Unlocking the metabolic potential of endophytic fungi through epigenetics: a paradigm shift for natural product discovery and plant-microbe interactions

Article

Liu, R, Peng, X-P, Newman, D.J., Purchase, D., Li, G. and Kusari, S. 2025. Unlocking the metabolic potential of endophytic fungi through epigenetics: a paradigm shift for natural product discovery and plant-microbe interactions. Natural Product Reports. https://doi.org/10.1039/D5NP00028A
TypeArticle
TitleUnlocking the metabolic potential of endophytic fungi through epigenetics: a paradigm shift for natural product discovery and plant-microbe interactions
AuthorsLiu, R, Peng, X-P, Newman, D.J., Purchase, D., Li, G. and Kusari, S.
Abstract

Microbial metabolic pathways, including those of endophytic fungi, offer significant potential for synthesizing secondary metabolites, regardless of their ecological niche. These pathways can be modulated at the molecular level through genome and epigenome manipulation. The metabolic activation of fungal endophytes using epigenetics presents an exciting frontier in science, paving the way for advanced biotechnological applications and enhancing our understanding of these microorganisms' roles in ecosystems. This review examines the significant role of epigenetics in the biosynthesis of secondary metabolites from fungal endophytes, which is vital for drug discovery. Our primary focus centers on studies that explore the epigenetic modulation of endophytic fungi up until December 2024. Acknowledging the rapidly evolving landscape of epigenetic research in this field, which has limited examples for endophytic fungi, we provide crucial foundational insights into fungal epigenetics and relate these insights to the broader context of plant–microbe interactions and endophytic fungal epigenetics, supported by relevant examples. Key mechanisms, such as histone acetylation, histone methylation, and DNA methylation, are discussed alongside recent advances in small-molecule epigenetic modulators that can activate silent biosynthetic gene clusters (BGCs). Further, chromatin-dependent regulation of these BGCs and methods for probing chromatin modifications and secondary metabolism in fungi are discussed. The role of CRISPR-Cas9 genome editing, combined with epigenetic strategies, is highlighted, showcasing its ability to alter the metabolite profiles of fungal endophytes. Finally, we explore how artificial intelligence (AI), machine learning (ML), and deep learning (DL) innovations are transforming research in chemical epigenomics at the plant–microbe interface. 

Keywordsendophyte fungi; natural products; epigenetic modification; AI
Sustainable Development Goals3 Good health and well-being
Middlesex University ThemeHealth & Wellbeing
PublisherRoyal Society of Chemistry
JournalNatural Product Reports
ISSN0265-0568
Electronic1460-4752
Publication dates
Online28 Jul 2025
Publication process dates
Submitted18 Apr 2025
Accepted17 Jul 2025
Deposited04 Aug 2025
Output statusPublished
Accepted author manuscript
File Access Level
Open
Digital Object Identifier (DOI)https://doi.org/10.1039/D5NP00028A
PubMed ID40719258
Web of Science identifierWOS:001538358700001
LanguageEnglish
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Phytoremediation of heavy metal-contaminated sites: Eco-environmental concerns, field studies, sustainability issues, and future prospects
Saxena, G., Purchase, D., Mulla, S., Saratale, G. and Bharagava, R. 2019. Phytoremediation of heavy metal-contaminated sites: Eco-environmental concerns, field studies, sustainability issues, and future prospects. in: de Voogt, P. (ed.) Reviews of Environmental Contamination and Toxicology Volume 249 Springer. pp. 71-131
Phytotoxicity, cytotoxicity and genotoxicity evaluation of organic and inorganic pollutants rich tannery wastewater from a Common Effluent Treatment Plant (CETP) in Unnao district, India using Vigna radiata and Allium cepa
Yadav, A., Raj, A., Purchase, D., Ferreira, L., Saratale, G. and Bharagava, R. 2019. Phytotoxicity, cytotoxicity and genotoxicity evaluation of organic and inorganic pollutants rich tannery wastewater from a Common Effluent Treatment Plant (CETP) in Unnao district, India using Vigna radiata and Allium cepa. Chemosphere. 224, pp. 324-332. https://doi.org/10.1016/j.chemosphere.2019.02.124
Acidomyces acidophilus: ecology, biochemical properties and application to bioremediation
