Minisatellite variants generated in yeast meiosis involve DNA removal during gene conversion

Variable Tandem Glycine-Rich Repeats Contribute to Cell Death-Inducing Activity of a Glycosylphosphatidylinositol-Anchored Cell Wall Protein That Is Associated with the Pathogenicity of Sclerotinia sclerotiorum

Glycosylphosphatidylinositol (GPI) anchoring of proteins is a conserved posttranslational modification in eukaryotes. GPI-anchored proteins are widely distributed in fungal plant pathogens, but the specific roles of the GPI-anchored proteins in the pathogenicity of Sclerotinia sclerotiorum, a devastating necrotrophic plant pathogen with a worldwide distribution, remain largely unknown. This research addresses SsGSR1, which encodes an S. sclerotiorum glycine- and serine-rich protein named SsGsr1 with an N-terminal secretory signal and a C-terminal GPI-anchor signal. SsGsr1 is located at the cell wall of hyphae, and deletion of SsGSR1 leads to abnormal cell wall architecture and impaired cell wall integrity of hyphae. The transcription levels of SsGSR1 were maximal in the initial stage of infection, and SsGSR1-deletion strains showed impaired virulence in multiple hosts, indicating that SsGSR1 is critical for the pathogenicity. Interestingly, SsGsr1 targeted the apoplast of host plants to induce cell death that relies on the glycine-rich 11-amino-acid repeats arranged in tandem. The homologs of SsGsr1 in Sclerotinia, Botrytis, and Monilinia species contain fewer repeat units and have lost their cell death activity. Moreover, allelic variants of SsGSR1 exist in field isolates of S. sclerotiorum from rapeseed, and one of the variants lacking one repeat unit results in a protein that exhibits loss of function relative to the cell death-inducing activity and the virulence of S. sclerotiorum. Taken together, our results demonstrate that a variation in tandem repeats provides the functional diversity of GPI-anchored cell wall protein that, in S. sclerotiorum and other necrotrophic pathogens, allows successful colonization of the host plants. IMPORTANCE Sclerotinia sclerotiorum is an economically important necrotrophic plant pathogen and mainly applies cell wall-degrading enzymes and oxalic acid to kill plant cells before colonization. In this research, we characterized a glycosylphosphatidylinositol (GPI)-anchored cell wall protein named SsGsr1, which is critical for the cell wall architecture and the pathogenicity of S. sclerotiorum. Additionally, SsGsr1 induces rapid cell death of host plants that is dependent on glycine-rich tandem repeats. Interestingly, the number of repeat units varies among homologs and alleles of SsGsr1, and such a variation creates alterations in the cell death-inducing activity and the role in pathogenicity. This work advances our understanding of the variation of tandem repeats in accelerating the evolution of a GPI-anchored cell wall protein associated with the pathogenicity of necrotrophic fungal pathogens and prepares the way toward a fuller understanding of the interaction between S. sclerotiorum and host plants.

Cell adaptation to aneuploidy by the environmental stress response dampens induction of the cytosolic unfolded-protein response

Aneuploid yeast cells are in a chronic state of proteotoxicity, yet do not constitutively induce the cytosolic unfolded protein response, or heat shock response (HSR) by heat shock factor 1 (Hsf1). Here, we demonstrate that an active environmental stress response (ESR), a hallmark of aneuploidy across different models, suppresses Hsf1 induction in models of single-chromosome gain. Furthermore, engineered activation of the ESR in the absence of stress was sufficient to suppress Hsf1 activation in euploid cells by subsequent heat shock while increasing thermotolerance and blocking formation of heat-induced protein aggregates. Suppression of the ESR in aneuploid cells resulted in longer cell doubling times and decreased viability in the presence of additional proteotoxicity. Last, we show that in euploids, Hsf1 induction by heat shock is curbed by the ESR. Strikingly, we found a similar relationship between the ESR and the HSR using an inducible model of aneuploidy. Our work explains a long-standing paradox in the field and provides new insights into conserved mechanisms of proteostasis with potential relevance to cancers associated with aneuploidy.

