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Ottilie S, Luth MR, Hellemann E, Goldgof GM, Vigil E, Kumar P, Cheung AL, Song M, Godinez-Macias KP, Carolino K, Yang J, Lopez G, Abraham M, Tarsio M, LeBlanc E, Whitesell L, Schenken J, Gunawan F, Patel R, Smith J, Love MS, Williams RM, McNamara CW, Gerwick WH, Ideker T, Suzuki Y, Wirth DF, Lukens AK, Kane PM, Cowen LE, Durrant JD, Winzeler EA. Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol 2022; 5:128. [PMID: 35149760 PMCID: PMC8837787 DOI: 10.1038/s42003-022-03076-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/21/2022] [Indexed: 12/24/2022] Open
Abstract
In vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in Saccharomyces cerevisiae. Sequence analysis identified many genes contributing to the resistance phenotype as well as numerous amino acids in potential targets that may play a role in compound binding. Our work shows that compound-target pairs can be conserved across multiple species. The set of 25 most frequently mutated genes was enriched for transcription factors, and for almost 25 percent of the compounds, resistance was mediated by one of 100 independently derived, gain-of-function SNVs found in a 170 amino acid domain in the two Zn2C6 transcription factors YRR1 and YRM1 (p < 1 × 10−100). This remarkable enrichment for transcription factors as drug resistance genes highlights their important role in the evolution of antifungal xenobiotic resistance and underscores the challenge to develop antifungal treatments that maintain potency. Ottilie et al. employ an experimental evolution approach to investigate the role of transcription factors in yeast chemical resistance. Most emergent mutations in resistant strains were enriched in transcription factor coding genes, highlighting their importance in drug resistance.
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Affiliation(s)
- Sabine Ottilie
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Madeline R Luth
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Erich Hellemann
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Gregory M Goldgof
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Eddy Vigil
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Prianka Kumar
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Andrea L Cheung
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Miranda Song
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Karla P Godinez-Macias
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Krypton Carolino
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Jennifer Yang
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Gisel Lopez
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Matthew Abraham
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
| | - Emmanuelle LeBlanc
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Jake Schenken
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Felicia Gunawan
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Reysha Patel
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Joshua Smith
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Melissa S Love
- Calibr, a division of The Scripps Research Institutes, La Jolla, CA, 92037, USA
| | - Roy M Williams
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA.,Aspen Neuroscience, San Diego, CA, 92121, USA
| | - Case W McNamara
- Calibr, a division of The Scripps Research Institutes, La Jolla, CA, 92037, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA, 92037, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yo Suzuki
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Amanda K Lukens
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA.
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Duplus-Bottin H, Spichty M, Triqueneaux G, Place C, Mangeot PE, Ohlmann T, Vittoz F, Yvert G. A single-chain and fast-responding light-inducible Cre recombinase as a novel optogenetic switch. eLife 2021; 10:61268. [PMID: 33620312 PMCID: PMC7997657 DOI: 10.7554/elife.61268] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/22/2021] [Indexed: 11/20/2022] Open
Abstract
Optogenetics enables genome manipulations with high spatiotemporal resolution, opening exciting possibilities for fundamental and applied biological research. Here, we report the development of LiCre, a novel light-inducible Cre recombinase. LiCre is made of a single flavin-containing protein comprising the AsLOV2 photoreceptor domain of Avena sativa fused to a Cre variant carrying destabilizing mutations in its N-terminal and C-terminal domains. LiCre can be activated within minutes of illumination with blue light without the need of additional chemicals. When compared to existing photoactivatable Cre recombinases based on two split units, LiCre displayed faster and stronger activation by light as well as a lower residual activity in the dark. LiCre was efficient both in yeast, where it allowed us to control the production of β-carotene with light, and human cells. Given its simplicity and performances, LiCre is particularly suited for fundamental and biomedical research, as well as for controlling industrial bioprocesses. In a biologist’s toolkit, the Cre protein holds a special place. Naturally found in certain viruses, this enzyme recognises and modifies specific genetic sequences, creating changes that switch on or off whatever gene is close by. Genetically engineering cells or organisms so that they carry Cre and its target sequences allows scientists to control the activation of a given gene, often in a single tissue or organ. However, this relies on the ability to activate the Cre protein ‘on demand’ once it is in the cells of interest. One way to do so is to split the enzyme into two pieces, which can then reassemble when exposed to blue light. Yet, this involves the challenging step of introducing both parts separately into a tissue. Instead, Duplus-Bottin et al. engineered LiCre, a new system where a large section of the Cre protein is fused to a light sensor used by oats to detect their environment. LiCre is off in the dark, but it starts to recognize and modify Cre target sequences when exposed to blue light. Duplus-Bottin et al. then assessed how LiCre compares to the two-part Cre system in baker's yeast and human kidney cells. This showed that the new protein is less ‘incorrectly’ active in the dark, and can switch on faster under blue light. The improved approach could give scientists a better tool to study the role of certain genes at precise locations and time points, but also help them to harness genetic sequences for industry or during gene therapy.
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Affiliation(s)
- Hélène Duplus-Bottin
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Martin Spichty
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Gérard Triqueneaux
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Christophe Place
- Laboratory of Physics, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5672, Universite Claude Bernard Lyon 1, Lyon, France
| | - Philippe Emmanuel Mangeot
- CIRI-Centre International de Recherche en Infectiologie, Universite Claude Bernard Lyon 1, Universite de Lyon, Inserm, U1111, CNRS, UMR5308, Ecole Normale Superieure de Lyon, Lyon, France
| | - Théophile Ohlmann
- CIRI-Centre International de Recherche en Infectiologie, Universite Claude Bernard Lyon 1, Universite de Lyon, Inserm, U1111, CNRS, UMR5308, Ecole Normale Superieure de Lyon, Lyon, France
| | - Franck Vittoz
- Laboratory of Physics, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5672, Universite Claude Bernard Lyon 1, Lyon, France
| | - Gaël Yvert
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
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Linscott KB, Niehaus TD, Zhuang X, Bell SA, Chappell J. Mapping a kingdom-specific functional domain of squalene synthase. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1049-1057. [PMID: 27320012 DOI: 10.1016/j.bbalip.2016.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/10/2016] [Accepted: 06/13/2016] [Indexed: 10/21/2022]
Abstract
Squalene synthase catalyzes the first committed step in sterol biosynthesis and consists of both an amino-terminal catalytic domain and a carboxy-terminal domain tethering the enzyme to the ER membrane. While the overall architecture of this enzyme is identical in eukaryotes, it was previously shown that plant and animal genes cannot complement a squalene synthase knockout mutation in yeast unless the carboxy-terminal domain is swapped for one of fungal origin. This implied a unique component of the fungal carboxy-terminal domain was responsible for the complementation phenotype. To identify this motif, we used Saccharomyces cerevisiae with a squalene synthase knockout mutation, and expressed intact and chimeric squalene synthases originating from fungi, plants, and animals. In contrast to previous observations, all enzymes tested could partially complement the knockout mutation when the genes were weakly expressed. However, when highly expressed, non-fungal squalene synthases could not complement the yeast mutation and instead led to the accumulation of a toxic intermediate(s) as defined by mutations of genes downstream in the ergosterol pathway. Restoration of the complete complementation phenotype was mapped to a 26-amino acid hinge region linking the catalytic and membrane-spanning domains specific to fungal squalene synthases. Over-expression of the C-terminal domain containing a hinge domain from fungi, not from animals or plants, led to growth inhibition of wild-type yeast. Because this hinge region is unique to and highly conserved within each kingdom of life, the data suggests that the hinge domain plays an essential functional role, such as assembly of ergosterol multi-enzyme complexes in fungi.