Purchase, D., Chan, W.K., Wildeboer, D. and Garelick, H. 2019. Acidomyces acidophilus: ecology, biochemical properties and application to bioremediation. in: Tiquia-Arashiro, S. and Grube, M. (ed.) Fungi in Extreme Environments: Ecological Role and Biotechnological Significance Springer. pp. 505-515
Levels of awareness and concentrations of heavy metals in the blood of electronic waste scavengers in Nigeria
Popoola, O., Popoola, A. and Purchase, D. 2019. Levels of awareness and concentrations of heavy metals in the blood of electronic waste scavengers in Nigeria. Journal of Health and Pollution. 9 (21), pp. 1-10. https://doi.org/10.5696/2156-9614-9.21.190311
Isolation and characterization of lignin-degrading bacterium Bacillus aryabhattai from pulp and paper mill wastewater and evaluation of its lignin-degrading potential
Zainith, S., Purchase, D., Saratale, G., Ferreira, L., Bilal, M. and Bharagava, R. 2019. Isolation and characterization of lignin-degrading bacterium Bacillus aryabhattai from pulp and paper mill wastewater and evaluation of its lignin-degrading potential. 3 Biotech. 9 (3). https://doi.org/10.1007/s13205-019-1631-x
A novel technology of solarization and phytoremediation enhanced with biosurfactant for sustainable treatment of PAH-contaminated soil
Futughe, A., Jones, H. and Purchase, D. 2018. A novel technology of solarization and phytoremediation enhanced with biosurfactant for sustainable treatment of PAH-contaminated soil. 15th International Phytotechnology Conference. Novi Sad, Serbia 01 - 05 Oct 2018
Global approaches to environmental exposure - assessment of e-wastes
Purchase, D., Bisschop, L., Ekberg, C., Fedotov, P., Garelick, H., Kandile, N., Luque, R., Popoola, O., Rüdel, H., Serpe, A., Surati, K. and Wilson, B. 2018. Global approaches to environmental exposure - assessment of e-wastes. SETAC Europe 28th Annual Meeting. Rome, Italy 13 - 17 May 2018
Chemistry and the environment
Purchase, D., Obare, S., Unsworth, J. and Garelick, H. 2018. Chemistry and the environment. Chemistry International. 40 (2), pp. 46-51. https://doi.org/10.1515/ci-2018-0230
Applications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup
Bharagava, R., Purchase, D., Saxena, G. and Mulla, S. 2018. Applications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup. in: Das, S. and Dash, H. (ed.) Microbial Diversity in the Genomic Era Oxford, UK Elsevier, Academic Press. pp. 459-477
Oxidative and monoxygenase enzymatic response in Eisenia hortensis and Lumbricus terrestiris exposed to 3-, 4- and 5-ring hydrocarbons amended with biosurfactant
Popoola, S., Purchase, D. and Jones, H. 2018. Oxidative and monoxygenase enzymatic response in Eisenia hortensis and Lumbricus terrestiris exposed to 3-, 4- and 5-ring hydrocarbons amended with biosurfactant. SETAC AP 2018: 11th Society of Environmental Toxicology and Chemistry – Asia Pacific 2018. Daegu, Korea 16 - 19 Sep 2018
Competition of As and other Group 15 elements for surface binding sites of an extremophilic Acidomyces acidophilus isolated from a historical tin mining site
Chan, W., Wildeboer, D., Garelick, H. and Purchase, D. 2018. Competition of As and other Group 15 elements for surface binding sites of an extremophilic Acidomyces acidophilus isolated from a historical tin mining site. Extremophiles. 22 (5), pp. 795-809. https://doi.org/10.1007/s00792-018-1039-2
Electronic waste – an emerging global environmental and health challenge in the 21st century
Purchase, D. 2017. Electronic waste – an emerging global environmental and health challenge in the 21st century. SmART Cities and Waste Research Workshop. London, United Kingdom 06 Apr 2017
Enhanced vermiremediation of hydrocarbon contamination using biosurfactant
Popoola, S., Jones, H. and Purchase, D. 2017. Enhanced vermiremediation of hydrocarbon contamination using biosurfactant. SETAC Europe 27th Annual Meeting. Brussels, Belgium 07 - 11 May 2017
A study of the inhibition of biofilm formation on multiple surfaces by a biosurfactant containing four discrete lipopeptides
Khonsari, S., Gonzalez Baez, A., Nguyen, H., Pantoja Munoz, L. and Purchase, D. 2017. A study of the inhibition of biofilm formation on multiple surfaces by a biosurfactant containing four discrete lipopeptides. Microbiology Society Annual Conference. Edinburgh, United Kingdom 03 - 06 Apr 2017
Coming of age
Purchase, D. 2011. Coming of age. Environmental Scientist. 20 (2), pp. 30-33.
