Fisher, M. C., Hawkins, N. J., Sanglard, D. & Gurr, S. J. Worldwide emergence of resistance to antifungal drugs challenges human health and food security. Science 360, 739–742 (2018).
Bongomin, F., Gago, S., Oladele, R. O. & Denning, D. W. Global and multi-national prevalence of fungal diseases-estimate precision. J. Fungi 3, 57 (2017).
Paulussen, C. et al. Ecology of aspergillosis: insights into the pathogenic potency of Aspergillus fumigatus and some other Aspergillus species. Microb. Biotechnol. 10, 296–322 (2017).
Myers, J. M. et al. Survey of early-diverging lineages of fungi reveals abundant and diverse mycoviruses. mBio 11, e02027-20 (2020).
Wu, M. et al. Characterization of a novel bipartite double-stranded RNA mycovirus conferring hypovirulence in the phytopathogenic fungus Botrytis porri. J. Virol. 86, 6605–6619 (2012).
Lau, S. K. et al. Novel partitivirus enhances virulence of and causes aberrant gene expression in Talaromyces marneffei. mBio 9, e00947-18 (2018).
Sass, G., Kotta-Loizou, I., Martinez, M., Larwood, D. J. & Stevens, D. A. Polymycovirus infection sensitizes Aspergillus fumigatus for antifungal effects of nikkomycin Z. Viruses 15, 197 (2023).
Nerva, L. et al. Mycoviruses mediate mycotoxin regulation in Aspergillus ochraceus. Environ. Microbiol. 21, 1957–1968 (2019).
Ninomiya, A. et al. Mycovirus-induced tenuazonic acid production in a rice blast fungus Magnaporthe oryzae. Front. Microbiol. 11, 1641 (2020).
Márquez, L. M., Redman, R. S., Rodriguez, R. J. & Roossinck, M. J. A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance. Science 315, 513–515 (2007).
Kanhayuwa, L., Kotta-Loizou, I., Özkan, S., Gunning, A. P. & Coutts, R. H. A. A novel mycovirus from Aspergillus fumigatus contains four unique dsRNAs as its genome and is infectious as dsRNA. Proc. Natl Acad. Sci. USA 112, 9100–9105 (2015).
Takahashi-Nakaguchi, A. et al. Phenotypic and molecular biological analysis of polymycovirus AfuPmV-1M from Aspergillus fumigatus: reduced fungal virulence in a mouse infection model. Front. Microbiol. 11, 3223 (2020).
Sass, G., Martinez, M., Kotta-Loizou, I. & Stevens, D. AfuPmV-1-infected Aspergillus fumigatus is more susceptible to stress than virus-free fungus. J. Fungi 9, 750 (2023).
Özkan, S. & Coutts, R. H. Aspergillus fumigatus mycovirus causes mild hypervirulent effect on pathogenicity when tested on Galleria mellonella. Fungal Genet. Biol. 76, 20–26 (2015).
Patil, R. H. et al. Freeing Aspergillus fumigatus of polymycovirus infection renders it more resistant to competition with Pseudomonas aeruginosa due to altered iron-acquiring tactics. J. Fungi 7, 497 (2021).
Han, Z., Jiang, J. & Xu, W. Novel polymycoviruses are encapsidated in filamentous virions. J. Virol. 99, e01515–e01524 (2025).
Filippou, C., Diss, R. M., Daudu, J. O., Coutts, R. H. A. & Kotta-Loizou, I. The polymycovirus-mediated growth enhancement of the entomopathogenic fungus Beauveria bassiana is dependent on carbon and nitrogen metabolism. Front. Microbiol. 12, 606366 (2021).
Clancey, S. A. et al. A novel mycovirus evokes transcriptional rewiring in the fungus Malassezia and stimulates beta interferon production in macrophages. mBio 11, e01534-20 (2020).
Park, M. et al. A novel virus alters gene expression and vacuolar morphology in Malassezia cells and induces a TLR3-mediated inflammatory immune response. mBio 11, e01521-20 (2020).
Cao, C., Li, H., Jones, M. G. K. & Wylie, S. J. Challenges to elucidating how endornaviruses influence fungal hosts: creating mycovirus-free isogenic fungal lines and testing them. J. Virol. Methods 274, 113745 (2019).
