A Phenotypic Profile of the Candida albicans Regulatory Network

Abstract

Candida albicans is a normal resident of the gastrointestinal tract and also the most prevalent fungal pathogen of humans. It last shared a common ancestor with the model yeast Saccharomyces cerevisiae over 300 million years ago. We describe a collection of 143 genetically matched strains of C. albicans, each of which has been deleted for a specific transcriptional regulator. This collection represents a large fraction of the non-essential transcription circuitry. A phenotypic profile for each mutant was developed using a screen of 55 growth conditions. The results identify the biological roles of many individual transcriptional regulators; for many, this work represents the first description of their functions. For example, a quarter of the strains showed altered colony formation, a phenotype reflecting transitions among yeast, pseudohyphal, and hyphal cell forms. These transitions, which have been closely linked to pathogenesis, have been extensively studied, yet our work nearly doubles the number of transcriptional regulators known to influence them. As a second example, nearly a quarter of the knockout strains affected sensitivity to commonly used antifungal drugs; although a few transcriptional regulators have previously been implicated in susceptibility to these drugs, our work indicates many additional mechanisms of sensitivity and resistance. Finally, our results inform how transcriptional networks evolve. Comparison with the existing S. cerevisiae data (supplemented by additional S. cerevisiae experiments reported here) allows the first systematic analysis of phenotypic conservation by orthologous transcriptional regulators over a large evolutionary distance. We find that, despite the many specific wiring changes documented between these species, the general phenotypes of orthologous transcriptional regulator knockouts are largely conserved. These observations support the idea that many wiring changes affect the detailed architecture of the circuit, but not its overall output.

Author Summary

A key goal in the understanding of the biology of an organism is the description of the regulatory networks that control the expression of its genes. Changes in gene expression result in new cellular phenotypes that can be acted upon by evolutionary forces to influence the configuration of these networks. We have developed a phenotypic description of the transcriptional regulatory networks of the major fungal pathogen of humans, Candida albicans, by individually deleting genes that encode transcriptional regulators and observing the resulting phenotypes in a variety of environmental conditions. This approach provides insight into the biological roles of many previously uncharacterized regulators, and allows us to assign groups of regulators to specific biological roles, many of which are relevant to pathogenesis. For example, we identified groups of regulators that influenced sensitivity to antifungal drugs, the ability to acquire iron (a challenge for organisms in a human host), and the ability to form complex multi-cellular colonies. Our results also allow us to analyze how the phenotypes associated with transcriptional regulators change as organisms diverge. A comparison of C. albicans data with that from the well-characterized yeast S. cerevisiae revealed strong phenotypic conservation between related transcriptional regulators, despite the more than 300 million years which separate the species.