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Ivamoto-Suzuki ST, Celedón JM, Yuen MMS, Kitzberger CSG, Silva Domingues D, Bohlmann J, Protasio Pereira LF. Functional Characterization of ent-Copalyl Diphosphate Synthase and Kaurene Synthase Genes from Coffea arabica L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15863-15873. [PMID: 37816128 DOI: 10.1021/acs.jafc.2c09087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
The biochemical profile of coffee beans translates directly into quality traits, nutraceutical and health promoting properties of the coffee beverage. Ent-kaurene is the ubiquitous precursor for gibberellin biosynthesis in plants, but it also serves as an intermediate in specialized (i.e., secondary) diterpenoid metabolism that leads to a diversity of more than 1,000 different metabolites. Nutraceutical effects on human health attributed to diterpenes include antioxidant, anticarcinogenic, and anti-inflammatory properties. Cafestol (CAF) and kahweol (KAH) are two diterpenes found exclusively in the Coffea genus. Our objective was to identify and functionally characterize genes involved in the central step of ent-kaurene production. We identified 17 putative terpene synthase genes in the transcriptome of Coffea arabica. Two ent-copalyl diphosphate synthase (CaCPS) and three kaurene synthase (CaKS) were selected and manually annotated. Transcript expression profiles of CaCPS1 and CaKS3 best matched the CAF and KAH metabolite profiles in different tissues. CaCPS1 and CaKS3 proteins were heterologously expressed and functionally characterized. CaCPS1 catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to ent-copalyl diphosphate (ent-CPP), which is converted to ent-kaurene by CaKS3. Knowledge about the central steps of diterpene formation in coffee provides a foundation for future characterization of the subsequent enzymes involved in CAF and KAH biosynthesis.
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Affiliation(s)
- Suzana Tiemi Ivamoto-Suzuki
- Grupo de Genômica e Transcriptômica em Plantas, Instituto de Biociências, Departamento de Biodiversidade, Universidade Estadual Paulista, CEP 13506-900 Rio Claro, Sao Paulo, Brazil
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver, BC, Canada
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina, 86057-970 Londrina, Brazil
| | - José Miguel Celedón
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver, BC, Canada
| | - Macaire M S Yuen
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver, BC, Canada
| | | | - Douglas Silva Domingues
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, 13418-900 Piracicaba, Brazil
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver, BC, Canada
| | - Luiz Filipe Protasio Pereira
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Café, 70770-901 Brasília, Brazil
- Laboratório de Biotecnologia Vegetal, Instituto de Desenvolvimento Rural do Paraná, 86047-902 Londrina, Brazil
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina, 86057-970 Londrina, Brazil
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Reyes-Calderón A, Gutiérrez-García C, Urióstegui-Pena AG, Srivastava A, Aguilar-Marcelino L, Iqbal HMN, Ahmed SSSJ, Paul S, Sharma A. Identification of Cumin ( Cuminum cyminum) MicroRNAs through Deep Sequencing and Their Impact on Plant Secondary Metabolism. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091756. [PMID: 37176813 PMCID: PMC10180537 DOI: 10.3390/plants12091756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
The pharmacological properties of plants lie in the content of secondary metabolites that are classified into different categories based on their biosynthesis, structures, and functions. MicroRNAs (miRNAs) are small non-coding RNA molecules that play crucial post-transcriptional regulatory roles in plants, including development and stress-response signaling; however, information about their involvement in secondary metabolism is still limited. Cumin is one of the most popular seeds from the plant Cuminum cyminum, with extensive applications in herbal medicine and cooking; nevertheless, no previous studies focus on the miRNA profile of cumin. In this study, the miRNA profile of C. cyminum and its association with the biosynthesis of secondary metabolites were determined using NGS technology. The sequencing data yielded 10,956,054 distinct reads with lengths ranging from 16 to 40 nt, of which 349 miRNAs were found to be conserved and 39 to be novel miRNAs. Moreover, this work identified 1959 potential target genes for C. cyminum miRNAs. It is interesting to note that several conserved and novel miRNAs have been found to specifically target important terpenoid backbone, flavonoid biosynthesis, and lipid/fatty acid pathways enzymes. We believe this investigation will aid in elucidating the implications of miRNAs in plant secondary metabolism.
