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Foresi N, De Marco MA, Del Castello F, Ramirez L, Nejamkin A, Calo G, Grimsley N, Correa-Aragunde N, Martínez-Noël GMA. The tiny giant of the sea, Ostreococcus's unique adaptations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108661. [PMID: 38735153 DOI: 10.1016/j.plaphy.2024.108661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.
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Affiliation(s)
- Noelia Foresi
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina.
| | - María Agustina De Marco
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | | | - Leonor Ramirez
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Andres Nejamkin
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina
| | - Gonzalo Calo
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | - Nigel Grimsley
- CNRS, LBBM, Sorbonne Université OOB, 1 Avenue de Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | | | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina.
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2
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Lu J, Yan S, Xue Z. Biosynthesis and functions of triterpenoids in cereals. J Adv Res 2024:S2090-1232(24)00211-X. [PMID: 38788922 DOI: 10.1016/j.jare.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/03/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Triterpenoids are versatile secondary metabolites with a diverse array of physiological activities, possessing valuable pharmacological effects and influencing the growth and development of plants. As more triterpenoids in cereals are unearthed and characterized, their biological roles in plant growth and development are gaining recognition. AIM OF THE REVIEW This review provides an overview of the structures, biosynthetic pathways, and diverse biological functions of triterpenoids identified in cereals. Our goal is to establish a basis for further exploration of triterpenoids with novel structures and functional activities in cereals, and to facilitate the potential application of triterpenoids in grain breeding, thus accelerating the development of superior grain varieties. KEY SCIENTIFIC CONCEPTS OF THE REVIEW This review consolidates information on various triterpenoid skeletons and derivatives found in cereals, and summarizes the pivotal enzyme genes involved, including oxidosqualene cyclase (OSC) and other triterpenoid modifying enzymes like cytochrome P450, glycosyltransferase, and acyltransferase. Triterpenoid-modifying enzymes exhibit specificity towards catalytic sites within triterpenoid skeletons, generating a diverse array of functional triterpenoid derivatives. Furthermore, triterpenoids have been shown to significantly impact the nutritional value, yield, disease resistance, and stress response of cereals.
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Affiliation(s)
- Jiaojiao Lu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, China
| | - Shan Yan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, China
| | - Zheyong Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, China; State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
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3
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Liu J, Yin X, Kou C, Thimmappa R, Hua X, Xue Z. Classification, biosynthesis, and biological functions of triterpene esters in plants. PLANT COMMUNICATIONS 2024; 5:100845. [PMID: 38356259 PMCID: PMC11009366 DOI: 10.1016/j.xplc.2024.100845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/12/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Triterpene esters comprise a class of secondary metabolites that are synthesized by decorating triterpene skeletons with a series of oxidation, glycosylation, and acylation modifications. Many triterpene esters with important bioactivities have been isolated and identified, including those with applications in the pesticide, pharmaceutical, and cosmetic industries. They also play essential roles in plant defense against pests, diseases, physical damage (as part of the cuticle), and regulation of root microorganisms. However, there has been no recent summary of the biosynthetic pathways and biological functions of plant triterpene esters. Here, we classify triterpene esters into five categories based on their skeletons and find that C-3 oxidation may have a significant effect on triterpenoid acylation. Fatty acid and aromatic moieties are common ligands present in triterpene esters. We further analyze triterpene ester synthesis-related acyltransferases (TEsACTs) in the triterpene biosynthetic pathway. Using an evolutionary classification of BAHD acyltransferases (BAHD-ATs) and serine carboxypeptidase-like acyltransferases (SCPL-ATs) in Arabidopsis thaliana and Oryza sativa, we classify 18 TEsACTs with identified functions from 11 species. All the triterpene-skeleton-related TEsACTs belong to BAHD-AT clades IIIa and I, and the only identified TEsACT from the SCPL-AT family belongs to the CP-I subfamily. This comprehensive review of the biosynthetic pathways and bioactivities of triterpene esters provides a foundation for further study of their bioactivities and applications in industry, agricultural production, and human health.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Xue Yin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Chengxi Kou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Ramesha Thimmappa
- Amity Institute of Genome Engineering, Amity University, Noida, UP India 201313, India
| | - Xin Hua
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Zheyong Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, P.R. China.
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4
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Dinday S, Ghosh S. Recent advances in triterpenoid pathway elucidation and engineering. Biotechnol Adv 2023; 68:108214. [PMID: 37478981 DOI: 10.1016/j.biotechadv.2023.108214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.
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Affiliation(s)
- Sandeep Dinday
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, Punjab, India
| | - Sumit Ghosh
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India.
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5
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Pu X, Chen M, Lei M, Lin X, Zhang J, Ai Z, He J, Liu Y, Yang S, Wang H, Liao J, Zhang L, Huang Q. Discovery of unique CYP716C oxidase involved in pentacyclic triterpene biosynthesis from Camptotheca acuminata. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107929. [PMID: 37542826 DOI: 10.1016/j.plaphy.2023.107929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
Dozens of triterpenes have been isolated from Camptotheca acuminata, however, triterpene metabolism in this plant remains poorly understood. The common C28 carboxy located in the oleanane-type and ursane-type triterpenes indicates the existence of a functionally active triterpene, C28 oxidase, in this plant. Thorough mining and screening of the CYP716 genes were initiated using the multi-omics database for C. acuminata. Two CYP716A (CYP716A394 and CYP716A395) and three CYP716C (CYP716C80-CYP716C82) were identified based on conserved domain analyses and hierarchical cluster analyses. CYP716 microsomal proteins were prepared and their enzymatic activities were evaluated in vitro. The CYP716 classified into the CYP716C subfamily displays β-amyrin oxidation activity, and CYP716A displays α-amyrin and lupeol oxidation activity, based on gas chromatography-mass spectrometry analyses. The oxidation products were determined based on their mass and nuclear magnetic resonance spectrums. The optimum reaction conditions and kinetic parameters for CYP716C were determined, and functions were verified in Nicotiana benthaminana. Relative quantitative analyses revealed that these CYP716C genes were enriched in the leaves of C. acuminata plantlets after 60 d. These results indicate that CYP716C plays a dominant role in oleanane-type triterpene metabolism in the leaves of C. acuminata via a substrate-specific manner, and CYP716A is responsible for ursane- and lupane-type triterpene metabolism in fruit. This study provides valuable insights into the unique CYP716C-mediated oxidation step of pentacyclic triterpene biosynthesis in C. acuminata.
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Affiliation(s)
- Xiang Pu
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China.
| | - Menghan Chen
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Ming Lei
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Xinyu Lin
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Jiahua Zhang
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Zhihui Ai
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Jinwei He
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Yuke Liu
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Shengnan Yang
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Hanguang Wang
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Jinqiu Liao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Li Zhang
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China
| | - Qianming Huang
- College of Science, Sichuan Agricultural University, Ya'an, 625104, PR China.
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6
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Wang D, Yu Z, Guan M, Cai Q, Wei J, Ma P, Xue Z, Ma R, Oksman-Caldentey KM, Rischer H. Comparative transcriptome analysis of Veratrum maackii and Veratrum nigrum reveals multiple candidate genes involved in steroidal alkaloid biosynthesis. Sci Rep 2023; 13:8198. [PMID: 37211560 DOI: 10.1038/s41598-023-35429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023] Open
Abstract
Veratrum (Melanthiaceae; Liliales) is a genus of perennial herbs known for the production of unique bioactive steroidal alkaloids. However, the biosynthesis of these compounds is incompletely understood because many of the downstream enzymatic steps have yet to be resolved. RNA-Seq is a powerful method that can be used to identify candidate genes involved in metabolic pathways by comparing the transcriptomes of metabolically active tissues to controls lacking the pathway of interest. The root and leaf transcriptomes of wild Veratrum maackii and Veratrum nigrum plants were sequenced and 437,820 clean reads were assembled into 203,912 unigenes, 47.67% of which were annotated. We identified 235 differentially expressed unigenes potentially involved in the synthesis of steroidal alkaloids. Twenty unigenes, including new candidate cytochrome P450 monooxygenases and transcription factors, were selected for validation by quantitative real-time PCR. Most candidate genes were expressed at higher levels in roots than leaves but showed a consistent profile across both species. Among the 20 unigenes putatively involved in the synthesis of steroidal alkaloids, 14 were already known. We identified three new CYP450 candidates (CYP76A2, CYP76B6 and CYP76AH1) and three new transcription factor candidates (ERF1A, bHLH13 and bHLH66). We propose that ERF1A, CYP90G1-1 and CYP76AH1 are specifically involved in the key steps of steroidal alkaloid biosynthesis in V. maackii roots. Our data represent the first cross-species analysis of steroidal alkaloid biosynthesis in the genus Veratrum and indicate that the metabolic properties of V. maackii and V. nigrum are broadly conserved despite their distinct alkaloid profiles.
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Affiliation(s)
- Dan Wang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
- College of Agricultural Sciences, Yanbian University, Yanji, 133000, Jilin Province, People's Republic of China
| | - Zhijing Yu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Meng Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin, People's Republic of China
| | - Qinan Cai
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Jia Wei
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Pengda Ma
- College of Life Sciences, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Zheyong Xue
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin, People's Republic of China
| | - Rui Ma
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China.
| | | | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd., P. O. Box 1000, 02044 VTT, Espoo, Finland.
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7
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Wang L, Fu J, Shen Q, Wang Q. OsWRKY10 extensively activates multiple rice diterpenoid phytoalexin biosynthesis to enhance rice blast resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37186469 DOI: 10.1111/tpj.16259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/14/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023]
Abstract
Phytoalexin is the main chemical weapon against disease pathogens in plants. Rice produces a number of phytoalexins to defend pathogens, most of which belong to diterpenoid phytoalexins. Three biosynthetic gene clusters (BGCs) and a few non-cluster genes are responsible for rice diterpenoid phytoalexin biosynthesis. The corresponding regulatory mechanism of these phytoalexins in response to pathogen challenges still remains unclear. Here we identified a transcription factor, OsWRKY10, positively regulating rice diterpenoid phytoalexin biosynthesis. Knockout mutants of OsWRKY10 obtained by the CRISPR/Cas9 technology are more susceptible to Magnaporthe oryzae infection, while overexpression of OsWRKY10 enhances resistance to rice blast. Further analysis reveals that overexpression of OsWRKY10 increases accumulation of multiple rice diterpenoid phytoalexins and expression of genes in three BGCs and non-clustered genes in response to M. oryzae infection. Knockout of OsWRKY10 impairs upregulation of rice diterpenoid phytoalexin biosynthesis gene expression by blast pathogen and CuCl2 treatment. OsWRKY10 directly binds to the W-boxes or W-box-like elements (WLEs) of rice diterpenoid phytoalexin biosynthesis gene promoters to regulate the corresponding gene expression. This study identified an extensive regulator (OsWRKY10) with the broad transcriptional regulation on rice diterpenoid phytoalexin biosynthesis, providing the insight to characterize regulation of rice chemical defense for improving disease resistance.
