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Bao T, Kimani S, Li Y, Li H, Yang S, Zhang J, Wang Q, Wang Z, Ning G, Wang L, Gao X. Allelic variation of terpene synthases drives terpene diversity in the wild species of the Freesia genus. PLANT PHYSIOLOGY 2023; 192:2419-2435. [PMID: 36932696 PMCID: PMC10315281 DOI: 10.1093/plphys/kiad172] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Terpene synthases (TPSs) play pivotal roles in conferring the structural diversity of terpenoids, which are mainly emitted from flowers, whereas the genetic basis of the release of floral volatile terpenes remains largely elusive. Though quite similar in sequence, TPS allelic variants still function divergently, and how they drive floral terpene diversity in closely related species remains unknown. Here, TPSs responsible for the floral scent of wild Freesia species were characterized, and the functions of their natural allelic variants, as well as the causal amino acid residues, were investigated in depth. Besides the 8 TPSs previously reported in modern cultivars, 7 additional TPSs were functionally evaluated to contribute to the major volatiles emitted from wild Freesia species. Functional characterization of allelic natural variants demonstrated that allelic TPS2 and TPS10 variants changed the enzymatic capacity while allelic TPS6 variants drove the diversity of floral terpene products. Further residue substitution analysis revealed the minor residues determining the enzyme catalytic activity and product specificity. The clarification of TPSs in wild Freesia species reveals that allelic TPS variants evolved differently to determine the interspecific floral volatile terpenes in the genus and might be used for modern cultivar improvement.
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Affiliation(s)
- Tingting Bao
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Shadrack Kimani
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
- School of Pure and Applied Sciences, Karatina University, Karatina 10101, Kenya
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Hongjie Li
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Song Yang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Jia Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Qiuyue Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Zhaoxuan Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
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Wen T, Xu X, Ren A, Zhao G, Wu J. Genome-wide identification of terpenoid synthase family genes in Gossypium hirsutum and functional dissection of its subfamily cadinene synthase A in gossypol synthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1162237. [PMID: 37180387 PMCID: PMC10169749 DOI: 10.3389/fpls.2023.1162237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/24/2023] [Indexed: 05/16/2023]
Abstract
Plant terpenoid synthase (TPS) family genes participate in metabolite synthesis, hormones, gossypol, etc. Here, we genome-widely identified TPS family genes in 12 land plant species. Four hundred and thirty TPS-related genes were divided into seven subfamilies. The TPS-c in Bryophytes was suggested to be the earliest subfamily, followed by the TPS-e/f and TPS-h presence in ferns. TPS-a, the largest number of genes, was derived from monocotyledonous and dicotyledonous plants. Collinearity analysis showed that 38 out of the 76 TPS genes in G. hirsutum were collinear within G. arboreum and G. raimondii. Twenty-one GhTPS-a genes belong to the cadinene synthase (GhCDN) subfamily and were divided into five groups, A, B, C, D, and E. The special cis-elements in the promoters of 12 GhCDN-A genes suggested that the JA and ethylene signaling pathways may be involved in their expression regulation. When 12 GhCDN-A genes were simultaneously silenced through virus-induced gene silencing, the glandular color of GhCDN-A-silenced plants was lighter than that of the control, supported by a gossypol content decrease based on HPLC testing, suggesting that GhCDN-A subgroup genes participate in gossypol synthesis. According to RNA-seq analysis, gossypol synthesis-related genes and disease-resistant genes in the glandular variety exhibited upregulated expression compared to the glandless variety, whereas hormone signaling-related genes were downregulated. All in all, these results revealed plant TPS gene evolution rules and dissected the TPS subfamily, GhCDN-A, function in gossypol synthesis in cotton.
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Affiliation(s)
- Tianyang Wen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiao Xu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Aiping Ren
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ge Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jiahe Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology Research, Chinese Academy of Sciences, Beijing, China
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Genome-wide identification, expression profile and evolutionary relationships of TPS genes in the neotropical fruit tree species Psidium cattleyanum. Sci Rep 2023; 13:3930. [PMID: 36894661 PMCID: PMC9998390 DOI: 10.1038/s41598-023-31061-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Terpenoids are essential for plant growth, development, defense, and adaptation mechanisms. Psidium cattleyanum (Myrtaceae) is a fleshy fruit tree species endemics from Atlantic Forest, known for its pleasant fragrance and sweet taste, attributed to terpenoids in its leaves and fruits. In this study, we conducted genome-wide identification, evolutionary and expression analyses of the terpene synthase gene (TPS) family in P. cattleyanum red guava (var. cattleyanum), and yellow guava (var. lucidum Hort.) morphotypes. We identified 32 full-length TPS in red guava (RedTPS) and 30 in yellow guava (YlwTPS). We showed different expression patterns of TPS paralogous in the two morphotypes, suggesting the existence of distinct gene regulation mechanisms and their influence on the final essential oil content in both morphotypes. Moreover, the oil profile of red guava was dominated by 1,8-cineole and linalool and yellow guava was enriched in α-pinene, coincident in proportion to TPS-b1 genes, which encode enzymes that produce cyclic monoterpenes, suggesting a lineage-specific subfamily expansion of this family. Finally, we identified amino acid residues near the catalytic center and functional areas under positive selection. Our findings provide valuable insights into the terpene biosynthesis in a Neotropical Myrtaceae species and their potential involvement in adaptation mechanisms.
