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Yang J, Wu Y, Zhang P, Ma J, Yao YJ, Ma YL, Zhang L, Yang Y, Zhao C, Wu J, Fang X, Liu J. Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family. Nat Commun 2023; 14:8457. [PMID: 38114555 PMCID: PMC10730914 DOI: 10.1038/s41467-023-44246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Hyoscyamine and scopolamine (HS), two valuable tropane alkaloids of significant medicinal importance, are found in multiple distantly related lineages within the Solanaceae family. Here we sequence the genomes of three representative species that produce HS from these lineages, and one species that does not produce HS. Our analysis reveals a shared biosynthetic pathway responsible for HS production in the three HS-producing species. We observe a high level of gene collinearity related to HS synthesis across the family in both types of species. By introducing gain-of-function and loss-of-function mutations at key sites, we confirm the reduced/lost or re-activated functions of critical genes involved in HS synthesis in both types of species, respectively. These findings indicate independent and repeated losses of the HS biosynthesis pathway since its origin in the ancestral lineage. Our results hold promise for potential future applications in the artificial engineering of HS biosynthesis in Solanaceae crops.
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Affiliation(s)
- Jiao Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Pan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianxiang Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Jun Yao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Lin Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan, 750021, Ningxia, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Changmin Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jihua Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiangwen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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Xu C, Su W. Hyperforin modulates MAPK/CCL11 signaling to reduce the inflammatory response of nasal mucosal epithelial cells caused by allergic rhinitis by targeting BCL6. Exp Ther Med 2023; 26:579. [PMID: 38023351 PMCID: PMC10655049 DOI: 10.3892/etm.2023.12278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/17/2023] [Indexed: 12/01/2023] Open
Abstract
Hyperforin is a type of bicyclic tetraketone with four isoprenoid chains extracted from Hypericum perforatum L. that has multiple biological activities such as anti-diabetes, antitumor and anti-inflammation. However, the role and potential mechanism of hyperforin in allergic rhinitis (AR) remains to be clarified. In the present study, cell viability was analyzed using Cell Counting Kit-8 assay, while inflammation was detected using ELISA and reverse transcription-quantitative PCR. Epithelial cell barrier damage was measured using western blotting and immunofluorescence staining. The expression levels of B-cell lymphoma 6 (BCL6) and the p38 MAPK/C-C motif chemokine 11 (CCL11) pathway were detected using western blotting. In addition, the association between hyperforin and BCL6 was analyzed by SWISS TargetPrediction, DisGeNET, Gene Ontology and Pathway databases. Molecular docking was performed using AutoDockTools 1.5.6 and Discovery Studio 4.5 software. The data demonstrated that there were 16 interlinking target genes of hyperforin with AR, in which BCL6 was the most relevant one with hyperforin in AR. The binding between hyperforin and BCL6 was verified, and molecular docking was modeled. The results revealed that hyperforin inhibited IL-13-induced nasal epithelial inflammatory cytokine release and repressed the damage to the cellular barrier from IL-13 stimulation. In addition, hyperforin activated BCL6 expression and significantly suppressed the expression of p38 MAPK/CCL11. Silencing of BCL6 reversed the effects of hyperforin on IL-13-induced inflammation and barrier damage. In summary, the present results revealed that hyperforin suppressed IL-13-induced nasal epithelial cell inflammation and barrier damage by targeting BCL6/p38 MAPK/CCL11, which may provide promising therapeutic targets for AR.
