A multi-omics analysis unveils functional and regulatory links between hydroxybenzene and aromatic amino acid metabolism in Candida albicans.

The fungus Candida albicans is a frequent colonizer of humans but also an opportunistic pathogen causing superficial to severe infections, especially in vulnerable individuals. Its broad metabolic flexibility is key for the fungal adaptation to host environments, evasion from immune attack, and virulence. Amino acid metabolism and homeostasis, in particular, are critical for fungal fitness-illustrated by a rapid metabolic shift in response to amino acid starvation to restore intracellular metabolic balance. To investigate the cellular mechanisms underlying such compensatory metabolic processes, we performed data-driven genome-scale metabolic modeling based on transcriptional metabolic profiles of amino acid-starved cells to identify condition-specific fungal metabolic fluxes and pathway activities specific to cellular response to amino acid starvation. Most prominently, we predicted altered activity of the shikimate pathway upon amino acid limitation and identified a simultaneous induction of aromatic amino acid (AAA) biosynthesis and a metabolic gene cluster required for the catabolism of hydroxybenzenes. Further phenotypic and transcriptional analyses not only verified the transcription factor Zcf25 as the central regulator of the catechol-branch of this pathway, but also condition-specific co-regulation of AAA and hydroxybenzene metabolism mediated by Zcf25 and the transcriptional regulator of amino acid metabolism Stp2. These findings propose a so far unknown metabolic link between amino acid and hydroxybenzene metabolism in C. albicans, therewith adding another layer to its metabolic plasticity.

Importance: The opportunistic human fungal pathogen Candida albicans possesses a remarkable metabolic plasticity, which is essential for both fungal commensalism and virulence and influences its physiology and behavior in multiple ways. The investigation of such processes particularly benefits from the emergence of multi-omics and in silico approaches. In this study, we combined a multi-omics approach with genome-scale metabolic modeling to investigate the fungal metabolic adaptation to amino acid utilization and starvation. Most strikingly, we found an altered activity of the shikimate pathway upon amino acid starvation, accompanied by a simultaneous induction of two metabolic gene clusters required for the metabolism of hydroxybenzenes. Further analyses revealed so far unknown potential functional and regulatory links between both metabolic pathways, which provide starting points for future research leading to a better understanding of the fungal adaptation to dynamic host conditions.