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Feng K, Liu J, Sun N, Zhou Z, Yang Z, Lv H, Yao C, Zou J, Zhao S, Wu P, Li L. Telomere-to-telomere genome assembly reveals insights into the adaptive evolution of herbivore-defense mediated by volatile terpenoids in Oenanthe javanica. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:2346-2357. [PMID: 40112135 PMCID: PMC12120883 DOI: 10.1111/pbi.70062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/28/2025] [Accepted: 03/07/2025] [Indexed: 03/22/2025]
Abstract
Releasing large quantities of volatiles is a defense strategy used by plants to resist herbivore attack. Oenanthe javanica, a perennial herb of the Apiaceae family, has a distinctive aroma due to volatile terpenoid accumulation. At present, the complete genome and genetic characteristics of volatile terpenoids in O. javanica remain largely unclear. Here, the telomere-to-telomere genome of O. javanica, with a size of 1012.13 Mb and a contig N50 of 49.55 Mb, was established by combining multiple sequencing technologies. Comparative genome analysis revealed that O. javanica experienced a recent species-specific whole-genome duplication event during the evolutionary process. Numerous gene family expansions were significantly enriched in the terpenoid biosynthesis process, monoterpenoid, and diterpenoid biosynthesis pathways, which resulted in abundant volatile substance accumulation in O. javanica. The volatile terpenoids of O. javanica showed repellent effects on herbivores. Terpenoid biosynthesis was activated by wounding signals under exogenous stimuli. The TPS gene family was significantly expanded in O. javanica compared to those in other species, and the members (OjTPS1, OjTPS3, OjTPS4, OjTPS5, OjTPS7, OjTPS16, OjTPS18, OjTPS30 and OjTPS58) responsible for different terpenoid biosynthesis were functionally characterized. These results reveal the genome evolution and molecular characteristics of volatile terpenoids in the process of plant-herbivore interactions. This study also provides genomic resources for genetic and molecular biology research on O. javanica and other plants.
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Affiliation(s)
- Kai Feng
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Jia‐Lu Liu
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Nan Sun
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Zi‐Qi Zhou
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Zhi‐Yuan Yang
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Hui Lv
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Cheng Yao
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Jin‐Ping Zou
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Shu‐Ping Zhao
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Peng Wu
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Liang‐Jun Li
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
- Key Laboratory of Biobreeding for Specialty Horticultural Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
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2
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Ji J, Han X, Zang L, Li Y, Lin L, Hu D, Sun S, Ren Y, Maker G, Lu Z, Wang L. Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica. Commun Biol 2025; 8:649. [PMID: 40269101 PMCID: PMC12019236 DOI: 10.1038/s42003-025-08076-x] [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: 10/01/2024] [Accepted: 04/10/2025] [Indexed: 04/25/2025] Open
Abstract
Furocoumarins (FCs), important natural compounds with biodefense roles and pharmacological activities, are notably abundant in medicinal plant Angelica dahurica. However, its accumulation patterns over development stages in FC-enriched tissue, biosynthetic pathways, and regulatory mechanisms in A. dahurica remain elusive. Here, we quantified the concentration dynamics of 17 coumarins across six developmental stages of root and found a gradual decrease in FC concentration as the roots develop. Using a de-novo assembled chromosome-level genome for A. dahurica, we conducted integrative multi-omics analyses to screen out candidate genes to fill in the sole missing step in the biosynthesis of imperatorin and isoimperatorin. This revealed that CYP71AZ18 catalyzes hydroxylation at the C-5 position of psoralen to generate bergaptol, while CYP71AZ19 and CYP83F95 catalyze hydroxylation at the C-8 position to produce xanthotoxol, notably indicating that a single step is catalyzed by two genes from distinct CYP450 subfamilies in this species. CYP71AZ19 originated from a proximal duplication event of CYP71AZ18, specific to A. dahurica, and subsequently underwent neofunctionalization. Accessible chromatin regions (ACRs), especially proximal ACRs, correlated with high gene expression levels, and the three validated genes exhibited strong signals of ACRs, showing the importance of chromosomal accessibility in regulating metabolite biosynthesis.