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Wang H, Zong C, Bai A, Yuan S, Li Y, Yu Z, Tian R, Liu T, Hou X, Li Y. Transcriptome sequencing and gas chromatography–mass spectrometry analyses provide insights into β-caryophyllene biosynthesis in Brassica campestris. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 5:100129. [PMID: 36060474 PMCID: PMC9428917 DOI: 10.1016/j.fochms.2022.100129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/28/2022] [Accepted: 08/06/2022] [Indexed: 11/24/2022]
Abstract
β-Caryophyllene (BCP) was detected in Brassica campestris. BCP content changed in cultivars during developmental stages and MeJA treatment. In the phylogenetic analysis, the TPSa gene subfamily was divided into four groups The potential regulatory and transporter network of BCP was constructed.
Sesquiterpenes are important defensive secondary metabolites and aroma components. However, limited information is available on the mechanism of sesquiterpene formation and composition in the non-heading Chinese cabbage (NHCC) leaf. Therefore, headspace solid-phase microextraction/gas chromatography–mass spectrometry (HS-SPME/GC–MS) combined with transcriptome analysis was used to study the mechanism of volatile organic compound formation. A total of 26 volatile organic compounds were identified in two NHCC cultivars ‘SZQ’ and ‘XQC’ and their F1 hybrids. Among these, sesquiterpene β-caryophyllene was identified only in ‘XQC’ and F1. Five genes encoding caryophyllene synthase were identified. The candidate β-caryophyllene synthase genes BcTPSa11 and BcTPSa21 had high expression levels only in ‘XQC’ and F1. In addition, several transcription factors of MYB-related, MYB, bHLH, and AP2/ERF families were identified by co-expression, suggesting that they regulate β-caryophyllene biosynthesis. Our results provide a molecular basis for sesquiterpene biosynthesis as well as insights into the regulatory network of β-caryophyllene in NHCC.
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Singh G, Sharma S, Rawat S, Sharma RK. Plant Specialised Glycosides (PSGs): their biosynthetic enzymatic machinery, physiological functions and commercial potential. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1009-1028. [PMID: 36038144 DOI: 10.1071/fp21294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Plants, the primary producers of our planet, have evolved from simple aquatic life to very complex terrestrial habitat. This habitat transition coincides with evolution of enormous chemical diversity, collectively termed as 'Plant Specialised Metabolisms (PSMs)', to cope the environmental challenges. Plant glycosylation is an important process of metabolic diversification of PSMs to govern their in planta stability, solubility and inter/intra-cellular transport. Although, individual category of PSMs (terpenoids, phenylpropanoids, flavonoids, saponins, alkaloids, phytohormones, glucosinolates and cyanogenic glycosides) have been well studied; nevertheless, deeper insights of physiological functioning and genomic aspects of plant glycosylation/deglycosylation processes including enzymatic machinery (CYPs, GTs, and GHs) and regulatory elements are still elusive. Therefore, this review discussed the paradigm shift on genomic background of enzymatic machinery, transporters and regulatory mechanism of 'Plant Specialised Glycosides (PSGs)'. Current efforts also update the fundamental understanding about physiological, evolutionary and adaptive role of glycosylation/deglycosylation processes during the metabolic diversification of PSGs. Additionally, futuristic considerations and recommendations for employing integrated next-generation multi-omics (genomics, transcriptomics, proteomics and metabolomics), including gene/genome editing (CRISPR-Cas) approaches are also proposed to explore commercial potential of PSGs.
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Affiliation(s)
- Gopal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India; and Present address: Department of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Shikha Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
| | - Sandeep Rawat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Present address: G. B. Pant National Institute of Himalayan Environment and Sustainable Development, Sikkim Regional Centre, Pangthang, Gangtok 737101, Sikkim, India
| | - Ram Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
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Parakkunnel R, Bhojaraja Naik K, Susmita C, Girimalla V, Bhaskar KU, Sripathy KV, Shantharaja CS, Aravindan S, Kumar S, Lakhanpaul S, Bhat KV. Evolution and co-evolution: insights into the divergence of plant heat shock factor genes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1029-1047. [PMID: 35722513 PMCID: PMC9203654 DOI: 10.1007/s12298-022-01183-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/04/2022] [Indexed: 05/03/2023]
Abstract
The Heat Shock Factor (Hsf) genes are widely distributed across the plant kingdom regulating the plant response to various abiotic stresses. In addition to natural selection, breeding and accelerated selection changed the structure and function of Hsf genes. 