Genome‐wide analysis of the regulation of Cu metabolism in Cryptococcus neoformans

Abstract

The ability of the human fungal pathogen Cryptococcus neoformans to adapt to variable copper (Cu) environments within the host is key for successful dissemination and colonization. During pulmonary infection, host alveolar macrophages compartmentalize Cu into the phagosome and C. neoformans Cu-detoxifying metallothioneins, MT1 and MT2, are required for survival of the pathogen. In contrast, during brain colonization the C. neoformans Cu importers Ctr1 and Ctr4 are required for virulence. Central for the regulation and expression of both the Cu detoxifying MT1/2 and the Cu acquisition Ctr1/4 proteins is the Cu-metalloregulatory transcription factor Cuf1, an established C. neoformans virulence factor. Due to the importance of the distinct C. neoformans Cu homeostasis mechanisms during host colonization and virulence, and to the central role of Cuf1 in regulating Cu homeostasis, we performed a combination of RNA-Seq and ChIP-Seq experiments to identify differentially transcribed genes between conditions of high and low Cu. We demonstrate that the transcriptional regulation exerted by Cuf1 is intrinsically complex and that Cuf1 also functions as a transcriptional repressor. The Cu- and Cuf1-dependent regulon in C. neoformans reveals new adaptive mechanisms for Cu homeostasis in this pathogenic fungus and identifies potential new pathogen-specific targets for therapeutic intervention in fungal infections.

Transcriptome Analysis Uncovers a Link Between Copper Metabolism, and Both Fungal Fitness and Antifungal Sensitivity in the Opportunistic Yeast Candida albicans

“…When grown under limiting concentrations, C. albicans activate Cu utilization genes such as the Cu transporter Ctr1 while under Cu excess genes involved in Cu detoxification (Crp1) and relocalization (Atx1, Cup1, Ccc2) were induced. As in other fungi (van Bakel et al, 2005;Rustici et al, 2007;Garcia-Santamarina et al, 2018), we also found that iron utilization genes were differentially modulated by Cu depletion which might reflect a situation of iron deficiency as well. Indeed, iron uptake depends on the multicopper ferroxidases and consequently Cu deprivation engender a subordinate iron depletion in C. albicans cells.…”

“…We also analyzed the 50 gene promoters that mac1 failed to activate for potential consensus binding motifs and identified two enriched mini-sequences one of which is the well-known Mac1 binding site (McDaniels et al, 1999;Garcia-Santamarina et al, 2018; Figure 4D). Mac1 binding motif was found in the promoters of Ctr1 and Sod3, as previously reported (Woodacre et al, 2008;Li et al, 2015), in addition to the ferric reductases Fre30 and Fre7 (Table 1).…”

“…C. neoformans depends on the Cu-transporters Ctr1 and Ctr4 for Cu uptake and on the Cu-metallothioneins MT1 and MT2 for Cu detoxification (Ding et al, 2011, p. 99). In this pathogenic fungus, both Cu uptake and detoxification are governed by the same transcriptional regulator Cuf1 (Ding et al, 2011, p. 99;Garcia-Santamarina et al, 2018). In Aspergillus fumigatus, intracellular Cu uptake relies on the Cu-transporters ctrA2 and ctrC that are both under the control of the transcriptional factor Afmac1 (Cai et al, 2017).…”

Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans

“…Bedgraphs were plotted using Integrative Genomics Viewer 2.0.30 (Broad Institute). Genes were determined as differentially bound if the fold change in ChIP signal between both conditions was greater than 1.5-fold in either direction (based on [50]).…”

New insights into copper homeostasis in filamentous fungi

“…The extracellular Cu 2+ is reduced by plasma membrane reductases prior to internalization. These plasma membrane reductases are equally widespread in eukaryotes (Garcia-Santamarina et al 2018;Marvin et al 2004).…”