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Claes K, Van Herpe D, Vanluchene R, Roels C, Van Moer B, Wyseure E, Vandewalle K, Eeckhaut H, Yilmaz S, Vanmarcke S, Çıtak E, Fijalkowska D, Grootaert H, Lonigro C, Meuris L, Michielsen G, Naessens J, van Schie L, De Rycke R, De Bruyne M, Borghgraef P, Callewaert N. OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression. Nat Microbiol 2024; 9:864-876. [PMID: 38443579 PMCID: PMC10914597 DOI: 10.1038/s41564-023-01574-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/01/2023] [Indexed: 03/07/2024]
Abstract
The industrial yeast Komagataella phaffii (formerly named Pichia pastoris) is commonly used to synthesize recombinant proteins, many of which are used as human therapeutics or in food. However, the basic strain, named NRRL Y-11430, from which all commercial hosts are derived, is not available without restrictions on its use. Comparative genome sequencing leaves little doubt that NRRL Y-11430 is derived from a K. phaffii type strain deposited in the UC Davis Phaff Yeast Strain Collection in 1954. We analysed four equivalent type strains in several culture collections and identified the NCYC 2543 strain, from which we started to develop an open-access Pichia chassis strain that anyone can use to produce recombinant proteins to industry standards. NRRL Y-11430 is readily transformable, which we found to be due to a HOC1 open-reading-frame truncation that alters cell-wall mannan. We introduced the HOC1 open-reading-frame truncation into NCYC 2543, which increased the transformability and improved secretion of some but not all of our tested proteins. We provide our genome-sequenced type strain, the hoc1tr derivative that we named OPENPichia as well as a synthetic, modular expression vector toolkit under liberal end-user distribution licences as an unencumbered OPENPichia resource for the microbial biotechnology community.
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Affiliation(s)
- Katrien Claes
- Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Dries Van Herpe
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Inbiose NV, Ghent, Belgium
| | - Robin Vanluchene
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Charlotte Roels
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Berre Van Moer
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Elise Wyseure
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kristof Vandewalle
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Hannah Eeckhaut
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Semiramis Yilmaz
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sandrine Vanmarcke
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Erhan Çıtak
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Hendrik Grootaert
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Chiara Lonigro
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Leander Meuris
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Gitte Michielsen
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Justine Naessens
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Loes van Schie
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- BioImaging Core, VIB, Ghent, Belgium
| | - Michiel De Bruyne
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- BioImaging Core, VIB, Ghent, Belgium
| | | | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
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Pastor-Vega N, Carbonero-Pacheco J, Mauricio JC, Moreno J, García-Martínez T, Nitin N, Ogawa M, Rai R, Moreno-García J. Flor yeast immobilization in microbial biocapsules for Sherry wine production: microvinification approach. World J Microbiol Biotechnol 2023; 39:271. [PMID: 37541980 PMCID: PMC10403390 DOI: 10.1007/s11274-023-03713-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/23/2023] [Indexed: 08/06/2023]
Abstract
Sherry wine is a pale-yellowish dry wine produced in Southern-Spain which features are mainly due to biological aging when the metabolism of biofilm-forming yeasts (flor yeasts) consumes ethanol (and other non-fermentable carbon sources) from a previous alcoholic fermentation, and produces volatile compounds such as acetaldehyde. To start aging and maintain the wine stability, a high alcohol content is required, which is achieved by the previous fermentation or by adding ethanol (fortification). Here, an alternative method is proposed which aims to produce a more economic, distinctive Sherry wine without fortification. For this, a flor yeast has been pre-acclimatized to glycerol consumption against ethanol, and later confined in a fungal-based immobilization system known as "microbial biocapsules", to facilitate its inoculum. Once aged, the wines produced using biocapsules and free yeasts (the conventional method) exhibited chemical differences in terms of acidity and volatile concentrations. These differences were evaluated positively by a sensory panel. Pre-acclimatization of flor yeasts to glycerol consumption was not successful but when cells were immobilized in fungal pellets, ethanol consumption was lower. We believe that immobilization of flor yeasts in microbial biocapsules is an economic technique that can be used to produce high quality differentiated Sherry wines.
