Transposable mating type genes in Saccharomyces cerevisiae

Homothallic mating type switching generates lethal chromosome breaks in rad52 strains of Saccharomyces cerevisiae

In homothallic cells of Saccharomyces cerevisiae, a or alpha mating type information at the mating type locus (MAT) is replaced by the transposition of the opposite mating type allele from HML alpha or HMRa. The rad52-1 mutation, which reduces mitotic and abolishes meiotic recombination, also affects homothallic switching (Malone and Esposito, Proc. Natl. Acad. Sci. U.S.A. 77:503-507, 1980). We have found that both HO rad52 MATa and HO rad52 MAT alpha cells die. This lethality is suppressed by mutations that substantially reduce but do not eliminate homothallic conversions. These mutations map at or near the MAT locus (MAT alpha inc, MATa-inc, MATa stk1) or are unlinked to MAT (HO-1 and swi1). These results suggest that the switching event itself is involved in the lethality. With the exception of swi1, HO rad52 strains carrying one of the above mutations cannot convert mating type at all. MAT alpha rad52 HO swi1 strains apparently can switch MAT alpha to MATa. However, when we analyzed these a maters, we found that few, if any, of them were bona fide MATa cells. These a-like cells were instead either deleted for part of chromosome III distal to and including MAT or had lost the entire third chromosome. Approximately 30% of the time, an a-like cell could be repaired to a normal MATa genotype if the cell was mated to a RAD52 MAT alpha-inc strain. The effects of rad52 were also studied in mata/MAT alpha-inc rad52/rad52 ho/HO diploids. When this diploid attempted to switch mata to MATa, an unstable broken chromosome was generated in nearly every cell. These studies suggest that homothallic switching involves the formation of a double-stranded deoxyribonucleic acid break or a structure which is labile in rad52 cells and results in a broken chromosome. We propose that the production of a double-stranded deoxyribonucleic acid break is the lethal event in rad52 HO cells.

Evolution of the 87A and 87C heat-shock loci in Drosophila

Several species related to Drosophila melanogaster have two loci containing sequences which code for the major heat-shock protein of molecular weight 70,000 (hsp70). These sequences are arranged as two pairs of inverted repeats. The structure of the 87C locus in D. melanogaster seems to have arisen through DNA insertion. Hsp70-coding sequences at the two loci are not evolving independently. Gene conversion between hsp70 genes has apparently occurred both within and between loci.

Physical evidence for a Saccharomyces cerevisiae transposable element which carries the his4C gene

A Saccharomyces cerevisiae transposable element which carries the his4C structural gene and which is capable of transposition, excision, and mutator activity is described. Physical evidence is presented for transposition of the his4C deoxyribonucleic acid sequences to a new location in the genome and for precise excision of these transposed deoxyribonucleic acid sequences in spontaneous his4C- segregants.

Mating-type differentiation by transposition of controlling elements in Saccharomyces cerevisiae

The nonfunctional mutation of the homothallic gene HML alpha, designated hml alpha, produced two mutant alleles, hml alpha-1 and hml alpha-2. Both mutant clones were mixed cultures consisting of a mating-type cells and nonmating haploid cells. The frequencies of the two cell types were different, and a few diploid cells able to sporulate were found in the hml alpha-2 mutant. Conversions of an a mating-type cell to nonmater, and vice versa, were observed in both mutants. The conversion of an a mating phenotype to nonmating is postulated to occur by alteration of the a mating type to the sterile mating-type allele in the hml alpha-1 mutant. In tetrad dissection of prototrophic diploids that were obtained by rare mating of hml alpha-1 mutants with a heterothallic strain having the MATa ho HMRa HMLa genotype, many mating-deficient haploid segregants were found, while alpha mating-type segregants were observed in a similar diploid using an hml alpha-2 mutant. The mating-type-deficient haploid segregants were supposed to have the sterile alpha mating-type allele because the nonmating genetic trait always segregated with the mating-type locus. Sporogenous diploid cells obtained in the hml alpha-2 mutant clone had the MATa/MAT alpha HO/HO HMRa/HMRa hml alpha-2/hml alpha-2 genotype. These observations suggested that the hml alpha-1 allele produces a transposable element that gives rise to the sterile alpha mating type by transposition into the mating-type locus, and that the hml alpha-2 allele produces an element that provides alpha mating-type information, but is defective in the structure for transposition.