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Affiliation(s)
- Chen Xu
- Department of Pediatrics, Wuhan Hospital of Integrated Traditional Chinese and Western Medicine (Wuhan No. 1 Hospital), Wuhan, Hubei 430022, P.R. China
| | - Wen Su
- Department of Pediatrics, Wuhan Hospital of Integrated Traditional Chinese and Western Medicine (Wuhan No. 1 Hospital), Wuhan, Hubei 430022, P.R. China
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Wu Y, Liu C, Koganitsky A, Gong FL, Li S. Discovering Dynamic Plant Enzyme Complexes in Yeast for Kratom Alkaloid Pathway Identification. Angew Chem Int Ed Engl 2023; 62:e202307995. [PMID: 37549372 PMCID: PMC10530425 DOI: 10.1002/anie.202307995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Discovering natural product biosynthetic pathways of medicinal plants is challenging and laborious. Capturing the coregulation patterns of pathway enzymes, particularly transcriptomic regulation, has proven an effective method to accelerate pathway identification. In this study, we developed a yeast-based screening method to capture the protein-protein interactions (PPI) between plant enzymes, which is another useful pattern to complement the prevalent approach. Combining this method with plant multiomics analysis, we discovered four enzyme complexes and their organized pathways from kratom, an alkaloid-producing plant. The four pathway branches involved six enzymes, including a strictosidine synthase, a strictosidine β-D-glucosidase (MsSGD), and four medium-chain dehydrogenase/reductases (MsMDRs). PPI screening selected six MsMDRs interacting with MsSGD from 20 candidates predicted by multiomics analysis. Four of the six MsMDRs were then characterized as functional, indicating the high selectivity of the PPI screening method. This study highlights the opportunity of leveraging post-translational regulation features to discover novel plant natural product biosynthetic pathways.
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Affiliation(s)
- Yinan Wu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Chang Liu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Anna Koganitsky
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Franklin L Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
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4
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Raj Y, Kumar A, Kumari S, Kumar R, Kumar R. Comparative Genomics and Physiological Investigations Supported Multifaceted Plant Growth-Promoting Activities in Two Hypericum perforatum L.-Associated Plant Growth-Promoting Rhizobacteria for Microbe-Assisted Cultivation. Microbiol Spectr 2023; 11:e0060723. [PMID: 37199656 PMCID: PMC10269543 DOI: 10.1128/spectrum.00607-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/01/2023] [Indexed: 05/19/2023] Open
Abstract
Plants are no longer considered standalone entities; instead, they harbor a diverse community of plant growth-promoting rhizobacteria (PGPR) that aid them in nutrient acquisition and can also deliver resilience. Host plants recognize PGPR in a strain-specific manner; therefore, introducing untargeted PGPR might produce unsatisfactory crop yields. Consequently, to develop a microbe-assisted Hypericum perforatum L. cultivation technique, 31 rhizobacteria were isolated from the plant's high-altitude Indian western Himalayan natural habitat and in vitro characterized for multiple plant growth-promoting attributes. Among 31 rhizobacterial isolates, 26 produced 0.59 to 85.29 μg mL-1 indole-3-acetic acid and solubilized 15.77 to 71.43 μg mL-1 inorganic phosphate; 21 produced 63.12 to 99.92% siderophore units, and 15 exhibited 103.60 to 1,296.42 nmol α-ketobutyrate mg-1 protein h-1 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity. Based on superior plant growth-promoting attributes, eight statistically significant multifarious PGPR were further evaluated for an in planta plant growth-promotion assay under poly greenhouse conditions. Plants treated with Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18 showed, by significant amounts, the highest photosynthetic pigments and performance, eventually leading to the highest biomass accumulation. Comparative genome analysis and comprehensive genome mining unraveled their unique genetic features, such as adaptation to the host plant's immune system and specialized metabolites. Moreover, the strains harbor several functional genes regulating direct and indirect plant growth-promotion mechanisms through nutrient acquisition, phytohormone production, and stress alleviation. In essence, the current study endorsed strains HypNH10 and HypNH18 as cogent candidates for microbe-assisted H. perforatum cultivation by highlighting their exclusive genomic signatures, which suggest their unison, compatibility, and multifaceted beneficial interactions with their host and support the excellent plant growth-promotion performance observed in the greenhouse trial. IMPORTANCE Hypericum perforatum L. (St. John's wort) herbal preparations are among the top-selling products to treat depression worldwide. A significant portion of the overall Hypericum supply is sourced through wild collection, prompting a rapid decline in their natural stands. Crop cultivation seems lucrative, although cultivable land and its existing rhizomicrobiome are well suited for traditional crops, and its sudden introduction can create soil microbiome dysbiosis. Also, the conventional plant domestication procedures with increased reliance on agrochemicals can reduce the diversity of the associated rhizomicrobiome and plants' ability to interact with plant growth-promoting microorganisms, leading to unsatisfactory crop production alongside harmful environmental effects. Cultivating H. perforatum with crop-associated beneficial rhizobacteria can reconcile such concerns. Based on a combinatorial in vitro, in vivo plant growth-promotion assay and in silico prediction of plant growth-promoting traits, here we recommend two H. perforatum-associated PGPR, Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18, to extrapolate as functional bioinoculants for H. perforatum sustainable cultivation.