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Affiliation(s)
- Liping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingye Fu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinqin Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
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8
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Chubatsu Nunes HH, Dang TTT. A booster for vaccines from plants. Science 2023; 379:1187-1188. [PMID: 36952422 DOI: 10.1126/science.adg8823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Reconstituting a plant biosynthetic pathway enables a sustainable supply of vaccine adjuvants.
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Affiliation(s)
- Helena H Chubatsu Nunes
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Thu-Thuy T Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
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9
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Bryson AE, Lanier ER, Lau KH, Hamilton JP, Vaillancourt B, Mathieu D, Yocca AE, Miller GP, Edger PP, Buell CR, Hamberger B. Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory. Nat Commun 2023; 14:343. [PMID: 36670101 PMCID: PMC9860074 DOI: 10.1038/s41467-023-35845-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions. Here, we report the genome assemblies of Prunella vulgaris, Plectranthus barbatus, and Leonotis leonurus. We investigate the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) together with other seven species within the Lamiaceae (mint) family. Based on core genes found in the BGCs of all species examined across the Lamiaceae, we predict a simplified version of this cluster evolved in an early Lamiaceae ancestor. The current composition of the extant BGCs highlights the dynamic nature of its evolution. We elucidate the terpene backbones generated by the Callicarpa americana BGC enzymes, including miltiradiene and the terpene (+)-kaurene, and show oxidization activities of BGC cytochrome P450s. Our work reveals the fluid nature of BGC assembly and the importance of genome structure in contributing to the origin of metabolites.
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Affiliation(s)
- Abigail E Bryson
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Emily R Lanier
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Kin H Lau
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Davis Mathieu
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Alan E Yocca
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Garret P Miller
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Björn Hamberger
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA.
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10
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Zhao Y, Yao S, Zhang X, Wang Z, Jiang C, Liu Y, Jiang X, Gao L, Xia T. Flavan-3-ol Galloylation-Related Functional Gene Cluster and the Functional Diversification of SCPL Paralogs in Camellia sp. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:488-498. [PMID: 36562642 DOI: 10.1021/acs.jafc.2c06433] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The high accumulation of galloylated flavan-3-ols in Camellia sp. is a noteworthy phenomenon. We identified a flavan-3-ol galloylation-related functional gene cluster in tannin-rich plant Camellia sp., which included UGT84A22 and SCPL-AT gene clusters. We investigated the possible correlation between the accumulation of metabolites and the expression of SCPL-ATs and UGT84A22. The results revealed that C. sinensis, C. ptilophylla, and C. oleifera accumulated galloylated cis-flavan-3-ols (EGCG), galloylated trans-flavan-3-ols (GCG), and hydrolyzed tannins, respectively; however, C. nitidissima did not accumulate any galloylated compounds. C. nitidissima exhibited no expression of SCPL-AT or UGT84A22, whereas the other three species of Camellia exhibited various expression patterns. This indicated that the functions of the paralogs of SCPL-AT vary. Enzymatic analysis revealed that SCPL5 was neofunctionalized as a noncatalytic chaperone paralog, a type of chaerone-like protein, associating with flavan-3-ol galloylation; moreover, CsSCPL4 was subfunctionalized in association with the galloylation of cis- and trans-flavan-3-ols. In C. nitidissima, an SCPL4 homolog was noted with mutations in two cysteine residues forming a disulfide bond, which suggested that this homolog was defunctionalized. The findings of this study improve our understanding of the functional diversification of SCPL paralogs in Camellia sp.
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Affiliation(s)
- Yue Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Anhui Provincial Laboratory, Hefei 230036, Anhui, People's Republic of China
| | - Shengbo Yao
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Anhui Provincial Laboratory, Hefei 230036, Anhui, People's Republic of China
| | - Xue Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Anhui Provincial Laboratory, Hefei 230036, Anhui, People's Republic of China
| | - Zhihui Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Anhui Provincial Laboratory, Hefei 230036, Anhui, People's Republic of China
| | - Changjuan Jiang
- School of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yajun Liu
- School of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Xiaolan Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Anhui Provincial Laboratory, Hefei 230036, Anhui, People's Republic of China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Anhui Provincial Laboratory, Hefei 230036, Anhui, People's Republic of China
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11
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Singh G, Agrawal H, Bednarek P. Specialized metabolites as versatile tools in shaping plant-microbe associations. MOLECULAR PLANT 2023; 16:122-144. [PMID: 36503863 DOI: 10.1016/j.molp.2022.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Plants are rich repository of a large number of chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes including responses against changing abiotic conditions and interactions with various co-existing organisms. One of the strikingly affirmed functions of these specialized metabolites is their involvement in plants' life-long interactions with complex multi-kingdom microbiomes including both beneficial and harmful microorganisms. Recent developments in genomic and molecular biology tools not only help to generate well-curated information about regulatory and structural components of biosynthetic pathways of plant specialized metabolites but also to create and screen mutant lines defective in their synthesis. In this review, we have comprehensively surveyed the function of these specialized metabolites and discussed recent research findings demonstrating the responses of various microbes on tested mutant lines having defective biosynthesis of particular metabolites. In addition, we attempt to provide key clues about the impact of these metabolites on the assembly of the plant microbiome by summarizing the major findings of recent comparative metagenomic analyses of available mutant lines under customized and natural microbial niches. Subsequently, we delineate benchmark initiatives that aim to engineer or manipulate the biosynthetic pathways to produce specialized metabolites in heterologous systems but also to diversify their immune function. While denoting the function of these metabolites, we also discuss the critical bottlenecks associated with understanding and exploiting their function in improving plant adaptation to the environment.
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Affiliation(s)
- Gopal Singh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Himani Agrawal
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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12
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Wang B, Li K, Wu G, Xu Z, Hou R, Guo B, Zhao Y, Liu F. Sulforaphane, a secondary metabolite in crucifers, inhibits the oxidative stress adaptation and virulence of Xanthomonas by directly targeting OxyR. MOLECULAR PLANT PATHOLOGY 2022; 23:1508-1523. [PMID: 35942507 PMCID: PMC9452769 DOI: 10.1111/mpp.13245] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 05/19/2023]
Abstract
Plant secondary metabolites perform numerous functions in the interactions between plants and pathogens. However, little is known about the precise mechanisms underlying their contribution to the direct inhibition of pathogen growth and virulence in planta. Here, we show that the secondary metabolite sulforaphane (SFN) in crucifers inhibits the growth, virulence, and ability of Xanthomonas species to adapt to oxidative stress, which is essential for the successful infection of host plants by phytopathogens. The transcription of oxidative stress detoxification-related genes (catalase [katA and katG] and alkylhydroperoxide-NADPH oxidoreductase subunit C [ahpC]) was substantially inhibited by SFN in Xanthomonas campestris pv. campestris (Xcc), and this phenomenon was most obvious in sax gene mutants sensitive to SFN. By performing microscale thermophoresis (MST) and electrophoretic mobility shift assay (EMSA), we observed that SFN directly bound to the virulence-related redox-sensing transcription factor OxyR and weakened the ability of OxyR to bind to the promoters of oxidative stress detoxification-related genes. Collectively, these results illustrate that SFN directly targets OxyR to inhibit the bacterial adaptation to oxidative stress, thereby decreasing bacterial virulence. Interestingly, this phenomenon occurs in multiple Xanthomonas species. This study provides novel insights into the molecular mechanisms by which SFN limits Xanthomonas adaptation to oxidative stress and virulence, and the findings will facilitate future studies on the use of SFN as a biopesticide to control Xanthomonas.
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Affiliation(s)
- Bo Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and SafetyState Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Kaihuai Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and SafetyState Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Guichun Wu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and SafetyState Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Zhizhou Xu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and SafetyState Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Rongxian Hou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and SafetyState Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Baodian Guo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and SafetyState Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and SafetyState Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and SafetyState Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
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13
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Zhan C, Shen S, Yang C, Liu Z, Fernie AR, Graham IA, Luo J. Plant metabolic gene clusters in the multi-omics era. TRENDS IN PLANT SCIENCE 2022; 27:981-1001. [PMID: 35365433 DOI: 10.1016/j.tplants.2022.03.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Secondary metabolism in plants gives rise to a vast array of small-molecule natural products. The discovery of operon-like gene clusters in plants has provided a new perspective on the evolution of specialized metabolism and the opportunity to rapidly advance the metabolic engineering of natural product production. Here, we review historical aspects of the study of plant metabolic gene clusters as well as general strategies for identifying plant metabolic gene clusters in the multi-omics era. We also emphasize the exploration of their natural variation and evolution, as well as new strategies for the prospecting of plant metabolic gene clusters and a deeper understanding of how their structure influences their function.
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Affiliation(s)
- Chuansong Zhan
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Shuangqian Shen
- College of Tropical Crops, Hainan University, Haikou 570228, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Alisdair R Fernie
- Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Ian A Graham
- Center for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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14
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Yu J, Tu X, Huang AC. Functions and biosynthesis of plant signaling metabolites mediating plant-microbe interactions. Nat Prod Rep 2022; 39:1393-1422. [PMID: 35766105 DOI: 10.1039/d2np00010e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2015-2022Plants and microbes have coevolved since their appearance, and their interactions, to some extent, define plant health. A reasonable fraction of small molecules plants produced are involved in mediating plant-microbe interactions, yet their functions and biosynthesis remain fragmented. The identification of these compounds and their biosynthetic genes will open up avenues for plant fitness improvement by manipulating metabolite-mediated plant-microbe interactions. Herein, we integrate the current knowledge on their chemical structures, bioactivities, and biosynthesis with the view of providing a high-level overview on their biosynthetic origins and evolutionary trajectory, and pinpointing the yet unknown and key enzymatic steps in diverse biosynthetic pathways. We further discuss the theoretical basis and prospects for directing plant signaling metabolite biosynthesis for microbe-aided plant health improvement in the future.