The intronic minisatellite OsMin1 within a serine protease gene in the Chinese caterpillar fungus Ophiocordyceps sinensis

Repetitive DNA sequences make up a significant portion of all genomes and may occur in intergenic, regulatory, coding, or even intronic regions. Partial sequences of a serine protease gene csp1 was previously used as a population genetic marker of the Chinese caterpillar fungus Ophiocordyceps sinensis, but its first intron region was excluded due to ambiguous alignment. Here in this study, we report the presence of a minisatellite OsMin1 within this intron, where a 20(19)-bp repeat motif is duplicated two to six times in different isolates. Fourteen intron alleles and 13 OsMin1 alleles were identified among 125 O. sinensis samples distributed broadly on the Tibetan Plateau. Two OsMin1 alleles were prevalent, corresponding to either two or five repeats of the core sequence motif. OsMin1 appears to be a single locus marker in the O. sinensis genome, but its origin is undetermined. Abundant recombination signals were detected between upstream and downstream flanking regions of OsMin1, suggesting that OsMin1 mutate by unequal crossing over. Geographic distribution, fungal phylogeny, and host insect phylogeny all significantly affected intron distribution patterns but with the greatest influence noted for fungal genotypes and the least for geography. As far as we know, OsMin1 is the first minisatellite found in O. sinensis and the second found in fungal introns. OsMin1 may be useful in designing an efficient protocol to discriminate authentic O. sinensis from counterfeits.

Heterozygosity and mutation rate: evidence for an interaction and its implications: the potential for meiotic gene conversions to influence both mutation rate and distribution

If natural selection chose where new mutations occur it might well favour placing them near existing polymorphisms, thereby avoiding disruption of areas that work while adding novelty to regions where variation is tolerated or even beneficial. Such a system could operate if heterozygous sites are recognised and 'repaired' during the initial stages of crossing over. Such repairs involve an extra round of DNA replication, providing an opportunity for further mutations, thereby raising the local mutation rate. If so, the changes in heterozygosity that occur when populations grow or shrink could feed back to modulate both the rate and the distribution of mutations. Here, I review evidence from isozymes, microsatellites and single nucleotide polymorphisms that this potential is realised in real populations. I then consider the likely implications, focusing particularly on how these processes might affect microsatellites, concluding that heterozygosity does impact on the rate and distribution of mutations.

Comparative genomics and molecular dynamics of DNA repeats in eukaryotes

Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

Mechanisms of human minisatellite mutation in yeast

Minisatellites are tandem repeat loci, with repeat units ranging in size from 5 bp to 100 bp. The total lengths of repeat arrays vary from about 0.5 kb to 30 kb, and excessive variability in allele length at human minisatellite loci is the result of germline-specific complex recombination events generating new length alleles. Minisatellite alleles also mutate to new lengths in somatic cells, but this occurs at a much lower rate than in the germline. Since recombination is involved in minisatellite mutation, the yeast Saccharomyces cerevisiae is a suitable model organism that has been employed to further dissect the molecular basis of mutation events at human minisatellites. These studies have shown that the mutational behaviour of a minisatellite in meiosis is not determined by the intrinsic properties of the repeat array, but are highly dependent on the position of the minisatellite in the genome. The processes for minisatellite mutation in yeast and humans are identical in the sense that mutation is indeed driven by meiotic recombination, but differ with regard to the types of structural changes that are generated by the recombination events. Tetrad analyses showed that inter-allelic transfers of repeats occur by conversion and not crossing over, and that several chromatids can be involved in successive recombination events in one meiosis, resulting in mutant alleles in several spores. It has been demonstrated that the genes SPO11 and RAD50, involved in the initiation of recombination events, are required for human minisatellite mutation in yeast meiosis. Intrinsic properties of the repeat array appear to determine the stability of human minisatellites in yeast mitosis, since mitotic mutation rates in yeast are highly variable between minisatellites. The repair genes RAD27 and DNA2 stabilise human minisatellites in yeast mitosis, while RAD5 has no effect on mitotic stability. MSH2 depresses human minisatellite frequency in meiotic cells of yeast.

Evidence that Protein Length Expansion and Contraction Is Partly Due to Mutational Events in Premeiotic Cells

Studies on the rate of evolution of proteins typically concentrate on rates of change of orthologous amino acids rather than on changes in size (i.e., generation of nonorthologous domains). Recent work has focused attention on Ser/Thr-rich regions in yeast as these tend to undergo size changes rapidly, with size polymorphisms commonly being found, especially in proteins with cell-surface localization. The underlying mechanism generating the indels is presently unclear though, due to a lack of correlation with the location of meiotic double-strand breaks, it has, by exclusion, been conjectured to be replication slippage. Here we provide new evidence to support this possibility. Notably, we show that Ser/Thr-rich repeat regions are more generally associated with the location of Mre11p in premeiotic cells. This is to be expected if the repeats were produced by mutational events in mitotic cells possibly through replication slippage.

