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Academic literature on the topic 'Saccharomyces cerevisiae genome codes'

Author: Grafiati

Published: 6 September 2023

Last updated: 7 September 2023

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Journal articles on the topic "Saccharomyces cerevisiae genome codes"

1

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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2

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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5

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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7

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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10

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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Dissertations / Theses on the topic "Saccharomyces cerevisiae genome codes"

1

Rowley, Neil K. "Studies on the Saccharomyces cerevisiae genome." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361615.

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Greig, Duncan. "Sex, species and Saccharomyces cerevisiae." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301401.

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Novarina, D. "MECHANISMS PRESERVING GENOME INTEGRITY IN SACCHAROMYCES CEREVISIAE." Doctoral thesis, Università degli Studi di Milano, 2013. http://hdl.handle.net/2434/215589.

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The integrity of the genome is continuously jeopardized by endogenous reactive byproducts of cellular metabolism and genotoxic insults by environmental agents, as well as by the DNA transactions (replication, transcription and recombination) required for cell survival and proliferation. Failure of the mechanisms deputed to the maintenance of genome integrity leads to genome instability, which is a hallmark of cancer and a driving force of tumorigenesis. To fully understand the mechanisms leading to genome instability and the cellular pathways counteracting them, three basic tasks must be achieved: i) identify all the genes implicated in the control of genome integrity; ii) unravel their biological role; iii) define the mechanistic molecular details of the processes in which they are implicated. This thesis describes work performed in the budding yeast Saccharomyces cerevisiae to explore the genome stability landscape at all these three levels. This model system is extremely useful for two main reasons: a) its high genetic tractability allows the application of genome-wide genetic screenings; b) the large conservation of the genome integrity pathways allows to extend the findings obtained in yeast to other eukaryotic organisms. We performed a genome-wide screen, based on the overexpression of the DDC2 DNA damage checkpoint gene in the yeast deletion collection, to identify genome stability genes on the basis of spontaneous accumulation of endogenous DNA damage in the corresponding mutant strains. Our screen identified several genes implicated in the control of genome integrity, highlighting, in particular, a key role for pathways protecting against oxidative stress. We present here the preliminary characterization of a new genome integrity gene, VID22. We also investigated the mechanisms counteracting a newly discovered source of genome instability, namely ribonucleotides (rNTPs) incorporated in genomic DNA during replication. We uncovered a role for RNase H enzymes, template switch pathways and Pol ζ translesion polymerase in protecting from misincorporated rNTPs. Given that mutations in any of the three human RNase H2 subunits were proven to cause Aicardi-Goutiéres Syndrome, these results might contribute to shed light on the complex and largely unknown pathogenetic mechanism of this rare genetic disease. Finally, we studied the molecular details underlying the role of Rad9 mediator protein in DNA damage checkpoint activation, exploring the dynamics of Rad9 dimerization, chromatin binding, CDK-dependent phosphorylation and checkpoint activation in G1 and M phases of the cell cycle; in particular, we characterized an M-phase specific pathway for checkpoint activation which is relies on Rad9-Dpb11 interaction.

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SHANMUGAN, MUTHU KUMAR. "EXPLORING GENOME INTEGRITY PATHWAYS IN SACCHAROMYCES CEREVISIAE." Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/229912.

