ABC transportome inventory of human pathogenic yeast Candida glabrata: Phylogenetic and expression analysis

Abstract

ATP-binding cassette (ABC) is one of the two major superfamilies of transporters present across the evolutionary scale. ABC superfamily members came to prominence due to their ability to extrude broad spectrum of substrates and to confer multi drug resistance (MDR). Overexpression of some ABC transporters in clinical isolates of Candida species was attributed to the development of MDR phenotypes. Among Candida species, Candida glabrata is an emerging drug resistant species in human fungal infections. A comprehensive analysis of such proteins in C. glabrata is required to untangle their role not only in MDR but also in other biological processes. Bioinformatic analysis of proteins encoded by genome of human pathogenic yeast C. glabrata identified 25 putative ABC protein coding genes. On the basis of phylogenetic analysis, domain organization and nomenclature adopted by the Human Genome Organization (HUGO) scheme, these proteins were categorized into six subfamilies such as Pleiotropic Drug Resistance (PDR)/ABCG, Multi Drug Resistance (MDR)/ABCB, Multi Drug Resistance associated Protein (MRP)/ABCC, Adrenoleukodystrophy protein (ALDp)/ABCD, RNase L Inhibitor (RLI)/ABCE and Elongation Factor 3 (EF3)/ABCF. Among these, only 18 ABC proteins contained transmembrane domains (TMDs) and were grouped as membrane proteins, predominantly belonging to PDR, MDR, MRP, and ALDp subfamilies. A comparative phylogenetic analysis of these ABC proteins with other yeast species revealed their orthologous relationship and pointed towards their conserved functions. Quantitative real time PCR (qRT-PCR) analysis of putative membrane localized ABC protein encoding genes of C. glabrata confirmed their basal expression and showed variable transcriptional response towards antimycotic drugs. This study presents first comprehensive overview of ABC superfamily proteins of a human fungal pathogen C. glabrata, which is expected to provide an important platform for in depth analysis of their physiological relevance in cellular processes and drug resistance.

ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes

“…CAUR_01852 (the homolog of STE6/HST6 ) showed the least basal expression among the 20 ABC transporter genes. Notably, similar low expression of C. glabrata CAGL0K00363g, an ortholog of S. cerevisiae STE6 has been reported (Kumari et al, 2018). SNQ2 orthologs, CAUR_01276 and CAUR_01285 , showed similar levels of basal expression.…”

“…The number of PDR members varies among different yeasts. While C. glabrata , C. albicans , and D. hansenii have higher numbers, the fission yeast Schizosaccharomyces pombe contains only two PDR genes (Lamping et al, 2010; Kumari et al, 2018; Wasi et al, 2018).…”

“…The basal expression profile of all the putative ABC transporter genes was quantified and normalized in comparison to TDH1 ( CAUR_02457 ) gene expression. TDH1 is a housekeeping gene, which is an ortholog of GAPDH , a housekeeping gene commonly used as internal control for qRT-PCR (Kumari et al, 2018). The expression profile of the CBS 10913T strain established the presence of transcripts of all the 20 predicted putative ABC transporter genes, and highlighted a variability of basal expression between them (Figure 4).…”

“…Among the MDR subfamily members, the homolog of STE6 ( CAUR_001852 ) was the only member that exhibited elevated expression in Isolate-1 and Isolate-2 (Figure 6A). Notably, Ste6 is not an established drug transporter, but a dedicated pheromone transporter in S. cerevisiae (Kumari et al, 2018). However, one study has reported that Ste6 could also impart resistance to valinomycin in S. pombe (Christensen et al, 1997).…”

“…However, one study has reported that Ste6 could also impart resistance to valinomycin in S. pombe (Christensen et al, 1997). In C. glabrata , the transcripts of a STE6 homolog (CAGL0K00363g) displayed variable response to drug exposure (Kumari et al, 2018), and also, the human Ste6 homolog, ABCB1, has been shown to extrude xenobiotics in various chemotherapy-resistant tumors (He et al, 2011). Notably, none of the MDR transporters showed more than or equal to twofold downregulation.…”