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Affiliation(s)
- Jingwei Yu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Xingzhao Tu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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15
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Yao S, Liu Y, Zhuang J, Zhao Y, Dai X, Jiang C, Wang Z, Jiang X, Zhang S, Qian Y, Tai Y, Wang Y, Wang H, Xie D, Gao L, Xia T. Insights into acylation mechanisms: co-expression of serine carboxypeptidase-like acyltransferases and their non-catalytic companion paralogs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:117-133. [PMID: 35437852 PMCID: PMC9541279 DOI: 10.1111/tpj.15782] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/12/2022] [Indexed: 05/18/2023]
Abstract
Serine carboxypeptidase-like acyltransferases (SCPL-ATs) play a vital role in the diversification of plant metabolites. Galloylated flavan-3-ols highly accumulate in tea (Camellia sinensis), grape (Vitis vinifera), and persimmon (Diospyros kaki). To date, the biosynthetic mechanism of these compounds remains unknown. Herein, we report that two SCPL-AT paralogs are involved in galloylation of flavan-3-ols: CsSCPL4, which contains the conserved catalytic triad S-D-H, and CsSCPL5, which has the alternative triad T-D-Y. Integrated data from transgenic plants, recombinant enzymes, and gene mutations showed that CsSCPL4 is a catalytic acyltransferase, while CsSCPL5 is a non-catalytic companion paralog (NCCP). Co-expression of CsSCPL4 and CsSCPL5 is likely responsible for the galloylation. Furthermore, pull-down and co-immunoprecipitation assays showed that CsSCPL4 and CsSCPL5 interact, increasing protein stability and promoting post-translational processing. Moreover, phylogenetic analyses revealed that their homologs co-exist in galloylated flavan-3-ol- or hydrolyzable tannin-rich plant species. Enzymatic assays further revealed the necessity of co-expression of those homologs for acyltransferase activity. Evolution analysis revealed that the mutations of the CsSCPL5 catalytic residues may have taken place about 10 million years ago. These findings show that the co-expression of SCPL-ATs and their NCCPs contributes to the acylation of flavan-3-ols in the plant kingdom.
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Affiliation(s)
- Shengbo Yao
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Yajun Liu
- School of Life ScienceAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Juhua Zhuang
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Yue Zhao
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Xinlong Dai
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Changjuan Jiang
- School of Life ScienceAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Zhihui Wang
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Xiaolan Jiang
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Shuxiang Zhang
- School of Life ScienceAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Yumei Qian
- School of Biological and Food EngineeringSuzhou UniversitySuzhou234000AnhuiChina
| | - Yuling Tai
- School of Life ScienceAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Yunsheng Wang
- School of Life ScienceAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Haiyan Wang
- School of Life ScienceAnhui Agricultural UniversityHefei230036AnhuiChina
| | - De‐Yu Xie
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - Liping Gao
- School of Life ScienceAnhui Agricultural UniversityHefei230036AnhuiChina
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefei230036AnhuiChina
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16
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Kharb A, Sharma S, Sharma A, Nirwal N, Pandey R, Bhattacharyya D, Chauhan RS. Capturing acyltransferase(s) transforming final step in the biosynthesis of a major Iridoid Glycoside, (Picroside-II) in a Himalayan Medicinal Herb, Picrorhiza kurroa. Mol Biol Rep 2022; 49:5567-5576. [PMID: 35581509 DOI: 10.1007/s11033-022-07489-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 02/02/2022] [Accepted: 04/19/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Picrorhiza kurroa has been reported as an age-old ayurvedic hepato-protection to treat hepatic disorders due to the presence of iridoids such as picroside-II (P-II), picroside-I, and kutkoside. The acylation of catalpol and vanilloyl coenzyme A by acyltransferases (ATs) is critical step in P-II biosynthesis. Since accumulation of P-II occurs only in roots, rhizomes and stolons in comparison to leaves uprooting of this critically endangered herb has been the only source of this compound. Recently, we reported that P-II acylation likely happen in roots, while stolons serve as the vital P-II storage compartment. Therefore, developing an alternate engineered platform for P-II biosynthesis require identification of P-II specific AT/s. METHODS AND RESULTS In that direction, egg-NOG function annotated 815 ATs from de novo RNA sequencing of tissue culture based 'shoots-only' system and nursery grown shoots, roots, and stolons varying in P-II content, were cross-compared in silico to arrive at ATs sequences unique and/or common to stolons and roots. Verification for organ and accession-wise upregulation in gene expression of these ATs by qRT-PCR has shortlisted six putative 'P-II-forming' ATs. Further, six-frame translation, ab initio protein structure modelling and protein-ligand molecular docking of these ATs signified one MBOAT domain containing AT with preferential binding to the vanillic acid CoA thiol ester as well as with P-II, implying that this could be potential AT decorating final structure of P-II. CONCLUSIONS Organ-wise comparative transcriptome mining coupled with reverse transcription real time qRT-PCR and protein-ligand docking led to the identification of an acyltransferases, contributing to the final structure of P-II.
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Affiliation(s)
- Anjali Kharb
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, 201310, Greater Noida, Uttar Pradesh, India
| | - Shilpa Sharma
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, 201310, Greater Noida, Uttar Pradesh, India
| | - Ashish Sharma
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, 201310, Greater Noida, Uttar Pradesh, India
| | - Neeti Nirwal
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, 201310, Greater Noida, Uttar Pradesh, India
| | - Roma Pandey
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, 201310, Greater Noida, Uttar Pradesh, India
| | - Dipto Bhattacharyya
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, 201310, Greater Noida, Uttar Pradesh, India
| | - Rajinder Singh Chauhan
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, 201310, Greater Noida, Uttar Pradesh, India.
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17
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Chen Q, Liang X, Wu C, Liu Y, Liu X, Zhao H, Li K, Chen S, Wang H, Han Z, Wu M, Yao X, Shui J, Qiao Y, Zhan X, Zhang Y. Overexpression of leucoanthocyanidin reductase or anthocyanidin reductase elevates tannins content and confers cassava resistance to two-spotted spider mite. FRONTIERS IN PLANT SCIENCE 2022; 13:994866. [PMID: 36061805 PMCID: PMC9433999 DOI: 10.3389/fpls.2022.994866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/01/2022] [Indexed: 05/09/2023]
Abstract
The two-spotted spider mite (TSSM) is a destructive cassava pest. Intensive demonstration of resistance mechanism greatly facilitates the creation of TSSM-resistant cassava germplasm. Gene to metabolite network plays a crucial role in modulating plant resistance, but little is known about the genes and related metabolites which are responsible for cassava resistance to TSSM. Here, a highly resistant (HR) and a highly susceptible (HS) cassava cultivar were used, integrative and comparative transcriptomic and metabolomic analyses between these two cultivars after TSSM infestation revealed that several genes and metabolites were closely related and significantly different in abundance. In particular, the expression of leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) genes showed a high positive correlation with most of the metabolites in the tannin biosynthesis pathway. Furthermore, transgenic cassava lines overexpressing either of the genes elevated tannin concentrations and conferred cassava resistance to TSSM. Additionally, different forms of tannins possessed distinct bioactivity on TSSM, of which total condensed tannins (LC50 = 375.68 mg/l) showed maximum lethal effects followed by procyanidin B1 (LC50 = 3537.10 mg/l). This study accurately targets LAR, ANR and specific tannin compounds as critical genes and metabolites in shaping cassava resistance to TSSM, which could be considered as biomarkers for evaluation and creation of pest-resistant cassava germplasm.
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Affiliation(s)
- Qing Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
- *Correspondence: Qing Chen,
| | - Xiao Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
- Xiao Liang,
| | - Chunling Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Ying Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Xiaoqiang Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Huiping Zhao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Haiyan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical, Haikou, China
| | - Zhiling Han
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Mufeng Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Xiaowen Yao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Jun Shui
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yang Qiao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Xue Zhan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yao Zhang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, Hainan, China
- Sanya Research Academy, Chinese Academy of Tropical Agriculture Science, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
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18
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Kumar A, Srivastava P, Srivastava G, Sandeep, Kumar N, Chanotiya CS, Ghosh S. BAHD acetyltransferase contributes to wound-induced biosynthesis of oleo-gum resin triterpenes in Boswellia. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1403-1419. [PMID: 34165841 DOI: 10.1111/tpj.15388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Triterpenes (30-carbon isoprene compounds) represent a large and highly diverse class of natural products that play various physiological functions in plants. The triterpene biosynthetic enzymes, particularly those catalyzing the late-stage regio-selective modifications are not well characterized. The bark of select Boswellia trees, e.g., B. serrata exudes specialized oleo-gum resin in response to wounding, which is enriched with boswellic acids (BAs), a unique class of C3α-epimeric pentacyclic triterpenes with medicinal properties. The bark possesses a network of resin secretory structures comprised of vertical and horizontal resin canals, and amount of BAs in bark increases considerably in response to wounding. To investigate BA biosynthetic enzymes, we conducted tissue-specific transcriptome profiling and identified a wound-responsive BAHD acetyltransferase (BsAT1) of B. serrata catalyzing the late-stage C3α-O-acetylation reactions in the BA biosynthetic pathway. BsAT1 catalyzed C3α-O-acetylation of αBA, βBA, and 11-keto-βBA in vitro and in planta assays to produce all the major C3α-O-acetyl-BAs (3-acetyl-αBA, 3-acetyl-βBA, and 3-acetyl-11-keto-βBA) found in B. serrata bark and oleo-gum resin. BsAT1 showed strict specificity for BA scaffold, whereas it did not acetylate the more common C3β-epimeric pentacyclic triterpenes. The analysis of steady-state kinetics using various BAs revealed distinct substrate affinity and catalytic efficiency. BsAT1 transcript expression coincides with increased levels of C3α-O-acetyl-BAs in bark in response to wounding, suggesting a role of BsAT1 in wound-induced biosynthesis of C3α-O-acetyl-BAs. Overall, the results provide new insights into the biosynthesis of principal chemical constituents of Boswellia oleo-gum resin.
