1
|
Li FR, Wang Q, Pan X, Xu HM, Dong LB. Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase. Angew Chem Int Ed Engl 2024; 63:e202401669. [PMID: 38651244 DOI: 10.1002/anie.202401669] [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: 01/24/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
cis-Prenyltransferases (cis-PTs) catalyze the sequential head-to-tail condensation of isopentenyl diphosphate (IPP) to allylic diphosphates, producing mixed E-Z prenyl diphosphates of varying lengths; however, the specific enzymes synthesizing cis-C25 prenyl diphosphates have not been identified. Herein, we present the discovery and characterization of a cis-geranylfarnesyl diphosphate synthase (ScGFPPS) from Streptomyces clavuligerus. This enzyme demonstrates high catalytic proficiency in generating six distinct cis-polyisoprenoids, including three C25 and three C20 variants. We determined the crystal structure of ScGFPPS. Additionally, we unveil the crystal structure of nerylneryl diphosphate synthase (NNPS), known for synthesizing an all-cis-C20 polyisoprenoid. Comparative structural analysis of ScGFPPS and NNPS has identified key differences that influence product specificity. Through site-directed mutagenesis, we have identified eight single mutations that significantly refine the selectivity of ScGFPPS for cis-polyisoprenoids. Our findings not only expand the functional spectrum of cis-PTs but also provide a structural comparison strategy in cis-PTs engineering.
Collapse
Affiliation(s)
- Fang-Ru Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Qingling Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xingming Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Hui-Min Xu
- The Public Laboratory Platform, China Pharmaceutical University, Nanjing, 211198, China
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| |
Collapse
|
2
|
Bergman ME, Kortbeek RWJ, Gutensohn M, Dudareva N. Plant terpenoid biosynthetic network and its multiple layers of regulation. Prog Lipid Res 2024; 95:101287. [PMID: 38906423 DOI: 10.1016/j.plipres.2024.101287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Terpenoids constitute one of the largest and most chemically diverse classes of primary and secondary metabolites in nature with an exceptional breadth of functional roles in plants. Biosynthesis of all terpenoids begins with the universal five‑carbon building blocks, isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), which in plants are derived from two compartmentally separated but metabolically crosstalking routes, the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. Here, we review the current knowledge on the terpenoid precursor pathways and highlight the critical hidden constraints as well as multiple regulatory mechanisms that coordinate and homeostatically govern carbon flux through the terpenoid biosynthetic network in plants.
Collapse
Affiliation(s)
- Matthew E Bergman
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Ruy W J Kortbeek
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Michael Gutensohn
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States.
| |
Collapse
|
3
|
Zhang Y, Kashkooli AB, Blom S, Zhao T, Bouwmeester HJ, Kappers IF. The Capsicum terpenoid biosynthetic module is affected by spider-mite herbivory. PLANT MOLECULAR BIOLOGY 2023; 113:303-321. [PMID: 37995005 PMCID: PMC10721696 DOI: 10.1007/s11103-023-01390-0] [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: 04/23/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
In response to herbivory, Capsicum annuum leaves adapt their specialized metabolome that may protect the plant against herbivore feeding either directly or indirectly through volatile metabolites acting as cues for natural enemies of the herbivore. The volatile blend of spider-mite infested leaves differs from non-challenged leaves predominantly by a higher contribution of mono- and sesquiterpenes. In addition to these terpenoids released into the headspace, the terpenoid composition of the leaves alters upon herbivory. All this suggests an important role for terpenoids and their biosynthetic machinery in the defence against herbivory. Here, we show that the C. annuum genome contains a terpene synthase (TPS) gene family of 103 putative members of which structural analysis revealed that 27 encode functional enzymes. Transcriptome analysis showed that several TPS loci were differentially expressed upon herbivory in leaves of two C. annuum genotypes, that differ in susceptibility towards spider mites. The relative expression of upstream biosynthetic genes from the mevalonate and the methylerythritol phosphate pathway also altered upon herbivory, revealing a shift in the metabolic flux through the terpene biosynthetic module. The expression of multiple genes potentially acting downstream of the TPSs, including cytochrome P450 monooxygenases, UDP-glucosyl transferases, and transcription factors strongly correlated with the herbivory-induced TPS genes. A selection of herbivory-induced TPS genes was functionally characterized through heterologous expression and the products that these enzymes catalysed matched with the volatile and non-volatile terpenoids induced in response to herbivory.
Collapse
Affiliation(s)
- Yuanyuan Zhang
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Arman B Kashkooli
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- Tarbiat Modares University, Tehran, Iran
| | - Suze Blom
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, The Netherlands
| | - Tao Zhao
- Biosystematics, Wageningen University, Wageningen, The Netherlands
- Northwest Agriculture and Forestry University, Xi'an, China
| | - Harro J Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Iris F Kappers
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands.
| |
Collapse
|
4
|
Lawas LMF, Kamileen MO, Buell CR, O'Connor SE, Leisner CP. Transcriptome-based identification and functional characterization of iridoid synthase involved in monotropein biosynthesis in blueberry. PLANT DIRECT 2023; 7:e512. [PMID: 37440931 PMCID: PMC10333835 DOI: 10.1002/pld3.512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Blueberries (Vaccinium spp.) are well known for their nutritional quality, and recent work has shown that Vaccinium spp. also produce iridoids, which are specialized metabolites with potent health-promoting benefits. The iridoid glycoside monotropein, which has anti-inflammatory and antinociceptive activities, has been detected in several wild blueberry species but in only a few cultivated highbush blueberry cultivars. How monotropein is produced in blueberry and the genes involved in its biosynthesis remain to be elucidated. Using a monotropein-positive (M+) and monotropein-negative (M-) cultivar of blueberry, we employed transcriptomics and comparative genomics to identify candidate genes in the blueberry iridoid biosynthetic pathway. Orthology analysis was completed using de novo transcript assemblies for both the M+ and M- blueberry cultivars along with the known iridoid-producing plant species Catharanthus roseus to identify putative genes involved in key steps in the early iridoid biosynthetic pathway. From the identified orthologs, we functionally characterized iridoid synthase (ISY), a key enzyme involved in formation of the iridoid scaffold, from both the M+ and M- cultivars. Detection of nepetalactol suggests that ISY from both the M+ and M- cultivars produce functional enzymes that catalyze the formation of iridoids. Transcript accumulation of the putative ISY gene did not correlate with monotropein production, suggesting other genes in the monotropein biosynthetic pathway may be more directly responsible for differential accumulation of the metabolite in blueberry. Mutual rank analysis revealed that ISY is co-expressed with UDP-glucuronosyltransferase, which encodes an enzyme downstream of the ISY step. Results from this study contribute new knowledge in our understanding of iridoid biosynthesis in blueberry and could lead to development of new cultivars with increased human health benefits.
Collapse
Affiliation(s)
| | - Mohamed O. Kamileen
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyJenaGermany
| | - C. Robin Buell
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Department of Crop and Soil SciencesInstitute of Plant Breeding, Genetics, & Genomics, University of GeorgiaAthensGeorgiaUSA
| | - Sarah E. O'Connor
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyJenaGermany
| | - Courtney P. Leisner
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
- School of Plant and Environmental SciencesVirginia TechBlacksburgVirginiaUSA
| |
Collapse
|
5
|
Habán M, Korczyk-Szabó J, Čerteková S, Ražná K. Lavandula Species, Their Bioactive Phytochemicals, and Their Biosynthetic Regulation. Int J Mol Sci 2023; 24:ijms24108831. [PMID: 37240177 DOI: 10.3390/ijms24108831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
Lavandula species are one of the most useful aromatic and medicinal plants and have great economic potential. The phytopharmaceutical contribution of the secondary metabolites of the species is unquestionable. Most recent studies have been focusing on the elucidation of the genetic background of secondary metabolite production in lavender species. Therefore, knowledge of not only genetic but especially epigenetic mechanisms for the regulation of secondary metabolites is necessary for the modification of those biosynthesis processes and the understanding of genotypic differences in the content and compositional variability of these products. The review discusses the genetic diversity of Lavandula species in relation to the geographic area, occurrence, and morphogenetic factors. The role of microRNAs in secondary-metabolites biosynthesis is described.
