Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway

Abstract

In haploid cells of Ogataea (Hansenula) polymorpha an environmental signal, nitrogen starvation, induces a reversible change in the structure of a chromosome. This process, mating-type switching, inverts a 19-kb DNA region to place either MATa or MATα genes under centromeric repression of transcription, depending on the orientation of the region. Here, we investigated the genetic pathway that controls switching. We characterized the transcriptomes of haploid and diploid O. polymorpha by RNAseq in rich and nitrogen-deficient media, and found that there are no constitutively a-specific or α-specific genes other than the MAT genes themselves. We mapped a switching defect in a sibling species (O. parapolymorpha strain DL-1) by interspecies bulk segregant analysis to a frameshift in the transcription factor EFG1, which in Candida albicans regulates filamentous growth and white-opaque switching. Gene knockout, overexpression and ChIPseq experiments show that EFG1 regulates RME1, which in turn regulates STE12, to achieve mating-type switching. All three genes are necessary both for switching and for mating. Overexpression of RME1 or STE12 is sufficient to induce switching without a nitrogen depletion signal. The homologous recombination genes RAD51 and RAD17 are also necessary for switching. The pathway controlling switching in O. polymorpha shares no components with the regulation of HO in S. cerevisiae, which does not involve any environmental signal, but it shares some components with mating-type switching in Kluyveromyces lactis and with white-opaque phenotypic switching in C. albicans.

A conserved regulator controls asexual sporulation in the fungal pathogen Candida albicans

“…Notably, Rme1 appears to play roles in various aspects of yeast sexuality although in a manner that varies from species to species. In Kluyveromyces lactis , Rme1 acts as a positive regulator of mating-type switching and expression of haploid-specific genes integrating starvation signals 49 while in Ogataea polymorpha , Rme1 positively regulates nitrogen-starvation-dependent mating-type switching and mating 50 . Our observation provides yet another function for Rme1, with a role in the formation of asexual chlamydospores, highlighting multiple events of functional rewiring during the evolution of the Saccharomycotina .…”

Functional duplication of Rap1 in methylotrophic yeasts

“…4F). Such short telomeric DNA fragments were observed in other yeast strains with increased telomere recombination 41,53 . Indeed, we found that disruption of the telomerase RNA gene (HpTER) in the B 1–526 strain neither changed telomere length nor induced senescence at any time point analyzed (Fig.…”

“…Since this analysis is not feasible in H . polymorpha DL-1 (due to its semi-sterility) 53 , we used its closest sibling H . polymorpha CBS4732 (a.k.a.…”

Carbon source requirements for mating and mating‐type switching in the methylotrophic yeasts Ogataea (Hansenula) polymorpha and Komagataella phaffii (Pichia pastoris)

“…Although these genes are expressed under rich media conditions, they are strongly induced in K. phaffii upon transfer of the cells to starvation conditions and in response to pheromone (Heistinger et al, ). In O. polymorpha , the pheromone receptors and other mating pathway genes are induced by activation of STE12 , which occurs in response to a nitrogen starvation signal (Hanson, Byrne, & Wolfe, ). These findings suggest that the low levels of expression of mating pathway genes in rich media is not sufficient to induce a response.…”