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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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2
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Klobucar K, Brown ED. Use of genetic and chemical synthetic lethality as probes of complexity in bacterial cell systems. FEMS Microbiol Rev 2018; 42:4563584. [PMID: 29069427 DOI: 10.1093/femsre/fux054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/23/2017] [Indexed: 12/22/2022] Open
Abstract
Different conditions and genomic contexts are known to have an impact on gene essentiality and interactions. Synthetic lethal interactions occur when a combination of perturbations, either genetic or chemical, result in a more profound fitness defect than expected based on the effect of each perturbation alone. Synthetic lethality in bacterial systems has long been studied; however, during the past decade, the emerging fields of genomics and chemical genomics have led to an increase in the scale and throughput of these studies. Here, we review the concepts of genomics and chemical genomics in the context of synthetic lethality and their revolutionary roles in uncovering novel biology such as the characterization of genes of unknown function and in antibacterial drug discovery. We provide an overview of the methodologies, examples and challenges of both genetic and chemical synthetic lethal screening platforms. Finally, we discuss how to apply genetic and chemical synthetic lethal approaches to rationalize the synergies of drugs, screen for new and improved antibacterial therapies and predict drug mechanism of action.
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Affiliation(s)
- Kristina Klobucar
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St West, Hamilton, ON L8N 3Z5, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St West, Hamilton, ON L8N 3Z5, Canada
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Helliwell SB, Karkare S, Bergdoll M, Rahier A, Leighton-Davis JR, Fioretto C, Aust T, Filipuzzi I, Frederiksen M, Gounarides J, Hoepfner D, Hofmann A, Imbert PE, Jeker R, Knochenmuss R, Krastel P, Margerit A, Memmert K, Miault CV, Rao Movva N, Muller A, Naegeli HU, Oberer L, Prindle V, Riedl R, Schuierer S, Sexton JA, Tao J, Wagner T, Yin H, Zhang J, Roggo S, Reinker S, Parker CN. FR171456 is a specific inhibitor of mammalian NSDHL and yeast Erg26p. Nat Commun 2015; 6:8613. [PMID: 26456460 PMCID: PMC4633953 DOI: 10.1038/ncomms9613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/10/2015] [Indexed: 01/07/2023] Open
Abstract
FR171456 is a natural product with cholesterol-lowering properties in animal models, but its molecular target is unknown, which hinders further drug development. Here we show that FR171456 specifically targets the sterol-4-alpha-carboxylate-3-dehydrogenase (Saccharomyces cerevisiae—Erg26p, Homo sapiens—NSDHL (NAD(P) dependent steroid dehydrogenase-like)), an essential enzyme in the ergosterol/cholesterol biosynthesis pathway. FR171456 significantly alters the levels of cholesterol pathway intermediates in human and yeast cells. Genome-wide yeast haploinsufficiency profiling experiments highlight the erg26/ERG26 strain, and multiple mutations in ERG26 confer resistance to FR171456 in growth and enzyme assays. Some of these ERG26 mutations likely alter Erg26 binding to FR171456, based on a model of Erg26. Finally, we show that FR171456 inhibits an artificial Hepatitis C viral replicon, and has broad antifungal activity, suggesting potential additional utility as an anti-infective. The discovery of the target and binding site of FR171456 within the target will aid further development of this compound. FR171456 is a bioactive chemical produced by some microorganisms. Here, the authors identify the enzyme NSDHL of the sterol synthesis pathway as the molecular target of FR171456, rendering it the first compound to specifically target this class of enzyme in yeast and mammalian cells.
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Affiliation(s)
- Stephen B Helliwell
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Shantanu Karkare
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Marc Bergdoll
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Strasbourg cedex 67083, France
| | - Alain Rahier
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Strasbourg cedex 67083, France
| | | | - Celine Fioretto
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Thomas Aust
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Ireos Filipuzzi
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Mathias Frederiksen
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - John Gounarides
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Andreas Hofmann
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Pierre-Eloi Imbert
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Rolf Jeker
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Richard Knochenmuss
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Anais Margerit
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Klaus Memmert
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Charlotte V Miault
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - N Rao Movva
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Alban Muller
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Hans-Ulrich Naegeli
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | | | - Ralph Riedl
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Jessica A Sexton
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | | | - Trixie Wagner
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Hong Yin
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Juan Zhang
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Silvio Roggo
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Stefan Reinker
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Christian N Parker
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
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4
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Production of the sesquiterpenoid (+)-nootkatone by metabolic engineering of Pichia pastoris. Metab Eng 2014; 24:18-29. [DOI: 10.1016/j.ymben.2014.04.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 04/02/2014] [Accepted: 04/08/2014] [Indexed: 11/18/2022]
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Zomorrodi AR, Maranas CD. Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC SYSTEMS BIOLOGY 2010; 4:178. [PMID: 21190580 PMCID: PMC3023687 DOI: 10.1186/1752-0509-4-178] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 12/29/2010] [Indexed: 11/29/2022]
Abstract
BACKGROUND Saccharomyces cerevisiae is the first eukaryotic organism for which a multi-compartment genome-scale metabolic model was constructed. Since then a sequence of improved metabolic reconstructions for yeast has been introduced. These metabolic models have been extensively used to elucidate the organizational principles of yeast metabolism and drive yeast strain engineering strategies for targeted overproductions. They have also served as a starting point and a benchmark for the reconstruction of genome-scale metabolic models for other eukaryotic organisms. In spite of the successive improvements in the details of the described metabolic processes, even the recent yeast model (i.e., iMM904) remains significantly less predictive than the latest E. coli model (i.e., iAF1260). This is manifested by its significantly lower specificity in predicting the outcome of grow/no grow experiments in comparison to the E. coli model. RESULTS In this paper we make use of the automated GrowMatch procedure for restoring consistency with single gene deletion experiments in yeast and extend the procedure to make use of synthetic lethality data using the genome-scale model iMM904 as a basis. We identified and vetted using literature sources 120 distinct model modifications including various regulatory constraints for minimal and YP media. The incorporation of the suggested modifications led to a substantial increase in the fraction of correctly predicted lethal knockouts (i.e., specificity) from 38.84% (87 out of 224) to 53.57% (120 out of 224) for the minimal medium and from 24.73% (45 out of 182) to 40.11% (73 out of 182) for the YP medium. Synthetic lethality predictions improved from 12.03% (16 out of 133) to 23.31% (31 out of 133) for the minimal medium and from 6.96% (8 out of 115) to 13.04% (15 out of 115) for the YP medium. CONCLUSIONS Overall, this study provides a roadmap for the computationally driven correction of multi-compartment genome-scale metabolic models and demonstrates the value of synthetic lethals as curation agents.