Ikeda, A., Chiba, Y., Kuroki, M., Urayama, S. & Hagiwara, D. Efficient elimination of RNA mycoviruses in Aspergillus species using RdRp-inhibitors ribavirin and 2′-C-methylribonucleoside derivatives. Front. Microbiol. 13, 1024933 (2022).
Mirabito, P. M., Adams, T. H. & Timberlake, W. E. Interactions of three sequentially expressed genes control temporal and spatial specificity in Aspergillus development. Cell 57, 859–868 (1989).
Alkhayyat, F., Chang Kim, S. & Yu, J.-H. Genetic control of asexual development in Aspergillus fumigatus. Adv. Appl. Microbiol. 90, 93–107 (2015).
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).
Shin, K.-S., Kim, Y. H. & Yu, J.-H. Proteomic analyses reveal the key roles of BrlA and AbaA in biogenesis of gliotoxin in Aspergillus fumigatus. Biochem. Biophys. Res. Commun. 463, 428–433 (2015).
Shlezinger, N. & Hohl, T. M. Mitochondrial reactive oxygen species enhance alveolar macrophage activity against Aspergillus fumigatus but are dispensable for host protection. mSphere 6, e00260-21 (2021).
Tekaia, F. & Latgé, J.-P. Aspergillus fumigatus: saprophyte or pathogen? Curr. Opin. Microbiol. 8, 385–392 (2005).
Witfeld, F., Begerow, D. & Guerreiro, M. A. Improved strategies to efficiently isolate thermophilic, thermotolerant, and heat-resistant fungi from compost and soil. Mycol. Prog. 20, 325–339 (2021).
Philippe, B. et al. Killing of Aspergillus fumigatus by alveolar macrophages is mediated by reactive oxidant intermediates. Infect. Immun. 71, 3034–3042 (2003).
Beffa, T. et al. Mycological control and surveillance of biological waste and compost. Med. Mycol. 36, 137–145 (1998).
Gouge, J. et al. Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation. Nat. Commun. 8, 130 (2017).
Van Bortle, K., Phanstiel, D. H. & Snyder, M. P. Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation. Genome Biol. 18, 180 (2017).
Yague‐Sanz, C. Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription? Yeast 41, 135–147 (2024).
Burke, M. F., Logan, M. K. & Hebert, M. D. Identification of additional regulatory RNPs that impact rRNA and U6 snRNA methylation. Biol. Open 7, bio036095 (2018).
Kedersha, N. et al. Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. J. Cell Biol. 169, 871–884 (2005).
Reineke, L. C. & Lloyd, R. E. Diversion of stress granules and P-bodies during viral infection. Virology 436, 255–267 (2013).
Onomoto, K. et al. Critical role of an antiviral stress granule containing RIG-I and PKR in viral detection and innate immunity. PLoS ONE 7, e43031 (2012).
Jain, S. et al. ATPase-modulated stress granules contain a diverse proteome and substructure. Cell 164, 487–498 (2016).
Schaefer, M. et al. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes Dev. 24, 1590–1595 (2010).
Kimball, S. R., Horetsky, R. L., Ron, D., Jefferson, L. S. & Harding, H. P. Mammalian stress granules represent sites of accumulation of stalled translation initiation complexes. Am. J. Physiol. Cell Physiol. 284, C273–C284 (2003).
Markmiller, S. et al. Context-dependent and disease-specific diversity in protein interactions within stress granules. Cell 172, 590–604.e13 (2018).
Kedersha, N. et al. Evidence that ternary complex (eIF2-GTP-tRNAiMet)-deficient preinitiation complexes are core constituents of mammalian stress granules. Mol. Biol. Cell 13, 195–210 (2002).
Reineke, L. C., Kedersha, N., Langereis, M. A., van Kuppeveld, F. J. M. & Lloyd, R. E. Stress granules regulate double-stranded RNA-dependent protein kinase activation through a complex containing G3BP1 and Caprin1. mBio 6, e02486-14 (2015).
Jovanovic, B. et al. Thioredoxin 1 is required for stress granule assembly upon arsenite-induced oxidative stress. Food Chem. Toxicol. 156, 112508 (2021).
Soukup, A. A., Fischer, G. J., Luo, J. & Keller, N. P. The Aspergillus nidulans Pbp1 homolog is required for normal sexual development and secondary metabolism. Fungal Genet. Biol. 100, 13–21 (2017).
Martani, F., Marano, F., Bertacchi, S., Porro, D. & Branduardi, P. The Saccharomyces cerevisiae poly(A) binding protein Pab1 as a target for eliciting stress tolerant phenotypes. Sci. Rep. 5, 18318 (2015).
