At least 10 genes on chromosome 5 ofCandida albicansare downregulated in concert to control cell wall and to confer adaptation to caspofungin

Abstract

Candida albicans is part of normal microbiota, however, can cause superficial and life threatening infection in immune-compromised individuals. Drugs from echinocandin (ECN) class that disrupt cell wall synthesis, are being used as a major treatment strategy against candidiasis. As the use of ECNs for the treatment of candidiasis is increasing, resistance against ECNs is also emerging. Previously, we reported involvement of 5 chromosome 2 (Ch2) genes in adaptation to ECN drugs. Here, we explored 22 candidate-genes on Ch5 that are consistently downregulated in independent mutants adapted to caspofungin (CAS), for their role in ECN adaptation. We also compared cell wall remodelling in CAS-adapted mutants and in 10 knockouts (KOs) from Ch5. Independent KO experiments as combined with broth microdilution assay, demonstrated that, as expected, 10 out of 22 Ch5 genes decrease ECN susceptibility by controlling the levels of three major components of the cell wall, glucan, mannan, and chitin. Some KOs decreased glucan or increased chitin or both. Similar cell wall remodelling, decreased glucan and increased chitin, was found in CAS-adapted mutants with no ploidy change. Some other KOs had no glucan change, but increased the level of either mannan or chitin. Our results identify the function of two uncharacterized genes, orf19.970 and orf19.4149.1, and expand the functions of DUS4, RPS25B, UAP1, URA7, RPO26, HAS1, and CKS1. The function of CHT2, as negative regulator of ECN susceptibility, has been previously established. Importantly, half of the above genes are essential indicating that essential processes are involved in cell wall remodelling for adaptation to ECNs. Also important, orf19.970 and orf19.4149.1 have no human orthologues. Finally, our work shows that multiple mechanisms are used by C. albicans cells to remodel cell wall in order to adapt to CAS. This work continues to identify common pathways that are involved in drug adaptation, as well as new genes controlling ECN susceptibility and reveals new targets for development of novel antifungal drugs.

Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants

“…In the aneuploid strain JMC200-3-4, the ORF INT1 (orf19.4257) is associated with five mutations ( Table S1 , summarized in Table S3 ). The INT1 gene with multiple mutations in aneuploid JMC200-3-4, resides on Ch5, which carries multiple genes for negative control of ECN susceptibility [ 7 , 10 ].…”

“…We also find that most genes sharing mutations between mutant strains acquired transcriptional changes ( Table 2 and Table S2 ). However, there is a lack of a direct correlation between shared or non-shared changes in the DNA sequences of caspofungin-adapted mutants analyzed in here and their DEGs that we published in [ 7 , 10 ]. Some examples include previously uncharacterized gene orf19.5069 that is upregulated in all three strains; however, it harbors an ORF mutation in one adapted strain only ( Table S3 ).…”

“…We characterized a total of 15 genes that are distributed non-randomly over two different chromosomes. These genes are simultaneously upregulated on Ch2, a total of five genes, and down-regulated on Ch5, a total of 10 genes, across all adapted mutants in order to control the cell wall of these mutants for adaptation to ECNs [ 7 , 10 ]. Here, we continue our search for the features that are implicated with adaptation to ECN drugs.…”