Dynamic genome plasticity during unisexual reproduction in the human fungal pathogen Cryptococcus deneoformans

Abstract

Genome copy number variation occurs during each mitotic and meiotic cycle and it is crucial for organisms to maintain their natural ploidy. Defects in ploidy transitions can lead to chromosome instability, which is a hallmark of cancer. Ploidy in the haploid human fungal pathogen Cryptococcus neoformans is exquisitely orchestrated and ranges from haploid to polyploid during sexual development and under various environmental and host conditions. However, the mechanisms controlling these ploidy transitions are largely unknown. During C. deneoformans (formerly C. neoformans var. neoformans, serotype D) unisexual reproduction, ploidy increases prior to the onset of meiosis, can be independent from cell-cell fusion and nuclear fusion, and likely occurs through an endoreplication pathway. To elucidate the molecular mechanisms underlying this ploidy transition, we identified twenty cell cycle-regulating genes encoding cyclins, cyclin-dependent kinases (CDK), and CDK regulators. We characterized four cyclin genes and two CDK regulator genes that were differentially expressed during unisexual reproduction and contributed to diploidization. To detect ploidy transition events, we generated a ploidy reporter, called NURAT, which can detect copy number increases via double selection for nourseothricin-resistant, uracil-prototrophic cells. Utilizing this ploidy reporter, we showed that ploidy transition from haploid to diploid can be detected during the early phases of unisexual reproduction. Interestingly, selection for the NURAT reporter revealed several instances of segmental aneuploidy of multiple chromosomes, which conferred azole resistance in some isolates. These findings provide further evidence of ploidy plasticity in fungi with significant biological and public health implications.

Ploidy changes in human fungal pathogens: Going beyond sexual reproduction

“…Studies in C . neoformans have linked ploidy increases to cell cycle regulation; one study revealed that suppression of the cell cycle regulator Cln1 can enable re-replication of DNA producing polyploid titan cells [ 31 ], while a related study showed a role for cyclins and cyclin-dependent kinases in regulating endoreplication [ 32 ]. Polyploidization can also be driven by genotoxic stresses that generate DNA double-strand breaks (DSBs) that subsequently can result in titan cell formation [ 33 ].…”

Genome-wide analysis of heat stress-stimulated transposon mobility in the human fungal pathogenCryptococcus deneoformans

“…The T1 DNA transposon and Tcn12 retrotransposon were previously identified as heatmobile elements using the URA3/URA5 reporters (31). To determine the endogenous chromosomal locations and copy numbers of these elements in C. deneoformans strain XL280α, the genome was assembled using Nanopore long-read and Illumina short-read sequencing (38).…”

HMMploidy: inference of ploidy levels from short-read sequencing data

“…Ploidy variation can be associated with a response or adaptation to environmental factors (Coward and Harding, 2014), and it is a phenomenon commonly detected in cancer cells (Davoli and Lange, 2011) and several pathogenic fungi (i.e. Cryptococcus neoformans, Candida albicans and Candida glabrata) and monocellular parasites (Avramovska et al, 2021;Farrer et al, 2013;Fu et al, 2021;Morrow and Fraser, 2013;Stone et al, 2019;Yang et al, 2021;Zhu et al, 2018).…”