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Affiliation(s)
- Noelia Pastor-Vega
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, 14014 Spain
| | - Juan Carbonero-Pacheco
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, 14014 Spain
| | - Juan Carlos Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, 14014 Spain
| | - Juan Moreno
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, 14014 Spain
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, 14014 Spain
| | - Nitin Nitin
- Department of Food Science and Technology, University of California, Davis, Davis, CA 95616 USA
| | - Minami Ogawa
- Department of Food Science and Technology, University of California, Davis, Davis, CA 95616 USA
| | - Rewa Rai
- Department of Food Science and Technology, University of California, Davis, Davis, CA 95616 USA
| | - Jaime Moreno-García
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, 14014 Spain
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Taylor MB, Skophammer R, Warwick AR, Geck RC, Boyer JM, yEvo Students, Walson M, Large CRL, Hickey ASM, Rowley PA, Dunham MJ. yEvo: experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2022; 12:jkac246. [PMID: 36173330 PMCID: PMC9635649 DOI: 10.1093/g3journal/jkac246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022]
Abstract
Antifungal resistance in pathogenic fungi is a growing global health concern. Nonpathogenic laboratory strains of Saccharomyces cerevisiae are an important model for studying mechanisms of antifungal resistance that are relevant to understanding the same processes in pathogenic fungi. We have developed a series of laboratory modules in which high school students used experimental evolution to study antifungal resistance by isolating azole-resistant S. cerevisiae mutants and examining the genetic basis of resistance. We have sequenced 99 clones from these experiments and found that all possessed mutations previously shown to impact azole resistance, validating our approach. We additionally found recurrent mutations in an mRNA degradation pathway and an uncharacterized mitochondrial protein (Csf1) that have possible mechanistic connections to azole resistance. The scale of replication in this initiative allowed us to identify candidate epistatic interactions, as evidenced by pairs of mutations that occur in the same clone more frequently than expected by chance (positive epistasis) or less frequently (negative epistasis). We validated one of these pairs, a negative epistatic interaction between gain-of-function mutations in the multidrug resistance transcription factors Pdr1 and Pdr3. This high school-university collaboration can serve as a model for involving members of the broader public in the scientific process to make meaningful discoveries in biomedical research.
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Affiliation(s)
- Matthew Bryce Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Program in Biology, Loras College, Dubuque, IA 52001, USA
| | | | - Alexa R Warwick
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Josephine M Boyer
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - yEvo Students
- Westridge School, Pasadena, CA 91105, USA
- Moscow High School, Moscow, ID 83843, USA
| | - Margaux Walson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christopher R L Large
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- UW Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Angela Shang-Mei Hickey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Present address: Department of Genetics, Stanford University, Biomedical Innovations Building, Palo Alto, CA 94304, USA
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Ruiz J, de Celis M, Martín-Santamaría M, Benito-Vázquez I, Pontes A, Lanza VF, Sampaio JP, Santos A, Belda I. Global distribution of IRC7 alleles in Saccharomyces cerevisiae populations: a genomic and phenotypic survey within the wine clade. Environ Microbiol 2021; 23:3182-3195. [PMID: 33973343 DOI: 10.1111/1462-2920.15540] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 11/28/2022]
Abstract
The adaptation to the different biotic and abiotic factors of wine fermentation has led to the accumulation of numerous genomic hallmarks in Saccharomyces cerevisiae wine strains. IRC7, a gene encoding a cysteine-S-β-lyase enzyme related volatile thiols production in wines, has two alleles: a full-length allele (IRC7F ) and a mutated one (IRC7S ), harbouring a 38 bp-deletion. Interestingly, IRC7S -encoding a less active enzyme - appears widespread amongst wine populations. Studying the global distribution of the IRC7S allele in different yeast lineages, we confirmed its high prevalence in the Wine clade and demonstrated a minority presence in other domesticated clades (Wine-PDM, Beer and Bread) while it is completely missing in wild clades. Here, we show that IRC7S -homozygous (HS) strains exhibited both fitness and competitive advantages compared with IRC7F -homozygous (HF) strains. There are some pieces of evidence of the direct contribution of the IRC7S allele to the outstanding behaviour of HS strains (i.e., improved response to oxidative stress conditions and higher tolerance to high copper levels); however, we also identified a set of sequence variants with significant co-occurrence patterns with the IRC7S allele, which can be co-contributing to the fitness and competitive advantages of HS strains in wine fermentations.
