A family of laboratory strains of Saccharomyces cerevisiae carry rearrangements involving chromosomes I and III

Fe-S coordination defects in the replicative DNA polymerase delta cause deleterious DNA replication in vivo and subsequent DNA damage in the yeast Saccharomyces cerevisiae

B-type eukaryotic polymerases contain a [4Fe-4S] cluster in their C-terminus domain, whose role is not fully understood yet. Among them, DNA polymerase delta (Polδ) plays an essential role in chromosomal DNA replication, mostly during lagging strand synthesis. Previous in vitro work suggested that the Fe-S cluster in Polδ is required for efficient binding of the Pol31 subunit, ensuring stability of the Polδ complex. Here we analyzed the in vivo consequences resulting from an impaired coordination of the Fe-S cluster in Polδ. We show that a single substitution of the very last cysteine coordinating the cluster by a serine is responsible for the generation of massive DNA damage during S phase, leading to checkpoint activation, requirement of homologous recombination for repair, and ultimately to cell death when the repair capacities of the cells are overwhelmed. These data indicate that impaired Fe-S cluster coordination in Polδ is responsible for aberrant replication. More generally, Fe-S in Polδ may be compromised by various stress including anti-cancer drugs. Possible in vivo Polδ Fe-S cluster oxidation and collapse may thus occur, and we speculate this could contribute to induced genomic instability and cell death, comparable to that observed in pol3-13 cells.

Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes

The study of mitogenomes allows the unraveling of some paths of yeast evolution that are often not exposed when analyzing the nuclear genome. Although both nuclear and mitochondrial genomes are known to determine phenotypic diversity and fitness, no concordance has yet established between the two, mainly regarding strains' technological uses and/or geographical distribution. In the current work, we proposed a new method to align and analyze yeast mitogenomes, overcoming current difficulties that make it impossible to obtain comparable mitogenomes for a large number of isolates. To this end, 12,016 mitogenomes were considered, and we developed a novel approach consisting of the design of a reference sequence intended to be comparable between all mitogenomes. Subsequently, the population structure of 6646 Saccharomyces cerevisiae mitogenomes was assessed. Results revealed the existence of particular clusters associated with the technological use of the strains, in particular regarding clinical isolates, laboratory strains, and yeasts used for wine-associated activities. As far as we know, this is the first time that a positive concordance between nuclear and mitogenomes has been reported for S. cerevisiae, in terms of strains' technological applications. The results obtained highlighted the importance of including the mtDNA genome in evolutionary analysis, in order to clarify the origin and history of yeast species.

Integration of new alternative reference strain genome sequences into the Saccharomyces genome database

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences.

Database URL:www.yeastgenome.org

Chromosomal rearrangements as a major mechanism in the onset of reproductive isolation in Saccharomyces cerevisiae

Understanding the molecular basis of how reproductive isolation evolves between individuals from the same species offers valuable insight into patterns of genetic differentiation as well as the onset of speciation [1, 2]. The yeast Saccharomyces cerevisiae constitutes an ideal model partly due to its vast ecological range, high level of genetic diversity [3-6], and laboratory-amendable sexual reproduction. Between S. cerevisiae and its sibling species in the Saccharomyces sensu stricto complex, reproductive isolation acts postzygotically and could be attributed to chromosomal rearrangements [7], cytonuclear incompatibility [8, 9], and antirecombination [10, 11], although the implication of these mechanisms at the incipient stage of speciation remains unclear due to further divergence in the nascent species. Recently, several studies assessed the onset of intraspecific reproductive isolation in S. cerevisiae by evaluating the effect of the mismatch repair system [12-14] or by fostering incipient speciation using the same initial genetic background [15-18]. Nevertheless, the overall genetic diversity within this species was largely overlooked, and no systematic evaluation has been performed. Here, we carried out the first species-wide survey for postzygotic reproductive isolation in S. cerevisiae. We crossed 60 natural isolates sampled from diverse niches with the reference strain S288c and identified 16 cases of reproductive isolation with reduced offspring viabilities ranging from 44% to 86%. Using different mapping strategies, we identified reciprocal translocations in a large fraction of all isolates surveyed, indicating that large-scale chromosomal rearrangements might play a major role in the onset of reproductive isolation in this species.

