Fungal secondary metabolism: regulation, function and drug discovery

Abstract

One of the exciting movements in microbial sciences has been a refocusing and revitalization of efforts to mine the fungal secondary metabolome. The magnitude of biosynthetic gene clusters (BGCs) in a single filamentous fungal genome combined with the historic number of sequenced genomes suggests that the secondary metabolite wealth of filamentous fungi is largely untapped. Mining algorithms and scalable expression platforms have greatly expanded access to the chemical repertoire of fungal-derived secondary metabolites. In this Review, I discuss new insights into the transcriptional and epigenetic regulation of BGCs and the ecological roles of fungal secondary metabolites in warfare, defence and development. I also explore avenues for the identification of new fungal metabolites and the challenges in harvesting fungal-derived secondary metabolites.

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Fig. 1: The typical building blocks of secondary metabolites and a schematic overview of a biosynthetic gene cluster.
Fig. 2: Regulation of the sterigmatocystin biosynthetic gene cluster.
Fig. 3: The ecological roles of secondary metabolites.
Fig. 4: Integration of genome mining with fungal biology yields valuable secondary metabolites.
Fig. 5: Chromosomal position of Aspergillus fumigatus biosynthetic gene clusters and their known or predicted products.

References

  1. 1.

    Nesbitt, B. F., O’Kelly, J., Sargeant, K. & Sheridan, A. Aspergillus flavus and turkey X disease: toxic metabolites of Aspergillus flavus. Nature 195, 1062–1063 (1962).

    CAS  PubMed  Google Scholar 

  2. 2.

    Quinn, R. Rethinking antibiotic research and development: World War II and the penicillin collaborative. Am. J. Public Health 103, 426–434 (2013).

    PubMed  PubMed Central  Google Scholar 

  3. 3.

    Krause, D. J. et al. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc. Natl Acad. Sci. USA 115, 11030–11035 (2018). This study characterizes the pulcherrimin cluster in K. lactis , a yeast that belongs to a taxon not associated with secondary metabolism.

    CAS  PubMed  Google Scholar 

  4. 4.

    Trail, F. et al. Physical and transcriptional map of an aflatoxin gene cluster in Aspergillus parasiticus and functional disruption of a gene involved early in the aflatoxin pathway. Appl. Environ. Microbiol. 61, 2665–2673 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Lind, A. L., Lim, F. Y., Soukup, A. A., Keller, N. P. & Rokas, A. An LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus. mSphere 3, e00050–18 (2018).

    PubMed  PubMed Central  Google Scholar 

  6. 6.

    Lysøe, E., Seong, K.-Y. & Kistler, H. C. The transcriptome of Fusarium graminearum during the infection of wheat. Mol. Plant Microbe Interact. 24, 995–1000 (2011).

    PubMed  Google Scholar 

  7. 7.

    Spraker, J. E. et al. Conserved responses in a war of small molecules between fungi and a bacterium. mBio 9, e00820–18 (2018). The paper reports the conserved induction of an antibacterial secondary metabolite cluster across disparate fungal genera in response to a lipopeptide that is secreted by the invading bacterium.

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Pelaez, F. in Handbook of Industrial Mycology (ed. Zhiqiang, A.) (Marcel Dekker, New York, NY, 2005).

  9. 9.

    Schueffler, A. & Anke, T. Fungal natural products in research and development. Nat. Prod. Rep. 31, 1425–1448 (2014).

    CAS  PubMed  Google Scholar 

  10. 10.

    Kück, U., Bloemendal, S. & Teichert, I. Putting fungi to work: harvesting a cornucopia of drugs, toxins, and antibiotics. PLOS Pathog. 10, e1003950 (2014).

    PubMed  PubMed Central  Google Scholar 

  11. 11.

    Caldwell, G. A., Naider, F. & Becker, J. M. Fungal lipopeptide mating pheromones: a model system for the study of protein prenylation. Microbiol. Rev. 59, 406–422 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Clevenger, K. D. et al. A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat. Chem. Biol. 13, 895–901 (2017). This paper presents a method to capture the entire secondary metabolome of a single species using FAC-MS technology.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Yun, C.-S., Motoyama, T. & Osada, H. Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS-PKS hybrid enzyme. Nat. Commun. 6, 8758 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Hur, G. H., Vickery, C. R. & Burkart, M. D. Explorations of catalytic domains in non-ribosomal peptide synthetase enzymology. Nat. Prod. Rep. 29, 1074 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Schmidt-Dannert, C. Biosynthesis of terpenoid natural products in fungi. Adv. Biochem. Eng. Biotechnol. 148, 19–61 (2014).

    Google Scholar 

  16. 16.

    Li, X.-W., Ear, A. & Nay, B. Hirsutellones and beyond: figuring out the biological and synthetic logics toward chemical complexity in fungal PKS-NRPS compounds. Nat. Prod. Rep. 30, 765 (2013).

    PubMed  Google Scholar 

  17. 17.

    Chiang, Y.-M., Oakley, B. R., Keller, N. P. & Wang, C. C. C. Unraveling polyketide synthesis in members of the genus Aspergillus. Appl. Microbiol. Biotechnol. 86, 1719–1736 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Umemura, M. et al. Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus. Fungal Genet. Biol. 68, 23–30 (2014). This study identifies the first BGC that produces a ribosomally encoded cyclic peptide.

