Summary: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Publications238 found, 100 shown here
- The genetic landscape of a cellMichael Costanzo
Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
Science 327:425-31. 2010..quantitative genetic interaction profiles for approximately 75% of all genes in the budding yeast, Saccharomyces cerevisiae. A network based on genetic interaction profiles reveals a functional map of the cell in which genes of ..
- The BioGRID Interaction Database: 2008 updateBobby Joe Breitkreutz
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
Nucleic Acids Res 36:D637-40. 2008..complete set of interactions reported to date in the primary literature for both the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe...
- Crystal structure of the eukaryotic ribosomeAdam Ben-Shem
IGBMC Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, BP10142, Illkirch F 67400, France
Science 330:1203-9. 2010..We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation...
- The transcriptional landscape of the yeast genome defined by RNA sequencingUgrappa Nagalakshmi
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
Science 320:1344-9. 2008..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated...
- Capturing chromosome conformationJob Dekker
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Science 295:1306-11. 2002..Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic ..
- Population genomics of domestic and wild yeastsGianni Liti
Institute of Genetics, Queen s Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
Nature 458:337-41. 2009Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution...
- Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profilingNicholas T Ingolia
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
Science 324:218-23. 2009..Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible...
- Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiaeM S Longtine
Department of Biology, University of North Carolina, Chapel Hill 27599 3280, USA
Yeast 14:953-61. 1998An important recent advance in the functional analysis of Saccharomyces cerevisiae genes is the development of the one-step PCR-mediated technique for deletion and modification of chromosomal genes...
- The chemical genomic portrait of yeast: uncovering a phenotype for all genesMaureen E Hillenmeyer
Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
Science 320:362-5. 2008..We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition...
- Saccharomyces Genome Database provides mutant phenotype dataStacia R Engel
Department of Genetics, Stanford University, Stanford, CA, USA
Nucleic Acids Res 38:D433-6. 2010..yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast...
- Stochastic switching as a survival strategy in fluctuating environmentsMurat Acar
Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nat Genet 40:471-5. 2008..explore how switching affects population growth by using the galactose utilization network of Saccharomyces cerevisiae. We engineered a strain that randomly transitions between two phenotypes as a result of stochastic gene ..
- A global protein kinase and phosphatase interaction network in yeastAshton Breitkreutz
Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1X5, Canada
Science 328:1043-6. 2010..An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses...
- The evolutionary fate and consequences of duplicate genesM Lynch
Department of Biology, University of Oregon, Eugene, OR 97403, USA
Science 290:1151-5. 2000..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
- Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespanKonrad T Howitz
BIOMOL Research Laboratories, Inc, 5120 Butler Pike, Plymouth Meeting, Pennsylvania 19462, USA
Nature 425:191-6. 2003..In the budding yeast Saccharomyces cerevisiae, calorie restriction extends lifespan by increasing the activity of Sir2 (ref...
- A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genomeTravis N Mavrich
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 18:1073-83. 2008..3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping...
- The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanismsM Kaeberlein
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genes Dev 13:2570-80. 1999..Sir2p is a limiting component in promoting yeast longevity, and increasing the gene dosage extends the life span in wild-type cells. A possible role of the conserved SIR2 in mammalian aging is discussed...
- Nonfilamentous C. albicans mutants are avirulentH J Lo
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA
Cell 90:939-49. 1997Candida albicans and Saccharomyces cerevisiae switch from a yeast to a filamentous form. In Saccharomyces, this switch is controlled by two regulatory proteins, Ste12p and Phd1p...
- Rewiring of genetic networks in response to DNA damageSourav Bandyopadhyay
Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
Science 330:1385-9. 2010..Differential networks chart a new type of genetic landscape that is invaluable for mapping cellular responses to stimuli...
- Global analysis of protein expression in yeastSina Ghaemmaghami
Howard Hughes Medical Institute, University of California-San Francisco, San Francisco, California 94143-2240, USA
Nature 425:737-41. 2003..To facilitate global protein analyses, we have created a Saccharomyces cerevisiae fusion library where each open reading frame is tagged with a high-affinity epitope and expressed from ..
- Extending healthy life span--from yeast to humansLuigi Fontana
Division of Geriatrics and Nutritional Science, Washington University School of Medicine, St Louis, MO 63110, USA
Science 328:321-6. 2010..We discuss these findings and their potential application to prevention of age-related disease and promotion of healthy aging in humans, and the challenge of possible negative side effects...
- Nucleosome positioning and gene regulation: advances through genomicsCizhong Jiang
Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
Nat Rev Genet 10:161-72. 2009..A detailed picture is starting to emerge of how diverse factors, including underlying DNA sequences and chromatin remodelling complexes, influence nucleosome positioning...