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Affiliation(s)
- Yog Raj
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anil Kumar
- High Altitude Microbiology Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sareeka Kumari
- High Altitude Microbiology Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rakshak Kumar
- High Altitude Microbiology Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rakesh Kumar
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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5
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Sayed HMB, Nassar S, Kaufholdt D, Beerhues L, Liu B, El-Awaad I. Biosynthesis of polyprenylated xanthones in Hypericum perforatum roots involves 4-prenyltransferase. PLANT PHYSIOLOGY 2023:kiad219. [PMID: 37061818 DOI: 10.1093/plphys/kiad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/24/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Polyprenylated xanthones are natural products with a multitude of biological and pharmacological activities. However, their biosynthetic pathway is not completely understood. In this study, metabolic profiling revealed the presence of 4-prenylated 1,3,5,6-tetrahydroxyxanthone derivatives in St. John's wort (Hypericum perforatum) root extracts. Transcriptomic data mining led to the detection of five variants of xanthone 4-prenyltransferase (HpPT4px) comprising four long variants (HpPT4px-v1 to HpPT4px-v4) and one short variant (HpPT4px-sh). The full-length sequences of all five variants were cloned and heterologously expressed in yeast (Saccharomyces cerevisiae). Microsomes containing HpPT4px-v2, HpPT4px-v4, and HpPT4px-sh catalyzed the addition of a prenyl group at the C-4 position of 1,3,5,6-tetrahydroxyxanthone, 1,3,5-trihydroxyxanthone, and 1,3,7-trihydroxyxanthone, whereas microsomes harboring HpPT4px-v1 and HpPT4px-v3 additionally accepted 1,3,6,7-tetrahydroxyxanthone. HpPT4px-v1 produced in Nicotiana benthamiana displayed the same activity as in yeast, while HpPT4px-sh was inactive. The kinetic parameters of HpPT4px-v1 and HpPT4px-sh chosen as representative variants indicated 1,3,5,6-tetrahydroxyxanthone as the preferred acceptor substrate, rationalizing that HpPT4px catalyzes the first prenylation step in the biosynthesis of polyprenylated xanthones in H. perforatum. Dimethylallyl pyrophosphate was the exclusive prenyl donor. Expression of the HpPT4px transcripts was highest in roots and leaves, raising the question of product translocation. C-terminal yellow fluorescent protein fusion of HpPT4px-v1 localized to the envelope of chloroplasts in N. benthamiana leaves, whereas short, truncated, and masked signal peptides led to the disruption of plastidial localization. These findings pave the way for a better understanding of the prenylation of xanthones in plants and the identification of additional xanthone-specific prenyltransferases.