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Affiliation(s)
- Ali R Zomorrodi
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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6
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Asadollahi MA, Maury J, Schalk M, Clark A, Nielsen J. Enhancement of farnesyl diphosphate pool as direct precursor of sesquiterpenes through metabolic engineering of the mevalonate pathway inSaccharomyces cerevisiae. Biotechnol Bioeng 2010; 106:86-96. [DOI: 10.1002/bit.22668] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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7
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Fang Y, Imagawa K, Zhou X, Kita A, Sugiura R, Jaiseng W, Kuno T. Pleiotropic phenotypes caused by an opal nonsense mutation in an essential gene encoding HMG-CoA reductase in fission yeast. Genes Cells 2009; 14:759-71. [PMID: 19486165 DOI: 10.1111/j.1365-2443.2009.01308.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Schizosaccharomyces pombe genome contains an essential gene hmg1(+) encoding the sterol biosynthetic enzyme, 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR). Here, we isolated an allele of the hmg1(+) gene, hmg1-1/its12, as a mutant that showed sensitivities to high temperature and to FK506, a calcineurin inhibitor. The hmg1-1 allele contained an opal nonsense mutation in its N-terminal transmembrane domain, yet in spite of the mutation a full-length protein was produced, suggesting a read-through termination codon. Consistently, overexpression of the hmg1-1 mutant gene suppressed the mutant phenotypes. The hmg1-1 mutant showed hypersensitivity to pravastatin, an HMGR inhibitor, suggesting a defective HMGR activity. The mutant treated with FK506 caused dramatic morphological changes and showed defects in cell wall integrity, as well as displayed synthetic growth phenotypes with the mutant alleles of genes involved in cytokinesis and cell wall integrity. The mutant exhibited different phenotypes from those of the disruption mutants of ergosterol biosynthesis genes, and it showed normal filipin staining as well as showed normal subcellular localization of small GTPases. These data suggest that the pleiotropic phenotypes reflect the integrated effects of the reduced availability of ergosterol and various intermediates of the mevalonate pathway.
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Affiliation(s)
- Yue Fang
- Division of Molecular Pharmacology and Pharmacogenomics, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
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8
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Boone C, Bussey H, Andrews BJ. Exploring genetic interactions and networks with yeast. Nat Rev Genet 2007; 8:437-49. [PMID: 17510664 DOI: 10.1038/nrg2085] [Citation(s) in RCA: 422] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The development and application of genetic tools and resources has enabled a partial genetic-interaction network for the yeast Saccharomyces cerevisiae to be compiled. Analysis of the network, which is ongoing, has already provided a clear picture of the nature and scale of the genetic interactions that robustly sustain biological systems, and how cellular buffering is achieved at the molecular level. Recent studies in yeast have begun to define general principles of genetic networks, and also pave the way for similar studies in metazoan model systems. A comparative understanding of genetic-interaction networks promises insights into some long-standing genetic problems, such as the nature of quantitative traits and the basis of complex inherited disease.
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Affiliation(s)
- Charles Boone
- Banting & Best Department of Medical Research and Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada.
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9
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Silva J, Chang K, Hannon GJ, Rivas FV. RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age. Oncogene 2004; 23:8401-9. [PMID: 15517022 DOI: 10.1038/sj.onc.1208176] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sequencing of complete genomes has provided researchers with a wealth of information to study genome organization, genetic instability, and polymorphisms, as well as a knowledge of all potentially expressed genes. The identification of all genes encoded in the human genome opens the door for large-scale systematic gene silencing using small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs). With the recent development of siRNA and shRNA expression libraries, the application of RNAi technology to assign function to cancer genes and to delineate molecular pathways in which these genes affect in normal and transformed cells, will contribute significantly to the knowledge necessary to develop new and also improve existing cancer therapy.