    CAS  PubMed  Google Scholar 

  19. 19.

    Pettit, R. K. Small-molecule elicitation of microbial secondary metabolites. Microb. Biotechnol. 4, 471–478 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Lim, F. Y. et al. Fungal isocyanide synthases and xanthocillin biosynthesis in Aspergillus fumigatus. mBio 9, e00785–18 (2018). This study identifies novel BGCs that contain isocyanide synthases.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Yu, J. et al. Clustered pathway genes in aflatoxin biosynthesis. Appl. Environ. Microbiol. 70, 1253–1262 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Amaike, S., Affeldt, K. J. & Keller, N. P. in The Mycota: Agricultural Applications 2nd edn Vol. 11 (ed. Kempken, F.) 59–74 (Springer, Berlin, 2013).

  23. 23.

    Neubauer, L., Dopstadt, J., Humpf, H.-U. & Tudzynski, P. Identification and characterization of the ergochrome gene cluster in the plant pathogenic fungus Claviceps purpurea. Fungal Biol. Biotechnol. 3, 2 (2016).

    PubMed  PubMed Central  Google Scholar 

  24. 24.

    Lebar, M. D. et al. Identification and functional analysis of the aspergillic acid gene cluster in Aspergillus flavus. Fungal Genet. Biol. 116, 14–23 (2018).

    CAS  PubMed  Google Scholar 

  25. 25.

    Keller, N. P. Translating biosynthetic gene clusters into fungal armor and weaponry. Nat. Chem. Biol. 11, 671–677 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Wiemann, P. et al. Prototype of an intertwined secondary-metabolite supercluster. Proc. Natl Acad. Sci. USA 110, 17065–17070 (2013). This report describes a supercluster in which the genes encoding the secondary metabolites fumagillin and pseurotin are intertwined.

    CAS  PubMed  Google Scholar 

  27. 27.

    Andersen, M. R. et al. Accurate prediction of secondary metabolite gene clusters in filamentous fungi. Proc. Natl Acad. Sci. USA 110, E99–E107 (2013). This study identifies non-contiguous members within a BGC through expression data.

    CAS  PubMed  Google Scholar 

  28. 28.

    Ohsato, S. et al. Transgenic rice plants expressing trichothecene 3-O-acetyltransferase show resistance to the Fusarium phytotoxin deoxynivalenol. Plant Cell Rep. 26, 531–538 (2007).

    CAS  PubMed  Google Scholar 

  29. 29.

    Bradshaw, R. E. et al. Fragmentation of an aflatoxin-like gene cluster in a forest pathogen. New Phytol. 198, 525–535 (2013). This study reports the fragmentation of a gene cluster dedicated to the production of a secondary metabolite.

    CAS  PubMed  Google Scholar 

  30. 30.

    Lim, F. Y. & Keller, N. P. Spatial and temporal control of fungal natural product synthesis. Nat. Prod. Rep. 31, 1277–1286 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Kalinina, S. A., Jagels, A., Cramer, B., Geisen, R. & Humpf, H.-U. Influence of environmental factors on the production of penitrems A–F by Penicillium crustosum. Toxins 9, 210 (2017).

    PubMed Central  Google Scholar 

  32. 32.

    Hewage, R. T., Aree, T., Mahidol, C., Ruchirawat, S. & Kittakoop, P. One strain-many compounds (OSMAC) method for production of polyketides, azaphilones, and an isochromanone using the endophytic fungus Dothideomycete sp. Phytochemistry 108, 87–94 (2014).

    CAS  PubMed  Google Scholar 

  33. 33.

    Joffe, A. Z. & Lisker, N. Effects of light, temperature, and pH value on aflatoxin production in vitro. Appl. Microbiol. 18, 517–518 (1969).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Lind, A. L., Smith, T. D., Saterlee, T., Calvo, A. M. & Rokas, A. Regulation of secondary metabolism by the Velvet complex is temperature-responsive in Aspergillus. G3 6, 4023–4033 (2016).

    CAS  PubMed  Google Scholar 

  35. 35.

    Hagiwara, D. et al. Temperature during conidiation affects stress tolerance, pigmentation, and trypacidin accumulation in the conidia of the airborne pathogen Aspergillus fumigatus. PLOS ONE 12, e0177050 (2017).

    PubMed  PubMed Central  Google Scholar 

  36. 36.

    Berthier, E. et al. Low-volume toolbox for the discovery of immunosuppressive fungal secondary metabolites. PLOS Pathog. 9, e1003289 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Nazari, L., Manstretta, V. & Rossi, V. A non-linear model for temperature-dependent sporulation and T-2 and HT-2 production of Fusarium langsethiae and Fusarium sporotrichioides. Fungal Biol. 120, 562–571 (2016).

    CAS  PubMed  Google Scholar 

  38. 38.

    Bazafkan, H. et al. SUB1 has photoreceptor dependent and independent functions in sexual development and secondary metabolism in Trichoderma reesei. Mol. Microbiol. 106, 742–759 (2017).

    CAS  PubMed  Google Scholar 

  39. 39.

    Bayram, O. et al. VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism. Science 320, 1504–1506 (2008). This paper describes the identification of a conserved transcriptional complex that coordinates global regulation of secondary metabolism.

    CAS  PubMed  Google Scholar 

  40. 40.

