Journal articles: 'Saccharomyces cerevisiae genome codes'

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Chow, T. Y., J. J. Ash, D. Dignard, and D. Y. Thomas. "Screening and identification of a gene, PSE-1, that affects protein secretion in Saccharomyces cerevisiae." Journal of Cell Science 101, no. 3 (March 1, 1992): 709–19. http://dx.doi.org/10.1242/jcs.101.3.709.

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Utilizing a screening method designed for the identification of genes involved with enhanced protein secretion in Saccharomyces cerevisiae we identified a gene, which we named PSE-1 (Protein Secretion Enhancer). Overexpression of PSE-1 in a multi-copy plasmid, as shown by Northern hybridization, gave a fourfold enhancement in total protein secretion. The repertoire of proteins that are found to be secreted in greater quantities include three known biologically active proteins: k1 killer toxin, alpha-factor, and acid phosphatase. The PSE-1 gene is located on chromosome XII of the yeast genome and codes for a hydrophobic protein containing 1089 amino acids. Haploid yeast cells that contained a LEU2 insertion mutation in PSE-1 grow very poorly, a phenotype similar to other conditional SEC mutants at restrictive temperature.

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Costanzo, Maria C., Nathalie Bonnefoy, Elizabeth H. Williams, G. Desmond Clark-Walker, and Thomas D. Fox. "Highly Diverged Homologs of Saccharomyces cerevisiae Mitochondrial mRNA-Specific Translational Activators Have Orthologous Functions in Other Budding Yeasts." Genetics 154, no. 3 (March 1, 2000): 999–1012. http://dx.doi.org/10.1093/genetics/154.3.999.

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Abstract Translation of mitochondrially coded mRNAs in Saccharomyces cerevisiae depends on membrane-bound mRNA-specific activator proteins, whose targets lie in the mRNA 5′-untranslated leaders (5′-UTLs). In at least some cases, the activators function to localize translation of hydrophobic proteins on the inner membrane and are rate limiting for gene expression. We searched unsuccessfully in divergent budding yeasts for orthologs of the COX2- and COX3-specific translational activator genes, PET111, PET54, PET122, and PET494, by direct complementation. However, by screening for complementation of mutations in genes adjacent to the PET genes in S. cerevisiae, we obtained chromosomal segments containing highly diverged homologs of PET111 and PET122 from Saccharomyces kluyveri and of PET111 from Kluyveromyces lactis. All three of these genes failed to function in S. cerevisiae. We also found that the 5′-UTLs of the COX2 and COX3 mRNAs of S. kluyveri and K. lactis have little similarity to each other or to those of S. cerevisiae. To determine whether the PET111 and PET122 homologs carry out orthologous functions, we deleted them from the S. kluyveri genome and deleted PET111 from the K. lactis genome. The pet111 mutations in both species prevented COX2 translation, and the S. kluyveri pet122 mutation prevented COX3 translation. Thus, while the sequences of these translational activator proteins and their 5′-UTL targets are highly diverged, their mRNA-specific functions are orthologous.

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Choe, J., T. Schuster, and M. Grunstein. "Organization, primary structure, and evolution of histone H2A and H2B genes of the fission yeast Schizosaccharomyces pombe." Molecular and Cellular Biology 5, no. 11 (November 1985): 3261–69. http://dx.doi.org/10.1128/mcb.5.11.3261-3269.1985.

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The histone H2A and H2B genes of the fission yeast Schizosaccharomyces pombe were cloned and sequenced. Southern blot and sequence analyses showed that, unlike other eucaryotes, Saccharomyces cerevisiae included, S. pombe has unequal numbers of these genes, containing two histone H2A genes (H2A-alpha and -beta) and only one H2B gene (H2B-alpha) per haploid genome. H2A- and H2B-alpha are adjacent to each other and are divergently transcribed. H2A-beta has no other histone gene in close proximity. Preceding both H2A-alpha and -beta is a highly conserved 19-base-pair sequence (5'-CATCAC/AAACCCTAACCCTG-3'). The H2A DNA sequences encode two histone H2A subtypes differing in amino acid sequence (three residues) and size (H2A-alpha, 131 residues; H2A-beta, 130 residues). H2B-alpha codes for a 125-amino-acid protein. Sequence evolution is extensive between S. pombe and S. cerevisiae and displays unique patterns of divergence. Certain N-terminal sequences normally divergent between eucaryotes are conserved between the two yeasts. In contrast, the normally conserved hydrophobic core of H2A is as divergent between the yeasts as between S. pombe and calf.

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Choe, J., T. Schuster, and M. Grunstein. "Organization, primary structure, and evolution of histone H2A and H2B genes of the fission yeast Schizosaccharomyces pombe." Molecular and Cellular Biology 5, no. 11 (November 1985): 3261–69. http://dx.doi.org/10.1128/mcb.5.11.3261.

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The histone H2A and H2B genes of the fission yeast Schizosaccharomyces pombe were cloned and sequenced. Southern blot and sequence analyses showed that, unlike other eucaryotes, Saccharomyces cerevisiae included, S. pombe has unequal numbers of these genes, containing two histone H2A genes (H2A-alpha and -beta) and only one H2B gene (H2B-alpha) per haploid genome. H2A- and H2B-alpha are adjacent to each other and are divergently transcribed. H2A-beta has no other histone gene in close proximity. Preceding both H2A-alpha and -beta is a highly conserved 19-base-pair sequence (5'-CATCAC/AAACCCTAACCCTG-3'). The H2A DNA sequences encode two histone H2A subtypes differing in amino acid sequence (three residues) and size (H2A-alpha, 131 residues; H2A-beta, 130 residues). H2B-alpha codes for a 125-amino-acid protein. Sequence evolution is extensive between S. pombe and S. cerevisiae and displays unique patterns of divergence. Certain N-terminal sequences normally divergent between eucaryotes are conserved between the two yeasts. In contrast, the normally conserved hydrophobic core of H2A is as divergent between the yeasts as between S. pombe and calf.

