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Huang J, Ma S, Zhou M, Liu Z, Liang Q. Cytochemical localization and synthesis mechanism of the glucomannan in pseudobulbs of Bletilla striata Reichb. f. HORTICULTURE RESEARCH 2024; 11:uhae092. [PMID: 38799126 PMCID: PMC11116825 DOI: 10.1093/hr/uhae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/25/2024] [Indexed: 05/29/2024]
Abstract
The dried pseudobulbs of Bletilla striata, an important traditional Chinese medicine named BaiJi, have an extraordinary polysaccharide content and excellent prospects for medicinal effects. However, the distribution and molecular mechanism underlying biosynthesis are poorly understood. In this study, chemical and immunologic analyses were performed in representative tissues of B. striata, and the results showed that what are conventionally termed Bletilla striata polysaccharides (BSPs) are water-soluble polysaccharides deposited only in pseudobulbs. The structural component of BSPs is glucomannan, with a mannose:glucose mass ratio of ~3:2. BSPs are present in the parenchyma of the pseudobulbs in cells known as glucomannan idioblasts and distributed in the cytoplasm within cellular membranes, but are not contained in the vacuole. Comparative transcriptomics and bioinformatics analyses mapped the pathway from sucrose to BSP and identified BsGPI, BsmanA, and BsCSLAs as the key genes of BSP biosynthesis, suggesting that the functional differentiation of the cellulose synthase-like family A (CSLA) may be critical for the flow of glucomannan to the BSP or cell wall. Subsequently, virus-mediated gene silencing showed that silencing of two CSLAs (Bs03G11846 and Bs03G11849) led to a decrease in BSP content, and yeast two-hybrid and luciferase complementation experiments confirmed that four CSLAs (Bs03G11846, Bs03G11847, Bs03G11848, and Bs03G11849) can form homo- or heterodimers, suggesting that multiple CSLAs may form a large complex that functions in BSP synthesis. Our results provide cytological evidence of BSP and describe the isolation and characterization of candidate genes involved in BSP synthesis, laying a solid foundation for further research on its regulation mechanisms and the genetic engineering breeding of B. striata.
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Affiliation(s)
- Junfeng Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Shuang Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ming Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhihao Liu
- Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi City 435002, China
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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2
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Ishikawa E, Kanai S, Shinozawa A, Hyakutake M, Sue M. Hordeum vulgare CYP76M57 catalyzes C 2 shortening of tryptophan side chain by C-N bond rearrangement in gramine biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:892-904. [PMID: 38281119 DOI: 10.1111/tpj.16644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/25/2023] [Accepted: 01/07/2024] [Indexed: 01/29/2024]
Abstract
The indole alkaloid gramine, 3-(dimethylaminomethyl)indole, is a defensive specialized metabolite found in some barley cultivars. In its biosynthetic process, the tryptophan (Trp) side chain is shortened by two carbon atoms to produce 3-(aminomethyl)indole (AMI), which is then methylated by N-methyltransferase (HvNMT) to produce gramine. Although side chain shortening is one of the crucial scaffold formation steps of alkaloids originating from aromatic amino acids, the gene and enzyme involved in the Trp-AMI conversion reactions are unknown. In this study, through RNA-seq analysis, 35 transcripts were shown to correlate with gramine production; among them, an uncharacterized cytochrome P450 (CYP) gene, CYP76M57, and HvNMT were identified as candidate genes for gramine production. Transgenic Arabidopsis thaliana and rice overexpressing CYP and HvNMT accumulate AMI, N-methyl-AMI, and gramine. CYP76M57, heterologously expressed in Pichia pastoris, was able to act on Trp to produce AMI. Furthermore, the amino group nitrogen of Trp was retained during the CYP76M57-catalyzed reaction, indicating that the C2 shortening of Trp proceeds with an unprecedented biosynthetic process, the removal of the carboxyl group and Cα and the rearrangement of the nitrogen atom to Cβ. In some gramine-non-accumulating barley cultivars, arginine 104 in CYP76M57 is replaced by threonine, which abolished the catalytic activity of CYP76M57 to convert Trp into AMI. These results uncovered the missing committed enzyme of gramine biosynthesis in barley and contribute to the elucidation of the potential functions of CYPs in plants and undiscovered specialized pathways.
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Affiliation(s)
- Erika Ishikawa
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Shion Kanai
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Akihisa Shinozawa
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
- The NODAI Genome Research Center (NGRC), Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Mami Hyakutake
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Masayuki Sue
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
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3
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Wu Y, Fu Y, Zhu Z, Hu Q, Sheng F, Du X. The Mediator Subunit OsMED16 Interacts with the WRKY Transcription Factor OsWRKY45 to Enhance Rice Resistance Against Magnaporthe oryzae. RICE (NEW YORK, N.Y.) 2024; 17:23. [PMID: 38558163 PMCID: PMC10984912 DOI: 10.1186/s12284-024-00698-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/03/2024] [Indexed: 04/04/2024]
Abstract
Rice blast, caused by Magnaporthe oryzae (M. oryzae), is one of the most common and damaging diseases of rice that limits rice yield and quality. The mediator complex plays a vital role in promoting transcription by bridging specific transcription factors and RNA polymerase II. Here, we show that the rice mediator subunit OsMED16 is essential for full induction of the diterpenoid phytoalexin biosynthesis genes and resistance to the ascomycetous fungus M. oryzae. Mutants of Osmed16 show reduced expression of the DP biosynthesis genes and are markedly more susceptible to M. oryzae, while transgenic plants overexpressing OsMED16 increased the expression of the DP biosynthesis genes and significantly enhanced resistance to M. oryzae. Interestingly, OsMED16 is physically associated with the WRKY family transcription factor OsWRKY45, which interacts with the phytoalexin synthesis key regulator transcription factor OsWRKY62. Further, OsMED16-OsWRKY45-OsWRKY62 complex could bind to the promoter regions of phytoalexin synthesis-related genes and activate their gene expression. Our results show that OsMED16 may enhance rice tolerance to M. oryzae via directly manipulating phytoalexin de novo biosynthesis.
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Affiliation(s)
- Yanfei Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yuquan Fu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Zhonglin Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Qin Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China.
| | - Feng Sheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Xuezhu Du
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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4
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Zhou H, Zhang J, Bai L, Liu J, Li H, Hua J, Luo S. Chemical Structure Diversity and Extensive Biological Functions of Specialized Metabolites in Rice. Int J Mol Sci 2023; 24:17053. [PMID: 38069376 PMCID: PMC10707428 DOI: 10.3390/ijms242317053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Rice (Oryza sativa L.) is thought to have been domesticated many times independently in China and India, and many modern cultivars are available. All rice tissues are rich in specialized metabolites (SPMs). To date, a total of 181 terpenoids, 199 phenolics, 41 alkaloids, and 26 other types of compounds have been detected in rice. Some volatile sesquiterpenoids released by rice are known to attract the natural enemies of rice herbivores, and play an indirect role in defense. Momilactone, phytocassane, and oryzalic acid are the most common diterpenoids found in rice, and are found at all growth stages. Indolamides, including serotonin, tryptamine, and N-benzoylserotonin, are the main rice alkaloids. The SPMs mainly exhibit defense functions with direct roles in resisting herbivory and pathogenic infections. In addition, phenolics are also important in indirect defense, and enhance wax deposition in leaves and promote the lignification of stems. Meanwhile, rice SPMs also have allelopathic effects and are crucial in the regulation of the relationships between different plants or between plants and microorganisms. In this study, we reviewed the various structures and functions of rice SPMs. This paper will provide useful information and methodological resources to inform the improvement of rice resistance and the promotion of the rice industry.
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Affiliation(s)
| | | | | | | | | | - Juan Hua
- Research Center of Protection and Utilization of Plant Resources, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China (J.L.)
| | - Shihong Luo
- Research Center of Protection and Utilization of Plant Resources, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China (J.L.)
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5
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Gong C, Liu D, Wang Q, Ma Y, Zhan X, Zhang S, Awais M, Pu J, Yang J, Wang X. Metabolic Resistance of Sogatella furcifera (Hemiptera: Delphacidae) toward Pymetrozine Involves the Overexpression of CYP6FJ3. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14179-14191. [PMID: 37660343 DOI: 10.1021/acs.jafc.3c03617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Sogatella furcifera (Horváth), which mainly threatens rice, shows various levels of pesticide resistance due to long-term overuse of pesticides. Our resistance monitoring of 20 field populations in Sichuan, China, revealed that they were susceptible to highly resistant toward pymetrozine (0.4-142.2 RR), and JL21 reached the highest level of resistance. The JL21 population exhibited cross-resistance to triflumezopyrim and dinotefuran but sensitivity to sulfoxaflor, acetamiprid, clothianidin, and nitenpyram. The increased P450 activity were support to involve in pymetrozine resistance by detoxification enzyme activities and synergist determination. Among 16 candidate P450 genes, CYP6FJ3 (5.25-fold) was the most up-regulated in JL21, while no significant change was found after LC25 pymetrozine treatment. Furthermore, the knockdown by RNAi and heterologous overexpression by the GAL4/UAS system confirmed that the CYP6FJ3 overexpression was involved in the pymetrozine resistance, and recombination in vitro confirmed that CYP6FJ3 could hydroxylate pymetrozine. Therefore, the overexpression of CYP6FJ3 promotes pymetrozine metabolic resistance in S. furcifera.
