Ploidy dynamics and evolvability in fungi

Abstract

Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Keywords: adaptation; aneuploidy; drug resistance; loss of heterozygosity; trimeras.

Figure 1.

Some aneuploidies and LOH events enable drug resistance. (a) Isochromosome (5 L) was detected in 12 fluconazole-resistant isolates from a survey of 90 clinical and laboratory isolates. Shown is comparative genome analysis performed with in-house produced microarrays [40] with the data displayed along the eight C. albicans chromosomes as log₂ ratios converted to ploidy levels (one, two, three or four gene copies) [40]. (b) Interpretation of i(5 L) geometry. CEN5 (magenta circle) maps to the breakpoint where extra copies of Chr5 L begin. Chr5 L includes ERG11, which encodes lanosterol 14-α-demethylase, the target of azole antifungals and TAC1, which encodes a transcription factor that positively regulates expression of efflux pump genes (CDR1 and CDR2). (c) The number of copies of ERG11 and TAC1-7 (a hyperactive allele of TAC1 [43]) correlate well with the level of resistance (MIC) of the strain as determined by deletion analysis of isogenic strains derived from parent strain carrying isochromosome (5 L) [34]. FLC, fluconazole.

Figure 2.

Antifungal drug exposure can induce aneuploidy and/or loss of heterozygosity. (a) Flow cytometry data comparing DNA content of Sytox green-stained cells with forward scatter levels as a proxy for cell size. Control diploids and tetraploid cells (derived by parasexual mating) were compared with samples without (top panels) or with (bottom panels) exposure to fluconazole for the indicated times. Note that DNA content and cell size increased in parallel in fluconazole-exposed cells. FSC, forward scatter. (b) A trimera cell after mitosis has four nuclei: the cell on the left contains two fused nuclei and subsequently underwent cytokinesis and cell separation to form a tetraploid; (c) example of multimera cells with multiple nucleoli detected using Nop1-GFP, green regions [110]; (d,e) time-lapse analysis of a cell that underwent unequal segregation of nucleoli (red) owing to failure of the two mitotic spindles (green) to remain parallel, resulting in very different amounts of nucleolar material being delivered to the two daughter cells (e) [110].

Figure 3.

Model for mechanisms of ploidy shift in C. albicans. Diploids that become mating type homozygous and switch to the opaque state can undergo mating to form tetraploids. Alternatively, in the presence of fluconazole (+FLC), trimeras form and yield tetraploids. Tetraploids produced in either way can undergo chromosome mis-segregation and a reduction in ploidy to return to a near-diploid state, which can include chromosomes that underwent a gain or loss and/or are aneuploid. This generates genotypic and phenotypic diversity without meiotic divisions [29,30]. Trimeras appeared after 4–24 h; mutlimeras were much less prevalent, but at least a few multimeras were evident by microscopy.