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Affiliation(s)
- Aashish Kumar
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Payal Srivastava
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gaurav Srivastava
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sandeep
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Narendra Kumar
- Plant Breeding and Genetic Resource Conservation Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Chandan S Chanotiya
- Phytochemistry Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sumit Ghosh
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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Bharadwaj R, Kumar SR, Sharma A, Sathishkumar R. Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2021; 12:697318. [PMID: 34490002 PMCID: PMC8418127 DOI: 10.3389/fpls.2021.697318] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 05/21/2023]
Abstract
Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Sarma R. Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Querétaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
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20
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Garagounis C, Delkis N, Papadopoulou KK. Unraveling the roles of plant specialized metabolites: using synthetic biology to design molecular biosensors. THE NEW PHYTOLOGIST 2021; 231:1338-1352. [PMID: 33997999 DOI: 10.1111/nph.17470] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 05/25/2023]
Abstract
Plants are a rich source of specialized metabolites with a broad range of bioactivities and many applications in human daily life. Over the past decades significant progress has been made in identifying many such metabolites in different plant species and in elucidating their biosynthetic pathways. However, the biological roles of plant specialized metabolites remain elusive and proposed functions lack an identified underlying molecular mechanism. Understanding the roles of specialized metabolites frequently is hampered by their dynamic production and their specific spatiotemporal accumulation within plant tissues and organs throughout a plant's life cycle. In this review, we propose the employment of strategies from the field of Synthetic Biology to construct and optimize genetically encoded biosensors that can detect individual specialized metabolites in a standardized and high-throughput manner. This will help determine the precise localization of specialized metabolites at the tissue and single-cell levels. Such information will be useful in developing complete system-level models of specialized plant metabolism, which ultimately will demonstrate how the biosynthesis of specialized metabolites is integrated with the core processes of plant growth and development.
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Affiliation(s)
- Constantine Garagounis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Nikolaos Delkis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
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21
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Palma-Guerrero J, Chancellor T, Spong J, Canning G, Hammond J, McMillan VE, Hammond-Kosack KE. Take-All Disease: New Insights into an Important Wheat Root Pathogen. TRENDS IN PLANT SCIENCE 2021; 26:836-848. [PMID: 33752966 DOI: 10.1016/j.tplants.2021.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Take-all disease, caused by the fungal root pathogen Gaeumannomyces tritici, is considered to be the most important root disease of wheat worldwide. Here we review the advances in take-all research over the last 15 years, focusing on the identification of new sources of genetic resistance in wheat relatives and the role of the microbiome in disease development. We also highlight recent breakthroughs in the molecular interactions between G. tritici and wheat, including genome and transcriptome analyses. These new findings will aid the development of novel control strategies against take-all disease. In light of this growing understanding, the G. tritici-wheat interaction could provide a model study system for root-infecting fungal pathogens of cereals.
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Affiliation(s)
- Javier Palma-Guerrero
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
| | - Tania Chancellor
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Jess Spong
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Gail Canning
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Jess Hammond
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Vanessa E McMillan
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
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22
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Diversity in Chemical Structures and Biological Properties of Plant Alkaloids. Molecules 2021; 26:molecules26113374. [PMID: 34204857 PMCID: PMC8199754 DOI: 10.3390/molecules26113374] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Phytochemicals belonging to the group of alkaloids are signature specialized metabolites endowed with countless biological activities. Plants are armored with these naturally produced nitrogenous compounds to combat numerous challenging environmental stress conditions. Traditional and modern healthcare systems have harnessed the potential of these organic compounds for the treatment of many ailments. Various chemical entities (functional groups) attached to the central moiety are responsible for their diverse range of biological properties. The development of the characterization of these plant metabolites and the enzymes involved in their biosynthesis is of an utmost priority to deliver enhanced advantages in terms of biological properties and productivity. Further, the incorporation of whole/partial metabolic pathways in the heterologous system and/or the overexpression of biosynthetic steps in homologous systems have both become alternative and lucrative methods over chemical synthesis in recent times. Moreover, in-depth research on alkaloid biosynthetic pathways has revealed numerous chemical modifications that occur during alkaloidal conversions. These chemical reactions involve glycosylation, acylation, reduction, oxidation, and methylation steps, and they are usually responsible for conferring the biological activities possessed by alkaloids. In this review, we aim to discuss the alkaloidal group of plant specialized metabolites and their brief classification covering major categories. We also emphasize the diversity in the basic structures of plant alkaloids arising through enzymatically catalyzed structural modifications in certain plant species, as well as their emerging diverse biological activities. The role of alkaloids in plant defense and their mechanisms of action are also briefly discussed. Moreover, the commercial utilization of plant alkaloids in the marketplace displaying various applications has been enumerated.
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23
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Li Y, Leveau A, Zhao Q, Feng Q, Lu H, Miao J, Xue Z, Martin AC, Wegel E, Wang J, Orme A, Rey MD, Karafiátová M, Vrána J, Steuernagel B, Joynson R, Owen C, Reed J, Louveau T, Stephenson MJ, Zhang L, Huang X, Huang T, Fan D, Zhou C, Tian Q, Li W, Lu Y, Chen J, Zhao Y, Lu Y, Zhu C, Liu Z, Polturak G, Casson R, Hill L, Moore G, Melton R, Hall N, Wulff BBH, Doležel J, Langdon T, Han B, Osbourn A. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals. Nat Commun 2021; 12:2563. [PMID: 33963185 PMCID: PMC8105312 DOI: 10.1038/s41467-021-22920-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat-the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a 'self-poisoning' scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity.
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Affiliation(s)
- Yan Li
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | | | - Qiang Zhao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qi Feng
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hengyun Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiashun Miao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zheyong Xue
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Eva Wegel
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Jing Wang
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Miroslava Karafiátová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - James Reed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Lei Zhang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xuehui Huang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Tao Huang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Danling Fan
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Congcong Zhou
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qilin Tian
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Wenjun Li
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yiqi Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiaying Chen
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yan Zhao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ying Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Chuanrang Zhu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guy Polturak
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Lionel Hill
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rachel Melton
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Bin Han
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China.
| | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich, UK.
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24
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Yonekura-Sakakibara K, Yamamura M, Matsuda F, Ono E, Nakabayashi R, Sugawara S, Mori T, Tobimatsu Y, Umezawa T, Saito K. Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis. THE PLANT CELL 2021; 33:129-152. [PMID: 33751095 PMCID: PMC8136895 DOI: 10.1093/plcell/koaa014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/20/2020] [Indexed: 05/03/2023]
Abstract
Lignans/neolignans are generally synthesized from coniferyl alcohol (CA) in the cinnamate/monolignol pathway by oxidation to generate the corresponding radicals with subsequent stereoselective dimerization aided by dirigent proteins (DIRs). Genes encoding oxidases and DIRs for neolignan biosynthesis have not been identified previously. In Arabidopsis thaliana, the DIR AtDP1/AtDIR12 plays an essential role in the 8-O-4' coupling in neolignan biosynthesis by unequivocal structural determination of the compound missing in the atdp1 mutant as a sinapoylcholine (SC)-conjugated neolignan, erythro-3-{4-[2-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-1-hydroxymethylethoxy]-3,5-dimethoxyphenyl}acryloylcholine. Phylogenetic analyses showed that AtDP1/AtDIR12 belongs to the DIR-a subfamily composed of DIRs for 8-8' coupling of monolignol radicals. AtDP1/AtDIR12 is specifically expressed in outer integument 1 cells in developing seeds. As a putative oxidase for neolignan biosynthesis, we focused on AtLAC5, a laccase gene coexpressed with AtDP1/AtDIR12. In lac5 mutants, the abundance of feruloylcholine (FC)-conjugated neolignans decreased to a level comparable to those in the atdp1 mutant. In addition, SC/FC-conjugated neolignans were missing in the seeds of mutants defective in SCT/SCPL19, an enzyme that synthesizes SC. These results strongly suggest that AtDP1/AtDIR12 and AtLAC5 are involved in neolignan biosynthesis via SC/FC. A tetrazolium penetration assay showed that seed coat permeability increased in atdp1 mutants, suggesting a protective role of neolignans in A. thaliana seeds.
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Affiliation(s)
- Keiko Yonekura-Sakakibara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masaomi Yamamura
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Fumio Matsuda
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Eiichiro Ono
- Research Institute, Suntory Global Innovation Center Ltd., 8-1-1 Seikadai, Seika, Soraku-gun, Kyoto 619-0284, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Satoko Sugawara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- Research Unit for Development of Global Sustainability, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Plant Molecular Science Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
- Author for correspondence: ,
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25
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Fu R, Zhang P, Jin G, Wang L, Qi S, Cao Y, Martin C, Zhang Y. Versatility in acyltransferase activity completes chicoric acid biosynthesis in purple coneflower. Nat Commun 2021; 12:1563. [PMID: 33692355 PMCID: PMC7946891 DOI: 10.1038/s41467-021-21853-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/11/2021] [Indexed: 02/05/2023] Open
Abstract
Purple coneflower (Echinacea purpurea (L.) Moench) is a popular native North American herbal plant. Its major bioactive compound, chicoric acid, is reported to have various potential physiological functions, but little is known about its biosynthesis. Here, taking an activity-guided approach, we identify two cytosolic BAHD acyltransferases that form two intermediates, caftaric acid and chlorogenic acid. Surprisingly, a unique serine carboxypeptidase-like acyltransferase uses chlorogenic acid as its acyl donor and caftaric acid as its acyl acceptor to produce chicoric acid in vacuoles, which has evolved its acyl donor specificity from the better-known 1-O-β-D-glucose esters typical for this specific type of acyltransferase to chlorogenic acid. This unusual pathway seems unique to Echinacea species suggesting convergent evolution of chicoric acid biosynthesis. Using these identified acyltransferases, we have reconstituted chicoric acid biosynthesis in tobacco. Our results emphasize the flexibility of acyltransferases and their roles in the evolution of specialized metabolism in plants.