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Affiliation(s)
- Changwei Gong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Dan Liu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiulin Wang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanxin Ma
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoxu Zhan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 611130, China
| | - Shuirong Zhang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Awais
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jian Pu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jizhi Yang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuegui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
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6
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Cunha E, Silva M, Chaves I, Demirci H, Lagoa DR, Lima D, Rocha M, Rocha I, Dias O. The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Comput Biol 2023; 19:e1011499. [PMID: 37729340 PMCID: PMC10545120 DOI: 10.1371/journal.pcbi.1011499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/02/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
Over the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behaviour at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871). The metabolic model comprises 7871 genes, 6231 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen, with specific biomass compositions. The tissue-specific models were merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyse the pathways associated with the synthesis of suberin monomers, namely the acyl-lipids, phenylpropanoids, isoprenoids, and flavonoids production. The models developed in this work provide a systematic overview of the metabolism of Q. suber, including its secondary metabolism pathways and cork formation.
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Affiliation(s)
- Emanuel Cunha
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Miguel Silva
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Huseyin Demirci
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
- SnT/University of Luxembourg, Luxembourg
| | | | - Diogo Lima
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga, Guimarães, Portugal
| | - Isabel Rocha
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, Oeiras, Portugal
| | - Oscar Dias
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga, Guimarães, Portugal
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7
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Lanier ER, Andersen TB, Hamberger B. Plant terpene specialized metabolism: complex networks or simple linear pathways? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1178-1201. [PMID: 36891828 PMCID: PMC11166267 DOI: 10.1111/tpj.16177] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 05/31/2023]
Abstract
From the perspectives of pathway evolution, discovery and engineering of plant specialized metabolism, the nature of the biosynthetic routes represents a critical aspect. Classical models depict biosynthesis typically from an end-point angle and as linear, for example, connecting central and specialized metabolism. As the number of functionally elucidated routes increased, the enzymatic foundation of complex plant chemistries became increasingly well understood. The perception of linear pathway models has been severely challenged. With a focus on plant terpenoid specialized metabolism, we review here illustrative examples supporting that plants have evolved complex networks driving chemical diversification. The completion of several diterpene, sesquiterpene and monoterpene routes shows complex formation of scaffolds and their subsequent functionalization. These networks show that branch points, including multiple sub-routes, mean that metabolic grids are the rule rather than the exception. This concept presents significant implications for biotechnological production.
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Affiliation(s)
| | | | - Björn Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, Molecular Plant Sciences Building, 1066 Bogue Street, East Lansing, Michigan, 48824, USA
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8
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Zhou M, Jiang Y, Liu X, Kong W, Zhang C, Yang J, Ke S, Li Y. Genome-Wide Identification and Evolution Analysis of the CYP76 Subfamily in Rice ( Oryza sativa). Int J Mol Sci 2023; 24:ijms24108522. [PMID: 37239869 DOI: 10.3390/ijms24108522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
The CYP76 subfamily, a member of the CYP superfamily, plays crucial roles in the biosynthesis of phytohormones in plants, involving biosynthesis of secondary metabolites, hormone signaling, and response to environmental stresses. Here, we conducted a genome-wide analysis of the CYP76 subfamily in seven AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, and Oryza glumaepatula. These were identified and classified into three groups, and it was found that Group 1 contained the largest number of members. Analysis of cis-acting elements revealed a large number of elements related to jasmonic acid and light response. The gene duplication analysis revealed that the CYP76 subfamily expanded mainly in SD/WGD and tandem forms and underwent strong purifying selection during evolution. Expression pattern analysis of OsCYP76s in various developmental stages revealed that the majority of OsCYP76s exhibit relatively restricted expression patterns in leaves and roots. We further analyzed the expression of CYP76s in O. sativa, japonica, and O. sativa, indica under cold, flooding, drought, and salt abiotic stresses by qRT-PCR. We found that OsCYP76-11 showed a huge increase in relative expression after drought and salt stresses. After flooding stress, OsiCYP76-4 showed a greater increase in expression compared to other genes. CYP76 in japonica and indica showed different response patterns to the same abiotic stresses, revealing functional divergence in the gene family during evolution; these may be the key genes responsible for the differences in tolerance to indica japonica. Our results provide valuable insights into the functional diversity and evolutionary history of the CYP76 subfamily and pave the way for the development of new strategies for improving stress tolerance and agronomic traits in rice.
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Affiliation(s)
- Mingao Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yifei Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xuhui Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Shenzhen Branch, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China
| | - Jian Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Simin Ke
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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9
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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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10
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Zhao L, Oyagbenro R, Feng Y, Xu M, Peters RJ. Oryzalexin S biosynthesis: a cross-stitched disappearing pathway. ABIOTECH 2023; 4:1-7. [PMID: 37220540 PMCID: PMC10199973 DOI: 10.1007/s42994-022-00092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/25/2023]
Abstract
Rice produces many diterpenoid phytoalexins and, reflecting the importance of these natural products in this important cereal crop plant, its genome contains three biosynthetic gene clusters (BGCs) for such metabolism. The chromosome 4 BGC (c4BGC) is largely associated with momilactone production, in part due to the presence of the initiating syn-copalyl diphosphate (CPP) synthase gene (OsCPS4). Oryzalexin S is also derived from syn-CPP. However, the relevant subsequently acting syn-stemarene synthase gene (OsKSL8) is not located in the c4BGC. Production of oryzalexin S further requires hydroxylation at carbons 2 and 19 (C2 and C19), presumably catalyzed by cytochrome P450 (CYP) monooxygenases. Here it is reported the closely related CYP99A2 and CYP99A3, whose genes are also found in the c4BGC catalyze the necessary C19-hydroxylation, while the closely related CYP71Z21 and CYP71Z22, whose genes are found in the recently reported chromosome 7 BGC (c7BGC), catalyze subsequent hydroxylation at C2α. Thus, oryzalexin S biosynthesis utilizes two distinct BGCs, in a pathway cross-stitched together by OsKSL8. Notably, in contrast to the widely conserved c4BGC, the c7BGC is subspecies (ssp.) specific, being prevalent in ssp. japonica and only rarely found in the other major ssp. indica. Moreover, while the closely related syn-stemodene synthase OsKSL11 was originally considered to be distinct from OsKSL8, it has now been reported to be a ssp. indica derived allele at the same genetic loci. Intriguingly, more detailed analysis indicates that OsKSL8(j) is being replaced by OsKSL11 (OsKSL8i), suggesting introgression from ssp. indica to (sub)tropical japonica, with concurrent disappearance of oryzalexin S production. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-022-00092-3.
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Affiliation(s)
- Le Zhao
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Richard Oyagbenro
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Yiling Feng
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Meimei Xu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
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11
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Zhao S, Zhang Q, Xiao W, Chen D, Hu J, Gao N, Huang M, Ye X. Comparative transcriptomic analysis reveals the important process in two rice cultivars with differences in cadmium accumulation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114629. [PMID: 36764070 DOI: 10.1016/j.ecoenv.2023.114629] [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: 08/23/2022] [Revised: 01/15/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
To date, Cd remains a major contaminant in rice production. An in-depth exploration of the mechanism that causes genotypic differences in Cd enrichment in rice is necessary to develop strategies to regulate Cd enrichment in rice. Here, two rice cultivars (low grain Cd, ZZ143; and high grain Cd, YX409) displayed different transcriptomic profile patterns when subjected to 100μmol/L Cd stress. In fact, 18,721(9833 upregulated and 8888 downregulated) and 16,403 (8366 upregulated and 8037 downregulated) differentially expressed genes (DEGs) were found in ZZ143 and YX409, respectively. Gene ontology (GO) classification revealed 28 and 26 terms enriched in ZZ143 and YX409, respectively. ZZ143 had more enriched DEGs than YX409, primarily in cellular processes, metabolic processes, binding terms, catalytic activity, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 21 and 24 pathways were significantly enriched in ZZ143 and YX409, respectively. Based on the DEGs, ZZ143 had a stronger ability for sulfur assimilation and Cys synthesis, whereas YX409 had a stronger ability to maintain cell wall stability. A series of DEGs involved in metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction pathways, and mitogen-activated protein kinase signaling pathways were identified, which maybe closely related to Cd resistance and the different Cd concentrations between cultivars. The above pathways and the greater number of identified DEGs in more than half of the GO terms and KEGG pathways suggest a higher absorption and stronger tolerance of the roots of ZZ143 than YX409 to Cd.
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Affiliation(s)
- Shouping Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wendan Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - De Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jing Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Na Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Miaojie Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xuezhu Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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12
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Wang Z, Nelson DR, Zhang J, Wan X, Peters RJ. Plant (di)terpenoid evolution: from pigments to hormones and beyond. Nat Prod Rep 2023; 40:452-469. [PMID: 36472136 PMCID: PMC9945934 DOI: 10.1039/d2np00054g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to 2014-2022.Diterpenoid biosynthesis in plants builds on the necessary production of (E,E,E)-geranylgeranyl diphosphate (GGPP) for photosynthetic pigment production, with diterpenoid biosynthesis arising very early in land plant evolution, enabling stockpiling of the extensive arsenal of (di)terpenoid natural products currently observed in this kingdom. This review will build upon that previously published in the Annual Review of Plant Biology, with a stronger focus on enzyme structure-function relationships, as well as additional insights into the evolution of (di)terpenoid metabolism since generated.
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Affiliation(s)
- Zhibiao Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China.,Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50014, USA.
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Juan Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50014, USA.
