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Li C, Haider I, Wang JY, Quinodoz P, Suarez Duran HG, Méndez LR, Horber R, Fiorilli V, Votta C, Lanfranco L, Correia de Lemos SM, Jouffroy L, Moegle B, Miesch L, De Mesmaeker A, Medema MH, Al-Babili S, Dong L, Bouwmeester HJ. OsCYP706C2 diverts rice strigolactone biosynthesis to a noncanonical pathway branch. SCIENCE ADVANCES 2024; 10:eadq3942. [PMID: 39196928 PMCID: PMC11352842 DOI: 10.1126/sciadv.adq3942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/24/2024] [Indexed: 08/30/2024]
Abstract
Strigolactones exhibit dual functionality as regulators of plant architecture and signaling molecules in the rhizosphere. The important model crop rice exudes a blend of different strigolactones from its roots. Here, we identify the inaugural noncanonical strigolactone, 4-oxo-methyl carlactonoate (4-oxo-MeCLA), in rice root exudate. Comprehensive, cross-species coexpression analysis allowed us to identify a cytochrome P450, OsCYP706C2, and two methyl transferases as candidate enzymes for this noncanonical rice strigolactone biosynthetic pathway. Heterologous expression in yeast and Nicotiana benthamiana indeed demonstrated the role of these enzymes in the biosynthesis of 4-oxo-MeCLA, which, expectedly, is derived from carlactone as substrate. The oscyp706c2 mutants do not exhibit a tillering phenotype but do have delayed mycorrhizal colonization and altered root phenotype. This work sheds light onto the intricate complexity of strigolactone biosynthesis in rice and delineates its role in symbiosis and development.
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Affiliation(s)
- Changsheng Li
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
- Yuelushan Laboratory, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, 410082, Changsha, P. R. China
| | - Imran Haider
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, The BioActives Lab, Thuwal, 23955-6900, Saudi Arabia
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Jian You Wang
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, The BioActives Lab, Thuwal, 23955-6900, Saudi Arabia
| | - Pierre Quinodoz
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | | | - Lucía Reyes Méndez
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Robin Horber
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Turin, Viale P.A. Mattioli 25, 10125 Turin, Italy
| | - Cristina Votta
- Department of Life Sciences and Systems Biology, University of Turin, Viale P.A. Mattioli 25, 10125 Turin, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Viale P.A. Mattioli 25, 10125 Turin, Italy
| | - Samara M. Correia de Lemos
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands
- Plant genomics and transcriptomics group, Institute of Biosciences, Sao Paulo State University, 13506-900 Rio Claro, Brazil
| | - Lucile Jouffroy
- Equipe Synthèse Organique et Phytochimie, Institut de Chimie du CNRS UMR 7177, Université de Strasbourg, Strasbourg, France
| | - Baptiste Moegle
- Equipe Synthèse Organique et Phytochimie, Institut de Chimie du CNRS UMR 7177, Université de Strasbourg, Strasbourg, France
| | - Laurence Miesch
- Equipe Synthèse Organique et Phytochimie, Institut de Chimie du CNRS UMR 7177, Université de Strasbourg, Strasbourg, France
| | - Alain De Mesmaeker
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Salim Al-Babili
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, The BioActives Lab, Thuwal, 23955-6900, Saudi Arabia
| | - Lemeng Dong
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Harro J. Bouwmeester
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
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2
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Baker RL, Brock GL, Newsome EL, Zhao M. Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11605. [PMID: 39184197 PMCID: PMC11342231 DOI: 10.1002/aps3.11605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 08/27/2024]
Abstract
Premise Most traits are polygenic and most genes are pleiotropic, resulting in complex, integrated phenotypes. Polyploidy presents an excellent opportunity to explore the evolution of phenotypic integration as entire genomes are duplicated, allowing for new associations among traits and potentially leading to enhanced or reduced phenotypic integration. Despite the multivariate nature of phenotypic evolution, studies often rely on simplistic bivariate correlations that cannot accurately represent complex phenotypes or data reduction techniques that can obscure specific trait relationships. Methods We apply network modeling, a common gene co-expression analysis, to the study of phenotypic integration to identify multivariate patterns of phenotypic evolution, including anatomy and morphology (structural) and physiology (functional) traits in response to whole genome duplication in the genus Brassica. Results We identify four key structural traits that are overrepresented in the evolution of phenotypic integration. Seeding networks with key traits allowed us to identify structure-function relationships not apparent from bivariate analyses. In general, allopolyploids exhibited larger, more robust networks indicative of increased phenotypic integration compared to diploids. Discussion Phenotypic network analysis may provide important insights into the effects of selection on non-target traits, even when they lack direct correlations with the target traits. Network analysis may allow for more nuanced predictions of both natural and artificial selection.