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Affiliation(s)
- Rao Fu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Pingyu Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Ge Jin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Lianglei Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Cathie Martin
- Department of Metabolic Biology and Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
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26
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Pei T, Yan M, Kong Y, Fan H, Liu J, Cui M, Fang Y, Ge B, Yang J, Zhao Q. The genome of Tripterygium wilfordii and characterization of the celastrol biosynthesis pathway. GIGABYTE 2021; 2021:gigabyte14. [PMID: 36967728 PMCID: PMC10038137 DOI: 10.46471/gigabyte.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/25/2021] [Indexed: 11/09/2022] Open
Abstract
Tripterygium wilfordii is a vine from the Celastraceae family that is used in traditional Chinese medicine (TCM). The active ingredient, celastrol, is a friedelane-type pentacyclic triterpenoid with putative roles as an antitumor, immunosuppressive, and anti-obesity agent. Here, we report a reference genome assembly of T. wilfordii with high-quality annotation using a hybrid sequencing strategy. The total genome size obtained is 340.12 Mb, with a contig N50 value of 3.09 Mb. We successfully anchored 91.02% of sequences into 23 pseudochromosomes using high-throughput chromosome conformation capture (Hi–C) technology. The super-scaffold N50 value was 13.03 Mb. We also annotated 31,593 structural genes, with a repeat percentage of 44.31%. These data demonstrate that T. wilfordii diverged from Malpighiales species approximately 102.4 million years ago. By integrating genome, transcriptome and metabolite analyses, as well as in vivo and in vitro enzyme assays of two cytochrome P450 (CYP450) genes, TwCYP712K1 and TwCYP712K2, it is possible to investigate the second biosynthesis step of celastrol and demonstrate that this was derived from a common ancestor. These data provide insights and resources for further investigation of pathways related to celastrol, and valuable information to aid the conservation of resources, as well as understand the evolution of Celastrales.
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Affiliation(s)
- Tianlin Pei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Hang Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Mengying Cui
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yumin Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Binjie Ge
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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27
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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.
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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.
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Zhou X, Liu L, Li Y, Li K, Liu X, Zhou J, Yang C, Liu X, Fang C, Luo J. Integrative Metabolomic and Transcriptomic Analyses Reveal Metabolic Changes and Its Molecular Basis in Rice Mutants of the Strigolactone Pathway. Metabolites 2020; 10:metabo10110425. [PMID: 33114491 PMCID: PMC7693813 DOI: 10.3390/metabo10110425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 11/24/2022] Open
Abstract
Plants have evolved many metabolites to meet the demands of growth and adaptation. Although strigolactones (SLs) play vital roles in controlling plant architecture, their function in regulating plant metabolism remains elusive. Here we report the integrative metabolomic and transcriptomic analyses of two rice SL mutants, d10 (a biosynthesis mutant) and d14 (a perception mutant). Both mutants displayed a series of metabolic and transcriptional alterations, especially in the lipid, flavonoid, and terpenoid pathways. Levels of several diterpenoid phytoalexins were substantially increased in d10 and d14, together with the induction of terpenoid gene cluster and the corresponding upstream transcription factor WRKY45, an established determinant of plant immunity. The fact that WRKY45 is a target of IPA1, which acted as a downstream transcription factor of SL signaling, suggests that SLs contribute to plant defense through WRKY45 and phytoalexins. Moreover, our data indicated that SLs may modulate rice metabolism through a vast number of clustered or tandemly duplicated genes. Our work revealed a central role of SLs in rice metabolism. Meanwhile, integrative analysis of the metabolome and transcriptome also suggested that SLs may contribute to metabolite-associated growth and defense.
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Affiliation(s)
- Xiujuan Zhou
- College of Tropical Crops, Hainan University, Haikou, Hainan 570288, China; (X.Z.); (L.L.); (K.L.); (X.L.); (J.Z.); (X.L.)
| | - Ling Liu
- College of Tropical Crops, Hainan University, Haikou, Hainan 570288, China; (X.Z.); (L.L.); (K.L.); (X.L.); (J.Z.); (X.L.)
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (C.Y.)
| | - Kang Li
- College of Tropical Crops, Hainan University, Haikou, Hainan 570288, China; (X.Z.); (L.L.); (K.L.); (X.L.); (J.Z.); (X.L.)
| | - Xiaoli Liu
- College of Tropical Crops, Hainan University, Haikou, Hainan 570288, China; (X.Z.); (L.L.); (K.L.); (X.L.); (J.Z.); (X.L.)
| | - Junjie Zhou
- College of Tropical Crops, Hainan University, Haikou, Hainan 570288, China; (X.Z.); (L.L.); (K.L.); (X.L.); (J.Z.); (X.L.)
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (C.Y.)
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou, Hainan 570288, China; (X.Z.); (L.L.); (K.L.); (X.L.); (J.Z.); (X.L.)
| | - Chuanying Fang
- College of Tropical Crops, Hainan University, Haikou, Hainan 570288, China; (X.Z.); (L.L.); (K.L.); (X.L.); (J.Z.); (X.L.)
- Correspondence: (C.F.); (J.L.)
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, Hainan 570288, China; (X.Z.); (L.L.); (K.L.); (X.L.); (J.Z.); (X.L.)
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (C.Y.)
- Correspondence: (C.F.); (J.L.)
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29
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Anderson O, Beckett J, Briggs CC, Natrass LA, Cranston CF, Wilkinson EJ, Owen JH, Mir Williams R, Loukaidis A, Bouillon ME, Pritchard D, Lahmann M, Baird MS, Denny PW. An investigation of the antileishmanial properties of semi-synthetic saponins. RSC Med Chem 2020; 11:833-842. [PMID: 33479679 PMCID: PMC7651632 DOI: 10.1039/d0md00123f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/21/2020] [Indexed: 12/25/2022] Open
Abstract
Leishmaniasis is a neglected tropical disease caused by insect-vector borne protozoan parasites of the, Leishmania species. Whilst infection threatens and affects millions of the global poor, vaccines are absent and drug therapy limited. Extensive efforts have recently been made to discover new leads from small molecule synthetic compound libraries held by industry; however, the number of new chemical entities identified and entering development as anti-leishmanials has been very low. This has led to increased interest in the possibility of discovering naturally derived compounds with potent antileishmanial activity which may be developed towards clinical applications. Plant-derived triterpenoid and steroidal saponins have long been considered as anti-microbials and here we describe an investigation of a library of 137 natural (9) and semi-synthetic saponins (128) for activity against Leishmania mexicana, a causative agent of cutaneous leishmaniasis. The triterpenoid sapogenin, hederagenin, readily obtained in large quantities from Hedera helix (common ivy), was converted into a range of 128 derivatives. These semi-synthetic compounds, as well as saponins isolated from ivy, were examined with a phenotypic screening approach to identify potent and selective anti-leishmanial hits. This led to the identification of 12 compounds, including the natural saponin gypsogenin, demonstrating high potency (ED50 < 10.5 μM) against axenic L. mexicana amastigotes, the mammalian pathogenic form. One of these, hederagenin disuccinate, was sufficiently non-toxic to the macrophage host cell to facilitate further analyses, selectivity index (SI) > 10. Whilst this was not active in an infected cell model, the anti-leishmanial properties of hederagenin-derivatives have been demonstrated, and the possibility of improving the selectivity of natural hederagenin through chemical modification has been established.
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Affiliation(s)
- Orlagh Anderson
- Department of Biosciences and Centre for Global Infectious Diseases , Durham University , Stockton Road , Durham , DH1 3LE , UK . ; Tel: +44 (0)191 3343983
| | - Joseph Beckett
- Department of Biosciences and Centre for Global Infectious Diseases , Durham University , Stockton Road , Durham , DH1 3LE , UK . ; Tel: +44 (0)191 3343983
| | - Carla C Briggs
- Department of Biosciences and Centre for Global Infectious Diseases , Durham University , Stockton Road , Durham , DH1 3LE , UK . ; Tel: +44 (0)191 3343983
| | - Liam A Natrass
- Department of Biosciences and Centre for Global Infectious Diseases , Durham University , Stockton Road , Durham , DH1 3LE , UK . ; Tel: +44 (0)191 3343983
- Department of Chemistry and Centre for Global Infectious Diseases , Durham University , Stockton Road , Durham , DH1 3LE , UK
| | - Charles F Cranston
- Department of Biosciences and Centre for Global Infectious Diseases , Durham University , Stockton Road , Durham , DH1 3LE , UK . ; Tel: +44 (0)191 3343983
| | - Elizabeth J Wilkinson
- Department of Chemistry , School of Natural Science , Bangor University , Gwynedd LL57 2UW , UK
| | - Jack H Owen
- Department of Chemistry , School of Natural Science , Bangor University , Gwynedd LL57 2UW , UK
| | - Rhodri Mir Williams
- Department of Chemistry , School of Natural Science , Bangor University , Gwynedd LL57 2UW , UK
| | - Angelos Loukaidis
- Department of Chemistry , School of Natural Science , Bangor University , Gwynedd LL57 2UW , UK
| | - Marc E Bouillon
- Department of Chemistry , School of Natural Science , Bangor University , Gwynedd LL57 2UW , UK
| | - Deiniol Pritchard
- Naturiol Bangor Ltd , Alun Roberts Building , Bangor University , Gwynedd LL57 2UW , UK
| | - Martina Lahmann
- Department of Chemistry , School of Natural Science , Bangor University , Gwynedd LL57 2UW , UK
| | - Mark S Baird
- Naturiol Bangor Ltd , Alun Roberts Building , Bangor University , Gwynedd LL57 2UW , UK
| | - Paul W Denny
- Department of Biosciences and Centre for Global Infectious Diseases , Durham University , Stockton Road , Durham , DH1 3LE , UK . ; Tel: +44 (0)191 3343983
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30
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Lacchini E, Goossens A. Combinatorial Control of Plant Specialized Metabolism: Mechanisms, Functions, and Consequences. Annu Rev Cell Dev Biol 2020; 36:291-313. [PMID: 32559387 DOI: 10.1146/annurev-cellbio-011620-031429] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plants constantly perceive internal and external cues, many of which they need to address to safeguard their proper development and survival. They respond to these cues by selective activation of specific metabolic pathways involving a plethora of molecular players that act and interact in complex networks. In this review, we illustrate and discuss the complexity in the combinatorial control of plant specialized metabolism. We hereby go beyond the intuitive concept of combinatorial control as exerted by modular-acting complexes of transcription factors that govern expression of specialized metabolism genes. To extend this discussion, we also consider all known hierarchical levels of regulation of plant specialized metabolism and their interfaces by referring to reported regulatory concepts from the plant field. Finally, we speculate on possible yet-to-be-discovered regulatory principles of plant specialized metabolism that are inspired by knowledge from other kingdoms of life and areas of biological research.
