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Chen X, Ren T, Mei D, Wei X, Guo Y, Li Y, Nan Z, Song Q. Infection of Various Medicago sativa Varieties by Ascochyta medicaginicola Triggers the Synthesis of Defensive Secondary Metabolites and Their Antifungal Mechanisms. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:6711-6723. [PMID: 40035699 DOI: 10.1021/acs.jafc.4c12848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2025]
Abstract
Infection with Ascochyta medicaginicola triggers the production of defensive secondary metabolites in plants, with varying levels observed across two alfalfa varieties. Among the six metabolites identified, 3-indoleacrylic acid (YD) and 3-ethynylaniline (EL) exhibited antifungal activity, achieving inhibition rates of 82.21 and 66.36% at 200 μg/mL, respectively. YD and EL exerted protective and therapeutic effects, reducing alfalfa leaf lesion areas by more than 96.00% compared to the blank control. The antifungal mechanisms of YD and EL against A. medicaginicola included the destruction of cellular structure (mycelial deformity, increased membrane permeability, impaired cell integrity with leakage of cellular contents), the induction of oxidative stress (elevated levels of reactive oxygen species, hydrogen peroxide, and malondialdehyde), and the reduction of mitochondrial membrane potential in hyphae cells. These results suggest that EL and YD hold promise as chemical defensive metabolites for controlling alfalfa spring black stem disease.
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Affiliation(s)
- Xunfeng Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ting Ren
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- Sichuan University of Arts and Science, Dazhou 635000, China
| | - Dahai Mei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xuhong Wei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Yongsha Guo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Yanzhong Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Qiuyan Song
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
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Han X, Li S, Zeng Q, Sun P, Wu D, Wu J, Yu X, Lai Z, Milne RJ, Kang Z, Xie K, Li G. Genetic engineering, including genome editing, for enhancing broad-spectrum disease resistance in crops. PLANT COMMUNICATIONS 2025; 6:101195. [PMID: 39568207 PMCID: PMC11897464 DOI: 10.1016/j.xplc.2024.101195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 11/01/2024] [Accepted: 11/19/2024] [Indexed: 11/22/2024]
Abstract
Plant diseases, caused by a wide range of pathogens, severely reduce crop yield and quality, posing a significant threat to global food security. Developing broad-spectrum resistance (BSR) in crops is a key strategy for controlling crop diseases and ensuring sustainable crop production. Cloning disease-resistance (R) genes and understanding their underlying molecular mechanisms provide new genetic resources and strategies for crop breeding. Novel genetic engineering and genome editing tools have accelerated the study and engineering of BSR genes in crops, which is the primary focus of this review. We first summarize recent advances in understanding the plant immune system, followed by an examination of the molecular mechanisms underlying BSR in crops. Finally, we highlight diverse strategies employed to achieve BSR, including gene stacking to combine multiple R genes, multiplexed genome editing of susceptibility genes and promoter regions of executor R genes, editing cis-regulatory elements to fine-tune gene expression, RNA interference, saturation mutagenesis, and precise genomic insertions. The genetic studies and engineering of BSR are accelerating the breeding of disease-resistant cultivars, contributing to crop improvement and enhancing global food security.
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Affiliation(s)
- Xinyu Han
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shumin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingdong Zeng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Peng Sun
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dousheng Wu
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Jianguo Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiao Yu
- National Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ricky J Milne
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Zhensheng Kang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guotian Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China.