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Affiliation(s)
- Robert L. Baker
- Inventory and Monitoring DivisionNational Park ServiceFort Collins80525ColoradoUSA
| | | | - Eastyn L. Newsome
- Department of Botany and Plant PathologyPurdue UniversityWest Lafayette47907IndianaUSA
| | - Meixia Zhao
- Department of Microbiology and Cell ScienceUniversity of FloridaGainesville32611FloridaUSA
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3
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Poretsky E, Cagirici HB, Andorf CM, Sen TZ. Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits. G3 (BETHESDA, MD.) 2024; 14:jkae059. [PMID: 38492232 PMCID: PMC11075552 DOI: 10.1093/g3journal/jkae059] [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: 10/20/2023] [Revised: 10/20/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein-protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.
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Affiliation(s)
- Elly Poretsky
- Crop Improvement and Genetics Research Unit, U.S. Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA
| | - Halise Busra Cagirici
- Crop Improvement and Genetics Research Unit, U.S. Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA
| | - Carson M Andorf
- Corn Insects and Crop Genetics Research, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA 50011, USA
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, U.S. Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA
- Department of Bioengineering, University of California, 306 Stanley Hall, Berkeley, CA 94720, USA
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4
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Wu M, Northen TR, Ding Y. Stressing the importance of plant specialized metabolites: omics-based approaches for discovering specialized metabolism in plant stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1272363. [PMID: 38023861 PMCID: PMC10663375 DOI: 10.3389/fpls.2023.1272363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
Plants produce a diverse range of specialized metabolites that play pivotal roles in mediating environmental interactions and stress adaptation. These unique chemical compounds also hold significant agricultural, medicinal, and industrial values. Despite the expanding knowledge of their functions in plant stress interactions, understanding the intricate biosynthetic pathways of these natural products remains challenging due to gene and pathway redundancy, multifunctionality of proteins, and the activity of enzymes with broad substrate specificity. In the past decade, substantial progress in genomics, transcriptomics, metabolomics, and proteomics has made the exploration of plant specialized metabolism more feasible than ever before. Notably, recent advances in integrative multi-omics and computational approaches, along with other technologies, are accelerating the discovery of plant specialized metabolism. In this review, we present a summary of the recent progress in the discovery of plant stress-related specialized metabolites. Emphasis is placed on the application of advanced omics-based approaches and other techniques in studying plant stress-related specialized metabolism. Additionally, we discuss the high-throughput methods for gene functional characterization. These advances hold great promise for harnessing the potential of specialized metabolites to enhance plant stress resilience in the future.
