The regulatory impact of transposable elements on drug resistance evolution in budding yeasts

Fungal human pathogens pose a high and increasing burden on global health. Many fungal pathogens infect predominantly immunosuppressed people, including organ transplant recipients and patients with viral infections like HIV or COVID-19. The number of antifungal drug classes is restricted, and drug resistance evolves quickly in patients. The use of antifungal drugs in agriculture can lead to environmental isolates that are already resistant prior to infection of a human. Another potential risk factor is global warming, as more fungal species are suspected to adapt to the high body temperatures of humans. An increasing threat by fungal pathogens combined with a reduced number of effective antifungal drugs makes it crucial to both understand how resistance emerges and what potential targets could be used for future treatment. Transposable elements (TEs) are important facilitators of fast adaptation to antifungal drug stress in plant pathogens, yet their impact on human pathogens is still understudied. TEs are mobile and can autonomously create new copies of themselves in the genome. New TE insertions are often deleterious, but can lead to a different expression of a nearby gene, lead to rearrangements or become part of a novel gene.Aim 1: Capture of structural variants and their impact on antifungal drug resistance in Candida auris. C. auris is a recently emerged pathogen with a fast adaptation to antifungal drugs. Currently there are 5 defined clades with differing phenotypes and different drug-resistant mutations. My comparisons of isolates show many large-scale structural variants (SVs), the complete absence of TE families in some isolates, and indication of exogenous DNA and minichromosomes. SVs might play an important role on the fast adaptation of C. auris. However, the reference genome is still fragmented and telomeric regions are not completely resolved. To detect and describe SVs, I will use a pangenomic approach, in which I will de novo assemble and compare high quality genomic sequences. I will define accessory regions that indicate local adaptation, and define the origin of exogenous DNA. The pangenome will be a valuable resource for further genetic analyses in C. auris.Aim 2: Determine the impact of antifungal drug stress on the activity and proliferation of TEs in C. albicans. C. albicans TEs are expressed under stress conditions13. However, it is not clear if expressed TEs will be able to successfully insert into the genome. Uncontrolled proliferation of TEs would have a dramatic impact on the pathogen, and might be an additional unintended consequence of the use of antifungal drugs. Utilizing TE could potentially be a treatment strategy as well. I will use an in vitro experiment in the presence and absence of antifungal drug stress to detect TE expression, combined with a screen for de novo TE insertions in the final population. I expect to see an increase in the expression of many TE families. However, the number of TEs likely not increases proportionally due to defense mechanisms or selection. I will create a list of genes and mechanisms that are likely involved in the regulation of TEs in C. albicans.Aim 3: Screen the subphylum of Saccharomycotina for proteins that control TE activity. In most organisms, TE activity is highly regulated. However, many defense mechanisms against TEs are missing in Candida species. Candida belongs to the subphylum Saccharomycotina, in which most studied species share genomic similarities with Candida genomes, including a low number of TEs. Potentially, Saccharomycotina share a not yet known mechanism to regulate TEs. Looking at the whole subphylum might show conserved mechanisms in TE regulation. Recently, I described several candidates of host-TE fusions that might be involved in TE regulation. I propose to screen the subphylum to find candidate proteins that might be involved in TE regulation. Understanding TE regulation will help to use TEs in future treatment strategies against fungal diseases.