Collapse
Affiliation(s)
- Miroslav Habán
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Pharmacognosy and Botany, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 83232 Bratislava, Slovakia
| | - Joanna Korczyk-Szabó
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Simona Čerteková
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Katarína Ražná
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Co-Localization of Resistance and Metabolic Quantitative Trait Loci on Carrot Genome Reveals Fungitoxic Terpenes and Related Candidate Genes Associated with the Resistance to Alternaria dauci. Metabolites 2023; 13:metabo13010071. [PMID: 36676996 PMCID: PMC9863879 DOI: 10.3390/metabo13010071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/03/2023] Open
Abstract
Alternaria leaf blight, caused by the fungus Alternaria dauci, is the most damaging foliar disease of carrot. Some carrot genotypes exhibit partial resistance to this pathogen and resistance Quantitative Trait Loci (rQTL) have been identified. Co-localization of metabolic QTL and rQTL identified camphene, α-pinene, α-bisabolene, β-cubebene, caryophyllene, germacrene D and α-humulene as terpenes potentially involved in carrot resistance against ALB. By combining genomic and transcriptomic analyses, we identified, under the co-localization regions, terpene-related genes which are differentially expressed between a resistant and a susceptible carrot genotype. These genes include five terpene synthases and twenty transcription factors. In addition, significant mycelial growth inhibition was observed in the presence of α-humulene and caryophyllene.
Collapse
|
8
|
Vasilev N. Medicinal Plants: Guests and Hosts in the Heterologous Expression of High-Value Products. PLANTA MEDICA 2022; 88:1175-1189. [PMID: 34521134 DOI: 10.1055/a-1576-4148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Medicinal plants play an important dual role in the context of the heterologous expression of high-value pharmaceutical products. On the one hand, the classical biochemical and modern omics approaches allowed for the discovery of various genes encoding biosynthetic pathways in medicinal plants. Recombinant DNA technology enabled introducing these genes and regulatory elements into host organisms and enhancing the heterologous production of the corresponding secondary metabolites. On the other hand, the transient expression of foreign DNA in plants facilitated the production of numerous proteins of pharmaceutical importance. This review summarizes several success stories of the engineering of plant metabolic pathways in heterologous hosts. Likewise, a few examples of recombinant protein expression in plants for therapeutic purposes are also highlighted. Therefore, the importance of medicinal plants has grown immensely as sources for valuable products of low and high molecular weight. The next step ahead for bioengineering is to achieve more success stories of industrial-scale production of secondary plant metabolites in microbial systems and to fully exploit plant cell factories' commercial potential for recombinant proteins.
Collapse
Affiliation(s)
- Nikolay Vasilev
- TU Dortmund University, Biochemical and Chemical Engineering, Technical Biochemistry, Dortmund, Germany
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Wu D, Hu Y, Akashi S, Nojiri H, Guo L, Ye C, Zhu Q, Okada K, Fan L. Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1354-1367. [PMID: 35781905 PMCID: PMC9544640 DOI: 10.1111/tpj.15893] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 05/31/2023]
Abstract
Momilactone A, an important plant labdane-related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the biosynthesis of momilactone A are found in clusters, i.e., momilactone A biosynthetic gene clusters (MABGCs), in the rice and barnyardgrass genomes. In addition, we know little about the origin and evolution of MABGCs. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC-like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC-like cluster in Triticeae (BOP clade) via lateral gene transfer (LGT) and followed by recruitment of MAS1/2 and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another LGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter originating from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate LGT-mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.
Collapse
Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang UniversityYonyou Industrial ParkSanya572025China
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Yiyu Hu
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Shota Akashi
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Hideaki Nojiri
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China
| | - Chu‐Yu Ye
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Qian‐Hao Zhu
- CSIRO Agriculture and Food, Black Mountain LaboratoriesCanberraACT2601Australia
| | - Kazunori Okada
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Longjiang Fan
- Hainan Institute of Zhejiang UniversityYonyou Industrial ParkSanya572025China
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| |
Collapse
|
12
|
Li CY, Yang L, Liu Y, Xu ZG, Gao J, Huang YB, Xu JJ, Fan H, Kong Y, Wei YK, Hu WL, Wang LJ, Zhao Q, Hu YH, Zhang YJ, Martin C, Chen XY. The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants. Cell Rep 2022; 40:111236. [PMID: 35977487 DOI: 10.1016/j.celrep.2022.111236] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/29/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022] Open
Abstract
The widely cultivated medicinal and ornamental plant sage (Salvia officinalis L.) is an evergreen shrub of the Lamiaceae family, native to the Mediterranean. We assembled a high-quality sage genome of 480 Mb on seven chromosomes, and identified a biosynthetic gene cluster (BGC) encoding two pairs of diterpene synthases (diTPSs) that, together with the cytochromes P450 (CYPs) genes located inside and outside the cluster, form two expression cascades responsible for the shoot and root diterpenoids, respectively, thus extending BGC functionality from co-regulation to orchestrating metabolite production in different organs. Phylogenomic analysis indicates that the Salvia clades diverged in the early Miocene. In East Asia, most Salvia species are herbaceous and accumulate diterpenoids in storage roots. Notably, in Chinese sage S. miltiorrhiza, the diterpene BGC has contracted and the shoot cascade has been lost. Our data provide genomic insights of micro-evolution of growth type-associated patterning of specialized metabolite production in plants.
Collapse
Affiliation(s)
- Chen-Yi Li
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yan Liu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Zhou-Geng Xu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Jian Gao
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Yan-Bo Huang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Jing-Jing Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Hang Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yu-Kun Wei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Wen-Li Hu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Ling-Jian Wang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yong-Hong Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yi-Jing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China.
| |
Collapse
|
13
|
Kutsukawa R, Imaizumi R, Suenaga‐Hiromori M, Takeshita K, Sakai N, Misawa S, Yamamoto M, Yamaguchi H, Miyagi‐Inoue Y, Waki T, Kataoka K, Nakayama T, Yamashita S, Takahashi S. Structure‐based engineering of a short‐chain
cis
‐prenyltransferase to biosynthesize nonnatural all‐
cis
‐polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain‐length determination. FEBS J 2022; 289:4602-4621. [DOI: 10.1111/febs.16392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 01/15/2023]
Affiliation(s)
- Ryo Kutsukawa
- Graduate School of Engineering Tohoku University Sendai Japan
| | - Riki Imaizumi
- Department of Material Chemistry Graduate School of Natural Science and Technology Kanazawa University Japan
| | | | | | | | - Shuto Misawa
- Department of Material Chemistry Graduate School of Natural Science and Technology Kanazawa University Japan
| | | | | | | | - Toshiyuki Waki
- Graduate School of Engineering Tohoku University Sendai Japan
| | - Kunishige Kataoka
- Department of Material Chemistry Graduate School of Natural Science and Technology Kanazawa University Japan
| | - Toru Nakayama
- Graduate School of Engineering Tohoku University Sendai Japan
| | - Satoshi Yamashita
- Department of Material Chemistry Graduate School of Natural Science and Technology Kanazawa University Japan
| | - Seiji Takahashi
- Graduate School of Engineering Tohoku University Sendai Japan
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Fiesel PD, Parks HM, Last RL, Barry CS. Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae. Nat Prod Rep 2022; 39:1438-1464. [PMID: 35332352 DOI: 10.1039/d2np00003b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: 2000-2022Plants collectively synthesize a huge repertoire of metabolites. General metabolites, also referred to as primary metabolites, are conserved across the plant kingdom and are required for processes essential to growth and development. These include amino acids, sugars, lipids, and organic acids. In contrast, specialized metabolites, historically termed secondary metabolites, are structurally diverse, exhibit lineage-specific distribution and provide selective advantage to host species to facilitate reproduction and environmental adaptation. Due to their potent bioactivities, plant specialized metabolites attract considerable attention for use as flavorings, fragrances, pharmaceuticals, and bio-pesticides. The Solanaceae (Nightshade family) consists of approximately 2700 species and includes crops of significant economic, cultural, and scientific importance: these include potato, tomato, pepper, eggplant, tobacco, and petunia. The Solanaceae has emerged as a model family for studying the biochemical evolution of plant specialized metabolism and multiple examples exist of lineage-specific metabolites that influence the senses and physiology of commensal and harmful organisms, including humans. These include, alcohols, phenylpropanoids, and carotenoids that contribute to fruit aroma and color in tomato (fruity), glandular trichome-derived terpenoids and acylsugars that contribute to plant defense (stinky & sticky, respectively), capsaicinoids in chilli-peppers that influence seed dispersal (spicy), and steroidal glycoalkaloids (bitter) from Solanum, nicotine (addictive) from tobacco, as well as tropane alkaloids (deadly) from Deadly Nightshade that deter herbivory. Advances in genomics and metabolomics, coupled with the adoption of comparative phylogenetic approaches, resulted in deeper knowledge of the biosynthesis and evolution of these metabolites. This review highlights recent progress in this area and outlines opportunities for - and challenges of-developing a more comprehensive understanding of Solanaceae metabolism.
Collapse
Affiliation(s)
- Paul D Fiesel
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Hannah M Parks
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L Last
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Prasanta Chakraborty
- Kalpana Chawla Center for Space and Nanoscience, Kolkata, Indian Institute of Chemical Biology (retd.), Kolkata, 700032, India.