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Grants
- 32300223, 32070242, and 82373837 National Natural Science Foundation of China (National Science Foundation of China)
- National Key Research and Development Program of China, grant 2023YFA0915800; Shenzhen Fundamental Research Program, grant 20220817165436004; Shenzhen Science and Technology Program, grant KQTD2016113010482651; Key Project at Central Government Level (The ability establishment of sustainable use for valuable Chinese medicine resources), grant 2060302; Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District, grants RC201901-05 and PT201901-19; Basic and Applied Basic Research Fund of Guangdong, grant 2020A1515110912; Science, Technology, and Innovation Commission of Shenzhen Municipality of China, grant ZDSYS20200811142605017
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Affiliation(s)
- Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Environmental and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Lanlan Zang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yushan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liqun Lin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Donghua Hu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yonglin Ren
- College of Environmental and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Garth Maker
- College of Environmental and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Zefu Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- Kunpeng Institute of Modern Agriculture at Foshan 528000, Foshan, China.
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Cheng LT, Wang ZL, Zhu QH, Ye M, Ye CY. A long road ahead to reliable and complete medicinal plant genomes. Nat Commun 2025; 16:2150. [PMID: 40032878 PMCID: PMC11876585 DOI: 10.1038/s41467-025-57448-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Accepted: 02/24/2025] [Indexed: 03/05/2025] Open
Abstract
Long-read DNA sequencing has propelled medicinal plant genomics forward, with over 400 genomes from 203 plants sequenced by February 2025. However, many genomes still have assembly and annotation flaws, with only 11 gapless telomere-to-telomere assemblies. The core challenge remains identifying genes linked to secondary metabolite biosynthesis, regulation and evolution. High-quality complete genomes are essential for characterizing biosynthetic gene clusters and for enabling robust functional genomics and synthetic biology applications. We propose to focus on achieving more complete genome assemblies in diverse varieties on the basis of refining the currently available ones, leverage lessons from crop genomics research, and apply the cutting-edge genomics technologies in research of medicinal plant genomics.
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Affiliation(s)
- Ling-Tong Cheng
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, Zhejiang University, Hangzhou, China
| | - Zi-Long Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Chu-Yu Ye
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, Zhejiang University, Hangzhou, China.
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Kong F, Kou Y, Zhang X, Tian Y, Yang B, Wang W. Comparative Analysis of Metabolites of Wild and Cultivated Notopterygium incisum from Different Origins and Evaluation of Their Anti-Inflammatory Activity. Molecules 2025; 30:468. [PMID: 39942574 PMCID: PMC11820002 DOI: 10.3390/molecules30030468] [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: 12/04/2024] [Revised: 01/16/2025] [Accepted: 01/19/2025] [Indexed: 02/16/2025] Open
Abstract
The dried rhizome of Notopterygium incisum (NI) from the Umbelliferae family, genuinely produced in Sichuan, China, is a classic traditional Chinese medicinal herb for treating wind-dampness arthralgia. Due to scarce natural resources, wild NI is gradually being replaced by cultivated types. However, knowledge is limited regarding the differences in chemical composition and pharmacological effects between wild and cultivated NI and between Sichuan-grown and other-region-grown NI. In this study, a plant metabolomics strategy, based on GC-MS and UHPLC-Orbitrap MS, was employed to compare metabolic profiles between wild and cultivated NI and between cultivated NI from Sichuan and cultivated NI from Gansu and Qinghai. In total, 195 metabolites were identified, and the biosynthetic pathways of coumarins and phenolic acids, which were the most abundant secondary metabolites in NI, were summarized. Additionally, seven key metabolic intermediates were uncovered, revealing the reasons for the differences in metabolic profiles between wild and cultivated NI. The anti-inflammatory effect of wild and cultivated NI was verified by inflammatory gene expression and neutrophil count using a zebrafish yolk sac inflammation model. Overall, this study presents information on the types and synthesis of pharmacodynamic substances in NI and provides a basis for its cultivation and applications.
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Affiliation(s)
- Fukang Kong
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (F.K.); (Y.K.); (X.Z.)
| | - Yannan Kou
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (F.K.); (Y.K.); (X.Z.)
| | - Xu Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (F.K.); (Y.K.); (X.Z.)
| | - Yue Tian
- School of Biomedicine, Beijing City University, No. 6 Huanghoudian Road, Haidian District, Beijing 100094, China;
| | - Bin Yang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (F.K.); (Y.K.); (X.Z.)
| | - Weihao Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (F.K.); (Y.K.); (X.Z.)