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Affiliation(s)
- Hesham M B Sayed
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt
| | - Sara Nassar
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, 11566 Cairo, Egypt
| | - David Kaufholdt
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, 38106 Braunschweig, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
| | - Islam El-Awaad
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt
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6
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Li H, Wu S, Lin R, Xiao Y, Malaco Morotti AL, Wang Y, Galilee M, Qin H, Huang T, Zhao Y, Zhou X, Yang J, Zhao Q, Kanellis AK, Martin C, Tatsis EC. The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae. MOLECULAR PLANT 2023; 16:549-570. [PMID: 36639870 DOI: 10.1016/j.molp.2023.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/21/2022] [Accepted: 01/09/2023] [Indexed: 06/09/2023]
Abstract
The presence of anticancer clerodane diterpenoids is a chemotaxonomic marker for the traditional Chinese medicinal plant Scutellaria barbata, although the molecular mechanisms behind clerodane biosynthesis are unknown. Here, we report a high-quality assembly of the 414.98 Mb genome of S. barbata into 13 pseudochromosomes. Using phylogenomic and biochemical data, we mapped the plastidial metabolism of kaurene (gibberellins), abietane, and clerodane diterpenes in three species of the family Lamiaceae (Scutellaria barbata, Scutellaria baicalensis, and Salvia splendens), facilitating the identification of genes involved in the biosynthesis of the clerodanes, kolavenol, and isokolavenol. We show that clerodane biosynthesis evolved through recruitment and neofunctionalization of genes from gibberellin and abietane metabolism. Despite the assumed monophyletic origin of clerodane biosynthesis, which is widespread in species of the Lamiaceae, our data show distinct evolutionary lineages and suggest polyphyletic origins of clerodane biosynthesis in the family Lamiaceae. Our study not only provides significant insights into the evolution of clerodane biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the production of anticancer clerodanes through future metabolic engineering efforts.
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Affiliation(s)
- Haixiu Li
- 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 200032, China
| | - 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 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruoxi Lin
- 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 200032, China
| | - Yiren Xiao
- 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 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 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 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meytal Galilee
- 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 200032, China
| | - Haowen Qin
- 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 200032, China
| | - Tao Huang
- Novogene Bioinformatics Institute, Beijing, China
| | - Yong Zhao
- Novogene Bioinformatics Institute, Beijing, China
| | - Xun Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Jun Yang
- 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 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - Qing Zhao
- 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 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - Angelos K Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Lab. of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | | | - 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 200032, China; CEPAMS - CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Shanghai 200032, China.
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7
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Wu Y, Gong FL, Li S. Leveraging yeast to characterize plant biosynthetic gene clusters. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102314. [PMID: 36463029 PMCID: PMC10664738 DOI: 10.1016/j.pbi.2022.102314] [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: 08/30/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Plant biosynthetic gene clusters (BGCs) contain multiple physically clustered non-homologous genes that encode enzymes catalyzing diverse reactions in one plant natural product biosynthetic pathway. A growing number of plant BGCs have emerged as an underlying resource for understanding plant specialized metabolism and evolution, but the characterization remains challenging. Recent studies have demonstrated that baker's yeast can serve as a versatile platform for the characterization of plant BGCs, from single-gene characterization to multiple genes and hitherto unknown putative BGC validation and elucidation. In this review, we will summarize the strategies and examples of the applications of yeast in plant BGC characterization and share our perspective on the development of a systematic pipeline to fully leverage yeast to advance the understanding of plant BGCs and plant natural product biomanufacturing.
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Affiliation(s)
- Yinan Wu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Franklin L Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA.
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8
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Drummond CP, Renner T. Genomic insights into the evolution of plant chemical defense. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102254. [PMID: 35777286 DOI: 10.1016/j.pbi.2022.102254] [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: 11/15/2021] [Revised: 04/22/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Plant trait evolution can be impacted by common mechanisms of genome evolution, including whole-genome and small-scale duplication, rearrangement, and selective pressures. With the increasing accessibility of genome sequencing for non-model species, comparative studies of trait evolution among closely related or divergent lineages have supported investigations into plant chemical defense. Plant defensive compounds include major chemical classes, such as terpenoids, alkaloids, and phenolics, and are used in primary and secondary plant functions. These include the promotion of plant health, facilitation of pollination, defense against pathogens, and responses to a rapidly changing climate. We discuss mechanisms of genome evolution and use examples from recent studies to impress a stronger understanding of the link between genotype and phenotype as it relates to the evolution of plant chemical defense. We conclude with considerations for how to leverage genomics, transcriptomics, metabolomics, and functional assays for studying the emergence and evolution of chemical defense systems.
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Affiliation(s)
- Chloe P Drummond
- The Pennsylvania State University, Department of Entomology, 501 ASI Building University Park, PA 16802, USA.
| | - Tanya Renner
- The Pennsylvania State University, Department of Entomology, 501 ASI Building University Park, PA 16802, USA
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