Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance

Yaseen, I., White, S.A., Torres-Garcia, S., Spanos, C., Lafos, M., Gaberdiel, E., Yeboah, R., El Karoui, M., Rappsilber, J., Pidoux, A.L., and Allshire, R.C.

Nature Structural & Molecular Biology (2022) 29, 745–758

We demonstrate that environmental insults such as fungicides trigger the truncation of a key epigenetic modifier (Epe1 H3K9 demthylase) that curtails its function. This proteasome-mediated processing of Epe1 allows heterochromatin to reprogram gene expression and as a consequence bestows resistance to some cells within a population. 

Summary of Paper by Lori Koch 

Certain fungi species are a major threat to crop yield and human health therefore understanding how they gain resistance to antifungal compounds is an important avenue of research. In their previous work, scientists in the Allshire group discovered that the single-celled fungus Schizosaccharomyces pombe can gain resistance to  caffeine or antifungal stresses epigenetically, meaning that the underlying DNA sequence  is not altered, rather chromatin modifications that influence whether genes are turned on or off change. Their work suggested that the enzyme Epe1, which removes methylation marks from chromatin, influenced the ability of the cells to resist external stress. However, how Epe1 itself senses or changes activity during stress was unknown. In their recent study published in Nature Structural & Molecular Biology, scientists led by Imtiyaz Yaseen and Sharon White uncovered that Epe1 is cleaved in response to stress and that this cleavage results in relocation from the nucleus to the cytoplasm. Western analysis of tagged Epe1 revealed that a shorter form of Epe1 appears upon treatment of cells with caffeine. Further analyses confirmed that this shorter form is due to proteolytic cleavage of the N-terminus of Epe1.  They hypothesized and confirmed that cleavage Epe1 depended on proteosome complexes within cells that routinely degrade undesired proteins by finding that Epe1 cleavage was blocked in cells with mutations in proteosome components and in cells treated with the proteasome inhibitor drug bortezomib. By tracking Epe1 protein with a fluorescent marker, they found that it relocates from the nucleus where genes reside, to the cytoplasm upon treatment with caffeine. Truncated Epe1 lacking the N-terminus was mostly located in the cytoplasm even in the absence of caffeine, suggesting that the cleavage is required for its relocation. Genetic analysis revealed that kinases in the cell integrity pathway (CIP) are involved in a pathway with Epe1 to confer resistance to caffeine or antifungals. Finally, both cells lacking Epe1 completely (epe1∆) and the N-terminus only (epe1∆N) showed increased methylation that correlated with resistance to caffeine. Together the work suggests that cleavage of the enzyme Epe1 by the proteosome causes reduced gene expression through increased methylation, which results in higher resistance to external stress.

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