1076 Hsf genes from 30 genera from primitive algae to the most advanced plant species and major crop plants were used for phylogenetic analysis. The interspecific divergence was studied with 11 members of genus Oryza while intraspecific divergence was studied with sesame pan-genome adapted to diverse ecological niches. B2 genes in eudicots and monocots originated separately while A1 gave rise to the recently evolved Class-C genes and land colonization happened with evolution of A1 genes. An increase in the number of lineages in the Oryza clade with the evolution of AA genome indicated independent domestication and positive selection was observed in > 53% of loci whereas the highly conserved homologues were under purifying selection. The paralogous genes under positive selection exhibited more domain changes for diversified function and increased fitness. A significant co-evolving cluster involving amino acids Phenylalanine, Lysine and Valine played crucial role in maintaining hydrophobic core along with highly conserved Tryptophan residues. A mutation of Glutamic acid to Glutamine was observed in A8 genes of Lamiales affecting protein solvency. Breeding resulted in accumulation of mutations reducing the hydrophobicity of proteins and a further reduction in protein aggregation. This study identify genome duplications, non-neutral selection and co-evolving residues as causing drastic changes in the conserved domain of Hsf proteins. Supplementary information The online version contains supplementary material available at 10.1007/s12298-022-01183-7.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - K Bhojaraja Naik
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - C Susmita
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh 275103 India
| | - Vanishree Girimalla
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - K Udaya Bhaskar
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - KV Sripathy
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - CS Shantharaja
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, Karnataka 560065 India
| | - S Aravindan
- 4Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, 110012 India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh 275103 India
| | | | - KV Bhat
- 4Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, 110012 India
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Kang M, Choi Y, Kim H, Kim S. Single-cell RNA-sequencing of Nicotiana attenuata corolla cells reveals the biosynthetic pathway of a floral scent. THE NEW PHYTOLOGIST 2022; 234:527-544. [PMID: 35075650 PMCID: PMC9305527 DOI: 10.1111/nph.17992] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/05/2022] [Indexed: 05/28/2023]
Abstract
High-throughput single-cell RNA sequencing (scRNA-Seq) identifies distinct cell populations based on cell-to-cell heterogeneity in gene expression. By examining the distribution of the density of gene expression profiles, we can observe the metabolic features of each cell population. Here, we employ the scRNA-Seq technique to reveal the entire biosynthetic pathway of a flower volatile. The corolla of the wild tobacco Nicotiana attenuata emits a bouquet of scents that are composed mainly of benzylacetone (BA). Protoplasts from the N. attenuata corolla limbs and throat cups were isolated at three different time points, and the transcript levels of > 16 000 genes were analyzed in 3756 single cells. We performed unsupervised clustering analysis to determine which cell clusters were involved in BA biosynthesis. The biosynthetic pathway of BA was uncovered by analyzing gene co-expression in scRNA-Seq datasets and by silencing candidate genes in the corolla. In conclusion, the high-resolution spatiotemporal atlas of gene expression provided by scRNA-Seq reveals the molecular features underlying cell-type-specific metabolism in a plant.
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Affiliation(s)
- Moonyoung Kang
- Department of Biological SciencesKorea Advanced Institute for Science and TechnologyDaejeon34141Korea
| | - Yuri Choi
- Department of Biological SciencesKorea Advanced Institute for Science and TechnologyDaejeon34141Korea
| | - Hyeonjin Kim
- Department of Biological SciencesKorea Advanced Institute for Science and TechnologyDaejeon34141Korea
| | - Sang‐Gyu Kim
- Department of Biological SciencesKorea Advanced Institute for Science and TechnologyDaejeon34141Korea
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Yang S, Wang N, Kimani S, Li Y, Bao T, Ning G, Li L, Liu B, Wang L, Gao X. Characterization of Terpene synthase variation in flowers of wild aquilegia species from Northeastern Asia. HORTICULTURE RESEARCH 2022; 9:uhab020. [PMID: 35039842 PMCID: PMC8771452 DOI: 10.1093/hr/uhab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 08/25/2021] [Accepted: 10/02/2021] [Indexed: 05/13/2023]
Abstract
There are several causes for the great diversity in floral terpenes. The terpene products are determined by the catalytic fidelity, efficiency and plasticity of the active sites of terpene synthases (TPSs). However, the molecular mechanism of TPS in catalyzing terpene biosynthesis and its evolutionary fate in wild plant species remain largely unknown. In this study, the functionality of terpene synthases and their natural variants were assessed in two Northeastern Asia endemic columbine species and their natural hybrid. Synoptically, TPS7, TPS8, and TPS9 were highly expressed in these Aquilegia species from the Zuojia population. The in vitro and in vivo enzymatic assays revealed that TPS7 and TPS8 mainly produced (+)-limonene and β-sesquiphellandrene, respectively, whereas TPS9 produced pinene, similar to the major components released from Aquilegia flowers. Multiple sequence alignment of Aquilegia TPS7 and TPS8 in the Zuojia population revealed amino acid polymorphisms. Domain swapping and amino acid substitution assays demonstrated that 413A, 503I and 529D had impacts on TPS7 catalytic activity, whereas 420G, 538F and 545 L affected the ratio of β-sesquiphellandrene to β-bisabolene in TPS8. Moreover, these key polymorphic amino acid residues were found in Aquilegia species from the Changbai Mountain population. Interestingly, amino acid polymorphisms in TPSs were present in individuals with low expression levels, and nonsynonymous mutations could impact the catalytic activity or product specificity of these genes. The results of this study will shed new light on the function and evolution of TPS genes in wild plant species and are beneficial to the modification of plant fragrances.
