belongs to the CP-I subfamily. This comprehensive review of the biosynthetic pathways and bioactivities of triterpene esters provides a foundation for further study of their bioactivities and applications in industry, agricultural production, and human health.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Xue Yin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Chengxi Kou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Ramesha Thimmappa
- Amity Institute of Genome Engineering, Amity University, Noida, UP India 201313, India
| | - Xin Hua
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Zheyong Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, P.R. China.
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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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Schelkunov MI, Shtratnikova VY, Klepikova AV, Makarenko MS, Omelchenko DO, Novikova LA, Obukhova EN, Bogdanov VP, Penin AA, Logacheva MD. The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole-genome duplications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:449-463. [PMID: 37846604 DOI: 10.1111/tpj.16500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
Heracleum sosnowskyi, belonging to a group of giant hogweeds, is a plant with large effects on ecosystems and human health. It is an invasive species that contributes to the deterioration of grassland ecosystems. The ability of H. sosnowskyi to produce linear furanocoumarins (FCs), photosensitizing compounds, makes it very dangerous. At the same time, linear FCs are compounds with high pharmaceutical value used in skin disease therapies. Despite this high importance, it has not been the focus of genetic and genomic studies. Here, we report a chromosome-scale assembly of Sosnowsky's hogweed genome. Genomic analysis revealed an unusually high number of genes (55106) in the hogweed genome, in contrast to the 25-35 thousand found in most plants. However, we did not find any traces of recent whole-genome duplications not shared with its confamiliar, Daucus carota (carrot), which has approximately thirty thousand genes. The analysis of the genomic proximity of duplicated genes indicates on tandem duplications as a main reason for this increase. We performed a genome-wide search of the genes of the FC biosynthesis pathway and surveyed their expression in aboveground plant parts. Using a combination of expression data and phylogenetic analysis, we found candidate genes for psoralen synthase and experimentally showed the activity of one of them using a heterologous yeast expression system. These findings expand our knowledge on the evolution of gene space in plants and lay a foundation for further analysis of hogweed as an invasive plant and as a source of FCs.
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Affiliation(s)
- Mikhail I Schelkunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Viktoria Yu Shtratnikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maksim S Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Denis O Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Lyudmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Viktor P Bogdanov
- Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
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5
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Sun W, Yin Q, Wan H, Gao R, Xiong C, Xie C, Meng X, Mi Y, Wang X, Wang C, Chen W, Xie Z, Xue Z, Yao H, Sun P, Xie X, Hu Z, Nelson DR, Xu Z, Sun X, Chen S. Characterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis. Nat Commun 2023; 14:6470. [PMID: 37833361 PMCID: PMC10576086 DOI: 10.1038/s41467-023-42253-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Horse chestnut (Aesculus chinensis) is an important medicinal tree that contains various bioactive compounds, such as aescin, barrigenol-type triterpenoid saponins (BAT), and aesculin, a glycosylated coumarin. Herein, we report a 470.02 Mb genome assembly and characterize an Aesculus-specific whole-genome duplication event, which leads to the formation and duplication of two triterpenoid biosynthesis-related gene clusters (BGCs). We also show that AcOCS6, AcCYP716A278, AcCYP716A275, and AcCSL1 genes within these two BGCs along with a seed-specific expressed AcBAHD6 are responsible for the formation of aescin. Furthermore, we identify seven Aesculus-originated coumarin glycoside biosynthetic genes and achieve the de novo synthesis of aesculin in E. coli. Collinearity analysis shows that the collinear BGC segments can be traced back to early-diverging angiosperms, and the essential gene-encoding enzymes necessary for BAT biosynthesis are recruited before the splitting of Aesculus, Acer, and Xanthoceras. These findings provide insight on the evolution of gene clusters associated with medicinal tree metabolites.
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Affiliation(s)
- Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Qinggang Yin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Ranran Gao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Chao Xiong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
- School of Life Science and Technology, Wuhan Polytechnic University, 430023, Wuhan, China
| | - Chong Xie
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Xiangxiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yaolei Mi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xiaotong Wang
- College of Life Science, Northeast Forestry University, 150040, Harbin, China
| | - Caixia Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Weiqiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Ziyan Xie
- College of Life Science, Northeast Forestry University, 150040, Harbin, China
| | - Zheyong Xue
- College of Life Science, Northeast Forestry University, 150040, Harbin, China
| | - Hui Yao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 100193, Beijing, China
| | - Peng Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xuehua Xie
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, 430065, Wuhan, China
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, 150040, Harbin, China.
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 100029, Beijing, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China.
