Untargeted metabolomics identifies a bacterial cyclic dipeptide that induces resistance to a rust fungus of beans

1. Piasecka, A., Jedrzejczak-Rey, N. & Bednarek, P. Secondary metabolites in plant innate immunity: conserved function of divergent chemicals. New Phytol. 206, 948–964 (2015).

   Google Scholar 

2. Kuc, J. Phytoalexins, stress metabolism, and disease resistance in plants. Annu. Rev. Phytopathol. 33, 275–297 (1995).

   Google Scholar 

3. Cooper, B., Campbell, K. B. & Garrett, W. M. Salicylic acid and phytoalexin induction by a bacterium that causes halo blight in beans. Phytopathology 112, 1766–1775 (2022).

   Google Scholar 

4. Thomma, B. P. H. J., Nelissen, I., Eggermont, K. & Broekaert, W. F. Deficiency in phytoalexin production causes enhanced susceptibility of Arabidopsis Thaliana to the fungus alternaria brassicicola. Plant J. 19, 163–171 (1999).

   Google Scholar 

5. Glazebrook, J. & Ausubel, F. M. Isolation of phytoalexin-deficient mutants of Arabidopsis Thaliana and characterization of their interactions with bacterial pathogens. Proc. Natl. Acad. Sci. U S A. 91, 8955–8959 (1994).

   Google Scholar 

6. Graham, T. L., Graham, M. Y., Subramanian, S. & Yu, O. RNAi Silencing of genes for elicitation or biosynthesis of 5-deoxyisoflavonoids suppresses race-specific resistance and hypersensitive cell death in phytophthora Sojae infected tissues. Plant. Physiol. 144, 728–740 (2007).

   Google Scholar 

7. Hain, R. et al. Disease resistance results from foreign phytoalexin expression in a novel plant. Nature 361, 153–156 (1993).

   Google Scholar 

8. He, X. Z. & Dixon, R. A. Genetic manipulation of isoflavone 7-O-methyltransferase enhances biosynthesis of 4’-O-methylated isoflavonoid phytoalexins and disease resistance in alfalfa. Plant. Cell. 12, 1689–1702 (2000).

   Google Scholar 

9. Ahuja, I., Kissen, R. & Bones, A. M. Phytoalexins in defense against pathogens. Trends Plant. Sci. 17, 73–90 (2012).

   Google Scholar 

10. Kim, M., Han, J. & Kim, S. U. Isoflavone daidzein: chemistry and bacterial metabolism. J. Appl. Biol. Chem. 51, 253–261 (2008).

    Google Scholar 

11. Ogawara, H., Akiyama, T., Ishida, J., Watanabe, S. & Suzuki, K. A specific inhibitor for tyrosine protein kinase from Pseudomonas. J. Antibiot. 39, 606–608 (1986).

    Google Scholar 

12. Akiyama, T. et al. Genistein, a specific inhibitor of tyrosine-specific protein kinases. J. Biol. Chem. 262, 5592–5595 (1987).

    Google Scholar 

13. Xagorari, A. et al. Luteolin inhibits an endotoxin-stimulated phosphorylation cascade and Proinflammatory cytokine production in macrophages. J. Pharmacol. Exp. Ther. 296, 181–187 (2001).

    Google Scholar 

14. Nakashima, S., Koike, T. & Nozawa, Y. Genistein, a protein tyrosine kinase inhibitor, inhibits thromboxane A2-mediated human platelet responses. Mol. Pharmacol. 39, 475–480 (1991).

    Google Scholar 

15. Hong, H., Landauer, M. R., Foriska, M. A. & Ledney, G. D. Antibacterial activity of the soy isoflavone genistein. J. Basic Microbiol. 46, 329–335 (2006).

    Google Scholar 

16. Wells, C. L., Jechorek, R. P., Kinneberg, K. M., Debol, S. M. & Erlandsen, S. L. The isoflavone genistein inhibits internalization of enteric bacteria by cultured Caco-2 and HT-29 enterocytes. J. Nutr. 129, 634–640 (1999).