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Affiliation(s)
- Javier Ruiz
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Miguel de Celis
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - María Martín-Santamaría
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Iván Benito-Vázquez
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Ana Pontes
- Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Val F Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, 28034, Spain
| | - José Paulo Sampaio
- Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Antonio Santos
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Ignacio Belda
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
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Brady JR, Whittaker CA, Tan MC, Kristensen DL, Ma D, Dalvie NC, Love KR, Love JC. Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain. Biotechnol Bioeng 2020; 117:543-555. [PMID: 31654411 PMCID: PMC7003935 DOI: 10.1002/bit.27209] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/04/2019] [Accepted: 10/22/2019] [Indexed: 01/08/2023]
Abstract
Komagataella phaffii, also known as Pichia pastoris, is a common host for the production of biologics and enzymes, due to fast growth, high productivity, and advancements in host engineering. Several K. phaffii variants are commonly used as interchangeable base strains, which confounds efforts to improve this host. In this study, genomic and transcriptomic analyses of Y-11430 (CBS7435), GS115, X-33, and eight other variants enabled a comparative assessment of the relative fitness of these hosts for recombinant protein expression. Cell wall integrity explained the majority of the variation among strains, impacting transformation efficiency, growth, methanol metabolism, and secretion of heterologous proteins. Y-11430 exhibited the highest activity of genes involved in methanol utilization, up to two-fold higher transcription of heterologous genes, and robust growth. With a more permeable cell wall, X-33 displayed a six-fold higher transformation efficiency and up to 1.2-fold higher titers than Y-11430. X-33 also shared nearly all mutations, and a defective variant of HIS4, with GS115, precluding robust growth. Transferring two beneficial mutations identified in X-33 into Y-11430 resulted in an optimized base strain that provided up to four-fold higher transformation efficiency and three-fold higher protein titers, while retaining robust growth. The approach employed here to assess unique banked variants in a species and then transfer key beneficial variants into a base strain should also facilitate rational assessment of a broad set of other recombinant hosts.
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Affiliation(s)
- Joseph R. Brady
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Charles A. Whittaker
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Melody C. Tan
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - D. Lee Kristensen
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Duanduan Ma
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Neil C. Dalvie
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Kerry Routenberg Love
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - J. Christopher Love
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
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Xiberras J, Klein M, Nevoigt E. Glycerol as a substrate for Saccharomyces cerevisiae based bioprocesses - Knowledge gaps regarding the central carbon catabolism of this 'non-fermentable' carbon source. Biotechnol Adv 2019; 37:107378. [PMID: 30930107 DOI: 10.1016/j.biotechadv.2019.03.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/14/2022]
Abstract
Glycerol is an interesting alternative carbon source in industrial bioprocesses due to its higher degree of reduction per carbon atom compared to sugars. During the last few years, significant progress has been made in improving the well-known industrial platform organism Saccharomyces cerevisiae with regard to its glycerol utilization capability, particularly in synthetic medium. This provided a basis for future metabolic engineering focusing on the production of valuable chemicals from glycerol. However, profound knowledge about the central carbon catabolism in synthetic glycerol medium is a prerequisite for such incentives. As a matter of fact, the current assumptions about the actual in vivo fluxes active on glycerol as the sole carbon source have mainly been based on omics data collected in complex media or were even deduced from studies with other non-fermentable carbon sources, such as ethanol or acetate. A number of uncertainties have been identified which particularly regard the role of the glyoxylate cycle, the subcellular localization of the respective enzymes, the contributions of mitochondrial transporters and the active anaplerotic reactions under these conditions. The review scrutinizes the current knowledge, highlights the necessity to collect novel experimental data using cells growing in synthetic glycerol medium and summarizes the current state of the art with regard to the production of valuable fermentation products from a carbon source that has been considered so far as 'non-fermentable' for the yeast S. cerevisiae.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany.