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Yang C, Marillonnet S, Tissier A. The scarecrow-like transcription factor SlSCL3 regulates volatile terpene biosynthesis and glandular trichome size in tomato (Solanum lycopersicum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1102-1118. [PMID: 34143914 DOI: 10.1111/tpj.15371] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 05/20/2023]
Abstract
Tomato (Solanum lycopersicum L.) type VI glandular trichomes that occur on the surface of leaves, stems, young fruits and flowers produce and store a blend of volatile monoterpenes and sesquiterpenes. These compounds play important roles in the interaction with pathogens and herbivorous insects. Although the function of terpene synthases in the biosynthesis of volatile terpenes in tomato has been comprehensively investigated, the deciphering of their transcriptional regulation is only just emerging. We selected transcription factors that are over-expressed in trichomes based on existing transcriptome data and silenced them individually by virus-induced gene silencing. Of these, SlSCL3, a scarecrow-like (SCL) subfamily transcription factor, led to a significant decrease in volatile terpene content and expression of the corresponding terpene synthase genes when its transcription level was downregulated. Overexpression of SlSCL3 dramatically increased both the volatile terpene content and glandular trichome size, whereas its homozygous mutants showed reduced terpene biosynthesis. However, its heterozygous mutants also showed a significantly elevated volatile terpene content and enlarged glandular trichomes, similar to the overexpression plants. SlSCL3 modulates the expression of terpene biosynthetic pathway genes by transcriptional activation, but neither direct protein-DNA binding nor interaction with known regulators was observed. Moreover, transcript levels of the endogenous copy of SlSCL3 were decreased in the overexpression plants but increased in the heterozygous and homozygous mutants, suggesting feedback repression of its own promoter. Taken together, our results provide new insights into the role of SlSCL3 in the complex regulation of volatile terpene biosynthesis and glandular trichome development in tomato.
Collapse
Affiliation(s)
- Changqing Yang
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, 266100, China
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
| |
Collapse
|
19
|
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
| |
Collapse
|
20
|
Huang LM, Huang H, Chuang YC, Chen WH, Wang CN, Chen HH. Evolution of Terpene Synthases in Orchidaceae. Int J Mol Sci 2021; 22:6947. [PMID: 34203299 PMCID: PMC8268431 DOI: 10.3390/ijms22136947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Terpenoids are the largest class of plant secondary metabolites and are one of the major emitted volatile compounds released to the atmosphere. They have functions of attracting pollinators or defense function, insecticidal properties, and are even used as pharmaceutical agents. Because of the importance of terpenoids, an increasing number of plants are required to investigate the function and evolution of terpene synthases (TPSs) that are the key enzymes in terpenoids biosynthesis. Orchidacea, containing more than 800 genera and 28,000 species, is one of the largest and most diverse families of flowering plants, and is widely distributed. Here, the diversification of the TPSs evolution in Orchidaceae is revealed. A characterization and phylogeny of TPSs from four different species with whole genome sequences is available. Phylogenetic analysis of orchid TPSs indicates these genes are divided into TPS-a, -b, -e/f, and g subfamilies, and their duplicated copies are increased in derived orchid species compared to that in the early divergence orchid, A. shenzhenica. The large increase of both TPS-a and TPS-b copies can probably be attributed to the pro-duction of different volatile compounds for attracting pollinators or generating chemical defenses in derived orchid lineages; while the duplications of TPS-g and TPS-e/f copies occurred in a species-dependent manner.
Collapse
Affiliation(s)
- Li-Min Huang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Yu-Chen Chuang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
| | - Wen-Huei Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Neng Wang
- Department of Life Sciences, Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106, Taiwan;
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; (L.-M.H.); (H.H.); (Y.-C.C.); (W.-H.C.)
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| |
Collapse
|
21
|
Therezan R, Kortbeek R, Vendemiatti E, Legarrea S, de Alencar SM, Schuurink RC, Bleeker P, Peres LEP. Introgression of the sesquiterpene biosynthesis from Solanum habrochaites to cultivated tomato offers insights into trichome morphology and arthropod resistance. PLANTA 2021; 254:11. [PMID: 34160697 PMCID: PMC8222033 DOI: 10.1007/s00425-021-03651-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/29/2021] [Indexed: 05/13/2023]
Abstract
Cultivated tomatoes harboring the plastid-derived sesquiterpenes from S. habrochaites have altered type-VI trichome morphology and unveil additional genetic components necessary for piercing-sucking pest resistance. Arthropod resistance in the tomato wild relative Solanum habrochaites LA1777 is linked to specific sesquiterpene biosynthesis. The Sesquiterpene synthase 2 (SsT2) gene cluster on LA1777 chromosome 8 controls plastid-derived sesquiterpene synthesis. The main genes at SsT2 are Z-prenyltransferase (zFPS) and Santalene and Bergamotene Synthase (SBS), which produce α-santalene, β-bergamotene, and α-bergamotene in LA1777 round-shaped type-VI glandular trichomes. Cultivated tomatoes have mushroom-shaped type-VI trichomes with much smaller glands that contain low levels of monoterpenes and cytosolic-derived sesquiterpenes, not presenting the same pest resistance as in LA1777. We successfully transferred zFPS and SBS from LA1777 to cultivated tomato (cv. Micro-Tom, MT) by a backcrossing approach. The trichomes of the MT-Sst2 introgressed line produced high levels of the plastid-derived sesquiterpenes. The type-VI trichome internal storage-cavity size increased in MT-Sst2, probably as an effect of the increased amount of sesquiterpenes, although it was not enough to mimic the round-shaped LA1777 trichomes. The presence of high amounts of plastid-derived sesquiterpenes was also not sufficient to confer resistance to various tomato piercing-sucking pests, indicating that the effect of the sesquiterpenes found in the wild S. habrochaites can be insect specific. Our results provide for a better understanding of the morphology of S. habrochaites type-VI trichomes and paves the way to obtain insect-resistant tomatoes.
Collapse
Affiliation(s)
- Rodrigo Therezan
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture, Laboratory of Plant Developmental Genetics, University of Sao Paulo, Piracicaba, SP, 13418-900, Brazil
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Ruy Kortbeek
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Eloisa Vendemiatti
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture, Laboratory of Plant Developmental Genetics, University of Sao Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Saioa Legarrea
- Molecular and Chemical Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - Severino M de Alencar
- Department of Agri-Food Industry, Food and Nutrition, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Robert C Schuurink
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Petra Bleeker
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| | - Lázaro E P Peres
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture, Laboratory of Plant Developmental Genetics, University of Sao Paulo, Piracicaba, SP, 13418-900, Brazil.
| |
Collapse
|
22
|
Scossa F, Fernie AR. Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? Comput Struct Biotechnol J 2021; 19:1579-1594. [PMID: 33868595 PMCID: PMC8039532 DOI: 10.1016/j.csbj.2021.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.
Collapse
Key Words
- APR, ancestral protein resurrection
- ASR, ancestral sequence reconstruction
- Ancestral sequence reconstruction
- CDS, coding sequence
- Evolution
- GR, glucocorticoid receptor
- GWAS, genome wide association study
- Genomics
- InDel, insertion/deletion
- MCMC, Markov Chain Monte Carlo
- ML, maximum likelihood
- MP, maximum parsimony
- MR, mineralcorticoid receptor
- MSA, multiple sequence alignment
- Metabolism
- NJ, neighbor-joining
- Phylogenetics
- Plants
- SFS, site frequency spectrum
Collapse
Affiliation(s)
- Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| |
Collapse
|
23
|
Dar MS, Dholakia BB, Kulkarni AP, Oak PS, Shanmugam D, Gupta VS, Giri AP. Influence of domestication on specialized metabolic pathways in fruit crops. PLANTA 2021; 253:61. [PMID: 33538903 DOI: 10.1007/s00425-020-03554-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 12/23/2020] [Indexed: 05/08/2023]
Abstract
During the process of plant domestication, the selection and traditional breeding for desired characters such as flavor, juiciness and nutritional value of fruits, probably have resulted in gain or loss of specialized metabolites contributing to these traits. Their appearance in fruits is likely due to the acquisition of novel and specialized metabolic pathways and their regulation, driven by systematic molecular evolutionary events facilitated by traditional breeding. Plants change their armory of specialized metabolism to adapt and survive in diverse ecosystems. This may occur through molecular evolutionary events, such as single nucleotide polymorphism, gene duplication and transposition, leading to convergent or divergent evolution of biosynthetic pathways producing such specialized metabolites. Breeding and selection for improved specific and desired traits (fruit size, color, taste, flavor, etc.) in fruit crops through conventional breeding approaches may further alter content and profile of specialized metabolites. Biosynthetic routes of these metabolites have been studied in various plants. Here, we explore the influence of plant domestication and breeding processes on the selection of biosynthetic pathways of favorable specialized metabolites in fruit crops. An orderly clustered arrangement of genes associated with their production is observed in many fruit crops. We further analyzed selection-based acquisition of specialized metabolic pathways comparing first the metabolic profiles and genes involved in their biosynthesis, followed by the genomic organization of such genes between wild and domesticated horticultural crops. Domestication of crop plants favored the acquisition and retention of metabolic pathways that enhanced the fruit value while eliminated those which produced toxic or unfavorable metabolites. Interestingly, unintentional reorganization of complex metabolic pathways by selection and traditional breeding processes has endowed us with flavorful, juicy and nutritionally rich fruits.