- An evolutionarily conserved mechanism for controlling the efficiency of protein translationTamir Tuller
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Cell 141:344-54. 2010..We suggest that the slow "ramp" at the beginning of mRNAs serves as a late stage of translation initiation, forming an optimal and robust means to reduce ribosomal traffic jams, thus minimizing the cost of protein expression...
- Lessons on longevity from budding yeastMatt Kaeberlein
Department of Pathology, University of Washington, Seattle, Washington 98195, USA
Nature 464:513-9. 2010..The first interventions to slow human ageing may spring from the humble yeast...
- Dissection of genetically complex traits with extremely large pools of yeast segregantsIan M Ehrenreich
Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA
Nature 464:1039-42. 2010..The method involves generating very large numbers of progeny from a cross between two Saccharomyces cerevisiae strains and then phenotyping and genotyping pools of these offspring...
- The DNA-encoded nucleosome organization of a eukaryotic genomeNoam Kaplan
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Nature 458:362-6. 2009..Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo...
- Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexesLee Zou
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Science 300:1542-8. 2003..Our data suggest that RPA-coated ssDNA is the critical structure at sites of DNA damage that recruits the ATR-ATRIP complex and facilitates its recognition of substrates for phosphorylation and the initiation of checkpoint signaling...
- Elevated histone expression promotes life span extensionJason Feser
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80010, USA
Mol Cell 39:724-35. 2010..This study indicates that maintenance of the fundamental chromatin structure is critical for slowing down the aging process and reveals that increasing the histone supply extends life span...
- High-resolution DNA-binding specificity analysis of yeast transcription factorsCong Zhu
Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
Genome Res 19:556-66. 2009..These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes...
- Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicityEsti Yeger-Lotem
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nat Genet 41:316-23. 2009..Bridging these data and data from mRNA profiling provided functional explanations for many of these genes and identified previously unknown relations between alpha-synuclein toxicity and basic cellular pathways...
- A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicingGwendolyn M Wilmes
Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143 2200, USA
Mol Cell 32:735-46. 2008..Finally, we show that Csn12 plays a role in pre-mRNA splicing, which is independent of other signalosome components. Thus, Sem1 is involved in three separate and functionally distinct complexes...
- Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolutionD Allan Drummond
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
Cell 134:341-52. 2008....
- Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcriptionMichael J Carrozza
Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
Cell 123:581-92. 2005..This erases transcription elongation-associated acetylation to suppress intragenic transcription initiation...
- Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth controlRobbie Loewith
Division of Biochemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
Mol Cell 10:457-68. 2002The target of rapamycin (TOR) proteins in Saccharomyces cerevisiae, TOR1 and TOR2, redundantly regulate growth in a rapamycin-sensitive manner...
- Cse4 is part of an octameric nucleosome in budding yeastRaymond Camahort
Stowers Institute for Medical Research, Kansas City, MO 64110, USA
Mol Cell 35:794-805. 2009..Taken together, our experimental evidence supports the model that the Cse4 nucleosome is an octamer, containing two copies each of Cse4, H2A, H2B, and H4...
- Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolutionJean Paul Armache
Gene Center, Department of Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
Proc Natl Acad Sci U S A 107:19748-53. 2010..5-Å resolution. This map, together with a 6.1-Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ∼98% of the rRNA...
- Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controlsR J Kaufman
Department of Biological Chemistry and Howard Hughes Medical Institute, The University of Michigan Medical Center, Ann Arbor, Michigan 48109-0650 USA
Genes Dev 13:1211-33. 1999
- GENECODIS: a web-based tool for finding significant concurrent annotations in gene listsPedro Carmona-Saez
Biocomputing Unit, National Center of Biotechnology CNB CSIC, C Darwin 3, Campus Universidad Autonoma de Madrid, 28049 Madrid, Spain
Genome Biol 8:R3. 2007..GENECODIS is publicly available at http://genecodis.dacya.ucm.es/...
- Translation efficiency is determined by both codon bias and folding energyTamir Tuller
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 107:3645-50. 2010..Using the Escherichia coli and Saccharomyces cerevisiae transcriptomes, we conducted a genome-scale study aiming at dissecting the determinants of translation ..
- A hierarchical combination of factors shapes the genome-wide topography of yeast meiotic recombination initiationJing Pan
Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Cell 144:719-31. 2011..This map illuminates the occurrence of DSBs in repetitive DNA elements, repair of which can lead to chromosomal rearrangements. We also discuss implications for evolutionary dynamics of recombination hot spots...