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Affiliation(s)
- Mengxi Wu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Trent R. Northen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yezhang Ding
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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5
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Que SJ, Zhong Q, Chen QY, Truty MJ, Yan S, Ma YB, Ding FH, Zheng CH, Li P, Wang JB, Lin JX, Lu J, Cao LL, Lin M, Tu RH, Lin JL, Zheng HL, Huang CM. A Novel ypTLM Staging System Based on LODDS for Gastric Cancer After Neoadjuvant Therapy: Multicenter and Large-Sample Retrospective Study. World J Surg 2023; 47:1762-1771. [PMID: 37069317 DOI: 10.1007/s00268-023-06994-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 04/19/2023]
Abstract
BACKGROUND The accuracy of the eighth AJCC ypTNM staging system on the prognosis of gastric cancer (GC) patients after neoadjuvant therapy (NAT) is controversial. This study aimed to develop and validate a novel staging system using the log odds of positive lymph nodes scheme (LODDS). METHODS A retrospective analysis of 606 GC patients who underwent radical gastrectomy after neoadjuvant therapy was conducted as the development cohort. (Fujian Medical University Affiliated Union Hospital (n = 183), Qinghai University Affiliated Hospital (n = 169), Mayo Clinic (n = 236), Lanzhou University First Hospital (n = 18)). The validation cohort came from the SEER database (n = 1701). A novel ypTLoddsS (ypTLM) staging system was established using the 3-year overall survival. The predictive performance of two systems was compared. RESULTS Two-step multivariate Cox regression analysis in both cohorts showed that ypTLM was an independent predictor of overall survival of GC patients after neoadjuvant therapy (HR: 1.57, 95% CI: 1.30-1.88, p < 0.001). In the development cohort, ypTLM had better discrimination ability than ypTNM (C-index: 0.663 vs 0.633, p < 0.001), better prediction homogeneity (LR: 97.7 vs. 70.9), and better prediction accuracy (BIC: 3067.01 vs 3093.82; NRI: 0.36). In the validation cohort, ypTLM had a better prognostic predictive ability (C-index: 0.614 vs 0.588, p < 0.001; LR: 11,909.05 vs. 11,975.75; BIC: 13,263.71 vs 13,328.24; NRI: 0.22). The time-dependent ROC curve shows that the predictive performance of ypTLM is better than ypTNM, and the analysis of the decision curve shows that ypTLM achieved better net benefits. CONCLUSION A LODDS-based ypTLM staging system based on multicenter data was established and validated. The predictive performance was superior to the eighth AJCC ypTNM staging system.
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Affiliation(s)
- Si-Jin Que
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Qing Zhong
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Qi-Yue Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Mark J Truty
- Section of Hepatobiliary and Pancreatic Surgery, Division of Subspecialty General Surgery, Department of Surgery, Mayo Clinic, Rochester, USA
| | - Su Yan
- Department of Gastrointestinal Surgery, Qinghai University Affiliated Hospital, Xining, China
| | - Yu-Bin Ma
- Department of Gastrointestinal Surgery, Qinghai University Affiliated Hospital, Xining, China
| | - Fang-Hui Ding
- Department of Gastrointestinal Surgery, First Hospital of Lanzhou University, Lanzhou, China
| | - Chao-Hui Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ping Li
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jia-Bin Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jian-Xian Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jun Lu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Long-Long Cao
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Mi Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ru-Hong Tu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ju-Li Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Hua-Long Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Chang-Ming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou, 350001, Fujian, China.
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China.
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6
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Saldivar EV, Ding Y, Poretsky E, Bird S, Block AK, Huffaker A, Schmelz EA. Maize Terpene Synthase 8 (ZmTPS8) Contributes to a Complex Blend of Fungal-Elicited Antibiotics. PLANTS (BASEL, SWITZERLAND) 2023; 12:1111. [PMID: 36903970 PMCID: PMC10005556 DOI: 10.3390/plants12051111] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
In maize (Zea mays), fungal-elicited immune responses include the accumulation of terpene synthase (TPS) and cytochrome P450 monooxygenases (CYP) enzymes resulting in complex antibiotic arrays of sesquiterpenoids and diterpenoids, including α/β-selinene derivatives, zealexins, kauralexins and dolabralexins. To uncover additional antibiotic families, we conducted metabolic profiling of elicited stem tissues in mapping populations, which included B73 × M162W recombinant inbred lines and the Goodman diversity panel. Five candidate sesquiterpenoids associated with a chromosome 1 locus spanning the location of ZmTPS27 and ZmTPS8. Heterologous enzyme co-expression studies of ZmTPS27 in Nicotiana benthamiana resulted in geraniol production while ZmTPS8 yielded α-copaene, δ-cadinene and sesquiterpene alcohols consistent with epi-cubebol, cubebol, copan-3-ol and copaborneol matching the association mapping efforts. ZmTPS8 is an established multiproduct α-copaene synthase; however, ZmTPS8-derived sesquiterpene alcohols are rarely encountered in maize tissues. A genome wide association study further linked an unknown sesquiterpene acid to ZmTPS8 and combined ZmTPS8-ZmCYP71Z19 heterologous enzyme co-expression studies yielded the same product. To consider defensive roles for ZmTPS8, in vitro bioassays with cubebol demonstrated significant antifungal activity against both Fusarium graminearum and Aspergillus parasiticus. As a genetically variable biochemical trait, ZmTPS8 contributes to the cocktail of terpenoid antibiotics present following complex interactions between wounding and fungal elicitation.