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5
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Liu SJ, Liu Z, Shao BY, Li T, Zhu X, Wang R, Shi L, Xu S, Van de Peer Y, Xue JY. Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e17220. [PMID: 39868644 DOI: 10.1111/tpj.17220] [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: 08/07/2024] [Revised: 11/04/2024] [Accepted: 12/11/2024] [Indexed: 01/28/2025]
Abstract
The traditional Chinese medicinal plant Prunella vulgaris contains numerous triterpene saponin metabolites, notably ursolic and oleanolic acid saponins, which have significant pharmacological values. Despite their importance, the genes responsible for synthesizing these triterpene saponins in P. vulgaris remain unidentified. This study used a comprehensive screening methodology, combining phylogenetic analysis, gene expression assessment, metabolome-transcriptome correlation and co-expression analysis, to identify candidate genes involved in triterpene saponins biosynthesis. Nine candidate genes - two OSCs, three CYP716s and four UGT73s - were precisely identified from large gene families comprising hundreds of members. These genes were subjected to heterologous expression and functional characterization, with enzymatic activity assays confirming their roles in the biosynthetic pathway, aligning with bioinformatics predictions. Analysis revealed that these genes originated from a whole-genome duplication (WGD) event in P. vulgaris, highlighting the potential importance of WGD for plant metabolism. This study addresses the knowledge gap in the biosynthesis of triterpene saponins in P. vulgaris, establishing a theoretical foundation for industrial production via synthetic biology. Additionally, we present an efficient methodological protocol that integrates evolutionary principles and bioinformatics techniques in metabolite biosynthesis research. This approach holds significant value for studies focused on unraveling various biosynthetic pathways.
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Affiliation(s)
- Si-Jie Liu
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhengtai Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Bing-Yan Shao
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Li
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinning Zhu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Ren Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Lei Shi
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yves Van de Peer
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, Ghent, B-9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Jia-Yu Xue
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
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6
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Ding Z, Liu Y, Zhang S, Wang F, Zong Q, Yang Y, Du A, Zheng Y, Zhu J, Jiang L. Investigation of the anti-Huanglongbing effects using antimicrobial lipopeptide and phytohormone complex powder prepared from Bacillus amyloliquefaciens MG-2 fermentation. Front Microbiol 2024; 15:1458051. [PMID: 39749134 PMCID: PMC11694225 DOI: 10.3389/fmicb.2024.1458051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 10/24/2024] [Indexed: 01/04/2025] Open
Abstract
Global citrus production has been severely affected by citrus Huanglongbing (HLB) disease, caused by Candidatus Liberibacter asiaticus (Clas), and the development of effective control methods are crucial. This study employed antimicrobial lipopeptide and phytohormone complex powder (L1) prepared from the fermentation broth of the endophytic plant growth promoting bacterium (PGPB) of Bacillus amyloliquefaciens strain MG-2 to treat Candidatus Liberibacter asiaticus (CLas)-infected 'Citrus reticulata 'Chun Jian' plants. Real-time fluorescence quantitative polymerase chain reaction (qPCR) and PCR were employed for disease detection. The results revealed that after 15 spray-drench treatments with L1 solution, the HLB infection rate decreased from 100 to 50%, the bacterial titer decreased by 51.9% compared with a 27.9% decrease in the control group. L1 treatment triggered the production of reactive oxygen species, increased lignin content, and increased defense enzyme activities (p < 0.05). Defense-related gene expression significantly increased within 12 h of treatment. In addition, L1 application also promoted plant growth, as evidenced by higher transpiration rates and net photosynthetic rates as well as increased leave or root density. Root flora analysis revealed that the abundances of Burkholderia_thailandensis, unclassified_g_Burkholderia-Caballeronia-Paraburkholderia, unclassified_g__Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Pseudomonas_mosselii were 1.64, 1.46, 5.84, and 6.93 times greater, respectively, than those in the control group. The levels of phenylpropanoids, polyketides, lipids, lipid-like molecules, organic acids, and derivatives, significantly increased following L1 treatment (FC > 2, p < 0.05). Additionally, salicylic acid, dihydrojasmonic acid, and isopentenyl adenosine levels in leaves markedly increased. High-performance liquid chromatography (HPLC) confirmed that L1 contained surfactin, iturin and fengycin cyclic-lipopeptides (CLPs) as well as indole-3-acetic acid (IAA), 3-indolebutyric acid (IBA), indole-3-carboxylic acid and indole-3-carboxaldehyde auxins, N6-entopentenyladenine and t-zeatin-riboside cytokinins, abscisic acid, 1-aminocyclicpanecarboxylic acid, salicylic acid, and gibberellin A1, A3 and A4 phytohormones. These findings provide insight into multiple mechanisms by which endophytic Bacillus PGPB L1 is able to combat HLB disease, to promote citrus plant growth, and to optimize the root flora for soil health which offering an innovative strategy for sustainable management of this severe disease and improving citrus plant growth and productivity.