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Kim JE, Jang IS, Sung BH, Kim SC, Lee JY. Rerouting of NADPH synthetic pathways for increased protopanaxadiol production in Saccharomyces cerevisiae. Sci Rep 2018; 8:15820. [PMID: 30361526 PMCID: PMC6202386 DOI: 10.1038/s41598-018-34210-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/11/2018] [Indexed: 11/17/2022] Open
Abstract
Ginseng (Panax ginseng) and its bioactive components, ginsenosides, are popular medicinal herbal products, exhibiting various pharmacological effects. Despite their advocated use for medication, the long cultivation periods of ginseng roots and their low ginsenoside content prevent mass production of this compound. Yeast Saccharomyces cerevisiae was engineered for production of protopanaxadiol (PPD), a type of aglycone characterizing ginsenoside. PPD-producing yeast cell factory was further engineered by obtaining a balance between enzyme expressions and altering cofactor availability. Different combinations of promoters (PGPD, PCCW12, and PADH2) were utilized to construct the PPD biosynthetic pathway. Rerouting the redox metabolism to improve NADPH availability in the engineered S. cerevisiae also increased PPD production. Combining these approaches resulted in more than an 11-fold increase in PPD titer over the initially constructed strain. The series of metabolic engineering strategies of this study provides a feasible approach for the microbial production of PPD and development of microbial platforms producing other industrially-relevant terpenoids.
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Affiliation(s)
- Jae-Eung Kim
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea
| | - In-Seung Jang
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea
| | - Bong Hyun Sung
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea.
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Santos MMS, Elsztein C, De Souza RB, Paiva SDSL, Silva JA, Crovella S, De Morais MA. Respiratory deficiency in yeast mevalonate kinase deficient may explain MKD-associate metabolic disorder in humans. Curr Genet 2018; 64:871-881. [PMID: 29374778 DOI: 10.1007/s00294-018-0803-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 01/28/2023]
Abstract
Mevalonate kinase deficiency (MKD) an orphan drug rare disease affecting humans with different clinical presentations, is still lacking information about its pathogenesis; no animal or cell model mimicking the genetic defect, mutations at MVK gene, and its consequences on the mevalonate pathway is available. Trying to clarify the effects of MVK gene impairment on the mevalonate pathway we used a yeast model, the erg12-d mutant strain Saccharomyces cerevisiae (orthologous of MKV) retaining only 10% of mevalonate kinase (MK) activity, to describe the effects of reduced MK activity on the mevalonate pathway. Since shortage of isoprenoids has been described in MKD, we checked this observation using a physiologic approach: while normally growing on glucose, erg12-d showed growth deficiency in glycerol, a respirable carbon source, that was not rescued by supplementation with non-sterol isoprenoids, such as farnesol, geraniol nor geranylgeraniol, produced by the mevalonate pathway. Erg12-d whole genome expression analysis revealed specific downregulation of RSF2 gene encoding general transcription factor for respiratory genes, explaining the absence of growth on glycerol. Moreover, we observed the upregulation of genes involved in sulphur amino acids biosynthesis that coincided with the increasing in the amount of proteins containing sulfhydryl groups; upregulation of ubiquinone biosynthesis genes was also detected. Our findings demonstrated that the shortage of isoprenoids is not the main mechanism involved in the respiratory deficit and mitochondrial malfunctioning of MK-defective cells, while the scarcity of ubiquinone plays an important role, as already observed in MKD patients.
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Affiliation(s)
- Manuella Maria Silva Santos
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Recife, PE, 50760-901, Brazil
- Department of Genetics, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Cidade Universitária, Recife, PE, 50760-901, Brazil
| | - Carolina Elsztein
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Recife, PE, 50760-901, Brazil
- Department of virology/CPqAM, Oswaldo Cruz Fundation, Avenida Moraes Rego, N/S, Recife, PE, 50760-901, Brazil
| | - Rafael Barros De Souza
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Recife, PE, 50760-901, Brazil
- Institute for Biologial Sciences, University of Pernambuco, Avenida Agamenon Magalhães, s/n, Recife, PE, 50100-010, Brazil
| | - Sérgio de Sá Leitão Paiva
- Laboratory of Bioinformatics and Evolutionary Biology, Federal Rural University Pernambuco, Rua Dom Manoel de Medeiros, s/n, Recife, PE, 52171-900, Brazil
| | - Jaqueline Azevêdo Silva
- Department of Genetics, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Cidade Universitária, Recife, PE, 50760-901, Brazil
- Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Recife, PE, 50760-901, Brazil
| | - Sergio Crovella
- Department of Genetics, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Cidade Universitária, Recife, PE, 50760-901, Brazil
- Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Recife, PE, 50760-901, Brazil
| | - Marcos Antonio De Morais
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Recife, PE, 50760-901, Brazil.