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13
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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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14
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Valletta A, Iozia LM, Fattorini L, Leonelli F. Rice Phytoalexins: Half a Century of Amazing Discoveries; Part I: Distribution, Biosynthesis, Chemical Synthesis, and Biological Activities. PLANTS (BASEL, SWITZERLAND) 2023; 12:260. [PMID: 36678973 PMCID: PMC9862927 DOI: 10.3390/plants12020260] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 06/17/2023]
Abstract
Cultivated rice is a staple food for more than half of the world's population, providing approximately 20% of the world's food energy needs. A broad spectrum of pathogenic microorganisms causes rice diseases leading to huge yield losses worldwide. Wild and cultivated rice species are known to possess a wide variety of antimicrobial secondary metabolites, known as phytoalexins, which are part of their active defense mechanisms. These compounds are biosynthesized transiently by rice in response to pathogens and certain abiotic stresses. Rice phytoalexins have been intensively studied for over half a century, both for their biological role and their potential application in agronomic and pharmaceutical fields. In recent decades, the growing interest of the research community, combined with advances in chemical, biological, and biomolecular investigation methods, has led to a notable acceleration in the growth of knowledge on rice phytoalexins. This review provides an overview of the knowledge gained in recent decades on the diversity, distribution, biosynthesis, chemical synthesis, and bioactivity of rice phytoalexins, with particular attention to the most recent advances in this research field.
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Affiliation(s)
- Alessio Valletta
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Maria Iozia
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Laura Fattorini
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Francesca Leonelli
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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15
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Zhan C, Lei L, Guo H, Zhou S, Xu C, Liu Z, Wu Z, Deng Y, Miao Y, Han Y, Zhang M, Li H, Huang S, Yang C, Zhang F, Li Y, Liu L, Liu X, Abbas HMK, Fernie AR, Yuan M, Luo J. Disease resistance conferred by components of essential chrysanthemum oil and the epigenetic regulation of OsTPS1. SCIENCE CHINA LIFE SCIENCES 2022; 66:1108-1118. [PMID: 36462108 DOI: 10.1007/s11427-022-2241-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/10/2022] [Indexed: 12/04/2022]
Abstract
The sesquiterpene alpha-bisabolol is the predominant active ingredient in essential oils that are highly valued in the cosmetics industry due to its wound healing, anti-inflammatory, and skin-soothing properties. Alpha-bisabolol was thought to be restricted to Compositae plants. Here we reveal that alpha-bisabolol is also synthesized in rice, a non-Compositae plant, where it acts as a novel sesquiterpene phytoalexin. Overexpressing the gene responsible for the biosynthesis of alpha-bisabolol, OsTPS1, conferred bacterial blight resistance in rice. Phylogenomic analyses revealed that alpha-bisabolol-synthesizing enzymes in rice and Compositae evolved independently. Further experiments demonstrated that the natural variation in the disease resistance level was associated with differential transcription of OsTPS1 due to polymorphisms in its promoter. We demonstrated that OsTPS1 was regulated at the epigenetic level by JMJ705 through the methyl jasmonate pathway. These data reveal the cross-family accumulation and regulatory mechanisms of alpha-bisabolol production.
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16
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Tiedge K, Li X, Merrill AT, Davisson D, Chen Y, Yu P, Tantillo DJ, Last RL, Zerbe P. Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum). THE NEW PHYTOLOGIST 2022; 236:1393-1408. [PMID: 36028985 PMCID: PMC9912200 DOI: 10.1111/nph.18443] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/09/2022] [Indexed: 05/13/2023]
Abstract
Switchgrass (Panicum virgatum) is a bioenergy model crop valued for its energy efficiency and drought tolerance. The related monocot species rice (Oryza sativa) and maize (Zea mays) deploy species-specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown. To investigate specialized metabolic drought responses in switchgrass, we integrated tissue-specific transcriptome and metabolite analyses of the genotypes Alamo and Cave-in-Rock that feature different drought tolerance. The more drought-susceptible Cave-in-Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid-biosynthetic genes showed drought-inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype-specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought-induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis verified select drought-responsive diterpenoids as oxygenated furanoditerpenoids. Drought-dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass drought responses. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance.
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Affiliation(s)
- Kira Tiedge
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
- Groningen Institute for Evolutionary Life SciencesUniversity of Groningen9747AG Groningenthe Netherlands
| | - Xingxing Li
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Amy T. Merrill
- Department of ChemistryUniversity of California, DavisDavisCA95616USA
| | - Danielle Davisson
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
| | - Yuxuan Chen
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
| | - Ping Yu
- NMR FacilityUniversity of California, DavisDavisCA95616USA
| | - Dean J. Tantillo
- Department of ChemistryUniversity of California, DavisDavisCA95616USA
| | - Robert L. Last
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
- Department Plant BiologyMichigan State UniversityEast LansingMI48824USA
| | - Philipp Zerbe
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
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17
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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: 44] [Impact Index Per Article: 22.0] [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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18
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Singh KS, van der Hooft JJJ, van Wees SCM, Medema MH. Integrative omics approaches for biosynthetic pathway discovery in plants. Nat Prod Rep 2022; 39:1876-1896. [PMID: 35997060 PMCID: PMC9491492 DOI: 10.1039/d2np00032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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19
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Li CY, Yang L, Liu Y, Xu ZG, Gao J, Huang YB, Xu JJ, Fan H, Kong Y, Wei YK, Hu WL, Wang LJ, Zhao Q, Hu YH, Zhang YJ, Martin C, Chen XY. The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants. Cell Rep 2022; 40:111236. [PMID: 35977487 DOI: 10.1016/j.celrep.2022.111236] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/29/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022] Open
Abstract
The widely cultivated medicinal and ornamental plant sage (Salvia officinalis L.) is an evergreen shrub of the Lamiaceae family, native to the Mediterranean. We assembled a high-quality sage genome of 480 Mb on seven chromosomes, and identified a biosynthetic gene cluster (BGC) encoding two pairs of diterpene synthases (diTPSs) that, together with the cytochromes P450 (CYPs) genes located inside and outside the cluster, form two expression cascades responsible for the shoot and root diterpenoids, respectively, thus extending BGC functionality from co-regulation to orchestrating metabolite production in different organs. Phylogenomic analysis indicates that the Salvia clades diverged in the early Miocene. In East Asia, most Salvia species are herbaceous and accumulate diterpenoids in storage roots. Notably, in Chinese sage S. miltiorrhiza, the diterpene BGC has contracted and the shoot cascade has been lost. Our data provide genomic insights of micro-evolution of growth type-associated patterning of specialized metabolite production in plants.
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Affiliation(s)
- Chen-Yi Li
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yan Liu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Zhou-Geng Xu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Jian Gao
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Yan-Bo Huang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Jing-Jing Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Hang Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yu-Kun Wei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Wen-Li Hu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Ling-Jian Wang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yong-Hong Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China
| | - Yi-Jing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Fenglin Road 300, Shanghai 201602, China.
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20
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Smit SJ, Lichman BR. Plant biosynthetic gene clusters in the context of metabolic evolution. Nat Prod Rep 2022; 39:1465-1482. [PMID: 35441651 PMCID: PMC9298681 DOI: 10.1039/d2np00005a] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 12/17/2022]
Abstract
Covering: up to 2022Plants produce a wide range of structurally and biosynthetically diverse natural products to interact with their environment. These specialised metabolites typically evolve in limited taxonomic groups presumably in response to specific selective pressures. With the increasing availability of sequencing data, it has become apparent that in many cases the genes encoding biosynthetic enzymes for specialised metabolic pathways are not randomly distributed on the genome. Instead they are physically linked in structures such as arrays, pairs and clusters. The exact function of these clusters is debated. In this review we take a broad view of gene arrangement in plant specialised metabolism, examining types of structures and variation. We discuss the evolution of biosynthetic gene clusters in the wider context of metabolism, populations and epigenetics. Finally, we synthesise our observations to propose a new hypothesis for biosynthetic gene cluster formation in plants.
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Affiliation(s)
- Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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21
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Jiang M, Yu N, Zhang Y, Liu L, Li Z, Wang C, Cheng S, Cao L, Liu Q. Deletion of Diterpenoid Biosynthetic Genes CYP76M7 and CYP76M8 Induces Cell Death and Enhances Bacterial Blight Resistance in Indica Rice ‘9311’. Int J Mol Sci 2022; 23:ijms23137234. [PMID: 35806236 PMCID: PMC9266670 DOI: 10.3390/ijms23137234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
Lesion mimic mutants (LMMs) are ideal materials for studying cell death and resistance mechanisms. Here, we identified and mapped a novel rice LMM, g380. The g380 exhibits a spontaneous hypersensitive response-like cell death phenotype accompanied by excessive accumulation of reactive oxygen species (ROS) and upregulated expression of pathogenesis-related genes, as well as enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo). Using a map-based cloning strategy, a 184,916 bp deletion on chromosome 2 that overlaps with the diterpenoid biosynthetic gene cluster was identified in g380. Accordingly, the content of diterpenoids decreased in g380. In addition, lignin, one of the physical lines of plant defense, was increased in g380. RNA-seq analysis showed 590 significantly differentially expressed genes (DEG) between the wild-type 9311 and g380, 585 of which were upregulated in g380. Upregulated genes in g380 were mainly enriched in the monolignol biosynthesis branches of the phenylpropanoid biosynthesis pathway, the plant–pathogen interaction pathway and the phytoalexin-specialized diterpenoid biosynthesis pathway. Taken together, our results indicate that the diterpenoid biosynthetic gene cluster on chromosome 2 is involved in immune reprogramming, which in turn regulates cell death in rice.
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Affiliation(s)
- Min Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
| | - Ning Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yingxin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
| | - Lin Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhi Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
| | - Chen Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
| | - Shihua Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
| | - Liyong Cao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
- Northern Center for China National Rice Research Institute, China National Rice Research Institute, Hangzhou 311400, China
- Correspondence: (L.C.); (Q.L.)
| | - Qunen Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (M.J.); (N.Y.); (Y.Z.); (L.L.); (Z.L.); (C.W.); (S.C.)