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Piombo E, Vetukuri RR, Konakalla NC, Kalyandurg PB, Sundararajan P, Jensen DF, Karlsson M, Dubey M. RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions. BMC Biol 2024; 22:219. [PMID: 39343898 PMCID: PMC11441109 DOI: 10.1186/s12915-024-02014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Small RNA (sRNAs)- mediated RNA silencing is emerging as a key player in host-microbe interactions. However, its role in fungus-plant interactions relevant to biocontrol of plant diseases is yet to be explored. This study aimed to investigate Dicer (DCL)-mediated endogenous and cross-kingdom gene expression regulation in the biocontrol fungus Clonostachys rosea and wheat roots during interactions. RESULTS C. rosea Δdcl2 strain exhibited significantly higher root colonization than the WT, whereas no significant differences were observed for Δdcl1 strains. Dual RNA-seq revealed the upregulation of CAZymes, membrane transporters, and effector coding genes in C. rosea, whereas wheat roots responded with the upregulation of stress-related genes and the downregulation of growth-related genes. The expression of many of these genes was downregulated in wheat during the interaction with DCL deletion strains, underscoring the influence of fungal DCL genes on wheat defense response. sRNA sequencing identified 18 wheat miRNAs responsive to C. rosea, and three were predicted to target the C. rosea polyketide synthase gene pks29. Two of these miRNAs (mir_17532_x1 and mir_12061_x13) were observed to enter C. rosea from wheat roots with fluorescence analyses and to downregulate the expression of pks29, showing plausible cross-kingdom RNA silencing of the C. rosea gene by wheat miRNAs. CONCLUSIONS We provide insights into the mechanisms underlying the interaction between biocontrol fungi and plant roots. Moreover, the study sheds light on the role of sRNA-mediated gene expression regulation in C. rosea-wheat interactions and provides preliminary evidence of cross-kingdom RNA silencing between plants and biocontrol fungi.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Naga Charan Konakalla
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Pruthvi B Kalyandurg
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Poorva Sundararajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Bian S, Li Z, Song S, Zhang X, Shang J, Wang W, Zhang D, Ni D. Enhancing Crop Resilience: Insights from Labdane-Related Diterpenoid Phytoalexin Research in Rice ( Oryza sativa L.). Curr Issues Mol Biol 2024; 46:10677-10695. [PMID: 39329985 PMCID: PMC11430374 DOI: 10.3390/cimb46090634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 09/16/2024] [Accepted: 09/20/2024] [Indexed: 09/28/2024] Open
Abstract
Rice (Oryza sativa L.), as one of the most significant food crops worldwide, holds paramount importance for global food security. Throughout its extensive evolutionary journey, rice has evolved a diverse array of defense mechanisms to fend off pest and disease infestations. Notably, labdane-related diterpenoid phytoalexins play a crucial role in aiding rice in its response to both biotic and abiotic stresses. This article provides a comprehensive review of the research advancements pertaining to the chemical structures, biological activities, and biosynthetic pathways, as well as the molecular regulatory mechanisms, underlying labdane-related diterpenoid phytoalexins discovered in rice. This insight into the molecular regulation of labdane-related diterpenoid phytoalexin biosynthesis offers valuable perspectives for future research aimed at improving crop resilience and productivity.
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Affiliation(s)
- Shiquan Bian
- Key Laboratory of Rice Germplasm Innovation and Molecular Improvement of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Zhong Li
- Key Laboratory of Rice Germplasm Innovation and Molecular Improvement of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shaojie Song
- Key Laboratory of Rice Germplasm Innovation and Molecular Improvement of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiao Zhang
- Key Laboratory of Rice Germplasm Innovation and Molecular Improvement of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jintao Shang
- Agricultural Technology Extension Center of Linping District, Hangzhou 311199, China
| | - Wanli Wang
- Key Laboratory of Rice Germplasm Innovation and Molecular Improvement of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Dewen Zhang
- Key Laboratory of Rice Germplasm Innovation and Molecular Improvement of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Dahu Ni