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Himmelfarb, H. J., E. Maicas, and J. D. Friesen. "Isolation of the SUP45 omnipotent suppressor gene of Saccharomyces cerevisiae and characterization of its gene product." Molecular and Cellular Biology 5, no. 4 (April 1985): 816–22. http://dx.doi.org/10.1128/mcb.5.4.816-822.1985.

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The Saccharomyces cerevisiae SUP45+ gene has been isolated from a genomic clone library by genetic complementation of paromomycin sensitivity, which is a property of a mutant strain carrying the sup45-2 allele. This plasmid complements all phenotypes associated with the sup45-2 mutation, including nonsense suppression, temperature sensitivity, osmotic sensitivity, and paromomycin sensitivity. Genetic mapping with a URA3+-marked derivative of the complementing plasmid that was integrated into the chromosome by homologous recombination demonstrated that the complementing fragment contained the SUP45+ gene and not an unlinked suppressor. The SUP45+ gene is present as a single copy in the haploid genome and is essential for viability. In vitro translation of the hybrid-selected SUP45+ transcript yielded a protein of Mr = 54,000, which is larger than any known ribosomal protein. RNA blot hybridization analysis showed that the steady-state level of the SUP45+ transcript is less than 10% of that for ribosomal protein L3 or rp59 transcripts. When yeast cells are subjected to a mild heat shock, the synthesis rate of the SUP45+ transcript was transiently reduced, approximately in parallel with ribosomal protein transcripts. Our data suggest that the SUP45+ gene does not encode a ribosomal protein. We speculate that it codes for a translation-related function whose precise nature is not yet known.

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Himmelfarb, H. J., E. Maicas, and J. D. Friesen. "Isolation of the SUP45 omnipotent suppressor gene of Saccharomyces cerevisiae and characterization of its gene product." Molecular and Cellular Biology 5, no. 4 (April 1985): 816–22. http://dx.doi.org/10.1128/mcb.5.4.816.

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The Saccharomyces cerevisiae SUP45+ gene has been isolated from a genomic clone library by genetic complementation of paromomycin sensitivity, which is a property of a mutant strain carrying the sup45-2 allele. This plasmid complements all phenotypes associated with the sup45-2 mutation, including nonsense suppression, temperature sensitivity, osmotic sensitivity, and paromomycin sensitivity. Genetic mapping with a URA3+-marked derivative of the complementing plasmid that was integrated into the chromosome by homologous recombination demonstrated that the complementing fragment contained the SUP45+ gene and not an unlinked suppressor. The SUP45+ gene is present as a single copy in the haploid genome and is essential for viability. In vitro translation of the hybrid-selected SUP45+ transcript yielded a protein of Mr = 54,000, which is larger than any known ribosomal protein. RNA blot hybridization analysis showed that the steady-state level of the SUP45+ transcript is less than 10% of that for ribosomal protein L3 or rp59 transcripts. When yeast cells are subjected to a mild heat shock, the synthesis rate of the SUP45+ transcript was transiently reduced, approximately in parallel with ribosomal protein transcripts. Our data suggest that the SUP45+ gene does not encode a ribosomal protein. We speculate that it codes for a translation-related function whose precise nature is not yet known.

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Storms, Reg K., Ying Wang, Natalie Fortin, John Hall, Danh H. Vo, Wu-Wei Zhong, Howard Bussey, et al. "Analysis of a 103 kbp cluster homology region from the left end of Saccharomyces cerevisiae chromosome I." Genome 40, no. 1 (February 1, 1997): 151–64. http://dx.doi.org/10.1139/g97-022.

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The DNA sequence and preliminary functional analysis of a 103-kbp section of the left arm of yeast chromosome I is presented. This region, from the left telomere to the LTE1 gene, can be divided into two distinct portions. One portion, the telomeric 29 kbp, has a very low gene density (only five potential genes and 21 kbp of noncoding sequence), does not encode any "functionally important" genes, and is rich in sequences repeated several times within the yeast genome. The other portion, with 37 genes and only 14.5 kbp of noncoding sequence, is gene rich and codes for at least 16 "functionally important" genes. The entire gene-rich portion is apparently duplicated on chromosome XV as an extensive region of partial gene synteney called a cluster homology region. A function can be assigned with varying degrees of precision to 23 of the 42 potential genes in this region; however, the precise function is know for only eight genes. Nineteen genes encode products presently novel to yeast, although five of these have homologs elsewhere in the yeast genome.Key words: Saccharomyces cerevisiae, chromosome I, cluster homology region, DNA sequence.

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Daròs, José-Antonio, Mary C. Schaad, and James C. Carrington. "Functional Analysis of the Interaction between VPg-Proteinase (NIa) and RNA Polymerase (NIb) of Tobacco Etch Potyvirus, Using Conditional and Suppressor Mutants." Journal of Virology 73, no. 10 (October 1, 1999): 8732–40. http://dx.doi.org/10.1128/jvi.73.10.8732-8740.1999.