- Unstable tandem repeats in promoters confer transcriptional evolvabilityMarcelo D Vinces
FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
Science 324:1213-6. 2009..A search for tandem repeats in the Saccharomyces cerevisiae genome revealed that the nucleosome-free region directly upstream of genes (the promoter region) is ..
- Two strategies for gene regulation by promoter nucleosomesItay Tirosh
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Genome Res 18:1084-91. 2008..Analysis of nucleosome positioning in human promoters reproduces the main observations. Our results suggest two distinct strategies for gene regulation by chromatin, which are selectively employed by different genes...
- Cell wall integrity signaling in Saccharomyces cerevisiaeDavid E Levin
Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
Microbiol Mol Biol Rev 69:262-91. 2005....
- Mechanism of eukaryotic homologous recombinationJoseph San Filippo
Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
Annu Rev Biochem 77:229-57. 2008..Recent progress on elucidating the mechanisms of action of Rad51 and Dmc1 and their cohorts of ancillary factors is reviewed here...
- Induction of autophagy by spermidine promotes longevityTobias Eisenberg
Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
Nat Cell Biol 11:1305-14. 2009..Finally, we found that enhanced autophagy is crucial for polyamine-induced suppression of necrosis and enhanced longevity...
- Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeastNorman Pavelka
Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
Nature 468:321-5. 2010....
- An ER-mitochondria tethering complex revealed by a synthetic biology screenBenoît Kornmann
Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
Science 325:477-81. 2009..The tethering complex localized to discrete foci, suggesting that discrete sites of close apposition between ER and mitochondria facilitate interorganelle calcium and phospholipid exchange...
- Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiaeJurgi Camblong
Department of Cell Biology, Sciences III, University of Geneva, 30 quai E Ansermet, 1211 Geneva 4, Switzerland
Cell 131:706-17. 2007....
- The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein responseC Sidrauski
Department of Biochemistry and Biophysics, University of California, School of Medicine, San Francisco 94143 0448, USA
Cell 90:1031-9. 1997..The addition of purified tRNA ligase completes splicing; we therefore have reconstituted HAC1 mRNA splicing in vitro from purified components...
- MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endingsMitch McVey
Department of Biology, Tufts University, 165 Packard Avenue, Medford, MA 02155, USA
Trends Genet 24:529-38. 2008..We propose a mechanistic model for MMEJ and highlight important questions for future research...
- A comprehensive strategy enabling high-resolution functional analysis of the yeast genomeDavid K Breslow
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA
Nat Methods 5:711-8. 2008Functional genomic studies in Saccharomyces cerevisiae have contributed enormously to our understanding of cellular processes...
- Full dynamic range proteome analysis of S. cerevisiae by targeted proteomicsPaola Picotti
Institute of Molecular Systems Biology, ETH Zurich, Zurich CH 8093, Switzerland
Cell 138:795-806. 2009..We therefore demonstrate the potential of SRM-based proteomics to provide assays for the measurement of any set of proteins of interest in yeast at high-throughput and quantitative accuracy...
- Systematic mapping of genetic interaction networksScott J Dixon
Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada
Annu Rev Genet 43:601-25. 2009..Systematic screens conducted in the yeast Saccharomyces cerevisiae have identified thousands of genetic interactions and provided insight into the global structure of ..
- Evolution of biomolecular networks: lessons from metabolic and protein interactionsTakuji Yamada
European Molecular Biology Laboratory, Heidelberg, Germany
Nat Rev Mol Cell Biol 10:791-803. 2009..However, many evolutionary constraints can be uncovered only if temporal and spatial aspects are included in the network analysis...
- Specificity and stability in topology of protein networksSergei Maslov
Department of Physics, Brookhaven National Laboratory, Upton, NY 11973, USA
Science 296:910-3. 2002..This effect decreases the likelihood of cross talk between different functional modules of the cell and increases the overall robustness of a network by localizing effects of deleterious perturbations...
- Systematic genetic analysis with ordered arrays of yeast deletion mutantsA H Tong
Banting and Best Department of Medical Research, University of Toronto, Toronto ON, Canada M5G 1L6
Science 294:2364-8. 2001In Saccharomyces cerevisiae, more than 80% of the approximately 6200 predicted genes are nonessential, implying that the genome is buffered from the phenotypic consequences of genetic perturbation...
- Translational regulation of GCN4 and the general amino acid control of yeastAlan G Hinnebusch
Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
Annu Rev Microbiol 59:407-50. 2005..The activator protein Gcn4 of the yeast Saccharomyces cerevisiae is regulated by an intricate translational control mechanism, which is the primary focus of this review, ..