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
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6
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Liu C, Smit SJ, Dang J, Zhou P, Godden GT, Jiang Z, Liu W, Liu L, Lin W, Duan J, Wu Q, Lichman BR. A chromosome-level genome assembly reveals that a bipartite gene cluster formed via an inverted duplication controls monoterpenoid biosynthesis in Schizonepeta tenuifolia. MOLECULAR PLANT 2023; 16:533-548. [PMID: 36609143 DOI: 10.1016/j.molp.2023.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 06/09/2023]
Abstract
Biosynthetic gene clusters (BGCs) are regions of a genome where genes involved in a biosynthetic pathway are in proximity. The origin and evolution of plant BGCs as well as their role in specialized metabolism remain largely unclear. In this study, we have assembled a chromosome-scale genome of Japanese catnip (Schizonepeta tenuifolia) and discovered a BGC that contains multiple copies of genes involved in four adjacent steps in the biosynthesis of p-menthane monoterpenoids. This BGC has an unprecedented bipartite structure, with mirrored biosynthetic regions separated by 260 kilobases. This bipartite BGC includes identical copies of a gene encoding an old yellow enzyme, a type of flavin-dependent reductase. In vitro assays and virus-induced gene silencing revealed that this gene encodes the missing isopiperitenone reductase. This enzyme evolved from a completely different enzyme family to isopiperitenone reductase from closely related Mentha spp., indicating convergent evolution of this pathway step. Phylogenomic analysis revealed that this bipartite BGC has emerged uniquely in the S. tenuifolia lineage and through insertion of pathway genes into a region rich in monoterpene synthases. The cluster gained its bipartite structure via an inverted duplication. The discovered bipartite BGC for p-menthane biosynthesis in S. tenuifolia has similarities to the recently described duplicated p-menthane biosynthesis gene pairs in the Mentha longifolia genome, providing an example of the convergent evolution of gene order. This work expands our understanding of plant BGCs with respect to both form and evolution, and highlights the power of BGCs for gene discovery in plant biosynthetic pathways.
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Affiliation(s)
- Chanchan Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Jingjie Dang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Peina Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Zheng Jiang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wukun Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Licheng Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Lin
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China; Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinao Duan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qinan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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7
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Tan D, Wang J, Cao L, Yang D, Lu Y, Wu D, Zhao Y, Wu X, Fan Q, Yang Z, Qin L, He Y. UDP-glycosyltransferases play a crucial role in the accumulation of alkaloids and sesquiterpene glycosides in Dendrobium nobile. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
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8
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Marszalek-Zenczak M, Satyr A, Wojciechowski P, Zenczak M, Sobieszczanska P, Brzezinski K, Iefimenko T, Figlerowicz M, Zmienko A. Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members. FRONTIERS IN PLANT SCIENCE 2023; 14:1104303. [PMID: 36778696 PMCID: PMC9909608 DOI: 10.3389/fpls.2023.1104303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity.
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Affiliation(s)
| | - Anastasiia Satyr
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Tetiana Iefimenko
- Department of Biology, National University of Kyiv-Mohyla Academy, Kyiv, Ukraine
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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9
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Bryson AE, Lanier ER, Lau KH, Hamilton JP, Vaillancourt B, Mathieu D, Yocca AE, Miller GP, Edger PP, Buell CR, Hamberger B. Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory. Nat Commun 2023; 14:343. [PMID: 36670101 PMCID: PMC9860074 DOI: 10.1038/s41467-023-35845-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions. Here, we report the genome assemblies of Prunella vulgaris, Plectranthus barbatus, and Leonotis leonurus. We investigate the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) together with other seven species within the Lamiaceae (mint) family. Based on core genes found in the BGCs of all species examined across the Lamiaceae, we predict a simplified version of this cluster evolved in an early Lamiaceae ancestor. The current composition of the extant BGCs highlights the dynamic nature of its evolution. We elucidate the terpene backbones generated by the Callicarpa americana BGC enzymes, including miltiradiene and the terpene (+)-kaurene, and show oxidization activities of BGC cytochrome P450s. Our work reveals the fluid nature of BGC assembly and the importance of genome structure in contributing to the origin of metabolites.
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Affiliation(s)
- Abigail E Bryson
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Emily R Lanier
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Kin H Lau
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Davis Mathieu
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Alan E Yocca
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Garret P Miller
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Björn Hamberger
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA.
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10
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Shen S, Zhan C, Yang C, Fernie AR, Luo J. Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives. MOLECULAR PLANT 2023; 16:43-63. [PMID: 36114669 DOI: 10.1016/j.molp.2022.09.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.
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Affiliation(s)
- Shuangqian Shen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chuansong Zhan
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chenkun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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11
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Ye L, Yang L, Wang B, Chen G, Jiang L, Hu Z, Shi Z, Liu Y, Chen S. The Chromosome-level genome of Aesculus wilsonii provides new insights into terpenoid biosynthesis and Aesculus evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:1022169. [PMID: 36388583 PMCID: PMC9642078 DOI: 10.3389/fpls.2022.1022169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Aesculus L. (buckeye and horse chestnut) are woody plant species with important horticultural and medicinal values. Aesculus seeds are widely used as biomedicine and cosmetic ingredients due to their saponins. We report a chromosomal-scale genome of Aesculus wilsonii. Sequences amounting to a total of 579.01 Mb were assembled into 20 chromosomes. More than half of the genome (54.46%) were annotated as repetitive sequences, and 46,914 protein-coding genes were predicted. In addition to the widespread gamma event with core eudicots, a unique whole-genome duplication (WGD) event (17.69 Mya) occurred in Aesculus after buckeye differentiated from longan. Due to WGD events and tandem duplications, the related synthetic genes of triterpene saponins unique to Aesculus increased significantly. Combined with transcriptome characterization, the study preliminarily resolved the biosynthetic pathway of triterpenoid saponins like aescin in A. wilsonii genome. Analyses of the resequencing of 104 buckeye accessions revealed clear relationship between the geographic distribution and genetic differentiation of buckeye trees in China. We found that the buckeye species found in southern Shaanxi is A. wilsonii rather than A. chinensis. Population dynamics analysis further suggests that the population size and evolution of existing buckeye species have been influenced by climate fluctuations during the Pleistocene and recent domestication events. The genome of A. wilsonii and population genomics of Aesculus provide a resource for future research on Hippocastanaceae. These findings will contribute to the utilization and diversity protection of Aesculus.