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ABSTRACT The tobacco etch potyvirus (TEV) RNA-dependent RNA polymerase (NIb) has been shown to interact with the proteinase domain of the VPg-proteinase (NIa). To investigate the significance of this interaction, a Saccharomyces cerevisiae two-hybrid assay was used to isolate conditional NIa mutant proteins with temperature-sensitive (ts) defects in interacting with NIb. Thirty-six unique tsNIa mutants with substitutions affecting the proteinase domain were recovered. Most of the mutants coded for proteins with little or no proteolytic activity at permissive and nonpermissive temperatures. However, three mutant proteins retained proteolytic activity at both temperatures and, in two cases (tsNIa-Q384P and tsNIa-N393D), the mutations responsible for the ts interaction phenotype could be mapped to single positions. One of the mutations (N393D) conferred ats-genome-amplification phenotype when it was placed in a recombinant TEV strain. Suppressor NIb mutants that restored interaction with the tsNIa-N393D protein at the restrictive temperature were recovered by a two-hybrid selection system. Although most of the suppressor mutants failed to stimulate amplification of genomes encoding the tsNIa-N393D protein, two suppressors (NIb-I94T and NIb-C380R) stimulated amplification of virus containing the N393D substitution by approximately sevenfold. These results support the hypothesis that interaction between NIa and NIb is important during TEV genome replication.

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Foroughmand-Araabi, Mohammad-Hadi, Sama Goliaei, and Bahram Goliaei. "A novel pattern matching algorithm for genomic patterns related to protein motifs." Journal of Bioinformatics and Computational Biology 18, no. 01 (February 2020): 2050011. http://dx.doi.org/10.1142/s0219720020500110.

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Background: Patterns on proteins and genomic sequences are vastly analyzed, extracted and collected in databases. Although protein patterns originate from genomic coding regions, very few works have directly or indirectly dealt with coding region patterns induced from protein patterns. Results: In this paper, we have defined a new genomic pattern structure suitable for representing induced patterns from proteins. The provided pattern structure, which is called “Consecutive Positions Scoring Matrix (CPSSM)”, is a replacement for protein patterns and profiles in the genomic context. CPSSMs can be identified, discovered, and searched in genomes. Then, we have presented a novel pattern matching algorithm between the defined genomic pattern and genomic sequences based on dynamic programming. In addition, we have modified the provided algorithm to support intronic gaps and huge sequences. We have implemented and tested the provided algorithm on real data. The results on Saccharomyces cerevisiae’s genome show 132% more true positives and no false negatives and the results on human genome show no false negatives and 10 times as many true positives as those in previous works. Conclusion: CPSSM and provided methods could be used for open reading frame detection and gene finding. The application is available with source codes to run and download at http://app.foroughmand.ir/cpssm/ .

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Fleckenstein, D., M. Rohde, D. J. Klionsky, and M. Rudiger. "Yel013p (Vac8p), an armadillo repeat protein related to plakoglobin and importin alpha is associated with the yeast vacuole membrane." Journal of Cell Science 111, no. 20 (October 15, 1998): 3109–18. http://dx.doi.org/10.1242/jcs.111.20.3109.

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Proteins of the armadillo family are involved in diverse cellular processes in higher eukaryotes. Some of them, like armadillo, beta-catenin and plakoglobins have dual functions in intercellular junctions and signalling cascades. Others, belonging to the importin-alpha-subfamily are involved in NLS recognition and nuclear transport, while some members of the armadillo family have as yet unknown functions. Here, we introduce the Saccharomyces cerevisiae protein Yel013p as a novel armadillo (arm) repeat protein. The ORF Yel013w was identified in the genome project on chromosome V (EMBL: U18530) and codes for an acidic protein of 578 residues with 8 central arm-repeats, which are closely related to the central repeat-domain of Xenopus laevis plakoglobin. We show that Yel013p (Vac8p) is constitutively expressed in diploid and haploid yeasts and that it is not essential for viability and growth. However, the vacuoles of mutant cells are multilobular or even fragmented into small vesicles and the processing of aminopeptidase I, representing the cytoplasm-to-vacuole transport pathway, is strongly impaired. Consistent with these observations, subcellular fractionation experiments, immunolocalization and expression of green fluorescent protein (GFP) fusion proteins revealed that Yel013p (Vac8p) is associated with the vacuolar membrane. Our data provide evidence for the involvement of an arm-family member in vacuolar morphology and protein targeting to the vacuole.

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Fleckenstein, Diana, Manfred Rohde, Daniel J. Klionsky, and Manfred Rüdiger. "Ye1013p (Vac8p), an armadillo repeat protein related to plakoglobin and importin α, is associated with the yeast vacuole membrane." Journal of Cell Science 111, no. 20 (January 15, 1998): 3109–18. http://dx.doi.org/10.1242/jcs.20.111.3109.

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ABSTRACT Proteins of the armadillo family are involved in diverse cellular processes in higher eukaryotes. Some of them, like armadillo, β-catenin and plakoglobins have dual functions in intercellular junctions and signalling cascades. Others, belonging to the importin-α-subfamily are involved in NLS recognition and nuclear transport, while some members of the armadillo family have as yet unknown functions. Here, we introduce the Saccharomyces cerevisiae protein Ye1013p as a novel armadillo (arm) repeat protein. The ORF Ye1013w was identified in the genome project on chromosome V (EMBL: U18530) and codes for an acidic protein of 578 residues with 8 central arm-repeats, which are closely related to the central repeat-domain of Xenopus laevis plakoglobin. We show that Ye1013p (Vac8p) is constitutively expressed in diploid and haploid yeasts and that it is not essential for viability and growth. However, the vacuoles of mutant cells are multilobular or even fragmented into small vesicles and the processing of aminopeptidase I, representing the cytoplasm-to-vacuole transport pathway, is strongly impaired. Consistent with these observations, subcellular fractionation experiments, immunolocalization and expression of green fluorescent protein (GFP) fusion proteins revealed that Ye1013p (Vac8p) is associated with the vacuolar membrane. Our data provide evidence for the involvement of an arm-family member in vacuolar morphology and protein targeting to the vacuole.

