Genome editing in the yeast Nakaseomyces delphensis and description of its complete sexual cycle

Lessons from the Nakaseomyces: mating-type switching, DSB repair and evolution of Ho

This short paper aims to review what our recent studies in the Nakaseomyces yeasts, principally Candida glabrata, reveal about the evolution of the mating-type switching system and its components, as well as about the repair of chromosomal double-strand breaks in this clade. In the model yeast Saccharomyces cerevisiae, the study of mating-type switching has, over the years, led to major discoveries in how cells process chromosomal breaks. Indeed, in this species, switching, which allows every haploid cell to produce cells of opposite mating types that can mate together, is initiated by the Ho endonuclease, linking sexual reproduction to a programmed chromosomal cut. More recently, the availability of other yeasts' genomes from type strains and from populations, and the ability to manipulate and edit the genomes of most yeasts in the laboratory, has enabled scientists to explore mating-type switching in new species, thus enriching our evolutionary perspective on this phenomenon. In this review, we will show how the study of mating-type switching in C. glabrata and Nakaseomyces delphensis has allowed us to reveal possible additional roles for Ho, and also to discover major differences in DSB repair at central and subtelomeric sexual loci. In addition, we report how the study of repair of chromosomal breaks induced by CRISPR-Cas9 reveals that efficient and faithful NHEJ is a major repair pathway in C. glabrata.

A single Ho-induced double-strand break at the MAT locus is lethal in Candida glabrata

Mating-type switching is a complex mechanism that promotes sexual reproduction in Saccharomycotina. In the model species Saccharomyces cerevisiae, mating-type switching is initiated by the Ho endonuclease that performs a site-specific double-strand break (DSB) at MAT, repaired by homologous recombination (HR) using one of the two silent mating-type loci, HMLalpha and HMRa. The reasons why all the elements of the mating-type switching system have been conserved in some Saccharomycotina, that do not show a sexual cycle nor mating-type switching, remain unknown. To gain insight on this phenomenon, we used the yeast Candida glabrata, phylogenetically close to S. cerevisiae, and for which no spontaneous and efficient mating-type switching has been observed. We have previously shown that expression of S. cerevisiae’s Ho (ScHo) gene triggers mating-type switching in C. glabrata, but this leads to massive cell death. In addition, we unexpectedly found, that not only MAT but also HML was cut in this species, suggesting the formation of multiple chromosomal DSBs upon HO induction. We now report that HMR is also cut by ScHo in wild-type strains of C. glabrata. To understand the link between mating-type switching and cell death in C. glabrata, we constructed strains mutated precisely at the Ho recognition sites. We find that even when HML and HMR are protected from the Ho-cut, introducing a DSB at MAT is sufficient to induce cell death, whereas one DSB at HML or HMR is not. We demonstrate that mating-type switching in C. glabrata can be triggered using CRISPR-Cas9, without high lethality. We also show that switching is Rad51-dependent, as in S. cerevisiae, but that donor preference is not conserved in C. glabrata. Altogether, these results suggest that a DSB at MAT can be repaired by HR in C. glabrata, but that repair is prevented by ScHo.

Mating-type switching is one of the strategies developed by fungi to promote sexual reproduction and propagation. This mechanism enables one haploid cell to give rise to a cell of the opposite mating-type so that they can mate. It has been extensively studied in the yeast S. cerevisiae in which it relies on a programmed double-strand break performed by the Ho endonuclease at the MAT locus which determines sexual identity. Little is known about why the mating-type switching components have been conserved in species like C. glabrata, in which neither sexual reproduction nor mating-type switching is observed. We have previously shown that mating-type switching can be triggered, in C. glabrata, by expression of the HO gene from S. cerevisiae but this leads to massive cell death. In this work, we show that mating-type switching in C. glabrata can be triggered by CRISPR-Cas9 and without any high lethality. We demonstrate that the cut at MAT is only lethal when the Ho endonuclease performs the break, a situation unique to C. glabrata. Our work points to a degeneration of the mating-type switching system in C. glabrata. Further studies of this phenomenon should shed light on the evolution of mating systems in asexual yeasts.