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Affiliation(s)
- Song Yang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Ning Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Shadrack Kimani
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
- School of Pure and Applied Sciences, Karatina University, Karatina, Kenya
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Tingting Bao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Guogui Ning
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
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Fan H, Wei G, Chen X, Guo H, Crandall-Stotler B, Köllner TG, Chen F. Sesquiterpene biosynthesis in a leafy liverwort Radula lindenbergiana Gottsche ex C. Hartm. PHYTOCHEMISTRY 2021; 190:112847. [PMID: 34237478 DOI: 10.1016/j.phytochem.2021.112847] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Liverworts (Marchantiophyta) are among the earliest diverging lineages of extant land plants. Among their unique features, most liverworts contain membrane-bound oil bodies, organelles that accumulate diverse secondary metabolites, especially terpenoids. In contrast to the rich information on liverwort terpenoid chemistry, little is known about their biosynthesis. Recently, terpenoid biosynthesis was studied in a model thalloid species Marchantiapolymorpha, in which sesquiterpenes and monoterpenes are biosynthesized by a new type of terpene synthases termed microbial terpene synthase-like (MTPSL) proteins. Here we study terpenoid biosynthesis in a leafy liverwort Radula lindenbergiana. Vegetative plants of R.lindenbergiana were found to contain a mixture of sesquiterpenes, with (E,E)-α-farnesene/β-curcumene and (Z)-β-bisabolene being the most abundant constituents. From the analysis of the R. lindenbergiana transcriptome, five full-length MTPSL genes were identified. They were designated RlMTPSL1-5, respectively. Recombinant RlMTPSL proteins were produced in Escherichia coli and tested for sesquiterpene synthase activities using farnesyl diphosphate (FPP) as substrate. All except RlMTPSL5 were demonstrated to catalyze the formation of different sesquiterpenes. RlMTPSL1 produced multiple sesquiterpenes with eremophilene and an unidentified sesquiterpene as major products. The major products of RlMTPSL2 and RlMTPSL3 were β-elemene and an unidentified sesquiterpene, respectively. RlMTPSL4 was also a multi-product sesquiterpene synthase with an unidentified sesquiterpene being the major product. Homology-based structural modeling was performed to understand the structural basis underlying different product profiles of the RlMTPSLs proteins. Most of the sesquiterpene products of the four active RlMTPSLs were also detected in R. lindenbergiana plants. Expression levels of the four RlMTPSL genes encoding active enzymes in vegetative plants were compared. In phylogenetic analysis, RlMTPSL genes were found to cluster together, indicating lineage-specific expansion of MTPSL genes in lineages leading to R.lindenbergiana and M. polymorpha. This study strengthens evidence for the contribution of MTPSL genes to terpenoid biosynthesis in liverworts.
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Affiliation(s)
- Honghong Fan
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA; School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Guo Wei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Tobias G Köllner
- Department of Biochemistry, Max-Planck-Institute for Chemical Ecology, Hans-Knöll Str. 8, D-07745, Jena, Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
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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.
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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
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Scandiffio R, Geddo F, Cottone E, Querio G, Antoniotti S, Gallo MP, Maffei ME, Bovolin P. Protective Effects of ( E)-β-Caryophyllene (BCP) in Chronic Inflammation. Nutrients 2020; 12:nu12113273. [PMID: 33114564 PMCID: PMC7692661 DOI: 10.3390/nu12113273] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
(E)-β-caryophyllene (BCP) is a bicyclic sesquiterpene widely distributed in the plant kingdom, where it contributes a unique aroma to essential oils and has a pivotal role in the survival and evolution of higher plants. Recent studies provided evidence for protective roles of BCP in animal cells, highlighting its possible use as a novel therapeutic tool. Experimental results show the ability of BCP to reduce pro-inflammatory mediators such as tumor necrosis factor-alfa (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), thus ameliorating chronic pathologies characterized by inflammation and oxidative stress, in particular metabolic and neurological diseases. Through the binding to CB2 cannabinoid receptors and the interaction with members of the family of peroxisome proliferator-activated receptors (PPARs), BCP shows beneficial effects on obesity, non-alcoholic fatty liver disease/nonalcoholic steatohepatitis (NAFLD/NASH) liver diseases, diabetes, cardiovascular diseases, pain and other nervous system disorders. This review describes the current knowledge on the biosynthesis and natural sources of BCP, and reviews its role and mechanisms of action in different inflammation-related metabolic and neurologic disorders.
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Affiliation(s)
- Rosaria Scandiffio
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.S.); (F.G.); (E.C.); (G.Q.); (S.A.); (M.P.G.)
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Via Quarello 15/a, 10135 Turin, Italy;
| | - Federica Geddo
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.S.); (F.G.); (E.C.); (G.Q.); (S.A.); (M.P.G.)
| | - Erika Cottone
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.S.); (F.G.); (E.C.); (G.Q.); (S.A.); (M.P.G.)
| | - Giulia Querio
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.S.); (F.G.); (E.C.); (G.Q.); (S.A.); (M.P.G.)
| | - Susanna Antoniotti
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.S.); (F.G.); (E.C.); (G.Q.); (S.A.); (M.P.G.)
| | - Maria Pia Gallo
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.S.); (F.G.); (E.C.); (G.Q.); (S.A.); (M.P.G.)
| | - Massimo E. Maffei
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Via Quarello 15/a, 10135 Turin, Italy;
| | - Patrizia Bovolin
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.S.); (F.G.); (E.C.); (G.Q.); (S.A.); (M.P.G.)
- Correspondence:
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12
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Evolution of isoprenyl diphosphate synthase-like terpene synthases in fungi. Sci Rep 2020; 10:14944. [PMID: 32913319 PMCID: PMC7484799 DOI: 10.1038/s41598-020-71219-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/27/2020] [Indexed: 01/21/2023] Open
Abstract
Terpene synthases (TPSs) and trans-isoprenyl diphosphate synthases (IDSs) are among the core enzymes for creating the enormous diversity of terpenoids. Despite having no sequence homology, TPSs and IDSs share a conserved “α terpenoid synthase fold” and a trinuclear metal cluster for catalysis, implying a common ancestry with TPSs hypothesized to evolve from IDSs anciently. Here we report on the identification and functional characterization of novel IDS-like TPSs (ILTPSs) in fungi that evolved from IDS relatively recently, indicating recurrent evolution of TPSs from IDSs. Through large-scale bioinformatic analyses of fungal IDSs, putative ILTPSs that belong to the geranylgeranyl diphosphate synthase (GGDPS) family of IDSs were identified in three species of Melampsora. Among the GGDPS family of the two Melampsora species experimentally characterized, one enzyme was verified to be bona fide GGDPS and all others were demonstrated to function as TPSs. Melampsora ILTPSs displayed kinetic parameters similar to those of classic TPSs. Key residues underlying the determination of GGDPS versus ILTPS activity and functional divergence of ILTPSs were identified. Phylogenetic analysis implies a recent origination of these ILTPSs from a GGDPS progenitor in fungi, after the split of Melampsora from other genera within the class of Pucciniomycetes. For the poplar leaf rust fungus Melampsora larici-populina, the transcripts of its ILTPS genes were detected in infected poplar leaves, suggesting possible involvement of these recently evolved ILTPS genes in the infection process. This study reveals the recurrent evolution of TPSs from IDSs since their ancient occurrence and points to the possibility of a wide distribution of ILTPS genes in three domains of life.