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Affiliation(s)
- Jose Silva
- Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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Youngman MJ, Hobbs AEA, Burgess SM, Srinivasan M, Jensen RE. Mmm2p, a mitochondrial outer membrane protein required for yeast mitochondrial shape and maintenance of mtDNA nucleoids. ACTA ACUST UNITED AC 2004; 164:677-88. [PMID: 14981098 PMCID: PMC2172170 DOI: 10.1083/jcb.200308012] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mitochondrial outer membrane protein, Mmm1p, is required for normal mitochondrial shape in yeast. To identify new morphology proteins, we isolated mutations incompatible with the mmm1-1 mutant. One of these mutants, mmm2-1, is defective in a novel outer membrane protein. Lack of Mmm2p causes a defect in mitochondrial shape and loss of mitochondrial DNA (mtDNA) nucleoids. Like the Mmm1 protein (Aiken Hobbs, A.E., M. Srinivasan, J.M. McCaffery, and R.E. Jensen. 2001. J. Cell Biol. 152:401–410.), Mmm2p is located in dot-like particles on the mitochondrial surface, many of which are adjacent to mtDNA nucleoids. While some of the Mmm2p-containing spots colocalize with those containing Mmm1p, at least some of Mmm2p is separate from Mmm1p. Moreover, while Mmm2p and Mmm1p both appear to be part of large complexes, we find that Mmm2p and Mmm1p do not stably interact and appear to be members of two different structures. We speculate that Mmm2p and Mmm1p are components of independent machinery, whose dynamic interactions are required to maintain mitochondrial shape and mtDNA structure.
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Affiliation(s)
- Matthew J Youngman
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
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Peña-Diaz J, Montalvetti A, Flores CL, Constán A, Hurtado-Guerrero R, De Souza W, Gancedo C, Ruiz-Perez LM, Gonzalez-Pacanowska D. Mitochondrial localization of the mevalonate pathway enzyme 3-Hydroxy-3-methyl-glutaryl-CoA reductase in the Trypanosomatidae. Mol Biol Cell 2003; 15:1356-63. [PMID: 14699057 PMCID: PMC363142 DOI: 10.1091/mbc.e03-10-0720] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
3-Hydroxy-3-methyl-glutaryl-CoA reductase (HMGR) is a key enzyme in the sterol biosynthesis pathway, but its subcellular distribution in the Trypanosomatidae family is somewhat controversial. Trypanosoma cruzi and Leishmania HMGRs are closely related in their catalytic domains to bacterial and eukaryotic enzymes described but lack an amino-terminal domain responsible for the attachment to the endoplasmic reticulum. In the present study, digitonin-titration experiments together with immunoelectron microscopy were used to establish the intracellular localization of HMGR in these pathogens. Results obtained with wild-type cells and transfectants overexpressing the enzyme established that HMGR in both T. cruzi and Leishmania major is localized primarily in the mitochondrion and that elimination of the mitochondrial targeting sequence in Leishmania leads to protein accumulation in the cytosolic compartment. Furthermore, T. cruzi HMGR is efficiently targeted to the mitochondrion in yeast cells. Thus, when the gene encoding T. cruzi HMGR was expressed in a hmg1 hmg2 mutant of Saccharomyces cerevisiae, the mevalonate auxotrophy of mutant cells was relieved, and immunoelectron analysis showed that the parasite enzyme exhibits a mitochondrial localization, suggesting a conservation between the targeting signals of both organisms.
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Affiliation(s)
- Javier Peña-Diaz
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas, 18001 Granada, Spain
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12
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Koren A, Ben-Aroya S, Steinlauf R, Kupiec M. Pitfalls of the synthetic lethality screen in Saccharomyces cerevisiae: an improved design. Curr Genet 2003; 43:62-9. [PMID: 12684846 DOI: 10.1007/s00294-003-0373-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2002] [Revised: 12/19/2002] [Accepted: 12/19/2002] [Indexed: 10/25/2022]
Abstract
The colony color assay in yeast enables the visual identification of plasmid-loss events. In combination with a plasmid-dependence assay, it is commonly used to identify synthetic interactions between functionally related genes. Frequently, the plasmid carries the ADE3 gene and mutants are recognized as red colonies that fail to produce sectors. In these assays, a high percentage of false-positives is obtained, most of which result from synthetic lethality with the ade3 mutation. Here, we study the nature of these mutants. We report that mutations in the HIP1 and SHM1 genes exhibit synthetic lethality with ade3 deletions. A similar interaction is found between the fur1 and ura3 mutations. Lethality in the absence of the mitochondrial Shm1 and the cytoplasmic Ade3 enzymes indicates that, under certain circumstances, these cellular compartments cooperate in carrying out essential metabolic processes. In addition, we report the identification of a truncated ADE3 allele with a unique coloration phenotype and show that it can be used to improve synthetic lethal screens.
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Affiliation(s)
- Amnon Koren
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Ramat Aviv, Israel
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Bensen ES, Costaguta G, Payne GS. Synthetic genetic interactions with temperature-sensitive clathrin in Saccharomyces cerevisiae. Roles for synaptojanin-like Inp53p and dynamin-related Vps1p in clathrin-dependent protein sorting at the trans-Golgi network. Genetics 2000; 154:83-97. [PMID: 10628971 PMCID: PMC1460916 DOI: 10.1093/genetics/154.1.83] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clathrin is involved in selective protein transport at the Golgi apparatus and the plasma membrane. To further understand the molecular mechanisms underlying clathrin-mediated protein transport pathways, we initiated a genetic screen for mutations that display synthetic growth defects when combined with a temperature-sensitive allele of the clathrin heavy chain gene (chc1-521) in Saccharomyces cerevisiae. Mutations, when present in cells with wild-type clathrin, were analyzed for effects on mating pheromone alpha-factor precursor maturation and sorting of the vacuolar protein carboxypeptidase Y as measures of protein sorting at the yeast trans-Golgi network (TGN) compartment. By these criteria, two classes of mutants were obtained, those with and those without defects in protein sorting at the TGN. One mutant with unaltered protein sorting at the TGN contains a mutation in PTC1, a type 2c serine/threonine phosphatase with widespread influences. The collection of mutants displaying TGN sorting defects includes members with mutations in previously identified vacuolar protein sorting genes (VPS), including the dynamin family member VPS1. Striking genetic interactions were observed by combining temperature-sensitive alleles of CHC1 and VPS1, supporting the model that Vps1p is involved in clathrin-mediated vesicle formation at the TGN. Also in the spectrum of mutants with TGN sorting defects are isolates with mutations in the following: RIC1, encoding a product originally proposed to participate in ribosome biogenesis; LUV1, encoding a product potentially involved in vacuole and microtubule organization; and INP53, encoding a synaptojanin-like inositol polyphosphate 5-phosphatase. Disruption of INP53, but not the related INP51 and INP52 genes, resulted in alpha-factor maturation defects and exacerbated alpha-factor maturation defects when combined with chc1-521. Our findings implicate a wide variety of proteins in clathrin-dependent processes and provide evidence for the selective involvement of Inp53p in clathrin-mediated protein sorting at the TGN.