Gene expression in eukaryotes

Gene expression in eukaryotes is influenced by a wide variety of mechanisms including the loss, amplification, and rearrangement of genes. Genes are differentially transcribed, and the RNA transcripts are variably utilized. Multigene families regulate the amount, the diversity, and the timing of gene expression. The present level of understanding of gene expression in eukaryotes is attributable mainly to biochemical methods rather than to traditional genetics. The new techniques that permit analysis and modification of purified genes of known function will identify both the control regions in eukaryotic genes as well as the molecules within cell that influence gene expression.

A mechanism of DNA transposition

Bacteriophage Mu and many other transposable elements undergo transposition by a process that involves replication of the element. We describe here a mechanism by which such integrative replication may take place. We hve examined electron microscopically the DNA structures generated in host cells after Mu induction and have deduced the following steps in the transposition process, (i) Association. A protein-mediated association is brought about between the transposable element and the target DNA. (ii) Attachment. One end of the element is nicked and attached to a site that undergoes a double-stranded cleavage. (iii) Roll-in replication. While one strand of the target DNA is linked to the nicked strand of the element, the complementary strand of the target DNA is used as a primer for replication into the element such that the replicating DNA is threaded through the replication complex. (iv) Roll-in termination. When the distal end of the element arrives at the replication complex, replication is terminated. The roll-in replication mechanism can also explain laying down of tandem repeats--i.e., amplification of circular DNA sequences.

Transposable elements associated with constitutive expression of yeast alcohol dehydrogenase II

The yeast structural gene ADR2, coding for the glucose-repressible alcohol dehydrogenase (ADHII), has been isolated by complementation of function in transformed yeast. The chromosomal DNA from nine yeast strains with cis-dominant constitutive mutations (ADR3c) has been investigated by restriction enzyme analysis, using the cloned ADR2 DNA as a hybridization probe. Seven mutants appear to have insertions of approximately 5.6 kg near the 5' end of the ADR2-coding region. Four of these insertions have the same restriction pattern as the yeast transposable element Ty1. Two differ from Ty1 by the presence of an additional Hind III site, and a seventh insertion differs from Ty1 at a number of restriction sites. All are inserted in the same orientation with respect to the structural gene. A DNA fragment containing the ADR2 gene and adjacent sequences from a constitutive mutant has been cloned and shown by heteroduplex analysis to contain an insertion near the 5' end of the structural gene. The cloned insertion sequence hybridizes to multiple genomic DNA fragments, indicating that it contains a moderately repetitive sequence. Thus it appears that insertion of a transposable element near the 5' terminus of the structural gene can produce constitutive expression of a normally glucose-repressed enzyme. Such insertions seem to be the most common way of generating cis-dominant constitutive mutations of ADHII.

Regulation of transcription in expressed and unexpressed mating type cassettes of yeast

The genes that control the a, alpha and a/alpha cell types in Saccharomyces are carried on transposable elements known as a and alpha cassettes which reside at three different chromosomal loci. Examination of the transcripts by R-looping and filter hybridization indicates that each cassette is capable of producing two divergent transcripts. Cassettes at the MAT locus are transcribed constitutively. Transcription of cassettes at HML and HMR is prevented by trans-acting negative regulators.

Gene conversion at the var1 locus on yeast mitochondrial DNA

Alleles of the var1 locus on yeast mtDNA determine the apparent size of the mitochondrial translation product, var1 polypeptide. We have analyzed most of the different var1 alleles in our collection, which number at least 15, and have developed procedures and a genetic rationale for determining their origin and predicting their behavior in crosses. The var1 alleles are characterized by two genetically defined segments, designated a and b, which can move from one var1 allele to another by asymmetric gene conversion. We show that the a segment behaves as an entity in recombination; it is either present in or absent from different var1 alleles. The b segment usually, but not always, recombines as an entity; in some cases, only portions of the b segment recombine by gene conversion. Thus, the total number of electrophoretically resolvable var1 species we observe is explained by the assortment of a, b, and partial b segments. Each segment recombines at a characteristic frequency; however, one example is presented which shows that the recipient can modulate the frequency of gene conversion. Finally, we show that, like the 21S rDNA region (omega), there is polarity of gene conversion within var1.