A proteomic study on the responses to arsenate stress by an acidophilic fungal strain Acidomyces acidophilus WKC1
Chan, W., Wildeboer, D., Garelick, H. and Purchase, D. 2016. A proteomic study on the responses to arsenate stress by an acidophilic fungal strain Acidomyces acidophilus WKC1. Biotechnology World Convention. Sao Paulo, Brazil 15 - 17 Aug 2016 OMICS International. pp. 35-35 https://doi.org/10.4172/2155-952X.C1.058
Informal recycling of electronic wastes in developing countries: challenges and solutions
Purchase, D. 2017. Informal recycling of electronic wastes in developing countries: challenges and solutions. 16th International Chemistry and the Environment (ICCE) Conference. Oslo, Norway 18 - 22 Jun 2017
To safeguard microgreens from contamination form Salmonella species
Selvam, S., Marvasi, M. and Purchase, D. 2017. To safeguard microgreens from contamination form Salmonella species. 2017 Middlesex University Postgraduate Researchers Summer Conference. Middlesex University London, UK 28 - 29 Jun 2017
Can metals be used as tracers for organic contaminants in potentially e-waste-polluted environmental media?
Rüdel, H., Abbasi, G., Popoola, O. and Purchase, D. 2017. Can metals be used as tracers for organic contaminants in potentially e-waste-polluted environmental media? 16th International Conference on Chemistry and the Environment (ICCE 2017). Oslo, Norway 18 - 22 Jun 2017
Heavy metals distribution and risk assessment in soil from an informal e-waste recycling site in Lagos State, Nigeria
Isimekhai, K., Garelick, H., Watt, J. and Purchase, D. 2017. Heavy metals distribution and risk assessment in soil from an informal e-waste recycling site in Lagos State, Nigeria. Environmental Science and Pollution Research. 24 (20), pp. 17206-17219. https://doi.org/10.1007/s11356-017-8877-9
Mycoremediation of heavy metal/metalloid-contaminated soil: current understanding and future prospects
Chan, W., Wildeboer, D., Garelick, H. and Purchase, D. 2016. Mycoremediation of heavy metal/metalloid-contaminated soil: current understanding and future prospects. in: Purchase, D. (ed.) Fungal Applications in Sustainable Environmental Biotechnology Cham, Switzerland Springer. pp. 249-272
Application of microalgae and fungal-microalgal associations for wastewater treatment
Egede, E., Jones, H., Cook, B., Purchase, D. and Mouradov, A. 2016. Application of microalgae and fungal-microalgal associations for wastewater treatment. in: Purchase, D. (ed.) Fungal Applications in Sustainable Environmental Biotechnology Cham Springer. pp. 143-181
The mechanisms of detoxification of As(III), dimethylarsinic acid (DMA) and As(V) in the microalga Chlorella vulgaris
Pantoja Munoz, L., Purchase, D., Jones, H., Raab, A., Urgast, D., Feldmann, J. and Garelick, H. 2016. The mechanisms of detoxification of As(III), dimethylarsinic acid (DMA) and As(V) in the microalga Chlorella vulgaris. Aquatic Toxicology. 175, pp. 56-72. https://doi.org/10.1016/j.aquatox.2016.02.020
Microbial keratinases: characteristics, biotechnological applications and potential
Purchase, D. 2016. Microbial keratinases: characteristics, biotechnological applications and potential. in: Gupta, V., Sharma, G., Tuohy, M. and Gaur, R. (ed.) The Handbook of Microbial Bioresources Wallingford, UK CAB International. pp. 634-674
Investigating arsenic resistance in fungi from tin-mining soil and the possible interaction between arsenic and tin/antimony
Chan, W., Wildeboer, D., Garelick, H. and Purchase, D. 2014. Investigating arsenic resistance in fungi from tin-mining soil and the possible interaction between arsenic and tin/antimony. 10th International Mycological Congress. Bangkok, Thailand 03 - 08 Aug 2014
Risk assessment at an informal e-waste recycling site in Lagos state, Nigeria
Isimekhai, K., Watt, J., Garelick, H. and Purchase, D. 2014. Risk assessment at an informal e-waste recycling site in Lagos state, Nigeria. Society for Risk Analysis Europe Conference. Istanbul, Turkey 16 - 18 Jun 2014