    Pruss, S. et al. Role of the Alternaria alternata blue-light receptor LreA (white-collar 1) in spore formation and secondary metabolism. Appl. Environ. Microbiol. 80, 2582–2591 (2014).

    PubMed  PubMed Central  Google Scholar 

  41. 41.

    Monroy, A. A., Stappler, E., Schuster, A., Sulyok, M. & Schmoll, M. A. CRE1-regulated cluster is responsible for light dependent production of dihydrotrichotetronin in Trichoderma reesei. PLOS ONE 12, e0182530 (2017).

    PubMed  PubMed Central  Google Scholar 

  42. 42.

    Purschwitz, J. et al. Functional and physical interaction of blue- and red-light sensors in Aspergillus nidulans. Curr. Biol. 18, 255–259 (2008).

    CAS  PubMed  Google Scholar 

  43. 43.

    Calvo, A. M. & Cary, J. W. Association of fungal secondary metabolism and sclerotial biology. Front. Microbiol. 6, 62 (2015).

    PubMed  PubMed Central  Google Scholar 

  44. 44.

    Kenne, G. et al. Activation of aflatoxin biosynthesis alleviates total ROS in Aspergillus parasiticus. Toxins 10, 57 (2018).

    PubMed Central  Google Scholar 

  45. 45.

    Montibus, M., Pinson-Gadais, L., Richard-Forget, F., Barreau, C. & Ponts, N. Coupling of transcriptional response to oxidative stress and secondary metabolism regulation in filamentous fungi. Crit. Rev. Microbiol. 41, 295–308 (2015).

    CAS  PubMed  Google Scholar 

  46. 46.

    Fountain, J. C. et al. Oxidative stress and carbon metabolism influence Aspergillus flavus transcriptome composition and secondary metabolite production. Sci. Rep. 6, 38747 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Macheleidt, J. et al. Regulation and role of fungal secondary metabolites. Annu. Rev. Genet. 50, 371–392 (2016).

    CAS  PubMed  Google Scholar 

  48. 48.

    Fernandes, M., Keller, N. P. & Adams, T. H. Sequence-specific binding by Aspergillus nidulans AflR, a C6 zinc cluster protein regulating mycotoxin biosynthesis. Mol. Microbiol. 28, 1355–1365 (1998).

    CAS  PubMed  Google Scholar 

  49. 49.

    Brown, D. W. et al. Identification of a 12-gene fusaric acid biosynthetic gene cluster in Fusarium species through comparative and functional genomics. Mol. Plant Microbe Interact. 28, 319–332 (2015).

    CAS  PubMed  Google Scholar 

  50. 50.

    Yin, W.-B. et al. A nonribosomal peptide synthetase-derived iron(III) complex from the pathogenic fungus. Aspergillus fumigatus. J. Am. Chem. Soc. 135, 2064–2067 (2013).

    CAS  PubMed  Google Scholar 

  51. 51.

    Wiemann, P. et al. Perturbations in small molecule synthesis uncovers an iron-responsive secondary metabolite network in Aspergillus fumigatus. Front. Microbiol. 5, 530 (2014).

    PubMed  PubMed Central  Google Scholar 

  52. 52.

    Bergmann, S. et al. Activation of a silent fungal polyketide biosynthesis pathway through regulatory cross talk with a cryptic nonribosomal peptide synthetase gene cluster. Appl. Environ. Microbiol. 76, 8143–8149 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Bok, J. W. & Keller, N. P. in The My cota: Biochemistry and Molecular Biology 3rd edn Vol. 3 (ed. Hoffmeister, D.) 21–29 (Springer International, Switzerland, 2016).

  54. 54.

    Chettri, P. & Bradshaw, R. E. LaeA negatively regulates dothistromin production in the pine needle pathogen Dothistroma septosporum. Fungal Genet. Biol. 97, 24–32 (2016).

    CAS  PubMed  Google Scholar 

  55. 55.

    Oakley, C. E. et al. Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol. Microbiol. 103, 347–365 (2017).

    CAS  PubMed  Google Scholar 

  56. 56.

    Lim, F. Y., Ames, B., Walsh, C. T. & Keller, N. P. Co-ordination between BrlA regulation and secretion of the oxidoreductase FmqD directs selective accumulation of fumiquinazoline C to conidial tissues in Aspergillus fumigatus. Cell. Microbiol. 16, 1267–1283 (2014).

    CAS  PubMed  Google Scholar 

  57. 57.

    Mulinti, P. et al. Accumulation of ergot alkaloids during conidiophore development in Aspergillus fumigatus. Curr. Microbiol. 68, 1–5 (2014).

    CAS  PubMed  Google Scholar 

  58. 58.

    Cichewicz, R. H. Epigenome manipulation as a pathway to new natural product scaffolds and their congeners. Nat. Prod. Rep. 27, 11–22 (2010).

    CAS  PubMed  Google Scholar 

  59. 59.

    Roze, L. V., Arthur, A. E., Hong, S.-Y., Chanda, A. & Linz, J. E. The initiation and pattern of spread of histone H4 acetylation parallel the order of transcriptional activation of genes in the aflatoxin cluster. Mol. Microbiol. 66, 713–726 (2007).

    CAS  PubMed  Google Scholar 

  60. 60.