Homothallic conversions of yeast mating-type genes occur by intrachromosomal recombination

The switching of yeast mating-type alleles involves a transposition of a copy of a sequence from HML or HMR to replace the sequences at MAT. Using diploid strains of yeast we have discovered that about 1% of the homothalic conversions of MAT alleles are accompanied by large intrachromosomal rearrangements. These rearrangements are highly specific fusions of part of MAT either with HMR (to produce a deficiency ring chromosome). We conclude that the mechanism of MAT conversions involves a highly specific pairing between the homologous sequences at MAT and the donor genes HML or HMR followed by a specialized gene conversion event, in which the original allele is replaced by a sequence copied from HMR or HML. At about a 1% frequency conversion of the MAT locus is accompanied by a reciprocal recombination event that results in an intrachromosomal deletion. This same preferential pairing is reflected in a high frequency (> 10(-3)) of site-specific mitotic recombination between MAT alleles on differenat chromosomes. A gene conversion model also allows us to explain the "illegal" transpositions of MAT alleles to HMR or HML that occur when normal excision of MAT is prevented.

Evidence for a physical interaction between the transposed and the substituted sequences during mating type gene transposition in yeast

Mating type switches in the yeast Saccharomyces cerevisiae occur by transposition of a replica of the "source" unexpressed loci HML and HMR to the mating type locus (MAT). The incoming information replaces previously expressed DNA, resulting in an interconversion of MAT alleles. A strain of genotype HML alpha/HML alpha MAT alpha/mata-missense HMR alpha/hmra-nonsense HO/ho generates cells with the genotype HML alpha/HML alpha MAT alpha/MAT a HMR alpha/hmra-nonsense HO/ho; that is, wild-type MATa+ recombinants are produced efficiently by a strain in which the incoming a information and the resident mata allele bear different mutations. Production of the wild-type MATa recombinants requires the homothallism (switching) function, and the incoming a information and the resident mata allele must bear different mutations. This result is consistent with the formation of a heteroduplex between the incoming and the outgoing DNA at MAT. Thus a process of unidirectional gene conversion as a mechanism for mating type gene transposition is favored. A molecular model based on a single-strand transfer is proposed. Results also favor the idea that the direction of switching is controlled by cell's mating phenotype rather than by the genetic content of MAT.

The trans action of HMRa in mating type interconversion

HML and HMR are the sites of cryptic mating type genes in the yeast Saccharomyces cerevisiae. In the presence of the HO gene, the information from HML or HMR (an a or alpha cassette) is transferred to the mating type locus (MAT). HML, HMR, and MAT are located on chromosome III, yet are widely separated. Similarly, in other yeasts, at least some of the genes involved in mating typing interconversion are linked to the mating type locus. We demonstrate here that a cassette donor (HMR) and the cassette target (MAT) need not be physically linked for successful mating type interconversion. In particular, we show that HMRa on one chromosome can donate an a cassette to the mating type locus on a homologous chromosome III.

Recombination of dispersed repeated DNA sequences in yeast

Yeast transformation can be used to insert new sequence arrangements into a variety of chromosomal locations by homologous recombination. These newly inserted sequences can recombine with similar sequences located on other chromosomes. In these events, information is duplicated without being lost at the site from which it is derived. Similar mechanisms might be utilized by cells to provide new functions during development or differentiation.

Functional equivalence and co-dominance of homothallic genes HM alpha/hm alpha and HMa/hma in Saccharomyces yeasts

The specificity of mating type in Saccharomyces yeasts is controlled by a pair of alleles, a and alpha, on chromosome III. They are mutually interconverted by the function of three kinds of homothallic genes, each consisting of a single pair of alleles, HO/ho, HM alpha/hma alpha and HMa/hma. For the a to alpha conversion, HO HM alpha, HMa, HO hm alpha HMa and HO hma alpha hma genotypes are effective; whereas the alpha to a conversion occurs in HO HM alpha HMa, HO HM alpha hma and HO hm alpha hma cells. To explain these observations, NAUMOV and TOLSTORUKOV (1973) and HARASHIMA, NOGI and OSHIMA (1974) suggested that hma and HM alpha are functionally equivalent and effective for the alpha to a conversion in combination with HO; whereas, hm alpha and HMa are functionally equivalent and effective for the a to alpha conversion with the function of HO. To test this idea and to compare it with two other possible mechanisms, some of the tetrad segregants from four kinds of a/a/alpha/alpha tetraploids homozygous for the HO allele and for one of the HM alpha/hm alpha and HMa/hma loci, while heterozygous for the other one with +/+/-/- configuration, were investigated with respect to their thallism by self-sporulation. Results indicated the functional equivalence of both the HM alpha and hma alleles and the hm alpha and HMa alleles in mating-type conversion, and the co-dominance of the alleles of each locus. From the findings and other data, we agree with the revision of the nomenclature of the HM alpha/hm alpha and HMa/hma genes to HMRa/HMR alpha and HML alpha/HMLa, respectively.