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Salzberg, Letal I., Alexandre A. R. Martos, Lisa Lombardi, Lars S. Jermiin, Alfonso Blanco, Kevin P. Byrne, and Kenneth H. Wolfe. "A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family." PLOS Genetics 18, no. 11 (November 28, 2022): e1010525. http://dx.doi.org/10.1371/journal.pgen.1010525.

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Saccharomyces genomes are highly collinear and show relatively little structural variation, both within and between species of this yeast genus. We investigated the only common inversion polymorphism known in S. cerevisiae, which affects a 24-kb ‘flip/flop’ region containing 15 genes near the centromere of chromosome XIV. The region exists in two orientations, called reference (REF) and inverted (INV). Meiotic recombination in this region is suppressed in crosses between REF and INV orientation strains such as the BY x RM cross. We find that the inversion polymorphism is at least 17 million years old because it is conserved across the genus Saccharomyces. However, the REF and INV isomers are not ancient alleles but are continually being re-created by re-inversion of the region within each species. Inversion occurs due to continual homogenization of two almost identical 4-kb sequences that form an inverted repeat (IR) at the ends of the flip/flop region. The IR consists of two pairs of genes that are specifically and strongly expressed during the late stages of sporulation. We show that one of these gene pairs, YNL018C/YNL034W, codes for a protein that is essential for spore formation. YNL018C and YNL034W are the founder members of a gene family, Centroid, whose members in other Saccharomycetaceae species evolve fast, duplicate frequently, and are preferentially located close to centromeres. We tested the hypothesis that Centroid genes are a meiotic drive system, but found no support for this idea.

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Franco, Leticia Veloso Ribeiro, Chen Hsien Su, and Alexander Tzagoloff. "Modular assembly of yeast mitochondrial ATP synthase and cytochrome oxidase." Biological Chemistry 401, no. 6-7 (May 26, 2020): 835–53. http://dx.doi.org/10.1515/hsz-2020-0112.

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AbstractThe respiratory pathway of mitochondria is composed of four electron transfer complexes and the ATP synthase. In this article, we review evidence from studies of Saccharomyces cerevisiae that both ATP synthase and cytochrome oxidase (COX) are assembled from independent modules that correspond to structurally and functionally identifiable components of each complex. Biogenesis of the respiratory chain requires a coordinate and balanced expression of gene products that become partner subunits of the same complex, but are encoded in the two physically separated genomes. Current evidence indicates that synthesis of two key mitochondrial encoded subunits of ATP synthase is regulated by the F1 module. Expression of COX1 that codes for a subunit of the COX catalytic core is also regulated by a mechanism that restricts synthesis of this subunit to the availability of a nuclear-encoded translational activator. The respiratory chain must maintain a fixed stoichiometry of the component enzyme complexes during cell growth. We propose that high-molecular-weight complexes composed of Cox6, a subunit of COX, and of the Atp9 subunit of ATP synthase play a key role in establishing the ratio of the two complexes during their assembly.

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Panwar, Sneh L., Melanie Legrand, Daniel Dignard, Malcolm Whiteway, and Paul T. Magee. "MFα1, the Gene Encoding the α Mating Pheromone of Candida albicans." Eukaryotic Cell 2, no. 6 (December 2003): 1350–60. http://dx.doi.org/10.1128/ec.2.6.1350-1360.2003.

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ABSTRACT Candida albicans, the single most frequently isolated human fungal pathogen, was thought to be asexual until the recent discovery of the mating-type-like locus (MTL). Homozygous MTL strains were constructed and shown to mate. Furthermore, it has been demonstrated that opaque-phase cells are more efficient in mating than white-phase cells. The similarity of the genes involved in the mating pathway in Saccharomyces cerevisiae and C. albicans includes at least one gene (KEX2) that is involved in the processing of the α mating pheromone in the two yeasts. Taking into account this similarity, we searched the C. albicans genome for sequences that would encode the α pheromone gene. Here we report the isolation and characterization of the gene MFα1, which codes for the precursor of the α mating pheromone in C. albicans. Two active α-peptides, 13 and 14 amino acids long, would be generated after the precursor molecule is processed in C. albicans. To examine the role of this gene in mating, we constructed an mfα1 null mutant of C. albicans. The mfα1 null mutant fails to mate as MTLα, while MTLa mfα1 cells are still mating competent. Experiments performed with the synthetic α-peptides show that they are capable of inducing growth arrest, as demonstrated by halo tests, and also induce shmooing in MTLa cells of C. albicans. These peptides are also able to complement the mating defect of an MTLα kex2 mutant strain when added exogenously, thereby confirming their roles as α mating pheromones.

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Zahedi, Rene P., Albert Sickmann, Andreas M. Boehm, Christiane Winkler, Nicole Zufall, Birgit Schönfisch, Bernard Guiard, Nikolaus Pfanner, and Chris Meisinger. "Proteomic Analysis of the Yeast Mitochondrial Outer Membrane Reveals Accumulation of a Subclass of Preproteins." Molecular Biology of the Cell 17, no. 3 (March 2006): 1436–50. http://dx.doi.org/10.1091/mbc.e05-08-0740.

