Transcriptomic and Metabolomic Analysis Revealed Roles of Yck2 in Carbon Metabolism and Morphogenesis of Candida albicans

Abstract

Candida albicans is a part of the normal microbiome of human mucosa and is able to thrive in a wide range of host environments. As an opportunistic pathogen, the virulence of C. albicans is tied to its ability to switch between yeast and hyphal morphologies in response to various environmental cues, one of which includes nutrient availability. Thus, metabolic flexibility plays an important role in the virulence of the pathogen. Our previous study has shown that C. albicans Yeast Casein Kinase 2 (CaYck2) regulates the yeast-to-hyphal switch, but its regulatory mechanisms remain unknown. This study further elucidated the role of Yck2 in governing morphology and carbon metabolism by analyzing the transcriptome and metabolome of the C. albicans YCK2 deletion mutant strain (yck2Δ strain) in comparison to the wild type strain. Our study revealed that loss of CaYck2 perturbs carbon metabolism, leading to a transcriptional response that resembles a transcriptional response to glucose starvation with coinciding intracellular accumulation of glucose and depletion of TCA cycle metabolites. This shift in the metabolome is likely mediated by derepression of glucose-repressed genes in the Mig1/2-mediated glucose sensing pathway and by downregulation of glycolytic genes, possibly through the Rgt1-mediated SRR pathway. In addition, genes involved in beta-oxidation, glyoxylate cycle, oxidative stress response, and arginine biosynthesis were upregulated in the yck2Δ strain, which is highly reminiscent of C. albicans engulfment by macrophages. This coincides with an increase in arginine degradation intermediates in the yck2Δ strain, suggesting arginine catabolism as a potential mechanism of CaYck2-mediated filamentation as seen during C. albicans escape from macrophages. Transcriptome analysis also shows differential expression of hyphal transcriptional regulators Nrg1 and Ume6. This suggests dysregulation of hyphal initiation and elongation in the yck2Δ strain which may lead to the constitutive pseudohyphal phenotype of this strain. Metabolome analysis also detected a high abundance of methyl citrate cycle intermediates in the yck2Δ strain, suggesting the importance of CaYck2 in this pathway. Taken together, we discovered that CaYck2 is an integral piece of carbon metabolism and morphogenesis of C. albicans.

An integrated transcriptomic and metabolomic approach to investigate the heterogeneous Candida albicans biofilm phenotype

“…Amino acids are thought to trigger signalling pathways in C. albicans , either directly or in directly, such as arginine in the activation of the SPS plasma sensor and/or indirectly through their biosynthesis leading to alkalinisation [ 59 ]. Similar to our observation that amino acids were spent in the media supplemented with FCS, it has also been observed that arginine metabolic processes play an important role in type strain studies utilising hyphal deficient knockouts, within which they suggest a role for the yck2 in the regulation of arginine metabolism and the ROS response of C. albicans [ 60 ]. It has also been observed that significant changes in the metabolic response to the environment are present in C. albicans SC5314.…”

“…The response in LBF isolates is similar to the transcriptional response observed in C. albicans in infected macrophages, where there is adaptation of the beta-oxidation and arginine metabolic pathways [ 68 ]. This adaptation has been linked to the yeast casein kinase 2 and is thought to regulate hyphal formation through the arginine degradation and beta-oxidation pathways that are observed in macrophage engulfment [ 60 ].The carbon metabolism plasticity and the utilisation of amino acids has been also hypothesised to sustain the growth of hyphae in diverse environments as well as provide a feedback mechanism for hyphal elongation [ 60 , 61 ]. Previously the PXP2, FOX2, FOX3 and POX1-3 genes involved in beta-oxidation were described in C. tropicalis and C. parapsilosis as significantly upregulated genes in response to blood [ 42 ].…”

Metabolic Plasticity of Candida albicans in Response to Different Environmental Conditions

“…In the hyphal form, carbon and nitrogen metabolic pathways are primarily perturbed, and the ATP level is reduced. Some studies explored the metabolic effects of molecules that suppress (phenylethyl alcohol [ 48 ]) or induce (N-acetylglucosamine [ 49 ]) yeast-to-hypha transition, while a recent transcriptomic and metabolomic study pointed out that the transition of C. albicans to its pathogenic form requires metabolic flexibility [ 50 ].…”

Integrative transcriptome analysis revealed the pathogenic molecular basis of Rhizoctonia solani AG-3 TB at three progressive stages of infection

“…In the early infection stage, fatty acid metabolism, amino sugar, nucleotide sugar metabolism, carbon metabolism and biosynthesis of amino acids were significantly enriched. Such metabolisms have been indicated to correlate with branching, initiation and elongation, cell wall and biofilm matrix of fungal hyphae ( Chen et al, 2020 ; Liboro et al, 2021 ). In the middle stage of infection, the cellular carbohydrate biosynthetic process of R. solani AG-3 TB began to be enriched.…”