Collapse
Affiliation(s)
- M Saleem Dar
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Bhushan B Dholakia
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
| | - Abhijeet P Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS, 411007, India
| | - Pranjali S Oak
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Dhanasekaran Shanmugam
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Vidya S Gupta
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Ashok P Giri
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India.
| |
Collapse
|
24
|
Wang P, Meng F, Moore BM, Shiu SH. Impact of short-read sequencing on the misassembly of a plant genome. BMC Genomics 2021; 22:99. [PMID: 33530937 PMCID: PMC7852129 DOI: 10.1186/s12864-021-07397-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/19/2021] [Indexed: 12/16/2022] Open
Abstract
Background Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively. Results To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads and the generality of these causes and factors should be tested further in other species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07397-5.
Collapse
Affiliation(s)
- Peipei Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,DOE Great Lake Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Fanrui Meng
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,DOE Great Lake Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Bethany M Moore
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,The Ecology, Evolution, and Behavioral Biology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. .,DOE Great Lake Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA. .,The Ecology, Evolution, and Behavioral Biology Program, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
| |
Collapse
|
25
|
Hua B, Chang J, Wu M, Xu Z, Zhang F, Yang M, Xu H, Wang L, Chen X, Wu S. Mediation of JA signalling in glandular trichomes by the woolly/SlMYC1 regulatory module improves pest resistance in tomato. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:375-393. [PMID: 32888338 PMCID: PMC7868972 DOI: 10.1111/pbi.13473] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 07/26/2020] [Accepted: 08/07/2020] [Indexed: 05/24/2023]
Abstract
Almost all plants form trichomes, which protect them against insect herbivores by forming a physical barrier and releasing chemical repellents. Glandular trichomes produce a variety of specialized defensive metabolites, including volatile terpenes. Previous studies have shown that the defence hormone jasmonic acid (JA) affects trichome development and induces terpene synthases (TPSs) but the underlying molecular mechanisms remain unclear. Here, we characterized a loss-of-function allele of the HD-ZIP IV transcription factor woolly (wo) and analysed its role in mediating JA signalling in tomato. We showed that knockout of wo led to extensive trichome defects, including structural and functional changes in type VI glandular trichomes, and a dramatic reduction in terpene levels. We further found that wo directly binds to TPS gene promoters to recruit SlMYC1, a JA signalling modulator, and that together these transcription factors promote terpene biosynthesis in tomato trichomes. The wo/SlMYC1 regulatory module is inhibited by SlJAZ2 through a competitive binding mechanism, resulting in a fine-tuned JA response in tomato trichomes. Enhanced expression of SlMYC1 substantially increased terpene levels and improved tomato resistance to spider mites. Interestingly, we also found that SlMYC1 plays an additional role in glandular cell division and expansion in type VI trichomes, independent of JA. Together, our results reveal a novel, JA-mediated regulatory mechanism that promotes insect resistance in tomato.
Collapse
Affiliation(s)
- Bing Hua
- College of HorticultureFAFU‐UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiang Chang
- College of HorticultureFAFU‐UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Minliang Wu
- College of HorticultureFAFU‐UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhijing Xu
- College of HorticultureFAFU‐UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Fanyu Zhang
- College of HorticultureFAFU‐UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Meina Yang
- College of HorticultureFAFU‐UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Huimin Xu
- College of HorticultureFAFU‐UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ling‐Jian Wang
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyShanghaiChina
| | - Xiao‐Ya Chen
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyShanghaiChina
| | - Shuang Wu
- College of HorticultureFAFU‐UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| |
Collapse
|
26
|
Zha WL, Zi JC. Advances in biotechnological production of santalenes and santalols. CHINESE HERBAL MEDICINES 2021; 13:90-97. [PMID: 36117763 PMCID: PMC9476758 DOI: 10.1016/j.chmed.2020.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 11/30/2022] Open
Abstract
Sandalwood essential oil has been widely used not only as natural medicines but also in perfumery and food industries, with sesquiterpenoids as its major components including (Z)- α-santalol and (Z)-β-santalol and so on. The mature heartwoods of Santalum album, Santalum austrocaledonicum and Santalum spicatum are the major plant resources for extracting sandalwood essential oil, which have been overexploited. Synthetic biology approaches have been successfully applied to produce natural products on large scale. In this review, we summarize biosynthetic enzymes of santalenes and santalols, including various santalene synthases (STSs) and cytochrome P450 monooxygenases (CYPs), and then highlight the advances of biotechnological production of santalenes and santalols in heterologous hosts, especially metabolic engineering strategies for constructing santalene- and santalol-producing Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Wen-long Zha
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jia-chen Zi
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
- College of Pharmacy, Jinan University, Guangzhou 510632, China
- Corresponding author.
| |
Collapse
|
27
|
Xu S, Kreitzer C, McGale E, Lackus ND, Guo H, Köllner TG, Schuman MC, Baldwin IT, Zhou W. Allelic differences of clustered terpene synthases contribute to correlated intraspecific variation of floral and herbivory-induced volatiles in a wild tobacco. THE NEW PHYTOLOGIST 2020; 228:1083-1096. [PMID: 32535930 DOI: 10.1111/nph.16739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/29/2020] [Indexed: 05/21/2023]
Abstract
Plant volatile emissions can recruit predators of herbivores for indirect defense and attract pollinators to aid in pollination. Although volatiles involved in defense and pollinator attraction are primarily emitted from leaves and flowers, respectively, they will co-evolve if their underlying genetic basis is intrinsically linked, due either to pleiotropy or to genetic linkage. However, direct evidence of co-evolving defense and floral traits is scarce. We characterized intraspecific variation of herbivory-induced plant volatiles (HIPVs), the key components of indirect defense against herbivores, and floral volatiles in wild tobacco Nicotiana attenuata. We found that variation of (E)-β-ocimene and (E)-α-bergamotene contributed to the correlated changes in HIPVs and floral volatiles among N. attenuata natural accessions. Intraspecific variations of (E)-β-ocimene and (E)-α-bergamotene emissions resulted from allelic variation of two genetically co-localized terpene synthase genes, NaTPS25 and NaTPS38, respectively. Analyzing haplotypes of NaTPS25 and NaTPS38 revealed that allelic variations of NaTPS25 and NaTPS38 resulted in correlated changes of (E)-β-ocimene and (E)-α-bergamotene emission in HIPVs and floral volatiles in N. attenuata. Together, these results provide evidence that pleiotropy and genetic linkage result in correlated changes in defenses and floral signals in natural populations, and the evolution of plant volatiles is probably under diffuse selection.
Collapse
Affiliation(s)
- Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany
| | - Christoph Kreitzer
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Erica McGale
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Nathalie D Lackus
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Han Guo
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Meredith C Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
- Department of Geography & Department of Chemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Wenwu Zhou
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
28
|
Lai D, Maimann AB, Macea E, Ocampo CH, Cardona G, Pičmanová M, Darbani B, Olsen CE, Debouck D, Raatz B, Møller BL, Rook F. Biosynthesis of cyanogenic glucosides in Phaseolus lunatus and the evolution of oxime-based defenses. PLANT DIRECT 2020; 4:e00244. [PMID: 32775954 PMCID: PMC7402084 DOI: 10.1002/pld3.244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 05/22/2020] [Accepted: 07/01/2020] [Indexed: 05/13/2023]
Abstract
Lima bean, Phaseolus lunatus, is a crop legume that produces the cyanogenic glucosides linamarin and lotaustralin. In the legumes Lotus japonicus and Trifolium repens, the biosynthesis of these two α-hydroxynitrile glucosides involves cytochrome P450 enzymes of the CYP79 and CYP736 families and a UDP-glucosyltransferase. Here, we identify CYP79D71 as the first enzyme of the pathway in P. lunatus, producing oximes from valine and isoleucine. A second CYP79 family member, CYP79D72, was shown to catalyze the formation of leucine-derived oximes, which act as volatile defense compounds in Phaseolus spp. The organization of the biosynthetic genes for cyanogenic glucosides in a gene cluster aided their identification in L. japonicus. In the available genome sequence of P. vulgaris, the gene orthologous to CYP79D71 is adjacent to a member of the CYP83 family. Although P. vulgaris is not cyanogenic, it does produce oximes as volatile defense compounds. We cloned the genes encoding two CYP83s (CYP83E46 and CYP83E47) and a UDP-glucosyltransferase (UGT85K31) from P. lunatus, and these genes combined form a complete biosynthetic pathway for linamarin and lotaustralin in Lima bean. Within the genus Phaseolus, the occurrence of linamarin and lotaustralin as functional chemical defense compounds appears restricted to species belonging to the closely related Polystachios and Lunatus groups. A preexisting ability to produce volatile oximes and nitriles likely facilitated evolution of cyanogenesis within the Phaseolus genus.