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Affiliation(s)
- Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; , .,Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; , .,Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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31
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Fermentative N-Methylanthranilate Production by Engineered Corynebacterium glutamicum. Microorganisms 2020; 8:microorganisms8060866. [PMID: 32521697 PMCID: PMC7356990 DOI: 10.3390/microorganisms8060866] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/20/2022] Open
Abstract
The N-functionalized amino acid N-methylanthranilate is an important precursor for bioactive compounds such as anticancer acridone alkaloids, the antinociceptive alkaloid O-isopropyl N-methylanthranilate, the flavor compound O-methyl-N-methylanthranilate, and as a building block for peptide-based drugs. Current chemical and biocatalytic synthetic routes to N-alkylated amino acids are often unprofitable and restricted to low yields or high costs through cofactor regeneration systems. Amino acid fermentation processes using the Gram-positive bacterium Corynebacterium glutamicum are operated industrially at the million tons per annum scale. Fermentative processes using C. glutamicum for N-alkylated amino acids based on an imine reductase have been developed, while N-alkylation of the aromatic amino acid anthranilate with S-adenosyl methionine as methyl-donor has not been described for this bacterium. After metabolic engineering for enhanced supply of anthranilate by channeling carbon flux into the shikimate pathway, preventing by-product formation and enhancing sugar uptake, heterologous expression of the gene anmt encoding anthranilate N-methyltransferase from Ruta graveolens resulted in production of N-methylanthranilate (NMA), which accumulated in the culture medium. Increased SAM regeneration by coexpression of the homologous adenosylhomocysteinase gene sahH improved N-methylanthranilate production. In a test bioreactor culture, the metabolically engineered C. glutamicum C1* strain produced NMA to a final titer of 0.5 g·L−1 with a volumetric productivity of 0.01 g·L−1·h−1 and a yield of 4.8 mg·g−1 glucose.
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32
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Cárdenas PD, Almeida A, Bak S. Evolution of Structural Diversity of Triterpenoids. FRONTIERS IN PLANT SCIENCE 2019; 10:1523. [PMID: 31921225 PMCID: PMC6929605 DOI: 10.3389/fpls.2019.01523] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/01/2019] [Indexed: 05/19/2023]
Abstract
Plants have evolved to produce a blend of specialized metabolites that serve functional roles in plant adaptation. Among them, triterpenoids are one of the largest subclasses of such specialized metabolites, with more than 14,000 known structures. They play a role in plant defense and development and have potential applications within food and pharma. Triterpenoids are cyclized from oxidized squalene precursors by oxidosqualene cyclases, creating more than 100 different cyclical triterpene scaffolds. This limited number of scaffolds is the first step towards creating the vast structural diversity of triterpenoids followed by extensive diversification, in particular, by oxygenation and glycosylation. Gene duplication, divergence, and selection are major forces that drive triterpenoid structural diversification. The triterpenoid biosynthetic genes can be organized in non-homologous gene clusters, such as in Avena spp., Cucurbitaceae and Solanum spp., or scattered along plant chromosomes as in Barbarea vulgaris. Paralogous genes organized as tandem repeats reflect the extended gene duplication activities in the evolutionary history of the triterpenoid saponin pathways, as seen in B. vulgaris. We review and discuss examples of convergent and divergent evolution in triterpenoid biosynthesis, and the apparent mechanisms occurring in plants that drive their increasing structural diversity within and across species. Using B. vulgaris' saponins as examples, we discuss the impact a single structural modification can have on the structure of a triterpenoid and how this affect its biological properties. These examples provide insight into how plants continuously evolve their specialized metabolome, opening the way to study uncharacterized triterpenoid biosynthetic pathways.
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Affiliation(s)
| | | | - Søren Bak
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
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33
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A noncanonical vacuolar sugar transferase required for biosynthesis of antimicrobial defense compounds in oat. Proc Natl Acad Sci U S A 2019; 116:27105-27114. [PMID: 31806756 PMCID: PMC6936528 DOI: 10.1073/pnas.1914652116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Plants produce an array of natural products with important ecological functions. These compounds are often decorated with oligosaccharide groups that influence bioactivity, but the biosynthesis of such sugar chains is not well understood. Triterpene glycosides (saponins) are a large family of plant natural products that determine important agronomic traits, as exemplified by avenacins, antimicrobial defense compounds produced by oats. Avenacins have a branched trisaccharide moiety consisting of l-arabinose linked to 2 d-glucose molecules that is critical for antifungal activity. Plant natural product glycosylation is usually performed by uridine diphosphate-dependent glycosyltransferases (UGTs). We previously characterized the arabinosyltransferase that initiates the avenacin sugar chain; however, the enzymes that add the 2 remaining d-glucose molecules have remained elusive. Here we characterize the enzymes that catalyze these last 2 glucosylation steps. AsUGT91G16 is a classical cytosolic UGT that adds a 1,2-linked d-glucose molecule to l-arabinose. Unexpectedly, the enzyme that adds the final 1,4-linked d-glucose (AsTG1) is not a UGT, but rather a sugar transferase belonging to Glycosyl Hydrolase family 1 (GH1). Unlike classical UGTs, AsTG1 is vacuolar. Analysis of oat mutants reveals that AsTG1 corresponds to Sad3, a previously uncharacterized locus shown by mutation to be required for avenacin biosynthesis. AsTG1 and AsUGT91G16 form part of the avenacin biosynthetic gene cluster. Our demonstration that a vacuolar transglucosidase family member plays a critical role in triterpene biosynthesis highlights the importance of considering other classes of carbohydrate-active enzymes in addition to UGTs as candidates when elucidating pathways for the biosynthesis of glycosylated natural products in plants.
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34
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Huang AC, Osbourn A. Plant terpenes that mediate below-ground interactions: prospects for bioengineering terpenoids for plant protection. PEST MANAGEMENT SCIENCE 2019; 75:2368-2377. [PMID: 30884099 PMCID: PMC6690754 DOI: 10.1002/ps.5410] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 05/03/2023]
Abstract
Plants are sessile organisms that have evolved various mechanisms to adapt to complex and changing environments. One important feature of plant adaption is the production of specialised metabolites. Terpenes are the largest class of specialised metabolites, with over 80 000 structures reported so far, and they have important ecological functions in plant adaptation. Here, we review the current knowledge on plant terpenes that mediate below-ground interactions between plants and other organisms, including microbes, herbivores and other plants. The discovery, functions and biosynthesis of these terpenes are discussed, and prospects for bioengineering terpenoids for plant protection are considered. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ancheng C Huang
- Department of Metabolic Biology, John Innes CentreNorwich Research ParkNorwichUK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes CentreNorwich Research ParkNorwichUK
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35
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Leveau A, Reed J, Qiao X, Stephenson MJ, Mugford ST, Melton RE, Rant JC, Vickerstaff R, Langdon T, Osbourn A. Towards take-all control: a C-21β oxidase required for acylation of triterpene defence compounds in oat. THE NEW PHYTOLOGIST 2019; 221:1544-1555. [PMID: 30294977 PMCID: PMC6446040 DOI: 10.1111/nph.15456] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/20/2018] [Indexed: 05/13/2023]
Abstract
Oats produce avenacins, antifungal triterpenes that are synthesized in the roots and provide protection against take-all and other soilborne diseases. Avenacins are acylated at the carbon-21 position of the triterpene scaffold, a modification critical for antifungal activity. We have previously characterized several steps in the avenacin pathway, including those required for acylation. However, transfer of the acyl group to the scaffold requires the C-21β position to be oxidized first, by an as yet uncharacterized enzyme. We mined oat transcriptome data to identify candidate cytochrome P450 enzymes that may catalyse C-21β oxidation. Candidates were screened for activity by transient expression in Nicotiana benthamiana. We identified a cytochrome P450 enzyme AsCYP72A475 as a triterpene C-21β hydroxylase, and showed that expression of this enzyme together with early pathway steps yields C-21β oxidized avenacin intermediates. We further demonstrate that AsCYP72A475 is synonymous with Sad6, a previously uncharacterized locus required for avenacin biosynthesis. sad6 mutants are compromised in avenacin acylation and have enhanced disease susceptibility. The discovery of AsCYP72A475 represents an important advance in the understanding of triterpene biosynthesis and paves the way for engineering the avenacin pathway into wheat and other cereals for control of take-all and other diseases.
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Affiliation(s)
- Aymeric Leveau
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - James Reed
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Xue Qiao
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Michael J. Stephenson
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sam T. Mugford
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rachel E. Melton
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jenni C. Rant
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Robert Vickerstaff
- Department of Genetics and Crop Improvement, East Malling Research, New Rd, East Malling, ME19 6BJ, UK
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FL, UK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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36
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Louveau T, Orme A, Pfalzgraf H, Stephenson MJ, Melton R, Saalbach G, Hemmings AM, Leveau A, Rejzek M, Vickerstaff RJ, Langdon T, Field RA, Osbourn A. Analysis of Two New Arabinosyltransferases Belonging to the Carbohydrate-Active Enzyme (CAZY) Glycosyl Transferase Family1 Provides Insights into Disease Resistance and Sugar Donor Specificity. THE PLANT CELL 2018; 30:3038-3057. [PMID: 30429223 PMCID: PMC6354260 DOI: 10.1105/tpc.18.00641] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/13/2018] [Indexed: 05/20/2023]
Abstract
Glycosylation of small molecules is critical for numerous biological processes in plants, including hormone homeostasis, neutralization of xenobiotics, and synthesis and storage of specialized metabolites. Glycosylation of plant natural products is usually performed by uridine diphosphate-dependent glycosyltransferases (UGTs). Triterpene glycosides (saponins) are a large family of plant natural products that determine important agronomic traits such as disease resistance and flavor and have numerous pharmaceutical applications. Most characterized plant natural product UGTs are glucosyltransferases, and little is known about enzymes that add other sugars. Here we report the discovery and characterization of AsAAT1 (UGT99D1), which is required for biosynthesis of the antifungal saponin avenacin A-1 in oat (Avena strigosa). This enzyme adds l-Ara to the triterpene scaffold at the C-3 position, a modification critical for disease resistance. The only previously reported plant natural product arabinosyltransferase is a flavonoid arabinosyltransferase from Arabidopsis (Arabidopsis thaliana). We show that AsAAT1 has high specificity for UDP-β-l-arabinopyranose, identify two amino acids required for sugar donor specificity, and through targeted mutagenesis convert AsAAT1 into a glucosyltransferase. We further identify a second arabinosyltransferase potentially implicated in the biosynthesis of saponins that determine bitterness in soybean (Glycine max). Our investigations suggest independent evolution of UDP-Ara sugar donor specificity in arabinosyltransferases in monocots and eudicots.