    Google Scholar 

17. Verdrengh, M., Collins, L. V., Bergin, P. & Tarkowski, A. Phytoestrogen genistein as an anti-staphylococcal agent. Microbes Infect. 6, 86–92 (2004).

    Google Scholar 

18. Cooper, B. et al. Quantitative proteomic analysis of Staphylococcus aureus treated with Punicalagin, a natural antibiotic from pomegranate that disrupts iron homeostasis and induces SOS. Proteomics 18, e1700461 (2018).

    Google Scholar 

19. Cooper, B. The detriment of Salicylic acid to the Pseudomonas Savastanoi pv. phaseolicola proteome. Mol. Plant. Microbe Interact. 35, 814–824 (2022).

    Google Scholar 

20. Cooper, B. Disruptive effects of Resveratrol on a bacterial pathogen of beans. J. Proteome Res. 22, 204–214 (2023).

    Google Scholar 

21. Cooper, B., Yang, R. & Campbell, K. B. Indole alkaloid production by the halo blight bacterium treated with the phytoalexin genistein. Phytopathology 114, 1196–1205 (2024).

    Google Scholar 

22. Kosslak, R. M., Bookland, R., Barkei, J., Paaren, H. E. & Appelbaum, E. R. Induction of Bradyrhizobium Japonicum common Nod genes by isoflavones isolated from Glycine max. Proc. Natl. Acad. Sci. U S A. 84, 7428–7432 (1987).

    Google Scholar 

23. Morris, P. F., Bone, E. & Tyler, B. M. Chemotropic and contact responses of phytophthora Sojae hyphae to soybean isoflavonoids and artificial substrates. Plant. Physiol. 117, 1171–1178 (1998).

    Google Scholar 

24. Cooper, B., Campbell, K. B., Beard, H. S., Garrett, W. M. & Ferreira, M. E. The proteomics of resistance to halo blight in common bean. Mol. Plant. Microbe Interact. 33, 1161–1175 (2020).

    Google Scholar 

25. Schymanski, E. L. et al. Identifying small molecules via high resolution mass spectrometry: communicating confidence. Environ. Sci. Technol. 48, 2097–2098 (2014).

    Google Scholar 

26. Sumner, L. W. et al. Proposed minimum reporting standards for chemical analysis chemical analysis working group (CAWG) metabolomics standards initiative (MSI). Metabolomics: Official J. Metabolomic Soc. 3, 211–221 (2007).

    Google Scholar 

27. Wheeler, A. W. Auxin-Like growth activity of phenylacetonitrile. Ann. Bot-London. 41, 867–872 (1977).

    Google Scholar 

28. Perez, V. C., Zhao, H., Lin, M., Kim, J. & Occurrence function, and biosynthesis of the natural auxin phenylacetic acid (PAA) in plants. Plants (Basel) 12 (2023).

29. Djami-Tchatchou, A. T. et al. Dual role of auxin in regulating plant defense and bacterial virulence gene expression during Pseudomonas syringae PtoDC3000 pathogenesis. Mol. plant-microbe Interactions: MPMI. 33, 1059–1071 (2020).

    Google Scholar 

30. Degrassi, G. et al. Plant growth-promoting Pseudomonas Putida WCS358 produces and secretes four Cyclic dipeptides: cross-talk with quorum sensing bacterial sensors. Curr. Microbiol. 45, 250–254 (2002).

    Google Scholar 

31. Ortiz-Castro, R. et al. Transkingdom signaling based on bacterial cyclodipeptides with auxin activity in plants. Proc. Natl. Acad. Sci. U S A. 108, 7253–7258 (2011).

    Google Scholar 

32. Hoch, H. C., Staples, R. C., Whitehead, B., Comeau, J. & Wolf, E. D. Signaling for growth orientation and cell differentiation by surface topography in Uromyces. Science 235, 1659–1662 (1987).

    Google Scholar 

33. Cooper, B., Beard, H. S., Garrett, W. M. & Campbell, K. B. Benzothiadiazole conditions the bean proteome for immunity to bean rust. Mol. Plant. Microbe Interact. 33, 600–611 (2020).