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Genomic DNA is under constant attack from both endogenous and exogenous DNA damaging agents like reactive oxygen species which include O2, H2O2, OH, reactive carbonyl species, alkylating agents such as estrogen and cholesterol metabolites, radiations (like UV, x-rays and gamma rays) and mutagenic chemicals. Moreover, threats to DNA integrity can also come from DNA metabolism such as replication, transcription and recombination. In order to survive and faithfully transmit the genetic material to the progeny, cells must detect the damage and activate repair mechanisms and, if the damage cannot be repaired, trigger the apoptotic program. All these processes, which are collectively known as DNA damage response (DDR), are coordinated by surveillance mechanisms often called DNA damage checkpoint, which temporarily halt or slow down cell cycle progression to provide enough time for DNA repair. The failure of the DNA damage response and other mechanisms deputed to the maintenance of genome integrity leads to a condition called “Genome Instability”, consisting in the accumulation of damage, genomic aberrations, such as mutations, gross chromosomal rearrangements and chromosome loss. Genome instability is a hallmark of cancer and a driving force in tumorigenesis. We exploit budding yeast Saccharomyces cerevisiae as a model system for studies on genome maintenance pathways which are highly conserved throughout evolution from yeast to human. Despite recent advances in the field, genome integrity pathways are not yet fully understood and not all the genes involved have been identified. We developed a screening strategy, based on the overexpression of DDC2, a critical DNA damage checkpoint gene in the contest of a yeast deletion collection, in order to identify genes controlling genome integrity on the basis of spontaneous accumulation of endogenous DNA damage. We identified several genes and pathways associated with genome integrity maintenance, among which are many genes induced in peroxisome biogenesis and mitochondria structure and function, as well as several uncharacterized ORFs.

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Bleackley, Mark Robert. "Transition metal tolerance and the Saccharomyces cerevisiae genome." Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/30821.

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Transition metal ions are essential nutrients to all forms of life. Iron, copper, zinc, manganese, cobalt and nickel all have unique chemical and physical properties that make them attractive molecules for use in biological systems. Many of these same properties that allow these metals to provide essential biochemical activities and structural motifs to a multitude of proteins including enzymes and other cellular constituents also leads to a potential for cytotoxicity. Organisms have been required to evolve a number of systems for the efficient uptake, intracellular transport, protein loading and storage of metal ions to ensure that the needs of the cells can be met while minimizing the associated toxic effects. The yeast Saccharomyces cerevisiae has been used as model organism for the investigation of these systems and a majority of the genes and biological systems that function in yeast metal homeostasis are conserved throughout eukaryotes to humans. Traditionally, genomic studies in metal homeostasis focus on the response to one, or in some cases two, metals. Here, I have used high density yeast arrays of a S. cerevisiae deletion collection to study the genes required for tolerance to six transition metals in parallel and I have used this data to examine the role of genes not only in the homeostasis of individual metals but to also gain insight into cellular transition metal homeostasis as a whole. Genes and pathways with novel function in the homeostasis of a particular metal have been identified along with the systems that function with broad spectrum metal specificity. Data generated in this screen has also be combined with previously published data sets that examine different aspects of yeast biology in an attempt to delve deeper in to the cellular machinery that allows yeast, and potentially the cells of other organisms, to maintain the balance between metal ions as essential nutrients as opposed to toxic moieties. Metallochaperones represent a relatively recent emerging class of proteins that play a central role in maintaining this balance. As part of the analysis of the high density array screens, putative chaperones have been identified. Additionally a yeast 2 hybrid screen using a cytoplasmic domain of the S. cerevisiae high affinity iron transporter Ftr1p has been performed to with the goal of discovering candidate iron chaperones. As a whole, the research discussed in this thesis has shed light on a number of new features of the homeostatic mechanisms that function in S. cerevisiae and will provide the basis for further investigation into the interactions between cells and metal ions eventually leading to implications in human health and disease.

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Minchell, Nicola E. "DNA topological stress during DNA replication in Saccharomyces cerevisiae." Thesis, University of Sussex, 2019. http://sro.sussex.ac.uk/id/eprint/81222/.

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DNA topological stress impedes normal DNA replication. If topological stress is allowed to build up in front of the replication fork, the fork rotates to overcome the stress, leading to formation of DNA pre-catenanes. The formation of DNA pre-catenanes is therefore a marker of DNA topological stress. In this study, I have examined how transcription linked DNA topological stress impacts on fork rotation and on endogenous DNA damage. Transcription, similar to replication, affects the topology of the DNA; and collision between the two machineries is likely to lead to high levels of DNA topological stress. I found that the frequency of fork rotation during DNA replication, increases with the number of genes present on a plasmid. Interestingly, I also found that this increase in pre-catenation is dependent on the cohesin complex. Cohesin and transcription are known to be linked, as transcription leads to the translocation of cohesin along budding yeast DNA away from its loading sites. Cohesin plays a major role in establishing chromosomal structure, influencing gene expression and genetic inheritance. In this work, I have analysed the relationship between cohesin and the generation of topological stress and found that topological stress associated with cohesin can lead to DNA replication stress and DNA damage.