- Department of Genetics, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Cidade Universitária, Recife, PE, 50760-901, Brazil.
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Klein M, Swinnen S, Thevelein JM, Nevoigt E. Glycerol metabolism and transport in yeast and fungi: established knowledge and ambiguities. Environ Microbiol 2017; 19:878-893. [DOI: 10.1111/1462-2920.13617] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/16/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Mathias Klein
- Department of Life Sciences and Chemistry; Jacobs University Bremen gGmbH; Campus Ring 1 Bremen 28759 Germany
| | - Steve Swinnen
- GlobalYeast NV; Kasteelpark Arenberg 31, Leuven-Heverlee 3001 Belgium
| | - Johan M. Thevelein
- GlobalYeast NV; Kasteelpark Arenberg 31, Leuven-Heverlee 3001 Belgium
- Laboratory of Molecular Cell Biology; Institute of Botany and Microbiology, KU Leuven; Leuven Belgium
- Department of Molecular Microbiology; VIB; Kasteelpark Arenberg 31, 3001 Heverlee-Leuven Flanders Belgium
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry; Jacobs University Bremen gGmbH; Campus Ring 1 Bremen 28759 Germany
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Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M. The metabolic background is a global player in Saccharomyces gene expression epistasis. Nat Microbiol 2016; 1:15030. [PMID: 27572163 PMCID: PMC5131842 DOI: 10.1038/nmicrobiol.2015.30] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/17/2015] [Indexed: 01/20/2023]
Abstract
The regulation of gene expression in response to nutrient availability is fundamental to the genotype-phenotype relationship. The metabolic-genetic make-up of the cell, as reflected in auxotrophy, is hence likely to be a determinant of gene expression. Here, we address the importance of the metabolic-genetic background by monitoring transcriptome, proteome and metabolome in a repertoire of 16 Saccharomyces cerevisiae laboratory backgrounds, combinatorially perturbed in histidine, leucine, methionine and uracil biosynthesis. The metabolic background affected up to 85% of the coding genome. Suggesting widespread confounding, these transcriptional changes show, on average, 83% overlap between unrelated auxotrophs and 35% with previously published transcriptomes generated for non-metabolic gene knockouts. Background-dependent gene expression correlated with metabolic flux and acted, predominantly through masking or suppression, on 88% of transcriptional interactions epistatically. As a consequence, the deletion of the same metabolic gene in a different background could provoke an entirely different transcriptional response. Propagating to the proteome and scaling up at the metabolome, metabolic background dependencies reveal the prevalence of metabolism-dependent epistasis at all regulatory levels. Urging a fundamental change of the prevailing laboratory practice of using auxotrophs and nutrient supplemented media, these results reveal epistatic intertwining of metabolism with gene expression on the genomic scale.