- Key Laboratory of Rice Germplasm Innovation and Molecular Improvement of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Xue Y, Wang S, Zhang Q, Wu F, Huang L, Qin S, Zhang M, Yang X, Deng Z, Jiang H, Li L, Chai Y. Brassica napus cytochrome P450 superfamily: Origin from parental species and involvement in diseases resistance, abiotic stresses tolerance, and seed quality traits. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116792. [PMID: 39096688 DOI: 10.1016/j.ecoenv.2024.116792] [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: 02/18/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/05/2024]
Abstract
Cytochromes P450 monooxygenases (CYP450s) constitute the largest enzymic protein family that is widely present in plants, animals, and microorganisms, participate in numerous metabolic pathways, and play diverse roles in development, metabolism, and defense. Rapeseed (Brassica napus) is an important oil crop worldwide and have many versions of reference genome. However, there is no systemically comparative genome-wide analysis of CYP450 family genes in rapeseed and its parental species B. rapa and B. oleracea. In this study, we identified 765, 293 and 437 CYP450 genes in B. napus, B. rapa and B. oleracea, respectively, which were unevenly located in A01-A10 and/or C01-C09 chromosomes in corresponding species. Phylogenetic relationship analysis indicated that 1745 CYP450 proteins from three Brassica species and Arabidopsis were divided into 4 groups. Whole genome duplication (WGD) or segmental duplication resulted in gene expansion of CYP450 family in three Brassica species. There were 33-83 SSR loci in CYP450 genes of three Brassica species, and numerous transcription factor binding sites were identified in their promoters. A total of 459-777 miRNAs were predicted to target 174-426 CYP450 genes in three Brassica species. Based on transcriptome data, BnCYP450s, BrCYP450s and BoCYP450s were differentially expressed in various tissues. There existed numerous BnCYP450 DEGs in response to pathogens and abiotic stresses. Besides, many BnCYP450 DEGs were involved in the regulation of important traits, such as seed germination, seed ALA content, and yellow-seed. The qRT-PCR experiment confirmed the transcriptome analysis results by validating two representative Sclerotinia-responsive BnCYP450 DEGs as an example. Three BnCYP450s genes (CYP707A1, CYP81F1, CYP81H1) might be regulated by seed-specific transcription factors BnTT1 and BnbZIP67 to participate in the development and metabolism of seed coat and embryo by undertaking related metabolic reactions.
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Affiliation(s)
- Yufei Xue
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Shanshan Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Qiheng Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Fangzhou Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Li Huang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Shujun Qin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Min Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Xiao Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Zihan Deng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Huanhuan Jiang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Lejing Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Yourong Chai
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing Key Laboratory of Crop Quality Improvement, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China.
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Yasmin F, Cowie AE, Zerbe P. Understanding the chemical language mediating maize immunity and environmental adaptation. THE NEW PHYTOLOGIST 2024; 243:2093-2101. [PMID: 39049575 DOI: 10.1111/nph.20000] [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: 05/03/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024]
Abstract
Diverse networks of specialized metabolites promote plant fitness by mediating beneficial and antagonistic environmental interactions. In maize (Zea mays), constitutive and dynamically formed cocktails of terpenoids, benzoxazinoids, oxylipins, and phenylpropanoids contribute to plant defense and ecological adaptation. Recent research has highlighted the multifunctional nature of many specialized metabolites, serving not only as elaborate chemical defenses that safeguard against biotic and abiotic stress but also as regulators in adaptive developmental processes and microbiome interactions. Great strides have also been made in identifying the modular pathway networks that drive maize chemical diversity. Translating this knowledge into strategies for enhancing stress resilience traits has the potential to address climate-driven yield losses in one of the world's major food, feed, and bioenergy crops.