    Shwab, E. K. et al. Histone deacetylase activity regulates chemical diversity in Aspergillus. Eukaryot. Cell 6, 1656–1664 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61.

    Gacek, A. & Strauss, J. The chromatin code of fungal secondary metabolite gene clusters. Appl. Microbiol. Biotechnol. 95, 1389–1404 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Fan, A. et al. Deletion of a histone acetyltransferase leads to the pleiotropic activation of natural products in Metarhizium robertsii. Org. Lett. 19, 1686–1689 (2017).

    CAS  PubMed  Google Scholar 

  63. 63.

    Gacek-Matthews, A. et al. KdmB, a Jumonji histone H3 demethylase, regulates genome-wide H3K4 trimethylation and is required for normal induction of secondary metabolism in Aspergillus nidulans. PLOS Genet. 12, e1006222 (2016). Using genome-wide chromatin immunoprecipitation coupled with RNA-seq and liquid chromatography with tandem mass spectrometry (LC-MS/MS), this study presents unprecedented insight into the global epigenetic regulation of cryptic BGCs in one species.

    PubMed  PubMed Central  Google Scholar 

  64. 64.

    Williams, R. B., Henrikson, J. C., Hoover, A. R., Lee, A. E. & Cichewicz, R. H. Epigenetic remodeling of the fungal secondary metabolome. Org. Biomol. Chem. 6, 1895 (2008).

    CAS  PubMed  Google Scholar 

  65. 65.

    Albright, J. C. et al. Large-scale metabolomics reveals a complex response of Aspergillus nidulans to epigenetic perturbation. ACS Chem. Biol. 10, 1535–1541 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66.

    Reyes-Dominguez, Y. et al. Heterochromatic marks are associated with the repression of secondary metabolism clusters in Aspergillus nidulans. Mol. Microbiol. 76, 1376–1386 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. 67.

    Karimi-Aghcheh, R. et al. Functional analyses of Trichoderma reesei LAE1 reveal conserved and contrasting roles of this regulator. G 3 3, 369–378 (2013).

  68. 68.

    Niehaus, E.-M. et al. Analysis of the global regulator Lae1 uncovers a connection between Lae1 and the histone acetyltransferase HAT1 in Fusarium fujikuroi. Appl. Microbiol. Biotechnol. 102, 279–295 (2018).

    CAS  PubMed  Google Scholar 

  69. 69.

    Nützmann, H.-W. et al. Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proc. Natl Acad. Sci. USA 108, 14282–14287 (2011). This paper reports the bacterial induction of a cryptic BGC via a chromatin remodelling enzyme complex.

    PubMed  Google Scholar 

  70. 70.

    Netzker, T. et al. Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front. Microbiol. 6, 299 (2015).

    PubMed  PubMed Central  Google Scholar 

  71. 71.

    Bok, J. W. et al. VeA and MvlA repression of the cryptic orsellinic acid gene cluster in Aspergillus nidulans involves histone 3 acetylation. Mol. Microbiol. 89, 963–974 (2013).

    CAS  PubMed  Google Scholar 

  72. 72.

    Tsai, H. F., Wheeler, M. H., Chang, Y. C. & Kwon-Chung, K. J. A developmentally regulated gene cluster involved in conidial pigment biosynthesis in Aspergillus fumigatus. J. Bacteriol. 181, 6469–6477 (1999). This article presents the first identification of a BGC required for fungal development.

    CAS  PubMed  Google Scholar 

  73. 73.

    Zhang, P. et al. A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development in Pestalotiopsis fici. Mol. Microbiol. 105, 469–483 (2017).

    CAS  PubMed  Google Scholar 

  74. 74.

    Leonard, K. J. Virulence, temperature optima, and competitive abilities of isolines of races T and 0 of Bipolaris maydis. Phytopathology 67, 1273–1279 (1977).

    Google Scholar 

  75. 75.

    Shukla, S. et al. Total phenolic content, antioxidant, tyrosinase and α-glucosidase inhibitory activities of water soluble extracts of noble starter culture Doenjang, a Korean fermented soybean sauce variety. Food Control 59, 854–861 (2016).

    CAS  Google Scholar 

  76. 76.

    Eisenman, H. C. & Casadevall, A. Synthesis and assembly of fungal melanin. Appl. Microbiol. Biotechnol. 93, 931–940 (2012).

    CAS  PubMed  Google Scholar 

  77. 77.

    Jacobson, E. S. Pathogenic roles for fungal melanins. Clin. Microbiol. Rev. 13, 708–717 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. 78.

    Zhao, L., Kim, J.-C., Paik, M.-J., Lee, W. & Hur, J.-S. A. Multifunctional and possible skin UV protectant, (3R)-5-hydroxymellein, produced by an endolichenic fungus isolated from Parmotrema austrosinense. Molecules 22, 26 (2016).

    PubMed Central  Google Scholar 

  79. 79.

    Zheng, H. et al. Redox metabolites signal polymicrobial biofilm development via the NapA oxidative stress cascade in Aspergillus. Curr. Biol. 25, 29–37 (2015).

    CAS  PubMed  Google Scholar 

  80. 80.

    Scherlach, K. & Hertweck, C. Mediators of mutualistic microbe-microbe interactions. Nat. Prod. Rep. 35, 303–308 (2018).

    CAS  PubMed  Google Scholar 

  81. 81.