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Affiliation(s)
- E S Bensen
- Department of Biological Chemistry, School of Medicine, University of California, Los Angeles, California 90095, USA
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14
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Profant DA, Roberts CJ, Koning AJ, Wright RL. The role of the 3-hydroxy 3-methylglutaryl coenzyme A reductase cytosolic domain in karmellae biogenesis. Mol Biol Cell 1999; 10:3409-23. [PMID: 10512876 PMCID: PMC25610 DOI: 10.1091/mbc.10.10.3409] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In all cells examined, specific endoplasmic reticulum (ER) membrane arrays are induced in response to increased levels of the ER membrane protein 3-hydroxy 3-methylglutaryl coenzyme A (HMG-CoA) reductase. In yeast, expression of Hmg1p, one of two yeast HMG-CoA reductase isozymes, induces assembly of nuclear-associated ER stacks called karmellae. Understanding the features of HMG-CoA reductase that signal karmellae biogenesis would provide useful insights into the regulation of membrane biogenesis. The HMG-CoA reductase protein consists of two domains, a multitopic membrane domain and a cytosolic catalytic domain. Previous studies had indicated that the HMG-CoA reductase membrane domain was exclusively responsible for generation of ER membrane proliferations. Surprisingly, we discovered that this conclusion was incorrect: sequences at the carboxyl terminus of HMG-CoA reductase can profoundly affect karmellae biogenesis. Specifically, truncations of Hmg1p that removed or shortened the carboxyl terminus were unable to induce karmellae assembly. This result indicated that the membrane domain of Hmg1p was not sufficient to signal for karmellae assembly. Using beta-galactosidase fusions, we demonstrated that the carboxyl terminus was unlikely to simply serve as an oligomerization domain. Our working hypothesis is that a truncated or misfolded cytosolic domain prevents proper signaling for karmellae by interfering with the required tertiary structure of the membrane domain.
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Affiliation(s)
- D A Profant
- Department of Zoology, University of Washington, Seattle, Washington 98195, USA
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15
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Nislow C, Ray E, Pillus L. SET1, a yeast member of the trithorax family, functions in transcriptional silencing and diverse cellular processes. Mol Biol Cell 1997; 8:2421-36. [PMID: 9398665 PMCID: PMC25717 DOI: 10.1091/mbc.8.12.2421] [Citation(s) in RCA: 197] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/1997] [Accepted: 09/03/1997] [Indexed: 02/05/2023] Open
Abstract
The trithorax gene family contains members implicated in the control of transcription, development, chromosome structure, and human leukemia. A feature shared by some family members, and by other proteins that function in chromatin-mediated transcriptional regulation, is the presence of a 130- to 140-amino acid motif dubbed the SET or Tromo domain. Here we present analysis of SET1, a yeast member of the trithorax gene family that was identified by sequence inspection to encode a 1080-amino acid protein with a C-terminal SET domain. In addition to its SET domain, which is 40-50% identical to those previously characterized, SET1 also shares dispersed but significant similarity to Drosophila and human trithorax homologues. To understand SET1 function(s), we created a null mutant. Mutant strains, although viable, are defective in transcriptional silencing of the silent mating-type loci and telomeres. The telomeric silencing defect is rescued not only by full-length episomal SET1 but also by the conserved SET domain of SET1. set1 mutant strains display other phenotypes including morphological abnormalities, stationary phase defects, and growth and sporulation defects. Candidate genes that may interact with SET1 include those with functions in transcription, growth, and cell cycle control. These data suggest that yeast SET1, like its SET domain counterparts in other organisms, functions in diverse biological processes including transcription and chromatin structure.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cell Division
- Cell Size
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- Cloning, Molecular
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Drosophila Proteins
- Fungal Proteins/chemistry
- Fungal Proteins/genetics
- Fungal Proteins/metabolism
- Gene Silencing
- Genes, Fungal/genetics
- Genes, Mating Type, Fungal
- Histone-Lysine N-Methyltransferase
- Humans
- Molecular Sequence Data
- Multigene Family/genetics
- Mutation/genetics
- Protein Structure, Tertiary
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/physiology
- Saccharomyces cerevisiae Proteins
- Sequence Alignment
- Sequence Homology, Amino Acid
- Spores, Fungal/genetics
- Telomere/genetics
- Telomere/metabolism
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptional Activation/genetics
- Transferases
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Affiliation(s)
- C Nislow
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA
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16
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Dimster-Denk D, Rine J. Transcriptional regulation of a sterol-biosynthetic enzyme by sterol levels in Saccharomyces cerevisiae. Mol Cell Biol 1996; 16:3981-9. [PMID: 8754796 PMCID: PMC231394 DOI: 10.1128/mcb.16.8.3981] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Sterols and all nonsterol isoprenoids are derived from the highly conserved mevalonate pathway. In animal cells, this pathway is regulated in part at the transcriptional level through the action of sterol response element-binding proteins acting at specific DNA sequences near promoters. Here we extend at least part of this regulatory paradigm to the ERG10 gene, which encodes a sterol-biosynthetic enzyme of Saccharomyces cerevisiae. Specifically, the discovery of sterol-mediated feedback control of ERG10 transcription is reported. Deletion analysis of the ERG10 promoter region identified sequences involved in the expression of ERG10. This regulatory axis appeared to involve sterol levels, as a late block in the pathway that depletes sterol, but not nonsterol isoprenoids, was able to elicit the regulatory response.
