Research in the Lewis Lab

Chromatin Structure and Function in Fungi

We are interested in understanding epigenetic and chromatin-based mechanisms that contribute to genome function and genome stability. In eukaryotes, chromosomal DNA is packaged with histone and non-histone proteins into chromatin. In the cell, this complex of DNA and protein is the relevant substrate for essential processes including transcription, DNA replication and DNA repair.

Virtually all DNA-based processes in the nucleus are regulated by local chromatin structure. Regulation is acheived through the action of  covalent modification of histone proteins, incorporation of histone variants, and in some organisms, methylation of cytosine bases in DNA. We are particularly interested in understanding how formation of repressive chromatin structures contributes to proper maintenance of genome stability (i.e. DNA replication and repair).

Eukaryotic genomes are spatially separated into structurally and functionally distinct chromatin domains. This image shows the arrangement of euchromatin (green) and heterochromatin (red) domains in N. crassa nuclei.

We found that two conserved histone methyltransferases, KMT1 and KMT6, have opposing effects on genome stability in the model fungus Neurospora crassa. These enzymes methylate histone H3 at specific lysine residues to establish two types of repressive chromatin.  In mammals, homologs of these enzymes are critical for development and defective function of  KMT6 has been tightly linked to cancer, but much is unknown about how they are regulated and how they function. Neurospora crassa is one of the simplest model systems that encodes both KMT1 and KMT6. Our work is focused on understanding these important enzymes. For all of our studies, we rely heavily on molecular, genetic, genomic, and proteomic methods.

Chromatin modifications establish functionally distinct chromatin environments. H3 lysine-9 methylation (blue), H3 lysine-27 methylation (green), and H3 lysine-4 methylation establish different chromatin architectures to regulate genome functions.

Developing new strategies to treat fungal infections

The fungal kingdom includes devastating pathogens of plants and animals (including humans). Current strategies for treating fungal infections in humans are limited by relatively low efficacy of antifungal drugs, high rates of antifungal drug resistance, and high toxicity in patients. We are working with the Meagher and Lin labs at UGA to develop strategies for delivering antifungal drugs directly to fungal cells using targeted liposomes. Briefly, antifungal drugs are loaded into liposomes, which are then coated with innate immune receptors that display high affinity for glycan molecules found on the surface of fungal cells. We have shown that targeted liposomes are concentrated on the surface of fungal cells, and that these targeted antifungal drugs are more effective at killing fungi and less toxic to human cells than untargeted drugs. Our current efforts are focused on optimizing the Dectisome delivery strategy.

Dectisomes are lipid nanoparticles coated with fungal binding proteins. We have developed drug-loaded liposomes coated with mammalian C-type lectin proteins to concentrate antifungal drugs on fungal cells and biofilms. The upper image illustrates the composition of a Dectisome nanoparticle. The lower image shows binding of drug loaded liposomes (red) to fungal cells (blue).