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Affiliation(s)
- Zhicheng Ding
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, National Fruit Free-Virus Germplasm Resource Indoor Conservation Center, Department of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Yang Liu
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, National Fruit Free-Virus Germplasm Resource Indoor Conservation Center, Department of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Shaoran Zhang
- National Key Laboratory of Agricultural Microbiology, Wuhan, China
| | - Fangkui Wang
- National Key Laboratory of Agricultural Microbiology, Wuhan, China
| | - Qi Zong
- National Key Laboratory of Agricultural Microbiology, Wuhan, China
| | - Yuehua Yang
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, National Fruit Free-Virus Germplasm Resource Indoor Conservation Center, Department of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Anna Du
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, National Fruit Free-Virus Germplasm Resource Indoor Conservation Center, Department of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Yajie Zheng
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, National Fruit Free-Virus Germplasm Resource Indoor Conservation Center, Department of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Jian Zhu
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, National Fruit Free-Virus Germplasm Resource Indoor Conservation Center, Department of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Ling Jiang
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, National Fruit Free-Virus Germplasm Resource Indoor Conservation Center, Department of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
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Martínez-Esteso MJ, Morante-Carriel J, Samper-Herrero A, Martínez-Márquez A, Sellés-Marchart S, Nájera H, Bru-Martínez R. Proteomics: An Essential Tool to Study Plant-Specialized Metabolism. Biomolecules 2024; 14:1539. [PMID: 39766246 PMCID: PMC11674799 DOI: 10.3390/biom14121539] [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: 10/29/2024] [Revised: 11/28/2024] [Accepted: 11/28/2024] [Indexed: 01/11/2025] Open
Abstract
Plants are a valuable source of specialized metabolites that provide a plethora of therapeutic applications. They are natural defenses that plants use to adapt and respond to their changing environment. Decoding their biosynthetic pathways and understanding how specialized plant metabolites (SPMs) respond to biotic or abiotic stress will provide vital knowledge for plant biology research and its application for the future sustainable production of many SPMs of interest. Here, we focus on the proteomic approaches and strategies that help with the study of plant-specialized metabolism, including the: (i) discovery of key enzymes and the clarification of their biosynthetic pathways; (ii) study of the interconnection of both primary (providers of carbon and energy for SPM production) and specialized (secondary) metabolism; (iii) study of plant responses to biotic and abiotic stress; (iv) study of the regulatory mechanisms that direct their biosynthetic pathways. Proteomics, as exemplified in this review by the many studies performed to date, is a powerful tool that forms part of omics-driven research. The proteomes analysis provides an additional unique level of information, which is absent from any other omics studies. Thus, an integrative analysis, considered versus a single omics analysis, moves us more closely toward a closer interpretation of real cellular processes. Finally, this work highlights advanced proteomic technologies with immediate applications in the field.
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Affiliation(s)
- María José Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil and Agricultural Chemistry, Faculty of Science, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (J.M.-C.); (A.S.-H.); (A.M.-M.); (S.S.-M.); (R.B.-M.)
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
| | - Jaime Morante-Carriel
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil and Agricultural Chemistry, Faculty of Science, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (J.M.-C.); (A.S.-H.); (A.M.-M.); (S.S.-M.); (R.B.-M.)
- Plant Biotechnology Group, Faculty of Forestry and Agricultural Sciences, Quevedo State Technical University, Av. Quito km 1 1/2 vía a Santo Domingo de los Tsachilas, Quevedo 120501, Ecuador
| | - Antonio Samper-Herrero
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil and Agricultural Chemistry, Faculty of Science, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (J.M.-C.); (A.S.-H.); (A.M.-M.); (S.S.-M.); (R.B.-M.)
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
| | - Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil and Agricultural Chemistry, Faculty of Science, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (J.M.-C.); (A.S.-H.); (A.M.-M.); (S.S.-M.); (R.B.-M.)
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil and Agricultural Chemistry, Faculty of Science, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (J.M.-C.); (A.S.-H.); (A.M.-M.); (S.S.-M.); (R.B.-M.)
- Research Technical Facility, Proteomics and Genomics Division, University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Hugo Nájera
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana–Cuajimalpa, Av. Vasco de Quiroga 4871, Colonia Santa Fe Cuajimalpa, Alcaldía Cuajimalpa de Morelos, Mexico City 05348, Mexico;
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil and Agricultural Chemistry, Faculty of Science, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain; (J.M.-C.); (A.S.-H.); (A.M.-M.); (S.S.-M.); (R.B.-M.)
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
- Multidisciplinary Institute for the Study of the Environment (IMEM), University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain
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