Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources

• DOI: 10.1371/journal.pgen.1009815
• Publication Date: 2022-03-07T18:40:43Z
• Authors: Andrea Cillingová; Renáta Tóth; Anna Mojáková; Igor Zeman; Romana Vrzoňová; Barbara Siváková; Peter Baráth; Martina Neboháčová; Zuzana Klepcová; Filip Brázdovič; Hana Lichancová; Viktória Hodorová; Broňa Brejová; Tomáš Vinař; Sofia Mutalová; Veronika Vozáriková; Giacomo Mutti; Ľubomír Tomáška; Atilla Gácser; Toni Gabaldón; Jozef Nosek
• Keywords: Proteome; Metabolic pathway; Candida parapsilosis

Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate gentisate pathways, whose components are encoded by two metabolic gene clusters. In this study, we determine chromosome level assembly C . strain CLIB214 use it for transcriptomic proteomic investigation cells cultivated on hydroxyaromatic substrates. We demonstrate that genes coding enzymes plasma membrane transporters involved in pathways highly upregulated their expression is controlled a substrate-specific manner. However, regulatory proteins process not known. Using knockout mutants, show putative transcriptional factors OTF1 GTF1 located within clusters function activators pathway, respectively. also activation both accompanied upregulation β-oxidation fatty acids, glyoxylate cycle, amino metabolism, peroxisome biogenesis. Transcriptome proteome profiles grown 4-hydroxybenzoate 3-hydroxybenzoate, which metabolized respectively, reflect different connection to central metabolism. Yet find differ assimilating hydroquinone, same pathway. This finding consistent with phenotype Otf1p-lacking mutant, exhibits impaired growth hydroxybenzoates, but still utilizes hydroxybenzenes, thus indicating additional, yet unidentified transcription factor could be pathway regulation. Moreover, propose bicarbonate ions resulting from decarboxylation hydroxybenzoates contribute differences cell responses hydroxybenzenes. Finally, our phylogenetic analysis highlights evolutionary paths leading adaptations