Patterns of polymorphism and divergence in stress-related yeast proteins

Yeast genomes contain variable number tandem repeats (VNTRs) within coding regions of DNA. A significant number of these genes are involved in cell rescue, defence and virulence and are regulated by genetic elements associated with stress. Alleles that encode variable length, single amino acid tracts, are mainly associated with transcription and proteins localized within the nucleus. Alleles that encode proteins containing oligopeptide repeats or minisatellites are over-represented in cell wall and extracellular space locations. Functional analysis of the latter group reveals that these proteins are involved in biogenesis of cellular components and in interaction with the cellular environment, especially in relation to stress resistance, heat shock response, temperature perception and adhesion. A significantly high number of these proteins have regions rich in threonine and/or serine that contain repeated sequences, variable in length within yeast species. DNA sequences encoding serine- and/or threonine-rich regions give rise to polymorphic alleles and therefore may confer a selective advantage to cells. We propose that these regions are the focus of mutational and recombination events that, when coupled with directed selection, may contribute to genetic variation within stress-related genes.

Minisatellites in Saccharomyces cerevisiae genes encoding cell wall proteins: a new way towards wine strain characterisation

With the aim of developing new tools for the characterisation of wine yeasts, by means of databases available on-line we scanned the genome of Saccharomyces cerevisiae in search of potentially polymorphic targets. As we have previously observed for SED1, we found that other genes coding for cell wall proteins contain minisatellite-like sequences. A polymerase chain reaction (PCR) survey of SED1 and three of these others, namely AGA1, DAN4 and HSP150, in a population of wild S. cerevisiae demonstrated that these genes are highly polymorphic in length and represent a sink of unexplored genetic variability. The primer pairs designed on the gene open reading frames yield stable and repeatable amplification profiles that show a level of resolution that allows the clear discriminate between different strains. These can therefore be utilised for PCR-based typing of S. cerevisiae.

SED1 gene length and sequence polymorphisms in feral strains of Saccharomyces cerevisiae

The SED1 gene (YDR077W), coding for the major cell wall glycoprotein of Saccharomyces cerevisiae stationary-phase cells, contains two blocks of tandem repeat units located within two distinct regions of the nucleotide sequence. A PCR survey of the SED1 open reading frames (ORFs) of 186 previously uncharacterized grape must isolates of S. cerevisiae yielded 13 PCR profiles arising from different combinations of seven SED1 length variants in individuals homozygous or heterozygous for the gene. Comparison of the nucleotide sequences of a group of representatives of each of the seven length variants with those of S288C and the type strain, CBS1171, unequivocally identified them as SED1 alleles and provided evidence for the presence of two minisatellite-like sequences, variable in length, within the ORF of an S. cerevisiae gene. The segregation analyses of the SED1 length variants and other genetic markers in 13 isolates representative of each PCR profile suggested that molecular mechanisms involved in minisatellite expansion and contraction may be responsible for SED1 heterozygosities within a population of homothallic must isolates of S. cerevisiae.

The influence of sequence divergence between alleles of the human MS205 minisatellite incorporated into the yeast genome on length-mutation rates and lethal recombination events during meiosis

Certain minisatellites exhibit hypervariability with respect to the number of repeat units and, thus, allele length. Such polymorphism is generated by germline-specific recombinational events that occur at high frequencies and lead to the gain or loss of repeat units. In order to elucidate the molecular details of mutagenesis in minisatellites, we have integrated human minisatellites into the yeast genome in the vicinity of a hotspot for meiotic double-strand breaks (DSBs). Here, we describe the results of tetrad analyses of mutations in the human MS205 minisatellite in yeast strains heterozygous for alleles composed of 51 and 31 repeat units, as well as in a strain homozygous for the same 51 repeat unit allele. The length-mutation rate was twice as high in the heterozygous strain as in the homozygous strain, suggesting that sequence divergence between alleles enhances the generation of length mutations. In the case of heterozygotes, the frequency of length mutants resulting from inter-allelic exchange was significantly higher in tetrads with three viable spores than in tetrads with four viable spores, indicating that there is a higher probability for spore mortality in tetrads originating from meioses during which inter-allelic exchange of repeat units occurs. In an attempt to explain these findings, we propose a model for minisatellite mutation involving recombination, in which sequence divergence between alleles results in a heteroduplex containing numerous mismatches. We suggest that convergent mismatch-repair tracts in this heteroduplex give rise to a DSB that may be repaired by an additional round of recombination resulting in mutation of a third allele, or be lethal if such recombination fails. It appears probable that the formation of such additional mutants is the major explanation for the difference in meiotic length-mutation rates between the heterozygous and homozygous yeast strains, and that this phenomenon contributes to high germline length-mutation frequencies at minisatellites in humans.