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Affiliation(s)
- Farida Yasmin
- Department of Plant Biology, University of California-Davis, Davis, CA, 95616, USA
| | - Anna E Cowie
- Department of Plant Biology, University of California-Davis, Davis, CA, 95616, USA
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, Davis, CA, 95616, USA
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Huang Q, Chen C, Wu X, Qin Y, Tan X, Zhang D, Liu Y, Li W, Chen Y. Overexpression of ATP Synthase Subunit Beta (Atp2) Confers Enhanced Blast Disease Resistance in Transgenic Rice. J Fungi (Basel) 2023; 10:5. [PMID: 38276021 PMCID: PMC10820023 DOI: 10.3390/jof10010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Previous research has shown that the pathogenicity and appressorium development of Magnaporthe oryzae can be inhibited by the ATP synthase subunit beta (Atp2) present in the photosynthetic bacterium Rhodopseudomonas palustris. In the present study, transgenic plants overexpressing the ATP2 gene were generated via genetic transformation in the Zhonghua11 (ZH11) genetic background. We compared the blast resistance and immune response of ATP2-overexpressing lines and wild-type plants. The expression of the Atp2 protein and the physiology, biochemistry, and growth traits of the mutant plants were also examined. The results showed that, compared with the wild-type plant ZH11, transgenic rice plants heterologously expressing ATP2 had no significant defects in agronomic traits, but the disease lesions caused by the rice blast fungus were significantly reduced. When infected by the rice blast fungus, the transgenic rice plants exhibited stronger antioxidant enzyme activity and a greater ratio of chlorophyll a to chlorophyll b. Furthermore, the immune response was triggered stronger in transgenic rice, especially the increase in reactive oxygen species (ROS), was more strongly triggered in plants. In summary, the expression of ATP2 as an antifungal protein in rice could improve the ability of rice to resist rice blast.
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Affiliation(s)
- Qiang Huang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Chunyan Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Xiyang Wu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Yingfei Qin
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Xinqiu Tan
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Yong Liu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Wei Li
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
| | - Yue Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
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8
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Nazari L, Aslan MF, Sabanci K, Ropelewska E. Integrated transcriptomic meta-analysis and comparative artificial intelligence models in maize under biotic stress. Sci Rep 2023; 13:15899. [PMID: 37741865 PMCID: PMC10517993 DOI: 10.1038/s41598-023-42984-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/17/2023] [Indexed: 09/25/2023] Open
Abstract
Biotic stress imposed by pathogens, including fungal, bacterial, and viral, can cause heavy damage leading to yield reduction in maize. Therefore, the identification of resistant genes paves the way to the development of disease-resistant cultivars and is essential for reliable production in maize. Identifying different gene expression patterns can deepen our perception of maize resistance to disease. This study includes machine learning and deep learning-based application for classifying genes expressed under normal and biotic stress in maize. Machine learning algorithms used are Naive Bayes (NB), K-Nearest Neighbor (KNN), Ensemble, Support Vector Machine (SVM), and Decision Tree (DT). A Bidirectional Long Short Term Memory (BiLSTM) based network with Recurrent Neural Network (RNN) architecture is proposed for gene classification with deep learning. To increase the performance of these algorithms, feature selection is made from the raw gene features through the Relief feature selection algorithm. The obtained finding indicated the efficacy of BiLSTM over other machine learning algorithms. Some top genes ((S)-beta-macrocarpene synthase, zealexin A1 synthase, polyphenol oxidase I, chloroplastic, pathogenesis-related protein 10, CHY1, chitinase chem 5, barwin, and uncharacterized LOC100273479 were proved to be differentially upregulated under biotic stress condition.