    Zeilinger, S. et al. Friends or foes? Emerging insights from fungal interactions with plants. FEMS Microbiol. Rev. 40, 182–207 (2016).

    CAS  PubMed  Google Scholar 

  82. 82.

    Rohlfs, M. Fungal secondary metabolite dynamics in fungus-grazer interactions: novel insights and unanswered questions. Front. Microbiol. 5, 788 (2014).

    PubMed  Google Scholar 

  83. 83.

    Partida-Martinez, L. P. & Hertweck, C. Pathogenic fungus harbours endosymbiotic bacteria for toxin production. Nature 437, 884–888 (2005).

    CAS  PubMed  Google Scholar 

  84. 84.

    Scherlach, K., Busch, B., Lackner, G., Paszkowski, U. & Hertweck, C. Symbiotic cooperation in the biosynthesis of a phytotoxin. Angew. Chem. Int. Ed. 51, 9615–9618 (2012).

    CAS  Google Scholar 

  85. 85.

    Spraker, J. E., Sanchez, L. M., Lowe, T. M., Dorrestein, P. C. & Keller, N. P. Ralstonia solanacearum lipopeptide induces chlamydospore development in fungi and facilitates bacterial entry into fungal tissues. ISME J. 10, 2317–2330 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. 86.

    Khalid, S. et al. NRPS-derived isoquinolines and lipopetides mediate antagonism between plant pathogenic fungi and bacteria. ACS Chem. Biol. 13, 171–179 (2018).

    CAS  PubMed  Google Scholar 

  87. 87.

    Schumacher, J. et al. A functional bikaverin biosynthesis gene cluster in rare strains of Botrytis cinerea is positively controlled by VELVET. PLOS ONE 8, e53729 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88.

    Campbell, M. A., Rokas, A. & Slot, J. C. Horizontal transfer and death of a fungal secondary metabolic gene cluster. Genome Biol. Evol. 4, 289–293 (2012).

    PubMed  PubMed Central  Google Scholar 

  89. 89.

    Oh, D.-C., Poulsen, M., Currie, C. R. & Clardy, J. Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis. Nat. Chem. Biol. 5, 391–393 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 90.

    Dhodary, B., Schilg, M., Wirth, R. & Spiteller, D. Secondary metabolites from Escovopsis weberi and their role in attacking the garden fungus of leaf-cutting ants. Chemistry 24, 4445–4452 (2018).

    CAS  PubMed  Google Scholar 

  91. 91.

    Tauber, J. P., Gallegos-Monterrosa, R., Kovács, Á. T., Shelest, E. & Hoffmeister, D. Dissimilar pigment regulation in Serpula lacrymans and Paxillus involutus during inter-kingdom interactions. Microbiology 164, 65–77 (2018).

    CAS  PubMed  Google Scholar 

  92. 92.

    Tauber, J. P., Schroeckh, V., Shelest, E., Brakhage, A. A. & Hoffmeister, D. Bacteria induce pigment formation in the basidiomycete Serpula lacrymans. Environ. Microbiol. 18, 5218–5227 (2016).

    CAS  PubMed  Google Scholar 

  93. 93.

    Fan, Y. et al. Regulatory cascade and biological activity of Beauveria bassiana oosporein that limits bacterial growth after host death. Proc. Natl Acad. Sci. USA 114, E1578–E1586 (2017). This paper reports the finding that a fungus-derived antibacterial compound poisons the food supply to limit microbial competition.

    CAS  PubMed  Google Scholar 

  94. 94.

    Drott, M. T., Lazzaro, B. P., Brown, D. L., Carbone, I. & Milgroom, M. G. Balancing selection for aflatoxin in Aspergillus flavus is maintained through interference competition with, and fungivory by insects. Proc. Biol. Sci. 284, 20172408 (2017). This article provides evidence that a toxic secondary metabolite provides a fitness advantage to the fungus during confrontations with insects.

    PubMed  PubMed Central  Google Scholar 

  95. 95.

    Dolan, S. K., O’Keeffe, G., Jones, G. W. & Doyle, S. Resistance is not futile: gliotoxin biosynthesis, functionality and utility. Trends Microbiol. 23, 419–428 (2015).

    CAS  PubMed  Google Scholar 

  96. 96.

    Teijeira, F. et al. The transporter CefM involved in translocation of biosynthetic intermediates is essential for cephalosporin production. Biochem. J. 418, 113–124 (2009).

    CAS  PubMed  Google Scholar 

  97. 97.

    Scharf, D. H. et al. Transannular disulfide formation in gliotoxin biosynthesis and its role in self-resistance of the human pathogen Aspergillus fumigatus. J. Am. Chem. Soc. 132, 10136–10141 (2010).

    CAS  PubMed  Google Scholar 

  98. 98.

    Abe, Y. et al. Effect of increased dosage of the ML-236B (compactin) biosynthetic gene cluster on ML-236B production in Penicillium citrinum. Mol. Genet. Genomics 268, 130–137 (2002).

    CAS  PubMed  Google Scholar 

  99. 99.

    Yeh, H.-H. et al. Resistance gene-guided genome mining: serial promoter exchanges in Aspergillus nidulans reveal the biosynthetic pathway for fellutamide B, a proteasome inhibitor. ACS Chem. Biol. 11, 2275–2284 (2016). This paper provides the first evidence that duplicated, resistant target genes within a BGC provide self-protection.