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Affiliation(s)
- Thomas Louveau
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Anastasia Orme
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Hans Pfalzgraf
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Rachel Melton
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Gerhard Saalbach
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Andrew M Hemmings
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Aymeric Leveau
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Robert J Vickerstaff
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FL, UK
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FL, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK
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Abstract
In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.
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Affiliation(s)
- Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom; .,Current affiliation: Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; .,Institute for Integrative Biology of the Cell, 91190 Gif-sur-Yvette, France
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom;
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38
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Ámon J, Fernández-Martín R, Bokor E, Cultrone A, Kelly JM, Flipphi M, Scazzocchio C, Hamari Z. A eukaryotic nicotinate-inducible gene cluster: convergent evolution in fungi and bacteria. Open Biol 2018; 7:rsob.170199. [PMID: 29212709 PMCID: PMC5746545 DOI: 10.1098/rsob.170199] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/09/2017] [Indexed: 12/23/2022] Open
Abstract
Nicotinate degradation has hitherto been elucidated only in bacteria. In the ascomycete Aspergillus nidulans, six loci, hxnS/AN9178 encoding the molybdenum cofactor-containing nicotinate hydroxylase, AN11197 encoding a Cys2/His2 zinc finger regulator HxnR, together with AN11196/hxnZ, AN11188/hxnY, AN11189/hxnP and AN9177/hxnT, are clustered and stringently co-induced by a nicotinate derivative and subject to nitrogen metabolite repression mediated by the GATA factor AreA. These genes are strictly co-regulated by HxnR. Within the hxnR gene, constitutive mutations map in two discrete regions. Aspergillus nidulans is capable of using nicotinate and its oxidation products 6-hydroxynicotinic acid and 2,5-dihydroxypyridine as sole nitrogen sources in an HxnR-dependent way. HxnS is highly similar to HxA, the canonical xanthine dehydrogenase (XDH), and has originated by gene duplication, preceding the origin of the Pezizomycotina. This cluster is conserved with some variations throughout the Aspergillaceae. Our results imply that a fungal pathway has arisen independently from bacterial ones. Significantly, the neo-functionalization of XDH into nicotinate hydroxylase has occurred independently from analogous events in bacteria. This work describes for the first time a gene cluster involved in nicotinate catabolism in a eukaryote and has relevance for the formation and evolution of co-regulated primary metabolic gene clusters and the microbial degradation of N-heterocyclic compounds.
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Affiliation(s)
- Judit Ámon
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH)
| | | | - Eszter Bokor
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH)
| | - Antonietta Cultrone
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Joan M Kelly
- Department of Biology, University of Essex, Colchester, UK
| | - Michel Flipphi
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Claudio Scazzocchio
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France .,Department of Biology, University of Essex, Colchester, UK.,Department of Microbiology, Imperial College, London, UK (present address of CS).,Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France (present address of CS)
| | - Zsuzsanna Hamari
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH) .,Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
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de Brito Francisco R, Martinoia E. The Vacuolar Transportome of Plant Specialized Metabolites. PLANT & CELL PHYSIOLOGY 2018; 59:1326-1336. [PMID: 29452376 DOI: 10.1093/pcp/pcy039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/05/2018] [Indexed: 05/21/2023]
Abstract
The plant vacuole is a cellular compartment that is essential to plant development and growth. Often plant vacuoles accumulate specialized metabolites, also called secondary metabolites, which constitute functionally and chemically diverse compounds that exert in planta many essential functions and improve the plant's fitness. These metabolites provide, for example, chemical defense against herbivorous and pathogens or chemical attractants (color and fragrance) to attract pollinators. The chemical composition of the vacuole is dynamic, and is altered during development and as a response to environmental changes. To some extent these alterations rely on vacuolar transporters, which import and export compounds into and out of the vacuole, respectively. During the past decade, significant progress was made in the identification and functional characterization of the transporters implicated in many aspects of plant specialized metabolism. Still, deciphering the molecular players underlying such processes remains a challenge for the future. In this review, we present a comprehensive summary of the most recent achievements in this field.
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Affiliation(s)
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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Silva MS, Arraes FBM, Campos MDA, Grossi-de-Sa M, Fernandez D, Cândido EDS, Cardoso MH, Franco OL, Grossi-de-Sa MF. Review: Potential biotechnological assets related to plant immunity modulation applicable in engineering disease-resistant crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:72-84. [PMID: 29576088 DOI: 10.1016/j.plantsci.2018.02.013] [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: 10/09/2017] [Revised: 02/01/2018] [Accepted: 02/04/2018] [Indexed: 05/21/2023]
Abstract
This review emphasizes the biotechnological potential of molecules implicated in the different layers of plant immunity, including, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), effector-triggered susceptibility (ETS), and effector-triggered immunity (ETI) that can be applied in the development of disease-resistant genetically modified (GM) plants. These biomolecules are produced by pathogens (viruses, bacteria, fungi, oomycetes) or plants during their mutual interactions. Biomolecules involved in the first layers of plant immunity, PTI and ETS, include inhibitors of pathogen cell-wall-degrading enzymes (CWDEs), plant pattern recognition receptors (PRRs) and susceptibility (S) proteins, while the ETI-related biomolecules include plant resistance (R) proteins. The biomolecules involved in plant defense PTI/ETI responses described herein also include antimicrobial peptides (AMPs), pathogenesis-related (PR) proteins and ribosome-inhibiting proteins (RIPs), as well as enzymes involved in plant defensive secondary metabolite biosynthesis (phytoanticipins and phytoalexins). Moreover, the regulation of immunity by RNA interference (RNAi) in GM disease-resistant plants is also considered. Therefore, the present review does not cover all the classes of biomolecules involved in plant innate immunity that may be applied in the development of disease-resistant GM crops but instead highlights the most common strategies in the literature, as well as their advantages and disadvantages.
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Affiliation(s)
- Marilia Santos Silva
- Embrapa Recursos Genéticos e Biotecnologia (Embrapa Cenargen), Brasília, DF, Brazil.
| | - Fabrício Barbosa Monteiro Arraes
- Embrapa Recursos Genéticos e Biotecnologia (Embrapa Cenargen), Brasília, DF, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), Post-Graduation Program in Molecular and Cellular Biology, Porto Alegre, RS, Brazil.
| | | | | | | | - Elizabete de Souza Cândido
- Universidade Católica de Brasília (UCB), Post-Graduation Program in Genomic Science and Biotechnology, Brasília, DF, Brazil; Universidade Católica Dom Bosco (UCDB), Campo Grande, MS, Brazil
| | - Marlon Henrique Cardoso
- Universidade Católica de Brasília (UCB), Post-Graduation Program in Genomic Science and Biotechnology, Brasília, DF, Brazil; Universidade Católica Dom Bosco (UCDB), Campo Grande, MS, Brazil; Universidade de Brasília (UnB), Brasilia, DF, Brazil
| | - Octávio Luiz Franco
- Universidade Católica de Brasília (UCB), Post-Graduation Program in Genomic Science and Biotechnology, Brasília, DF, Brazil; Universidade Católica Dom Bosco (UCDB), Campo Grande, MS, Brazil; Universidade de Brasília (UnB), Brasilia, DF, Brazil
| | - Maria Fátima Grossi-de-Sa
- Embrapa Recursos Genéticos e Biotecnologia (Embrapa Cenargen), Brasília, DF, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), Post-Graduation Program in Molecular and Cellular Biology, Porto Alegre, RS, Brazil; Universidade Católica de Brasília (UCB), Post-Graduation Program in Genomic Science and Biotechnology, Brasília, DF, Brazil; Universidade de Brasília (UnB), Brasilia, DF, Brazil.
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41
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Ciarkowska A, Ostrowski M, Jakubowska A. A serine carboxypeptidase-like acyltransferase catalyzes synthesis of indole-3-acetic (IAA) ester conjugate in rice (Oryza sativa). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 125:126-135. [PMID: 29448154 DOI: 10.1016/j.plaphy.2018.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/16/2018] [Accepted: 02/06/2018] [Indexed: 05/16/2023]
Abstract
Indole-3-acetic acid (IAA) conjugation is one of mechanisms responsible for regulation of free auxin levels in plants. A new member of the serine carboxypeptidase-like (SCPL) acyltransferases family from Oryza sativa has been cloned and characterized. 1-O-indole-3-acetyl-β-D-glucose (1-O-IAGlc): myo-inositol acyltransferase (IAInos synthase) is an enzyme of IAA ester conjugates biosynthesis pathway that catalyzes transfer of IAA moiety from 1-O-IAGlc to myo-inositol forming IA-myo-inositol (IAInos). The OsIAA-At cDNA has been cloned and expressed using yeast and bacterial expression systems. Proteins produced in Saccharomyces cerevisiae and Escherichia coli contained 483 and 517 amino acids, respectively. The enzyme functionally expressed in both expression systems exhibits 1-O-IAGlc-dependent acyltransferase activity. Analysis of amino acid sequence confirmed that rice IAInos synthase belongs to the SCPL protein family. Recombinant IAInos synthases produced in yeast and bacterial expression systems have been partially characterized and their properties have been compared to those of the native enzyme obtained from 6-days-old rice seedlings by biochemical approach. The oligosaccharide component of the protein enzyme is not necessary for its catalytic activity. The native enzyme showed the lowest specific activity of 5.01 nmol min-1 mg-1 protein, whereas the recombinant enzymes produced in yeast and bacteria showed specific activity of 18.75 nmol min-1 mg-1 protein and 18.09 nmol min-1 mg-1 protein, respectively. The KM values for myo-inositol were similar for all three forms of the enzyme: 1.38, 0.83, 1.0 mM for native, bacterial and yeast protein, respectively. Both recombinant forms of IAInos synthase and the native enzyme also have the same optimal pH of 7.4 and all of them are inhibited by phenylmethylsulfonyl fluoride (PMSF), specific inhibitor of serine carboxypeptidases.