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Affiliation(s)
- Lichun Ye
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Lulu Yang
- Genomics Project Department, Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Bo Wang
- Hubei Institute for Drug Control, Wuhan, China
| | - Gang Chen
- Genomics Project Department, Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Liping Jiang
- Department of Pharmacy, Wuhan Hospital of Traditional and Western Medicine, Wuhan, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Zhaohua Shi
- Key Laboratory of Chinese Medicine Resource and Compound Prescription, Ministry of Education, Hubei University of Chinese Medicine, Wuhan, China
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Shilin Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Institute of herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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12
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Zhan C, Shen S, Yang C, Liu Z, Fernie AR, Graham IA, Luo J. Plant metabolic gene clusters in the multi-omics era. TRENDS IN PLANT SCIENCE 2022; 27:981-1001. [PMID: 35365433 DOI: 10.1016/j.tplants.2022.03.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Secondary metabolism in plants gives rise to a vast array of small-molecule natural products. The discovery of operon-like gene clusters in plants has provided a new perspective on the evolution of specialized metabolism and the opportunity to rapidly advance the metabolic engineering of natural product production. Here, we review historical aspects of the study of plant metabolic gene clusters as well as general strategies for identifying plant metabolic gene clusters in the multi-omics era. We also emphasize the exploration of their natural variation and evolution, as well as new strategies for the prospecting of plant metabolic gene clusters and a deeper understanding of how their structure influences their function.
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Affiliation(s)
- Chuansong Zhan
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Shuangqian Shen
- College of Tropical Crops, Hainan University, Haikou 570228, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Alisdair R Fernie
- Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Ian A Graham
- Center for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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13
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Singh KS, van der Hooft JJJ, van Wees SCM, Medema MH. Integrative omics approaches for biosynthetic pathway discovery in plants. Nat Prod Rep 2022; 39:1876-1896. [PMID: 35997060 PMCID: PMC9491492 DOI: 10.1039/d2np00032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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14
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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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15
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Wu S, Malaco Morotti AL, Wang S, Wang Y, Xu X, Chen J, Wang G, Tatsis EC. Convergent gene clusters underpin hyperforin biosynthesis in St John's wort. THE NEW PHYTOLOGIST 2022; 235:646-661. [PMID: 35377483 DOI: 10.1111/nph.18138] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The meroterpenoid hyperforin is responsible for the antidepressant activity of St John's wort extracts, but the genes controlling its biosynthesis are unknown. Using genome mining and biochemical work, we characterize two biosynthetic gene clusters (BGCs) that encode the first three steps in the biosynthesis of hyperforin precursors. The findings of syntenic and phylogenetic analyses reveal the parallel assembly of the two BGCs. The syntenous BGC in Mesua ferrea indicates that the first cluster was assembled before the divergence of the Hypericaceae and Calophyllaceae families. The assembly of the second cluster is the result of a coalescence of genomic fragments after a major duplication event. The differences between the two BGCs - in terms of gene expression, response to methyl jasmonate, substrate specificity and subcellular localization of key enzymes - suggest that the presence of the two clusters could serve to generate separate pools of precursors. The parallel assembly of two BGCs with similar compositions in a single plant species is uncommon, and our work provides insights into how and when these gene clusters form. Our discovery helps to advance our understanding of the evolution of plant specialized metabolism and its genomic organization. Additionally, our results offer a foundation from which hyperforin biosynthesis can be more fully understood, and which can be used in future metabolic engineering applications.
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Affiliation(s)
- Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
| | - Shanshan Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
| | - Ya Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyan Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla County, 666303, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Evangelos C Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 300 Feng Lin Road, 200032, China
- CEPAMS - Centre of Excellence for Plant and Microbial Science, Shanghai, 200032, China
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16
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Du Y, Song W, Yin Z, Wu S, Liu J, Wang N, Jin H, Qiao J, Huo YX. Genomic Analysis Based on Chromosome-Level Genome Assembly Reveals an Expansion of Terpene Biosynthesis of Azadirachta indica. FRONTIERS IN PLANT SCIENCE 2022; 13:853861. [PMID: 35528946 PMCID: PMC9069239 DOI: 10.3389/fpls.2022.853861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Azadirachta indica (neem), an evergreen tree of the Meliaceae family, is a source of the potent biopesticide azadirachtin. The lack of a chromosome-level assembly impedes an in-depth understanding of its genome architecture and the comparative genomic analysis of A. indica. Here, a high-quality genome assembly of A. indica was constructed using a combination of data from Illumina, PacBio, and Hi-C technology, which is the first chromosome-scale genome assembly of A. indica. Based on the length of our assembly, the genome size of A. indica is estimated to be 281 Mb anchored to 14 chromosomes (contig N50 = 6 Mb and scaffold N50 = 19 Mb). The genome assembly contained 115 Mb repetitive elements and 25,767 protein-coding genes. Evolutional analysis revealed that A. indica didn't experience any whole-genome duplication (WGD) event after the core eudicot γ event, but some genes and genome segment might likely experienced recent duplications. The secondary metabolite clusters, TPS genes, and CYP genes were also identified. Comparative genomic analysis revealed that most of the A. indica-specific TPS genes and CYP genes were located on the terpene-related clusters on chromosome 13. It is suggested that chromosome 13 may play an important role in the specific terpene biosynthesis of A. indica. The gene duplication events may be responsible for the terpene biosynthesis expansion in A. indica. The genomic dataset and genomic analysis created for A. indica will shed light on terpene biosynthesis in A. indica and facilitate comparative genomic research of the family Meliaceae.