Dynamic large-scale chromosomal rearrangements fuel rapid adaptation in yeast populations

Large-scale genome rearrangements have been observed in cells adapting to various selective conditions during laboratory evolution experiments. However, it remains unclear whether these types of mutations can be stably maintained in populations and how they impact the evolutionary trajectories. Here we show that chromosomal rearrangements contribute to extremely high copper tolerance in a set of natural yeast strains isolated from Evolution Canyon (EC), Israel. The chromosomal rearrangements in EC strains result in segmental duplications in chromosomes 7 and 8, which increase the copy number of genes involved in copper regulation, including the crucial transcriptional activator CUP2 and the metallothionein CUP1. The copy number of CUP2 is correlated with the level of copper tolerance, indicating that increasing dosages of a single transcriptional activator by chromosomal rearrangements has a profound effect on a regulatory pathway. By gene expression analysis and functional assays, we identified three previously unknown downstream targets of CUP2: PHO84, SCM4, and CIN2, all of which contributed to copper tolerance in EC strains. Finally, we conducted an evolution experiment to examine how cells maintained these changes in a fluctuating environment. Interestingly, the rearranged chromosomes were reverted back to the wild-type configuration at a high frequency and the recovered chromosome became fixed in less selective conditions. Our results suggest that transposon-mediated chromosomal rearrangements can be highly dynamic and can serve as a reversible mechanism during early stages of adaptive evolution.

Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae

High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.

Balanced structural polymorphisms are differences in the relative arrangement of genomic features within species that do not affect DNA copy number. Little is known about their prevalence or importance because they are difficult to observe. Here, we present a novel methodology for systematically identifying such polymorphisms based on the idea that single-copy DNA that occupies different genomic locations in two parents will segregate independently during meiosis and will therefore reveal itself as a copy number difference among a fraction of progeny. Comparative hybridization reveals multiple balanced structural polymorphisms that involve changes to gene order in two strains of yeast; the results are independently validated using paired-end whole genome shotgun sequencing. The longest transposed segment we identify comprises 13.5 kb near the telomere of chromosome XV in the S288C reference strain and contains several annotated genes. We map the location of this polymorphism in the non-reference strain using genome-wide genotypic data, which also reveals an appreciable frequency of ectopic recombination among transposed segment pairs. The breakpoints of the remaining polymorphisms are localized by the paired-end sequence data. Our work provides proof-of-principle for a very general approach to systematically identify all balanced genomic polymorphisms in two different genotypes and is a starting point for understanding the frequency, evolutionary origins, and functional consequences of this seldom-studied class of genomic structural variation in eukaryotes.

Saccharomyces cerevisiae as a model system to define the chromosomal instability phenotype

Translocations, deletions, and chromosome fusions are frequent events seen in cancers with genome instability. Here we analyzed 358 genome rearrangements generated in Saccharomyces cerevisiae selected by the loss of the nonessential terminal segment of chromosome V. The rearrangements appeared to be generated by both nonhomologous end joining and homologous recombination and targeted all chromosomes. Fifteen percent of the rearrangements occurred independently more than once. High levels of specific classes of rearrangements were isolated from strains with specific mutations: translocations to Ty elements were increased in telomerase-defective mutants, potential dicentric translocations and dicentric isochromosomes were associated with cell cycle checkpoint defects, chromosome fusions were frequent in strains with both telomerase and cell cycle checkpoint defects, and translocations to homolog genes were seen in strains with defects allowing homoeologous recombination. An analysis of human cancer-associated rearrangements revealed parallels to the effects that strain genotypes have on classes of rearrangement in S. cerevisiae.

Reciprocal translocations in Saccharomyces cerevisiae formed by nonhomologous end joining

Reciprocal translocations are common in cancer cells, but their creation is poorly understood. We have developed an assay system in Saccharomyces cerevisiae to study reciprocal translocation formation in the absence of homology. We induce two specific double-strand breaks (DSBs) simultaneously on separate chromosomes with HO endonuclease and analyze the subsequent chromosomal rearrangements among surviving cells. Under these conditions, reciprocal translocations via nonhomologous end joining (NHEJ) occur at frequencies of approximately 2-7 x 10(-5)/cell exposed to the DSBs. Yku80p is a component of the cell's NHEJ machinery. In its absence, reciprocal translocations still occur, but the junctions are associated with deletions and extended overlapping sequences. After induction of a single DSB, translocations and inversions are recovered in wild-type and rad52 strains. In these rearrangements, a nonrandom assortment of sites have fused to the DSB, and their junctions show typical signs of NHEJ. The sites tend to be between open reading frames or within Ty1 LTRs. In some cases the translocation partner is formed by a break at a cryptic HO recognition site. Our results demonstrate that NHEJ-mediated reciprocal translocations can form in S. cerevisiae as a consequence of DSB repair.

Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays

To analyse the reliability and accuracy of genotype analysis with high-density oligonucleotide microarrays, this method and other experimental approaches were used to analyse genomic DNA of two popular Saccharomyces cerevisiae laboratory strains. S288C was used for systematic sequencing of 'the' S. cerevisiae genome; CEN.PK113-7D is a popular strain for physiological studies and functional genomics. Random amplified polymorphic DNA, electrophoretic karyotyping and microarray analysis all indicated a high level of sequence similarity between the two strains. In the microarray analysis, as few as 288 (4.5%) of the ca. 6300 represented yeast genes were identified that yielded significantly different hybridisation intensities between the two strains. These could be classified as amplified, absent, or with sequence polymorphism in CEN.PK113-7D compared to S288C. A detailed analysis focused on the subset of 25 genes called absent in CEN.PK113-7D. Among these absent genes, 17 were clustered together on five chromosomes, mainly in subtelomeric regions. Thorough analysis of these regions by polymerase chain reaction (PCR) and restriction fragment length polymorphism confirmed the absence of these genes in CEN.PK113-7D. Surprisingly, three of these regions were not smaller in CEN.PK113-7D chromosomes, indicating that they may harbour unidentified and potentially new sequences. In addition, eight genes called absent by the microarrays were scattered over the chromosomes. Using diagnostic PCR most of these genes were actually found to be present in CEN.PK113-7D, but after sequencing were found to differ significantly at the DNA level from S288C, explaining the poor hybridisation to the arrays. Our results indicate that DNA microarrays are a powerful tool for determining genotypic similarity between different yeast strains. However, to obtain meaningful information at the individual gene level, this method should be backed up by additional techniques.

Correlations among measures of phenotypic and genetic variation within an oligotrophic asexual yeast, Candida sonorensis, collected from Opuntia

Many descriptions of yeast species are based on a limited number of strains collected at one time from a single locale. Often, little is known of phenotypic or genotypic variation and covariation within species. We compare 36 strains of an asexual cactophilic yeast, Candida sonorensis, collected from Opuntia cacti. Comparisons were based on geographical distances between collection locales, responses to physiological assimilation and stress tests, random amplified polymorphic DNA (RAPD) profiles, partial Lage Subunit (LSU) rDNA sequences, relative DNA-DNA hybridization values, and electrokaryotypes. There was significant variation among strains in all types of data collected. Comparisons among the different data types found significant positive associations between RAPD profiles, geographical distances, physiologies, reassociation values, and electrokaryotypes. No significant associations were found between rDNA sequences and any other type of variation measured. Based on RAPD, reassociation, electrokaryotype, and physiological data, the 36 strains could be divided into two groups: those collected in West Texas (nine strains) and all others. RAPD data indicated that 10 (of 12) Australian strains also formed a distinct clade. The taxonomic and phylogenetic status of these clades is discussed. Evidence that new genotypes can sweep through large geographic areas is also discussed.

Reciprocal Translocations in Saccharomyces cerevisiae Formed by Nonhomologous End Joining

Reciprocal translocations are common in cancer cells, but their creation is poorly understood. We have developed an assay system in Saccharomyces cerevisiae to study reciprocal translocation formation in the absence of homology. We induce two specific double-strand breaks (DSBs) simultaneously on separate chromosomes with HO endonuclease and analyze the subsequent chromosomal rearrangements among surviving cells. Under these conditions, reciprocal translocations via nonhomologous end joining (NHEJ) occur at frequencies of ∼2-7 × 10-5/cell exposed to the DSBs. Yku80p is a component of the cell’s NHEJ machinery. In its absence, reciprocal translocations still occur, but the junctions are associated with deletions and extended overlapping sequences. After induction of a single DSB, translocations and inversions are recovered in wild-type and rad52 strains. In these rearrangements, a nonrandom assortment of sites have fused to the DSB, and their junctions show typical signs of NHEJ. The sites tend to be between open reading frames or within Ty1 LTRs. In some cases the translocation partner is formed by a break at a cryptic HO recognition site. Our results demonstrate that NHEJ-mediated reciprocal translocations can form in S. cerevisiae as a consequence of DSB repair.