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Cook, Kristen. "Regulation of Genome-Wide Transcriptional Stress Responses in Saccharomyces cerevisiae." Thesis, Harvard University, 2011. http://dissertations.umi.com/gsas.harvard:10032.

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In response to osmotic shock in Saccharomyces cerevisiae the MAP kinase Hog1 coordinates a large-scale transcriptional stress response, rapidly producing hundreds of copies of specified transcripts. Many of the most highly induced genes are bound and regulated by a transcription factor, Sko1, but lack the canonical binding site for this factor. We use ChIP-seq to demonstrate a stress-specific binding mode of Sko1. In stress, Sko1 binds to promoters in close proximity to Hog1, and another Hog1-regulated transcription factor, Hot1. This mode of Sko1 binding requires the physical presence of Hog1, but not Hog1 phosphorylation of Sko1. We identify candidate Sko1 and Hot1 binding motifs that predict co-localization of Sko1, Hot1, and Hog1 at promoters. We then demonstrate a role for Sko1 and Hot1 in directing Hog1-associated RNA Pol II to target genes, where Hog1 is present with the elongating polymerase. We suggest a possible model for Hog1 reprogramming of transcription in the early stages of the osmotic stress response. We then determine the extent and structure of the Hog1 controlled transcriptional program in a related stress, damage to the cell wall. We find that Sko1 and Hot1 have different apparent thresholds for activation by Hog1. In addition, in cell wall damage, Hog1 regulates an additional transcription factor, Rlm1, that is not involved in other Hog1 regulated stress responses. This factor is activated by the coincidence of a signal from Hog1 with that of another MAP kinase, Slt2.

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Coissac, Éric. "Analyse structurale et fonctionnelle du genome de la levure saccharomyces cerevisiae." Paris 6, 1996. http://www.theses.fr/1996PA066520.

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Dans le cadre d'une collaboration internationale, la sequence nucleotidique du genome de la levure saccharomyces cerevisiae a ete entierement determinee. Au sein de ce projet, nous avons sequence un fragment d'adn de 39411 paires de bases correspondant aux regions telomerique et subtelomerique gauches du chromosome vii. Cette region comporte dix-huit phases ouvertes de lectures longues de plus de cent codons et une de soixante-seize. Parmi elles, six correspondent a des genes precedemment identifies : adh4, fzf1, hxk2, rtg2, hfm1 et pde1. La deletion de cinq autres a ete realisee (ygl257c, ygl255w, ygl250w, ygl249w et ygl246c). Deux de ces deletions (ygl250w et ygl246c) provoquent un retard de croissance sur milieu complet a une temperature de 28c. La phase ouverte ygl261c est un nouveau membre de la famille des seripauperines. Les caracteristiques de cette famille ont ete intensement etudiees. Cette etude montre qu'une pression de selection doit s'exercer sur cette famille afin de maintenir un de ces membres localise sur chacun des seize chromosomes. La deuxieme partie de cette these est consacree a l'analyse exhaustive des duplications de genes chez s. Cerevisiae et dans quatres organismes eucaryotes et bacteriens. Nos resultats montrent que le niveau de duplication de l'ensemble des genomes etudies est equivalent. Une etude plus approfondie demontre l'importance des telomeres dans les mecanismes de duplication chez la levure. Ces resultats suggerent qu'ils pourraient jouer le role de guides dans les processus de recombinaison ectopique.

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Teixeira, Maria Teresa. "Organisation du noyau et analyse fonctionnelle du genome de saccharomyces cerevisiae." Paris 11, 2000. http://www.theses.fr/2000PA112033.