Defined oligomeric SV40 DNA: a sensitive probe of general recombination in somatic cells

We have constructed well defined oligomeric molecules of simian virus 40 (SV40) DNA as probes for investigating mechanisms by which cultured somatic cells recombine DNA. Restriction enzyme fragments from different temperature-sensitive mutants were joined in a head-to-tail orientation to create partial dimers 1.84 genome lengths in size. These molecules are too large to fit into a viral capsid. Therefore an assay that depends on production of progeny virus after infection with oligomeric DNA is a selective measure of precise conversion of oligomers to monomers. By constructing oligomers from appropriate combinations of temperature-sensitive DNAs, we have been able to study the conversion process in several defined regions of the SV40 genome. Our results indicate that conversion of oligomers to monomers occurs uniformly throughout the genome and is not dependent on normal viral DNA replication. These data indicate that conversion occurs primarily by general, homology-dependent recombination. At least one secondary mechanism that generates a low level of wild-type progeny was also detected. Studies with heteroduplex molecules indicate that repair of mismatched bases may be the secondary mechanism.

Structure and organization of transposable mating type cassettes in Saccharomyces yeasts

Cell type in Saccharomyces yeasts is regulated by two transposable blocks of DNA, the a and alpha cassettes. There are three loci where either cassette can exist. At the HML and HMR loci the cassettes are not expressed. The cassette at the MAT locus is expressed and controls the cell type. Changes of cell type involve transposition-substitution of cassettes from HML or HMR into MAT. We recently reported the molecular cloning of the alpha cassette at the HML locus, HML alpha, and showed that it contained sequences homologous to HMR and MAT. Using HML alpha as a hybridization probe, we have isolated HMLa, HMR alpha, HMRa, MAT alpha, and MATa. Heteroduplex analysis and restriction endonuclease mapping studies indicate that the a and alpha cassettes differ by a substitution corresponding to about 750 base pairs in alpha and about 600 base pairs in a. The HML, HMR, and MAT loci have regions of homology flanking the position of the a versus alpha substitution. We have used specific chromosome rearrangements fusing MAT and HML and MAT with HMR to orient the cloned sequences on the genetic map and have found that all three genes have the same left-to-right polarity on the chromosome.

Mutations preventing transpositions of yeast mating type alleles

Homothallic strains of Saccharomyces cerevisiae can switch from one mating type to the other as often as every cell division. The conversion of mating type alleles (from MATa to MATalpha or vice versa) depends on other, unexpressed copies of a or alpha information that can be transposed to MAT. Previously, "inconvertible" mutations within MATalpha and MATa have been described that block the excision of the MAT allele. In this paper we describe two cis-acting mutations that also impair mating type switching and lie very near, but outside, the MAT locus. Both "stuck" mutations, stk1 and stk2, diminish the efficiency of converting MATa to MATalpha to less than 10% of normal. The stk1 mutation also slightly reduces conversion of MATalpha to MATa, whereas stk2 has no discernible effect. Unlike the inconvertible MATalpha-inc and MATa-inc mutations within MAT, the stk mutations are not replaced by wild-type sequences after the "stuck" cells occasionally switch to the opposite mating type. Because these mutations are not "healed" by mating type conversions, they must lie in sequences outside of the transposable mating type information. These results indicate that the efficient replacement of MAT alleles depends on sequences both within and adjacent to the MAT locus. Among subclones of homothallic stk MATa strains, approximately 2% show "illegal" transpositions of mating type genes. In these colonies the silent copy of alpha information at the HMLalpha locus has been converted to a, without any change of MATa or the silent a copy at HMRa. Such conversions of the unexpressed library genes are not found in wild-type homothallic strains that can switch mating type efficiently, but they are found in MATa-inc and MATalpha-inc strains. It appears that all of the cis-acting mutations within or adjacent to mating type result in these unusual switches of mating type information at HML and HMR.