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Affiliation(s)
- Kristin B Linscott
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40506-9983, United States
| | - Thomas D Niehaus
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536-0596, United States
| | - Xun Zhuang
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536-0596, United States
| | - Stephen A Bell
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536-0596, United States
| | - Joe Chappell
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40506-9983, United States; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536-0596, United States.
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Brockman IM, Prather KLJ. Dynamic metabolic engineering: New strategies for developing responsive cell factories. Biotechnol J 2015; 10:1360-9. [PMID: 25868062 DOI: 10.1002/biot.201400422] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/02/2015] [Accepted: 03/15/2015] [Indexed: 12/22/2022]
Abstract
Metabolic engineering strategies have enabled improvements in yield and titer for a variety of valuable small molecules produced naturally in microorganisms, as well as those produced via heterologous pathways. Typically, the approaches have been focused on up- and downregulation of genes to redistribute steady-state pathway fluxes, but more recently a number of groups have developed strategies for dynamic regulation, which allows rebalancing of fluxes according to changing conditions in the cell or the fermentation medium. This review highlights some of the recently published work related to dynamic metabolic engineering strategies and explores how advances in high-throughput screening and synthetic biology can support development of new dynamic systems. Dynamic gene expression profiles allow trade-offs between growth and production to be better managed and can help avoid build-up of undesired intermediates. The implementation is more complex relative to static control, but advances in screening techniques and DNA synthesis will continue to drive innovation in this field.
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Affiliation(s)
- Irene M Brockman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Sørensen DM, Holen HW, Holemans T, Vangheluwe P, Palmgren MG. Towards defining the substrate of orphan P5A-ATPases. Biochim Biophys Acta Gen Subj 2014; 1850:524-35. [PMID: 24836520 DOI: 10.1016/j.bbagen.2014.05.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND P-type ATPases are ubiquitous ion and lipid pumps found in cellular membranes. P5A-ATPases constitute a poorly characterized subfamily of P-type ATPases present in all eukaryotic organisms but for which a transported substrate remains to be identified. SCOPE OF REVIEW This review aims to discuss the available evidence which could lead to identification of possible substrates of P5A-ATPases. MAJOR CONCLUSIONS The complex phenotypes resulting from the loss of P5A-ATPases in model organisms can be explained by a role of the P5A-ATPase in the endoplasmic reticulum (ER), where loss of function leads to broad and unspecific phenotypes related to the impairment of basic ER functions such as protein folding and processing. Genetic interactions in Saccharomyces cerevisiae point to a role of the endogenous P5A-ATPase Spf1p in separation of charges in the ER, in sterol metabolism, and in insertion of tail-anchored proteins in the ER membrane. A role for P5A-ATPases in vesicle formation would explain why sterol transport and distribution are affected in knock out cells, which in turn has a negative impact on the spontaneous insertion of tail-anchored proteins. It would also explain why secretory proteins destined for the Golgi and the cell wall have difficulties in reaching their final destination. Cations and phospholipids could both be transported substrates of P5A-ATPases and as each carry charges, transport of either might explain why a charge difference arises across the ER membrane. GENERAL SIGNIFICANCE Identification of the substrate of P5A-ATPases would throw light on an important general process in the ER that is still not fully understood. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Danny Mollerup Sørensen
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Henrik Waldal Holen
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Tine Holemans
- Department of Cellular and Molecular Medicine, ON1 Campus Gasthuisberg, Katholieke Universiteit Leuven, Herestraat 49, Box 802, B3000 Leuven, Belgium
| | - Peter Vangheluwe
- Department of Cellular and Molecular Medicine, ON1 Campus Gasthuisberg, Katholieke Universiteit Leuven, Herestraat 49, Box 802, B3000 Leuven, Belgium
| | - Michael G Palmgren
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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High-quality lycopene overaccumulation via inhibition of γ-carotene and ergosterol biosyntheses in Blakeslea trispora. J Funct Foods 2014. [DOI: 10.1016/j.jff.2014.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Sun J, Li H, Sun X, Yuan Q. Trisporic acid stimulates gene transcription of terpenoid biosynthesis in Blakeslea trispora. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.06.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bhargava P, Kumar K, Chaudhaery SS, Saxena AK, Roy U. Cloning, overexpression and characterization of Leishmania donovani squalene synthase. FEMS Microbiol Lett 2010; 311:82-92. [DOI: 10.1111/j.1574-6968.2010.02071.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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9
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Cheng B, Yuan QP, Sun XX, Li WJ. Methods on erg9 gene deletion in Schizosaccharomyces pombe. ASIA-PAC J CHEM ENG 2009. [DOI: 10.1002/apj.333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Sealey-Cardona M, Cammerer S, Jones S, Ruiz-Pérez LM, Brun R, Gilbert IH, Urbina JA, González-Pacanowska D. Kinetic characterization of squalene synthase from Trypanosoma cruzi: selective inhibition by quinuclidine derivatives. Antimicrob Agents Chemother 2007; 51:2123-9. [PMID: 17371809 PMCID: PMC1891404 DOI: 10.1128/aac.01454-06] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biosynthesis of sterols is a major route for the development of antitrypanosomals. Squalene synthase (SQS) catalyzes the first step committed to the biosynthesis of sterols within the isoprenoid pathway, and several inhibitors of the enzyme have selective antitrypanosomal activity both in vivo and in vitro. The enzyme from Trypanosoma cruzi is a 404-amino-acid protein with a clearly identifiable membrane-spanning region. In an effort to generate soluble recombinant enzyme, we have expressed in Escherichia coli several truncated versions of T. cruzi SQS with a His tag attached to the amino terminus. Deletions of both the amino- and carboxyl-terminal regions generated active and soluble forms of the enzyme. The highest levels of soluble protein were achieved when 24 and 36 amino acids were eliminated from the amino and carboxyl regions, respectively, yielding a protein of 41.67 kDa. The Michaelis-Menten constants of the purified enzyme for farnesyl diphosphate and NAD (NADPH) were 5.25 and 23.34 microM, respectively, whereas the V(max) was 1,428.56 nmol min(-1)mg(-1). Several quinuclidine derivatives with antiprotozoal activity in vitro were found to be selective inhibitors of recombinant T. cruzi SQS in comparative assays with the human enzyme, with 50% inhibitory concentration values in the nanomolar range. These data suggest that selective inhibition of T. cruzi SQS may be an efficient strategy for the development of new antitrypanosomal agents.
