Abstract
Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metabolic gene clusters. In this study, we determine the chromosome level assembly of the C. parapsilosis strain CLIB214 and use it for transcriptomic and proteomic investigation of cells cultivated on hydroxyaromatic substrates. We demonstrate that the genes coding for enzymes and plasma membrane transporters involved in the 3-oxoadipate and gentisate pathways are highly upregulated and their expression is controlled in a substrate-specific manner. However, regulatory proteins involved in this process are not known. Using the knockout mutants, we show that putative transcriptional factors encoded by the genes OTF1 and GTF1 located within these gene clusters function as transcriptional activators of the 3-oxoadipate and gentisate pathway, respectively. We also show that the activation of both pathways is accompanied by upregulation of genes for the enzymes involved in β-oxidation of fatty acids, glyoxylate cycle, amino acid metabolism, and peroxisome biogenesis. Transcriptome and proteome profiles of the cells grown on 4-hydroxybenzoate and 3-hydroxybenzoate, which are metabolized via the 3-oxoadipate and gentisate pathway, respectively, reflect their different connection to central metabolism. Yet we find that the expression profiles differ also in the cells assimilating 4-hydroxybenzoate and hydroquinone, which are both metabolized in the same pathway. This finding is consistent with the phenotype of the Otf1p-lacking mutant, which exhibits impaired growth on hydroxybenzoates, but still utilizes hydroxybenzenes, thus indicating that additional, yet unidentified transcription factor could be involved in the 3-oxoadipate pathway regulation. Moreover, we propose that bicarbonate ions resulting from decarboxylation of hydroxybenzoates also contribute to differences in the cell responses to hydroxybenzoates and hydroxybenzenes. Finally, our phylogenetic analysis highlights evolutionary paths leading to metabolic adaptations of yeast cells assimilating hydroxyaromatic substrates.
Highlights
Metabolic gene clusters (MGCs) are composed of co-localized genes, whose products participate in the same metabolic pathway
While benzene itself is toxic and carcinogenic, benzoic acid is commonly used in the food industry and some of its derivatives are used in pharmacology or cosmetics
We show that the genes coding for the substrate transporters and enzymes involved in both pathways are coexpressed and regulated by the transcriptional activators Otf1p and Gtf1p, respectively
Summary
Metabolic gene clusters (MGCs) are composed of co-localized genes, whose products participate in the same metabolic pathway. In most cases, their functions are linked to the production of secondary metabolites or the assimilation of unconventional substrates. Their functions are linked to the production of secondary metabolites or the assimilation of unconventional substrates Such biochemical pathways are usually nonessential, but in specific circumstances they may provide a growth benefit for the host organism. Investigations of MGCs provide a venue for elucidating their evolutionary origin, genetic organization, and expression, as well as the coordination of the corresponding biochemical pathways with the central cellular metabolism
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