Consideration of the bioavailability of metal/metalloid species in freshwaters: experiences regarding the implementation of biotic ligand model-based approaches in risk assessment frameworks
Rüdel, H., Diaz Muñiz, C., Garelick, H., Kandile, N., Miller, B., Pantoja Munoz, L., Peijnenburg, W., Purchase, D., Shevah, Y., Van Sprang, P., Vijer, M. and Vink, J. 2015. Consideration of the bioavailability of metal/metalloid species in freshwaters: experiences regarding the implementation of biotic ligand model-based approaches in risk assessment frameworks. Environmental Science and Pollution Research. 22 (10), pp. 7405-7421. https://doi.org/10.1007/s11356-015-4257-5
The mechanisms of arsenic bioremediation from water by the green microalgae Chlorella vulgaris
Pantoja Munoz, L., Purchase, D., Jones, H., Feldmann, J. and Garelick, H. 2014. The mechanisms of arsenic bioremediation from water by the green microalgae Chlorella vulgaris. THE BNASS / TraceSpec Tandem Conference. Aberdeen, Scotland, UK 31 Aug - 04 Sep 2014
Enhanced determination of As-phytochelatin complexes in Chlorella vulgaris using focused sonication for extraction of water-soluble species
Pantoja Munoz, L., Purchase, D., Jones, H., Feldmann, J. and Garelick, H. 2014. Enhanced determination of As-phytochelatin complexes in Chlorella vulgaris using focused sonication for extraction of water-soluble species. Analytical Methods. 6 (3), pp. 791-797. https://doi.org/10.1039/C3AY41629A
Enzymatic formulation capable of degrading scrapie prion under mild digestion conditions
Okoroma, E., Purchase, D., Garelick, H., Morris, R., Neale, M., Windl, O. and Abiola, O. 2013. Enzymatic formulation capable of degrading scrapie prion under mild digestion conditions. PLoS ONE. 8 (7), pp. 1-7. https://doi.org/10.1371/journal.pone.0068099
Identification and characterisation of a Bacillus licheniformis strain with profound keratinase activity for degradation of melanised feather
Okoroma, E., Garelick, H., Abiola, O. and Purchase, D. 2012. Identification and characterisation of a Bacillus licheniformis strain with profound keratinase activity for degradation of melanised feather. International Biodeterioration and Biodegradation. 74, pp. 54-60. https://doi.org/10.1016/j.ibiod.2012.07.013
Mathematical models to predict soil heavy metal toxicity in the 2012 Olympic site
Radiar, A. and Purchase, D. 2012. Mathematical models to predict soil heavy metal toxicity in the 2012 Olympic site. International Journal of Environmental Science and Technology. 9 (2), pp. 219-226. https://doi.org/10.1007/s13762-012-0027-9
Technical note: effects of arsenate (AS5+) on growth and production of glutathione (GSH) and phytochelatins (PCS) in Chlorella Vulgaris
Jiang, Y., Purchase, D., Jones, H. and Garelick, H. 2011. Technical note: effects of arsenate (AS5+) on growth and production of glutathione (GSH) and phytochelatins (PCS) in Chlorella Vulgaris. International Journal of Phytoremediation. 13 (8), pp. 834-844. https://doi.org/10.1080/15226514.2010.525560
A novel enzymatic composition effective for prion degradation
Okoroma, E., Purchase, D., Garelick, H. and Abiola, O. 2011. A novel enzymatic composition effective for prion degradation. Society for General Microbiology Spring Conference. Harrogate, UK 11 - 14 Apr 2011
Keratin degradation by proteolytic microorganisms isolated from activated sludge and farmyard manure: possible application in decontamination of prion protein
Purchase, D., Garelick, H., Okoroma, E., Christen, H. and Abiola, O. 2007. Keratin degradation by proteolytic microorganisms isolated from activated sludge and farmyard manure: possible application in decontamination of prion protein. BAGECO 9: 9th Symposium on Bacterial Genetics and Ecology. Wernigerode, Germany
Keratinase production by proteolytic micro-organisms in activated sludge and farmyard waste.