- Kinetochore recruitment of two nucleolar proteins is required for homolog segregation in meiosis IKirsten P Rabitsch
Research Institute of Molecular Pathology, Dr Bohr Gasse 7, A 1030 Vienna, Austria
Dev Cell 4:535-48. 2003..of a protein complex, Csm1/Lrs4, that is essential for monoorientation of sister kinetochores in Saccharomyces cerevisiae. Both proteins are present in vegetative cells, where they reside in the nucleolus...
- Increased mutagenesis and unique mutation signature associated with mitotic gene conversionWade M Hicks
Department of Biology and Rosenstiel Center, Brandeis University, Waltham, MA 02454 9110, USA
Science 329:82-5. 2010To examine the fidelity of DNA synthesis during double-strand break (DSB) repair in Saccharomyces cerevisiae we studied gene conversion in which both strands of DNA are newly synthesized...
- Identification of aneuploidy-tolerating mutationsEduardo M Torres
David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Cell 143:71-83. 2010....
- Uniform transitions of the general RNA polymerase II transcription complexAndreas Mayer
Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science, Ludwig Maximilians Universitat Munchen, Munich, Germany
Nat Struct Mol Biol 17:1272-8. 2010..Transitions are uniform and independent of gene length, type and expression...
- SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeastS Strahl-Bolsinger
Department of Biological Chemistry, University of California, Los Angeles 90095, USA
Genes Dev 11:83-93. 1997..RAP1 binding at the core region is unaffected by SIR3 overproduction and RAP1 shows no evidence of spreading. Thus, we propose that the structure of core telomeric heterochromatin differs from that extended by SIR3...
- A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promotersGwenael Badis
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
Mol Cell 32:878-87. 2008....
- A ubiquitin-like system mediates protein lipidationY Ichimura
Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
Nature 408:488-92. 2000..11) and Apg3, respectively. These reactions are necessary for the formation of Apg8-phosphatidylethanolamine. This lipidation has an essential role in membrane dynamics during autophagy...
- Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networksXionglei He
Department of Ecology and Evolutionary Biology, Ann Arbor, Michigan, USA
Nat Genet 42:272-6. 2010..interactions amongst biochemical reactions within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis...
- Comprehensive characterization of genes required for protein folding in the endoplasmic reticulumMartin C Jonikas
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
Science 323:1693-7. 2009..The use of a quantitative reporter in a comprehensive screen followed by systematic analysis of genetic dependencies should be broadly applicable to functional dissection of complex cellular processes from yeast to human...
- Abundance of ribosomal RNA gene copies maintains genome integritySatoru Ide
National Institute of Genetics, SOKENDAI, 1111 Yata, Mishima, 411 8540 Japan
Science 327:693-6. 2010..These results suggest that high concentrations of heavily transcribed genes are toxic to the cells, and therefore amplified genes, such as rDNA, have evolved...
- N-terminal acetylation of cellular proteins creates specific degradation signalsCheol Sang Hwang
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
Science 327:973-7. 2010..Using the yeast Saccharomyces cerevisiae, we found that the Nt-acetylated Met residue could act as a degradation signal (degron), targeted by the ..
- Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiaeAlexandra B Lantermann
Adolf Butenandt Institut, University of Munich, Munich, Germany
Nat Struct Mol Biol 17:251-7. 2010..differences from the previously published nucleosome organization of the distantly related yeast Saccharomyces cerevisiae. DNA sequence guides nucleosome positioning differently: for example, poly(dA-dT) elements are not ..
- Global analysis of nascent RNA reveals transcriptional pausing in terminal exonsFernando Carrillo Oesterreich
Max Planck Institute of Molecular Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
Mol Cell 40:571-81. 2010..The discovery of terminal exon pausing demonstrates functional coupling of transcription and splicing near gene ends...
- Frequent gain and loss of functional transcription factor binding sitesScott W Doniger
Computational Biology Program, Washington University School of Medicine, St Louis, Missouri, United States of America
PLoS Comput Biol 3:e99. 2007..The frequent gain and loss of TFBSs implies that cis-regulatory sequences are labile and, in the absence of turnover, may contribute to species-specific patterns of gene expression...
- A consensus of core protein complex compositions for Saccharomyces cerevisiaeJoris J Benschop
Department of Physiological Chemistry, University Medical Centre Utrecht, 3584 CG Utrecht, The Netherlands
Mol Cell 38:916-28. 2010..We determine consensus compositions for 409 core protein complexes from Saccharomyces cerevisiae by merging previous predictions with a new approach...
- Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosomeJean Paul Armache
Gene Center, Department of Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
Proc Natl Acad Sci U S A 107:19754-9. 2010..5-Å resolution, together with a 6.1-Å map of a translating Saccharomyces cerevisiae 80S ribosome, we have localized and modeled 74/80 (92...
- Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiaeGregory I Lang
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genetics 178:67-82. 2008..44x10(-10) at CAN1) and we propose a definition for the effective target size of genes (the probability that a mutation inactivates the gene) that acknowledges that the mutation rate is nonuniform across the genome...
- The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosolY Ye
Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 414:652-6. 2001..We propose that the Cdc48/p97-Ufd1-Npl4 complex extracts proteins from the ER membrane for cytosolic degradation...
- How common are extraribosomal functions of ribosomal proteins?Jonathan R Warner
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Mol Cell 34:3-11. 2009..Is this due to a lack of imaginative evolution by cells and viruses, or to a lack of imaginative experiments by molecular biologists?..
- The biomass objective functionAdam M Feist
GT Life Sciences, Inc, 10520 Wateridge Circle, San Diego, CA 92122, USA
Curr Opin Microbiol 13:344-9. 2010..Here we review fundamental issues associated with its formulation and use to compute optimal growth states...
- Genome-wide views of chromatin structureOliver J Rando
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
Annu Rev Biochem 78:245-71. 2009....
- tRNA cleavage is a conserved response to oxidative stress in eukaryotesDebrah M Thompson
Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
RNA 14:2095-103. 2008..In this work, we demonstrate that Saccharomyces cerevisiae contains a small RNA population consisting primarily of tRNA halves and rRNA fragments...
- Histone H4 lysine 16 acetylation regulates cellular lifespanWeiwei Dang
Gene Expression and Regulation Program, The Wistar Institute Philadelphia, Pennsylvania 19104, USA
Nature 459:802-7. 2009..This pathway, distinct from existing ageing models for yeast, may represent an evolutionarily conserved function of sirtuins in regulation of replicative ageing by maintenance of intact telomeric chromatin...
- The glyoxylate cycle is required for fungal virulenceM C Lorenz
Whitehead Institute for Biomedical Research, Nine Cambridge Center, Massachusetts 02142, USA
Nature 412:83-6. 2001..Here we use genome-wide expression profiles of the related yeast Saccharomyces cerevisiae to obtain a signature of the events that take place in the fungus on ingestion by a mammalian macrophage...
- Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusionHitoshi Nakatogawa
Department of Cell Biology, National Institute for Basic Biology, Okazaki 444 8585, Japan
Cell 130:165-78. 2007..Atg8 is a ubiquitin-like protein required for this process in Saccharomyces cerevisiae that can be conjugated to the lipid phosphatidylethanolamine by a ubiquitin-like system...
- Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifsJanine Mok
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
Sci Signal 3:ra12. 2010..approach to determine consensus phosphorylation site motifs targeted by 61 of the 122 kinases in Saccharomyces cerevisiae. By correlating these motifs with kinase primary sequence, we uncovered previously unappreciated rules ..
- Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALSAndrew C Elden
Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Nature 466:1069-75. 2010..Furthermore, these findings indicate that the TDP-43-ATXN2 interaction may be a promising target for therapeutic intervention in ALS and other TDP-43 proteinopathies...
- Defining genetic interactionRamamurthy Mani
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 105:3461-6. 2008..Although 52% of known synergistic genetic interactions in Saccharomyces cerevisiae were inferred according to the Min definition, we find that both Product and Log definitions (shown here ..
- An E3 ubiquitin ligase prevents ectopic localization of the centromeric histone H3 variant via the centromere targeting domainPrerana Ranjitkar
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, P O Box 19024, Seattle, WA 98109, USA
Mol Cell 40:455-64. 2010..Taken together, we propose that the CATD has a previously unknown role in maintaining the exclusive localization of Cse4 by preventing its mislocalization to euchromatin via Psh1-mediated degradation...
- Genome-wide patterns of histone modifications in yeastCatherine B Millar
Department of Biological Chemistry, Geffen School of Medicine and the Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
Nat Rev Mol Cell Biol 7:657-66. 2006..Recent studies have mapped histone modifications across the Saccharomyces cerevisiae genome...
- Origin and evolution of the mitochondrial proteomeC G Kurland
Department of Molecular Evolution, Evolutionary Biology Centre, University of Uppsala, Uppsala SE 752 36, Lund University, Lund SE 223 62, Sweden
Microbiol Mol Biol Rev 64:786-820. 2000..There are no indications of a specific alpha-proteobacterial origin to genes for glycolysis. In the absence of data to the contrary, it is assumed that the ancestral host cell was a heterotroph...