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Affiliation(s)
- Almendra Reyes-Calderón
- Tecnologico de Monterrey, Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Queretaro 76130, Mexico
| | - Claudia Gutiérrez-García
- Tecnologico de Monterrey, Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Queretaro 76130, Mexico
| | - Andrea G Urióstegui-Pena
- Tecnologico de Monterrey, Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Queretaro 76130, Mexico
| | - Aashish Srivastava
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Liliana Aguilar-Marcelino
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, INIFAP, Jiutepec 62550, Mexico
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico
| | - Shiek S S J Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, India
| | - Sujay Paul
- Tecnologico de Monterrey, Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Queretaro 76130, Mexico
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Queretaro 76130, Mexico
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T R, Sharma D, Lin F, Choong YK, Lim C, Jobichen C, Zhang C. Structural Understanding of Fungal Terpene Synthases for the Formation of Linear or Cyclic Terpene Products. ACS Catal 2023; 13:4949-4959. [PMID: 37066048 PMCID: PMC10088877 DOI: 10.1021/acscatal.2c05598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/31/2023] [Indexed: 03/29/2023]
Abstract
Terpene synthases (TPSs), known gatekeepers of terpenoid diversity, are the main targets for enzyme engineering attempts. To this end, we have determined the crystal structure of Agrocybe pediades linalool synthase (Ap.LS), which has been recently reported to be 44-fold and 287-fold more efficient than bacterial and plant counterparts, respectively. Structure-based molecular modeling followed by in vivo as well as in vitro tests confirmed that the region of 60-69aa and Tyr299 (adjacent to the motif "WxxxxxRY") are essential for maintaining Ap.LS specificity toward a short-chain (C10) acyclic product. Ap.LS Y299 mutants (Y299A, Y299C, Y299G, Y299Q, and Y299S) yielded long-chain (C15) linear or cyclic products. Molecular modeling based on the Ap.LS crystal structure indicated that farnesyl pyrophosphate in the binding pocket of Ap.LS Y299A has less torsion strain energy compared to the wild-type Ap.LS, which can be partially attributed to the larger space in Ap.LS Y299A for better accommodation of the longer chain (C15). Linalool/nerolidol synthase Y298 and humulene synthase Y302 mutations also produced C15 cyclic products similar to Ap.LS Y299 mutants. Beyond the three enzymes, our analysis confirmed that most microbial TPSs have asparagine at the position and produce mainly cyclized products (δ-cadinene, 1,8-cineole, epi-cubebol, germacrene D, β-barbatene, etc.). In contrast, those producing linear products (linalool and nerolidol) typically have a bulky tyrosine. The structural and functional analysis of an exceptionally selective linalool synthase, Ap.LS, presented in this work provides insights into factors that govern chain length (C10 or C15), water incorporation, and cyclization (cyclic vs acyclic) of terpenoid biosynthesis.
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Wang Z, Nelson DR, Zhang J, Wan X, Peters RJ. Plant (di)terpenoid evolution: from pigments to hormones and beyond. Nat Prod Rep 2023; 40:452-469. [PMID: 36472136 PMCID: PMC9945934 DOI: 10.1039/d2np00054g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to 2014-2022.Diterpenoid biosynthesis in plants builds on the necessary production of (E,E,E)-geranylgeranyl diphosphate (GGPP) for photosynthetic pigment production, with diterpenoid biosynthesis arising very early in land plant evolution, enabling stockpiling of the extensive arsenal of (di)terpenoid natural products currently observed in this kingdom. This review will build upon that previously published in the Annual Review of Plant Biology, with a stronger focus on enzyme structure-function relationships, as well as additional insights into the evolution of (di)terpenoid metabolism since generated.
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Affiliation(s)
- Zhibiao Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China.,Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50014, USA.
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Juan Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50014, USA.
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Abstract
As a midsized gene family conserved more by lineage than function, the typical plant terpene synthases (TPSs) could be a valuable tool to examine plant evolution. TPSs are pivotal in biosynthesis of gibberellins and related phytohormones as well as in formation of the extensive arsenal of specialized plant metabolites mediating ecological interactions whose production is often lineage specific. Yet the origin and early evolution of the TPS family is not well understood. Systematic analysis of an array of transcriptomes and sequenced genomes indicated that the TPS family originated after the divergence of land plants from charophytic algae. Phylogenetic and biochemical analyses support the hypothesis that the ancestral TPS gene encoded a bifunctional class I and II diterpene synthase producing the ent-kaurene required for phytohormone production in all extant lineages of land plants. Moreover, the ancestral TPS gene likely underwent duplication at least twice early in land plant evolution. Together these two gave rise to three TPS lineages leading to the extant TPS-c, TPS-e/f, and the remaining TPS (h/d/a/b/g) subfamilies, with the latter dedicated to secondary rather than primary metabolism while the former two contain those genes involved in ent-kaurene production. Nevertheless, parallel evolution from the ent-kaurene–producing class I and class II diterpene synthases has led to roles for TPS-e/f and -c subfamily members in secondary metabolism as well. These results clarify TPS evolutionary history and provide context for the role of these genes in producing the vast diversity of terpenoid natural products observed today in various land plant lineages.
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Lou YR, Pichersky E, Last RL. Deep roots and many branches: Origins of plant-specialized metabolic enzymes in general metabolism. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102192. [PMID: 35217473 DOI: 10.1016/j.pbi.2022.102192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Collectively, plants produce hundreds of thousands of specialized metabolites from simple building blocks such as amino acids, fatty acids, and isoprenoids. As additional specialized metabolic enzymes are described, there is increasing recognition of the importance of cooption of general metabolic enzymes to specialized metabolism by gene duplication, narrowing of expression, and alteration of enzymatic activities. Here, we examine how several classes of enzymes were each coopted multiple times. We demonstrate the simplicity of achieving the synthesis of analogous chemicals by coopting existing enzymes and summarize emerging insights that could inform rational metabolic engineering of both general and specialized metabolic enzymes.
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Affiliation(s)
- Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
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