Okoroma, E., Purchase, D., Garelick, H. and Abiola, O. 2008. Keratinase production by proteolytic micro-organisms in activated sludge and farmyard waste. Society for General Microbiology, Autumn Meeting. Trinity College, Dublin, Ireland 08 - 11 Sep 2008
Bacterial keratinase: prospects for prion degradation.
Okoroma, E., Purchase, D., Garelick, H. and Abiola, O. 2009. Bacterial keratinase: prospects for prion degradation. Society for General Microbiology, Spring Meeting. Harrogate, UK 30 Mar - 02 Apr 2009
Degradation of scrapie infected brain homogenateby a novel bacterial keratinase
Okoroma, E., Purchase, D., Garelick, H., Jen, A., Morris, R. and Abiola, O. 2009. Degradation of scrapie infected brain homogenateby a novel bacterial keratinase. Prion 2009. Chalkidiki, Greece 23 - 25 Sep 2009
Effects of temperature on metal tolerance and the accumulation of Zn and Pb by metal-tolerant fungi isolated from urban runoff treatment wetlands
Purchase, D., Lundy, L., Revitt, D. and Shutes, B. 2009. Effects of temperature on metal tolerance and the accumulation of Zn and Pb by metal-tolerant fungi isolated from urban runoff treatment wetlands. Journal of Applied Microbiology. 106 (4), pp. 1163-1174. https://doi.org/10.1111/j.1365-2672.2008.04082.x
Effectiveness of domestic antibacterial products in decontaminating food contact surfaces
De Vere, E. and Purchase, D. 2007. Effectiveness of domestic antibacterial products in decontaminating food contact surfaces. Food Microbiology. 24 (4), pp. 425-430. https://doi.org/10.1016/j.fm.2006.07.013
Survival and nodulating ability of indigenous and inoculated rhizobium leguminosarum biovar trifolii in sterilized and unsterilized soil treated with sewage sludge
Purchase, D. and Miles, R. 2001. Survival and nodulating ability of indigenous and inoculated rhizobium leguminosarum biovar trifolii in sterilized and unsterilized soil treated with sewage sludge. Current Microbiology. 42 (1), pp. 59-64. https://doi.org/10.1007/s002840010179
Use of sequential extraction procedures for the analysis of cadmium and lead in sediment samples from a constructed wetland
Carapeto, C. and Purchase, D. 2000. Use of sequential extraction procedures for the analysis of cadmium and lead in sediment samples from a constructed wetland. Bulletin of Environmental Contamination and Toxicology. 64 (1), pp. 51-58. https://doi.org/10.1007/s001289910009
Distribution and removal of cadmium and lead in a constructed wetland receiving urban runoff
Carapeto, C. and Purchase, D. 2000. Distribution and removal of cadmium and lead in a constructed wetland receiving urban runoff. Bulletin of Environmental Contamination and Toxicology. 65 (3), pp. 322-329. https://doi.org/10.1007/s0012800131
The removal of urban pollutants by constructed wetlands during wet weather
Scholes, L., Shutes, R., Revitt, D., Purchase, D. and Forshaw, M. 1999. The removal of urban pollutants by constructed wetlands during wet weather. Water Science & Technology. 40 (3), pp. 333-340. https://doi.org/10.1016/S0273-1223(99)00467-9
The treatment of metals in urban runoff by constructed wetlands
Scholes, L., Shutes, R., Revitt, D., Forshaw, M. and Purchase, D. 1998. The treatment of metals in urban runoff by constructed wetlands. Science of the Total Environment. 214 (1-3), pp. 211-219. https://doi.org/10.1016/S0048-9697(98)00072-2
Expression and content of terminal oxidases in Azotobacter vinelandii grown with excess NH4+ are modulated by O-2 supply
Dmello, R., Purchase, D., Poole, R. and Hill, S. 1997. Expression and content of terminal oxidases in Azotobacter vinelandii grown with excess NH4+ are modulated by O-2 supply. Microbiology. 143 (1), pp. 231-237. https://doi.org/10.1099/00221287-143-1-231
Cadmium uptake and nitrogen fixing ability in heavy-metal-resistant laboratory and field strains of Rhizobium leguminosarum biovar trifolii
Purchase, D., Miles, R. and Young, T. 1997. Cadmium uptake and nitrogen fixing ability in heavy-metal-resistant laboratory and field strains of Rhizobium leguminosarum biovar trifolii. FEMS Microbiology Ecology. 22 (1), pp. 85-93. https://doi.org/10.1111/j.1574-6941.1997.tb00359.x