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 311400, China
- Correspondence: (L.C.); (Q.L.)
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22
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Gong C, Ruan Y, Zhang Y, Wang Q, Wu Y, Zhan X, He Y, Liu X, Liu X, Pu J, Wang X. Resistance of Sogatella furcifera to triflumezopyrim mediated with the overexpression of CYPSF01 which was regulated by nuclear receptor USP. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 238:113575. [PMID: 35500402 DOI: 10.1016/j.ecoenv.2022.113575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Sogatella furcifera is one of the main agricultural pests in many Asian countries, bringing about enormous injury. A triflumezopyrim-resistant (Tri) strain of S. furcifera was established through continuous screening in laboratory. The determination of synergist and enzyme activity indicated that P450s, especially for the upregulation expression of CYPSF01, played a key role in the increased resistance, confirmed by RNAi, and the recombinant protein of CYPSF01 and NADPH-P450 reductase was able to degrade triflumezopyrim. CYPSF01 had an obviously co-expression relationship with nuclear receptor ultraspiracle (USP), which were all significantly up-regulated when exposed to triflumezopyrim. Further, a USP-binding motif MA0534.1 was enriched from the upregulated peaks by Assay for Transposase Accessible Chromatin (ATAC-seq) analysis, which exited in the peaks located on the promoter of CYPSF01; the yeast one-hybrid experiments confirmed that USP could bind to the CYPSF01 promoter. And the USP interference significantly down-regulated CYPSF01 expression, and resulted in the significantly increasing sensitivity to triflumezopyrim, its mortality rate increased 28.37%. Therefore, the overexpression of USP could cause to the overexpression of CYPSF01, ultimately resulting in the resistance to triflumezopyrim in S. furcifera.
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Affiliation(s)
- Changwei Gong
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanwei Ruan
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuming Zhang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiulin Wang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yutong Wu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoxu Zhan
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yunfeng He
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinxian Liu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuemei Liu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jian Pu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuegui Wang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China.
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23
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Lin M, Jian JB, Zhou ZQ, Chen CH, Wang W, Xiong H, Mei ZN. Chromosome-level genome of Entada phaseoloides provides insights into genome evolution and triterpenoid saponins biosynthesis. Mol Ecol Resour 2022; 22:3049-3067. [PMID: 35661414 DOI: 10.1111/1755-0998.13662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 11/26/2022]
Abstract
As a medicinal herbal plant, Entada phaseoloides has high levels of secondary metabolites, particularly triterpenoid saponins, which are important resources for scientific research and medical applications. However, the lack of a reference genome for this genus has limited research on its evolution and utilization of its medicinal potential. In this study, we report a chromosome-scale genome assembly for E. phaseoloides using Illumina, Nanopore long reads, and high-throughput chromosome conformation capture technology. The assembled reference genome is 456.18 Mb (scaffold N50=30.9 Mb; contig N50=6.34 Mb) with 95.71 % of the sequences anchored onto 14 pseudochromosomes. E. phaseoloides was estimated to diverge from the Leguminosae lineage at approximately 72.0 million years ago. With the integration of transcriptomic and metabolomic data, gene expression patterns and metabolite profiling of E. phaseoloides were determined in different tissues. The pattern of gene expression and metabolic profile of the kernel were distinct from those of other tissues. Furthermore, the evolution of certain gene families involved in the biosynthesis of triterpenoid saponins and terpenes was analyzed and offer new insights into the formation of these two metabolites. Four CYP genes, one UGT gene and related transcription factors were identified as candidate genes contributing to regulation of triterpenoid saponins biosynthesis. As the first high-quality assembled reference genome in the genus Entada, it will not only provide new information for the evolutionary study of this genus and conservation biology of E. phaseoloides but also lay a foundation for the formation and utilization of secondary metabolites in medicinal plants.
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Affiliation(s)
- Min Lin
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
| | - Jian-Bo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Zhu-Qing Zhou
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
| | | | - Wen Wang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
| | - Hui Xiong
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
| | - Zhi-Nan Mei
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
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24
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Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, Akmakjian GZ, Deal RB, Sinha NR, Brady SM, Girke T, Bailey-Serres J. Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Dev Cell 2022; 57:1177-1192.e6. [PMID: 35504287 DOI: 10.1016/j.devcel.2022.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/10/2022] [Accepted: 04/07/2022] [Indexed: 12/11/2022]
Abstract
Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; IBBM, FCE-UNLP CONICET, La Plata 1900, Argentina
| | - Alexander T Borowsky
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Germain C Pauluzzi
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Elaine Yeung
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Jianhai Zhang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Elide Formentin
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, University of Padova, Padova, Italy
| | - Joel Velasco
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Sean Cabanlit
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Christine Duvenjian
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew J Prior
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Garo Z Akmakjian
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Thomas Girke
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands.
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25
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Polturak G, Dippe M, Stephenson MJ, Chandra Misra R, Owen C, Ramirez-Gonzalez RH, Haidoulis JF, Schoonbeek HJ, Chartrain L, Borrill P, Nelson DR, Brown JK, Nicholson P, Uauy C, Osbourn A. Pathogen-induced biosynthetic pathways encode defense-related molecules in bread wheat. Proc Natl Acad Sci U S A 2022; 119:e2123299119. [PMID: 35412884 PMCID: PMC9169793 DOI: 10.1073/pnas.2123299119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/14/2022] [Indexed: 12/23/2022] Open
Abstract
Wheat is a widely grown food crop that suffers major yield losses due to attack by pests and pathogens. A better understanding of biotic stress responses in wheat is thus of major importance. The recently assembled bread wheat genome coupled with extensive transcriptomic resources provides unprecedented new opportunities to investigate responses to pathogen challenge. Here, we analyze gene coexpression networks to identify modules showing consistent induction in response to pathogen exposure. Within the top pathogen-induced modules, we identify multiple clusters of physically adjacent genes that correspond to six pathogen-induced biosynthetic pathways that share a common regulatory network. Functional analysis reveals that these pathways, all of which are encoded by biosynthetic gene clusters, produce various different classes of compounds—namely, flavonoids, diterpenes, and triterpenes, including the defense-related compound ellarinacin. Through comparative genomics, we also identify associations with the known rice phytoalexins momilactones, as well as with a defense-related gene cluster in the grass model plant Brachypodium distachyon. Our results significantly advance the understanding of chemical defenses in wheat and open up avenues for enhancing disease resistance in this agriculturally important crop. They also exemplify the power of transcriptional networks to discover the biosynthesis of chemical defenses in plants with large, complex genomes.
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Affiliation(s)
- Guy Polturak
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Martin Dippe
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Michael J. Stephenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rajesh Chandra Misra
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Charlotte Owen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - John F. Haidoulis
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Henk-Jan Schoonbeek
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Laetitia Chartrain
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Philippa Borrill
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
| | - James K.M. Brown
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
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26
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Yan N, Yang T, Yu XT, Shang LG, Guo DP, Zhang Y, Meng L, Qi QQ, Li YL, Du YM, Liu XM, Yuan XL, Qin P, Qiu J, Qian Q, Zhang ZF. Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis. Commun Biol 2022; 5:36. [PMID: 35017643 PMCID: PMC8752815 DOI: 10.1038/s42003-021-02993-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 12/21/2021] [Indexed: 12/25/2022] Open
Abstract
Chinese wild rice (Zizania latifolia; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 38,852 genes, with 52.89% of the genome comprising repetitive sequences. Phylogenetic analyses revealed close relation of Z. latifolia to Leersia perrieri and Oryza species, with a divergence time of 19.7-31.0 million years. Collinearity and transcriptome analyses revealed candidate genes related to seed shattering, providing basic information on abscission layer formation and degradation in Z. latifolia. Moreover, two genomic blocks in the Z. latifolia genome showed good synteny with the rice phytocassane biosynthetic gene cluster. The updated genome will support future studies on the genetic improvement of Chinese wild rice and comparative analyses between Z. latifolia and other plants.
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Affiliation(s)
- Ning Yan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Ting Yang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xiu-Ting Yu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lian-Guang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - De-Ping Guo
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yu Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Lin Meng
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Qian-Qian Qi
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ya-Li Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yong-Mei Du
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xin-Min Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xiao-Long Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
| | - Zhong-Feng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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27
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Li R, Zhang J, Li Z, Peters RJ, Yang B. Dissecting the labdane-related diterpenoid biosynthetic gene clusters in rice reveals directional cross-cluster phytotoxicity. THE NEW PHYTOLOGIST 2022; 233:878-889. [PMID: 34655492 PMCID: PMC8688320 DOI: 10.1111/nph.17806] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/12/2021] [Indexed: 05/23/2023]
Abstract
Rice (Oryza sativa) is a staple food crop and serves as a model cereal plant. It contains two biosynthetic gene clusters (BGCs) for the production of labdane-related diterpenoids (LRDs), which serve important roles in combating biotic and abiotic stress. While plant BGCs have been subject to genetic analyses, these analyses have been largely confined to the investigation of single genes. CRISPR/Cas9-mediated genome editing was used to precisely remove each of these BGCs, as well as simultaneously knock out both BGCs. Deletion of the BGC from chromosome 2 (c2BGC), which is associated with phytocassane biosynthesis, but not that from chromosome 4 (c4BGC), which is associated with momilactone biosynthesis, led to a lesion mimic phenotype. This phenotype is dependent on two closely related genes encoding cytochrome P450 (CYP) mono-oxygenases, CYP76M7 and CYP76M8, from the c2BGC. However, rather than being redundant, CYP76M7 has been associated with the production of phytocassanes, whereas CYP76M8 is associated with momilactone biosynthesis. Intriguingly, the lesion mimic phenotype is not present in a line with both BGCs deleted. These results reveal directional cross-cluster phytotoxicity, presumably arising from the accumulation of LRD intermediates dependent on the c4BGC in the absence of CYP76M7 and CYP76M8, further highlighting their interdependent evolution and the selective pressures driving BGC assembly.