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Affiliation(s)
- Marco Sealey-Cardona
- Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas, Avda. del Conocimiento s/n, Parque Tecnológico de Ciencias de la Salud, 18100-Armilla, Granada, Spain
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Malathi K, Higaki K, Tinkelenberg AH, Balderes DA, Almanzar-Paramio D, Wilcox LJ, Erdeniz N, Redican F, Padamsee M, Liu Y, Khan S, Alcantara F, Carstea ED, Morris JA, Sturley SL. Mutagenesis of the putative sterol-sensing domain of yeast Niemann Pick C-related protein reveals a primordial role in subcellular sphingolipid distribution. ACTA ACUST UNITED AC 2004; 164:547-56. [PMID: 14970192 PMCID: PMC2171978 DOI: 10.1083/jcb.200310046] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lipid movement between organelles is a critical component of eukaryotic membrane homeostasis. Niemann Pick type C (NP-C) disease is a fatal neurodegenerative disorder typified by lysosomal accumulation of cholesterol and sphingolipids. Expression of yeast NP-C–related gene 1 (NCR1), the orthologue of the human NP-C gene 1 (NPC1) defective in the disease, in Chinese hamster ovary NPC1 mutant cells suppressed lipid accumulation. Deletion of NCR1, encoding a transmembrane glycoprotein predominantly residing in the vacuole of normal yeast, gave no phenotype. However, a dominant mutation in the putative sterol-sensing domain of Ncr1p conferred temperature and polyene antibiotic sensitivity without changes in sterol metabolism. Instead, the mutant cells were resistant to inhibitors of sphingolipid biosynthesis and super sensitive to sphingosine and C2-ceramide. Moreover, plasma membrane sphingolipids accumulated and redistributed to the vacuole and other subcellular membranes of the mutant cells. We propose that the primordial function of these proteins is to recycle sphingolipids and that defects in this process in higher eukaryotes secondarily result in cholesterol accumulation.
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Affiliation(s)
- Krishnamurthy Malathi
- Institute of Human Nutrition, Columbia University Medical Center, 630 W. 168 St., New York, NY 10032, USA
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12
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Akamine S, Nakamori K, Chechetka SA, Banba M, Umehara Y, Kouchi H, Izui K, Hata S. cDNA cloning, mRNA expression, and mutational analysis of the squalene synthase gene of Lotus japonicus. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1626:97-101. [PMID: 12697335 DOI: 10.1016/s0167-4781(03)00042-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A full-length cDNA for squalene synthase was isolated from Lotus japonicus, a model leguminous plant. The transcript was abundant in roots, symbiotic root nodules, and shoots, in that order. In situ hybridization revealed that the mRNA level is high in expanding root cells but low in dividing root tip ones. The transcript is also abundant in vascular bundles and the basal portions of mature nodules. L. japonicus squalene synthase has an unusual Asp residue near the active site, where mammalian enzymes have Gln, and replacement of the Gln by Glu has been reported to cause severe inactivation. Site-directed mutagenesis of the L. japonicus enzyme and assaying in vitro showed that this Asp residue can be substituted by not only Gln but also Glu, suggesting that the local structure of plant squalene synthases is different from that of mammalian enzymes.
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Affiliation(s)
- Satomi Akamine
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, 606-8502, Kyoto, Japan
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Sturley SL. Conservation of eukaryotic sterol homeostasis: new insights from studies in budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1529:155-63. [PMID: 11111085 DOI: 10.1016/s1388-1981(00)00145-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The model eukaryote Saccharomyces cerevisiae (budding yeast) has provided significant insight into sterol homeostasis. The study of sterol metabolism in a genetically amenable model organism such as yeast is likely to have an even greater impact and relevance to human disease with the advent of the complete human genome sequence. In addition to definition of the sterol biosynthetic pathway, almost to completion, the remarkable conservation of other components of sterol homeostasis are described in this review.
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Affiliation(s)
- S L Sturley
- Institute of Human Nutrition, Department of Pediatrics, Columbia University College of Physicians and Surgeons, 630 W168th St., New York, NY 10032, USA.
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14
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Tansey TR, Shechter I. Structure and regulation of mammalian squalene synthase. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1529:49-62. [PMID: 11111077 DOI: 10.1016/s1388-1981(00)00137-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Mammalian squalene synthase (SQS) catalyzes the first reaction of the branch of the isoprenoid metabolic pathway committed specifically to sterol biosynthesis. SQS produces squalene in an unusual two-step reaction in which two molecules of farnesyl diphosphate are condensed head-to-head. Recent studies have advanced understanding of the reaction mechanism, the functional domains of the enzyme, and transcriptional regulation of the gene. Site-directed mutagenesis has identified conserved Asp, Tyr, and Phe residues that are essential for SQS activity. The Asp residues are hypothesized to be required for substrate binding; the Tyr and Phe residues may stabilize carbocation reaction intermediates. The elucidation of SQS crystal structure will most likely direct future research on the relationship between enzyme structure and function. SQS activity, protein, and mRNA levels are regulated by cholesterol status and by the cytokines TNF-alpha and IL-1beta. Activation of the SQS promoter in response to cholesterol deficit is mediated by sterol regulatory element binding proteins SREBP-1a and SREBP-2. The precise contributions made by individual SREBPs and accessory transcription factors to SQS transcriptional control, and the mechanisms underlying cytokine regulation of SQS are major foci of current research.
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Affiliation(s)
- T R Tansey
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, 430l Jones Bridge Road, Bethesda, MD 20814-4799, USA
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15
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Tansey TR, Shechter I. Squalene synthase: structure and regulation. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2000; 65:157-95. [PMID: 11008488 DOI: 10.1016/s0079-6603(00)65005-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Squalene synthase (SQS) catalyzes the first reaction of the branch of the isoprenoid metabolic pathway committed specifically to sterol biosynthesis. Regulation of SQS is thought to direct proximal intermediates in the pathway into either sterol or nonsterol branches in response to changing cellular requirements. The importance of SQS in cholesterol metabolism has stimulated research on the mechanism, structure, and regulation of the enzyme. SQS produces squalene, a C30 isoprenoid, in a two-step reaction in which two molecules of farnesyl diphosphate are condensed head to head. Site-directed mutagenesis of rat SQS has identified conserved Tyr, Phe, and Asp residues that are essential for function. The aromatic rings of Tyr and Phe are postulated to stabilize carbocation intermediates of the first and second half-reactions, respectively; the acidic Asp residues may be required for substrate binding. SQS activity, protein level, and gene transcription are strictly and coordinately regulated by cholesterol status, decreasing with cholesterol surfeit and increasing with cholesterol deficit. The human SQS (hSQS) gene has an unusually complex promoter with multiple binding sites for the sterol regulatory element binding proteins SREBP-1a and SREBP-2, and for accessory transcription factors known to be involved in the control of other sterol-responsive genes. SREBP-1a and SREBP-2 require different subsets of hSQS regulatory DNA elements to achieve maximal promoter activation. Current research is directed at elucidating the precise contribution made by individual SREBPs and accessory transcription factors to hSQS transcriptional control.
