Chapter 39 : Switching of Mating-Type Genes

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Homothallic switching of the budding yeast mating-type (MAT) genes has provided one of the most intensively studied examples of a programmed genetic rearrangement. A site-specific double-strand break (DSB) at the locus, induced by HO endonuclease, provokes the replacement of mating-type specific sequences through homologous recombination. Homothallic organisms have the capacity to self-diploidize by converting some offspring of a haploid cell of one mating type to cells of the opposite mating type. This chapter briefly looks at the determination of cell lineage and at the mechanism of silencing the donor sequences. The conversion of one mating type to the other involves the replacement at the locus of Ya or Yα by a gene conversion induced by a DSB. Additional information has been gleaned from the analysis of DSB-induced recombination in meiotic cells. has evolved an elaborate mechanism that gives it the ability to choose between its two donors. It makes sense that should seek out and recombine with rather than , so that the recombinational repair of the DSB will lead to a switch to the opposite mating type. By comparing the recombination enhancer (RE) sequences of and (which is functional in ), it was possible to narrow down the RE to 270 contiguous base pairs in or 244 in , within which are four well-conserved subdomains.

Citation: Haber J. 2002. Switching of Mating-Type Genes, p 927-952. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch39
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Image of Figure 1.
Figure 1.

Mating-type loci on chromosome III. In addition to the expressed locus, chromosome III harbors two unexpressed donor loci, and These donors are maintained in a heterochromatic structure (diagonal lines) enforced by two adjacent silencer sequences -E (E) and -I (I), and -E (E) and -I (I). The locus shares X and Z1 regions of homology with both and whereas the W and Z2 regions are shared only with When the HO endonuclease is expressed, alleles can be switched by repair of a double-strand break, leading to a gene conversion event in which the -Y region is replaced without altering the donor sequences. The choice of or is mating-type dependent and is enforced by a small -acting element, the RE. Reprinted from reference 57 with permission from the (© 1998 by Annual Reviews).

Citation: Haber J. 2002. Switching of Mating-Type Genes, p 927-952. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch39
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Image of Figure 2.
Figure 2.

Homothallic life cycle of A homothallic () haploid cell that has divided can switch to the opposite mating type, and the original cell and its switched partner can conjugate to form a diploid cell. switching usually occurs only in the G1 phase of the cell cycle and only in haploid cells that have divided previously (i.e., in mother cells). The restriction of switching to mother cells depends on a novel regulatory mechanism in which the mRNA of a repressor protein, Ash1p, is localized only to the daughter cell and thus prevents expression in those cells. A cell that has switched but fails to conjugate can switch again. The efficiency of switching and conjugation is very high, so that colonies derived from single haploid spores are composed only of nonmating diploid cells, where is turned off. With appropriate carbon sources and under nitrogen starvation, diploid cells can undergo meiosis and sporulation, which will regenerate haploid cells. Reprinted in part from reference 57 with permission from the (© 1998 by Annual Reviews).

Citation: Haber J. 2002. Switching of Mating-Type Genes, p 927-952. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch39
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Image of Figure 3.
Figure 3.

Mating-type regulation of -specific, α-specific, and haploid-specific genes. (A) Expression of haploid and matingtype- specific genes depends on several combinations of regulatory proteins expressed by and , in combination with the Mcm1p. (B) Structure of and alleles, distinguished by their Y(650 bp) or Y(750 bp) regions and the expression of genes in different cell types. contains two transcripts. 1 encodes a corepressor that acts in / diploids to turn off haploid-specific genes, along with the homeodomain protein 2, 2 may have a role in the pheromone response pathway. In the 1 gene encodes a coactivator of transcription of -specific genes, acting in conjunction with Mcm1p. 2 encodes a corepressor that acts with the Mcm1 protein to turn off specific genes. In a diploid, Mata1p and Mat2p repress 1 transcription.

Citation: Haber J. 2002. Switching of Mating-Type Genes, p 927-952. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch39
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Image of Figure 4.
Figure 4.

