Transcriptomic and proteomic profiling revealed reprogramming of carbon metabolism in acetate-grown human pathogen Candida glabrata

Abstract

Background: Emergence of Candida glabrata, which causes potential life-threatening invasive candidiasis, has been widely associated with high morbidity and mortality. In order to cause disease in vivo, a robust and highly efficient metabolic adaptation is crucial for the survival of this fungal pathogen in human host. In fact, reprogramming of the carbon metabolism is believed to be indispensable for phagocytosed C. glabrata within glucose deprivation condition during infection.

Methods: In this study, the metabolic responses of C. glabrata under acetate growth condition was explored using high-throughput transcriptomic and proteomic approaches.

Results: Collectively, a total of 1482 transcripts (26.96%) and 242 proteins (24.69%) were significantly up- or down-regulated. Both transcriptome and proteome data revealed that the regulation of alternative carbon metabolism in C. glabrata resembled other fungal pathogens such as Candida albicans and Cryptococcus neoformans, with up-regulation of many proteins and transcripts from the glyoxylate cycle and gluconeogenesis, namely isocitrate lyase (ICL1), malate synthase (MLS1), phosphoenolpyruvate carboxykinase (PCK1) and fructose 1,6-biphosphatase (FBP1). In the absence of glucose, C. glabrata shifted its metabolism from glucose catabolism to anabolism of glucose intermediates from the available carbon source. This observation essentially suggests that the glyoxylate cycle and gluconeogenesis are potentially critical for the survival of phagocytosed C. glabrata within the glucose-deficient macrophages.

Conclusion: Here, we presented the first global metabolic responses of C. glabrata to alternative carbon source using transcriptomic and proteomic approaches. These findings implicated that reprogramming of the alternative carbon metabolism during glucose deprivation could enhance the survival and persistence of C. glabrata within the host.

Keywords: Acetate; Candida; Candida glabrata; Carbon metabolism; Liquid chromatography tandem-mass spectrometry; Proteomic; RNA-sequencing; Transcriptomic.

Fig. 1

Verification of the RNA sequencing data. a Comparison of gene expression levels of 15 DEGs between RNA sequencing and RT-qPCR analyses. b Correlation between gene expression levels of 15 DEGs obtained from RNA sequencing and RT-qPCR analyses. Statistically significant Pearson correlation (r² = 0.7824) was observed between the two quantitative methods

Fig. 2

Scatter plot indicates the mass versus retention time of the peptides identified from glucose-grown and acetate-grown C. glabrata. Most of the separated peptides from these two growth conditions had masses between 300 and 1500 Da, and most of the separated peptides eluting from 10 to 80 min

Fig. 3

Abundance and detection range of the proteins identified from glucose-grown and acetate-grown C. glabrata. Highly abundance proteins identified were up to 5-log higher abundance in comparison to the lowest abundance proteins identified

Fig. 4

Venn diagram showing total proteins identified between the two treatment groups, glucose-grown and acetate-grown C. glabrata. A total of 855 proteins identified were expressed in both growth conditions, while only 19 and 106 proteins identified were expressed exclusively in glucose-grown and acetate-grown C. glabrata cells, respectively

Fig. 5

Hierarchical clustering analysis of the proteins identified from glucose-grown and acetate-grown C. glabrata cells. Hierarchical clustering analysis demonstrated a clear divergent in the proteomes of the glucose-grown and acetate-grown C. glabrata cells, with only minimal differences between the biological replicates

Fig. 6

Induction of the glyoxylate cycle and gluconeogenesis in acetate-grown C. glabrata. The glyoxylate cycle and glycolysis (dashed arrows)/gluconeogenesis (full line arrows) are shown, along with the log2 fold changes of transcripts (italic) and proteins (bold) obtained from the transcriptomic and proteomic analyses in this study, respectively. ND indicates the transcript or protein is not detected