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Affiliation(s)
- T R Tansey
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
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16
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Nakayama H, Izuta M, Nakayama N, Arisawa M, Aoki Y. Depletion of the squalene synthase (ERG9) gene does not impair growth of Candida glabrata in mice. Antimicrob Agents Chemother 2000; 44:2411-8. [PMID: 10952588 PMCID: PMC90078 DOI: 10.1128/aac.44.9.2411-2418.2000] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Squalene synthase (farnesyl-diphosphate farnesyltransferase, EC 2.5. 1.21) is the first committed enzyme of the sterol biosynthesis pathway. Inhibitors of this enzyme have been intensively studied as potential antifungal agents. To assess the effect of deactivating squalene synthase on the growth of fungi in mice, we isolated the squalene synthase (ERG9) gene from the pathogenic fungus Candida glabrata and generated strains in which the CgERG9 gene was under the control of the tetracycline-regulatable promoter. Depletion of the ERG9 gene by doxycycline (DOX), a derivative of tetracycline, decreased the cell viability in laboratory media, whereas it did not affect cell growth in mice at all. The growth defect caused by DOX in laboratory media was suppressed by the addition of serum. Analyses of the sterol composition of the restored cells in serum-containing media suggest that the defect of ergosterol biosynthesis can be complemented by the incorporation of exogenous cholesterol into the cells. Thus, deactivation of squalene synthase did not affect fungal growth in mice, presumably because the cells were able to incorporate cholesterol from the serum. These results showed that squalene synthase could not be a suitable target of antifungals for the treatment of C. glabrata infection.
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Affiliation(s)
- H Nakayama
- Department of Mycology, Nippon Roche K. K. Research Center, Kanagawa, Japan.
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Merkulov S, van Assema F, Springer J, Fernandez Del Carmen A, Mooibroek H. Cloning and characterization of the Yarrowia lipolytica squalene synthase (SQS1) gene and functional complementation of the Saccharomyces cerevisiae erg9 mutation. Yeast 2000; 16:197-206. [PMID: 10649449 DOI: 10.1002/(sici)1097-0061(200002)16:3<197::aid-yea513>3.0.co;2-l] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The squalene synthase (SQS) gene encodes a key regulatory enzyme, farnesyl-diphosphate farnesyltransferase (EC 2.5.1.21), in sterol biosynthesis. The SQS1 gene was isolated from a subgenomic library of the industrially important yeast Yarrowia lipolytica, using PCR-generated probes. Probes were based on conserved regions of homologues from different organisms. The complete nucleotide sequence of the coding region and the corresponding amino acid sequence were determined. The sequences showed extensive homologies with squalene synthase genes and enzymes from a number of other organisms and extreme amino acid conservation within the binding and catalytic domains. Direct cloning of a 4.3 kb genomic Y. lipolytica fragment, also comprising its own promoter and terminator sequences, into autonomously replicating plasmid YEp352 and subsequent transformation of a Saccharomyces cerevisiae mutant strain with relevant erg9: ura3-1 markers, resulted in functional complementation of these deficiencies, although Northern blot analyses did not reveal a unique full-length messenger. The availability of the Y. lipolytica SQS1 gene (GenBank Accession No. AF092497) offers prospects for metabolic engineering of the isoprenoid and sterol biosynthetic pathways.
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Affiliation(s)
- S Merkulov
- Agrotechnological Research Institute ATO-DLO, Bornsesteeg 59, NL-6708 PD Wageningen, The Netherlands
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18
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Gardner RG, Hampton RY. A highly conserved signal controls degradation of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase in eukaryotes. J Biol Chem 1999; 274:31671-8. [PMID: 10531376 DOI: 10.1074/jbc.274.44.31671] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sterol synthesis by the mevalonate pathway is modulated, in part, through feedback-regulated degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR). In both mammals and yeast, a non-sterol isoprenoid signal positively regulates the rate of HMGR degradation. To define more precisely the molecule that serves as the source of this signal, we have conducted both pharmacological and genetic manipulations of the mevalonate pathway in yeast. We now demonstrate that farnesyl diphosphate (FPP) is the source of the positive signal for Hmg2p degradation in yeast. This FPP-derived signal does not act by altering the endoplasmic reticulum degradation machinery in general. Rather, the FPP-derived signal specifically modulates Hmg2p stability. In mammalian cells, an FPP-derived molecule also serves as a positive signal for HMGR degradation. Thus, both yeast and mammalian cells employ the same strategy for regulation of HMGR degradation, perhaps by conserved molecular processes.
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Affiliation(s)
- R G Gardner
- Department of Biology, University of California, San Diego, La Jolla, California 92093, USA
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Kennedy MA, Barbuch R, Bard M. Transcriptional regulation of the squalene synthase gene (ERG9) in the yeast Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1445:110-22. [PMID: 10209263 DOI: 10.1016/s0167-4781(99)00035-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The ergosterol biosynthetic pathway is a specific branch of the mevalonate pathway. Since the cells requirement for sterols is greater than for isoprenoids, sterol biosynthesis must be regulated independently of isoprenoid biosynthesis. In this study we explored the transcriptional regulation of squalene synthase (ERG9) in Saccharomyces cerevisiae, the first enzyme dedicated to the synthesis of sterols. A mutant search was performed to identify genes that were involved in the regulation of the expression of an ERG9-lacZ promoter fusion. Mutants with phenotypes consistent with known sterol biosynthetic mutations (ERG3, ERG7, ERG24) increased expression of ERG9. In addition, treatment of wild-type cells with the sterol inhibitors zaragozic acid and ketoconazole, which target squalene synthase and the C-14 sterol demethylase respectively, also caused an increase in ERG9 expression. The data also demonstrate that heme mutants increased ERG9 expression while anaerobic conditions decreased expression. Additionally, the heme activator protein transcription factors HAP1 and HAP2/3/4, the yeast activator protein transcription factor yAP-1, and the phospholipid transcription factor complex INO2/4 regulate ERG9 expression. ERG9 expression is decreased in hap1, hap2/3/4, and yap-1 mutants while ino2/4 mutants showed an increase in ERG9 expression. This study demonstrates that ERG9 transcription is regulated by several diverse factors, consistent with the idea that as the first step dedicated to the synthesis of sterols, squalene synthase gene expression and ultimately sterol biosynthesis is highly regulated.