    CAS  PubMed  Google Scholar 

  100. 100.

    Yue, Q. et al. Genomics-driven discovery of a novel self-resistance mechanism in the echinocandin-producing fungus Pezicula radicicola. Environ. Microbiol. 20, 3154–3167 (2018).

    CAS  PubMed  Google Scholar 

  101. 101.

    Yan, Y. et al. Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action. Nature 559, 415–418 (2018). This study describes a genomics approach to identify duplicated resistance genes and the discovery of a bioactive natural-product herbicide.

    CAS  PubMed  PubMed Central  Google Scholar 

  102. 102.

    Hansen, B. G. et al. A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi. BMC Microbiol. 11, 202 (2011). This study reports on the initial demonstration that a duplicated target gene within a BGC can provide resistance to the BGC product using a heterologous host.

    CAS  PubMed  PubMed Central  Google Scholar 

  103. 103.

    Larkin, E. L., Dharmaiah, S. & Ghannoum, M. A. Biofilms and beyond: expanding echinocandin utility. J. Antimicrob. Chemother. 73, i73–i81 (2018).

    CAS  PubMed  Google Scholar 

  104. 104.

    Studt, L., Wiemann, P., Kleigrewe, K., Humpf, H.-U. & Tudzynski, B. Biosynthesis of fusarubins accounts for pigmentation of Fusarium fujikuroi perithecia. Appl. Environ. Microbiol. 78, 4468–4480 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. 105.

    Zhao, Y. et al. Production of a fungal furocoumarin by a polyketide synthase gene cluster confers the chemo-resistance of Neurospora crassa to the predation by fungivorous arthropods. Environ. Microbiol. 19, 3920–3929 (2017).

    CAS  PubMed  Google Scholar 

  106. 106.

    Schindler, D. & Nowrousian, M. The polyketide synthase gene pks4 is essential for sexual development and regulates fruiting body morphology in Sordaria macrospora. Fungal Genet. Biol. 68, 48–59 (2014).

    CAS  PubMed  Google Scholar 

  107. 107.

    Becker, J., Liermann, J. C., Opatz, T., Anke, H. & Thines, E. GKK1032A2, a secondary metabolite from Penicillium sp. IBWF-029-96, inhibits conidial germination in the rice blast fungus Magnaporthe oryzae. J. Antibiot. 65, 99–102 (2012).

    CAS  PubMed  Google Scholar 

  108. 108.

    Nielsen, J. C. et al. Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species. Nat. Microbiol. 2, 17044 (2017).

    CAS  PubMed  Google Scholar 

  109. 109.

    Medema, M. H. et al. Minimum information about a biosynthetic gene cluster. Nat. Chem. Biol. 11, 625–631 (2015). This article presents a community effort to standardize annotations and metadata on BGCs and their products.

    CAS  PubMed  PubMed Central  Google Scholar 

  110. 110.

    Alberti, F., Foster, G. D. & Bailey, A. M. Natural products from filamentous fungi and production by heterologous expression. Appl. Microbiol. Biotechnol. 101, 493–500 (2017).

    CAS  PubMed  Google Scholar 

  111. 111.

    Chavali, A. K. & Rhee, S. Y. Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites. Brief. Bioinform. 19, 1022–1034 (2017).

    PubMed Central  Google Scholar 

  112. 112.

    Khaldi, N. et al. SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet. Biol. 47, 736–741 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. 113.

    Medema, M. H. et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39, W339–W346 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. 114.

    Galagan, J. E. et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438, 1105–1115 (2005).

    CAS  PubMed  Google Scholar 

  115. 115.

    Machida, M. et al. Genome sequencing and analysis of Aspergillus oryzae. Nature 438, 1157–1161 (2005).

    PubMed  Google Scholar 

  116. 116.

    Nierman, W. C. et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438, 1151–1156 (2005).

    CAS  PubMed  Google Scholar 

  117. 117.

    Mohimani, H. et al. Dereplication of microbial metabolites through database search of mass spectra. Nat. Commun. 9, 4035 (2018).

    PubMed  PubMed Central  Google Scholar 

  118. 118.

    Janevska, S. et al. Establishment of the inducible Tet-On system for the activation of the silent trichosetin gene cluster in Fusarium fujikuroi. Toxins 9, 126 (2017).

    PubMed Central  Google Scholar 

  119. 119.

    Jiang, T. et al. Overexpression of the global regulator LaeA in Chaetomium globosum leads to the biosynthesis of chaetoglobosin Z. J. Nat. Prod. 79, 2487–2494 (2016).

    CAS  PubMed  Google Scholar 

  120. 120.

    Palonen, E. K. et al. Transcriptomic complexity of Aspergillus terreus Velvet gene family under the influence of butyrolactone I. Microorganisms 5, 12 (2017).

    PubMed Central  Google Scholar 

  121. 121.

    Adnani, N., Rajski, S. R. & Bugni, T. S. Symbiosis-inspired approaches to antibiotic discovery. Nat. Prod. Rep. 34, 784–814 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. 122.

    Billingsley, J. M., DeNicola, A. B. & Tang, Y. Technology development for natural product biosynthesis in Saccharomyces cerevisiae. Curr. Opin. Biotechnol. 42, 74–83 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. 123.