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Luck K, Chen X, Norris AM, Chen F, Gershenzon J, Köllner TG. The reconstruction and biochemical characterization of ancestral genes furnish insights into the evolution of terpene synthase function in the Poaceae. PLANT MOLECULAR BIOLOGY 2020; 104:203-215. [PMID: 32683610 PMCID: PMC7417412 DOI: 10.1007/s11103-020-01037-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/12/2020] [Indexed: 05/05/2023]
Abstract
Distinct catalytic features of the Poaceae TPS-a subfamily arose early in grass evolution and the reactions catalyzed have become more complex with time. The structural diversity of terpenes found in nature is mainly determined by terpene synthases (TPS). TPS enzymes accept ubiquitous prenyl diphosphates as substrates and convert them into the various terpene skeletons by catalyzing a carbocation-driven reaction. Based on their sequence similarity, terpene synthases from land plants can be divided into different subfamilies, TPS-a to TPS-h. In this study, we aimed to understand the evolution and functional diversification of the TPS-a subfamily in the Poaceae (the grass family), a plant family that contains important crops such as maize, wheat, rice, and sorghum. Sequence comparisons showed that aside from one clade shared with other monocot plants, the Poaceae TPS-a subfamily consists of five well-defined clades I-V, the common ancestor of which probably originated very early in the evolution of the grasses. A survey of the TPS literature and the characterization of representative TPS enzymes from clades I-III revealed clade-specific substrate and product specificities. The enzymes in both clade I and II function as sesquiterpene synthases with clade I enzymes catalyzing initial C10-C1 or C11-C1 ring closures and clade II enzymes catalyzing C6-C1 closures. The enzymes of clade III mainly act as monoterpene synthases, forming cyclic and acyclic monoterpenes. The reconstruction and characterization of clade ancestors demonstrated that the differences among clades I-III were already present in their ancestors. However, the ancestors generally catalyzed simpler reactions with less double-bond isomerization and fewer cyclization steps. Overall, our data indicate an early origin of key enzymatic features of TPS-a enzymes in the Poaceae, and the development of more complex reactions over the course of evolution.
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Affiliation(s)
- Katrin Luck
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll Straße 8, 07745 Jena, Germany
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Ayla M. Norris
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll Straße 8, 07745 Jena, Germany
| | - Tobias G. Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll Straße 8, 07745 Jena, Germany
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Nagegowda DA, Gupta P. Advances in biosynthesis, regulation, and metabolic engineering of plant specialized terpenoids. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110457. [PMID: 32234216 DOI: 10.1016/j.plantsci.2020.110457] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/18/2020] [Accepted: 02/22/2020] [Indexed: 05/28/2023]
Abstract
Plant specialized terpenoids are natural products that have no obvious role in growth and development, but play many important functional roles to improve the plant's overall fitness. Besides, plant specialized terpenoids have immense value to humans due to their applications in fragrance, flavor, cosmetic, and biofuel industries. Understanding the fundamental aspects involved in the biosynthesis and regulation of these high-value molecules in plants not only paves the path to enhance plant traits, but also facilitates homologous or heterologous engineering for overproduction of target molecules of importance. Recent developments in functional genomics and high-throughput analytical techniques have led to unraveling of several novel aspects involved in the biosynthesis and regulation of plant specialized terpenoids. The knowledge thus derived has been successfully utilized to produce target specialized terpenoids of plant origin in homologous or heterologous host systems by metabolic engineering and synthetic biology approaches. Here, we provide an overview and highlights on advances related to the biosynthetic steps, regulation, and metabolic engineering of plant specialized terpenoids.