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Affiliation(s)
- Riqing Li
- Division of Plant SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMO65211USA
| | - Juan Zhang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIA50011USA
| | - Zhaohu Li
- State Key Laboratory of Physiology and BiochemistryCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100193China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIA50011USA
| | - Bing Yang
- Division of Plant SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMO65211USA
- Donald Danforth Plant Science CenterSt LouisMO63132USA
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28
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Samal P, Molla KA, Bal A, Ray S, Swain H, Khandual A, Sahoo P, Behera M, Jaiswal S, Iquebal A, Chakraborti M, Behera L, Kar MK, Mukherjee AK. Comparative transcriptome profiling reveals the basis of differential sheath blight disease response in tolerant and susceptible rice genotypes. PROTOPLASMA 2022; 259:61-73. [PMID: 33811539 DOI: 10.1007/s00709-021-01637-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/17/2021] [Indexed: 05/27/2023]
Abstract
Rice sheath blight (ShB) disease, caused by the fungal pathogen Rhizoctonia solani AG1-IA, is one of the devastating diseases and causes severe yield losses all over the world. No completely resistant germplasm is known till now, and as a result, the progress in resistance breeding is unsatisfactory. Basic studies to identify candidate genes, QTLs, and to better understand the host-pathogen interaction are also scanty. In this study, we report the identification of a new ShB-tolerant rice germplasm, CR 1014. Further, we investigated the basis of tolerance by exploring the disease responsive differentially expressed transcriptome and comparing them with that of a susceptible variety, Swarna-Sub1. A total of 815 and 551 genes were found to be differentially regulated in CR 1014 and Swarna-Sub1, respectively, at two different time points. The result shows that the ability to upregulate genes for glycosyl hydrolase, secondary metabolite biosynthesis, cytoskeleton and membrane integrity, the glycolytic pathway, and maintaining photosynthesis make CR 1014 a superior performer in resisting the ShB pathogen. We discuss several putative candidate genes for ShB resistance. The present study, for the first time, revealed the basis of ShB tolerance in the germplasm CR1014 and should prove to be particularly valuable in understanding molecular response to ShB infection. The knowledge could be utilized to devise strategies to manage the disease better.
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Affiliation(s)
| | | | - Archana Bal
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Soham Ray
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
- ICAR-Central Research Institute for Jute and Allied Fibers, Barrackpore, Kolkata, West Bengal, India
| | - Harekrushna Swain
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Ansuman Khandual
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Pritiranjan Sahoo
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Motilal Behera
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistical Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Asif Iquebal
- ICAR-Indian Agricultural Statistical Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Mridul Chakraborti
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Meera K Kar
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India
| | - Arup K Mukherjee
- ICAR-National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, 753006, India.
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29
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Chakraborty P. Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery. Biochimie 2021; 193:1-15. [PMID: 34890733 DOI: 10.1016/j.biochi.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023]
Abstract
Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organised in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.
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Affiliation(s)
- Prasanta Chakraborty
- Kalpana Chawla Center for Space and Nanoscience, Kolkata, Indian Institute of Chemical Biology (retd.), Kolkata, 700032, India.
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Muchlinski A, Jia M, Tiedge K, Fell JS, Pelot KA, Chew L, Davisson D, Chen Y, Siegel J, Lovell JT, Zerbe P. Cytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1053-1068. [PMID: 34514645 PMCID: PMC9292899 DOI: 10.1111/tpj.15492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 05/02/2023]
Abstract
Specialized diterpenoid metabolites are important mediators of plant-environment interactions in monocot crops. To understand metabolite functions in plant environmental adaptation that ultimately can enable crop improvement strategies, a deeper knowledge of the underlying species-specific biosynthetic pathways is required. Here, we report the genomics-enabled discovery of five cytochrome P450 monooxygenases (CYP71Z25-CYP71Z29) that form previously unknown furanoditerpenoids in the monocot bioenergy crop Panicum virgatum (switchgrass). Combinatorial pathway reconstruction showed that CYP71Z25-CYP71Z29 catalyze furan ring addition directly to primary diterpene alcohol intermediates derived from distinct class II diterpene synthase products. Transcriptional co-expression patterns and the presence of select diterpenoids in switchgrass roots support the occurrence of P450-derived furanoditerpenoids in planta. Integrating molecular dynamics, structural analysis and targeted mutagenesis identified active site determinants that contribute to the distinct catalytic specificities underlying the broad substrate promiscuity of CYP71Z25-CYP71Z29 for native and non-native diterpenoids.
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Affiliation(s)
- Andrew Muchlinski
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
- Present address:
Firmenich Inc.4767 Nexus Center Dr.San DiegoCalifornia9212USA
| | - Meirong Jia
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
- Present address:
State Key Laboratory of Bioactive Substance and Function of Natural Medicines & NHC Key Laboratory of Biosynthesis of Natural ProductsInstitute of Materia MedicaChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100050China
| | - Kira Tiedge
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Jason S. Fell
- Genome CenterUniversity of California – DavisDavisCalifornia95616USA
| | - Kyle A. Pelot
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Lisl Chew
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Danielle Davisson
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Yuxuan Chen
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Justin Siegel
- Genome CenterUniversity of California – DavisDavisCalifornia95616USA
- Department of ChemistryUniversity of California – DavisDavisCalifornia95616USA
- Department of Biochemistry & Molecular MedicineUniversity of California – DavisDavisCalifornia95616USA
| | - John T. Lovell
- Genome Sequencing CenterHudson Alpha Institute for BiotechnologyHuntsvilleAlabama35806USA
| | - Philipp Zerbe
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
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Liang J, An T, Zhu JX, Chen S, Zhu JH, Peters RJ, Yu R, Zi J. Mining of the Catharanthus roseus Genome Leads to Identification of a Biosynthetic Gene Cluster for Fungicidal Sesquiterpenes. JOURNAL OF NATURAL PRODUCTS 2021; 84:2709-2716. [PMID: 34644092 PMCID: PMC8627374 DOI: 10.1021/acs.jnatprod.1c00588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Characterization of cryptic biosynthetic gene clusters (BGCs) from microbial genomes has been proven to be a powerful approach to the discovery of new natural products. However, such a genome mining approach to the discovery of bioactive plant metabolites has been muted. The plant BGCs characterized to date encode pathways for antibiotics important in plant defense against microbial pathogens, providing a means to discover such phytoalexins by mining plant genomes. Here is reported the discovery and characterization of a minimal BGC from the medicinal plant Catharanthus roseus, consisting of an adjacent pair of genes encoding a terpene synthase (CrTPS18) and cytochrome P450 (CYP71D349). These two enzymes act sequentially, with CrTPS18 acting as a sesquiterpene synthase, producing 5-epi-jinkoheremol (1), which CYP71D349 further hydroxylates to debneyol (2). Infection studies with maize revealed that 1 and 2 exhibit more potent fungicidal activity than validamycin. Accordingly, this study demonstrates that characterization of such cryptic plant BGCs is a promising strategy for the discovery of potential agrochemical leads. Moreover, despite the observed absence of 1 and 2 in C. roseus, the observed transcriptional regulation is consistent with their differential fungicidal activity, suggesting that such conditional coexpression may be sufficient to drive BGC assembly in plants.
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Affiliation(s)
- Jincai Liang
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
| | - Tianyue An
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
| | - Jian-Xun Zhu
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
| | - Shan Chen
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
| | - Jian-Hua Zhu
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics, Molecular Biology, Iowa State University, Ames, IA 50011, United States
- Jiachen Zi – Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China; ; Rongmin Yu – Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China; ; Reuben J. Peters – Roy J. Carver Department of Biochemistry, Biophysics, Molecular Biology, Iowa State University, Ames, IA 50011, United States;
| | - Rongmin Yu
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
- Jiachen Zi – Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China; ; Rongmin Yu – Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China; ; Reuben J. Peters – Roy J. Carver Department of Biochemistry, Biophysics, Molecular Biology, Iowa State University, Ames, IA 50011, United States;
| | - Jiachen Zi
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China
- Jiachen Zi – Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China; ; Rongmin Yu – Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou 510632, China; ; Reuben J. Peters – Roy J. Carver Department of Biochemistry, Biophysics, Molecular Biology, Iowa State University, Ames, IA 50011, United States;
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Wang K, Yu H, Zhang X, Ye D, Huang H, Wang Y, Zheng Z, Li T. A transcriptomic view of cadmium retention in roots of cadmium-safe rice line (Oryza sativa L.). JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126379. [PMID: 34329031 DOI: 10.1016/j.jhazmat.2021.126379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
A better understanding of the mechanisms controlling cadmium (Cd) accumulation in rice will benefit the development of strategies to minimize Cd accumulation in grains. A Cd-safe rice line designated D62B accumulated less than 0.2 mg Cd kg-1 in brown rice due to its strong capacity for Cd retention in roots. Here transcriptomic was used to clarify the underlying mechanisms of Cd response in roots of D62B compared with a high Cd-accumulating line (Wujin4B). There were 777, 1058 differentially expressed genes (DEGs) in D62B and Wujin4B, respectively, when exposed to Cd. The functions of DEGs were clearly line-specific. Cell wall biosynthesis responded more intensively to Cd stress in D62B, facilitating Cd restriction. Meanwhile, more glutathione (GSH) and phytochelatins synthesized in D62B with the upregulation of sulphur and GSH metabolism. Besides, membrane proteins played critical roles in Cd response in D62B, whereas 18 terms involved in regulation were enriched in Wujin4B. Exogenous GSH further induced the expression of genes related to GSH metabolism and cell wall biosynthesis, leading to the retention of more Cd. Great responsiveness of cell wall biosynthesis and GSH metabolism could be considered the most important specific mechanisms for Cd retention in the roots of Cd-safe rice line.