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Affiliation(s)
- Leyla Nazari
- Crop and Horticultural Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | - Muhammet Fatih Aslan
- Electrical and Electronics Engineering, Karamanoglu Mehmetbey University, Karaman, Turkey
| | - Kadir Sabanci
- Electrical and Electronics Engineering, Karamanoglu Mehmetbey University, Karaman, Turkey
| | - Ewa Ropelewska
- Fruit and Vegetable Storage and Processing Department, The National Institute of Horticultural Research, Skierniewice, Poland
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Wang L, Xu G, Li L, Ruan M, Bennion A, Wang GL, Li R, Qu S. The OsBDR1-MPK3 module negatively regulates blast resistance by suppressing the jasmonate signaling and terpenoid biosynthesis pathway. Proc Natl Acad Sci U S A 2023; 120:e2211102120. [PMID: 36952381 PMCID: PMC10068787 DOI: 10.1073/pnas.2211102120] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/17/2023] [Indexed: 03/24/2023] Open
Abstract
Receptor-like kinases (RLKs) may initiate signaling pathways by perceiving and transmitting environmental signals to cellular machinery and play diverse roles in plant development and stress responses. The rice genome encodes more than one thousand RLKs, but only a small number have been characterized as receptors for phytohormones, polypeptides, elicitors, and effectors. Here, we screened the function of 11 RLKs in rice resistance to the blast fungus Magnaporthe oryzae (M. oryzae) and identified a negative regulator named BDR1 (Blast Disease Resistance 1). The expression of BDR1 was rapidly increased under M. oryzae infection, while silencing or knockout of BDR1 significantly enhanced M. oryzae resistance in two rice varieties. Protein interaction and kinase activity assays indicated that BDR1 directly interacted with and phosphorylated mitogen-activated kinase 3 (MPK3). Knockout of BDR1 compromised M. oryzae-induced MPK3 phosphorylation levels. Moreover, transcriptome analysis revealed that M. oryzae-elicited jasmonate (JA) signaling and terpenoid biosynthesis pathway were negatively regulated by BDR1 and MPK3. Mutation of JA biosynthetic (allene oxide cyclase (AOC)/signaling (MYC2) genes decreased rice resistance to M. oryzae. Besides diterpenoid, the monoterpene linalool and the sesquiterpene caryophyllene were identified as unique defensive compounds against M. oryzae, and their biosynthesis genes (TPS3 and TPS29) were transcriptionally regulated by JA signaling and suppressed by BDR1 and MPK3. These findings demonstrate the existence of a BDR1-MPK3 cascade that negatively mediates rice blast resistance by affecting JA-related defense responses.
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Affiliation(s)
- Lanlan Wang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 310021Hangzhou, China
| | - Guojuan Xu
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 310021Hangzhou, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193Beijing, China
| | - Lihua Li
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 310021Hangzhou, China
| | - Meiying Ruan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences,310021Hangzhou, China
| | - Anne Bennion
- SynMikro Center for Synthetic Microbiology, Philipps University Marburg, 35032Marburg, Germany
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, 43210Columbus, OH
| | - Ran Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 310058Hangzhou, China
| | - Shaohong Qu
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 310021Hangzhou, China
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10
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Nan J, Ling Y, An J, Wang T, Chai M, Fu J, Wang G, Yang C, Yang Y, Han B. Genome resequencing reveals independent domestication and breeding improvement of naked oat. Gigascience 2022; 12:giad061. [PMID: 37524540 PMCID: PMC10390318 DOI: 10.1093/gigascience/giad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/04/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
As an important cereal crop, common oat, has attracted more and more attention due to its healthy nutritional components and bioactive compounds. Here, high-depth resequencing of 115 oat accessions and closely related hexaploid species worldwide was performed. Based on genetic diversity and linkage disequilibrium analysis, it was found that hulled oat (Avena sativa) experienced a more severe bottleneck than naked oat (Avena sativa var. nuda). Combined with the divergence time of ∼51,200 years ago, the previous speculation that naked oat was a variant of hulled oat was rejected. It was found that the common segments that hulled oat introgressed to naked oat cultivars contained 444 genes, mainly enriched in photosynthetic efficiency-related pathways. Selective sweeps during environmental adaptation and breeding improvement were identified in the naked oat genome. Candidate genes associated with smut resistance and the days to maturity phenotype were also identified. Our study provides genomic resources and new insights into naked oat domestication and breeding.