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Affiliation(s)
- Yuhui Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Wei Song
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Zhiqiu Yin
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, China
| | - Shengbo Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jiaheng Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Hua Jin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
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17
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Liu S, Xie L, Su J, Tian B, Fang A, Yu Y, Bi C, Yang Y. Integrated Metabolo-transcriptomics Reveals the Defense Response of Homogentisic Acid in Wheat against Puccinia striiformis f. sp. tritici. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3719-3729. [PMID: 35293725 DOI: 10.1021/acs.jafc.2c00231] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Stripe rust is a widespread and harmful wheat disease caused by Puccinia striiformis f. sp. tritici (Pst) worldwide. Targeted metabolome and transcriptomics analyses of CYR23 infected leaves were performed to identify the differential metabolites and differentially expressed genes related to wheat disease resistance. We observed upregulation of 33 metabolites involved in the primary and secondary metabolism, especially for homogentisic acid (HGA), p-coumaroylagmatine, and saccharopine. These three metabolites were mainly involved in the phenylpropanoid metabolic pathway, hydroxycinnamic acid amides pathway, and saccharopine pathway. Combined with transcriptome data on non-compatible interaction, the synthesis-related genes of these three differential metabolites were all upregulated significantly. The gene regulatory network involved in response to Pst infection was constructed, which revealed that several transcription factor families including WRKYs, MYBs, and bZIPs were identified as potentially hubs in wheat resistance response against Pst. An in vitro test showed that HGA effectively inhibited the germination of stripe rust fungus urediniospores and reduced the occurrence of wheat stripe rust. The results of gene silencing and overexpression of HGA synthesis-related gene 4-hydroxyphenylpyruvate dioxygenase proved that HGA was involved in wheat disease resistance. These results provided a further understanding of the disease resistance of wheat and indicated that HGA can be developed as a potential agent against Pst.
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Affiliation(s)
- Saifei Liu
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Liyang Xie
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Jiaxuan Su
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Binnian Tian
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Anfei Fang
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yang Yu
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Chaowei Bi
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yuheng Yang
- College of Plant Protection, Southwest University, Chongqing 400715, China
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18
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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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19
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Lu Y, Luo Y, Zhou J, Hu T, Tu L, Tong Y, Su P, Liu Y, Wang J, Jiang Z, Wu X, Chen X, Huang L, Gao W. Probing the functions of friedelane-type triterpene cyclases from four celastrol-producing plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:555-567. [PMID: 34750899 DOI: 10.1111/tpj.15575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Triterpenes are among the most diverse plant natural products, and their diversity is closely related to various triterpene skeletons catalyzed by different 2,3-oxidosqualene cyclases (OSCs). Celastrol, a friedelane-type triterpene with significant bioactivities, is specifically distributed in higher plants, such as Celastraceae species. Friedelin is an important precursor for the biosynthesis of celastrol, and it is synthesized through the cyclization of 2,3-oxidosqualene, with the highest number of rearrangements being catalyzed by friedelane-type triterpene cyclases. However, the molecular mechanisms underlying the catalysis of friedelin production by friedelane-type triterpene cyclases have not yet been fully elucidated. In this study, transcriptome data of four celastrol-producing plants from Celastraceae were used to identify a total of 21 putative OSCs. Through functional characterization, the friedelane-type triterpene cyclases were separately verified in the four plants. Analysis of the selection pressure showed that purifying selection acted on these OSCs, and the friedelane-type triterpene cyclases may undergo weaker selective restriction during evolution. Molecular docking and site-directed mutagenesis revealed that changes in some amino acids that are unique to friedelane-type triterpene cyclases may lead to variations in catalytic specificity or efficiency, thereby affecting the synthesis of friedelin. Our research explored the functional diversity of triterpene synthases from a multispecies perspective. It also provides some references for further research on the relative mechanisms of friedelin biosynthesis.
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Affiliation(s)
- Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yunfeng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jiawei Zhou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Tianyuan Hu
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Ping Su
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jiadian Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Zhouqian Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xiaoyi Wu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xiaochao Chen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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20
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Chakraborty P. Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery. Biochimie 2021; 193:1-15. [PMID: 34890733 DOI: 10.1016/j.biochi.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023]
Abstract
Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organised in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.
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Affiliation(s)
- Prasanta Chakraborty
- Kalpana Chawla Center for Space and Nanoscience, Kolkata, Indian Institute of Chemical Biology (retd.), Kolkata, 700032, India.
