Duplication processes in Saccharomyces cerevisiae haploid strains

Duplication is thought to be one of the main processes providing a substrate on which the effects of evolution are visible. The mechanisms underlying this chromosomal rearrangement were investigated here in the yeast Saccharomyces cerevisiae. Spontaneous revertants containing a duplication event were selected and analyzed. In addition to the single gene duplication described in a previous study, we demonstrated here that direct tandem duplicated regions ranging from 5 to 90 kb in size can also occur spontaneously. To further investigate the mechanisms in the duplication events, we examined whether homologous recombination contributes to these processes. The results obtained show that the mechanisms involved in segmental duplication are RAD52-independent, contrary to those involved in single gene duplication. Moreover, this study shows that the duplication of a given gene can occur in S.cerevisiae haploid strains via at least two ways: single gene or segmental duplication

Influence of genetic background on the occurrence of chromosomal rearrangements in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Chromosomal rearrangements such as duplications and deletions are key factors in evolutionary processes because they promote genomic plasticity. Although the genetic variations in the <it>Saccharomyces cerevisiae </it>species have been well documented, there is little known to date about the impact of the genetic background on the appearance of rearrangements.</p> <p>Results</p> <p>Using the same genetic screening, the type of rearrangements and the mutation rates observed in the S288c <it>S. cerevisiae </it>strain were compared to previous findings obtained in the FL100 background. Transposon-associated rearrangements, a major chromosomal rearrangement event selected in FL100, were not detected in S288c. The mechanisms involved in the occurrence of deletions and duplications in the S288c strain were also tackled, using strains deleted for genes implicated in homologous recombination (HR) or non-homologous end joining (NHEJ). Our results indicate that an Yku80p-independent NHEJ pathway is involved in the occurrence of these rearrangements in the S288c background.</p> <p>Conclusion</p> <p>The comparison of two different <it>S</it>. <it>cerevisiae </it>strains, FL100 and S288c, allowed us to conclude that intra-species genomic variations have an important impact on the occurrence of chromosomal rearrangement and that this variability can partly be explained by differences in Ty1 retrotransposon activity.</p

Ploidy influences cellular responses to gross chromosomal rearrangements in saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Gross chromosomal rearrangements (GCRs) such as aneuploidy are key factors in genome evolution as well as being common features of human cancer. Their role in tumour initiation and progression has not yet been completely elucidated and the effects of additional chromosomes in cancer cells are still unknown. Most previous studies in which <it>Saccharomyces cerevisiae </it>has been used as a model for cancer cells have been carried out in the haploid context. To obtain new insights on the role of ploidy, the cellular effects of GCRs were compared between the haploid and diploid contexts.</p> <p>Results</p> <p>A total number of 21 haploid and diploid <it>S. cerevisiae </it>strains carrying various types of GCRs (aneuploidies, nonreciprocal translocations, segmental duplications and deletions) were studied with a view to determining the effects of ploidy on the cellular responses. Differences in colony and cell morphology as well as in the growth rates were observed between mutant and parental strains. These results suggest that cells are impaired physiologically in both contexts. We also investigated the variation in genomic expression in all the mutants. We observed that gene expression was significantly altered. The data obtained here clearly show that genes involved in energy metabolism, especially in the tricarboxylic acid cycle, are up-regulated in all these mutants. However, the genes involved in the composition of the ribosome or in RNA processing are down-regulated in diploids but up-regulated in haploids. Over-expression of genes involved in the regulation of the proteasome was found to occur only in haploid mutants.</p> <p>Conclusion</p> <p>The present comparisons between the cellular responses of strains carrying GCRs in different ploidy contexts bring to light two main findings. First, GCRs induce a general stress response in all studied mutants, regardless of their ploidy. Secondly, the ploidy context plays a crucial role in maintaining the stoichiometric balance of the proteins: the translation rates decrease in diploid strains, whereas the excess protein synthesized is degraded in haploids by proteasome activity.</p

Genomic Exploration of the Hemiascomycetous Yeasts: 1. A set of yeast species for molecular evolution studies11Sequences and annotations are accessible at: Génoscope (http://www.genoscope.cns.fr), FEBS Letters Website (http://www.elsevier.nl/febs/show/), Bordeaux (http://cbi.genopole-bordeaux.fr/Genolevures) and were deposited into the EMBL database (accession number from AL392203 to AL441602).

AbstractThe identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20 000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the ‘yeast-specific’ genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated ‘Génolevures’

Genomic Exploration of the Hemiascomycetous Yeasts: 19. Ascomycetes-specific genes

AbstractComparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from ‘maverick’ genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the ‘maverick’ genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear ‘Ascomycetes-specific’. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein-coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the ‘Ascomycetes-specific’ genes tend to diverge more rapidly in evolution than that of other genes. Half of the ‘Ascomycetes-specific’ genes are functionally characterized in S. cerevisiae, and a few functional categories are over-represented in them

Réarrangements chromosomiques chez Saccharomyces cerevisiae (Influence du contexte génétique et mécanismes impliqués dans leur apparition)