Collapse
Affiliation(s)
- Daniela Lai
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Alexandra B. Maimann
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Eliana Macea
- International Center for Tropical AgricultureCaliColombia
| | | | | | - Martina Pičmanová
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Behrooz Darbani
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
- Present address:
The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Carl Erik Olsen
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Daniel Debouck
- International Center for Tropical AgricultureCaliColombia
| | - Bodo Raatz
- International Center for Tropical AgricultureCaliColombia
| | - Birger Lindberg Møller
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Fred Rook
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| |
Collapse
|
29
|
Bagnaresi P, Cattivelli L. Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomes. PLoS One 2020; 15:e0234782. [PMID: 32559249 PMCID: PMC7304597 DOI: 10.1371/journal.pone.0234782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 11/20/2022] Open
Abstract
A functional Non-Tandem Duplicated Cluster (FNTDC) is a group of non-tandem-duplicated genes that are located closer than expected by mere chance and have a role in the same biological function. The identification of secondary-compounds–related FNTDC has gained increased interest in recent years, but little ab-initio attempts aiming to the identification of FNTDCs covering all biological functions, including primary metabolism compounds, have been carried out. We report an extensive FNTDC dataset accompanied by a detailed assessment on parameters used for genome scanning and their impact on FNTDC detection. We propose 70% identity and 70% alignment coverage as intermediate settings to exclude tandem duplicated genes and a dynamic scanning window of 24 genes. These settings were applied to rice, arabidopsis and grapevine genomes to call for FNTDCs. Besides the best-known secondary metabolism clusters, we identified many FNTDCs associated to primary metabolism ranging from macromolecules synthesis/editing, TOR signalling, ubiquitination, proton and electron transfer complexes. Using the intermediate FNTDC setting parameters (at P-value 1e-6), 130, 70 and 140 candidate FNTDCs were called in rice, arabidopsis and grapevine, respectively, and 20 to 30% of GO tags associated to called FNTDC were common among the 3 genomes. The datasets developed along with this work provide a rich framework for pinpointing candidate FNTDCs reflecting all GO-BP tags covering both primary and secondary metabolism with large macromolecular complexes/metabolons as the most represented FNTDCs. Noteworthy, several FNTDCs are tagged with GOs referring to organelle-targeted multi-enzyme complex, a finding that suggest the migration of endosymbiont gene chunks towards nuclei could be at the basis of these class of candidate FNTDCs. Most FNTDC appear to have evolved prior of genome duplication events. More than one-third of genes interspersed/adjacent to called FNTDCs lacked any functional annotation; however, their co-localization may provide hints towards a candidate biological role.
Collapse
Affiliation(s)
- Paolo Bagnaresi
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
- * E-mail:
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| |
Collapse
|
30
|
Zhou F, Pichersky E. More is better: the diversity of terpene metabolism in plants. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:1-10. [PMID: 32088555 DOI: 10.1016/j.pbi.2020.01.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 05/18/2023]
Abstract
All plants synthesize a diverse array of terpenoid metabolites. Some are common to all, but many are synthesized only in specific taxa and presumably evolved as adaptations to specific ecological conditions. While the basic terpenoid biosynthetic pathways are common in all plants, recent discoveries have revealed many variations in the way plants synthesized specific terpenes. A major theme is the much greater number of substrates that can be used by enzymes belonging to the terpene synthase (TPS) family. Other recent discoveries include non-TPS enzymes that catalyze the formation of terpenes, and novel transport mechanisms.
Collapse
Affiliation(s)
- Fei Zhou
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
31
|
Lichman BR, Godden GT, Buell CR. Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:74-83. [PMID: 32344371 DOI: 10.1016/j.pbi.2020.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/19/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.
Collapse
Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Carol Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA.
| |
Collapse
|
32
|
Zhou F, Pichersky E. The complete functional characterisation of the terpene synthase family in tomato. THE NEW PHYTOLOGIST 2020; 226:1341-1360. [PMID: 31943222 PMCID: PMC7422722 DOI: 10.1111/nph.16431] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/05/2020] [Indexed: 05/14/2023]
Abstract
Analysis of the updated reference tomato genome found 34 full-length TPS genes and 18 TPS pseudogenes. Biochemical analysis has now identified the catalytic activities of all enzymes encoded by the 34 TPS genes: one isoprene synthase, 10 exclusively or predominantly monoterpene synthases, 17 sesquiterpene synthases and six diterpene synthases. Among the monoterpene and sesquiterpene and diterpene synthases, some use trans-prenyl diphosphates, some use cis-prenyl diphosphates and some use both. The isoprene synthase is cytosolic; six monoterpene synthases are plastidic, and four are cytosolic; the sesquiterpene synthases are almost all cytosolic, with the exception of one found in the mitochondria; and three diterpene synthases are found in the plastids, one in the cytosol and two in the mitochondria. New trans-prenyltransferases (TPTs) were characterised; together with previously characterised TPTs and cis-prenyltransferases (CPTs), tomato plants can make all cis and trans C10 , C15 and C20 prenyl diphosphates. Every type of plant tissue examined expresses some TPS genes and some TPTs and CPTs. Phylogenetic comparison of the TPS genes from tomato and Arabidopsis shows expansions in each clade of the TPS gene family in each lineage (and inferred losses), accompanied by changes in subcellular localisations and substrate specificities.
Collapse
Affiliation(s)
- Fei Zhou
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMI48109USA
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Lichman BR, Godden GT, Hamilton JP, Palmer L, Kamileen MO, Zhao D, Vaillancourt B, Wood JC, Sun M, Kinser TJ, Henry LK, Rodriguez-Lopez C, Dudareva N, Soltis DE, Soltis PS, Buell CR, O’Connor SE. The evolutionary origins of the cat attractant nepetalactone in catnip. SCIENCE ADVANCES 2020; 6:eaba0721. [PMID: 32426505 PMCID: PMC7220310 DOI: 10.1126/sciadv.aba0721] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/02/2020] [Indexed: 05/07/2023]
Abstract
Catnip or catmint (Nepeta spp.) is a flowering plant in the mint family (Lamiaceae) famed for its ability to attract cats. This phenomenon is caused by the compound nepetalactone, a volatile iridoid that also repels insects. Iridoids are present in many Lamiaceae species but were lost in the ancestor of the Nepetoideae, the subfamily containing Nepeta. Using comparative genomics, ancestral sequence reconstructions, and phylogenetic analyses, we probed the re-emergence of iridoid biosynthesis in Nepeta. The results of these investigations revealed mechanisms for the loss and subsequent re-evolution of iridoid biosynthesis in the Nepeta lineage. We present evidence for a chronology of events that led to the formation of nepetalactone biosynthesis and its metabolic gene cluster. This study provides insights into the interplay between enzyme and genome evolution in the origins, loss, and re-emergence of plant chemical diversity.
Collapse
Affiliation(s)
- Benjamin R. Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
- Corresponding author. (B.R.L.); (C.R.B.); (S.E.O.)
| | - Grant T. Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - John P. Hamilton
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Lira Palmer
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Mohamed O. Kamileen
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Dongyan Zhao
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Brieanne Vaillancourt
- 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
| | - Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Taliesin J. Kinser
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Laura K. Henry
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Carlos Rodriguez-Lopez
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA
- Corresponding author. (B.R.L.); (C.R.B.); (S.E.O.)