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Affiliation(s)
- Evan V. Saldivar
- Department of Cell and Developmental Biology, University of California at San Diego, San Diego, CA 92093, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford University, Palo Alto, CA 94305, USA
| | - Yezhang Ding
- Department of Cell and Developmental Biology, University of California at San Diego, San Diego, CA 92093, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elly Poretsky
- Department of Cell and Developmental Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Skylar Bird
- Department of Cell and Developmental Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Anna K. Block
- Chemistry Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, FL 32608, USA
| | - Alisa Huffaker
- Department of Cell and Developmental Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Eric A. Schmelz
- Department of Cell and Developmental Biology, University of California at San Diego, San Diego, CA 92093, USA
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7
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Li C, Dong L, Durairaj J, Guan JC, Yoshimura M, Quinodoz P, Horber R, Gaus K, Li J, Setotaw YB, Qi J, De Groote H, Wang Y, Thiombiano B, Floková K, Walmsley A, Charnikhova TV, Chojnacka A, Correia de Lemos S, Ding Y, Skibbe D, Hermann K, Screpanti C, De Mesmaeker A, Schmelz EA, Menkir A, Medema M, Van Dijk ADJ, Wu J, Koch KE, Bouwmeester HJ. Maize resistance to witchweed through changes in strigolactone biosynthesis. Science 2023; 379:94-99. [PMID: 36603079 DOI: 10.1126/science.abq4775] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Maize (Zea mays) is a major staple crop in Africa, where its yield and the livelihood of millions are compromised by the parasitic witchweed Striga. Germination of Striga is induced by strigolactones exuded from maize roots into the rhizosphere. In a maize germplasm collection, we identified two strigolactones, zealactol and zealactonoic acid, which stimulate less Striga germination than the major maize strigolactone, zealactone. We then showed that a single cytochrome P450, ZmCYP706C37, catalyzes a series of oxidative steps in the maize-strigolactone biosynthetic pathway. Reduction in activity of this enzyme and two others involved in the pathway, ZmMAX1b and ZmCLAMT1, can change strigolactone composition and reduce Striga germination and infection. These results offer prospects for breeding Striga-resistant maize.