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Affiliation(s)
- Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
| | - Priyanka Gupta
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
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15
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Zhang K, Jiang Y, Zhao H, Köllner TG, Chen S, Chen F, Chen F. Diverse Terpenoids and Their Associated Antifungal Properties from Roots of Different Cultivars of Chrysanthemum Morifolium Ramat. Molecules 2020; 25:molecules25092083. [PMID: 32365690 PMCID: PMC7248984 DOI: 10.3390/molecules25092083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/18/2020] [Accepted: 04/23/2020] [Indexed: 12/05/2022] Open
Abstract
Roots provide anchorage and enable the absorption of water and micronutrients from the soil for plants. Besides these essential functions, roots are increasingly being recognized as an important organ for the production of diverse secondary metabolites. The goal of this study was to investigate the chemical composition and function of terpenoid secondary metabolites in roots of different cultivars of the popular ornamental plant Chrysanthemum morifolium Ramat. Although C. morifolium is known for rich production of secondary metabolites in its flower heads and leaves, the diversity of secondary metabolites in roots remains poorly characterized. In this study, 12 cultivars of C. morifolium were selected for comparative analysis. From their roots, a total of 20 terpenoids were detected, including four monoterpenes, 15 sesquiterpenes, and one diterpene. The cultivar ‘She Yang Hong Xin Ju’ exhibited the highest concentration of total terpenoids at approximately 730 µg·g−1 fresh weight. Most cultivars contained sesquiterpenes as the predominant terpenoids. Of them, (E)-β-farnesene was detected in all cultivars. Based on their terpenoid composition, the 12 cultivars were planed into four groups. To gain insights into the function of root secondary metabolites, we performed bioassays to assess their effects on growth of three species of pathogenic fungi: Fusarium oxysporum, Magnaporthe oryzae, and Verticillium dahliae. Significant variability in antifungal activity of the root extracts among different cultivars were observed. The cultivar ‘Xiao Huang Ju’ was the only cultivar that had significant inhibitory effects on all three species of fungi. Our study reveals the diversity of terpenoids in roots of C. morifolium and their function as a chemical defense against fungi.
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Affiliation(s)
- Kaige Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (K.Z.); (S.C.); (F.C.)
| | - Yifan Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (K.Z.); (S.C.); (F.C.)
- Correspondence: (Y.J.); (F.C.); Tel.: +86-25-8439-5262 (Y.J.); +1-865-974-8521 (F.C.)
| | - Hongwei Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Tobias G. Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll Str. 8, 07745 Jena, Germany;
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (K.Z.); (S.C.); (F.C.)
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (K.Z.); (S.C.); (F.C.)
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (Y.J.); (F.C.); Tel.: +86-25-8439-5262 (Y.J.); +1-865-974-8521 (F.C.)
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16
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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17
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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.
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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
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18
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Abstract
Plants produce a diverse portfolio of sesquiterpenes that are important in their response to herbivores and the interaction with other plants. Their biosynthesis from farnesyl diphosphate depends on the sesquiterpene synthases that admit different cyclizations and rearrangements to yield a blend of sesquiterpenes. Here, we investigate to what extent sesquiterpene biosynthesis metabolic pathways can be reconstructed just from the knowledge of the final product and the reaction mechanisms catalyzed by sesquiterpene synthases. We use the software package MedØlDatschgerl (MØD) to generate chemical networks and to elucidate pathways contained in them. As examples, we successfully consider the reachability of the important plant sesquiterpenes β -caryophyllene, α -humulene, and β -farnesene. We also introduce a graph database to integrate the simulation results with experimental biological evidence for the selected predicted sesquiterpenes biosynthesis.
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Zhang X, Niu M, Teixeira da Silva JA, Zhang Y, Yuan Y, Jia Y, Xiao Y, Li Y, Fang L, Zeng S, Ma G. Identification and functional characterization of three new terpene synthase genes involved in chemical defense and abiotic stresses in Santalum album. BMC PLANT BIOLOGY 2019; 19:115. [PMID: 30922222 PMCID: PMC6437863 DOI: 10.1186/s12870-019-1720-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/14/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND It is well known that aromatic essential oils extracted from the heartwood of Santalum album L. have wide economic value. However, little is known about the role of terpenoids in response to various adverse environmental stresses as other plants do in the form of signals during plant-environment interactions. RESULTS In this study, trace amounts of volatiles consisting of α-santalene, epi-β-santalene, β-santalene, α-santalol, β-santalol, (E)-α-bergamotene, (E)-β-farnesene and β-bisabolene were found in the leaves of mature S. album trees. We identified more than 40 candidate terpene synthase (TPS) unigenes by mining publicly-available RNA-seq data and characterized the enzymes encoded by three cDNAs: one mono-TPS catalyzes the formation of mostly α-terpineol, and two multifunctional sesqui-TPSs, one of which produces (E)-α-bergamotene and sesquisabinene as major products and another which catalyzes the formation of (E)-β-farnesene, (E)-nerolidol and (E,E)-farnesol as main products. Metabolite signatures and gene expression studies confirmed that santalol content is closely related with santalene synthase (SaSSY) transcripts in heartwood, which is key enzyme responsible for santalol biosynthesis. However, the expression of three new SaTPS genes differed significantly from SaSSY in the essential oil-producing heartwood. Increased activities of antioxidant enzymes, superoxide dismutase, catalase, peroxidase and ascorbate peroxidase, were detected in different tissues of S. album plants after applying 1 mM methyl jasmonate (MeJA) and 1 mM salicylic acid (SA), or exposure to 4°C, 38°C and high light intensity. MeJA and SA dramatically induced the expression of SaTPS1 and SaTPS2 in leaves. SaTPS1 to 3 transcripts were differentially activated among different tissues under adverse temperature and light stresses. In contrast, almost all SaSSY transcripts decreased in response to these environmental stresses, unlike SaTPS1 to 3. CONCLUSIONS Multifunctional enzymes were biochemically characterized, including one chloroplastic mono-TPS and two cytosolic sesqui-TPSs in sandalwood. Our results suggest the ecological importance of these three new SaTPS genes in defensive response to biotic attack and abiotic stresses in S. album.