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21
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Chevrette MG, Gavrilidou A, Mantri S, Selem-Mojica N, Ziemert N, Barona-Gómez F. The confluence of big data and evolutionary genome mining for the discovery of natural products. Nat Prod Rep 2021; 38:2024-2040. [PMID: 34787598 DOI: 10.1039/d1np00013f] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review covers literature between 2003-2021The development and application of genome mining tools has given rise to ever-growing genetic and chemical databases and propelled natural products research into the modern age of Big Data. Likewise, an explosion of evolutionary studies has unveiled genetic patterns of natural products biosynthesis and function that support Darwin's theory of natural selection and other theories of adaptation and diversification. In this review, we aim to highlight how Big Data and evolutionary thinking converge in the study of natural products, and how this has led to an emerging sub-discipline of evolutionary genome mining of natural products. First, we outline general principles to best utilize Big Data in natural products research, addressing key considerations needed to provide evolutionary context. We then highlight successful examples where Big Data and evolutionary analyses have been combined to provide bioinformatic resources and tools for the discovery of novel natural products and their biosynthetic enzymes. Rather than an exhaustive list of evolution-driven discoveries, we highlight examples where Big Data and evolutionary thinking have been embraced for the evolutionary genome mining of natural products. After reviewing the nascent history of this sub-discipline, we discuss the challenges and opportunities of genomic and metabolomic tools with evolutionary foundations and/or implications and provide a future outlook for this emerging and exciting field of natural product research.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Athina Gavrilidou
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany.
| | - Shrikant Mantri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany. .,Computational Biology Laboratory, National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Nelly Selem-Mojica
- Laboratorio de Evolución de la Diversidad Metabólica, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico.
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany.
| | - Francisco Barona-Gómez
- Laboratorio de Evolución de la Diversidad Metabólica, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico.
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22
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Wang J, Guo Y, Yin X, Wang X, Qi X, Xue Z. Diverse triterpene skeletons are derived from the expansion and divergent evolution of 2,3-oxidosqualene cyclases in plants. Crit Rev Biochem Mol Biol 2021; 57:113-132. [PMID: 34601979 DOI: 10.1080/10409238.2021.1979458] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Triterpenoids are one of the largest groups of secondary metabolites and exhibit diverse structures, which are derived from C30 skeletons that are biosynthesized via the isoprenoid pathway by cyclization of 2,3-oxidosqualene. Triterpenoids have a wide range of biological activities, and are used in functional foods, drugs, and as industrial materials. Due to the low content levels in their native plants and limited feasibility and efficiency of chemical synthesis, heterologous biosynthesis of triterpenoids is the most promising strategy. Herein, we classified 121 triterpene alcohols/ketones according to their conformation and ring numbers, among which 51 skeletons have been experimentally characterized as the products of oxidosqualene cyclases (OSCs). Interestingly, 24 skeletons that have not been reported from nature source were generated by OSCs in heterologous expression. Comprehensive evolutionary analysis of the identified 152 OSCs from 75 species in 25 plant orders show that several pentacyclic triterpene synthases repeatedly originated in multiple plant lineages. Comparative analysis of OSC catalytic reaction revealed that stabilization of intermediate cations, steric hindrance, and conformation of active center amino acid residues are primary factors affecting triterpene formation. Optimization of OSC could be achieved by changing of side-chain orientations of key residues. Recently, methods, such as rationally design of pathways, regulation of metabolic flow, compartmentalization engineering, etc., were introduced in improving chassis for the biosynthesis of triterpenoids. We expect that extensive study of natural variation of large number of OSCs and catalytical mechanism will provide basis for production of high level of triterpenoids by application of synthetic biology strategies.
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Affiliation(s)
- Jing Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.,Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China.,Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, PR China
| | - Yanhong Guo
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.,Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Xue Yin
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.,Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Xiaoning Wang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, PR China
| | - Zheyong Xue
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.,Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
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23
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Kumar A, Srivastava P, Srivastava G, Sandeep, Kumar N, Chanotiya CS, Ghosh S. BAHD acetyltransferase contributes to wound-induced biosynthesis of oleo-gum resin triterpenes in Boswellia. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1403-1419. [PMID: 34165841 DOI: 10.1111/tpj.15388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Triterpenes (30-carbon isoprene compounds) represent a large and highly diverse class of natural products that play various physiological functions in plants. The triterpene biosynthetic enzymes, particularly those catalyzing the late-stage regio-selective modifications are not well characterized. The bark of select Boswellia trees, e.g., B. serrata exudes specialized oleo-gum resin in response to wounding, which is enriched with boswellic acids (BAs), a unique class of C3α-epimeric pentacyclic triterpenes with medicinal properties. The bark possesses a network of resin secretory structures comprised of vertical and horizontal resin canals, and amount of BAs in bark increases considerably in response to wounding. To investigate BA biosynthetic enzymes, we conducted tissue-specific transcriptome profiling and identified a wound-responsive BAHD acetyltransferase (BsAT1) of B. serrata catalyzing the late-stage C3α-O-acetylation reactions in the BA biosynthetic pathway. BsAT1 catalyzed C3α-O-acetylation of αBA, βBA, and 11-keto-βBA in vitro and in planta assays to produce all the major C3α-O-acetyl-BAs (3-acetyl-αBA, 3-acetyl-βBA, and 3-acetyl-11-keto-βBA) found in B. serrata bark and oleo-gum resin. BsAT1 showed strict specificity for BA scaffold, whereas it did not acetylate the more common C3β-epimeric pentacyclic triterpenes. The analysis of steady-state kinetics using various BAs revealed distinct substrate affinity and catalytic efficiency. BsAT1 transcript expression coincides with increased levels of C3α-O-acetyl-BAs in bark in response to wounding, suggesting a role of BsAT1 in wound-induced biosynthesis of C3α-O-acetyl-BAs. Overall, the results provide new insights into the biosynthesis of principal chemical constituents of Boswellia oleo-gum resin.