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Mitochondria consist of four compartments–outer membrane, intermembrane space, inner membrane, and matrix—with crucial but distinct functions for numerous cellular processes. A comprehensive characterization of the proteome of an individual mitochondrial compartment has not been reported so far. We used a eukaryotic model organism, the yeast Saccharomyces cerevisiae, to determine the proteome of highly purified mitochondrial outer membranes. We obtained a coverage of ∼85% based on the known outer membrane proteins. The proteome represents a rich source for the analysis of new functions of the outer membrane, including the yeast homologue (Hfd1/Ymr110c) of the human protein causing Sjögren–Larsson syndrome. Surprisingly, a subclass of proteins known to reside in internal mitochondrial compartments were found in the outer membrane proteome. These seemingly mislocalized proteins included most top scorers of a recent genome-wide analysis for mRNAs that were targeted to mitochondria and coded for proteins of prokaryotic origin. Together with the enrichment of the precursor form of a matrix protein in the outer membrane, we conclude that the mitochondrial outer membrane not only contains resident proteins but also accumulates a conserved subclass of preproteins destined for internal mitochondrial compartments.

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Mulero, J. J., and T. D. Fox. "Alteration of the Saccharomyces cerevisiae COX2 mRNA 5'-untranslated leader by mitochondrial gene replacement and functional interaction with the translational activator protein PET111." Molecular Biology of the Cell 4, no. 12 (December 1993): 1327–35. http://dx.doi.org/10.1091/mbc.4.12.1327.

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The ability to replace wild-type mitochondrial DNA sequences in yeast with in vitro-generated mutations has been exploited to study the mechanism by which the nuclearly encoded PET111 protein specifically activates translation of the mitochondrially coded COX2 mRNA. We have generated three mutations in vitro that alter the COX2 mRNA 5'-untranslated leader (UTL) and introduced them into the mitochondrial genome, replacing the wild-type sequence. None of the mutations significantly affected the steady-state level of COX2 mRNA. Deletion of a single base at position -24 (relative to the translation initiation codon) in the 5'-UTL (cox2-11) reduced COX2 mRNA translation and respiratory growth, whereas insertion of four bases in place of the deleted base (cox2-12) and deletion of bases -30 to -2 (cox2-13) completely blocked both. Six spontaneous nuclear mutations were selected as suppressors of the single-base 5'-UTL deletion, cox2-11. One of these mapped to PET111 and was shown to be a missense mutation that changed residue 652 from Ala to Thr. This suppressor, PET111-20, failed to suppress the 29-base deletion, cox2-13, but very weakly suppressed the insertion mutation, cox2-12. PET111-20 also enhanced translation of a partially functional COX2 mRNA with a wild-type 5'-UTL but a mutant initiation codon. Although overexpression of the wild-type PET111 protein caused weak suppression of the single-base deletion, cox2-11, the PET111-20 suppressor mutation did not function simply by increasing the level of the protein. These results demonstrate an intimate functional interaction between the translational activator protein and the mRNA 5'-UTL and suggest that they may interact directly.

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Belloch, Carmela, Roberto Pérez-Torrado, Sara S. González, José E. Pérez-Ortín, José García-Martínez, Amparo Querol, and Eladio Barrio. "Chimeric Genomes of Natural Hybrids of Saccharomyces cerevisiae and Saccharomyces kudriavzevii." Applied and Environmental Microbiology 75, no. 8 (February 27, 2009): 2534–44. http://dx.doi.org/10.1128/aem.02282-08.

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ABSTRACT Recently, a new type of hybrid resulting from the hybridization between Saccharomyces cerevisiae and Saccharomyces kudriavzevii was described. These strains exhibit physiological properties of potential biotechnological interest. A preliminary characterization of these hybrids showed a trend to reduce the S. kudriavzevii fraction of the hybrid genome. We characterized the genomic constitution of several wine S. cerevisiae × S. kudriavzevii strains by using a combined approach based on the restriction fragment length polymorphism analysis of gene regions, comparative genome hybridizations with S. cerevisiae DNA arrays, ploidy analysis, and gene dose determination by quantitative real-time PCR. The high similarity in the genome structures of the S. cerevisiae × S. kudriavzevii hybrids under study indicates that they originated from a single hybridization event. After hybridization, the hybrid genome underwent extensive chromosomal rearrangements, including chromosome losses and the generation of chimeric chromosomes by the nonreciprocal recombination between homeologous chromosomes. These nonreciprocal recombinations between homeologous chromosomes occurred in highly conserved regions, such as Ty long terminal repeats (LTRs), rRNA regions, and conserved protein-coding genes. This study supports the hypothesis that chimeric chromosomes may have been generated by a mechanism similar to the recombination-mediated chromosome loss acting during meiosis in Saccharomyces hybrids. As a result of the selective processes acting during fermentation, hybrid genomes maintained the S. cerevisiae genome but reduced the S. kudriavzevii fraction.

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Wodicka, Lisa, Helin Dong, Michael Mittmann, Ming-Hsiu Ho, and David J. Lockhart. "Genome-wide expression monitoring in Saccharomyces cerevisiae." Nature Biotechnology 15, no. 13 (December 1997): 1359–67. http://dx.doi.org/10.1038/nbt1297-1359.