Protter, D. S. W. & Parker, R. Principles and properties of stress granules. Trends Cell Biol. 26, 668–679 (2016).
Meyer, Y., Buchanan, B. B., Vignols, F. & Reichheld, J.-P. Thioredoxins and glutaredoxins: unifying elements in redox biology. Annu. Rev. Genet. 43, 335–367 (2009).
Jhingran, A. et al. Tracing conidial fate and measuring host cell antifungal activity using a reporter of microbial viability in the lung. Cell Rep. 2, 1762–1773 (2012).
Shlezinger, N. et al. Sterilizing immunity in the lung relies on targeting fungal apoptosis-like programmed cell death. Science 357, 1037–1041 (2017).
Mekada, K. & Yoshiki, A. Substrains matter in phenotyping of C57BL/6 mice. Exp. Anim. 70, 145–160 (2021).
Kotta-Loizou, I. & Coutts, R. H. A. Mycoviruses in Aspergilli: a comprehensive review. Front. Microbiol. 8, 1699 (2017).
Kotta-Loizou, I. Mycoviruses and their role in fungal pathogenesis. Curr. Opin. Microbiol. 63, 10–18 (2021).
Ali, A. Fungal viruses: an unlikely ally. Appl. Plant Virol. https://doi.org/10.1016/B978-0-12-818654-1.00017-7 (2020).
Zwanzig, M. et al. Mobile compensatory mutations promote plasmid survival. mSystems https://doi.org/10.1128/msystems.00186-18 (2019).
Harrison, E., Guymer, D., Spiers, A. J., Paterson, S. & Brockhurst, M. A. Parallel compensatory evolution stabilizes plasmids across the parasitism–mutualism continuum. Curr. Biol. 25, 2034–2039 (2015).
Twumasi-Boateng, K. et al. Transcriptional profiling identifies a role for BrlA in the response to nitrogen depletion and for StuA in the regulation of secondary metabolite clusters in Aspergillus fumigatus. Eukaryot. Cell 8, 104–115 (2009).
Lin, H., Kazlauskas, R. J. & Travisano, M. Developmental evolution facilitates rapid adaptation. Sci. Rep. 7, 15891 (2017).
Stewart, J. I. P. et al. Reducing Aspergillus fumigatus virulence through targeted dysregulation of the conidiation pathway. mBio 11, e03202–e03219 (2020).
Wang, P., Yang, G., Lu, H. & Huang, B. Infection with a novel polymycovirus enhances growth, conidiation and sensitivity to UV-B irradiation of the entomopathogenic fungus Metarhizium anisopliae. Front. Microbiol. 14, 1214133 (2023).
Jahn, B. et al. Interaction of human phagocytes with pigmentless Aspergillus conidia. Infect. Immun. 68, 3736–3739 (2000).
Tsai, H.-F., Chang, Y. C., Washburn, R. G., Wheeler, M. H. & Kwon-Chung, K. J. The developmentally regulated alb1 gene of Aspergillus fumigatus: Its role in modulation of conidial morphology and virulence. J. Bacteriol. 180, 3031–3038 (1998).
Hohl, T. M. et al. Aspergillus fumigatus triggers inflammatory responses by stage-specific β-glucan display. PLoS Pathog. 1, e30 (2005).
Balloy, V. & Chignard, M. The innate immune response to Aspergillus fumigatus. Microbes Infect. 11, 919–927 (2009).
Segal, B. H. Aspergillosis. N. Engl. J. Med. 360, 1870–1884 (2009).
Hampton, M. B., Kettle, A. J. & Winterbourn, C. C. Inside the neutrophil phagosome: oxidants, myeloperoxidase, and bacterial killing. Blood 92, 3007–3017 (1998).
Liu, Y. et al. N6-methyladenosine RNA modification-mediated cellular metabolism rewiring inhibits viral replication. Science 365, 1171–1176 (2019).
Wickner, R. B., Fujimura, T. & Esteban, R. Viruses and prions of Saccharomyces cerevisiae. Adv. Virus Res. 86, 1–36 (2013).
Kedersha, N. et al. G3BP–Caprin1–USP10 complexes mediate stress granule condensation and associate with 40S subunits. J. Cell Biol. 212, e201508028 (2016).