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
- Corresponding author. (B.R.L.); (C.R.B.); (S.E.O.)
| |
Collapse
|
35
|
Zeng Y, Wang MY, Hunter DC, Matich AJ, McAtee PA, Knäbel M, Hamiaux C, Popowski EA, Jaeger SR, Nieuwenhuizen NJ, Yauk YK, Atkinson RG. Sensory-Directed Genetic and Biochemical Characterization of Volatile Terpene Production in Kiwifruit. PLANT PHYSIOLOGY 2020; 183:51-66. [PMID: 32184346 PMCID: PMC7210626 DOI: 10.1104/pp.20.00186] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/01/2020] [Indexed: 05/12/2023]
Abstract
Terpene volatiles are found in many important fruit crops, but their relationship to flavor is poorly understood. Here, we demonstrate using sensory descriptive and discriminant analysis that 1,8-cineole contributes a key floral/eucalyptus note to the aroma of ripe 'Hort16A' kiwifruit (Actinidia chinensis). Two quantitative trait loci (QTLs) for 1,8-cineole production were identified on linkage groups 27 and 29a in a segregating A. chinensis population, with the QTL on LG29a colocating with a complex cluster of putative terpene synthase (TPS)-encoding genes. Transient expression in Nicotiana benthamiana and analysis of recombinant proteins expressed in Escherichia coli showed four genes in the cluster (AcTPS1a-AcTPS1d) encoded functional TPS enzymes, which produced predominantly sabinene, 1,8-cineole, geraniol, and springene, respectively. The terpene profile produced by AcTPS1b closely resembled the terpenes detected in red-fleshed A chinensis AcTPS1b expression correlated with 1,8-cineole content in developing/ripening fruit and also showed a positive correlation with 1,8-cineole content in the mapping population, indicating the basis for segregation is an expression QTL. Transient overexpression of AcTPS1b in Actinidia eriantha fruit confirmed this gene produced 1,8-cineole in Actinidia Structure-function analysis showed AcTPS1a and AcTPS1b are natural variants at key TPS catalytic site residues previously shown to change enzyme specificity in vitro. Together, our results indicate that AcTPS1b is a key gene for production of the signature flavor terpene 1,8-cineole in ripe kiwifruit. Using a sensory-directed strategy for compound identification provides a rational approach for applying marker-aided selection to improving flavor in kiwifruit as well as other fruits.
Collapse
Affiliation(s)
- Yunliu Zeng
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, P.R. China
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| | - Mindy Y Wang
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| | - Denise C Hunter
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| | | | - Peter A McAtee
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| | | | - Cyril Hamiaux
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| | | | - Sara R Jaeger
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| | - Niels J Nieuwenhuizen
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| | - Yar-Khing Yauk
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Auckland 1142, New Zealand
| |
Collapse
|
36
|
Kuhalskaya A, Wijesingha Ahchige M, Perez de Souza L, Vallarino J, Brotman Y, Alseekh S. Network Analysis Provides Insight into Tomato Lipid Metabolism. Metabolites 2020; 10:metabo10040152. [PMID: 32295308 PMCID: PMC7240963 DOI: 10.3390/metabo10040152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/26/2020] [Accepted: 04/11/2020] [Indexed: 11/16/2022] Open
Abstract
Metabolic correlation networks have been used in several instances to obtain a deeper insight into the complexity of plant metabolism as a whole. In tomato (Solanum lycopersicum), metabolites have a major influence on taste and overall fruit quality traits. Previously a broad spectrum of metabolic and phenotypic traits has been described using a Solanum pennellii introgression-lines (ILs) population. To obtain insights into tomato fruit metabolism, we performed metabolic network analysis from existing data, covering a wide range of metabolic traits, including lipophilic and volatile compounds, for the first time. We provide a comprehensive fruit correlation network and show how primary, secondary, lipophilic, and volatile compounds connect to each other and how the individual metabolic classes are linked to yield-related phenotypic traits. Results revealed a high connectivity within and between different classes of lipophilic compounds, as well as between lipophilic and secondary metabolites. We focused on lipid metabolism and generated a gene-expression network with lipophilic metabolites to identify new putative lipid-related genes. Metabolite–transcript correlation analysis revealed key putative genes involved in lipid biosynthesis pathways. The overall results will help to deepen our understanding of tomato metabolism and provide candidate genes for transgenic approaches toward improving nutritional qualities in tomato.
Collapse
Affiliation(s)
- Anastasiya Kuhalskaya
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Department of Life Sciences, Ben Gurion University of the Negev, 84105 Beersheva, Israel
| | - Micha Wijesingha Ahchige
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - José Vallarino
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Department of Life Sciences, Ben Gurion University of the Negev, 84105 Beersheva, Israel
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +49-(0)331-567-8211
| |
Collapse
|
37
|
Li Q, Ramasamy S, Singh P, Hagel JM, Dunemann SM, Chen X, Chen R, Yu L, Tucker JE, Facchini PJ, Yeaman S. Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy. Nat Commun 2020; 11:1190. [PMID: 32132540 PMCID: PMC7055283 DOI: 10.1038/s41467-020-15040-2] [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: 08/08/2018] [Accepted: 02/10/2020] [Indexed: 02/08/2023] Open
Abstract
Genes in plant secondary metabolic pathways enable biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression of BIA genes increases within clusters and identify candidates with unknown function based on clustering and covariation in expression and alkaloid production. Copy number variation in critical BIA genes correlates with stark differences in alkaloid production, linking noscapine production with an 11-gene deletion, and increased thebaine/decreased morphine production with deletion of a T6ODM cluster. Our results show that the opium poppy genome is still dynamically evolving in ways that contribute to medically and industrially important phenotypes.
Collapse
Affiliation(s)
- Qiushi Li
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sukanya Ramasamy
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Sonja M Dunemann
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Xue Chen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Rongji Chen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Lisa Yu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Joseph E Tucker
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
| |
Collapse
|
38
|
Schuurink R, Tissier A. Glandular trichomes: micro-organs with model status? THE NEW PHYTOLOGIST 2020; 225:2251-2266. [PMID: 31651036 DOI: 10.1111/nph.16283] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/01/2019] [Indexed: 05/19/2023]
Abstract
Glandular trichomes are epidermal outgrowths that are the site of biosynthesis and storage of large quantities of specialized metabolites. Besides their role in the protection of plants against biotic and abiotic stresses, they have attracted interest owing to the importance of the compounds they produce for human use; for example, as pharmaceuticals, flavor and fragrance ingredients, or pesticides. Here, we review what novel concepts investigations on glandular trichomes have brought to the field of specialized metabolism, particularly with respect to chemical and enzymatic diversity. Furthermore, the next challenges in the field are understanding the metabolic network underlying the high productivity of glandular trichomes and the transport and storage of metabolites. Another emerging area is the development of glandular trichomes. Studies in some model species, essentially tomato, tobacco, and Artemisia, are now providing the first molecular clues, but many open questions remain: How is the distribution and density of different trichome types on the leaf surface controlled? When is the decision for an epidermal cell to differentiate into one type of trichome or another taken? Recent advances in gene editing make it now possible to address these questions and promise exciting discoveries in the near future.
Collapse
Affiliation(s)
- Robert Schuurink
- Swammerdam Institute for Life Sciences, Green Life Science Research Cluster, University of Amsterdam, Postbus 1210, 1000 BE, Amsterdam, the Netherlands
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| |
Collapse
|
39
|
Gericke O, Hansen NL, Pedersen GB, Kjaerulff L, Luo D, Staerk D, Møller BL, Pateraki I, Heskes AM. Nerylneryl diphosphate is the precursor of serrulatane, viscidane and cembrane-type diterpenoids in Eremophila species. BMC PLANT BIOLOGY 2020; 20:91. [PMID: 32111159 PMCID: PMC7049213 DOI: 10.1186/s12870-020-2293-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/17/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Eremophila R.Br. (Scrophulariaceae) is a diverse genus of plants with species distributed across semi-arid and arid Australia. It is an ecologically important genus that also holds cultural significance for many Indigenous Australians who traditionally use several species as sources of medicines. Structurally unusual diterpenoids, particularly serrulatane and viscidane-types, feature prominently in the chemical profile of many species and recent studies indicate that these compounds are responsible for much of the reported bioactivity. We have investigated the biosynthesis of diterpenoids in three species: Eremophila lucida, Eremophila drummondii and Eremophila denticulata subsp. trisulcata. RESULTS In all studied species diterpenoids were localised to the leaf surface and associated with the occurrence of glandular trichomes. Trichome-enriched transcriptome databases were generated and mined for candidate terpene synthases (TPS). Four TPSs with diterpene biosynthesis activity were identified: ElTPS31 and ElTPS3 from E. lucida were found to produce (3Z,7Z,11Z)-cembratrien-15-ol and 5-hydroxyviscidane, respectively, and EdTPS22 and EdtTPS4, from E. drummondii and E. denticulata subsp. trisulcata, respectively, were found to produce 8,9-dihydroserrulat-14-ene which readily aromatized to serrulat-14-ene. In all cases, the identified TPSs used the cisoid substrate, nerylneryl diphosphate (NNPP), to form the observed products. Subsequently, cis-prenyl transferases (CPTs) capable of making NNPP were identified in each species. CONCLUSIONS We have elucidated two biosynthetic steps towards three of the major diterpene backbones found in this genus. Serrulatane and viscidane-type diterpenoids are promising candidates for new drug leads. The identification of an enzymatic route to their synthesis opens up the possibility of biotechnological production, making accessible a ready source of scaffolds for further modification and bioactivity testing.