    He, Y. et al. Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp. Biotechnol. Adv. 36, 739–783 (2018).

    CAS  PubMed  Google Scholar 

  124. 124.

    Yin, W.-B. et al. Discovery of cryptic polyketide metabolites from dermatophytes using heterologous expression in Aspergillus nidulans. ACS Synth. Biol. 2, 629–634 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  125. 125.

    Harvey, C. J. B. et al. HEx: a heterologous expression platform for the discovery of fungal natural products. Sci. Adv. 4, eaar5459 (2018). This paper describes the tool and protocol development that led to the expression of 41 BGCs and 22 compounds in a yeast heterologous expression system.

    PubMed  PubMed Central  Google Scholar 

  126. 126.

    Stepien, Ł. The use of Fusarium secondary metabolite biosynthetic genes in chemotypic and phylogenetic studies. Crit. Rev. Microbiol. 40, 176–185 (2014).

    CAS  PubMed  Google Scholar 

  127. 127.

    Khaldi, N., Collemare, J., Lebrun, M.-H. & Wolfe, K. H. Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol. 9, R18 (2008). This early phylogenetic study provides evidence for horizontal transfer of natural-product BGCs in fungi.

    PubMed  PubMed Central  Google Scholar 

  128. 128.

    Reynolds, H. T. et al. Differential retention of gene functions in a secondary metabolite cluster. Mol. Biol. Evol. 34, 2002–2015 (2017).

    CAS  PubMed  Google Scholar 

  129. 129.

    Bignell, E., Cairns, T. C., Throckmorton, K., Nierman, W. C. & Keller, N. P. Secondary metabolite arsenal of an opportunistic pathogenic fungus. Phil. Trans. R. Soc. B 371, 20160023 (2016).

    PubMed  Google Scholar 

  130. 130.

    Perrin, R. M. et al. Transcriptional regulation of chemical diversity in Aspergillus fumigatus by LaeA. PLOS Pathog. 3, e50 (2007).

    PubMed  PubMed Central  Google Scholar 

  131. 131.

    Lind, A. L. et al. Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species. PLOS Biol. 15, e2003583 (2017). This study compares DNA sequences of the BGCs of 66 A. fumigatus isolates and establishes 5 drivers of genetic diversity that explain BGC macroevolutionary patterns.

    PubMed  PubMed Central  Google Scholar 

  132. 132.

    Droce, A. et al. Functional analysis of the fusarielin biosynthetic gene cluster. Molecules 21, 1710 (2016).

    PubMed Central  Google Scholar 

  133. 133.

    Campbell, M. A., Staats, M., van Kan, J. A. L., Rokas, A. & Slot, J. C. Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia 105, 1126–1134 (2013).

    PubMed  Google Scholar 

  134. 134.

    Nielsen, K. F. & Larsen, T. O. The importance of mass spectrometric dereplication in fungal secondary metabolite analysis. Front. Microbiol. 6, 71 (2015).

    PubMed  PubMed Central  Google Scholar 

  135. 135.

    Chiang, Y.-M. et al. Development of genetic dereplication strains in Aspergillus nidulans results in the discovery of aspercryptin. Angew. Chem. Int. Ed. 55, 1662–1665 (2016).

    CAS  Google Scholar 

  136. 136.

    Díez, B. et al. The cluster of penicillin biosynthetic genes: identification and characterization of the pcbAB gene encoding the alpha-aminoadipyl-cysteinyl-valine synthetase and linkage to the pcbC and penDE genes. J. Biol. Chem. 265, 16358–16365 (1990).

    PubMed  Google Scholar 

  137. 137.

    Smith, D. J., Burnham, M. K., Edwards, J., Earl, A. J. & Turner, G. Cloning and heterologous expression of the penicillin biosynthetic gene cluster from Penicillum chrysogenum. Biotechnology 8, 39–41 (1990).

    CAS  PubMed  Google Scholar 

  138. 138.

    Keller, N. P. & Hohn, T. M. Metabolic pathway gene clusters in filamentous fungi. Fungal Genet. Biol. 21, 17–29 (1997).

    CAS  PubMed  Google Scholar 

  139. 139.

    Goffeau, A. et al. Life with 6000 genes. Science 274, 546–567 (1996).

    CAS  PubMed  Google Scholar 

  140. 140.

    Inglis, D. O. et al. Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. BMC Microbiol. 13, 91 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  141. 141.

    Samson, R. A. et al. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud. Mycol. 78, 141–173 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  142. 142.

    Visagie, C. M. et al. Identification and nomenclature of the genus Penicillium. Stud. Mycol. 78, 343–371 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  143. 143.

    Kirk, P. M., Cannon, P. F., David, J. C. & Stalpers, J. A. (eds) Ainsworth & Bisby’s Dictionary of the Fungi 9th edn (CABI, 2001).

  144. 144.

    Schoch, C. L. et al. A class-wide phylogenetic assessment of Dothideomycetes. Stud. Mycol. 64, 1–15 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  145. 145.

    Jahn, L. et al. Linking secondary metabolites to biosynthesis genes in the fungal endophyte Cyanodermella asteris: the anti-cancer bisanthraquinone skyrin. J. Biotechnol. 257, 233–239 (2017).

    CAS  PubMed  Google Scholar 

  146. 146.