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Affiliation(s)
- M A Kennedy
- Department of Biology, Indiana University-Purdue University at Indianapolis, 723 W. Michigan Street, SL324, Indianapolis, IN 46202, USA
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Koohang A, Coates RM, Owen D, Poulter CD. Synthesis and Evaluation of Aziridine Analogues of Presqualene Diphosphate as Squalene Synthase Inhibitors. J Org Chem 1999; 64:6-7. [PMID: 11674074 DOI: 10.1021/jo981833z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ali Koohang
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
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21
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22
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Perzl M, Reipen IG, Schmitz S, Poralla K, Sahm H, Sprenger GA, Kannenberg EL. Cloning of conserved genes from Zymomonas mobilis and Bradyrhizobium japonicum that function in the biosynthesis of hopanoid lipids. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1393:108-18. [PMID: 9714766 DOI: 10.1016/s0005-2760(98)00064-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The squalene-hopene cyclase (SHC) is the only enzyme involved in the biosynthesis of hopanoid lipids that has been characterized on the genetic level. To investigate if additional genes involved in hopanoid biosynthesis are clustered with the shc gene, we cloned and analyzed the nucleotide sequences located immediately upstream of the shc genes from Zymomonas mobilis and Bradyrhizobium japonicum. In Z. mobilis, five open reading frames (ORFs, designated as hpnA-E) were detected in a close arrangement with the shc gene. In B. japonicum, three similarly arranged ORFs (corresponding to hpnC-E from Z. mobilis) were found. The deduced amino acid sequences of hpnC-E showed significant similarity (58-62%) in both bacteria. Similarities to enzymes of other terpenoid biosynthesis pathways (carotenoid and steroid biosynthesis) suggest that these ORFs encode proteins involved in the biosynthesis of hopanoids and their intermediates. Expression of hpnC to hpnE from Z. mobilis as well as expression of hpnC from B. japonicum in Escherichia coli led to the formation of the hopanoid precursor squalene. This indicates that hpnC encodes a squalene synthase. The two additional ORFs (hpnA and hpnB) in Z. mobilis showed similarities to enzymes involved in the transfer and modification of sugars, indicating that they may code for enzymes involved in the biosynthesis of the complex, sugar-containing side chains of hopanoids.
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Affiliation(s)
- M Perzl
- Mikrobiologie/Biotechnologie, Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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Gu P, Ishii Y, Spencer TA, Shechter I. Function-structure studies and identification of three enzyme domains involved in the catalytic activity in rat hepatic squalene synthase. J Biol Chem 1998; 273:12515-25. [PMID: 9575210 DOI: 10.1074/jbc.273.20.12515] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rat hepatic squalene synthase (RSS, EC 2.5.1.21) contains three conserved sections, A, B, and C, that were proposed to be involved in catalysis (McKenzie, T. L., Jiang, G., Straubhaar, J. R., Conrad, D., and Shechter, I. (1992) J. Biol. Chem. 267, 21368-21374). Here we use the high expression vector pTrxRSS and site-directed mutagenesis to determine the specific residues in these sections that are essential for the two reactions catalyzed by RSS. Section C mutants F288Y, F288L, F286Y, F286W, F286L, Q293N, and Q283E accumulate presqualene diphosphate (PSPP) from trans-farnesyl diphosphate (FPP) with reduced production of squalene. F288L, which retains approximately 50% first step activity, displays only residual activity (0.2%) in the production of squalene from either FPP or PSPP. Substitution of either Phe288 or Phe286 with charged residues completely abolishes the enzyme activity. Thus, F288W, F288D, F288R, F286D, and F286R cannot produce squalene from either FPP or PSPP. All single residue mutants in Section A, except Tyr171, retain most of the RSS activity, with no detectable accumulation of PSPP in an assay mixture complete with NADPH. Y171F, Y171S, and Y171W are all inactive. Section B, which binds the diphosphate moieties of the allylic diphosphate subtrates, contains four negatively charged residues: Glu222, Glu226, Asp219, and Asp223. The two Glu residues can be replaced with neutral or with positively charged residues without signficantly affecting enzyme activity. However, replacement of either Asp residues with Asn eliminates all but a residual level of activity, and substitution with Glu abolishes all activity. These results indicate that 1) Section C, in particular Phe288, may be involved in the second step of catalysis, 2) Tyr171 of Section A is essential for catalysis, most likely for the first reaction, 3) the two Asp residues in Section B are essential for the activity and most likely bind the substrate via magnesium salt bridges. Based on these results, a mechanism for the first reaction is proposed.
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Affiliation(s)
- P Gu
- Department of Biochemistry and Molecular Biology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799, USA
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Ness F, Achstetter T, Duport C, Karst F, Spagnoli R, Degryse E. Sterol uptake in Saccharomyces cerevisiae heme auxotrophic mutants is affected by ergosterol and oleate but not by palmitoleate or by sterol esterification. J Bacteriol 1998; 180:1913-9. [PMID: 9537392 PMCID: PMC107107 DOI: 10.1128/jb.180.7.1913-1919.1998] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The relationship between sterol uptake and heme competence in two yeast strains impaired in heme synthesis, namely, G204 and H12-6A, was analyzed. To evaluate heme availability, a heterologous 17alpha-hydroxylase cytochrome P-450 cDNA (P-450c17) was expressed in these strains, and its activity was measured in vivo. Heme deficiency in G204 led to accumulation of squalene and lethality. The heterologous cytochrome P-450 was inactive in this strain. The leaky H12-6A strain presented a slightly modified sterol content compared to that for the wild type, and the P-450c17 recovered partial activity. By analyzing sterol transfer on nongrowing cells, it was shown that the cells were permeable toward exogenous cholesterol when they were depleted of endogenous sterols, which was the case for G204 but not for H12-6A. It was concluded that the fully blocked heme mutant (G204) replenishes its diminishing endogenous sterol levels during growth by replacement with sterol from the outside medium. Endogenous sterol biosynthesis appears to be the primary factor capable of excluding exogenous sterol. Oleate but not palmitoleate was identified as a component that reduced but did not prevent sterol transfer. Sterol transfer was only slightly affected by a lack of esterification. It is described herein how avoidance of the potential cytotoxicity of the early intermediates of the mevalonate pathway could be achieved by a secondary heme mutation in erg auxotrophs.