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Affiliation(s)
- D Dimster-Denk
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA
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17
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Koning AJ, Roberts CJ, Wright RL. Different subcellular localization of Saccharomyces cerevisiae HMG-CoA reductase isozymes at elevated levels corresponds to distinct endoplasmic reticulum membrane proliferations. Mol Biol Cell 1996; 7:769-89. [PMID: 8744950 PMCID: PMC275929 DOI: 10.1091/mbc.7.5.769] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In all eucaryotic cell types analyzed, proliferations of the endoplasmic reticulum (ER) can be induced by increasing the levels of certain integral ER proteins. One of the best characterized of these proteins is HMG-CoA reductase, which catalyzes the rate-limiting step in sterol biosynthesis. We have investigated the subcellular distributions of the two HMG-CoA reductase isozymes in Saccharomyces cerevisiae and the types of ER proliferations that arise in response to elevated levels of each isozyme. At endogenous expression levels, Hmg1p and Hmg2p were both primarily localized in the nuclear envelope. However, at increased levels, the isozymes displayed distinct subcellular localization patterns in which each isozyme was predominantly localized in a different region of the ER. Specifically, increased levels of Hmg1p were concentrated in the nuclear envelope, whereas increased levels of Hmg2p were concentrated in the peripheral ER. In addition, an Hmg2p chimeric protein containing a 77-amino acid lumenal segment from Hmg1p was localized in a pattern that resembled that of Hmg1p when expressed at increased levels. Reflecting their different subcellular distributions, elevated levels of Hmg1p and Hmg2p induced sets of ER membrane proliferations with distinct morphologies. The ER membrane protein, Sec61p, was localized in the membranes induced by both Hmg1p and Hmg2p green fluorescent protein (GFP) fusions. In contrast, the lumenal ER protein, Kar2p, was present in Hmg1p:GFP membranes, but only rarely in Hmg2p:GFP membranes. These results indicated that the membranes synthesized in response to Hmg1p and Hmg2p were derived from the ER, but that the membranes were not identical in protein composition. We determined that the different types of ER proliferations were not simply due to quantitative differences in protein amounts or to the different half-lives of the two isozymes. It is possible that the specific distributions of the two yeast HMG-CoA reductase isozymes and their corresponding membrane proliferations may reveal regions of the ER that are specialized for certain branches of the sterol biosynthetic pathway.
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Affiliation(s)
- A J Koning
- Department of Zoology, University of Washington, Seattle 98195, USA
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18
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Smith V, Botstein D, Brown PO. Genetic footprinting: a genomic strategy for determining a gene's function given its sequence. Proc Natl Acad Sci U S A 1995; 92:6479-83. [PMID: 7604017 PMCID: PMC41541 DOI: 10.1073/pnas.92.14.6479] [Citation(s) in RCA: 136] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This report describes an efficient strategy for determining the functions of sequenced genes in microorganisms. A large population of cells is subjected to insertional mutagenesis. The mutagenized population is then divided into representative samples, each of which is subjected to a different selection. DNA is prepared from each sample population after the selection. The polymerase chain reaction is then used to determine retrospectively whether insertions into a particular sequence affected the outcome of any selection. The method is efficient because the insertional mutagenesis and each selection need only to be performed once to enable the functions of thousands of genes to be investigated, rather than once for each gene. We tested this "genetic footprinting" strategy using the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- V Smith
- Department of Genetics, Stanford University, CA, USA
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19
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Abstract
The function and activity of a protein are often modulated by other proteins with which it interacts. This review is intended as a practical guide to the analysis of such protein-protein interactions. We discuss biochemical methods such as protein affinity chromatography, affinity blotting, coimmunoprecipitation, and cross-linking; molecular biological methods such as protein probing, the two-hybrid system, and phage display: and genetic methods such as the isolation of extragenic suppressors, synthetic mutants, and unlinked noncomplementing mutants. We next describe how binding affinities can be evaluated by techniques including protein affinity chromatography, sedimentation, gel filtration, fluorescence methods, solid-phase sampling of equilibrium solutions, and surface plasmon resonance. Finally, three examples of well-characterized domains involved in multiple protein-protein interactions are examined. The emphasis of the discussion is on variations in the approaches, concerns in evaluating the results, and advantages and disadvantages of the techniques.