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Affiliation(s)
- Xinhua Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Meiyun Niu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | | | - Yueya Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yunfei Yuan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yongxia Jia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yangyang Xiao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yuan Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Lin Fang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Songjun Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Guohua Ma
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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20
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Wei G, Jia Q, Chen X, Köllner TG, Bhattacharya D, Wong GKS, Gershenzon J, Chen F. Terpene Biosynthesis in Red Algae Is Catalyzed by Microbial Type But Not Typical Plant Terpene Synthases. PLANT PHYSIOLOGY 2019; 179:382-390. [PMID: 30538166 PMCID: PMC6426406 DOI: 10.1104/pp.18.01413] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 11/30/2018] [Indexed: 05/27/2023]
Abstract
Red algae (Rhodophyta) and land plants belong to the monophyletic clade Archaeplastida, and taxa of both groups are rich producers of terpene secondary metabolites. The terpene carbon skeletons of land plants are made by two types of terpene synthases: typical plant terpene synthases and microbial-type terpene synthases (MTPSLs); however, terpene biosynthesis in red algae is poorly understood. By systematic sequence analysis of seven genomes and 34 transcriptomes of red algae, MTPSL homologs were identified within one genome and two transcriptomes, whereas no homolog of typical plant terpene synthase genes was found. Phylogenetic analysis showed that red algae MTPSLs group with bacterial terpene synthases. Analysis of the genome assembly and characterization of neighboring genes demonstrated red algal MTPSLs to be bona fide red algal genes and not microbial contaminants. MTPSL genes from Porphyridium purpureum and Erythrolobus australicus were characterized via heterologous expression in Escherichia coli and demonstrated to have sesquiterpene synthase activities. We detected a number of volatile sesquiterpenes in the headspace of P. purpureum and E. australicus cultures, most identical to the in vitro products of the respective MTPSLs. Expression of the MTPSL gene in P. purpureum was found to be induced by methyl jasmonate, suggesting a role for this gene in host defense. In summary, this study indicates that the formation of terpene carbon skeletons in red algae is carried out by MTPSLs that are phylogenetically unrelated to typical plant terpene synthases and most likely originated in Rhodophyta via horizontal gene transfer from bacteria.
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Affiliation(s)
- Guo Wei
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Qidong Jia
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996
| | - Xinlu 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
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2E1
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996
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21
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Muchlinski A, Chen X, Lovell JT, Köllner TG, Pelot KA, Zerbe P, Ruggiero M, Callaway L, Laliberte S, Chen F, Tholl D. Biosynthesis and Emission of Stress-Induced Volatile Terpenes in Roots and Leaves of Switchgrass ( Panicum virgatum L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1144. [PMID: 31608090 PMCID: PMC6761604 DOI: 10.3389/fpls.2019.01144] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/21/2019] [Indexed: 05/18/2023]
Abstract
Switchgrass (Panicum virgatum L.), a perennial C4 grass, represents an important species in natural and anthropogenic grasslands of North America. Its resilience to abiotic and biotic stress has made switchgrass a preferred bioenergy crop. However, little is known about the mechanisms of resistance of switchgrass against pathogens and herbivores. Volatile compounds such as terpenes have important activities in plant direct and indirect defense. Here, we show that switchgrass leaves emit blends of monoterpenes and sesquiterpenes upon feeding by the generalist insect herbivore Spodoptera frugiperda (fall armyworm) and in a systemic response to the treatment of roots with defense hormones. Belowground application of methyl jasmonate also induced the release of volatile terpenes from roots. To correlate the emission of terpenes with the expression and activity of their corresponding biosynthetic genes, we identified a gene family of 44 monoterpene and sesquiterpene synthases (mono- and sesqui-TPSs) of the type-a, type-b, type-g, and type-e subfamilies, of which 32 TPSs were found to be functionally active in vitro. The TPS genes are distributed over the K and N subgenomes with clusters occurring on several chromosomes. Synteny analysis revealed syntenic networks for approximately 30-40% of the switchgrass TPS genes in the genomes of Panicum hallii, Setaria italica, and Sorghum bicolor, suggesting shared TPS ancestry in the common progenitor of these grass lineages. Eighteen switchgrass TPS genes were substantially induced upon insect and hormone treatment and the enzymatic products of nine of these genes correlated with compounds of the induced volatile blends. In accordance with the emission of volatiles, TPS gene expression was induced systemically in response to belowground treatment, whereas this response was not observed upon aboveground feeding of S. frugiperda. Our results demonstrate complex above and belowground responses of induced volatile terpene metabolism in switchgrass and provide a framework for more detailed investigations of the function of terpenes in stress resistance in this monocot crop.
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Affiliation(s)
- Andrew Muchlinski
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - John T. Lovell
- Genome Sequencing Center, Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Tobias G. Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Kyle A. Pelot
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Philipp Zerbe
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Meredith Ruggiero
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - LeMar Callaway
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Suzanne Laliberte
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- *Correspondence: Feng Chen, ; Dorothea Tholl,
| | - Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: Feng Chen, ; Dorothea Tholl,
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Shen F, Wu X, Shi L, Zhang H, Chen Y, Qi X, Wang Z, Li X. Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development. BMC SYSTEMS BIOLOGY 2018; 12:47. [PMID: 29745852 PMCID: PMC5998905 DOI: 10.1186/s12918-018-0574-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Rice (Oryza sativa) is one of the most important grain crops, which serves as food source for nearly half of the world population. The study of rice development process as well as related strategies for production has made significant progress. However, the comprehensive study on development of different rice tissues at both transcriptomic and metabolic flux level across different stages was lacked. RESULTS In this study, we performed RNA-Seq and characterized the expression profiles of differentiated tissues from Oryza sativa Zhonghua 11, including leaves, sheath, stamen, pistil, lemma and palea of the booting stage, and embryo, endosperm, lemma and palea of the mature grain stage. By integrating this set of transcriptome data of different rice tissues at different stages with a genome-scale rice metabolic model, we generated tissue-specific models and investigated the shift of metabolic patterns, and the discrepancy between transcriptomic and metabolic level. We found although the flux patterns are not very similar with the gene expression pattern, the tissues at booting stage and mature grain stage can be separately clustered by primary metabolism at either level. While the gene expression and flux distribution of secondary metabolism is more diverse across tissues and stages. The critical rate-limiting reactions and pathways were also identified. In addition, we compared the patterns of the same tissue at different stages and the different tissues at same stage. There are more altered pathways at gene expression level than metabolic level, which indicate the metabolism is more robust to reflect the phenotype, and might largely because of the complex post-transcriptional modification. CONCLUSIONS The tissue-specific models revealed more detail metabolic pattern shift among different tissues and stages, which is of great significance to uncover mechanism of rice grain development and further improve production and quality of rice.