Anderson, P. & Kedersha, N. RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nat. Rev. Mol. Cell Biol. 10, 430–436 (2009).
Redding, A. & Grabocka, E. Stress granules and hormetic adaptation of cancer. Trends Cancer https://doi.org/10.1016/j.trecan.2023.08.005 (2023).
Wesener, F. & Tietjen, B. Primed to be strong, primed to be fast: modeling benefits of microbial stress responses. FEMS Microbiol. Ecol. 95, fiz114 (2019).
Hillmann, F. et al. The crystal structure of peroxiredoxin Asp f3 provides mechanistic insight into oxidative stress resistance and virulence of Aspergillus fumigatus. Sci. Rep. 6, 33396 (2016).
Zhai, P. et al. The OxrA protein of Aspergillus fumigatus is required for the oxidative stress response and fungal pathogenesis. Appl. Environ. Microbiol. 87, e01120–e01121 (2021).
Binder, J., Shadkchan, Y., Osherov, N. & Krappmann, S. The essential thioredoxin reductase of the human pathogenic mold Aspergillus fumigatus is a promising antifungal target. Front. Microbiol. 11, 1383 (2020).
Mirkov, I. et al. Strain differences in the immune mechanisms of resistance of immunocompetent rats to pulmonary aspergillosis. Immunobiology 220, 1075–1084 (2015).
Clemons, K. V. & Stevens, D. A. The contribution of animal models of aspergillosis to understanding pathogenesis, therapy and virulence. Med. Mycol. 43, 101–110 (2005).
Kuhlmann, F. M. et al. Antiviral screening identifies adenosine analogs targeting the endogenous dsRNA Leishmania RNA virus 1 (LRV1) pathogenicity factor. Proc. Natl Acad. Sci. USA 114, E811–E819 (2017).
Bhatti, M. F. et al. The effects of dsRNA mycoviruses on growth and murine virulence of Aspergillus fumigatus. Fungal Genet. Biol. 48, 1071–1075 (2011).
Crabtree, A. et al. A rapid method for sequencing double-stranded RNAs purified from yeasts and the identification of a potent K1 killer toxin isolated from Saccharomyces cerevisiae. Viruses 11, 70 (2019).
Bustin, S. A. et al. The MIQE Guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55, 611–622 (2009).
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the \(2^{-\Delta\Delta {\rm C}_{\rm{T}}}\) method. Methods 25, 402–408 (2001).
Beattie, S. R. et al. Filamentous fungal carbon catabolite repression supports metabolic plasticity and stress responses essential for disease progression. PLoS Pathog. 13, e1006340 (2017).
Levanova, A. & Poranen, M. M. Application of steric exclusion chromatography on monoliths for separation and purification of RNA molecules. J. Chromatogr. A 1574, 50–59 (2018).
Biel, S. W. & Parrish, F. W. Isolation of DNA from fungal mycelia and sclerotia without use of density gradient ultracentrifugation. Anal. Biochem. 154, 21–25 (1986).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Vasimuddin, M., Misra, S., Li, H. & Aluru, S. Efficient architecture-aware acceleration of BWA-MEM for multicore systems. In Proc. IEEE International Parallel and Distributed Processing Symposium 314–324 (IEEE, 2019).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Rimmer, A et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat. Genet. 46, 912–918 (2014).
Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).
Boeva, V. et al. Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28, 423–425 (2012).
Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333–i339 (2012).
Liu, L. et al. Calcineurin signaling pathway influences Aspergillus niger biofilm formation by affecting hydrophobicity and cell wall integrity. Biotechnol. Biofuels 13, 54 (2020).
Muñiz-Buenrostro, A., Arce-Mendoza, A. Y., Montes-Zapata, E. I., Calderón-Meléndez, R. C. & Montelongo-RodrÍguez, M. J. Simplified neutrophil isolation protocol. Int. J. Immunol. Immunother. https://doi.org/10.23937/2378-3672/1410041 (2020).
Segal, G. & Shuman, H. A. Legionella pneumophila utilizes the same genes to multiply within Acanthamoeba castellanii and human macrophages. Infect. Immun. 67, 2117–2124 (1999).
De Gouvêa, P. F. et al. Functional characterization of the Aspergillus fumigatus PHO80 homologue. Fungal Genet. Biol. 45, 1135–1146 (2008).
Adeoye, J. & Fabre, M. L. Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host. Zenodo https://doi.org/10.5281/zenodo.16698311 (2025).