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Affiliation(s)
- F Ness
- Yeast Department, Transgène S.A., Strasbourg, France
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25
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Thompson JF, Danley DE, Mazzalupo S, Milos PM, Lira ME, Harwood HJ. Truncation of human squalene synthase yields active, crystallizable protein. Arch Biochem Biophys 1998; 350:283-90. [PMID: 9473303 DOI: 10.1006/abbi.1997.0502] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Squalene synthase catalyzes the first committed step in cholesterol biosynthesis and thus is important as a potential target for therapeutic intervention. In order to determine the important functional domains of the protein, the amino and carboxyl terminal regions thought to be involved in membrane association of the enzyme were removed genetically. The 30 N-terminal amino acids were deleted with no apparent effect on activity. Additional deletion of 81 or 97 amino acids from the C-terminus completely ablated activity. However, a protein with a C-terminal deletion of 47 amino acids retained full activity. The latter enzyme was readily overexpressed in Escherichia coli and purified to homogeneity. The pure, doubly truncated enzyme exhibited a specific activity similar to that reported for the protease-solubilized rat liver enzyme, had a KM for farnesyl diphosphate similar to that observed for native enzyme, and was inhibited by anionic compounds to the same degree as native enzyme. Using the vapor diffusion method, the protein was crystallized as an enzyme-inhibitor complex, yielding orthorhombic crystals which diffracted to 2.2 A.
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Affiliation(s)
- J F Thompson
- Central Research Division, Pfizer Inc., Groton, Connecticut 06340, USA.
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26
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Kribii R, Arró M, Del Arco A, González V, Balcells L, Delourme D, Ferrer A, Karst F, Boronat A. Cloning and characterization of the Arabidopsis thaliana SQS1 gene encoding squalene synthase--involvement of the C-terminal region of the enzyme in the channeling of squalene through the sterol pathway. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 249:61-9. [PMID: 9363754 DOI: 10.1111/j.1432-1033.1997.00061.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Squalene synthase (SQS) catalyzes the first committed step of the sterol biosynthetic pathway. A full-length Arabidopsis thaliana SQS cDNA has been isolated by combining library screening and PCR-based approaches. Arabidopsis SQS is encoded by a small gene family of two genes (SQS1 and SQS2) which are organized in a tandem array. SQS1 and SQS2 have an identical organization with regard to intron positions and exon sizes and encode SQS isoforms showing a high level of sequence conservation (79% identity and 88% similarity). The isolated cDNA has been assigned to the SQS1 gene product, SQS1. RNA blot analysis has shown that the 1.6-kb SQS1 mRNA is detected in all plant tissues analyzed (inflorescenses, leaves, stems and roots) although the transcript is especially abundant in roots. Arabidopsis SQS1 isoform is unable to complement the SQS-defective Saccharomyces cerevisiae strain 5302, although SQS activity was detected in the microsomal fraction of the transformed yeast strain. However, a chimeric SQS resulting from the replacement of the 66 C-terminal residues of the Arabidopsis enzyme by the 111 C-terminal residues of the Schizosaccharomyces pombe enzyme was able to confer ergosterol prototrophy to strain 5302. Labeling studies using [3H]farnesyl-P2 and microsomal fractions obtained from yeast strains expressing either Arabidopsis SQS1 or chimeric Arabidopsis/S. pombe SQS derivatives indicated that the C-terminal region of the enzyme is involved in the channeling of squalene through the yeast sterol pathway.
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Affiliation(s)
- R Kribii
- Laboratoire de Génétique Physiologique et Moléculaire, Institut de Biologie Moléculaire et d'Ingénierie Génétique, Université de Poitiers, France
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Bach TJ, Benveniste P. Cloning of cDNAs or genes encoding enzymes of sterol biosynthesis from plants and other eukaryotes: heterologous expression and complementation analysis of mutations for functional characterization. Prog Lipid Res 1997; 36:197-226. [PMID: 9624427 DOI: 10.1016/s0163-7827(97)00009-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- T J Bach
- Institut de Biologie Moléculaire des Plantes (C.N.R.S., UPR 0406), Université Louis Pasteur, Strasbourg, France
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Bergès T, Guyonnet D, Karst F. The Saccharomyces cerevisiae mevalonate diphosphate decarboxylase is essential for viability, and a single Leu-to-Pro mutation in a conserved sequence leads to thermosensitivity. J Bacteriol 1997; 179:4664-70. [PMID: 9244250 PMCID: PMC179309 DOI: 10.1128/jb.179.15.4664-4670.1997] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The mevalonate diphosphate decarboxylase is an enzyme which converts mevalonate diphosphate to isopentenyl diphosphate, the building block of isoprenoids. We used the Saccharomyces cerevisiae temperature-sensitive mutant defective for mevalonate diphosphate decarboxylase previously described (C. Chambon, V. Ladeveve, M. Servouse, L. Blanchard, C. Javelot, B. Vladescu, and F. Karst, Lipids 26:633-636, 1991) to characterize the mutated allele. We showed that a single change in a conserved amino acid accounts for the temperature-sensitive phenotype of the mutant. Complementation experiments were done both in the erg19-mutated background and in a strain in which the ERG19 gene, which was shown to be an essential gene for yeast, was disrupted. Epitope tagging of the wild-type mevalonate diphosphate decarboxylase allowed us to isolate the enzyme in an active form by a versatile one-step immunoprecipitation procedure. Furthermore, during the course of this study, we observed that a high level of expression of the wild-type ERG19 gene led to a lower sterol steady-state accumulation compared to that of a wild-type strain, suggesting that this enzyme may be a key enzyme in mevalonate pathway regulation.
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Affiliation(s)
- T Bergès
- Faculté des Sciences, Institut de Biologie Moléculaire et d'Ingénierie Génétique, Université de Poitiers, France.
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Watson NS, Procopiou PA. Squalene synthase inhibitors: their potential as hypocholesterolaemic agents. PROGRESS IN MEDICINAL CHEMISTRY 1996; 33:331-78. [PMID: 8776946 DOI: 10.1016/s0079-6468(08)70308-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- N S Watson
- Medicinal Chemistry 3 Department, Glaxo Wellcome Medicines Research Centre, Stevenage, Hertfordshire, U.K
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Nakashima T, Inoue T, Oka A, Nishino T, Osumi T, Hata S. Cloning, expression, and characterization of cDNAs encoding Arabidopsis thaliana squalene synthase. Proc Natl Acad Sci U S A 1995; 92:2328-32. [PMID: 7892265 PMCID: PMC42476 DOI: 10.1073/pnas.92.6.2328] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We have isolated and characterized two overlapping cDNA clones for Arabidopsis thaliana squalene synthase. Their nucleotide sequences contained an open reading frame for a 410-amino acid polypeptide (calculated molecular mass, 47 kDa). The deduced amino acid sequence of the Arabidopsis polypeptide was significantly homologous (42-44% identical) to the sequences of known squalene synthases of several species, from yeast to man, but it was much less homologous to that of tomato phytoene synthase. To express the Arabidopsis enzyme in Escherichia coli, the entire coding region was subcloned into an expression vector. A cell-free extract of E. coli transformed with the recombinant plasmid, in the presence of NADPH and Mg2+, efficiently converted [14C]farnesyl diphosphate into squalene. On the other hand, in the absence of NADPH and the presence of Mn2+, the cell-free extract formed dehydrosqualene as a secondary product. Another E. coli extract expressing mouse squalene synthase showed the same activity as the Arabidopsis enzyme. Therefore, both the structure and reaction mechanism of squalene synthases are markedly conserved in taxonomically remote eukaryotes.