Allelic variation of a Beauveria bassiana (Ascomycota: Hypocreales) minisatellite is independent of host range and geographic origin

The minisatellite locus, BbMin1, was isolated from a partial Beauveria bassiana genomic library that consisted of poly(GA) flanked inserts. Polymerase chain reaction (PCR) of the BbMin1 repeat demonstrated allele size variation among 95 B. bassiana isolates. Amplification was also observed from single isolates of Beauveria amorpha, Beauveria brongniartii, and Beauveria caledonica. Eight alleles were identified at the haploid locus, where repeat number fluctuated between one and fourteen. AMOVA and theta (Fst) indicated that fixation of repeat number has not occurred within pathogenic ecotypes or geographically isolated samples of B. bassiana. Selective neutrality of allele size, the rate of BbMin1 mutation, and the age of the species may contribute to host and geographic independence of the marker. Presence of alleles with a large number of repeat units may be attributed to the rare occurrence of somatic recombination or DNA replication error. The molecular genetic marker was useful for the identification of genetic types of B. bassiana and related species.

RAD1 controls the meiotic expansion of the human HRAS1 minisatellite in Saccharomyces cerevisiae

Minisatellite DNA is repetitive DNA with a repeat unit length from 15 to 100 bp. While stable during mitosis, it destabilizes during meiosis, altering both in length and in sequence composition. The basis for this instability is unknown. To investigate the factors controlling minisatellite stability, a minisatellite sequence 3' of the human HRAS1 gene was introduced into the Saccharomyces cerevisiae genome, replacing the wild-type HIS4 promoter. The minisatellite tract exhibited the same phenotypes in yeast that it exhibited in mammalian systems. The insertion stimulated transcription of the HIS4 gene; mRNA production was detected at levels above those seen with the wild-type promoter. The insertion stimulated meiotic recombination and created a hot spot for initiation of double-strand breaks during meiosis in the regions immediately flanking the repetitive DNA. The tract length altered at a high frequency during meiosis, and both expansions and contractions in length were detected. Tract expansion, but not contraction, was controlled by the product of the RAD1 gene. RAD1 is the first gene identified that controls specifically the expansion of minisatellite tracts. A model for tract length alteration based on these results is presented.

Expansions and contractions in 36-bp minisatellites by gene conversion in yeast

The instability of simple tandem repeats, such as human minisatellite loci, has been suggested to arise by gene conversions. In Saccharomyces cerevisiae, a double-strand break (DSB) was created by the HO endonuclease so that DNA polymerases associated with gap repair must traverse an artificial minisatellite of perfect 36-bp repeats or a yeast Y' minisatellite containing diverged 36-bp repeats. Gene conversions are frequently accompanied by changes in repeat number when the template contains perfect repeats. When the ends of the DSB have nonhomologous tails of 47 and 70 nucleotides that must be removed before repair DNA synthesis can begin, 16% of gene conversions had rearrangements, most of which were contractions, almost always in the recipient locus. When efficient removal of nonhomologous tails was prevented in rad1 and msh2 strains, repair was reduced 10-fold, but among survivors there was a 10-fold reduction in contractions. Half the remaining events were expansions. A similar decrease in the contraction rate was observed when the template was modified so that DSB ends were homologous to the template; and here, too, half of the remaining rearrangements were expansions. In this case, efficient repair does not require RAD1 and MSH2, consistent with our previous observations. In addition, without nonhomologous DSB ends, msh2 and rad1 mutations did not affect the frequency or the distribution of rearrangements. We conclude that the presence of nonhomologous ends alters the mechanism of DSB repair, likely through early recruitment of repair proteins including Msh2p and Rad1p, resulting in more frequent contractions of repeated sequences.