    Yin, W.-B. et al. An Aspergillus nidulans bZIP response pathway hardwired for defensive secondary metabolism operates through aflR. Mol. Microbiol. 83, 1024–1034 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  147. 147.

    Soukup, A. A. et al. Overexpression of the Aspergillus nidulans histone 4 acetyltransferase EsaA increases activation of secondary metabolite production. Mol. Microbiol. 86, 314–330 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  148. 148.

    Itoh, E. et al. Sirtuin A regulates secondary metabolite production by Aspergillus nidulans. J. Gen. Appl. Microbiol. 63, 228–235 (2017).

    CAS  PubMed  Google Scholar 

  149. 149.

    Ahuja, M. et al. Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J. Am. Chem. Soc. 134, 8212–8221 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  150. 150.

    Brakhage, A. A. Regulation of fungal secondary metabolism. Nat. Rev. Microbiol. 11, 21–32 (2013).

    CAS  PubMed  Google Scholar 

  151. 151.

    Pfannenstiel, B. T. et al. Revitalization of a forward genetic screen identifies three new regulators of fungal secondary metabolism in the genus Aspergillus. mBio 8, e01246–17 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  152. 152.

    Gacek-Matthews, A. et al. KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. Mol. Microbiol. 96, 839–860 (2015).

    CAS  Google Scholar 

  153. 153.

    Strauss, J. & Reyes-Dominguez, Y. Regulation of secondary metabolism by chromatin structure and epigenetic codes. Fungal Genet. Biol. 48, 62–69 (2011).

    CAS  PubMed  Google Scholar 

  154. 154.

    Wiemann, P. et al. CoIN: co-inducible nitrate expression system for secondary metabolites in Aspergillus nidulans. Fungal Biol. Biotechnol. 5, 6 (2018).

  155. 155.

    Blin, K. et al. antiSMASH 4.0 — improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 45, W36–W41 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  156. 156.

    Skinnider, M. A. et al. Genomes to natural products prediction informatics for secondary metabolomes (PRISM). Nucleic Acids Res. 43, 9645–9662 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  157. 157.

    Wolf, T., Shelest, V., Nath, N. & Shelest, E. CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes. Bioinformatics 32, 1138–1143 (2016).

    CAS  PubMed  Google Scholar 

  158. 158.

    Vesth, T. C., Brandl, J. & Andersen, M. R. FunGeneClusterS: predicting fungal gene clusters from genome and transcriptome data. Synth. Syst. Biotechnol. 1, 122–129 (2016).

    PubMed  PubMed Central  Google Scholar 

  159. 159.

    Zierep, P. F. et al. SeMPI: a genome-based secondary metabolite prediction and identification web server. Nucleic Acids Res. 45, W64–W71 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  160. 160.

    Conway, K. R. & Boddy, C. N. ClusterMine360: a database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res. 41, D402–D407 (2013).

    CAS  PubMed  Google Scholar 

  161. 161.

    Hadjithomas, M. et al. IMG-ABC: a knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. mBio 6, e00932 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  162. 162.

    Medema, M. H. et al. Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products. PLOS Comput. Biol. 10, e1003822 (2014).

    PubMed  PubMed Central  Google Scholar 

  163. 163.

    Dejong, C. A. et al. Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching. Nat. Chem. Biol. 12, 1007–1014 (2016).

    CAS  PubMed  Google Scholar 

  164. 164.

    Röttig, M. et al. NRPSpredictor2 — a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res. 39, W362–W367 (2011).

    PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The author thanks F. Y. Lim for generating the original figure 5 and J. Winans and C. D. Nwagwu for help with formatting the text. N.P.K. is funded by US National Institutes of Health (NIH) grants R01GM112739-01 and R01 AI065728-01.

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Nature Reviews Microbiology thanks M. Andersen, J. Cary, D. Hoffmeister and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Glossary

Metabolome

The total number of small molecules in a biological sample.

Primary metabolites

Metabolites that are produced by many unrelated taxa and are required for normal growth, development and reproduction.

Tailoring enzymes

Enzymes that modify non-ribosomal peptides, polyketide backbones and/or terpenoid backbones after chain elongation from respective synthetases, synthases or cyclases.

Velvet complex

A conserved transcriptional complex in filamentous fungi that is critical for the regulation of fungal secondary metabolism and reproduction in response to light and other environmental signals.

Phytochrome

A red-light photoreceptor found in fungi, bacteria and plants.

Conidiophore

The asexual spore (called conidium) bearing structure that is produced by many filamentous fungi. Specific secondary metabolites are associated with asexual spore formation.

Heterochromatin

Highly condensed chromatin tightly wound around histones and less available to the transcriptional machinery. The heterochromatin state is dependent on specific post-translational histone modifications, such as deacetylation.

Euchromatin

Lightly packed chromatin with looser arrangement around histones and accessible to the transcriptional machinery. The euchromatin state is dependent on specific post-translational histone modifications, such as acetylation and methylation.

Perithecia

Sexual fruiting bodies containing sexual spores of some Ascomycete fungi.

Dereplication

A screen in secondary metabolite analysis to eliminate already-known compounds from the discovery process.

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Keller, N.P. Fungal secondary metabolism: regulation, function and drug discovery. Nat Rev Microbiol 17, 167–180 (2019). https://doi.org/10.1038/s41579-018-0121-1

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