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Affiliation(s)
- Jinsheng Nan
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Yu Ling
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Jianghong An
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Ting Wang
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Mingna Chai
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Jun Fu
- Beijing 8omics Gene Technology Co. Ltd, Beijing 100080, China
| | - Gaochao Wang
- Beijing 8omics Gene Technology Co. Ltd, Beijing 100080, China
| | - Cai Yang
- Inner Mongolia Guomai Agriculture Co. Ltd, Xilingol League, Xilinhot City 026005, China
| | - Yan Yang
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Bing Han
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
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11
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Jiang H, Jia H, Hao X, Li K, Gai J. Mapping Locus R SC11K and predicting candidate gene resistant to Soybean mosaic virus strain SC11 through linkage analysis combined with genome resequencing of the parents in soybean. Genomics 2022; 114:110387. [PMID: 35569732 DOI: 10.1016/j.ygeno.2022.110387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 04/29/2022] [Accepted: 05/07/2022] [Indexed: 11/26/2022]
Abstract
Soybean mosaic virus (SMV) strain SC11 was prevalent in middle China. Its resistance was controlled by a Mendelian single dominant gene RSC11K in soybean Kefeng-1. This study aimed at mapping RSC11K and identifying its candidate gene. RSC11K locus was mapped ~217 kb interval between two SNP-linkage-disequilibrium-blocks (Gm02_BLOCK_11273955_11464884 and Gm02_BLOCK_11486875_11491354) in W82.a1.v1 genome using recombinant inbred lines population derived from Kefeng-1 (Resistant) × NN1138-2 (Susceptible), but inserted with a ~245 kb segment in W82.a2.v1 genome. In the entire 462 kb RSC11K region, 429 SNPs, 142 InDels and 34 putative genes were identified with more SNPs/InDels distributed in non-functional regions. Thereinto, ten genes contained SNP/InDel variants with high and moderate functional impacts on proteins, among which Glyma.02G119700 encoded a typical innate immune receptor-like kinase involving in virus disease process and responded to SMV inoculation, therefore was recognized as RSC11K's candidate gene. The novel RSC11K locus and candidate genes may help developing SMV resistance germplasm.
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Affiliation(s)
- Hua Jiang
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Huiying Jia
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaoshuai Hao
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kai Li
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Junyi Gai
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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12
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Yuan X, Wang H, Bi Y, Yan Y, Gao Y, Xiong X, Wang J, Li D, Song F. ONAC066, A Stress-Responsive NAC Transcription Activator, Positively Contributes to Rice Immunity Against Magnaprothe oryzae Through Modulating Expression of OsWRKY62 and Three Cytochrome P450 Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:749186. [PMID: 34567053 PMCID: PMC8458891 DOI: 10.3389/fpls.2021.749186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
NAC transcriptional factors constitute a large family in rice and some of them have been demonstrated to play crucial roles in rice immunity. The present study investigated the function and mechanism of ONAC066 in rice immunity. ONAC066 shows transcription activator activity that depends on its C-terminal region in rice cells. ONAC066-OE plants exhibited enhanced resistance while ONAC066-Ri and onac066-1 plants showed attenuated resistance to Magnaporthe oryzae. A total of 81 genes were found to be up-regulated in ONAC066-OE plants, and 26 of them were predicted to be induced by M. oryzae. Four OsWRKY genes, including OsWRKY45 and OsWRKY62, were up-regulated in ONAC066-OE plants but down-regulated in ONAC066-Ri plants. ONAC066 bound to NAC core-binding site in OsWRKY62 promoter and activated OsWRKY62 expression, indicating that OsWRKY62 is a ONAC066 target. A set of cytochrome P450 genes were found to be co-expressed with ONAC066 and 5 of them were up-regulated in ONAC066-OE plants but down-regulated in ONAC066-Ri plants. ONAC066 bound to promoters of cytochrome P450 genes LOC_Os02g30110, LOC_Os06g37300, and LOC_Os02g36150 and activated their transcription, indicating that these three cytochrome P450 genes are ONAC066 targets. These results suggest that ONAC066, as a transcription activator, positively contributes to rice immunity through modulating the expression of OsWRKY62 and a set of cytochrome P450 genes to activate defense response.