    Google Scholar 

34. Bernsdorff, F. et al. Pipecolic acid orchestrates plant systemic acquired resistance and defense priming via Salicylic acid-Dependent and -Independent pathways. Plant. Cell. 28, 102–129 (2016).

    Google Scholar 

35. Klessig, D. F., Choi, H. W. & Dempsey, D. A. Systemic acquired resistance and Salicylic acid: Past, Present, and future. Mol. Plant. Microbe Interact. 31, 871–888 (2018).

    Google Scholar 

36. Jirage, D. et al. Constitutive Salicylic acid-dependent signaling in cpr1 and cpr6 mutants requires PAD4. Plant. J. 26, 395–407 (2001).

    Google Scholar 

37. Wang, W. et al. An Arabidopsis secondary metabolite directly targets expression of the bacterial type III secretion system to inhibit bacterial virulence. Cell. Host Microbe. 27, 601–613e607 (2020).

    Google Scholar 

38. Ngou, B. P. M., Ding, P. & Jones, J. D. G. Thirty years of resistance: Zig-zag through the plant immune system. Plant. Cell. 34, 1447–1478 (2022).

    Google Scholar 

39. Cooper, B., Beard, H. S., Yang, R., Garrett, W. M. & Campbell, K. B. Bacterial immobilization and toxicity induced by a bean plant immune system. J. Proteome Res. 20, 3664–3677 (2021).

    Google Scholar 

40. O’Leary, B. M. et al. Early changes in Apoplast composition associated with defence and disease in interactions between phaseolus vulgaris and the halo blight pathogen Pseudomonas syringae Pv. phaseolicola. Plant. Cell. Environ. 39, 2172–2184 (2016).

    Google Scholar 

41. Freeman, B. C. & Beattie, G. A. Bacterial growth restriction during host resistance to Pseudomonas syringae is associated with leaf water loss and localized cessation of vascular activity in Arabidopsis Thaliana. Mol. Plant. Microbe Interact. 22, 857–867 (2009).

    Google Scholar 

42. Yamada, K., Saijo, Y., Nakagami, H. & Takano, Y. Regulation of sugar transporter activity for antibacterial defense in Arabidopsis. Science 354, 1427–1430 (2016).

    Google Scholar 

43. Parniske, M., Ahlborn, B. & Werner, D. Isoflavonoid-inducible resistance to the phytoalexin Glyceollin in soybean rhizobia. J. Bacteriol. 173, 3432–3439 (1991).

    Google Scholar 

44. Kapadia, C. et al. Pseudomonas aeruginosa inhibits quorum-sensing mechanisms of soft rot pathogen Lelliottia Amnigena RCE to regulate its virulence factors and biofilm formation. Front. Microbiol. 13, 977669 (2022).

    Google Scholar 

45. Wu, L., Wu, H., Chen, L., Zhang, H. & Gao, X. Induction of systemic disease resistance in Nicotiana benthamiana by the cyclodipeptides cyclo (l-Pro-l-Pro) and cyclo (d-Pro-d-Pro). Mol. Plant Pathol. 18, 67–74 (2017).

    Google Scholar 

46. Minen, R. I. et al. Characterization of the cyclic dipeptide cyclo(His-Pro) in arabidopsis. Plant Physiol. 198 (2025).

47. Cooper, B. & Yang, R. Genomic resources for Pseudomonas Savastanoi pv. phaseolicola races 5 and 8. Phytopathology 111, 893–895 (2021).

    Google Scholar 

48. Cooper, B. & Yang, R. An assessment of acquirex and compound discoverer software 3.3 for non-targeted metabolomics. Sci. Rep. 14, 4841 (2024).

    Google Scholar 

49. Lee, J. et al. Quantitative proteomic analysis of bean plants infected by a virulent and avirulent obligate rust fungus. Mol. Cell. Proteom. 8, 19–31 (2009).

    Google Scholar 

Download references