Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locusSaccharomyces cerevisiaesystem

Abstract

Saccharomyces cerevisiae has a complex system for switching the mating type of haploid cells, requiring the genome to have three mating-type (MAT)-like loci and a mechanism for silencing two of them. How this system originated is unknown, because the threelocus system is present throughout the family Saccharomycetaceae, whereas species in the sister Candida clade have only one locus and do not switch. Here we show that yeasts in a third clade, the methylotrophs, have a simpler two-locus switching system based on reversible inversion of a section of chromosome with MATa genes at one end and MATalpha genes at the other end. In Hansenula polymorpha the 19-kb invertible region lies beside a centromere so that, depending on the orientation, either MATa or MATalpha is silenced by centromeric chromatin. In Pichia pastoris, the orientation of a 138-kb invertible region puts either MATa or MATalpha beside a telomere and represses transcription of MATa2 or MATalpha2. Both species are homothallic, and inversion of their MAT regions can be induced by crossing two strains of the same mating type. The three-locus system of S. cerevisiae, which uses a nonconservative mechanism to replace DNA at MAT, likely evolved from a conservative two-locus system that swapped genes between expression and nonexpression sites by inversion. The increasing complexity of the switching apparatus, with three loci, donor bias, and cell lineage tracking, can be explained by continuous selection to increase sporulation ability in young colonies. Our results provide an evolutionary context for the diversity of switching and silencing mechanisms.Hansenula polymorpha | Pichia pastoris | yeast genetics | comparative genomics M ating-type switching in yeasts is a highly regulated process that converts a haploid cell of one mating type into a haploid of the opposite type (1-5). Switching involves the complete deactivation of one set of regulatory genes and activation of an alternative set, but, unlike most regulatory changes, the switch is achieved by physically replacing the DNA at an expression site that is shared by both types of cell. In Saccharomyces cerevisiae the switching system uses a menagerie of molecular components (3) including three mating-type (MAT)-like loci (the expressed MAT locus and the silent loci HML and HMR); an endonuclease (HO) that creates a double-strand break at the MAT locus, which then is repaired using HMLalpha or HMRa as a donor; a mechanism (Sir1 and Sir2/3/4 proteins) for repressing transcription and HO cleavage at the silent loci; two triplicated sequences (the Z and X regions) that guide repair of the dsDNA break; a donorbias mechanism (the recombination enhancer, RE) to ensure that switching happens in the correct direction; and a cell lineagetracking mechanism (Ash1 mRNA localization) to ensure that switching occurs only in particular cells. Most of these components have no function other than facilitating switching.

The frequency of sex in fungi

“…These mating-type switchers have the genes for both mating types in their haploid genome, but only the genes at one specific physical location are expressed, while the genes of the other mating type at another locus are silenced [30,31]. During asexual growth, the genes from the silent locus are moved into the active locus, such that the daughter cell becomes the opposite mating type, and thus now is compatible with the mother cell [31]. A single individual can thus reproduce sexually after a single round of asexual reproduction without the need of another genotype.…”

Genomics and the making of yeast biodiversity

“…Interestingly, Kluyveromyces lactis HO has been replaced by MATα3 , another selfish element co-opted from a DNA transposon [19,20]. A simpler two-locus system that switches mating types by inversion has evolved in the clade containing Ogataea (Hansenula) polymorpha and Komagataella (Pichia) pastoris [21]. Here inversion simply switches which of the two mating loci is present in active chromatin, and thus determines which is expressed.…”

“…For example, dozens of species evolved from clades associated with fruit-rot and tree-flux habitats to exploit the diverse chemistries associated with different species of cacti, which, in turn, have been exploited by several different cactophilic Drosophila and sap beetle species that feed on these yeasts [27,28]. Most species of the Starmerella clade are associated with Hymenoptera species, while yeasts of the genus Ogataea frequently inhabit leaf litter where methanol consumption may be beneficial [21,27,40]. Little is known about the genetic underpinnings of these ecological innovations, except that they must rely, at least partly, on metabolism.…”

1 Running Hot and Cold: Recombination Around and Within Mating-Type Loci of Fungi and Other Eukaryotes

“…Specifically, in H. polymorpha, the MATa and MATa loci are located approximately 19 kb apart on the same chromosome, and the chromosomal region encompassing the two MAT loci lies beside the centromere. As a consequence, depending on the orientation of this chromosomal region, one of the two MAT loci will be silenced by the centromeric chromatin due to its proximity to the centromere, leaving the other MAT locus active and capable of defining the mating type of the cell (Hanson et al 2014;Maekawa and Kaneko 2014). In P. pastoris, the two MAT loci are approximately 123 kb apart on the same chromosome, and depending on the orientation, one of the two MAT loci will be located close to the end of the chromosome and consequently silenced due to its close proximity to the telomere.…”

“…In P. pastoris, the two MAT loci are approximately 123 kb apart on the same chromosome, and depending on the orientation, one of the two MAT loci will be located close to the end of the chromosome and consequently silenced due to its close proximity to the telomere. The inversion that results in switching between the mating types occurs by recombination between inverted-repeat sequences flanking the MAT loci (Hanson et al 2014) (Fig. 1.1).…”