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Affiliation(s)
- Aashish Kumar
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Payal Srivastava
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gaurav Srivastava
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sandeep
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Narendra Kumar
- Plant Breeding and Genetic Resource Conservation Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Chandan S Chanotiya
- Phytochemistry Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sumit Ghosh
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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24
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Medema MH, de Rond T, Moore BS. Mining genomes to illuminate the specialized chemistry of life. Nat Rev Genet 2021; 22:553-571. [PMID: 34083778 PMCID: PMC8364890 DOI: 10.1038/s41576-021-00363-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.
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Affiliation(s)
- Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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25
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Bharadwaj R, Kumar SR, Sharma A, Sathishkumar R. Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2021; 12:697318. [PMID: 34490002 PMCID: PMC8418127 DOI: 10.3389/fpls.2021.697318] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 05/21/2023]
Abstract
Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Sarma R. Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Querétaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
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26
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Gilchrist CLM, Booth TJ, van Wersch B, van Grieken L, Medema MH, Chooi YH. cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters. BIOINFORMATICS ADVANCES 2021; 1:vbab016. [PMID: 36700093 PMCID: PMC9710679 DOI: 10.1093/bioadv/vbab016] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 01/28/2023]
Abstract
Motivation Genes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalized as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however, existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data. Results Here, we present cblaster, a Python-based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface. It generates outputs that enable intuitive visualizations of large datasets and can be readily incorporated into larger bioinformatic pipelines. cblaster is a significant update to the comparative genomics toolbox. Availability and implementation cblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Cameron L M Gilchrist
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia,To whom correspondence should be addressed. or or
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Bram van Wersch
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands
| | - Liana van Grieken
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands,To whom correspondence should be addressed. or or
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia,To whom correspondence should be addressed. or or
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27
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van Velzen R, Schranz ME. Origin and Evolution of the Cannabinoid Oxidocyclase Gene Family. Genome Biol Evol 2021; 13:evab130. [PMID: 34100927 PMCID: PMC8521752 DOI: 10.1093/gbe/evab130] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 12/21/2022] Open
Abstract
Cannabis is an ancient crop representing a rapidly increasing legal market, especially for medicinal purposes. Medicinal and psychoactive effects of Cannabis rely on specific terpenophenolic ligands named cannabinoids. Recent whole-genome sequencing efforts have uncovered variation in multiple genes encoding the final steps in cannabinoid biosynthesis. However, the origin, evolution, and phylogenetic relationships of these cannabinoid oxidocyclase genes remain unclear. To elucidate these aspects, we performed comparative genomic analyses of Cannabis, related genera within the Cannabaceae family, and selected outgroup species. Results show that cannabinoid oxidocyclase genes originated in the Cannabis lineage from within a larger gene expansion in the Cannabaceae family. Localization and divergence of oxidocyclase genes in the Cannabis genome revealed two main syntenic blocks, each comprising tandemly repeated cannabinoid oxidocyclase genes. By comparing these blocks with those in genomes from closely related species, we propose an evolutionary model for the origin, neofunctionalization, duplication, and diversification of cannabinoid oxidocycloase genes. Based on phylogenetic analyses, we propose a comprehensive classification of three main clades and seven subclades that are intended to aid unequivocal referencing and identification of cannabinoid oxidocyclase genes. Our data suggest that cannabinoid phenotype is primarily determined by the presence/absence of single-copy genes. Although wild populations of Cannabis are still unknown, increased sampling of landraces and wild/feral populations across its native geographic range is likely to uncover additional cannabinoid oxidocyclase sequence variants.
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Affiliation(s)
- Robin van Velzen
- Plant Sciences, Biosystematics Group, Wageningen University, Wageningen, The Netherlands
- Bedrocan International, Veendam, The Netherlands
| | - M Eric Schranz
- Plant Sciences, Biosystematics Group, Wageningen University, Wageningen, The Netherlands
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28
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Garagounis C, Delkis N, Papadopoulou KK. Unraveling the roles of plant specialized metabolites: using synthetic biology to design molecular biosensors. THE NEW PHYTOLOGIST 2021; 231:1338-1352. [PMID: 33997999 DOI: 10.1111/nph.17470] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 05/25/2023]
Abstract
Plants are a rich source of specialized metabolites with a broad range of bioactivities and many applications in human daily life. Over the past decades significant progress has been made in identifying many such metabolites in different plant species and in elucidating their biosynthetic pathways. However, the biological roles of plant specialized metabolites remain elusive and proposed functions lack an identified underlying molecular mechanism. Understanding the roles of specialized metabolites frequently is hampered by their dynamic production and their specific spatiotemporal accumulation within plant tissues and organs throughout a plant's life cycle. In this review, we propose the employment of strategies from the field of Synthetic Biology to construct and optimize genetically encoded biosensors that can detect individual specialized metabolites in a standardized and high-throughput manner. This will help determine the precise localization of specialized metabolites at the tissue and single-cell levels. Such information will be useful in developing complete system-level models of specialized plant metabolism, which ultimately will demonstrate how the biosynthesis of specialized metabolites is integrated with the core processes of plant growth and development.