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Affiliation(s)
- Anna Ciarkowska
- Department of Biochemistry, Nicolaus Copernicus University, Torun, Lwowska 1, Poland
| | - Maciej Ostrowski
- Department of Biochemistry, Nicolaus Copernicus University, Torun, Lwowska 1, Poland.
| | - Anna Jakubowska
- Department of Biochemistry, Nicolaus Copernicus University, Torun, Lwowska 1, Poland
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Dingkuhn M, Pasco R, Pasuquin JM, Damo J, Soulié JC, Raboin LM, Dusserre J, Sow A, Manneh B, Shrestha S, Kretzschmar T. Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. Thermal stress and spikelet sterility. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4389-4406. [PMID: 28922773 DOI: 10.1093/jxb/erx250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology. The objectives were to improve the RIDEV model of rice thermal sterility, to estimate response traits by fitting model parameters, and to link the response traits to genomic regions through genome-wide association studies (GWAS). RIDEV captured 64% of variation of sterility when cold acclimation during vegetative stage was simulated, but only 38% when it was not. The RIDEV parameters gave more and stronger quantitative trait loci (QTLs) than index variables derived more directly from observation. The 15 QTLs identified at P<1 × 10-5 (33 at P<1 × 10-4) were related to sterility effects of heat, cold, cold acclimation, or unexplained causes (baseline sterility). Nine annotated genes were found on average within the 50% linkage disequilibrium (LD) region. Among them, one to five plausible candidate genes per QTL were identified based on known expression profiles (organ, stage, stress factors) and function. Meiosis-, development- and flowering-related genes were frequent, as well a stress signaling kinases and transcription factors. Putative epigenetic factors such as DNA methylases or histone-related genes were frequent in cold-acclimation QTLs, and positive-effect alleles were frequent in cold-tolerant highland rice from Madagascar. The results indicate that epigenetic control of acclimation may be important in indica rice genotypes adapted to cool environments.
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Affiliation(s)
- Michael Dingkuhn
- Cirad, Umr AGAP (Dept BIOS) and Upr AIDA (Dept ES), F-34398, Montpellier, France
| | - Richard Pasco
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | | | - Jean Damo
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | | | - Louis-Marie Raboin
- Cirad, Umr AGAP (Dept BIOS) and Upr AIDA (Dept ES), F-34398, Montpellier, France
| | - Julie Dusserre
- Cirad, Umr AGAP (Dept BIOS) and Upr AIDA (Dept ES), F-34398, Montpellier, France
| | - Abdoulaye Sow
- Africa Rice Center, Sahel Station, PB 96, St Louis, Senegal
| | | | - Suchit Shrestha
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
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43
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Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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Ghosh S. Triterpene Structural Diversification by Plant Cytochrome P450 Enzymes. FRONTIERS IN PLANT SCIENCE 2017; 8:1886. [PMID: 29170672 PMCID: PMC5684119 DOI: 10.3389/fpls.2017.01886] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 10/18/2017] [Indexed: 05/06/2023]
Abstract
Cytochrome P450 monooxygenases (P450s) represent the largest enzyme family of the plant metabolism. Plants typically devote about 1% of the protein-coding genes for the P450s to execute primary metabolism and also to perform species-specific specialized functions including metabolism of the triterpenes, isoprene-derived 30-carbon compounds. Triterpenes constitute a large and structurally diverse class of natural products with various industrial and pharmaceutical applications. P450-catalyzed structural modification is crucial for the diversification and functionalization of the triterpene scaffolds. In recent times, a remarkable progress has been made in understanding the function of the P450s in plant triterpene metabolism. So far, ∼80 P450s are assigned biochemical functions related to the plant triterpene metabolism. The members of the subfamilies CYP51G, CYP85A, CYP90B-D, CYP710A, CYP724B, and CYP734A are generally conserved across the plant kingdom to take part in plant primary metabolism related to the biosynthesis of essential sterols and steroid hormones. However, the members of the subfamilies CYP51H, CYP71A,D, CYP72A, CYP81Q, CYP87D, CYP88D,L, CYP93E, CYP705A, CYP708A, and CYP716A,C,E,S,U,Y are required for the metabolism of the specialized triterpenes that might perform species-specific functions including chemical defense toward specialized pathogens. Moreover, a recent advancement in high-throughput sequencing of the transcriptomes and genomes has resulted in identification of a large number of candidate P450s from diverse plant species. Assigning biochemical functions to these P450s will be of interest to extend our knowledge on triterpene metabolism in diverse plant species and also for the sustainable production of valuable phytochemicals.
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45
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O’Neill EC, Kelly S. Engineering biosynthesis of high-value compounds in photosynthetic organisms. Crit Rev Biotechnol 2016; 37:779-802. [DOI: 10.1080/07388551.2016.1237467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, UK
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46
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Medema MH, Osbourn A. Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways. Nat Prod Rep 2016; 33:951-62. [PMID: 27321668 PMCID: PMC4987707 DOI: 10.1039/c6np00035e] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 01/09/2023]
Abstract
Covering: 2003 to 2016The last decade has seen the first major discoveries regarding the genomic basis of plant natural product biosynthetic pathways. Four key computationally driven strategies have been developed to identify such pathways, which make use of physical clustering, co-expression, evolutionary co-occurrence and epigenomic co-regulation of the genes involved in producing a plant natural product. Here, we discuss how these approaches can be used for the discovery of plant biosynthetic pathways encoded by both chromosomally clustered and non-clustered genes. Additionally, we will discuss opportunities to prioritize plant gene clusters for experimental characterization, and end with a forward-looking perspective on how synthetic biology technologies will allow effective functional reconstitution of candidate pathways using a variety of genetic systems.
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Affiliation(s)
- Marnix H. Medema
- Bioinformatics Group , Wageningen University , Wageningen , The Netherlands .
| | - Anne Osbourn
- Department of Metabolic Biology , John Innes Centre , Norwich Research Park , Norwich , UK .
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Nützmann HW, Huang A, Osbourn A. Plant metabolic clusters - from genetics to genomics. THE NEW PHYTOLOGIST 2016; 211:771-89. [PMID: 27112429 PMCID: PMC5449196 DOI: 10.1111/nph.13981] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/22/2016] [Indexed: 05/18/2023]
Abstract
Contents 771 I. 771 II. 772 III. 780 IV. 781 V. 786 786 References 786 SUMMARY: Plant natural products are of great value for agriculture, medicine and a wide range of other industrial applications. The discovery of new plant natural product pathways is currently being revolutionized by two key developments. First, breakthroughs in sequencing technology and reduced cost of sequencing are accelerating the ability to find enzymes and pathways for the biosynthesis of new natural products by identifying the underlying genes. Second, there are now multiple examples in which the genes encoding certain natural product pathways have been found to be grouped together in biosynthetic gene clusters within plant genomes. These advances are now making it possible to develop strategies for systematically mining multiple plant genomes for the discovery of new enzymes, pathways and chemistries. Increased knowledge of the features of plant metabolic gene clusters - architecture, regulation and assembly - will be instrumental in expediting natural product discovery. This review summarizes progress in this area.
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Affiliation(s)
- Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ancheng Huang
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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A conserved amino acid residue critical for product and substrate specificity in plant triterpene synthases. Proc Natl Acad Sci U S A 2016; 113:E4407-14. [PMID: 27412861 DOI: 10.1073/pnas.1605509113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Triterpenes are structurally complex plant natural products with numerous medicinal applications. They are synthesized through an origami-like process that involves cyclization of the linear 30 carbon precursor 2,3-oxidosqualene into different triterpene scaffolds. Here, through a forward genetic screen in planta, we identify a conserved amino acid residue that determines product specificity in triterpene synthases from diverse plant species. Mutation of this residue results in a major change in triterpene cyclization, with production of tetracyclic rather than pentacyclic products. The mutated enzymes also use the more highly oxygenated substrate dioxidosqualene in preference to 2,3-oxidosqualene when expressed in yeast. Our discoveries provide new insights into triterpene cyclization, revealing hidden functional diversity within triterpene synthases. They further open up opportunities to engineer novel oxygenated triterpene scaffolds by manipulating the precursor supply.
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49
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Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
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Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
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50
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Ono NN, Qin X, Wilson AE, Li G, Tian L. Two UGT84 Family Glycosyltransferases Catalyze a Critical Reaction of Hydrolyzable Tannin Biosynthesis in Pomegranate (Punica granatum). PLoS One 2016; 11:e0156319. [PMID: 27227328 PMCID: PMC4882073 DOI: 10.1371/journal.pone.0156319] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022] Open
Abstract
Hydrolyzable tannins (HTs) play important roles in plant herbivore deterrence and promotion of human health. A critical step in HT production is the formation of 1-O-galloyl-β-D-glucopyranoside (β-glucogallin, ester-linked gallic acid and glucose) by a UDP-glucosyltransferase (UGT) activity. We cloned and biochemically characterized four candidate UGTs from pomegranate (Punica granatum), of which only UGT84A23 and UGT84A24 exhibited β-glucogallin forming activities in enzyme assays. Although overexpression and single RNAi knockdown pomegranate hairy root lines of UGT84A23 or UGT84A24 did not lead to obvious alterations in punicalagin (the prevalent HT in pomegranate) accumulation, double knockdown lines of the two UGTs resulted in largely reduced levels of punicalagins and bis-hexahydroxydiphenyl glucose isomers. An unexpected accumulation of galloyl glucosides (ether-linked gallic acid and glucose) was also detected in the double knockdown lines, suggesting that gallic acid was utilized by an unidentified UGT activity for glucoside formation. Transient expression in Nicotiana benthamiana leaves and immunogold labeling in roots of pomegranate seedlings collectively indicated cytosolic localization of UGT84A23 and UGT84A24. Overall, functional characterization and localization of UGT84A23 and UGT84A24 open up opportunities for further understanding the regulatory control of HT metabolism in plants and its coordination with other biochemical pathways in the metabolic network.
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Affiliation(s)
- Nadia N. Ono
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Xiaoqiong Qin
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Alexander E. Wilson
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Gang Li
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Li Tian
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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