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Affiliation(s)
- E M Phizicky
- Department of Biochemistry, University of Rochester Medical School, New York 14642
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20
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Hiser L, Basson ME, Rine J. ERG10 from Saccharomyces cerevisiae encodes acetoacetyl-CoA thiolase. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)31705-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Ozier-Kalogeropoulos O, Adeline MT, Yang WL, Carman GM, Lacroute F. Use of synthetic lethal mutants to clone and characterize a novel CTP synthetase gene in Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1994; 242:431-9. [PMID: 8121398 DOI: 10.1007/bf00281793] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the pyrimidine biosynthetic pathway, CTP synthetase catalyses the conversion of uridine 5'-triphosphate (UTP) to cytidine 5'-triphosphate (CTP). In the yeast Saccharomyces cerevisiae, the URA7 gene encoding this enzyme was previously shown to be nonessential for cell viability. The present paper describes the selection of synthetic lethal mutants in the CTP biosynthetic pathway that led us to clone a second gene, named URA8, which also encodes a CTP synthetase. Comparison of the predicted amino acid sequences of the products of URA7 and URA8 shows 78% identity. Deletion of the URA8 gene is viable in a haploid strain but simultaneous presence of null alleles both URA7 and URA8 is lethal. Based on the codon bias values for the two genes and the intracellular concentrations of CTP in strains deleted for one of the two genes, relative to the wild-type level, URA7 appears to be the major gene for CTP biosynthesis. Nevertheless, URA8 alone also allows yeast growth, at least under standard laboratory conditions.
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Affiliation(s)
- O Ozier-Kalogeropoulos
- Centre de Génétique Moléculaire du C.N.R.S., Laboratoire propre associé, Université Pierre et Marie Curie, Gif-sur-Yvette, France
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22
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Abstract
Many bacterial signaling pathways involve a two-component design. In these pathways, a sensor kinase, when activated by a signal, phosphorylates its own histidine, which then serves as a phosphoryl donor to an aspartate in a response regulator protein. The Sln1 protein of the yeast Saccharomyces cerevisiae has sequence similarities to both the histidine kinase and the response regulator proteins of bacteria. A missense mutation in SLN1 is lethal in the absence but not in the presence of the N-end rule pathway, a ubiquitin-dependent proteolytic system. The finding of SLN1 demonstrates that a mode of signal transduction similar to the bacterial two-component design operates in eukaryotes as well.
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Affiliation(s)
- I M Ota
- Division of Biology, California Institute of Technology, Pasadena 91125
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23
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Vinh DB, Welch MD, Corsi AK, Wertman KF, Drubin DG. Genetic evidence for functional interactions between actin noncomplementing (Anc) gene products and actin cytoskeletal proteins in Saccharomyces cerevisiae. Genetics 1993; 135:275-86. [PMID: 8243993 PMCID: PMC1205634 DOI: 10.1093/genetics/135.2.275] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We describe here genetic interactions between mutant alleles of Actin-NonComplementing (ANC) genes and actin (ACT1) or actin-binding protein (SAC6, ABP1, TPM1) genes. The anc mutations were found to exhibit allele-specific noncomplementing interactions with different act1 mutations. In addition, mutant alleles of four ANC genes (ANC1, ANC2, ANC3 and ANC4) were tested for interactions with null alleles of actin-binding protein genes. An anc1 mutant allele failed to complement null alleles of the SAC6 and TPM1 genes that encode yeast fimbrin and tropomyosin, respectively. Also, synthetic lethality between anc3 and sac6 mutations, and between anc4 and tpm1 mutations was observed. Taken together, the above results strongly suggest that the ANC gene products contribute to diverse aspects of actin function. Finally, we report the results of tests of two models previously proposed to explain extragenic noncomplementation.
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Affiliation(s)
- D B Vinh
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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24
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HAP1 and ROX1 form a regulatory pathway in the repression of HEM13 transcription in Saccharomyces cerevisiae. Mol Cell Biol 1992. [PMID: 1588959 DOI: 10.1128/mcb.12.6.2616] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HEM13 of Saccharomyces cerevisiae encodes coproporphyrinogen oxidase, an enzyme in the heme biosynthetic pathway. Expression of HEM13 is repressed by oxygen and heme. This study investigated the regulatory pathway responsible for the regulation of HEM13 expression. The transcriptional activator HAP1 is demonstrated to be required for the full-level expression of HEM13 in the absence of heme. It is also shown that the repression of HEM13 transcription caused by heme involves the HAP1 and ROX1 gene products; a mutation in either gene results in derepression of HEM13 expression. The heme-dependent expression of ROX1 was found to require functional HAP1, leading one to propose that repression of HEM13 results from a pathway involving HAP1-mediated regulation of ROX1 transcription in response to heme levels followed by ROX1-mediated repression of HEM13 transcription. In support of this model, expression of ROX1 under control of the GAL promoter was found to result in repression of HEM13 transcription in a hap1 mutant strain. The ability of ROX1 encoded by the galactose-inducible ROX1 construct to function in the absence of HAP1 indicates that the only role of HAP1 in repression of HEM13 is to activate ROX1 transcription.