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Affiliation(s)
- Constantine Garagounis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Nikolaos Delkis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
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29
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Dong L, Almeida A, Pollier J, Khakimov B, Bassard JE, Miettinen K, Stærk D, Mehran R, Olsen CE, Motawia MS, Goossens A, Bak S. An independent evolutionary origin for insect deterrent cucurbitacins in Iberis amara. Mol Biol Evol 2021; 38:4659-4673. [PMID: 34264303 PMCID: PMC8557398 DOI: 10.1093/molbev/msab213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pieris rapae and Phyllotreta nemorum are Brassicaceae specialists, but do not feed on Iberis amara spp. that contain cucurbitacins. The cucurbitacins are highly oxygenated triterpenoid, occurring widespread in cucurbitaceous species and in a few other plant families. Using de-novo assembled transcriptomics from I. amara, gene co-expression analysis and comparative genomics, we unraveled the evolutionary origin of the insect deterrent cucurbitacins in I. amara. Phylogenetic analysis of five oxidosqualene cyclases and heterologous expression allowed us to identify the first committed enzyme in cucurbitacin biosynthesis in I. amara, cucurbitadienol synthase (IaCPQ). In addition, two species-specific cytochrome P450s (CYP708A16 and CYP708A15) were identified that catalyse the unique C16 and C22 hydroxylation of the cucurbitadienol backbone, enzymatic steps that have not been reported before. Furthermore, the draft genome assembly of I. amara showed that the IaCPQ was localized to the same scaffold together with CYP708A15 but spanning over 100 kb, this contrasts with the highly organized cucurbitacin gene cluster in the cucurbits. These results reveal that cucurbitacin biosynthesis has evolved convergently via different biosynthetic routes in different families rather than through divergence from an ancestral pathway. This study thus provides new insight into the mechanism of recurrent evolution and diversification of a plant defensive chemical.
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Affiliation(s)
- Lemeng Dong
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.,Plant Hormone Biology group, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Aldo Almeida
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jacob Pollier
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Bekzod Khakimov
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Jean-Etienne Bassard
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Karel Miettinen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dan Stærk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Rahimi Mehran
- Plant Hormone Biology group, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Carl Erik Olsen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Søren Bak
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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30
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Teresa B. Fitzpatrick. THE NEW PHYTOLOGIST 2021; 231:537-539. [PMID: 34132415 DOI: 10.1111/nph.17439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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31
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Polturak G, Osbourn A. The emerging role of biosynthetic gene clusters in plant defense and plant interactions. PLoS Pathog 2021; 17:e1009698. [PMID: 34214143 PMCID: PMC8253395 DOI: 10.1371/journal.ppat.1009698] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Guy Polturak
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
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32
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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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Ma Y, Cui G, Chen T, Ma X, Wang R, Jin B, Yang J, Kang L, Tang J, Lai C, Wang Y, Zhao Y, Shen Y, Zeng W, Peters RJ, Qi X, Guo J, Huang L. Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza. Nat Commun 2021; 12:685. [PMID: 33514704 PMCID: PMC7846762 DOI: 10.1038/s41467-021-20959-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/01/2021] [Indexed: 11/09/2022] Open
Abstract
Tanshinones are the bioactive nor-diterpenoid constituents of the Chinese medicinal herb Danshen (Salvia miltiorrhiza). These groups of chemicals have the characteristic furan D-ring, which differentiates them from the phenolic abietane-type diterpenoids frequently found in the Lamiaceae family. However, how the 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly of Danshen using a highly homozygous genotype. We identify a cytochrome P450 (CYP71D) tandem gene array through gene expansion analysis. We show that CYP71D373 and CYP71D375 catalyze hydroxylation at carbon-16 (C16) and 14,16-ether (hetero)cyclization to form the D-ring, whereas CYP71D411 catalyzes upstream hydroxylation at C20. In addition, we discover a large biosynthetic gene cluster associated with tanshinone production. Collinearity analysis indicates a more specific origin of tanshinones in Salvia genus. It illustrates the evolutionary origin of abietane-type diterpenoids and those with a furan D-ring in Lamiaceae.
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Affiliation(s)
- Ying Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guanghong Cui
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Tong Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaohui Ma
- College of Pharmaceutical Science, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Ruishan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baolong Jin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jian Yang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Liping Kang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jinfu Tang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Changjiangsheng Lai
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yujun Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ye Shen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wen Zeng
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Reuben J Peters
- Roy J. Carver Dep. of Biochem., Biophys. & Mol. Biol., Iowa State University, Ames, IA, USA
| | - Xiaoquan Qi
- Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
| | - Juan Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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Eljounaidi K, Lichman BR. Nature's Chemists: The Discovery and Engineering of Phytochemical Biosynthesis. Front Chem 2020; 8:596479. [PMID: 33240856 PMCID: PMC7680914 DOI: 10.3389/fchem.2020.596479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Abstract
Plants produce a diverse array of natural products, many of which have high pharmaceutical value or therapeutic potential. However, these compounds often occur at low concentrations in uncultivated species. Producing phytochemicals in heterologous systems has the potential to address the bioavailability issues related to obtaining these molecules from their natural source. Plants are suitable heterologous systems for the production of valuable phytochemicals as they are autotrophic, derive energy and carbon from photosynthesis, and have similar cellular context to native producer plants. In this review we highlight the methods that are used to elucidate natural product biosynthetic pathways, including the approaches leading to proposing the sequence of enzymatic steps, selecting enzyme candidates and characterizing gene function. We will also discuss the advantages of using plant chasses as production platforms for high value phytochemicals. In addition, through this report we will assess the emerging metabolic engineering strategies that have been developed to enhance and optimize the production of natural and novel bioactive phytochemicals in heterologous plant systems.
