Abstract
ABSTRACTThe diploid genome of the yeast Candida albicans is highly plastic, exhibiting frequent loss-of-heterozygosity (LOH) events. To provide a deeper understanding of the mechanisms leading to LOH, we investigated the repair of a unique DNA double-strand break (DSB) in the laboratory C. albicans SC5314 strain using the I-SceI meganuclease. Upon I-SceI induction, we detected a strong increase in the frequency of LOH events at an I-SceI target locus positioned on chromosome 4 (Chr4), including events spreading from this locus to the proximal telomere. Characterization of the repair events by single nucleotide polymorphism (SNP) typing and whole-genome sequencing revealed a predominance of gene conversions, but we also observed mitotic crossover or break-induced replication events, as well as combinations of independent events. Importantly, progeny that had undergone homozygosis of part or all of Chr4 haplotype B (Chr4B) were inviable. Mining of genome sequencing data for 155 C. albicans isolates allowed the identification of a recessive lethal allele in the GPI16 gene on Chr4B unique to C. albicans strain SC5314 which is responsible for this inviability. Additional recessive lethal or deleterious alleles were identified in the genomes of strain SC5314 and two clinical isolates. Our results demonstrate that recessive lethal alleles in the genomes of C. albicans isolates prevent the occurrence of specific extended LOH events. While these and other recessive lethal and deleterious alleles are likely to accumulate in C. albicans due to clonal reproduction, their occurrence may in turn promote the maintenance of corresponding nondeleterious alleles and, consequently, heterozygosity in the C. albicans species.
Highlights
Candida albicans is a quasi-obligate diploid yeast [1] whose 32 Mb genome is organized in eight pairs of chromosomes with, on average, one heterozygous position every ~250 bp [2,3,4]
To study the mechanisms involved in the repair of a single DNA double-strand break (DSB) in C. albicans, we took advantage of the I-SceI meganuclease, an intron-encoded homing endonuclease isolated from the yeast Saccharomyces cerevisiae
Our results revealed that a majority of C. albicans cells repaired an I-SceI-induced DNA DSB on Chr4 haplotype B (Chr4B) by gene conversion without crossover (GC) but that BIR or mitotic crossover (MCO) could be used, at lower frequency
Summary
Candida albicans is a quasi-obligate diploid yeast [1] whose 32 Mb genome is organized in eight pairs of chromosomes with, on average, one heterozygous position every ~250 bp [2,3,4]. An investigation of the events associated with LOH at a specific locus on C. albicans Chr revealed that WCL events leaving haplotype B as the sole remaining haplotype were never observed [27] Taken together, these studies have led to the hypothesis that recessive lethal alleles are present on C. albicans chromosome homologs and prevent some LOH events from being detected. The mechanisms by which DNA DSBs are repaired can greatly influence the nature of the LOH events that affect the C. albicans genome. Our detailed analysis of LOH events resulting from an induced DNA DSB in strain SC5314 allowed us to identify recessive deleterious alleles on C. albicans Chr haplotype B (Chr4B) that explain why haplotype A for this chromosome cannot be lost. Our results suggest that recessive deleterious alleles could play a role in the maintenance of heterozygosity in the C. albicans species
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