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25
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Keng T. HAP1 and ROX1 form a regulatory pathway in the repression of HEM13 transcription in Saccharomyces cerevisiae. Mol Cell Biol 1992; 12:2616-23. [PMID: 1588959 PMCID: PMC364455 DOI: 10.1128/mcb.12.6.2616-2623.1992] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
HEM13 of Saccharomyces cerevisiae encodes coproporphyrinogen oxidase, an enzyme in the heme biosynthetic pathway. Expression of HEM13 is repressed by oxygen and heme. This study investigated the regulatory pathway responsible for the regulation of HEM13 expression. The transcriptional activator HAP1 is demonstrated to be required for the full-level expression of HEM13 in the absence of heme. It is also shown that the repression of HEM13 transcription caused by heme involves the HAP1 and ROX1 gene products; a mutation in either gene results in derepression of HEM13 expression. The heme-dependent expression of ROX1 was found to require functional HAP1, leading one to propose that repression of HEM13 results from a pathway involving HAP1-mediated regulation of ROX1 transcription in response to heme levels followed by ROX1-mediated repression of HEM13 transcription. In support of this model, expression of ROX1 under control of the GAL promoter was found to result in repression of HEM13 transcription in a hap1 mutant strain. The ability of ROX1 encoded by the galactose-inducible ROX1 construct to function in the absence of HAP1 indicates that the only role of HAP1 in repression of HEM13 is to activate ROX1 transcription.
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Affiliation(s)
- T Keng
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
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26
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Barnes G, Louie KA, Botstein D. Yeast proteins associated with microtubules in vitro and in vivo. Mol Biol Cell 1992; 3:29-47. [PMID: 1348005 PMCID: PMC275500 DOI: 10.1091/mbc.3.1.29] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Conditions were established for the self-assembly of milligram amounts of purified Saccharomyces cerevisiae tubulin. Microtubules assembled with pure yeast tubulin were not stabilized by taxol; hybrid microtubules containing substoichiometric amounts of bovine tubulin were stabilized. Yeast microtubule-associated proteins (MAPs) were identified on affinity matrices made from hybrid and all-bovine microtubules. About 25 yeast MAPs were isolated. The amino-terminal sequences of several of these were determined: three were known metabolic enzymes, two were GTP-binding proteins (including the product of the SAR1 gene), and three were novel proteins not found in sequence databases. Affinity-purified antisera were generated against synthetic peptides corresponding to two of the apparently novel proteins (38 and 50 kDa). Immunofluorescence microscopy showed that both these proteins colocalize with intra- and extranuclear microtubules in vivo.
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Affiliation(s)
- G Barnes
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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27
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Ota IM, Varshavsky A. A gene encoding a putative tyrosine phosphatase suppresses lethality of an N-end rule-dependent mutant. Proc Natl Acad Sci U S A 1992; 89:2355-9. [PMID: 1549598 PMCID: PMC48656 DOI: 10.1073/pnas.89.6.2355] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. In the yeast Saccharomyces cerevisiae, mutational inactivation of the N-end rule pathway is neither lethal nor phenotypically conspicuous. We have used a "synthetic lethal" screen to isolate a mutant that requires the N-end rule pathway for viability. An extragenic suppressor of this mutation was cloned and found to encode a 750-residue protein with strong sequence similarities to protein phosphotyrosine phosphatases. This heat-inducible gene was named PTP2. Null ptp2 mutants grow slowly, are hypersensitive to heat, and are viable in either the presence or absence of the N-end rule pathway. We discuss possible connections between dephosphorylation of phosphotyrosine in proteins and the N-end rule pathway of protein degradation.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- Drosophila/genetics
- Genes, Fungal
- Genes, Lethal
- Genotype
- Hot Temperature
- Humans
- Molecular Sequence Data
- Open Reading Frames
- Protein Tyrosine Phosphatases/genetics
- RNA, Fungal/genetics
- RNA, Fungal/isolation & purification
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Schizosaccharomyces/enzymology
- Schizosaccharomyces/genetics
- Sequence Homology, Nucleic Acid
- Suppression, Genetic
- TATA Box
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Affiliation(s)
- I M Ota
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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28
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Ozier-Kalogeropoulos O, Fasiolo F, Adeline MT, Collin J, Lacroute F. Cloning, sequencing and characterization of the Saccharomyces cerevisiae URA7 gene encoding CTP synthetase. MOLECULAR & GENERAL GENETICS : MGG 1991; 231:7-16. [PMID: 1753946 DOI: 10.1007/bf00293815] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The URA7 gene of Saccharomyces cerevisiae encodes CTP synthetase (EC 6.3.4.2) which catalyses the conversion of uridine 5'-triphosphate to cytidine 5'-triphosphate, the last step of the pyrimidine biosynthetic pathway. We have cloned and sequenced the URA7 gene. The coding region is 1710 bp long and the deduced protein sequence shows a strong degree of homology with bacterial and human CTP synthetases. Gene disruption shows that URA7 is not an essential gene: the level of the intracellular CTP pool is roughly the same in the deleted and the wild-type strains, suggesting that an alternative pathway for CTP synthesis exists in yeast. This could involve either a divergent duplicated gene or a different route beginning with the amination of uridine mono- or diphosphate.
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Affiliation(s)
- O Ozier-Kalogeropoulos
- Centre de Génétique Moléculaire du C.N.R.S. Université Pierre et Marie Curie, Gif-sur-Yvette, France
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29
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Qin S, Nakajima B, Nomura M, Arfin S. Cloning and characterization of a Saccharomyces cerevisiae gene encoding a new member of the ubiquitin-conjugating protein family. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)98652-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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30
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Lorenz RT, Parks LW. Involvement of heme components in sterol metabolism of Saccharomyces cerevisiae. Lipids 1991; 26:598-603. [PMID: 1779707 DOI: 10.1007/bf02536423] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There is an intimate association between sterol biosynthesis in yeast and aerobicity. Besides the requirement for molecular oxygen for the epoxidation of squalene, cytochrome hemoproteins are involved in demethylation and desaturation steps. Regulatory effects of hemes on sterol formation have been demonstrated using specifically defective mutants of yeast. Heme competency participates in a mechanism whereby wild-type cells are prevented from taking exogenous sterols from the growth media. The multiple interactions of hemes and sterols appear to be associated with the variously defined functions for sterols in the yeast cells.