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Giaever, Guri, Angela M. Chu, Li Ni, Carla Connelly, Linda Riles, Steeve Véronneau, Sally Dow, et al. "Functional profiling of the Saccharomyces cerevisiae genome." Nature 418, no. 6896 (July 25, 2002): 387–91. http://dx.doi.org/10.1038/nature00935.

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Peter, Jackson, Matteo De Chiara, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergström, Anastasie Sigwalt, et al. "Genome evolution across 1,011 Saccharomyces cerevisiae isolates." Nature 556, no. 7701 (April 2018): 339–44. http://dx.doi.org/10.1038/s41586-018-0030-5.

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Kolodner, R. D. "Maintenance of Genome Stability in Saccharomyces cerevisiae." Science 297, no. 5581 (July 26, 2002): 552–57. http://dx.doi.org/10.1126/science.1075277.

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Waldrip, Zachary J., Piroon Jenjaroenpun, Oktawia DeYoung, Intawat Nookaew, Sean D. Taverna, Kevin D. Raney, and Alan J. Tackett. "Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae." PeerJ 8 (July 29, 2020): e9442. http://dx.doi.org/10.7717/peerj.9442.

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The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potential for site-specific chromosomal studies in organisms with relatively small genomes such as yeasts.

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Gibney, Patrick A., Mark J. Hickman, Patrick H. Bradley, John C. Matese, and David Botstein. "Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome." G3: Genes|Genomes|Genetics 3, no. 8 (June 7, 2013): 1335–40. http://dx.doi.org/10.1534/g3.113.006585.

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Schmuckli-Maurer, J. "Genome instability in rad54 mutants of Saccharomyces cerevisiae." Nucleic Acids Research 31, no. 3 (February 1, 2003): 1013–23. http://dx.doi.org/10.1093/nar/gkg190.

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Generoso, Wesley Cardoso, Manuela Gottardi, Mislav Oreb, and Eckhard Boles. "Simplified CRISPR-Cas genome editing for Saccharomyces cerevisiae." Journal of Microbiological Methods 127 (August 2016): 203–5. http://dx.doi.org/10.1016/j.mimet.2016.06.020.

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Hoang, Stephen A., and Stefan Bekiranov. "The Network Architecture of the Saccharomyces cerevisiae Genome." PLoS ONE 8, no. 12 (December 9, 2013): e81972. http://dx.doi.org/10.1371/journal.pone.0081972.

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Hou, Lihua. "Novel methods of genome shuffling in Saccharomyces cerevisiae." Biotechnology Letters 31, no. 5 (January 20, 2009): 671–77. http://dx.doi.org/10.1007/s10529-009-9916-5.

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Dymond, Jessica, and Jef Boeke. "The Saccharomyces cerevisiae SCRaMbLE system and genome minimization." Bioengineered 3, no. 3 (May 2012): 170–73. http://dx.doi.org/10.4161/bbug.19543.

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Ryan, Owen W., Snigdha Poddar, and Jamie H. D. Cate. "CRISPR–Cas9 Genome Engineering in Saccharomyces cerevisiae Cells." Cold Spring Harbor Protocols 2016, no. 6 (June 2016): pdb.prot086827. http://dx.doi.org/10.1101/pdb.prot086827.

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Lisnić, Berislav, Ivan-Krešimir Svetec, Hrvoje Šarić, Ivan Nikolić, and Zoran Zgaga. "Palindrome content of the yeast Saccharomyces cerevisiae genome." Current Genetics 47, no. 5 (March 18, 2005): 289–97. http://dx.doi.org/10.1007/s00294-005-0573-5.

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Fisk, Dianna G., Catherine A. Ball, Kara Dolinski, Stacia R. Engel, Eurie L. Hong, Laurie Issel-Tarver, Katja Schwartz, Anand Sethuraman, David Botstein, and J. Michael Cherry. "Saccharomyces cerevisiae S288C genome annotation: a working hypothesis." Yeast 23, no. 12 (2006): 857–65. http://dx.doi.org/10.1002/yea.1400.

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32

Imran, Yaseen Ismael, Ibrahim Abdulla Ahmed, and Ahmed Ali Muhawesh. "Genome Editing of Saccharomyces Cerevisiae Using CRISPR-Cas9 System." Journal La Lifesci 2, no. 1 (March 22, 2021): 20–28. http://dx.doi.org/10.37899/journallalifesci.v2i1.318.

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Saccharomyces cerevisiae is an important yeast has been exploited for a long time to produce alcohol or bread. Moreover, genetically engineered S. cerevisiae cells continue to be used as cell factories for production of biofuels, pharmaceutical proteins and food additives. Genetically modified strain of S. cerevisiae created using traditional methods is laborious and time consuming. Recently, originally an immune system in archaea and bacteria, Clustered regularly interspaced short palindromic repeats “CRISPR” and CRISPR-associated “Cas” have been used exploited as a flexible tool for genome editing. Until now, this tool has been applied to many organisms including yeast. Here, we review the importance of S. cerevisiae as an industrial platform and the use of CRISPR/Cas system and its applications in research and industry of this yeast.

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33

Ng, Patrick C., Edith D. Wong, Kevin A. MacPherson, Suzi Aleksander, Joanna Argasinska, Barbara Dunn, Robert S. Nash, et al. "Transcriptome visualization and data availability at the Saccharomyces Genome Database." Nucleic Acids Research 48, no. D1 (October 15, 2019): D743—D748. http://dx.doi.org/10.1093/nar/gkz892.