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La structure du noyau semble etre hautement organisee : de nombreux facteurs nucleaires sont adresses a des domaines discrets, en concordance avec leur role localise. Cette regionalisation spatiale et fonctionnelle est particulierement bien etablie dans le cas du nucleole, site d'assemblage des sous-unites ribosomiques et dans le cas du pore nucleaire, site du trafic nucleo-cytoplasmique. Ce travail de these a pour but de participer a la caracterisation moleculaire de certains constituants du noyau impliques dans cette organisation fonctionnelle en prenant comme modele experimental la levure saccharomyces cerevisi. Dans une phase initiale du travail, nous nous sommes focalises dans l'etude d'une proteine constitutive du pore nucleaire, nup145p, impliquee dans l'export des arnm du noyau vers le cytoplasme. Nous avons montre que nup145p est clive in vivo en deux domaines, n- et c- nup145p, qui agissent de facon independante au niveau du pore nucleaire. En particulier, le c- nup145p s'associe avec d'autres nucleoporines pour former un sous-complexe du pore nucleaire implique dans l'export des arnm du noyau vers le cytoplasme, dans la distribution des pores nucleaires au sein de l'enveloppe nucleaire et dans l'integrite du nucleole. La maturation post-traductionelle de nup145p est essentielle a la localisation et l'activite du n-nup145p. Cette proteolyse specifique est autocatalytique et le site catalytique reside dans le n-nup145p. Nous avons egalement participe a l'analyse fonctionnelle du genome de saccharomyces cerevisi au sein du programme eurofan. 417 souches de levure individuellement deletees pour chacun des genes de fonction inconnue (collection euroscarf) ont ete analysees de facon independante pour la distribution de trois marqueurs nucleaires. Ainsi, nous avons selectionne 14 genes candidats potentiellement impliques dans l'organisation de l'architecture nucleaire et/ou dans le transport nucleo-cytoplasmique.

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Amai, Takamitsu. "Development of genome editing technology of mitochondrial DNA in Saccharomyces cerevisiae." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263707.

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Books on the topic "Saccharomyces cerevisiae genome codes"

1

Ray, Malay Kumar. Studies of cytoplasmically inherited genes for components of the mitochondrial ATP ase complex: Analysis of the Oli-2 region of the mitrochondrial genome of 'Saccharomyces cerevisiae'. [s.l.]: typescript, 1985.

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Edmonds, Dawn Elaine. A genome-wide screen in Saccharomyces cerevisiae to identify novel genes that interact with telomerase. 2006.

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(Editor), Peter Fantes, and Jean Beggs (Editor), eds. The Yeast Nucleus (Frontiers in Molecular Biology). Oxford University Press, USA, 2000.

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Book chapters on the topic "Saccharomyces cerevisiae genome codes"

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Dannenmaier, Stefan, Silke Oeljeklaus, and Bettina Warscheid. "2nSILAC for Quantitative of Prototrophic Baker’s Yeast." In Methods in Molecular Biology, 253–70. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_18.

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AbstractStable isotope labeling by amino acids in cell culture (SILAC) combined with high-resolution mass spectrometry is a quantitative strategy for the comparative analysis of (sub)proteomes. It is based on the metabolicincorporation of stable isotope-coded amino acids during growth of cells or organisms. Here, complete labeling of proteins with the amino acid(s) selected for incorporation needs to be guaranteed to enable accurate quantification on a proteomic scale. Wild-type strains of baker’s yeast (Saccharomyces cerevisiae), which is a widely accepted and well-studied eukaryotic model organism, are generally able to synthesize all amino acids on their own (i.e., prototrophic). To render them amenable to SILAC, auxotrophies are introduced by genetic manipulations. We addressed this limitation by developing a generic strategy for complete “native” labeling of prototrophic S. cerevisiae with isotope-coded arginine and lysine, referred to as “2nSILAC”. It allows for directly using and screening several genome-wide yeast mutant collections that are easily accessible to the scientific community for functional proteomic studies but are based on prototrophic variants of S. cerevisiae.

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Srivatsan, Anjana, Christopher D. Putnam, and Richard D. Kolodner. "Analyzing Genome Rearrangements in Saccharomyces cerevisiae." In Methods in Molecular Biology, 43–61. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7306-4_5.