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Affiliation(s)
- C Li
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - L Dong
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - J Durairaj
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands
| | - J-C Guan
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - M Yoshimura
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.,Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland.,Kyoto University, iCeMS, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - P Quinodoz
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - R Horber
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - K Gaus
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - J Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Y B Setotaw
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - J Qi
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - H De Groote
- International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041-00621, Nairobi, Kenya
| | - Y Wang
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - B Thiombiano
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - K Floková
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands.,Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - A Walmsley
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - T V Charnikhova
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - A Chojnacka
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - S Correia de Lemos
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands.,Plant genomics and transcriptomics group, Institute of Biosciences, Sao Paulo State University, 13506-900 Rio Claro, Brazil
| | - Y Ding
- Section of Cell and Developmental Biology, University of California at San Diego; La Jolla, CA 92093, USA
| | - D Skibbe
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC 27709, USA
| | - K Hermann
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - C Screpanti
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - A De Mesmaeker
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - E A Schmelz
- Section of Cell and Developmental Biology, University of California at San Diego; La Jolla, CA 92093, USA
| | - A Menkir
- International Institute of Tropical Agriculture, PMB 5320 Oyo Road, Ibadan, Nigeria
| | - M Medema
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands
| | - A D J Van Dijk
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands
| | - J Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - K E Koch
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - H J Bouwmeester
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
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8
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Chen QY, Que SJ, Chen JY, Qing-Zhong, Liu ZY, Wang JB, Lin JX, Lu J, Cao LL, Lin M, Tu RH, Huang ZN, Lin JL, Zheng HL, Xie JW, Zheng CH, Li P, Huang CM. Development and validation of metabolic scoring to individually predict prognosis and monitor recurrence early in gastric cancer: A large-sample analysis. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2022; 48:2149-2158. [PMID: 35864012 DOI: 10.1016/j.ejso.2022.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 05/14/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE To develop and validate a simple metabolic score (Metabolic score, MS) for use in evaluating the prognosis of gastric cancer (GC) patients and dynamically monitor for early recurrence. METHODS We retrospectively collected general clinicopathological data of patients who underwent radical gastrectomy for GC between September 2012 and December 2017 in the Department of Gastric Surgery of the Fujian Medical University Union Hospital. Using a random forest algorithm to screen preoperative blood indicators into the Least absolute shrinkage and selection operator (LASSO) model, we developed a novel MS to predict prognosis. RESULTS Data of 1974 patients were used to develop and validate the model. Total cholesterol (TCHO), bilirubin (TBIL), direct bilirubin (DBIL), and 15 other metabolic indicators had significant predictive value for the prognosis using the random forest algorithm. In the overall population, 533 patients (27.0%) had high and 1441 (73%) had low MS status. High MS status was related to tumor progression. The KM curves of 3-year OS and RFS for training set patients showed low MS had a better prognosis than high MS (OS: 79.4% vs 59.7%, P < 0.001; RFS: 76.0% vs 56.2%, P < 0.001). CONCLUSIONS We have developed and validated MS to predict the long-term survival of GC patients and allow early monitoring of recurrence. This will provide physicians with simple, economical, and dynamic tumor monitoring information.
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Affiliation(s)
- Qi-Yue Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Si-Jin Que
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jun-Yu Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Qing-Zhong
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Zhi-Yu Liu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jia-Bin Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jian-Xian Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jun Lu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Long-Long Cao
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Mi Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ru-Hong Tu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ze-Ning Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ju-Li Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Hua-Long Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jian-Wei Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Chao-Hui Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ping Li
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Chang-Ming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China.
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9
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Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses. Int J Mol Sci 2021; 22:ijms222313048. [PMID: 34884850 PMCID: PMC8657681 DOI: 10.3390/ijms222313048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 01/12/2023] Open
Abstract
SIMILAR TO RCD-ONEs (SROs) comprise a small plant-specific gene family which play important roles in regulating numerous growth and developmental processes and responses to environmental stresses. However, knowledge of SROs in sesame (Sesamum indicum L.) is limited. In this study, four SRO genes were identified in the sesame genome. Phylogenetic analysis showed that 64 SROs from 10 plant species were divided into two groups (Group I and II). Transcriptome data revealed different expression patterns of SiSROs over various tissues. Expression analysis showed that Group II SROs, especially SiSRO2b, exhibited a stronger response to various abiotic stresses and phytohormones than those in Group I, implying their crucial roles in response to environmental stimulus and hormone signals. In addition, the co-expression network and protein-protein interaction network indicated that SiSROs are associated with a wide range of stress responses. Moreover, transgenic yeast harboring SiSRO2b showed improved tolerance to salt, osmotic and oxidative stress, indicating SiSRO2b could confer multiple tolerances to transgenic yeast. Taken together, this study not only lays a foundation for further functional dissection of the SiSRO gene family, but also provides valuable gene candidates for genetic improvement of abiotic stress tolerance in sesame.
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10
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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: 2.3] [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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