Collapse
Affiliation(s)
- Oliver Gericke
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Nikolaj Lervad Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Gustav Blichfeldt Pedersen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Louise Kjaerulff
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Dan Luo
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Irini Pateraki
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Allison Maree Heskes
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
- Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
| |
Collapse
|
40
|
Chen H, Köllner TG, Li G, Wei G, Chen X, Zeng D, Qian Q, Chen F. Combinatorial Evolution of a Terpene Synthase Gene Cluster Explains Terpene Variations in Oryza. PLANT PHYSIOLOGY 2020; 182:480-492. [PMID: 31712306 PMCID: PMC6945850 DOI: 10.1104/pp.19.00948] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/28/2019] [Indexed: 05/21/2023]
Abstract
Terpenes are specialized metabolites ubiquitously produced by plants via the action of terpene synthases (TPSs). There are enormous variations in the types and amounts of terpenes produced by individual species. To understand the mechanisms responsible for such vast diversity, here we investigated the origin and evolution of a cluster of tandemly arrayed TPS genes in Oryza In the Oryza species analyzed, TPS genes occur as a three-TPS cluster, a two-TPS cluster, and a single TPS gene in five, one, and one species, respectively. Phylogenetic analysis revealed the origins of the two-TPS and three-TPS clusters and the role of species-specific losses of TPS genes. Within the three-TPS clusters, one orthologous group exhibited conserved catalytic activities. The other two groups, both of which contained pseudogenes and/or nonfunctional genes, exhibited distinct profiles of terpene products. Sequence and structural analyses combined with functional validation identified several amino acids in the active site that are critical for catalytic activity divergence of the three orthologous groups. In the five Oryza species containing the three-TPS cluster, their functional TPS genes showed both conserved and species-specific expression patterns in insect-damaged and untreated plants. Emission patterns of volatile terpenes from each species were largely consistent with the expression of their respective TPS genes and the catalytic activities of the encoded enzymes. This study indicates the importance of combinatorial evolution of TPS genes in determining terpene variations among individual species, which includes gene duplication, retention/loss/degradation of duplicated genes, varying selection pressure, retention/divergence in catalytic activities, and divergence in expression regulation.
Collapse
Affiliation(s)
- Hao Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Guanglin Li
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Guo Wei
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Dali Zeng
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| |
Collapse
|
41
|
Chen X, Liu F, Liu L, Qiu J, Fang D, Wang W, Zhang X, Ye C, Timko MP, Zhu QH, Fan L, Xiao B. Characterization and evolution of gene clusters for terpenoid phytoalexin biosynthesis in tobacco. PLANTA 2019; 250:1687-1702. [PMID: 31414203 DOI: 10.1007/s00425-019-03255-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
MAIN CONCLUSION The study performed genome-wide identification, characterization and evolution analysis of gene clusters for phytoalexin terpenoid biosynthesis in tobacco, and specifically illustrated ones for capsidiol, an efficient defensive specialized metabolite. Terpenoid phytoalexins play an important role in plant self-defense against pest and pathogen attack. Terpenoid biosynthesis involves terpene synthase and cytochrome P450, which always locate and function as cluster(s). In this study, we performed genome-wide investigation of metabolic gene clusters involved in terpenoid production in tobacco (Nicotiana tabacum). Due to the complexity of the tobacco genome, we modified a published prediction pipeline to reduce the influence of the large number of repeats and to improve the annotation of tobacco genes with respect to their metabolic functions. We identified 1181 metabolic gene clusters with 34 of them potentially being involved in terpenoid biosynthesis. Through integration with transcriptome and metabolic pathway annotation analyses, 3 of the 34 terpenoid biosynthesis-related gene clusters were determined to be high-confidence ones, with 2 involved in biosynthesis of capsidiol, a terpenoid recognized as 1 of the effective resistance compounds in the Nicotiana species. The capsidiol-related gene cluster was conserved in N. sylvestris, N. tomentosiformis and N. attenuate. Our findings demonstrate that phytoalexins in tobacco can arise from operon-like gene clusters, a genomic pattern characterized as being beneficial for rapid stress response, gene co-regulation, co-function and co-heredity.
Collapse
Affiliation(s)
- Xi Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China
| | - Fangjie Liu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China
| | - Lu Liu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Jie Qiu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Dunhuang Fang
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Weidi Wang
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Xingcheng Zhang
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Chuyu Ye
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Michael Paul Timko
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China
| | - Bingguang Xiao
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
| |
Collapse
|
42
|
Identification and Functional Characterization of a Soybean ( Glycine max) Thioesterase that Acts on Intermediates of Fatty Acid Biosynthesis. PLANTS 2019; 8:plants8100397. [PMID: 31597241 PMCID: PMC6843456 DOI: 10.3390/plants8100397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/21/2019] [Accepted: 10/02/2019] [Indexed: 11/16/2022]
Abstract
(1) Background: Plants possess many acyl-acyl carrier protein (acyl-ACP) thioesterases (TEs) with unique specificity. One such TE is methylketone synthase 2 (MKS2), an enzyme with a single-hotdog-fold structure found in several tomato species that hydrolyzes 3-ketoacyl-ACPs to give free 3-ketoacids. (2) Methods: In this study, we identified and characterized a tomato MKS2 homolog gene, namely, GmMKS2, in the genome of soybean (Glycine max). (3) Results: GmMKS2 underwent alternative splicing to produce three alternative transcripts, but only one encodes a protein with thioesterase activity when recombinantly expressed in Escherichia coli. Heterologous expression of the main transcript of GmMKS2, GmMKS2-X2, in E. coli generated various types of fatty acids, including 3-ketoacids-with 3-ketotetradecenoic acid (14:1) being the most abundant-cis-Δ5-dodecanoic acid, and 3-hydroxyacids, suggesting that GmMKS2 acts as an acyl-ACP thioesterase. In plants, the GmMKS2-X2 transcript level was found to be higher in the roots compared to other examined organs. In silico analysis revealed that there is a substantial enrichment of putative cis-regulatory elements related to disease-resistance responses and abiotic stress responses in the promoter of this gene. (4) Conclusions: GmMKS2 showed broad substrate specificities toward a wide range of acyl-ACPs that varied in terms of chain length, oxidation state, and saturation degree. Our results suggest that GmMKS2 might have a stress-related physiological function in G. max.
Collapse
|
43
|
Rokas A, Wisecaver JH, Lind AL. The birth, evolution and death of metabolic gene clusters in fungi. Nat Rev Microbiol 2019; 16:731-744. [PMID: 30194403 DOI: 10.1038/s41579-018-0075-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.
Collapse
Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Abigail L Lind
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.,Gladstone Institutes, San Francisco, CA, USA
| |
Collapse
|
44
|
Johnson SR, Bhat WW, Sadre R, Miller GP, Garcia AS, Hamberger B. Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution. THE NEW PHYTOLOGIST 2019; 223:323-335. [PMID: 30843212 PMCID: PMC6593445 DOI: 10.1111/nph.15778] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/22/2019] [Indexed: 05/20/2023]
Abstract
The mint family (Lamiaceae) is well documented as a rich source of terpene natural products. More than 200 diterpene skeletons have been reported from mints, but biosynthetic pathways are known for just a few of these. We crossreferenced chemotaxonomic data with publicly available transcriptomes to select common selfheal (Prunella vulgaris) and its highly unusual vulgarisin diterpenoids as a case study for exploring the origins of diterpene skeletal diversity in Lamiaceae. Four terpene synthases (TPS) from the TPS-a subfamily, including two localised to the plastid, were cloned and functionally characterised. Previous examples of TPS-a enzymes from Lamiaceae were cytosolic and reported to act on the 15-carbon farnesyl diphosphate. Plastidial TPS-a enzymes using the 20-carbon geranylgeranyl diphosphate are known from other plant families, having apparently arisen independently in each family. All four new enzymes were found to be active on multiple prenyl-diphosphate substrates with different chain lengths and stereochemistries. One of the new enzymes catalysed the cyclisation of geranylgeranyl diphosphate into 11-hydroxy vulgarisane, the likely biosynthetic precursor of the vulgarisins. We uncovered the pathway to a rare diterpene skeleton. Our results support an emerging paradigm of substrate and compartment switching as important aspects of TPS evolution and diversification.
