Evolution of stress response transcription factors and adhesin gene families in yeast opportunistic pathogens
Creators: name: Snyder, Lindsey Faye
Publisher: name: University of Iowa
Year: 2024
Subjects: Biochemistry

description: Studying genomic differences between pathogens and their less pathogenic relatives is critical for thinking about potential treatments and host adaptation. By comparing yeasts rarely associated with disease to those that are commonly involved in infection, we can learn more about what makes them pathogenic and better able to survive in a human host and how differences in environment can influence function and evolution. For my thesis, I studied two specific examples of this.
description: In the second chapter, I investigated two orthologous stress response transcription factors to better understand how they function and how one evolved to be more self-sufficient. Stress responses are critical for survival in a host as a host will provide a unique combination of stresses. Combinatorial regulation, or the requirement of two or more transcription factors (TFs) to regulate a gene, is a cornerstone in eukaryotic transcription. This allows multiple upstream signals to influence downstream gene expression and provides a way to tune specificity by requiring a defined binding configuration for activation to occur. We take advantage of the natural variation in cofactor dependence present in the Phosphate Starvation response TF in two yeast species to study the genetic and biophysical basis for coactivator dependence. In S. cerevisiae, the TF Pho4 (ScPho4) relies on the TF Pho2, whereas in C. glabrata, Pho4 (CgPho4) exhibits lower dependence on Pho2 and activates 2-3 times more targets. Using chimeras of ScPho4 and CgPho4 coupled with a dual fluorescence reporter, we discovered that the putative Pho2-interaction domain determines Pho2 dependence versus independence. CgPho4 contains two activation boosting regions that increase overall activity when assayed as Gal4DBD fusions. Biolayer Interferometry and EMSA showed that CgPho4DBD binds ~4 times tighter than ScPho4DBD to the consensus motif in vitro, but the two TFs have no significant differences in specificity. Lastly, the two Pho4 orthologs differed significantly in their ability to interact and thus collaborate with Pho2. Our findings thus provide a detailed molecular picture of how co-TF dependence is mediated and how mutations and insertions in a TF can lead to changes in codependency, which results in significant consequences in the regulatory output.
description: In the third chapter, I characterized a family of cell wall proteins called adhesins. Cell wall proteins are critical for the survival of fungal pathogens in a host, as they play a role in host immune evasion. Adhesins are proteins that allow cells to adhere to one another as well as to living and non-living surfaces. The ability to adhere to a surface and to each other is the first step in pathogenesis and biofilm formation. Adhesins in the emerging pathogen, Candida auris, need to be studied because the species has been described as hyperadhesive, requiring additional hospital sanitation protocols. Many of the well-known adhesin families like the Als family in other Candida pathogens are poorly represented in C. auris, indicating the presence of additional adhesin families. The family of adhesins we studied is related to and shares the hyphally regulated cell wall protein N terminal effector domain with the Hyr/Iff family in C. albicans, so we referred to them as the Hil (Hyr/Iff like) family. Using bioinformatic tools, we investigated the evolutionary history and sequence divergence of the Hil family and showed that this family has expanded in pathogenic yeasts compared to their relatives with lower pathogenic potential. We also found that the N terminal domain is structurally similar to an unrelated family of bacterial adhesins, indicating that they indeed function as adhesins. Lastly, we showed that the Hil family genes are largely located at chromosome ends suggesting that the family expansion was caused by recombination and break induced replication events.