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Abstract The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.

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34

Ostergaard, Simon, Lisbeth Olsson, and Jens Nielsen. "Metabolic Engineering of Saccharomyces cerevisiae." Microbiology and Molecular Biology Reviews 64, no. 1 (March 1, 2000): 34–50. http://dx.doi.org/10.1128/mmbr.64.1.34-50.2000.

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SUMMARY Comprehensive knowledge regarding Saccharomyces cerevisiae has accumulated over time, and today S. cerevisiae serves as a widley used biotechnological production organism as well as a eukaryotic model system. The high transformation efficiency, in addition to the availability of the complete yeast genome sequence, has facilitated genetic manipulation of this microorganism, and new approaches are constantly being taken to metabolicially engineer this organism in order to suit specific needs. In this paper, strategies and concepts for metabolic engineering are discussed and several examples based upon selected studies involving S. cerevisiae are reviewed. The many different studies of metabolic engineering using this organism illustrate all the categories of this multidisciplinary field: extension of substrate range, improvements of producitivity and yield, elimination of byproduct formation, improvement of process performance, improvements of cellular properties, and extension of product range including heterologous protein production.

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35

Gerstein, Aleeza C., Rachel M. McBride, and Sarah P. Otto. "Ploidy reduction in Saccharomyces cerevisiae." Biology Letters 4, no. 1 (October 30, 2007): 91–94. http://dx.doi.org/10.1098/rsbl.2007.0476.

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Large-scale transitions in genome size from tetraploid to diploid were observed during a previous 1800-generation evolution experiment in Saccharomyces cerevisiae . Whether the transitions occurred via a one-step process (tetraploid to diploid) or through multiple steps (through ploidy intermediates) remained unclear. To provide insight into the mechanism involved, we investigated whether triploid-sized cells sampled from the previous experiment could also undergo ploidy loss. A batch culture experiment was conducted for approximately 200 generations, starting from four triploid-sized colonies and one contemporaneous tetraploid-sized colony. Ploidy reduction towards diploidy was observed in both triploid and tetraploid lines. Comparative genomic hybridization indicated the presence of aneuploidy in both the founder and the evolved colonies. The specific aneuploidies involved suggest that chromosome loss was not haphazard but that nearly full sets of chromosomes were lost at once, with some additional chromosome mis-segregation events. These results suggest the existence of a mitotic mechanism allowing the elimination of an entire set of chromosomes in S. cerevisiae , thereby reducing the ploidy level.

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36

Lemmon, S. K., C. Freund, K. Conley, and E. W. Jones. "Genetic instability of clathrin-deficient strains of Saccharomyces cerevisiae." Genetics 124, no. 1 (January 1, 1990): 27–38. http://dx.doi.org/10.1093/genetics/124.1.27.

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Abstract Saccharomyces cerevisiae strains carrying a mutation in the clathrin heavy chain gene (CHC1) are genetically unstable and give rise to heterogeneous populations of cells. Manifestations of the instability include increases in genome copy number as well as compensatory genetic changes that allow better growing clathrin-deficient cells to take over the population. Increases in genome copy number appear to result from changes in ploidy as well as alterations in normal nuclear number. Genetic background influences the frequency at which cells with increased genome content are observed in different Chc- strains. We cannot distinguish whether genetic background affects the rate at which aberrant nuclear division events occur or a growth advantage of cells with increased nuclear and/or genome content. However, survival of chc1-delta cells does not require an increase in genome copy number. The clathrin heavy chain gene was mapped 1-2 cM distal to KEX1 on the left arm of chromosome VII by making use of integrated 2 mu plasmid sequences to destabilize distal chromosome segments and allow ordering of the genes.

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Stepchenkova, Elena I., Sergey P. Zadorsky, Andrey R. Shumega, and Anna Y. Aksenova. "Practical Approaches for the Yeast Saccharomyces cerevisiae Genome Modification." International Journal of Molecular Sciences 24, no. 15 (July 26, 2023): 11960. http://dx.doi.org/10.3390/ijms241511960.

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The yeast S. cerevisiae is a unique genetic object for which a wide range of relatively simple, inexpensive, and non-time-consuming methods have been developed that allow the performing of a wide variety of genome modifications. Among the latter, one can mention point mutations, disruptions and deletions of particular genes and regions of chromosomes, insertion of cassettes for the expression of heterologous genes, targeted chromosomal rearrangements such as translocations and inversions, directed changes in the karyotype (loss or duplication of particular chromosomes, changes in the level of ploidy), mating-type changes, etc. Classical yeast genome manipulations have been advanced with CRISPR/Cas9 technology in recent years that allow for the generation of multiple simultaneous changes in the yeast genome. In this review we discuss practical applications of both the classical yeast genome modification methods as well as CRISPR/Cas9 technology. In addition, we review methods for ploidy changes, including aneuploid generation, methods for mating type switching and directed DSB. Combined with a description of useful selective markers and transformation techniques, this work represents a nearly complete guide to yeast genome modification.

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38

Jordan, I. King, and John F. McDonald. "Tempo and Mode of Ty Element Evolution in Saccharomyces cerevisiae." Genetics 151, no. 4 (April 1, 1999): 1341–51. http://dx.doi.org/10.1093/genetics/151.4.1341.