- Nascent transcript sequencing visualizes transcription at nucleotide resolutionL Stirling Churchman
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, USA
Nature 469:368-73. 2011..Application of NET-seq in Saccharomyces cerevisiae reveals that although promoters are generally capable of divergent transcription, the Rpd3S deacetylation ..
- Modelling neurodegeneration in Saccharomyces cerevisiae: why cook with baker's yeast?Vikram Khurana
Department of Neurology, Brigham and Women s and Massachusetts General Hospitals, Harvard Medical School, Boston, Massachusetts, USA
Nat Rev Neurosci 11:436-49. 2010..Here, we describe why the budding yeast Saccharomyces cerevisiae has a unique role in the neurodegeneration armamentarium...
- Structure and function of a transcriptional network activated by the MAPK Hog1Andrew P Capaldi
Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Department of Molecular and Cellular Biology, Cambridge, Massachusetts 02138, USA
Nat Genet 40:1300-6. 2008..This study lays out a path to identifying and characterizing the role of signal integration and processing in other gene regulatory networks...
- RNA polymerase II-TFIIB structure and mechanism of transcription initiationDirk Kostrewa
Gene Center Munich and Center for Integrated Protein Science Munich CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
Nature 462:323-30. 2009..Synthesis of the RNA chain and rewinding of upstream DNA displace the B-reader and B-linker, respectively, to trigger B release and elongation complex formation...
- How do Cdc7 and cyclin-dependent kinases trigger the initiation of chromosome replication in eukaryotic cells?Karim Labib
Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, United Kingdom
Genes Dev 24:1208-19. 2010..A series of recent studies has shed new light on the targets of Cdc7 and CDK, indicating that chromosome replication probably initiates by a fundamentally similar mechanism in all eukaryotes...
- A yeast TDP-43 proteinopathy model: Exploring the molecular determinants of TDP-43 aggregation and cellular toxicityBrian S Johnson
Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
Proc Natl Acad Sci U S A 105:6439-44. 2008..This work provides a mechanistic framework for investigating the toxicity of TDP-43 aggregation relevant to human disease and establishes a manipulable, high-throughput model for discovering potential therapeutic strategies...
- Growth signaling promotes chronological aging in budding yeast by inducing superoxide anions that inhibit quiescenceMartin Weinberger
Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
Aging (Albany NY) 2:709-26. 2010..Here we report that in Saccharomyces cerevisiae, alterations in growth signaling pathways impact levels of superoxide anions that promote chronological ..
- Signalling pathways in the unfolded protein response: development from yeast to mammalsKazutoshi Mori
Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake, Sakyo ku, Kyoto 606 8502, Japan
J Biochem 146:743-50. 2009..functional sensors/transducers, ubiquitously expressed, has increased with evolution, for example, one in Saccharomyces cerevisiae, two in Caenorhabditis elegans and Drosophila melanogaster, and three in mammals...
- Storage lipid synthesis is non-essential in yeastLine Sandager
Department of Crop Science, Swedish University of Agricultural Sciences, Box 44, S 230 53 Alnarp, Sweden
J Biol Chem 277:6478-82. 2002Steryl esters and triacylglycerol (TAG) are the main storage lipids in eukaryotic cells. In the yeast Saccharomyces cerevisiae, these storage lipids accumulate during stationary growth phase within organelles known as lipid bodies...
- Genetic basis of individual differences in the response to small-molecule drugs in yeastEthan O Perlstein
Howard Hughes Medical Institute, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Genet 39:496-502. 2007..Our results provide a step toward a systematic understanding of small-molecule drug action in genetically distinct individuals...
- TDP-43 mediates degeneration in a novel Drosophila model of disease caused by mutations in VCP/p97Gillian P Ritson
Department of Neurology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
J Neurosci 30:7729-39. 2010..VCP (p97 in mouse, TER94 in Drosophila melanogaster, and CDC48 in Saccharomyces cerevisiae) is a highly conserved AAA(+) (ATPases associated with multiple cellular activities) ATPase that ..
- Characterization of mutations in NOT2 indicates that it plays an important role in maintaining the integrity of the CCR4-NOT complexPamela Russell
Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham 03824, USA
J Mol Biol 322:27-39. 2002..of the CCR4-NOT complex that plays multiple roles in the regulation of mRNA production in the yeast Saccharomyces cerevisiae. We have identified four novel not2 mutations and have characterized these and two previously described ..
- Contribution of Msh2 and Msh6 subunits to the asymmetric ATPase and DNA mismatch binding activities of Saccharomyces cerevisiae Msh2-Msh6 mismatch repair proteinEdwin Antony
Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
DNA Repair (Amst) 5:153-62. 2006Previous analyses of both Thermus aquaticus MutS homodimer and Saccharomyces cerevisiae Msh2-Msh6 heterodimer have revealed that the subunits in these protein complexes bind and hydrolyze ATP asymmetrically, emulating their asymmetric DNA ..
