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The Contribution of Romidepsin to the Herbicidal Activity of Burkholderia rinojensis Biopesticide

Cite this: J. Nat. Prod. 2020, 83, 4, 843–851
Publication Date (Web):February 24, 2020
https://doi.org/10.1021/acs.jnatprod.9b00405
Copyright © 2020 American Chemical Society and American Society of Pharmacognosy
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    The culture broth of Burkholderia rinojensis strain A396 is herbicidal to a number of weed species with greater observed efficacy against broadleaf than grass weeds. A portion of this activity is attributed to romidepsin, a 16-membered cyclic depsipeptide bridged by a 15-membered macrocyclic disulfide. Romidepsin, which is present in small amounts in the broth (18 to 25 μg mL–1), was isolated and purified using standard chromatographic techniques. It was established that romidepsin is a natural proherbicide that targets the activity of plant histone deacetylases (HDAC). Assays to measure plant HDAC activity were optimized by testing a number of HDAC substrates. The activity of romidepsin was greater when its macrocyclic-forming disulfide bridge was reduced to liberate a highly reactive free butenyl thiol side chain. Reduction was achieved using 200 mM tris(2-carboxyethyl)phosphine hydrochloride. A similar bioactivation of the proherbicide via reduction of the disulfide bridge of romidepsin was observed in plant-cell-free extracts. Molecular dynamic simulation of the binding of romidepsin to Arabidopsis thaliana HDAC19 indicated the reduced form of the compound could reach deep inside the catalytic domain and interact with an associated zinc atom required for enzyme activity.

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jnatprod.9b00405.

    • 1H NMR, 13C NMR, DEPT, HMQC, COSY, HMBC, NOESY, and HR-ESIMS spectra (PDF)

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    Cited By

    This article is cited by 12 publications.

    1. Thomas C. Sparks, Janine M. Sparks, Stephen O. Duke. Natural Product-Based Crop Protection Compounds─Origins and Future Prospects. Journal of Agricultural and Food Chemistry 2023, 71 (5) , 2259-2269. https://doi.org/10.1021/acs.jafc.2c06938
    2. Sean B. Romanowski, Sanghoon Lee, Sylvia Kunakom, Bruno S. Paulo, Michael J. J. Recchia, Dennis Y. Liu, Hannah Cavanagh, Roger G. Linington, Alessandra S. Eustáquio. Identification of the lipodepsipeptide selethramide encoded in a giant nonribosomal peptide synthetase from a Burkholderia bacterium. Proceedings of the National Academy of Sciences 2023, 120 (42) https://doi.org/10.1073/pnas.2304668120
    3. Stephen O Duke. Why are there no widely successful microbial bioherbicides for weed management in crops?. Pest Management Science 2023, 53 https://doi.org/10.1002/ps.7595
    4. Stephen O. Duke, Zhiqiang Pan, Amar G. Chittiboyina, Daniel R. Swale, Thomas C. Sparks. Molecular targets of insecticides and herbicides – Are there useful overlaps?. Pesticide Biochemistry and Physiology 2023, 191 , 105340. https://doi.org/10.1016/j.pestbp.2023.105340
    5. Yi-Meng Zhang, De-Xing Ye, Yan Liu, Xin-Yuan Zhang, Yuan-Lin Zhou, Li Zhang, Xin-Ling Yang. Peptides, new tools for plant protection in eco-agriculture. Advanced Agrochem 2023, 2 (1) , 58-78. https://doi.org/10.1016/j.aac.2023.01.003
    6. Pamela G. Marrone. Status of the biopesticide market and prospects for new bioherbicides. Pest Management Science 2023, 18 https://doi.org/10.1002/ps.7403
    7. Joanna Bajsa-Hirschel, Zhiqiang Pan, Pankaj Pandey, Ratnakar N. Asolkar, Amar G. Chittiboyina, Louis Boddy, Marylou C. Machingura, Stephen O. Duke. Spliceostatin C, a component of a microbial bioherbicide, is a potent phytotoxin that inhibits the spliceosome. Frontiers in Plant Science 2023, 13 https://doi.org/10.3389/fpls.2022.1019938
    8. Debora Luiza Costa Barreto, Camila Rodrigues de Carvalho, Tânia Maria de Almeida Alves, Carlos Leomar Zani, Charles Lowell Cantrell, Stephen Oscar Duke, Luiz Henrique Rosa. Influence of Genetics on the Secondary Metabolism of Fungi. 2023, 687-704. https://doi.org/10.1007/978-3-031-18587-8_22
    9. R.J. Kremer. Bioherbicide development and commercialization. 2023, 119-148. https://doi.org/10.1016/B978-0-323-95290-3.00016-9
    10. Stephen O Duke, Franck E Dayan. The search for new herbicide mechanisms of action: Is there a ‘holy grail’?. Pest Management Science 2022, 78 (4) , 1303-1313. https://doi.org/10.1002/ps.6726
    11. Stephen O. Duke, Zhiqiang Pan, Joanna Bajsa-Hirschel, C. Douglas Boyette. The potential future roles of natural compounds and microbial bioherbicides in weed management in crops. Advances in Weed Science 2022, 40 (spe1) https://doi.org/10.51694/AdvWeedSci/2022;40:seventy-five003
    12. Peter Maienfisch, Sven Mangelinckx. Recent innovation in crop protection research. 2021, 1-23. https://doi.org/10.1016/B978-0-12-821035-2.00001-2
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