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Nookaew, Intawat, Roberto Olivares-Hernández, Sakarindr Bhumiratana, and Jens Nielsen. "Genome-Scale Metabolic Models of Saccharomyces cerevisiae." In Methods in Molecular Biology, 445–63. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-173-4_25.

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Si, Tong, and Huimin Zhao. "RNAi-Assisted Genome Evolution (RAGE) in Saccharomyces cerevisiae." In Methods in Molecular Biology, 183–98. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6337-9_15.

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Weining, Song, and Dongyou Liu. "Genetic Manipulation and Genome Editing of Saccharomyces cerevisiae." In Molecular Food Microbiology, 329–36. 3rd ed. First edition. | Boca Raton : Taylor & Francis, 2021. |: CRC Press, 2021. http://dx.doi.org/10.1201/9781351120388-25.

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Jordan, King, and John F. McDonald. "Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements." In Transposable Elements and Genome Evolution, 3–13. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4156-7_2.

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Caspeta, Luis, and Prisciluis Caheri Salas Navarrete. "Reduction of the Saccharomyces cerevisiae Genome: Challenges and Perspectives." In Minimal Cells: Design, Construction, Biotechnological Applications, 117–39. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-31897-0_5.

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Xu, Tao, Nikë Bharucha, and Anuj Kumar. "Genome-Wide Transposon Mutagenesis in Saccharomyces cerevisiae and Candida albicans." In Methods in Molecular Biology, 207–24. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-197-0_13.

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Korbel, J. O., H. E. Assmus, S. M. Kielbasa, and H. Herzel. "Compositional Asymmetries and Predicted Origins of Replication of the Saccharomyces Cerevisiae Genome." In Bioinformatics of Genome Regulation and Structure, 33–38. Boston, MA: Springer US, 2004. http://dx.doi.org/10.1007/978-1-4419-7152-4_4.

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Sasano, Yu, Minetaka Sugiyama, and Satoshi Harashima. "Development and Application of Novel Genome Engineering Technologies in Saccharomyces cerevisiae." In Microbial Production, 53–62. Tokyo: Springer Japan, 2014. http://dx.doi.org/10.1007/978-4-431-54607-8_5.

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Conference papers on the topic "Saccharomyces cerevisiae genome codes"

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Heath, Allison P., Lydia Kavraki, and Gabor Balazsi. "Bipolarity of the Saccharomyces Cerevisiae Genome." In 2008 2nd International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2008. http://dx.doi.org/10.1109/icbbe.2008.84.

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Cifuentes, Yina, Sergio Latorre, Andres Pinzon, and Mario Velasquez. "Draft genome sequence of a natural isolated Saccharomyces cerevisiae from Colombia." In 2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2015. http://dx.doi.org/10.1109/iccabs.2015.7344727.

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Li, Mingtao, Xiaoyu You, and Kunrong Mei. "Site-directed mutagenesis of Saccharomyces cerevisiae genome using mismatch PCR product." In International Conference on Biomedical and Intelligent Systems (IC-BIS 2022), edited by Ahmed El-Hashash. SPIE, 2022. http://dx.doi.org/10.1117/12.2660375.

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Guo, Shou-Hui, Li-Qin Xu, Wei Chen, Guo-Qing Liu, and Hao Lin. "Recombination spots prediction using DNA physical properties in the saccharomyces cerevisiae genome." In NUMERICAL ANALYSIS AND APPLIED MATHEMATICS ICNAAM 2012: International Conference of Numerical Analysis and Applied Mathematics. AIP, 2012. http://dx.doi.org/10.1063/1.4756460.

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"Whole genome sequencing and assembly of Saccharomyces cerevisiae genomes using Oxford Nanopore data." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-037.

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CHEN, YU, and DONG XU. "GENOME-SCALE PROTEIN FUNCTION PREDICTION IN YEAST SACCHAROMYCES CEREVISIAE THROUGH INTEGRATING MULTIPLE SOURCES OF HIGH-THROUGHPUT DATA." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2004. http://dx.doi.org/10.1142/9789812702456_0045.

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Reports on the topic "Saccharomyces cerevisiae genome codes"

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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.

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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.

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