Heterochromatin epimutations impose mitochondrial dysfunction to confer antifungal resistance

Abstract

Global health and food supply are endangered by an increasing frequency of antifungal resistance in pathogenic fungi. Wild-type fission yeast, Schizosaccharomyces pombe, can gain resistance to insults such as caffeine and antifungal compounds through reversible epimutations. Resistant epimutants exhibit histone H3K9 methylation-dependent heterochromatin islands at various chromosomal locations, reducing expression of underlying genes. Two genes whose heterochromatin island-induced repression causes resistance encode mitochondrial proteins: the LYR domain protein Cup1 and the Cox1 translation regulator Ppr4. Genetic mutations, cup1-tt and ppr4{Delta}, that phenocopy their respective epimutants, cause mitochondrial dysfunction, including respiratory deficiency, poor growth on non-glucose carbon sources, and elevated reactive oxygen species. RNA-Seq analyses indicate that cup1-tt and ppr4{Delta} cells activate the mitonuclear retrograde pathway and the Pap1 transcription factor-dependent oxidative stress response pathways. Both mutants show increased nuclear localisation of Pap1 and its recruitment to promoters of genes encoding oxidoreductases and membrane transporters, causing increased efflux activity. cup1 and ppr4 epimutants also show mitochondrial dysfunction phenotypes and increased efflux, explaining how heterochromatin-island epimutations cause drug resistance. Thus, wild-type cells harness epimutations that impose mitochondrial dysfunction to bypass external insults. As mitochondrial dysfunction has been linked to antifungal resistance in several fungi, similar epimutations likely contribute to development of resistance in fungal pathogens.