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Affiliation(s)
- Fangzhou Shen
- Bio-X Institutes, Key laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Xueting Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People's Republic of China
| | - Luoxi Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.,Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, 55455, USA
| | - Hang Zhang
- Bio-X Institutes, Key laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yangmin Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiaoquan Qi
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Zhuo Wang
- Bio-X Institutes, Key laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China. .,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People's Republic of China.
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Genome-wide identification, functional and evolutionary analysis of terpene synthases in pineapple. Comput Biol Chem 2017; 70:40-48. [DOI: 10.1016/j.compbiolchem.2017.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/19/2017] [Accepted: 05/24/2017] [Indexed: 12/22/2022]
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24
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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25
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Wang X, Zhou C, Yang X, Miao D, Zhang Y. De Novo Transcriptome Analysis of Warburgia ugandensis to Identify Genes Involved in Terpenoids and Unsaturated Fatty Acids Biosynthesis. PLoS One 2015; 10:e0135724. [PMID: 26305373 PMCID: PMC4549110 DOI: 10.1371/journal.pone.0135724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/24/2015] [Indexed: 12/24/2022] Open
Abstract
The bark of Warburgia ugandensis (Canellaceae family) has been used as a medicinal source for a long history in many African countries. The presence of diverse terpenoids and abundant polyunsaturated fatty acids (PUFAs) in this organ contributes to its broad range of pharmacological properties. Despite its medicinal and economic importance, the knowledge on the biosynthesis of terpenoid and unsaturated fatty acid in W. ugandensis bark remains largely unknown. Therefore, it is necessary to construct a genomic and/or transcriptomic database for the functional genomics study on W. ugandensis. The chemical profiles of terpenoids and fatty acids between the bark and leaves of W. ugandensis were compared by gas chromatography-mass spectrometry (GC-MS) analysis. Meanwhile, the transcriptome database derived from both tissues was created using Illumina sequencing technology. In total, about 17.1 G clean nucleotides were obtained, and de novo assembled into 72,591 unigenes, of which about 38.06% can be aligned to the NCBI non-redundant protein database. Many candidate genes in the biosynthetic pathways of terpenoids and unsaturated fatty acids were identified, including 14 unigenes for terpene synthases. Furthermore, 2,324 unigenes were discovered to be differentially expressed between both tissues; the functions of those differentially expressed genes (DEGs) were predicted by gene ontology enrichment and metabolic pathway enrichment analyses. In addition, the expression of 12 DEGs with putative roles in terpenoid and unsaturated fatty acid metabolic pathways was confirmed by qRT-PCRs, which was consistent with the data of the RNA-sequencing. In conclusion, we constructed a comprehensive transcriptome dataset derived from the bark and leaf of W. ugandensis, which forms the basis for functional genomics studies on this plant species. Particularly, the comparative analysis of the transcriptome data between the bark and leaf will provide critical clues to reveal the regulatory mechanisms underlying the biosynthesis of terpenoids and PUFAs in W. ugandensis.
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Affiliation(s)
- Xin Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chen Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xianpeng Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Di Miao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yansheng Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail:
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26
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The Origin and Evolution of Baeyer-Villiger Monooxygenases (BVMOs): An Ancestral Family of Flavin Monooxygenases. PLoS One 2015; 10:e0132689. [PMID: 26161776 PMCID: PMC4498894 DOI: 10.1371/journal.pone.0132689] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/18/2015] [Indexed: 12/13/2022] Open
Abstract
The Baeyer-Villiger Monooxygenases (BVMOs) are enzymes belonging to the "Class B" of flavin monooxygenases and are capable of performing exquisite selective oxidations. These enzymes have been studied from a biotechnological perspective, but their physiological substrates and functional roles are widely unknown. Here, we investigated the origin, taxonomic distribution and evolutionary history of the BVMO genes. By using in silico approaches, 98 BVMO encoding genes were detected in the three domains of life: Archaea, Bacteria and Eukarya. We found evidence for the presence of these genes in Metazoa (Hydra vulgaris, Oikopleura dioica and Adineta vaga) and Haptophyta (Emiliania huxleyi) for the first time. Furthermore, a search for other "Class B" monooxygenases (flavoprotein monooxygenases--FMOs--and N-hydroxylating monooxygenases--NMOs) was conducted. These sequences were also found in the three domains of life. Phylogenetic analyses of all "Class B" monooxygenases revealed that NMOs and BVMOs are monophyletic, whereas FMOs form a paraphyletic group. Based on these results, we propose that BVMO genes were already present in the last universal common ancestor (LUCA) and their current taxonomic distribution is the result of differential duplication and loss of paralogous genes.
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