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Affiliation(s)
- Keji Wang
- College of Resource, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China
| | - Haiying Yu
- College of Resource, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China
| | - Xizhou Zhang
- College of Resource, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China
| | - Daihua Ye
- College of Resource, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China
| | - Huagang Huang
- College of Resource, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China
| | - Yongdong Wang
- College of Resource, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China
| | - Zicheng Zheng
- College of Resource, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China
| | - Tingxuan Li
- College of Resource, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
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33
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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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Hansen CC, Nelson DR, Møller BL, Werck-Reichhart D. Plant cytochrome P450 plasticity and evolution. MOLECULAR PLANT 2021; 14:1244-1265. [PMID: 34216829 DOI: 10.1016/j.molp.2021.06.028] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/28/2021] [Accepted: 06/30/2021] [Indexed: 05/27/2023]
Abstract
The superfamily of cytochrome P450 (CYP) enzymes plays key roles in plant evolution and metabolic diversification. This review provides a status on the CYP landscape within green algae and land plants. The 11 conserved CYP clans known from vascular plants are all present in green algae and several green algae-specific clans are recognized. Clan 71, 72, and 85 remain the largest CYP clans and include many taxa-specific CYP (sub)families reflecting emergence of linage-specific pathways. Molecular features and dynamics of CYP plasticity and evolution are discussed and exemplified by selected biosynthetic pathways. High substrate promiscuity is commonly observed for CYPs from large families, favoring retention of gene duplicates and neofunctionalization, thus seeding acquisition of new functions. Elucidation of biosynthetic pathways producing metabolites with sporadic distribution across plant phylogeny reveals multiple examples of convergent evolution where CYPs have been independently recruited from the same or different CYP families, to adapt to similar environmental challenges or ecological niches. Sometimes only a single or a few mutations are required for functional interconversion. A compilation of functionally characterized plant CYPs is provided online through the Plant P450 Database (erda.dk/public/vgrid/PlantP450/).
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Affiliation(s)
- Cecilie Cetti Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Copenhagen, Denmark; VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark.
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, Copenhagen, Denmark; VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
| | - Daniele Werck-Reichhart
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique (CNRS), University of Strasbourg, Strasbourg, France.
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35
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Liang J, Shen Q, Wang L, Liu J, Fu J, Zhao L, Xu M, Peters RJ, Wang Q. Rice contains a biosynthetic gene cluster associated with production of the casbane-type diterpenoid phytoalexin ent-10-oxodepressin. THE NEW PHYTOLOGIST 2021; 231:85-93. [PMID: 33892515 PMCID: PMC9044444 DOI: 10.1111/nph.17406] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/14/2021] [Indexed: 05/03/2023]
Abstract
Diterpenoids play important roles in rice microbial disease resistance as phytoalexins, as well as acting in allelopathy and abiotic stress responses. Recently, the casbane-type phytoalexin ent-10-oxodepressin was identified in rice, but its biosynthesis has not yet been elucidated. Here ent-10-oxodepressin biosynthesis was investigated via co-expression analysis and biochemical characterisation, with use of the CRISPR/Cas9 technology for genetic analysis. The results identified a biosynthetic gene cluster (BGC) on rice chromosome 7 (c7BGC), containing the relevant ent-casbene synthase (OsECBS), and four cytochrome P450 (CYP) genes from the CYP71Z subfamily. Three of these CYPs were shown to act on ent-casbene, with CYP71Z2 able to produce a keto group at carbon-5 (C5), while the closely related paralogues CYP71Z21 and CYP71Z22 both readily produce a keto group at C10. Together these C5 and C10 oxidases can elaborate ent-casbene to ent-10-oxodepressin (5,10-diketo-ent-casbene). OsECBS knockout lines no longer produce casbane-type diterpenoids and exhibit impaired resistance to the rice fungal blast pathogen Magnaporthe oryzae. Elucidation of ent-10-oxodepressin biosynthesis and the associated c7BGC provides not only a potential target for molecular breeding, but also, gives the intriguing parallels to the independently assembled BGCs for casbene-derived diterpenoids in the Euphorbiaceae, further insight into plant BGC evolution, as discussed here.
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Affiliation(s)
- Jin Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan 611130, China; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Qinqin Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan 611130, China; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Liping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan 611130, China; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jiang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan 611130, China; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jingye Fu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan 611130, China; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Le Zhao
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Meimei Xu
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Qiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan 611130, China; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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Polturak G, Osbourn A. The emerging role of biosynthetic gene clusters in plant defense and plant interactions. PLoS Pathog 2021; 17:e1009698. [PMID: 34214143 PMCID: PMC8253395 DOI: 10.1371/journal.ppat.1009698] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Guy Polturak
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
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37
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Kitaoka N, Zhang J, Oyagbenro RK, Brown B, Wu Y, Yang B, Li Z, Peters RJ. Interdependent evolution of biosynthetic gene clusters for momilactone production in rice. THE PLANT CELL 2021; 33:290-305. [PMID: 33793769 PMCID: PMC8136919 DOI: 10.1093/plcell/koaa023] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/23/2020] [Indexed: 05/20/2023]
Abstract
Plants can contain biosynthetic gene clusters (BGCs) that nominally resemble those found in microbes. However, while horizontal gene transmission is often observed in microbes, plants are limited to vertical gene transmission, implying that their BGCs may exhibit distinct inheritance patterns. Rice (Oryza sativa) contains two unlinked BGCs involved in diterpenoid phytoalexin metabolism, with one clearly required for momilactone biosynthesis, while the other is associated with production of phytocassanes. Here, in the process of elucidating momilactone biosynthesis, genetic evidence was found demonstrating a role for a cytochrome P450 (CYP) from the other "phytocassane" BGC. This CYP76M8 acts after the CYP99A2/3 from the "momilactone" BGC, producing a hemiacetal intermediate that is oxidized to the eponymous lactone by a short-chain alcohol dehydrogenase also from this BGC. Thus, the "momilactone" BGC is not only incomplete, but also fractured by the need for CYP76M8 to act in between steps catalyzed by enzymes from this BGC. Moreover, as supported by similar activity observed with orthologs from the momilactone-producing wild-rice species Oryza punctata, the presence of CYP76M8 in the other "phytocassane" BGC indicates interdependent evolution of these two BGCs, highlighting the distinct nature of BGC assembly in plants.
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Affiliation(s)
- Naoki Kitaoka
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Juan Zhang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
- State Key Laboratory of Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Richard K Oyagbenro
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Benjamin Brown
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Yisheng Wu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Bing Yang
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | - Zhaohu Li
- State Key Laboratory of Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Authors for correspondence: ,
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
- Authors for correspondence: ,
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38
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Zhan C, Lei L, Liu Z, Zhou S, Yang C, Zhu X, Guo H, Zhang F, Peng M, Zhang M, Li Y, Yang Z, Sun Y, Shi Y, Li K, Liu L, Shen S, Wang X, Shao J, Jing X, Wang Z, Li Y, Czechowski T, Hasegawa M, Graham I, Tohge T, Qu L, Liu X, Fernie AR, Chen LL, Yuan M, Luo J. Selection of a subspecies-specific diterpene gene cluster implicated in rice disease resistance. NATURE PLANTS 2020; 6:1447-1454. [PMID: 33299150 DOI: 10.1038/s41477-020-00816-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/04/2020] [Indexed: 05/24/2023]
Abstract
Diterpenoids are the major group of antimicrobial phytoalexins in rice1,2. Here, we report the discovery of a rice diterpenoid gene cluster on chromosome 7 (DGC7) encoding the entire biosynthetic pathway to 5,10-diketo-casbene, a member of the monocyclic casbene-derived diterpenoids. We revealed that DGC7 is regulated directly by JMJ705 through methyl jasmonate-mediated epigenetic control3. Functional characterization of pathway genes revealed OsCYP71Z21 to encode a casbene C10 oxidase, sought after for the biosynthesis of an array of medicinally important diterpenoids. We further show that DGC7 arose relatively recently in the Oryza genus, and that it was partly formed in Oryza rufipogon and positively selected for in japonica during domestication. Casbene-synthesizing enzymes that are functionally equivalent to OsTPS28 are present in several species of Euphorbiaceae but gene tree analysis shows that these and other casbene-modifying enzymes have evolved independently. As such, combining casbene-modifying enzymes from these different families of plants may prove effective in producing a diverse array of bioactive diterpenoid natural products.
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Affiliation(s)
- Chuansong Zhan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Long Lei
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zixin Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shen Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xitong Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Hao Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Feng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Meng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Zixin Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yangyang Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yuheng Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Kang Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Ling Liu
- College of Tropical Crops, Hainan University, Haikou, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xuyang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jiawen Shao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xinyu Jing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Zixuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Tomasz Czechowski
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | | | - Ian Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Takayuki Tohge
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Lianghuan Qu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xianqing Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China.
