Chapter 23 : Mating-type Gene Switching in Saccharomyces cerevisiae

Homothallic life cycle of S. cerevisiae. A homothallic MAT a (pink) mother cell and its new daughter can switch to MATα (light blue). This lineage is established by the asymmetric partitioning of the mRNA encoding the Ash1 repressor of HO gene expression in daughter cells (light green). These cells can conjugate to form a zygote that gives rise to MAT a/MATα diploids (lilac), in which HO gene expression is repressed. Under nitrogen starvation, diploids undergo meiosis and sporulation to produce four haploid spores (two MAT a and two MATα) in an ascus. The spores germinate and grow vegetatively and can repeat the homothallic cycle. Heterothallic cells have stable mating types and grow vegetatively until they exhaust their nutrients and enter stationary phase. Used with permission from the Genetics Society of America.

(A) Arrangement of MAT, HML, and HMR on chromosome 3. The gene conversion between MAT a and MATα is illustrated. Both HML and HMR could be transcribed but are silenced by the creation of short regions of heterochromatin (ordered nucleosomes are presented as blue circles) by the interaction of silencing proteins with flanking cis-acting silencer E and I sequences. The recombination enhancer (RE), located 17 kb centromere-proximal to HML, acts to promote the usage of HML as the donor in MAT a cells. (B) Control of mating type-specific genes. Transcription of a- and α-regulatory genes at MAT occurs from a bidirectional promoter. The Mcm1 protein, in combination with Matα1 and Matα2, activates the transcription of α-specific genes or represses a-specific genes, respectively, while a Mata1–Matα2 repressor turns off haploid-specific genes. Mata2 has no known function.

Silencing of HMR and HML. The processive process of silencing establishment from HMR-E is illustrated. Proteins (ORC proteins, Rap1, and Abf1, all in gray) bound to the three elements [autonomously replicating sequence consensus sequence (ACS), Rap1-binding site, and Abf1-binding site] of the HMR-E silencer recruit Sir1 that in turn recruits the Sir2–Sir3–Sir4 complex. The NAD+- dependent HDAC Sir2 deacetylates lysines on the N-terminal tails of histones H3 and H4, which allows the Sir3–Sir4 complex to bind and stabilize the position of the nucleosome. Sir2 can then deactylate the next nucleosome and silencing spreads further. The progressing spread of silencing in the simplified figure is shown only in one direction and from one of the two silencers.

Physical monitoring of MAT switching. Southern blot analysis of StyI-digested DNA after galactose induction of the HO endonuclease. The probe detects sequences just distal to MAT- Z1/Z2 and shows a difference in the size of the StyI restriction fragments of MAT a and MATα. In this experiment, an ade3::GAL::HO strain carrying HMLα MAT a hmrΔ was used. The cleavage of MAT a into a smaller HO-cut segment was followed by the appearance of the MATα product. (Figure modified from 149 ).

Mechanism of MAT switching. Key steps in the switching of MAT a to MATα by a synthesis-dependent strand-annealing (SDSA) mechanism. An HO-induced DSB is resected by 5′-to-3′ exonucleases or helicase endonucleases to produce a 3′-end single-stranded DNA (ssDNA) tail, on which assembles a Rad51 filament (shown only on one side of the DSB). The Rad51::ssDNA complex engages in a search for homology. Strand invasion of MAT-Z into the homologous HML-Z can be detected by anti-Rad51 chromatin immunoprecipitation followed by quantitative PCR using the primer pair Pz and P HML . Strand invasion can form an interwound (plectonemic) joint molecule (D-loop) that can assemble DNA replication factors to copy the Yα sequences, which can be monitored by a primer extension assay using the primer pair Pα and P MAT . The D-loop is thought to migrate as DNA synthesis proceeds. Unlike normal replication, the newly copied strand is postulated to dissociate from the template and, when sufficiently extended, anneal with the second end, still blocked from forming a plectonemic structure by the long nonhomologous Ya tail. The single-stranded tail is clipped off once strand annealing occurs by the Rad1– Rad10 flap endonuclease, so that the new 3′ end can also be used as a primer to fill in the gap. Consequently, all newly synthesized DNA is found at the MAT locus, while the donor is unaltered. However, a small fraction of DSB repair events apparently proceed by a different repair mechanism involving the formation of a double Holliday junction.

Protein binding to consensus elements in the RE. In MAT a cells, Mcm1 binding facilitates the binding of Swi4–Swi6 and multiple copies of Fkh1. These proteins are important for the ability of RE in promoting HML usage in MAT a cells. In MATα cells, binding of the Matα2–Mcm1 repressor to a 31-bp conserved operator, shared by a-specific genes, leads to the formation of highly positioned nucleosomes between the two flanking genes and excludes binding of Fkh1 or Swi4–Swi6.

Role of the recombination enhancer in MAT a donor preference. (A) Arrangement of HMLα, MAT a, and HMRα–BamHI (HMRα-B). When RE is replaced by four LexA-binding sites (LexABS), HML usage is strongly impaired. Expression of LexA–FHA (the phosphothreonine-binding domain of Fkh1) fusion protein completely rescues HML usage, while expression of the mutant LexA–FHAR80A, which has lost phosphothreonine-binding activity, fails to rescue it. (B) Southern blot data after induction of switching showing the proportion of BamHI-digested MATα or MATα-B DNA in the strains depicted above. (Figure modified from 85 .)

Model for Fkh1-regulated donor preference. A cluster of Fkh1 bound to RE in MAT a cells can associate with phosphothreonine residues that are located near the DSB and created by casein kinase II, and possibly other kinases, in response to the DSB. The association of Fkh1 and the DSB, which has been demonstrated by ChIP, tethers HML within ∼20 kb of the DSB ends and facilitates its use over HMR, located 100 kb away.