Les remaniements chromosomiques tels que les délétions, les duplications ou les insertions de rétrotransposons Ty1 représentent des événements moteurs dans l évolution. Ils sont à l origine de la variabilité inter- et intra-espèces. Cependant, l influence des variations intra-espèces ainsi que les mécanismes à l origine de la formation des remaniements chromosomiques sont encore peu connus. Au laboratoire, un crible génétique basé sur un allèle particulier du gène URA2 a été développé permettant ainsi de sélectionner des révertants porteurs de remaniements chromosomiques spontanés chez la levure S. cerevisiae. Afin d appréhender l impact du contexte génétique sur l apparition des remaniements chromosomiques, nous avons comparé deux souches de S. cerevisiae utilisées en laboratoire à savoir la souche FL100 et la souche de référence séquencée S288c. On a ainsi pu montrer que la variabilité intra-espèces a une influence sur les types de remaniements obtenus et que cette variation est due à une différence d activité des rétrotransposons Ty1. L étude des mécanismes permettant l apparition des réarrangements a également été réalisée. Des souches de levure ont été construites portant des mutations dans des gènes dont les produits sont impliqués dans la voie de recombinaison homologue (RAD52 et RAD59) et dans celle du non-homologous end joining (NHEJ) (YKU80 et LIG4). Les résultats obtenus suggèrent qu un mécanisme de NHEJ indépendant de la protéine Yku80p est impliqué dans l apparition des délétions et des duplications. Enfin, nous avons appréhendé la variabilité inter-espèces et l évolution des génomes par l étude in silico de deux familles multigéniques codant pour des perméases.Chromosomal rearrangements such as deletions, duplications or Ty1 retrotransposons insertions represent key events in evolution processes. They are responsible for inter- and intra-species variability. However, little is known about the influence of the intra-species variations and the mechanisms responsible for the formation of chromosomal rearrangements. In our laboratory, a genetic screening based on a particular allele of the URA2 gene was developed allowing the selection of revertants carrying spontaneous chromosomal rearrangements in yeast S. cerevisiae. In order to understand the impact of the genetic background on the occurrence of chromosomal rearrangements, we compared two laboratory strains of S. cerevisiae, the FL100 strain and the sequenced reference strain S288c. It was thus showed that intra-species variability has an influence on the type of obtained rearrangements and that the variation between the two backgrounds is due to a difference of activity for the Ty1 retrotransposons. The study of the mechanisms allowing the occurrence of rearrangements in genomes was also carried out. Strains of S. cerevisiae mutated for genes whose products are involved in homologous recombination (RAD52 and RAD59) or non-homologous end-joining (NHEJ) (YKU80 et LIG4) were constructed. The results obtained during this study suggest that a Yku80p-independent NHEJ mechanism is involved in the appearance of deletions and duplications. Finally, we considered inter-species variability and genome evolution by an in silico study of two multigenic families coding for permeases.STRASBOURG-Sc. et Techniques (674822102) / SudocSudocFranceF

The characterization of two new clusters of duplicated genes suggests a 'Lego' organization of the yeast Saccharomyces cerevisiae chromosomes.

The systematic sequencing of 42,485 bp of yeast chromosome VII (nucleotides 377948 to 420432) has revealed the presence of 27 putative open reading frames (ORFs) coding for proteins of at least 100 amino acids. The degree of redundancy observed is elevated since five of the 27 ORFs are duplications of a previously identified gene. These duplicated copies may be classified in two types of cluster organization. The first type includes genes sharing a significant level of identity in the amino acid sequences of their predicted protein product. They are recovered on two different chromosomes, transcribed in the same orientation and the distance between them is conserved. The second type of cluster is based on one gene unit tandemly repeated. This duplication is itself repeated elsewhere in the genome. The level of nucleic acid identity is high within the coding sequence and the non-coding region between the two repeats. In addition, the basic gene unit is recovered many times in the genome and is a component of a multigene family of unknown function. These organizations in clusters of genes suggest a 'Lego organization' of the yeast chromosomes, as recently proposed for the genome of plants (Moore, 1995). The sequence is deposited in the Yeast Genome Databank under Accession Number from Z72562 to Z72586.journal articleresearch support, non-u.s. gov't1997 Julimporte

Delta sequence of Ty1 transposon can initiate transcription of the distal part of the URA2 gene complex in Saccharomyces cerevisiae.

Expression of a silent aspartate transcarbamylase (ATCase) domain can occur by insertion of a Tyl retrotransposon within the coding sequence of a mutated ura2 allele. This unusual type of Ty-mediated gene activation is possible as the URA2 gene product is a multifunctional protein containing the carbamoyl phosphate synthetase (CPSase), the ATCase and a cryptic dihydroorotase (DHOase) domain. The region in which transcription of the corresponding allele is initiated was determined by RT-PCR experiments. Expression is initiated by a sequence located in the delta element of the Tyl and not by a sequence of the URA2 gene itself. This situation differs with the Ty-mediated gene activation described thus far, in which the transposon substitutes only the 5' regulatory sequences and in which the normal transcription start point is used. The corresponding protein carries both the DHOase-like domain and the ATCase domain, suggesting that the DHOase-like domain is at least involved in the architecture of the protein and necessary to render the ATCase domain functional.journal articleresearch support, non-u.s. gov't1997 Mar 01importe

Involvement of very short DNA tandem repeats and the influence of the RAD52 gene on the occurrence of deletions in Saccharomyces cerevisiae.

Chromosomal rearrangements, such as deletions, duplications, or Ty transposition, are rare events. We devised a method to select for such events as Ura(+) revertants of a particular ura2 mutant. Among 133 Ura(+) revertants, 14 were identified as the result of a deletion in URA2. Of seven classes of deletions, six had very short regions of identity at their junctions (from 7 to 13 bp long). This strongly suggests a nonhomologous recombination mechanism for the formation of these deletions. The total Ura(+) reversion rate was increased 4.2-fold in a rad52Delta strain compared to the wild type, and the deletion rate was significantly increased. All the deletions selected in the rad52Delta context had microhomologies at their junctions. We propose two mechanisms to explain the occurrence of these deletions and discuss the role of microhomology stretches in the formation of fusion proteins.journal articleresearch support, non-u.s. gov't2000 Octimporte