Uncovering Gene Function Using Preserved Regulatory Network and Gene Expression Analyses in Candida albicans Clinical Isolates

The opportunistic pathogen, Candida albicans is a diploid fungus which colonizes most humans and is the primary cause of a significant portion of severe fungal infections. There exists significant natural variation among clinical isolates of C. albicans which includes genome sequence heterogeneity, gene regulatory network rewiring, and differential virulence associated phenotypic output. Here we utilize CRISPR-Cas9 based methods in conjunction with preserved gene expression analyses to uncover novel function of transcriptional regulators of natural variation among C. albicans clinical isolate strains. Herein WOR3, which is known to regulate mating, was identified as a novel regulator of biofilm formation as it mediates the expression of preserved direct and indirect targets of the master biofilm regulator, EFG1, independently of EFG1. Additionally, RME1, which is required for chlamydospore formation, was identified as a repressor of epithelial cell damage through the use of gene co-expression clustering analysis via repression of ECE1, ALS3, and HWP1.