Chromosomes of the budding yeast Saccharomyces cerevisiae

The mitotic chromosomes of the baker's yeast, Saccharomyces cerevisiae, cannot be visualized by standard cytological methods. Only the study of meiotic bivalents and the synaptonemal complex and the visualization of chromosome-sized DNA molecules on pulsed-field gels have provided some insight into chromosome structure and behavior. More recently, advanced techniques such as in situ hybridization, the illumination of chromosomal loci by GFP-tagged DNA-binding proteins, and immunostaining of chromosomal proteins have promoted our knowledge about yeast chromosomes. These novel cytological approaches in combination with the yeast's advanced biochemistry and genetics have produced a great wealth of information on the interplay between molecular and cytological processes and have strengthened the role of yeast as a leading cell biological model organism. Recent cytological studies have revealed much about the chromosomal organization in interphase nuclei and have contributed significantly to our current understanding of chromosome condensation, sister chromatid cohesion, and centromere orientation in mitosis. Moreover, important details about the biochemistry and ultrastructure of meiotic pairing and recombination have been revealed by combined cytological and molecular approaches. This article covers several aspects of yeast chromosome structure, including their organization within interphase nuclei and their behavior during mitosis and meiosis.

Ku-dependent and Ku-independent end-joining pathways lead to chromosomal rearrangements during double-strand break repair in Saccharomyces cerevisiae

Chromosomal double-strand breaks (DSBs) can be repaired by either homology-dependent or homology-independent pathways. Nonhomologous repair mechanisms have been relatively less well studied, despite their potential importance in generating chromosomal rearrangements. We have developed a Saccharomyces cerevisiae-based assay to identify and characterize homology-independent chromosomal rearrangements associated with repair of a unique DSB generated within an engineered URA3 gene. Approximately 1% of successfully repaired cells have accompanying chromosomal rearrangements consisting of large insertions, deletions, aberrant gene conversions, or other more complex changes. We have analyzed rearrangements in isogenic wild-type, rad52, yku80, and rad52 yku80 strains, to determine the types of events that occur in the presence or absence of these key repair proteins. Deletions were found in all strain backgrounds, but insertions were dependent upon the presence of Yku80p. A rare RAD52- and YKU80-independent form of deletion was present in all strains. These events were characterized by long one-sided deletions (up to 13 kb) and extensive imperfect overlapping sequences (7-22 bp) at the junctions. Our results demonstrate that the frequency and types of repair events depend on the specific genetic context. This approach can be applied to a number of problems associated with chromosome stability.

Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strains

Wine yeast strains show a high level of chromosome length polymorphism. This polymorphism is mainly generated by illegitimate recombination mediated by Ty transposons or subtelomeric repeated sequences. We have found, however, that the SSU1-R allele, which confers sulfite resistance to yeast cells, is the product of a reciprocal translocation between chromosomes VIII and XVI due to unequal crossing-over mediated by microhomology between very short sequences on the 5' upstream regions of the SSU1 and ECM34 genes. We also show that this translocation is only present in wine yeast strains, suggesting that the use for millennia of sulfite as a preservative in wine production could have favored its selection. This is the first time that a gross chromosomal rearrangement is shown to be involved in the adaptive evolution of Saccharomyces cerevisiae.

Ylli, a non-LTR retrotransposon L1 family in the dimorphic yeast Yarrowia lipolytica

During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side of this zone of homology allowed the definition of an element over 6 kb long. The conceptual translation of this sequence revealed two open reading frames (ORFs) that displayed several characteristics of non-LTR retrotransposons: a Cys-rich motif in the ORF1, an N-terminal endonuclease, a central RT, and a C-terminal zinc finger domain in the ORF2. We called this element Ylli (for Y. lipolytica LINE). A total of 19 distinct repeats carrying the 3' untranslated region (UTR) and all ending with a poly-A tail were detected. Most of them were very short, 17 being 134 bp long or less. The number of copies of Ylli was estimated to be around 100 if these short repeats are 5' truncations. No 5' UTR was clearly identified, indicating that entire and therefore active elements might be very rare in the Y. lipolytica strain tested. Ylli does not seem to have any insertion specificity. Phylogenetic analysis of the RT domain unambiguously placed Ylli within the L1 clade. It forms a monophyletic group with the Zorro non-LTR retrotransposons discovered in another dimorphic yeast Candida albicans. BLAST comparisons showed that ORF2 of Ylli is closely related to that of the slime mold Dictyostelium discoideum L1 family, TRE.