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Affiliation(s)
- T Nakashima
- Faculty of Science, Himeji Institute of Technology, Hyogo, Japan
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32
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Lees ND, Skaggs B, Kirsch DR, Bard M. Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiae--a review. Lipids 1995; 30:221-6. [PMID: 7791529 DOI: 10.1007/bf02537824] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Research on the ergosterol biosynthetic pathway in fungi has focused on the identification of the specific sterol structure required for normal membrane structure and function and for completion of the cell cycle. The pathway and its end product are also the targets for a number of antifungal drugs. Identification of essential steps in ergo-sterol biosynthesis could provide new targets for the development of novel therapeutic agents. Nine of the eleven genes in the portion of the pathway committed exclusively to ergosterol biosynthesis have been cloned, and their essentiality for aerobic growth has been determined. The first three genes, ERG9 (squalene synthase), ERG1 (squalene epoxidase), and ERG7 (lanosterol synthase), have been cloned and found to be essential for aerobic viability since their absence would result in the cell being unable to synthesize a sterol molecule. The remaining eight genes encode enzymes which metabolize the first sterol, lanosterol, to ultimately form ergosterol. The two earliest genes, ERG11 (lanosterol demethylase) and ERG24 (C-14 reductase), have been cloned and found to be essential for aerobic growth but are suppressed by mutations in the C-5 desaturase (ERG3) gene and fen1 and fen2 mutations, respectively. The remaining cloned genes, ERG6 (C-24 methylase), ERG2 (D8AE7 isomerase), ERG3 (C-5 desaturase), and ERG4 (C-24(28) reductase), have been found to be nonessential. The remaining genes not yet cloned are the C-4 demethylase and the C-22 desaturase (ERG5).
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Affiliation(s)
- N D Lees
- Department of Biology, Indiana University-Purdue University at Indianapolis 46202-5132, USA
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33
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Inoue T, Osumi T, Hata S. Molecular cloning and functional expression of a cDNA for mouse squalene synthase. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1260:49-54. [PMID: 7999794 DOI: 10.1016/0167-4781(94)00178-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using a probe obtained by PCR amplification, a full-length cDNA encoding squalene synthase was isolated from a mouse liver cDNA library. Its nucleotide sequence had an open reading frame fro a 416 amino acid polypeptide (calculated molecular mass, 48 kDa). In vitro transcription of the cDNA followed by in vitro translation produced a protein of the expected size. The deduced amino acid sequence was 93%, 88% and 46% identical to those of the rat, human and budding yeast squalene synthases, respectively. Blotting analyses showed that the mRNA is 1.6 kb in size and that less than two copies of the gene are present in the mouse genome. To establish the enzyme activity, the entire coding region was subcloned into an expression plasmid so that it was in frame with the N-terminal region of beta-galactosidase. Escherichia coli, which was transformed with the recombinant plasmid, expressed high activity of converting farnesyl diphosphate into squalene.
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Affiliation(s)
- T Inoue
- Department of Life Science, Faculty of Science, Himeji Institute of Technology, Hyogo, Japan
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34
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Affiliation(s)
- D E Cane
- Chemistry Department, Brown University, Providence, RI 02912, USA
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35
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Novotn� ?, Karst F. Sterol dependent growth and ethanol tolerance of a sterol-auxotrophicerg9::HIS3 mutant ofSaccharomyces cerevisiae. Biotechnol Lett 1994. [DOI: 10.1007/bf01023340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Mookhtiar K, Kalinowski S, Zhang D, Poulter C. Yeast squalene synthase. A mechanism for addition of substrates and activation by NADPH. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(19)78111-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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37
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Corey EJ, Matsuda SP, Bartel B. Molecular cloning, characterization, and overexpression of ERG7, the Saccharomyces cerevisiae gene encoding lanosterol synthase. Proc Natl Acad Sci U S A 1994; 91:2211-5. [PMID: 8134375 PMCID: PMC43340 DOI: 10.1073/pnas.91.6.2211] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We report the cloning, characterization, and overexpression of Saccharomyces cerevisiae ERG7, which encodes lanosterol synthase [(S)-2,3-epoxysqualene mutase (cyclizing, lanosterol forming), EC 5.4.99.7], the enzyme responsible for the complex cyclization/rearrangement step in sterol biosynthesis. Oligonucleotide primers were designed corresponding to protein sequences conserved between Candida albicans ERG7 and the related Arabidopsis thaliana cycloartenol synthase [(S)-2,3-epoxysqualene mutase (cyclizing, cycloartenol forming), EC 5.4.99.8]. A PCR product was amplified from yeast genomic DNA using these primers and was used to probe yeast libraries by hybridization. Partial-length clones homologous to the two known epoxysqualene mutases were isolated, but a full-length sequence was found neither in cDNA nor genomic libraries, whether in phage or plasmids. Two overlapping clones were assembled to make a functional reconstruction of the gene, which contains a 2196-bp open reading frame capable of encoding an 83-kDa protein. The reconstruction complemented the erg7 mutation when driven from either its native promoter or the strong ADH1 promoter.
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Affiliation(s)
- E J Corey
- Department of Chemistry, Harvard University, Cambridge, MA 02138
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38
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Summers C, Karst F, Charles AD. Cloning, expression and characterisation of the cDNA encoding human hepatic squalene synthase, and its relationship to phytoene synthase. Gene 1993; 136:185-92. [PMID: 8294001 DOI: 10.1016/0378-1119(93)90462-c] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The reaction catalysed by squalene synthase (SQS) shows many similarities to that performed by another polyisoprene synthase, phytoene synthase (PhS). By identifying sequences conserved between yeast SQS (ySQS) and PhS, we have cloned a 2-kb cDNA (hSQS) encoding human SQS, a protein of 417 amino acids with a predicted M(r) of 48,041, which has only limited homology to ySQS. When expressed in E. coli, the hSQS cDNA directed the production of active enzyme. Two hSQS mRNA species of 2.0 and 1.55 kb have been identified which differ in their 3' untranslated sequences. The two mRNAs are present in roughly equal amounts in heart, placenta, lung, liver, kidney and pancreas, but the 2-kb mRNA predominates in brain and skeletal muscle. In HepG2 cells, both mRNAs are induced 2-4-fold by the 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitor, lovastatin. In contrast, Northern blot analysis of rat tissues reveals only a 2.0-kb mRNA, which is considerably up-regulated in vivo by lovastatin.