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Abstract The Saccharomyces cerevisiae genome contains five families of long terminal repeat (LTR) retrotransposons, Ty1–Ty5. The sequencing of the S. cerevisiae genome provides an unprecedented opportunity to examine the patterns of molecular variation existing among the entire genomic complement of Ty retrotransposons. We report the results of an analysis of the nucleotide and amino acid sequence variation within and between the five Ty element families of the S. cerevisiae genome. Our results indicate that individual Ty element families tend to be highly homogenous in both sequence and size variation. Comparisons of within-element 5′ and 3′ LTR sequences indicate that the vast majority of Ty elements have recently transposed. Furthermore, intrafamily Ty sequence comparisons reveal the action of negative selection on Ty element coding sequences. These results taken together suggest that there is a high level of genomic turnover of S. cerevisiae Ty elements, which is presumably in response to selective pressure to escape host-mediated repression and elimination mechanisms.

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39

Rainha, João, Joana L. Rodrigues, and Lígia R. Rodrigues. "CRISPR-Cas9: A Powerful Tool to Efficiently Engineer Saccharomyces cerevisiae." Life 11, no. 1 (December 26, 2020): 13. http://dx.doi.org/10.3390/life11010013.

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Saccharomyces cerevisiae has been for a long time a common model for fundamental biological studies and a popular biotechnological engineering platform to produce chemicals, fuels, and pharmaceuticals due to its peculiar characteristics. Both lines of research require an effective editing of the native genetic elements or the inclusion of heterologous pathways into the yeast genome. Although S. cerevisiae is a well-known host with several molecular biology tools available, a more precise tool is still needed. The clustered, regularly interspaced, short palindromic repeats–associated Cas9 (CRISPR-Cas9) system is a current, widespread genome editing tool. The implementation of a reprogrammable, precise, and specific method, such as CRISPR-Cas9, to edit the S. cerevisiae genome has revolutionized laboratory practices. Herein, we describe and discuss some applications of the CRISPR-Cas9 system in S. cerevisiae from simple gene knockouts to more complex processes such as artificial heterologous pathway integration, transcriptional regulation, or tolerance engineering.

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40

KANEKO, Yoshinobu. "New Genetic Map of Saccharomyces cerevisiae and Genome Analysis." JOURNAL OF THE BREWING SOCIETY OF JAPAN 85, no. 8 (1990): 545–50. http://dx.doi.org/10.6013/jbrewsocjapan1988.85.545.

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41

McKinlay, Anastasia, Carlos L. Araya, and Stanley Fields. "Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae." G3: Genes|Genomes|Genetics 1, no. 7 (December 2011): 549–58. http://dx.doi.org/10.1534/g3.111.000810.

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42

Dunham, M. J., H. Badrane, T. Ferea, J. Adams, P. O. Brown, F. Rosenzweig, and D. Botstein. "Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae." Proceedings of the National Academy of Sciences 99, no. 25 (November 21, 2002): 16144–49. http://dx.doi.org/10.1073/pnas.242624799.

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43

DiCarlo, James E., Julie E. Norville, Prashant Mali, Xavier Rios, John Aach, and George M. Church. "Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems." Nucleic Acids Research 41, no. 7 (March 4, 2013): 4336–43. http://dx.doi.org/10.1093/nar/gkt135.

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44

Forster, J. "Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network." Genome Research 13, no. 2 (February 1, 2003): 244–53. http://dx.doi.org/10.1101/gr.234503.

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Oberbeckmann, Elisa, Michael Wolff, Nils Krietenstein, Mark Heron, Jessica L. Ellins, Andrea Schmid, Stefan Krebs, Helmut Blum, Ulrich Gerland, and Philipp Korber. "Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome." Genome Research 29, no. 12 (November 6, 2019): 1996–2009. http://dx.doi.org/10.1101/gr.253419.119.

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Rybarczyk-Filho, José Luiz, Mauro A. A. Castro, Rodrigo J. S. Dalmolin, José C. F. Moreira, Leonardo G. Brunnet, and Rita M. C. de Almeida. "Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case." Nucleic Acids Research 39, no. 8 (December 15, 2010): 3005–16. http://dx.doi.org/10.1093/nar/gkq1269.

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47

Auxillos, Jamie Y., Eva Garcia-Ruiz, Sally Jones, Tianyi Li, Shuangying Jiang, Junbiao Dai, and Yizhi Cai. "Multiplex Genome Engineering for Optimizing Bioproduction in Saccharomyces cerevisiae." Biochemistry 58, no. 11 (February 28, 2019): 1492–500. http://dx.doi.org/10.1021/acs.biochem.8b01086.

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Ohkuni, Kentaro, Katsuhiko Shirahige, and Akihiko Kikuchi. "Genome-wide expression analysis of NAP1 in Saccharomyces cerevisiae." Biochemical and Biophysical Research Communications 306, no. 1 (June 2003): 5–9. http://dx.doi.org/10.1016/s0006-291x(03)00907-0.

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Sambasivam, Vijayan, Desirazu N. Rao, and Srinivasan Chandrasegaran. "Rewriting the Genome of the Model Eukaryote Saccharomyces cerevisiae." Resonance 25, no. 6 (June 2020): 801–16. http://dx.doi.org/10.1007/s12045-020-0997-8.

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Kakimoto, Masayuki, Atsushi Kobayashi, Ryouichi Fukuda, Yasuke Ono, Akinori Ohta, and Etsuro Yoshimura. "Genome-Wide Screening of Aluminum Tolerance in Saccharomyces cerevisiae." BioMetals 18, no. 5 (October 2005): 467–74. http://dx.doi.org/10.1007/s10534-005-4663-0.

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Journal articles on the topic 'Saccharomyces cerevisiae genome codes'

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