- Ssn6, an important factor of morphological conversion and virulence in Candida albicansCheol-Sang Hwang
Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
Mol Microbiol 47:1029-43. 2003..namely SSN6, encoding a putative global transcriptional co-repressor that is highly homologous to the Saccharomyces cerevisiae Ssn6. The isolated C. albicans SSN6 complemented the pleiotropic phenotypes of S...
- Role of the OPI1 gene in controlling viability of Candida glabrataTODD REYNOLDS; Fiscal Year: 2007..CgOpi1p is similar to the Opi1p protein in the bakers' yeast Saccharomyces cerevisiae. S...
- ENZYMATIC MECHANISMS OF GENETIC RECOMBINATIONRichard D Kolodner; Fiscal Year: 2010..In the proposed studies, Saccharomyces cerevisiae will be used as a model system to identify the genes and pathways that act to suppress GCRs...
- INTEGRATION SPECIFICITY OF THE TY3 RETROTRANSPOSONSuzanne Sandmeyer; Fiscal Year: 1999..TFIIIC suppressors identified in the Sentenac lab will be analyzed for affects on Ty3 transposition. As residues in Ty3 are identified which are critical to targeting, suppressor screens for interacting host factors will be performed. ..
- HTLV-I Tax activates the anaphase promoting complexChou Zen Giam; Fiscal Year: 2009....
- MECHANISM OF PRE-MRNA SPLICINGMAGDA KONARSKA; Fiscal Year: 2009..By contrast, splice site signals in Saccharomyces cerevisiae fit well to the consensus and alternative splicing is thought not to occur in yeast...
- Regulation of nitrogen catabolic gene expression in S cerevisiaeTERRANCE COOPER; Fiscal Year: 2007..More importantly it will serve as an efficient model system that generates information, much of which will be directly applicable to mammalian cells because the Tor pathway is so well conserved between these organisms. ..
- Regulation of nitrogen catabolic gene expression in S cerevisiaeTerrance G Cooper; Fiscal Year: 2010..More importantly it will serve as an efficient model system that generates information, much of which will be directly applicable to mammalian cells because the Tor pathway is so well conserved between these organisms. ..
- MECHANISM OF PRE-MRNA SPLICINGMAGDA KONARSKA; Fiscal Year: 2010..By contrast, splice site signals in Saccharomyces cerevisiae fit well to the consensus and alternative splicing is thought not to occur in yeast...
- MANNOPROTEIN BIOSYNTHESIS IN SACCHAROMYCES CEREVISIAEAnnette Herscovics; Fiscal Year: 2000..Large quantities of the catalytic domain of the al,2-mannosidase from Saccharomyces cerevisiae that trims Man9GlcNAc2 to Man8GlcNAc2 have been produced in Pichia pastoris...
- MECHANISM OF SITE SPECIFIC DNA RECOMBINATIONMakkuni Jayaram; Fiscal Year: 2001..The tests involve the building synthetic substrates to test both questions. ..
- GLYCOPROTEIN BIOSYNTHESIS IN YEASTRobert Trimble; Fiscal Year: 1999..The current application proposes in four Aims studies in the small eukaryotes Saccharomyces cerevisiae and schizosaccharomyces pombe to determine the extent to which the substrate specificity of glycan ..
- DNA REPLICATION AND CHROMOSOME STRUCTURE IN YEASTVirginia A Zakian; Fiscal Year: 2011..These studies will lay the groundwork for the identification and analysis of human proteins with similar functions. ..
- DNA REPLICATION AND CHROMOSOME STRUCTURE IN YEASTVirginia A Zakian; Fiscal Year: 2010..These studies will lay the groundwork for the identification and analysis of human proteins with similar functions. ..
- SORTING AND TRANSPORT OF YEAST MEMBRANE PROTEINSTom Stevens; Fiscal Year: 2009..of the vacuolar-type proton-translocating ATPase (V-ATPase) in the simple model eukaryote, the yeast Saccharomyces cerevisiae. Yeast has proved to be an excellent model system, both for identifying the proteins regulating membrane ..
- REGULATION OF RETROTRANSPOSITION IN S. CEREVISIAEM Joan Curcio; Fiscal Year: 2011..Cellular proteins that are required for retroviral replication are potential targets for the development of new drugs to treat AIDS. ..
- REGULATION OF RETROTRANSPOSITION IN S. CEREVISIAEM Joan Curcio; Fiscal Year: 2010..Cellular proteins that are required for retroviral replication are potential targets for the development of new drugs to treat AIDS. ..