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Affiliation(s)
- Kaouthar Eljounaidi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
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35
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Formation and diversification of a paradigm biosynthetic gene cluster in plants. Nat Commun 2020; 11:5354. [PMID: 33097700 PMCID: PMC7584637 DOI: 10.1038/s41467-020-19153-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Numerous examples of biosynthetic gene clusters (BGCs), including for compounds of agricultural and medicinal importance, have now been discovered in plant genomes. However, little is known about how these complex traits are assembled and diversified. Here, we examine a large number of variants within and between species for a paradigm BGC (the thalianol cluster), which has evolved recently in a common ancestor of the Arabidopsis genus. Comparisons at the species level reveal differences in BGC organization and involvement of auxiliary genes, resulting in production of species-specific triterpenes. Within species, the thalianol cluster is primarily fixed, showing a low frequency of deleterious haplotypes. We further identify chromosomal inversion as a molecular mechanism that may shuffle more distant genes into the cluster, so enabling cluster compaction. Antagonistic natural selection pressures are likely involved in shaping the occurrence and maintenance of this BGC. Our work sheds light on the birth, life and death of complex genetic and metabolic traits in plants.
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36
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Hamilton JP, Godden GT, Lanier E, Bhat WW, Kinser TJ, Vaillancourt B, Wang H, Wood JC, Jiang J, Soltis PS, Soltis DE, Hamberger B, Buell CR. Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana. Gigascience 2020; 9:giaa093. [PMID: 32893861 PMCID: PMC7476102 DOI: 10.1093/gigascience/giaa093] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/03/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance. FINDINGS We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs. CONCLUSIONS Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.
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Affiliation(s)
- John P Hamilton
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611, USA
| | - Emily Lanier
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI 48824, USA
| | - Wajid Waheed Bhat
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI 48824, USA
| | - Taliesin J Kinser
- Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, 876 Newell Dr, Gainesville, Florida, 32611 USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Haiyan Wang
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Joshua C Wood
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
- MSU AgBioResearch, Michigan State University, 446 W. Circle Drive, East Lansing, MI 48824, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, 876 Newell Dr, Gainesville, Florida, 32611 USA
| | - Bjoern Hamberger
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI 48824, USA
- MSU AgBioResearch, Michigan State University, 446 W. Circle Drive, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- MSU AgBioResearch, Michigan State University, 446 W. Circle Drive, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
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37
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Peters RJ. Doing the gene shuffle to close synteny: dynamic assembly of biosynthetic gene clusters. THE NEW PHYTOLOGIST 2020; 227:992-994. [PMID: 32433781 PMCID: PMC7856633 DOI: 10.1111/nph.16631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
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38
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Fan P, Wang P, Lou YR, Leong BJ, Moore BM, Schenck CA, Combs R, Cao P, Brandizzi F, Shiu SH, Last RL. Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity. eLife 2020; 9:e56717. [PMID: 32613943 PMCID: PMC7386920 DOI: 10.7554/elife.56717] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity and recruitment of primary metabolic enzymes and examples of genomic clustering of pathway genes. Solanaceae glandular trichomes produce defensive acylsugars, with sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals insights into the dynamics behind gene cluster evolution and cell-type specific metabolite diversity.
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Affiliation(s)
- Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Peipei Wang
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
| | - Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Bryan J Leong
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
| | - Bethany M Moore
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- University of WisconsinMadisonUnited States
| | - Craig A Schenck
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Rachel Combs
- Division of Biological Sciences, University of MissouriColumbusUnited States
| | - Pengfei Cao
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast LansingUnited States
| | - Federica Brandizzi
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast LansingUnited States
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
- Department of Computational Mathematics, Science, and Engineering, Michigan State UniversityEast LansingUnited States
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
- Department of Plant Biology, Michigan State UniversityEast LansingUnited States
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39
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Tohge T, Fernie AR. Co-Regulation of Clustered and Neo-Functionalized Genes in Plant-Specialized Metabolism. PLANTS (BASEL, SWITZERLAND) 2020; 9:E622. [PMID: 32414181 PMCID: PMC7285293 DOI: 10.3390/plants9050622] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 01/20/2023]
Abstract
Current findings of neighboring genes involved in plant specialized metabolism provide the genomic signatures of metabolic evolution. Two such genomic features, namely, (i) metabolic gene cluster and (ii) neo-functionalization of tandem gene duplications, represent key factors corresponding to the creation of metabolic diversity of plant specialized metabolism. So far, several terpenoid and alkaloid biosynthetic genes have been characterized with gene clusters in some plants. On the other hand, some modification genes involved in flavonoid and glucosinolate biosynthesis were found to arise via gene neo-functionalization. Although the occurrence of both types of metabolic evolution are different, the neighboring genes are generally regulated by the same or related regulation factors. Therefore, the translation-based approaches associated with genomics, and transcriptomics are able to be employed for functional genomics focusing on plant secondary metabolism. Here, we present a survey of the current understanding of neighboring genes involved in plant secondary metabolism. Additionally, a genomic overview of neighboring genes of four model plants and transcriptional co-expression network neighboring genes to detect metabolic gene clusters in Arabidopsis is provided. Finally, the insights functional genomics have provided concerning the evolution and mechanistic regulation of both the formation and operation of metabolic neighboring clusters is discussed.
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Affiliation(s)
- Takayuki Tohge
- Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma 630-0192, Japan
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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