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Affiliation(s)
- Xi Yuan
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Hui Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Bi
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuqing Yan
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yizhou Gao
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaohui Xiong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiajing Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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13
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Ding Y, Northen TR, Khalil A, Huffaker A, Schmelz EA. Getting back to the grass roots: harnessing specialized metabolites for improved crop stress resilience. Curr Opin Biotechnol 2021; 70:174-186. [PMID: 34129999 DOI: 10.1016/j.copbio.2021.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Roots remain an understudied site of complex and important biological interactions mediating plant productivity. In grain and bioenergy crops, grass root specialized metabolites (GRSM) are central to key interactions, yet our basic knowledge of the chemical language remains fragmentary. Continued improvements in plant genome assembly and metabolomics are enabling large-scale advances in the discovery of specialized metabolic pathways as a means of regulating root-biotic interactions. Metabolomics, transcript coexpression analyses, forward genetic studies, gene synthesis and heterologous expression assays drive efficient pathway discoveries. Functional genetic variants identified through genome wide analyses, targeted CRISPR/Cas9 approaches, and both native and non-native overexpression studies critically inform novel strategies for bioengineering metabolic pathways to improve plant traits.
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Affiliation(s)
- Yezhang Ding
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Ahmed Khalil
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Alisa Huffaker
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Eric A Schmelz
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA.
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14
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Wang L, Liang J, Xie X, Liu J, Shen Q, Li L, Wang Q. Direct formation of the sesquiterpeonid ether liguloxide by a terpene synthase in Senecio scandens. PLANT MOLECULAR BIOLOGY 2021; 105:55-64. [PMID: 32915351 DOI: 10.1007/s11103-020-01068-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
SsLOS directly catalyzed formation of the sesquiterpenoid ether liguloxide in the medicinal plant Senecio scandens. Terpene synthases determine the diversity of terpene skeletons and corresponding terpenoid natural products. Oxygenated groups introduced in catalysis of terpene synthases are important for solubility, potential bioactivity and further elaboration of terpenoids. Here we identified one terpene synthase, SsLOS, in the Chinese medicinal plant Senecio scandens. SsLOS acted as the sesquiterpene synthase and utilized (E,E)-farnesyl diphosphate as the substrate to produce a blend of sesquiterpenoids. GC-MS analysis and NMR structure identification demonstrated that SsLOS directly produced the sesquiterpenoid ether, liguloxide, as well as its alcoholic isomer, 6-epi-guaia-2(3)-en-11-ol. Homology modeling and site-directed mutagenesis were combined to explore the catalytic mechanism of SsLOS. A few key residues were identified in the active site and hedycaryol was identified as the neutral intermediate of SsLOS catalysis. The plausible catalytic mechanism was proposed as well. Altogether, SsLOS was identified and characterized as the sesquiterpenoid ether synthase, which is the second terpenoid ether synthase after 1,8-cineol synthase, suggesting some insights for the universal mechanism of terpene synthases using the water molecule in the catalytic cavity.
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Affiliation(s)
- Liping Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Liang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xin Xie
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiang Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Qinqin Shen
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lixia Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China.
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15
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Ding Y, Weckwerth PR, Poretsky E, Murphy KM, Sims J, Saldivar E, Christensen SA, Char SN, Yang B, Tong AD, Shen Z, Kremling KA, Buckler ES, Kono T, Nelson DR, Bohlmann J, Bakker MG, Vaughan MM, Khalil AS, Betsiashvili M, Dressano K, Köllner TG, Briggs SP, Zerbe P, Schmelz EA, Huffaker A. Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity. NATURE PLANTS 2020; 6:1375-1388. [PMID: 33106639 DOI: 10.1038/s41477-020-00787-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/11/2020] [Indexed: 05/24/2023]
Abstract
Specialized metabolites constitute key layers of immunity that underlie disease resistance in crops; however, challenges in resolving pathways limit our understanding of the functions and applications of these metabolites. In maize (Zea mays), the inducible accumulation of acidic terpenoids is increasingly considered to be a defence mechanism that contributes to disease resistance. Here, to understand maize antibiotic biosynthesis, we integrated association mapping, pan-genome multi-omic correlations, enzyme structure-function studies and targeted mutagenesis. We define ten genes in three zealexin (Zx) gene clusters that encode four sesquiterpene synthases and six cytochrome P450 proteins that collectively drive the production of diverse antibiotic cocktails. Quadruple mutants in which the ability to produce zealexins (ZXs) is blocked exhibit a broad-spectrum loss of disease resistance. Genetic redundancies ensuring pathway resiliency to single null mutations are combined with enzyme substrate promiscuity, creating a biosynthetic hourglass pathway that uses diverse substrates and in vivo combinatorial chemistry to yield complex antibiotic blends. The elucidated genetic basis of biochemical phenotypes that underlie disease resistance demonstrates a predominant maize defence pathway and informs innovative strategies for transferring chemical immunity between crops.