Potential role of transposable elements in the rapid reorganization of the Fusarium oxysporum genome

The activity of several families of transposable elements (TEs) in the genome of Fusarium oxysporum represents a potential source of karyotypic instability. We investigated transposon-mediated chromosome rearrangements by analyzing the karyotypes of a set of strains in which transposition events had occurred. We uncovered exceptional electrophoretic karyotype (EK) variability, in both number and size of chromosomal bands. We showed that EK differences result from chromosomal translocations, large deletions, and even more complex rearrangements. We also revealed many duplicated chromosomal regions. By following transposition of two elements and analyzing the distribution of different families of TEs on whole chromosomes, we find (i) no evidence of chromosomal breakages induced by transposition, (ii) a clustering of TEs in some regions, and (iii) a correlation between the high level of chromosomal polymorphism and the concentration of TEs. These results suggest that chromosome length polymorphisms likely result from ectopic recombination between TEs that can serve as substrates for these changes.

Mitotic recombination and genetic changes in Saccharomyces cerevisiae during wine fermentation

Natural strains of Saccharomyces cerevisiae are prototrophic homothallic yeasts that sporulate poorly, are often heterozygous, and may be aneuploid. This genomic constitution may confer selective advantages in some environments. Different mechanisms of recombination, such as meiosis or mitotic rearrangement of chromosomes, have been proposed for wine strains. We studied the stability of the URA3 locus of a URA3/ura3 wine yeast in consecutive grape must fermentations. ura3/ura3 homozygotes were detected at a rate of 1 x 10(-5) to 3 x 10(-5) per generation, and mitotic rearrangements for chromosomes VIII and XII appeared after 30 mitotic divisions. We used the karyotype as a meiotic marker and determined that sporulation was not involved in this process. Thus, we propose a hypothesis for the genome changes in wine yeasts during vinification. This putative mechanism involves mitotic recombination between homologous sequences and does not necessarily imply meiosis.

Molecular typing demonstrates homogeneity of Saccharomyces uvarum strains and reveals the existence of hybrids between S. uvarum and S. cerevisiae, including the S. bayanus type strain CBS 380

PCR/RFLP of the NTS2 sequence of rDNA was shown to be suitable for differentiating Saccharomyces sensu stricto species. We previously showed that, within the presently accepted S. bayanus taxon, strains formerly classified as S. uvarum represented a distinct subgroup (Nguyen and Gaillardin, 1997). In this study, we reidentified 43 more strains isolated recently from wine, cider and various fermentation habitats, and confirmed by karyotyping, hybridization and mtDNA analysis the homogeneity of strains from the S. uvarum subspecies. Molecular typing of nuclear and mitochondrial genomes of strains preserved in collections, and often originating from beer like S. pastorianusNT, revealed the existence of hybrids between S. uvarum and S. cerevisiae. Surprisingly, S. bayanusT CBS380 appeared itself to be a hybrid between S. uvarum and S. cerevisiae. This strain has a mitochondrial genome identical to that of S. uvarum, and a very similar karyotype with 13 isomorphic chromosomes, six of which at least hybridize strongly with S. uvarum chromosomes or with a S. uvarum specific sequence. However, four of the chromosome bands of S. bayanusT bear Y' sequences indistinguishable from those of S. cerevisiae, a feature that is not observed among presently isolated S. uvarum strains. Because of the hybrid nature of S. bayanus(T) and of the scarcity of similar hybrids among present days isolates, we propose to reinstate S. uvarum as a proper species among the Saccharomyces sensu stricto complex.

Inter- and intraspecific chromosome pattern variation in the yeast genus Kluyveromyces

The analysis of the electrophoretic chromosome patterns of the species of the genus Kluyveromyces, reveals a high polymorphism in size, number and intensity of bands. Different sets of electrophoresis running conditions were used to establish species-specific patterns and also to detect intraspecific variation. According to their karyotypes, the species of this genus can be divided into two major groups. The first group includes the species K. africanus, K. bacillisporus, K. delphensis, K. lodderae, K. phaffi, K. polysporus and K. yarrowii, composing the so-called 'Saccharomyces cerevisiae-like' group, because their karyotypes resemble that of the species S. cerevisiae. The second group comprises the species K. aestuarii, K. blattae, K. dobzhanskii, K. lactis, K. marxianus, K. thermotolerans, K. waltii and K. wickerhamii, whose chromosomal patterns exhibit common characteristics very different to those of the species included in the 'S. cerevisiae-like' group. This division is concordant with the position of these species in previous phylogenetic reconstructions. Additionally, the intraspecific analysis of the chromosome patterns show a rich polymorphism in the heterogeneous species K. dobzhanskii, K. lactis, and K. marxianus, which is in concordance with the variability observed with other phenotypic or genetic markers. On the contrary, K. thermotolerans exhibits a homogeneous karyotype indicative of a very low level of chromosomal polymorphism, which is congruent with the reduced variability found in this species with other molecular markers.