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Affiliation(s)
- R T Lorenz
- Department of Microbiology, North Carolina State University, Raleigh 27695-7615
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31
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Bonneaud N, Ozier-Kalogeropoulos O, Li GY, Labouesse M, Minvielle-Sebastia L, Lacroute F. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast 1991; 7:609-15. [PMID: 1767589 DOI: 10.1002/yea.320070609] [Citation(s) in RCA: 451] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We describe a set of replicative, integrative and single-stranded shuttle vectors constructed from the pUC19 plasmid that we use routinely in our experiments. They bear a yeast selectable marker: URA3, TRP1 or LEU2. Replicative vectors carrying different yeast replication origins have been constructed in order to have plasmids based on the same construction with a high or low copy number per cell and with different mitotic stabilities. All the vectors are small in size, provide a high yield in Escherichia coli and efficiently transform Saccharomyces cerevisiae. These plasmids have many of the unique sites of the pUC19 multicloning region and many of them allow for the screening of plasmids with an insert by alpha-complementation. The nucleotide sequence of each of them is completely known.
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Affiliation(s)
- N Bonneaud
- Centre de Génétique Moléculaire du C.N.R.S., Laboratoire propre associé à l'Université Pierre et Marie Curie, Gif sur Yvette, France
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32
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Pelsy F, Gonneau M. Genetic and biochemical analysis of intragenic complementation events among nitrate reductase apoenzyme-deficient mutants of Nicotiana plumbaginifolia. Genetics 1991; 127:199-204. [PMID: 2016042 PMCID: PMC1204304 DOI: 10.1093/genetics/127.1.199] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Intragenic complementation has been observed between apoenzyme nitrate reductase-deficient mutants (nia) of Nicotiana plumbaginifolia. In vivo as in vitro, the NADH-nitrate reductase (NR) activity in plants heterozygous for two different nia alleles was lower than in the wild type plant, but the plants were able to grow on nitrate as a sole nitrogen source. NR activity, absent in extracts of homozygous nia mutants was restored by mixing extracts from two complementing nia mutants. These observations suggest that NR intragenic complementation results from either the formation of heteromeric NR or from the interaction between two modified enzymes. Complementation was only observed between mutants retaining different partial catalytic activities of the enzyme. Results are in agreement with molecular data suggesting the presence of three catalytic domains in the subunit of the enzyme.
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Affiliation(s)
- F Pelsy
- Laboratoire de Biologie Cellulaire, INRA-Versailles, Versailles, France
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33
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Lorenz RT, Parks LW. Effects of lovastatin (mevinolin) on sterol levels and on activity of azoles in Saccharomyces cerevisiae. Antimicrob Agents Chemother 1990; 34:1660-5. [PMID: 2285278 PMCID: PMC171901 DOI: 10.1128/aac.34.9.1660] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The hypocholesterolemic drug lovastatin (mevinolin) was found to be very effective in lowering the sterol levels of the wild-type yeast Saccharomyces cerevisiae. Lovastatin dramatically decreased the steryl ester content from 2.62 to 0.8 micrograms/mg (dry weight), whereas the free sterol content decreased only from 2.79 to 2.24 micrograms/mg (dry weight) when lovastatin was present in the medium at 10 micrograms/ml. At higher concentrations (100 micrograms/ml), lovastatin nearly abolished the accumulation of steryl esters and decreased the free sterol concentration to less than 1.3 micrograms/mg (dry weight). As a result of the lowered sterol levels, proportional amounts of exogenous sterol were taken up from the medium during aerobic, respiratory conditions. Nearly all of the exogenous sterol taken up was partitioned into the free sterol fraction. The inhibition of sterol esterification in the presence of lovastatin was dependent on heme synthesis. The result of these combined effects caused the MICs of three azole antifungal drugs (ketoconazole, clotrimazole, and miconazole) to be lowered from 6- to 32-fold when lovastatin was present in the medium at 10 micrograms/ml.
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Affiliation(s)
- R T Lorenz
- Department of Microbiology, North Carolina State University, Raleigh 27695-7615
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34
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Positive and negative transcriptional control by heme of genes encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase in Saccharomyces cerevisiae. Mol Cell Biol 1990. [PMID: 2685574 DOI: 10.1128/mcb.9.12.5702] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Responses of the yeast genes encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase, HMG1 and HMG2, to in vivo changes in heme concentrations were investigated. Expression of the genes was determined by direct measurement of the mRNA transcribed from each gene, by direct assay of the enzyme activity encoded by each gene, and by measurement of the expression of lacZ fusions to the control regions of each gene. These studies indicated that expression of HMG1 was stimulated by heme, whereas expression of HMG2 was repressed by heme. The effect of heme on HMG1 expression was mediated by the HAP1 transcriptional regulator and was independent of HAP2. Thus, the genes encoding the 3-hydroxy-3-methylglutaryl coenzyme A reductase isozymes join a growing list of gene pairs that are regulated by heme in opposite ways.
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35
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Mortimer RK, Schild D, Contopoulou CR, Kans JA. Genetic map of Saccharomyces cerevisiae, edition 10. Yeast 1989; 5:321-403. [PMID: 2678811 DOI: 10.1002/yea.320050503] [Citation(s) in RCA: 250] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- R K Mortimer
- Department of Molecular and Cellular Biology, University of California, Berkeley 94720
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