- MOLECULAR MARKER FOR INVASIVE CANDIDA ALBICANSMARGARET HOSTETTER; Fiscal Year: 2001..albicans and thereby bring forward new strategies for the control of candidal infection. ..
- FUNCTION OF AXR1 AND AXR1 LIKE GENES IN ARABIDOPSISMark Estelle; Fiscal Year: 2000..is to determine the biochemical and cellular function of the AXR1 family of proteins in Arabidopsis and Saccharomyces cerevisiae. This family of proteins is related to the ubiquitin-activating enzyme (E1) and genetic studies have ..
- Methods for engineering S. cerevisiae strains carrying multiple precise deletionsFREDERICK ROTH; Fiscal Year: 2007..Multiply-deleted strains allow functional study of genes in gene families, while multiply-inserted strains allow the study of human protein complexes in a tractable model organism. ..
- ROLE OF PROTEIN KINASE C IN YEAST GROWTH CONTROLDavid Levin; Fiscal Year: 1993..Other known cell lysis mutants will also be examined for genetic interactions with PKC1 and BCK1...
- SORTING AND TRANSPORT OF YEAST MEMBRANE PROTEINSTOM HALL STEVENS; Fiscal Year: 2010..of the vacuolar-type proton-translocating ATPase (V-ATPase) in the simple model eukaryote, the yeast Saccharomyces cerevisiae. Yeast has proved to be an excellent model system, both for identifying the proteins regulating membrane ..
- Control of Yeast Life SpanKurt W Runge; Fiscal Year: 2010..pathway that revealed the importance of the b-subunit of the F1F0-ATP synthase complex, encoded in Saccharomyces cerevisiae by the ATP2 gene...
- CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORAMATTHEW SACHS; Fiscal Year: 2009..AAP-mediated regulation is observed in vivo in both Neurospora crassa and Saccharomyces cerevisiae and in vitro, using fungal, plant and animal extracts...
- CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORAMATTHEW SACHS; Fiscal Year: 2006..AAP-mediated regulation is observed in vivo in both Neurospora crassa and Saccharomyces cerevisiae and in vitro, using fungal, plant and animal extracts...
- Assembly and Function of the Yeast Spore WallAaron M Neiman; Fiscal Year: 2010..The spore wall of Saccharomyces cerevisiae is a complex structure that forms de novo during the process of sporulation...
- CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORAMATTHEW SACHS; Fiscal Year: 2007..AAP-mediated regulation is observed in vivo in both Neurospora crassa and Saccharomyces cerevisiae and in vitro, using fungal, plant and animal extracts...
- CONTROL OF ARG-2 GENE EXPRESSION IN NEUROSPORAMATTHEW SACHS; Fiscal Year: 2007
- GENETIC ANALYSIS OF PLEIOTROPIC DRUG RESISTANCEW Moye Rowley; Fiscal Year: 2009..We are using the yeast Saccharomyces cerevisiae as a model eukaryotic system that has a well described set of multidrug resistance loci called ..
- GENETIC ANALYSIS OF PLEIOTROPIC DRUG RESISTANCEW Scott Moye Rowley; Fiscal Year: 2010..We are using the yeast Saccharomyces cerevisiae as a model eukaryotic system that has a well described set of multidrug resistance loci called ..
- MANNOPROTEIN BIOSYNTHESIS IN SACCHAROMYCES CEREVISIAEAnnette Herscovics; Fiscal Year: 2005....
- SACCHAROMYCES CEREVISIAE MICROTUBULE CYTOSKELETONGeorjana Barnes; Fiscal Year: 1993Having used biochemical approaches to identify components of the Saccharomyces cerevisiae microtubule cytoskeleton, we will now determine how these components function during mitosis, meiosis, and nuclear fusion...
- Arrest, Recovery, and Adaptation from DNA DamageJames Haber; Fiscal Year: 2009We will continue and extend our analysis of the DNA damage checkpoint in the model organism, Saccharomyces cerevisiae. In yeast, as well as in human cells, the DNA damage checkpoint acts to prevent mitosis until DNA has been repaired...
- YEAST GENETIC RESEARCH RESOURCE CENTERSHUNG CHANG JONG; Fiscal Year: 2002..abstract_text> ..
- Molecular Structure of Yeast Chromosome 1DAVID KABACK; Fiscal Year: 2005We propose to continue functional genomic studies on the model eukaryote Saccharomyces cerevisiae and will investigate a proposed function for subtelomeric DNA that comprises approximately 7 percent of its genome...