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Affiliation(s)
- Yezhang Ding
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Philipp R Weckwerth
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Elly Poretsky
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Katherine M Murphy
- Department of Plant Biology, University of California Davis, Davis, CA, USA
| | - James Sims
- ETH Zurich, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Evan Saldivar
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Shawn A Christensen
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Department of Agriculture, Agricultural Research Service, Gainesville, FL, USA
| | - Si Nian Char
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Anh-Dao Tong
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Zhouxin Shen
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Karl A Kremling
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Edward S Buckler
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
- Robert W. Holley Center for Agriculture and Health, Ithaca, US Department of Agriculture, Agricultural Research Service, New York, NY, USA
| | - Tom Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - David R Nelson
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew G Bakker
- National Center for Agricultural Utilization Research, US Department of Agriculture, Agricultural Research Service, Peoria, IL, USA
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Martha M Vaughan
- National Center for Agricultural Utilization Research, US Department of Agriculture, Agricultural Research Service, Peoria, IL, USA
| | - Ahmed S Khalil
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Mariam Betsiashvili
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Keini Dressano
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | | | - Steven P Briggs
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Philipp Zerbe
- Department of Plant Biology, University of California Davis, Davis, CA, USA
| | - Eric A Schmelz
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Alisa Huffaker
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA.
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16
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Zhang X, Zhang R, Li L, Yang Y, Ding Y, Guan H, Wang X, Zhang A, Wen H. Negligible transcriptome and metabolome alterations in RNAi insecticidal maize against Monolepta hieroglyphica. PLANT CELL REPORTS 2020; 39:1539-1547. [PMID: 32869121 PMCID: PMC7554010 DOI: 10.1007/s00299-020-02582-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/17/2020] [Indexed: 06/01/2023]
Abstract
RNAi-based genetically modified maize resistant to Monolepta hieroglyphica (Motschulsky) was demonstrated with negligible transcriptome and metabolome alterations compared to its unmodified equivalent. As one of the most prevalent insect pests afflicting various crops, Monolepta hieroglyphica (Motschulsky) causes severe loss of agricultural and economic productivity for many years in China. In an effort to reduce damages, in this study, an RNA interference (RNAi)-based genetically modified (GM) maize was developed. It was engineered to produce MhSnf7 double-stranded RNAs (dsRNAs), which can suppress the Snf7 gene expression and then lead M. hieroglyphica to death. Field trail analysis confirmed the robustly insecticidal ability of the MhSnf7 GM maize to resist damages by M. hieroglyphica. RNA sequencing analysis identified that only one gene was differentially expressed in the MhSnf7 GM maize compared to non-GM maize, indicating that the transcriptome in MhSnf7 GM maize is principally unaffected by the introduction of the MhSnf7 dsRNA expression vector. Likewise, metabolomics analysis identified that only 8 out of 5787 metabolites were significantly changed. Hence, the integration of transcriptomics and metabolomics demonstrates that there are negligible differences between MhSnf7 GM maize and its unmodified equivalent. This study not only presents a comprehensive assessment of cellular alteration in terms of gene transcription and metabolite abundance in RNAi-based GM maize, but also could be used as a reference for evaluating the unintended effect of GM crops.
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Affiliation(s)
- Xiaolei Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ruiying Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Yang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yijia Ding
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Haitao Guan
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaoqin Wang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Aihong Zhang
- Beijing DaBeiNong Biotechnology Co., Ltd., Beijing, 100080, China
| | - Hongtao Wen
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
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17
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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: 48] [Impact Index Per Article: 9.6] [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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