A basic model for switching, based on the DSB repair model of Szostak et al. (185). After HO endonuclease cleavage, a 3′ end in Z1 is exposed by 5′-to-3′ exonuclease. Strand invasion allows the initiation of new DNA synthesis from the 3′ end of the invading strand, copying the donor locus. This intermediate step can be monitored by PCR amplification between a primer homologous to a region distal to and one homologous to the Y region of the donor locus; amplification is only possible when there is a covalent DNA intermediate that connects both primer sites. Removal of the original Y region allows a second strand of new DNA synthesis. The completion of switching can be detected by Southern blot hybridization or by a second PCR primer set. Experimentally, the intermediate measured by the first PCR reaction occurs 30 min before the process is completed ( ). Reprinted in part from reference 57 with permission from the (© 1998 by Annual Reviews).

Citation: Haber J. 2002. Switching of Mating-Type Genes, p 927-952. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch39
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Image of Figure 5.
Figure 5.

Silencing of and (A) A cartoon of heterochromatic structure of the silent locus A highly positioned array of nucleosomes (large circles) are established between -E and -1, which contain binding sites for the DNA replication complex, ORC, and the DNA-binding proteins Rap1 and Abf1. Silencing depends also on the deacetylation of histones and the interactions of four Sir proteins. (B) Schematic representation of the chromatin maps of the silent mating type loci and adapted from the data of Weiss and Simpson ( ) and Ravindra et al. ( ). Map units correspond to base pair positions of the sequence of chromosome III. White boxes labeled E and I identify the silencer sequences, boxes labeled W, X,Yα and YZ1 and Z2 identify the mating-type loci regions. Black arrowheads identify sites that are hypersensitive to micrococcal nuclease, with thicker arrows indicating more pronounced cleavage; tick marks correspond to regions generally sensitive to nuclease cleavage. Open ellipses with heavy borders indicate precisely positioned nucleosomes. Light gray and striped ellipses indicate more loosely positioned nucleosomes and the less-defined chromatin structure of the W region, respectively. The 1, 2, a1, and a2 coding regions are identified by horizontal arrows.

Citation: Haber J. 2002. Switching of Mating-Type Genes, p 927-952. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch39
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Image of Figure 6.
Figure 6.

A synthesis-dependent, strand-annealing model for switching. Proteins involved at different stages of the process are shown. In this mechanism, the DSB is first converted into 3′-ended single-stranded tails. -dependent strand invasion allows the invading 3′ end to initiate new DNA synthesis, requiring RFC, PCNA, and either Polδ and Polϵ; but, at the same time, a second strand is synthesized by lagging-strand replication, requiring Polδ and primase. Experiments have shown that leading-strand synthesis is impaired when lagging-strand polymerase is inactive ( ). Unlike normal semiconservative DNA replication, it is proposed that the newly synthesized strands are displaced from the template by branch migration. Removal of the original Y region is excised by a flap endonuclease including Rad1/Rad10, Msh2/Msh3, and Srs2. Reprinted in part from reference 57 with permission from the (© 1998 by Annual Reviews).

Citation: Haber J. 2002. Switching of Mating-Type Genes, p 927-952. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch39
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Image of Figure 7.
Figure 7.

Donor preference in switching. (A) Control of an entire chromosome arm for recombination depends on an intact RE. In cells, or a donor placed at other sites along the left arm of chromosome III, is activated to be the preferred donor. In α, the RE is turned off and the entire left arm and part of the right arm become “cold,” allowing to be the preferred donor. When the RE is deleted in a cell, the left arm becomes inaccessible and becomes the preferred donor. (B) General features and chromatin structure of the RE region in and α cells, as determined by Wu et al. ( ). The 2.5-kb intergenic region containing the RE contains a 753-bp RE region that is sufficient for full donor preference, in either orientation. In cells this region contains two prominent protein footprints (FP1 and FP2) and a DNase I hypersensitive (HS) region, and one or more transcripts (arrow). Both this region and another site with the 2.5-kb region contain binding sites for the Matα2p-Mcm1p repressor (dark boxes). In α cells, the region is covered by positioned nucleosomes that do not extend into adjacent coding regions. (C) A 270-bp “minimum enhancer” was identified by comparing the and RE regions ( ). Regions A, C, and D are essential for activity. Region C contains the Matα2p-Mcm1p binding site necessary for repressing the RE in α cells. The region of that is located where the transcripts have been seen in ( ) is not well conserved, nor is a second region, similar to region D containing repeats of TTT(A/G). Reprinted in part from reference 57 with permission from the (© 1998 by Annual Reviews).

Citation: Haber J. 2002. Switching of Mating-Type Genes, p 927-952. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch39
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