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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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Lai D, Maimann AB, Macea E, Ocampo CH, Cardona G, Pičmanová M, Darbani B, Olsen CE, Debouck D, Raatz B, Møller BL, Rook F. Biosynthesis of cyanogenic glucosides in Phaseolus lunatus and the evolution of oxime-based defenses. PLANT DIRECT 2020; 4:e00244. [PMID: 32775954 PMCID: PMC7402084 DOI: 10.1002/pld3.244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 05/22/2020] [Accepted: 07/01/2020] [Indexed: 05/13/2023]
Abstract
Lima bean, Phaseolus lunatus, is a crop legume that produces the cyanogenic glucosides linamarin and lotaustralin. In the legumes Lotus japonicus and Trifolium repens, the biosynthesis of these two α-hydroxynitrile glucosides involves cytochrome P450 enzymes of the CYP79 and CYP736 families and a UDP-glucosyltransferase. Here, we identify CYP79D71 as the first enzyme of the pathway in P. lunatus, producing oximes from valine and isoleucine. A second CYP79 family member, CYP79D72, was shown to catalyze the formation of leucine-derived oximes, which act as volatile defense compounds in Phaseolus spp. The organization of the biosynthetic genes for cyanogenic glucosides in a gene cluster aided their identification in L. japonicus. In the available genome sequence of P. vulgaris, the gene orthologous to CYP79D71 is adjacent to a member of the CYP83 family. Although P. vulgaris is not cyanogenic, it does produce oximes as volatile defense compounds. We cloned the genes encoding two CYP83s (CYP83E46 and CYP83E47) and a UDP-glucosyltransferase (UGT85K31) from P. lunatus, and these genes combined form a complete biosynthetic pathway for linamarin and lotaustralin in Lima bean. Within the genus Phaseolus, the occurrence of linamarin and lotaustralin as functional chemical defense compounds appears restricted to species belonging to the closely related Polystachios and Lunatus groups. A preexisting ability to produce volatile oximes and nitriles likely facilitated evolution of cyanogenesis within the Phaseolus genus.
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Affiliation(s)
- Daniela Lai
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Alexandra B. Maimann
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Eliana Macea
- International Center for Tropical AgricultureCaliColombia
| | | | | | - Martina Pičmanová
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Behrooz Darbani
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
- Present address:
The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Carl Erik Olsen
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Daniel Debouck
- International Center for Tropical AgricultureCaliColombia
| | - Bodo Raatz
- International Center for Tropical AgricultureCaliColombia
| | - Birger Lindberg Møller
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
| | - Fred Rook
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
- VILLUM Center for Plant PlasticityUniversity of CopenhagenFrederiksbergDenmark
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Yu XZ, Lu CJ, Tang S, Zhang Q. Transcriptomic analysis of cytochrome P450 genes and pathways involved in chromium toxicity in Oryza sativa. ECOTOXICOLOGY (LONDON, ENGLAND) 2020; 29:503-513. [PMID: 31119592 DOI: 10.1007/s10646-019-02046-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 06/09/2023]
Abstract
In plants, cytochrome P450 monooxygenase (CYP) plays an important role in detoxifying xenobiotic chemicals and coordinating abiotic stresses. Agilent 44 K rice microarray has been used to focus on the transcriptional profile of osCYP genes in rice seedling exposed to Cr solution containing K2CrO4 or Cr(NO3)3. Our study showed that expression profiles of 264 osCYP genes identified were tissue, dose and stimulus specific in rice seedlings. Comparative genomics analysis revealed that more differentially expressed osCYP genes were discovered in roots than in shoots under both Cr exposures. Results from Venn diagram analysis of differentially expressed osCYP genes demonstrated that there were common osCYP genes and unique osCYP genes present in different rice tissue as well as in different Cr treatments, which may control and/or regulate involvement of different CYP isoenzymes under Cr exposure individually or combinedly. KEGG analysis indicated that significant up- and down-regulated osCYP genes in rice tissues were chiefly related to "biosynthesis of secondary metabolites". However, involvements of osCYP genes mapped in the "biosynthesis of secondary metabolites" were tissue and dose specific, implying their distinctly responsive and adaptive mechanisms during Cr exposure. Overall, our findings are evident to describe and clarify their individual roles of specific osCYP genes in regulating involvement of CYP isoforms in Cr detoxification by rice seedlings.
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Affiliation(s)
- Xiao-Zhang Yu
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China.
| | - Chun-Jiao Lu
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
| | - Shen Tang
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
| | - Qing Zhang
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
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42
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Karunanithi PS, Berrios DI, Wang S, Davis J, Shen T, Fiehn O, Maloof JN, Zerbe P. The foxtail millet (Setaria italica) terpene synthase gene family. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:781-800. [PMID: 32282967 PMCID: PMC7497057 DOI: 10.1111/tpj.14771] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/15/2020] [Accepted: 03/24/2020] [Indexed: 05/18/2023]
Abstract
Terpenoid metabolism plays vital roles in stress defense and the environmental adaptation of monocot crops. Here, we describe the identification of the terpene synthase (TPS) gene family of the panicoid food and bioenergy model crop foxtail millet (Setaria italica). The diploid S. italica genome contains 32 TPS genes, 17 of which were biochemically characterized in this study. Unlike other thus far investigated grasses, S. italica contains TPSs producing all three ent-, (+)- and syn-copalyl pyrophosphate stereoisomers that naturally occur as central building blocks in the biosynthesis of distinct monocot diterpenoids. Conversion of these intermediates by the promiscuous TPS SiTPS8 yielded different diterpenoid scaffolds. Additionally, a cytochrome P450 monooxygenase (CYP99A17), which genomically clustered with SiTPS8, catalyzes the C19 hydroxylation of SiTPS8 products to generate the corresponding diterpene alcohols. The presence of syntenic orthologs to about 19% of the S. italica TPSs in related grasses supports a common ancestry of selected pathway branches. Among the identified enzyme products, abietadien-19-ol, syn-pimara-7,15-dien-19-ol and germacrene-d-4-ol were detectable in planta, and gene expression analysis of the biosynthetic TPSs showed distinct and, albeit moderately, inducible expression patterns in response to biotic and abiotic stress. In vitro growth-inhibiting activity of abietadien-19-ol and syn-pimara-7,15-dien-19-ol against Fusarium verticillioides and Fusarium subglutinans may indicate pathogen defensive functions, whereas the low antifungal efficacy of tested sesquiterpenoids supports other bioactivities. Together, these findings expand the known chemical space of monocot terpenoid metabolism to enable further investigations of terpenoid-mediated stress resilience in these agriculturally important species.
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Affiliation(s)
- Prema S. Karunanithi
- Department of Plant BiologyUniversity of California–DavisOne Shields AvenueDavis95616CAUSA
| | - David I. Berrios
- Department of Plant BiologyUniversity of California–DavisOne Shields AvenueDavis95616CAUSA
| | - Sadira Wang
- Department of Plant BiologyUniversity of California–DavisOne Shields AvenueDavis95616CAUSA
| | - John Davis
- Department of Plant BiologyUniversity of California–DavisOne Shields AvenueDavis95616CAUSA
| | - Tong Shen
- West Coast Metabolomics CenterUniversity of California–DavisOne Shields AvenueDavis95616CAUSA
| | - Oliver Fiehn
- West Coast Metabolomics CenterUniversity of California–DavisOne Shields AvenueDavis95616CAUSA
| | - Julin N. Maloof
- Department of Plant BiologyUniversity of California–DavisOne Shields AvenueDavis95616CAUSA
| | - Philipp Zerbe
- Department of Plant BiologyUniversity of California–DavisOne Shields AvenueDavis95616CAUSA
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43
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Active and repressed biosynthetic gene clusters have spatially distinct chromosome states. Proc Natl Acad Sci U S A 2020; 117:13800-13809. [PMID: 32493747 DOI: 10.1073/pnas.1920474117] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes in Arabidopsis thaliana Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.
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Tohge T, Fernie AR. Co-Regulation of Clustered and Neo-Functionalized Genes in Plant-Specialized Metabolism. PLANTS (BASEL, SWITZERLAND) 2020; 9:E622. [PMID: 32414181 PMCID: PMC7285293 DOI: 10.3390/plants9050622] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 01/20/2023]
Abstract
Current findings of neighboring genes involved in plant specialized metabolism provide the genomic signatures of metabolic evolution. Two such genomic features, namely, (i) metabolic gene cluster and (ii) neo-functionalization of tandem gene duplications, represent key factors corresponding to the creation of metabolic diversity of plant specialized metabolism. So far, several terpenoid and alkaloid biosynthetic genes have been characterized with gene clusters in some plants. On the other hand, some modification genes involved in flavonoid and glucosinolate biosynthesis were found to arise via gene neo-functionalization. Although the occurrence of both types of metabolic evolution are different, the neighboring genes are generally regulated by the same or related regulation factors. Therefore, the translation-based approaches associated with genomics, and transcriptomics are able to be employed for functional genomics focusing on plant secondary metabolism. Here, we present a survey of the current understanding of neighboring genes involved in plant secondary metabolism. Additionally, a genomic overview of neighboring genes of four model plants and transcriptional co-expression network neighboring genes to detect metabolic gene clusters in Arabidopsis is provided. Finally, the insights functional genomics have provided concerning the evolution and mechanistic regulation of both the formation and operation of metabolic neighboring clusters is discussed.