Collapse
Affiliation(s)
- Sean R. Johnson
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
| | - Wajid Waheed Bhat
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Pharmacology and ToxicologyMichigan State UniversityEast LansingMI48824USA
| | - Radin Sadre
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
| | - Garret P. Miller
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
| | - Alekzander Sky Garcia
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
| | - Björn Hamberger
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
| |
Collapse
|
45
|
Nunes-Nesi A, Alseekh S, de Oliveira Silva FM, Omranian N, Lichtenstein G, Mirnezhad M, González RRR, Sabio Y Garcia J, Conte M, Leiss KA, Klinkhamer PGL, Nikoloski Z, Carrari F, Fernie AR. Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds. Metabolomics 2019; 15:46. [PMID: 30874962 PMCID: PMC6420416 DOI: 10.1007/s11306-019-1503-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 01/12/2019] [Indexed: 01/10/2023]
Abstract
INTRODUCTION To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. OBJECTIVE This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. METHODS The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. RESULTS Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. CONCLUSIONS Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.
Collapse
Affiliation(s)
- Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany.
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany
- Center of Plant System Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | | | - Nooshin Omranian
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany
- Center of Plant System Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Gabriel Lichtenstein
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | - Mohammad Mirnezhad
- Plant Ecology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Roman R Romero González
- Plant Ecology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Julia Sabio Y Garcia
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | - Mariana Conte
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | - Kirsten A Leiss
- Plant Ecology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Business Unit Horticulture, Wageningen University & Research, Postbus 20, 2665 ZG, Bleiswijk, The Netherlands
| | - Peter G L Klinkhamer
- Plant Ecology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Zoran Nikoloski
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany
- Center of Plant System Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| |
Collapse
|
46
|
Smith SD, Angelovici R, Heyduk K, Maeda HA, Moghe GD, Pires JC, Widhalm JR, Wisecaver JH. The renaissance of comparative biochemistry. AMERICAN JOURNAL OF BOTANY 2019; 106:3-13. [PMID: 30629738 DOI: 10.1002/ajb2.1216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
47
|
Guo L, Qiu J, Li LF, Lu B, Olsen K, Fan L. Genomic Clues for Crop-Weed Interactions and Evolution. TRENDS IN PLANT SCIENCE 2018; 23:1102-1115. [PMID: 30293809 DOI: 10.1016/j.tplants.2018.09.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/10/2018] [Accepted: 09/11/2018] [Indexed: 05/11/2023]
Abstract
Agronomically critical weeds that have evolved alongside crop species are characterized by rapid adaptation and invasiveness, which can result in an enormous reduction in annual crop yield worldwide. We discuss here recent genome-based research studies on agricultural weeds and crop-weed interactions that reveal several major evolutionary innovations such as de-domestication, interactions mediated by allelochemical secondary metabolites, and parasitic genetic elements that play crucial roles in enhancing weed invasiveness in agricultural settings. We believe that these key studies will guide future research into the evolution of crop-weed interactions, and further the development of practical applications in agricultural weed control and crop breeding.
Collapse
Affiliation(s)
- Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; These authors contributed equally to this work
| | - Jie Qiu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; These authors contributed equally to this work
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Baorong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kenneth Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Longjiang Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
48
|
Gao F, Liu B, Li M, Gao X, Fang Q, Liu C, Ding H, Wang L, Gao X. Identification and characterization of terpene synthase genes accounting for volatile terpene emissions in flowers of Freesia x hybrida. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4249-4265. [PMID: 29901784 PMCID: PMC6093421 DOI: 10.1093/jxb/ery224] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/06/2017] [Indexed: 05/19/2023]
Abstract
The development of flower scents was a crucial event in biological evolution, providing olfactory signals by which plants can attract pollinators. In this study, bioinformatics, metabolomics, and biochemical and molecular methodologies were integrated to investigate the candidate genes involved in the biosynthesis of volatile components in two cultivars of Freesia x hybrida, Red River® and Ambiance, which release different categories of compounds. We found that terpene synthase (TPS) genes were the pivotal genes determining spatiotemporal release of volatile compounds in both cultivars. Eight FhTPS genes were isolated and six were found to be functional: FhTPS1 was a single-product enzyme catalyzing the formation of linalool, whereas the other four FhTPS proteins were multi-product enzymes, among which FhTPS4, FhTPS6, and FhTPS7 could recognize geranyl diphosphate and farnesyl diphosphate simultaneously. The FhTPS enzymatic products closely matched the volatile terpenes emitted from flowers, and significant correlations were found between release of volatile terpenes and FhTPS gene expression. Graphical models based on these results are proposed that summarize the biosynthesis of Freesia floral volatile terpenes. The characterization of FhTPS genes paves the way to decipher their roles in the speciation and fitness of Freesia, and this knowledge could also be used to introduce or enhance scent in other plants.
Collapse
Affiliation(s)
- Fengzhan Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Baofeng Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Min Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xiaoyan Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Qiang Fang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Chang Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Hui Ding
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
- Correspondence: or
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
- Correspondence: or
| |
Collapse
|
49
|
Olsen KM, Small LL. Micro- and macroevolutionary adaptation through repeated loss of a complete metabolic pathway. THE NEW PHYTOLOGIST 2018; 219:757-766. [PMID: 29708583 DOI: 10.1111/nph.15184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 05/27/2023]
Abstract
There is growing evidence for the convergent evolution of physically linked gene clusters encoding chemical defense pathways. Metabolic clusters are proposed to evolve because they ensure co-inheritance of all required genes where the defense is favored, and prevent inheritance of toxic partial pathways where it is not. This hypothesis rests on the assumption that clusters evolve in species where selection favors intraspecific polymorphism for the defense; however, they have not been examined in polymorphic species. We examined metabolic cluster evolution in relation to an adaptive polymorphism for cyanogenic glucoside (CNglc) production in clover. Using 163 accessions, we performed CNglc assays, BAC sequencing, Southern hybridizations and molecular evolutionary analyses. We find that the CNglc pathway forms a 138-kb cluster in white clover, and that the adaptive polymorphism occurs through presence/absence of the complete cluster. Component genes are orthologous to those in the distantly related legume Lotus japonicus. These findings provide empirical support for the co-inheritance hypothesis, and they indicate that adaptive CNglc variation in white clover evolves through recurrent deletions of the entire pathway. They further indicate that the shared ancestor of many important legume crops was likely cyanogenic and that this defense was lost repeatedly over the last 50 Myr.
Collapse
Affiliation(s)
- Kenneth M Olsen
- Biology Department, Washington University, Campus Box 1137, St Louis, MO, 63130-4899, USA
| | - Linda L Small
- Biology Department, Washington University, Campus Box 1137, St Louis, MO, 63130-4899, USA
| |
Collapse
|
50
|
Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots. Proc Natl Acad Sci U S A 2018; 115:E6650-E6658. [PMID: 29941591 PMCID: PMC6048515 DOI: 10.1073/pnas.1721318115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Recently discovered biosynthetic gene clusters in plants are a striking example of the nonrandom complex structure of eukaryotic genomes. The mechanisms underpinning the formation of these clustered pathways are not understood. Here we carry out a systematic analysis of transposable elements associated with clustered terpene biosynthetic genes in plant genomes, and find evidence to suggest a role for miniature inverted-repeat transposable elements in cluster formation in eudicots. Our analyses provide insights into potential mechanisms of cluster assembly. They also shed light on the emergence of a “block” mechanism for the foundation of new terpene clusters in the eudicots in which microsyntenic blocks of terpene synthase and cytochrome P450 gene pairs duplicate, providing templates for the evolution of new pathways. Plants produce a plethora of natural products, including many drugs. It has recently emerged that the genes encoding different natural product pathways may be organized as biosynthetic gene clusters in plant genomes, with >30 examples reported so far. Despite superficial similarities with microbes, these clusters have not arisen by horizontal gene transfer, but rather by gene duplication, neofunctionalization, and relocation via unknown mechanisms. Previously we reported that two Arabidopsis thaliana biosynthetic gene clusters are located in regions of the genome that are significantly enriched in transposable elements (TEs). Other plant biosynthetic gene clusters also harbor abundant TEs. TEs can mediate genomic rearrangement by providing homologous sequences that enable illegitimate recombination and gene relocation. Thus, TE-mediated recombination may contribute to plant biosynthetic gene cluster formation. TEs may also facilitate establishment of regulons. However, a systematic analysis of the TEs associated with plant biosynthetic gene clusters has not been carried out. Here we investigate the TEs associated with clustered terpene biosynthetic genes in multiple plant genomes and find evidence to suggest a role for miniature inverted-repeat transposable elements in cluster formation in eudicots. Through investigation of the newly sequenced Amborella trichopoda, Aquilegia coerulea, and Kalanchoe fedtschenkoi genomes, we further show that the “block” mechanism of founding of biosynthetic gene clusters through duplication and diversification of pairs of terpene synthase and cytochrome P450 genes that is prevalent in the eudicots arose around 90–130 million years ago, after the appearance of the basal eudicots and before the emergence of the superrosid clade.
Collapse
|