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Affiliation(s)
- C Summers
- Cardiovascular Department, ZENECA Pharmaceuticals, Macclesfield, Cheshire, UK
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39
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Ciosek CP, Magnin DR, Harrity TW, Logan JV, Dickson JK, Gordon EM, Hamilton KA, Jolibois KG, Kunselman LK, Lawrence RM. Lipophilic 1,1-bisphosphonates are potent squalene synthase inhibitors and orally active cholesterol lowering agents in vivo. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74540-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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40
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Conservation between human and fungal squalene synthetases: similarities in structure, function, and regulation. Mol Cell Biol 1993. [PMID: 8474436 DOI: 10.1128/mcb.13.5.2706] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Squalene synthetase (farnesyl diphosphate:farnesyl diphosphate farnesyltransferase; EC 2.5.1.21) is thought to represent a major control point of isoprene and sterol biosynthesis in eukaryotes. We demonstrate structural and functional conservation between the enzymes from humans, a budding yeast (Saccharomyces cerevisiae), and a fission yeast (Schizosaccharomyces pombe). The amino acid sequences of the human and S. pombe proteins deduced from cloned cDNAs were compared to those of the known S. cerevisiae protein. All are predicted to encode C-terminal membrane-spanning proteins of approximately 50 kDa with similar hydropathy profiles. Extensive sequence conservation exists in regions of the enzyme proposed to interact with its prenyl substrates (i.e., two farnesyl diphosphate molecules). Many of the highly conserved regions are also present in phytoene and prephytoene diphosphate synthetases, enzymes which catalyze prenyl substrate condensation reactions analogous to that of squalene synthetase. Expression of cDNA clones encoding S. pombe or hybrid human-S. cerevisiae squalene synthetases reversed the ergosterol requirement of S. cerevisiae cells bearing ERG9 gene disruptions, showing that these enzymes can functionally replace the S. cerevisiae enzyme. Inhibition of sterol synthesis in S. cerevisiae and S. pombe cells or in cultured human fibroblasts by treatment with the 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor lovastatin resulted in elevated levels of squalene synthetase mRNA in all three cell types.
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41
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Robinson GW, Tsay YH, Kienzle BK, Smith-Monroy CA, Bishop RW. Conservation between human and fungal squalene synthetases: similarities in structure, function, and regulation. Mol Cell Biol 1993; 13:2706-17. [PMID: 8474436 PMCID: PMC359645 DOI: 10.1128/mcb.13.5.2706-2717.1993] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Squalene synthetase (farnesyl diphosphate:farnesyl diphosphate farnesyltransferase; EC 2.5.1.21) is thought to represent a major control point of isoprene and sterol biosynthesis in eukaryotes. We demonstrate structural and functional conservation between the enzymes from humans, a budding yeast (Saccharomyces cerevisiae), and a fission yeast (Schizosaccharomyces pombe). The amino acid sequences of the human and S. pombe proteins deduced from cloned cDNAs were compared to those of the known S. cerevisiae protein. All are predicted to encode C-terminal membrane-spanning proteins of approximately 50 kDa with similar hydropathy profiles. Extensive sequence conservation exists in regions of the enzyme proposed to interact with its prenyl substrates (i.e., two farnesyl diphosphate molecules). Many of the highly conserved regions are also present in phytoene and prephytoene diphosphate synthetases, enzymes which catalyze prenyl substrate condensation reactions analogous to that of squalene synthetase. Expression of cDNA clones encoding S. pombe or hybrid human-S. cerevisiae squalene synthetases reversed the ergosterol requirement of S. cerevisiae cells bearing ERG9 gene disruptions, showing that these enzymes can functionally replace the S. cerevisiae enzyme. Inhibition of sterol synthesis in S. cerevisiae and S. pombe cells or in cultured human fibroblasts by treatment with the 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor lovastatin resulted in elevated levels of squalene synthetase mRNA in all three cell types.
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Affiliation(s)
- G W Robinson
- Department of Metabolic Diseases, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543
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42
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Blanchard L, Karst F. Characterization of a lysine-to-glutamic acid mutation in a conservative sequence of farnesyl diphosphate synthase from Saccharomyces cerevisiae. Gene X 1993; 125:185-9. [PMID: 8096487 DOI: 10.1016/0378-1119(93)90326-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The mutant gene erg20-2 was isolated from a yeast strain defective in farnesyl diphosphate synthase (FPPS). This strain had the unusual property of excreting prenyl alcohols such as geraniol. The nucleotide (nt) sequence, compared with that of the wild-type gene, showed a single nt change, resulting in a Lys197-->Glu substitution in FPPS which is directly involved in terpenic alcohol formation. In addition, disruption of ERG20 revealed that in yeast no other prenyl transferase is able to synthesize the FPP molecules required for essential non-sterol metabolites.
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Affiliation(s)
- L Blanchard
- Laboratoire de Biochimie et Génétique des Microorganismes, Université de Poitiers, France
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43
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Marcireau C, Guyonnet D, Karst F. Construction and growth properties of a yeast strain defective in sterol 14-reductase. Curr Genet 1992; 22:267-72. [PMID: 1394506 DOI: 10.1007/bf00317919] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have transformed Saccharomyces cerevisiae with a genomic library contained in the replicative vector pFL44. The resulting transformants were screened for resistance to fenpropidin, a specific inhibitor of sterol 14-reductase. A plasmid was isolated that transformed yeast both to resistance to fenpropidin and to an increased specific activity of sterol 14-reductase. Sterol analysis of transformed cells grown in the presence of increasing concentrations of the inhibitor confirmed that resistance was a consequence of over-production of sterol 14-reductase. By chromosomal gene disruption, we have, for the first time, constructed yeast strains defective in sterol 14-reductase. As expected, since yeast in unable to take up sterols in aerobiosis, the disrupted strains do not grow in the presence of oxygen, even if exogenous sterols are supplied. However, disrupted cells grow in anaerobiosis with exogenous oleic acid and ergosterol supplements. They also grow in aerobiosis if they bear an additional mutation allowing sterol uptake. In this last growth condition the cells require a "sparking" ergosterol supplementation (25 nM) and accumulate ignosterol (ergosta-8,14-dienol) as the end-product of the sterol pathway. These results reveal that ignosterol is not obviously toxic to yeast membranes and strongly suggest that the molecular basis of the antifungal-activity morpholine and piperidine is directly related to the specific inhibition of ergosterol formation.
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Affiliation(s)
- C Marcireau
- Laboratoire de Biochimie et Génétique des Microorganismes, Université de Poitiers, France
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