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Affiliation(s)
- Takayuki Tohge
- Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma 630-0192, Japan
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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45
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Murphy KM, Zerbe P. Specialized diterpenoid metabolism in monocot crops: Biosynthesis and chemical diversity. PHYTOCHEMISTRY 2020; 172:112289. [PMID: 32036187 DOI: 10.1016/j.phytochem.2020.112289] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 05/27/2023]
Abstract
Among the myriad specialized metabolites that plants employ to mediate interactions with their environment, diterpenoids form a chemically diverse group with vital biological functions. A few broadly abundant diterpenoids serve as core pathway intermediates in plant general metabolism. The majority of plant diterpenoids, however, function in specialized metabolism as often species-specific chemical defenses against herbivores and microbial diseases, in below-ground allelopathic interactions, as well as abiotic stress responses. Dynamic networks of anti-microbial diterpenoids were first demonstrated in rice (Oryza sativa) over four decades ago, and more recently, unique diterpenoid blends with demonstrated antibiotic bioactivities were also discovered in maize (Zea mays). Enabled by advances in -omics and biochemical approaches, species-specific diterpenoid-diversifying enzymes have been identified in these and other Poaceous species, including wheat (Triticum aestivum) and switchgrass (Panicum virgatum), and are discussed in this article with an emphasis on the critical diterpene synthase and cytochrome P450 monooxygenase families and their products. The continued investigation of the biosynthesis, diversity, and function of terpenoid-mediated crop defenses provides foundational knowledge to enable the development of strategies for improving crop resistance traits in the face of impeding pest, pathogen, and climate pressures impacting global agricultural production.
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Affiliation(s)
- Katherine M Murphy
- Department of Plant Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA.
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Yang J, Liang J, Shao L, Liu L, Gao K, Zhang JL, Sun Z, Xu W, Lin P, Yu R, Zi J. Green production of silybin and isosilybin by merging metabolic engineering approaches and enzymatic catalysis. Metab Eng 2020; 59:44-52. [PMID: 32004707 DOI: 10.1016/j.ymben.2020.01.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 01/30/2023]
Abstract
Silymarin extracted from milk thistle seeds, is used for treating hepatic diseases. Silybin and isosilybin are its main components, and synthesized from coupling of taxifolin and coniferyl alcohol. Here, the biosynthetic pathways of taxifolin and coniferyl alcohol were reconstructed in Saccharomyces cerevisiae for the first time. To alleviate substantial burden caused by a great deal of genetic manipulation, expression of the enzymes (e.g. ZWF1, TYR1 and ARO8) playing multiple roles in the relevant biosynthetic pathways was selectively optimized. The strain YT1035 overexpressing seven heterologous enzymes and five native enzymes and the strain YC1053 overexpressing seven heterologous enzymes and four native enzymes, respectively produce 336.8 mg/L taxifolin and 201.1 mg/L coniferyl alcohol. Silybin and isosilybin are synthesized from taxifolin and coniferyl alcohol under catalysis of APX1t (the truncated milk thistle peroxidase), with a yield of 62.5%. This study demonstrates an approach for producing silybin and isosilybin from glucose for the first time.
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Affiliation(s)
- Jiazeng Yang
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou, 510632, China
| | - Jincai Liang
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou, 510632, China
| | - Lei Shao
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Lihong Liu
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou, 510632, China
| | - Ke Gao
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou, 510632, China
| | - Jun-Liang Zhang
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai, 200040, China
| | - Zhenjiao Sun
- Guangdong Qingyunshan Pharmaceutical Co., Ltd., Shaoguan, 512600, China
| | - Wendong Xu
- National Engineering Research Center for Modernization of Extraction and Separation Process of TCM/Guangzhou Hanfang Pharmaceutical Co., Ltd., Guangzhou, 510240, China
| | - Pengcheng Lin
- College of Pharmacy, Qinghai Nationalities University, Xining, 810007, China
| | - Rongmin Yu
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou, 510632, China
| | - Jiachen Zi
- Biotechnological Institute of Chinese Materia Medic, Jinan University, Guangzhou, 510632, China.
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47
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Chen X, Liu F, Liu L, Qiu J, Fang D, Wang W, Zhang X, Ye C, Timko MP, Zhu QH, Fan L, Xiao B. Characterization and evolution of gene clusters for terpenoid phytoalexin biosynthesis in tobacco. PLANTA 2019; 250:1687-1702. [PMID: 31414203 DOI: 10.1007/s00425-019-03255-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
MAIN CONCLUSION The study performed genome-wide identification, characterization and evolution analysis of gene clusters for phytoalexin terpenoid biosynthesis in tobacco, and specifically illustrated ones for capsidiol, an efficient defensive specialized metabolite. Terpenoid phytoalexins play an important role in plant self-defense against pest and pathogen attack. Terpenoid biosynthesis involves terpene synthase and cytochrome P450, which always locate and function as cluster(s). In this study, we performed genome-wide investigation of metabolic gene clusters involved in terpenoid production in tobacco (Nicotiana tabacum). Due to the complexity of the tobacco genome, we modified a published prediction pipeline to reduce the influence of the large number of repeats and to improve the annotation of tobacco genes with respect to their metabolic functions. We identified 1181 metabolic gene clusters with 34 of them potentially being involved in terpenoid biosynthesis. Through integration with transcriptome and metabolic pathway annotation analyses, 3 of the 34 terpenoid biosynthesis-related gene clusters were determined to be high-confidence ones, with 2 involved in biosynthesis of capsidiol, a terpenoid recognized as 1 of the effective resistance compounds in the Nicotiana species. The capsidiol-related gene cluster was conserved in N. sylvestris, N. tomentosiformis and N. attenuate. Our findings demonstrate that phytoalexins in tobacco can arise from operon-like gene clusters, a genomic pattern characterized as being beneficial for rapid stress response, gene co-regulation, co-function and co-heredity.
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Affiliation(s)
- Xi Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China
| | - Fangjie Liu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China
| | - Lu Liu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Jie Qiu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Dunhuang Fang
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Weidi Wang
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Xingcheng Zhang
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Chuyu Ye
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Michael Paul Timko
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China
| | - Bingguang Xiao
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
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Rokas A, Wisecaver JH, Lind AL. The birth, evolution and death of metabolic gene clusters in fungi. Nat Rev Microbiol 2019; 16:731-744. [PMID: 30194403 DOI: 10.1038/s41579-018-0075-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Abigail L Lind
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.,Gladstone Institutes, San Francisco, CA, USA
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Gene Modules Co-regulated with Biosynthetic Gene Clusters for Allelopathy between Rice and Barnyardgrass. Int J Mol Sci 2019; 20:ijms20163846. [PMID: 31394718 PMCID: PMC6719971 DOI: 10.3390/ijms20163846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/13/2022] Open
Abstract
Allelopathy is a central process in crop–weed interactions and is mediated by the release of allelochemicals that result in adverse growth effects on one or the other plant in the interaction. The genomic mechanism for the biosynthesis of many critical allelochemicals is unknown but may involve the clustering of non-homologous biosynthetic genes involved in their formation and regulatory gene modules involved in controlling the coordinated expression within these gene clusters. In this study, we used the transcriptomes from mono- or co-cultured rice and barnyardgrass to investigate the nature of the gene clusters and their regulatory gene modules involved in the allelopathic interactions of these two plants. In addition to the already known biosynthetic gene clusters in barnyardgrass we identified three potential new clusters including one for quercetin biosynthesis and potentially involved in allelopathic interaction with rice. Based on the construction of gene networks, we identified one gene regulatory module containing hub transcription factors, significantly positively co-regulated with both the momilactone A and phytocassane clusters in rice. In barnyardgrass, gene modules and hub genes co-expressed with the gene clusters responsible for 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) biosynthesis were also identified. In addition, we found three genes in barnyardgrass encoding indole-3-glycerolphosphate synthase that regulate the expression of the DIMBOA cluster. Our findings offer new insights into the regulatory mechanisms of biosynthetic gene clusters involved in allelopathic interactions between rice and barnyardgrass, and have potential implications in controlling weeds for crop protection.
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Shen Q, Pu Q, Liang J, Mao H, Liu J, Wang Q. CYP71Z18 overexpression confers elevated blast resistance in transgenic rice. PLANT MOLECULAR BIOLOGY 2019; 100:579-589. [PMID: 31093900 DOI: 10.1007/s11103-019-00881-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
CYP71Z18 exhibited plastic substrate specificity to catalyze oxidation of multiple rice diterpenes and elevated chemical defense against the blast fungus in transgenic rice. Diversified plant specialized metabolism relies on corresponding biosynthetic enzymes with differential substrate specificity. CYP71Z18 catalyzed formation of maize phytoalexins including zealexin A1, the sesquiterpenoid phytoalexin, and diterpenoid phytoalexin dolabralexin, indicating catalytic promiscuity on different terpene substrates. Here substrate specificity of CYP71Z18 was further explored through microbial metabolic engineering and it was identified to accept multiple rice diterpenes as substrates for oxidation. One CYP71Z18 enzymatic product derived from syn-pimaradiene was identified as 15,16-epoxy-syn-pimaradiene by NMR analysis, which was further elaborated by CYP99A3 to generate C19 hydroxylated product. 15,16-epoxy-syn-pimaradien-19-ol exhibited inhibitory effect on spore germination and appressorium formation of the blast pathogen Magnaporthe oryzae. Overexpression of CYP71Z18 in rice resulted in accumulation of several new diterpenoids, indicating promiscuous activity in planta. Transgenic rice also showed stronger resistance against M. oryzae infection, suggesting elevated chemical defense through changed diterpenoid metabolism by CYP71Z18 overexpression. This investigation sheds light on plant metabolic engineering using plastic substrate specificity of P450s to strengthen disease resistance and potentially provide abundant lead compounds.
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Affiliation(s)
- Qinqin Shen
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qingyu Pu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Liang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongjie Mao
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiang Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China.
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