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Affiliation(s)
- Mohammad Tauqeer Alam
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Aleksej Zelezniak
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
| | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Pavel Shliaha
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Roland Schwarz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Elahe Radmanesfahar
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Antje Krüger
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Enrica Calvani
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Steve Michel
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Stefan Christen
- Department of Molecular Systems Biology, Eidgenoessische Technische Hochschule, Zurich, Switzerland
| | | | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Kathryn S Lilley
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
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11
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Swinnen S, Klein M, Carrillo M, McInnes J, Nguyen HTT, Nevoigt E. Re-evaluation of glycerol utilization in Saccharomyces cerevisiae: characterization of an isolate that grows on glycerol without supporting supplements. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:157. [PMID: 24209984 PMCID: PMC3835864 DOI: 10.1186/1754-6834-6-157] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 10/29/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Glycerol has attracted attention as a carbon source for microbial production processes due to the large amounts of crude glycerol waste resulting from biodiesel production. The current knowledge about the genetics and physiology of glycerol uptake and catabolism in the versatile industrial biotechnology production host Saccharomyces cerevisiae has been mainly based on auxotrophic laboratory strains, and carried out in the presence of growth-supporting supplements such as amino acids and nucleic bases. The latter may have resulted in ambiguous conclusions concerning glycerol growth in this species. The purpose of this study was to re-evaluate growth of S. cerevisiae in synthetic glycerol medium without the addition of supplements. RESULTS Initial experiments showed that prototrophic versions of the laboratory strains CEN.PK, W303, and S288c did not exhibit any growth in synthetic glycerol medium without supporting supplements. However, a screening of 52 S. cerevisiae isolates for growth in the same medium revealed a high intraspecies diversity. Within this group significant variation with respect to the lag phase and maximum specific growth rate was observed. A haploid segregant of one good glycerol grower (CBS 6412-13A) was selected for detailed analysis. Single deletions of the genes encoding for the glycerol/H+ symporter (STL1), the glycerol kinase (GUT1), and the mitochondrial FAD+-dependent glycerol 3-phosphate dehydrogenase (GUT2) abolished glycerol growth in this strain, implying that it uses the same glycerol utilization pathway as previously identified in auxotrophic laboratory strains. Segregant analysis of a cross between CBS 6412-13A and CEN.PK113-1A revealed that the glycerol growth phenotype is a quantitative trait. Genetic linkage and reciprocal hemizygosity analysis demonstrated that GUT1CBS 6412-13A is one of the multiple genetic loci contributing to the glycerol growth phenotype. CONCLUSION The S. cerevisiae intraspecies diversity with regard to glycerol growth is a valuable starting point to identify the genetic and molecular basis of this phenotype. This knowledge can be applied for further rational strain improvement with the goal of using glycerol as a carbon source in industrial biotechnology processes based on S. cerevisiae as a production organism.
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Affiliation(s)
- Steve Swinnen
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Martina Carrillo
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Joseph McInnes
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Huyen Thi Thanh Nguyen
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- School of Engineering and Science, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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12
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Luo Z, Walkey CJ, Madilao LL, Measday V, Van Vuuren HJJ. Functional improvement of Saccharomyces cerevisiae to reduce volatile acidity in wine. FEMS Yeast Res 2013; 13:485-94. [PMID: 23692528 DOI: 10.1111/1567-1364.12053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/15/2013] [Accepted: 05/16/2013] [Indexed: 01/07/2023] Open
Abstract
Control of volatile acidity (VA) is a major issue for wine quality. In this study, we investigated the production of VA by a deletion mutant of the fermentation stress response gene AAF1 in the budding yeast Saccharomyces cerevisiae. Fermentations were carried out in commercial Chardonnay grape must to mimic industrial wine-making conditions. We demonstrated that a wine yeast strain deleted for AAF1 reduced acetic acid levels in wine by up to 39.2% without increasing the acetaldehyde levels, revealing a potential for industrial application. Deletion of the cytosolic aldehyde dehydrogenase gene ALD6 also reduced acetic acid levels dramatically, but increased the acetaldehyde levels by 41.4%, which is not desired by the wine industry. By comparison, ALD4 and the AAF1 paralog RSF2 had no effects on acetic acid production in wine. Deletion of AAF1 was detrimental to the growth of ald6Δ and ald4Δald6Δ mutants, but had no effect on acetic acid production. Overexpression of AAF1 dramatically increased acetic acid levels in wine in an Ald6p-dependent manner, indicating that Aaf1p regulates acetic acid production mainly via Ald6p. Overexpression of AAF1 in an ald4Δald6Δ strain produced significantly more acetic acid in wine than the ald4Δald6Δ mutant, suggesting that Aaf1p may also regulate acetic acid synthesis independently of Ald4p and Ald6p.
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Affiliation(s)
- Zongli Luo
- Wine Research Centre, The University of British Columbia, Vancouver, BC, Canada
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13
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Jung JY, Kim TY, Ng CY, Oh MK. Characterization of GCY1 in Saccharomyces cerevisiae by metabolic profiling. J Appl Microbiol 2012; 113:1468-78. [PMID: 22979944 DOI: 10.1111/jam.12013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/29/2012] [Accepted: 09/07/2012] [Indexed: 12/20/2022]
Abstract
AIMS The analytical study of intracellular (IC) metabolites has developed with advances in chromatography-linked mass spectrometry and fast sampling procedures. We applied the IC metabolite analysis to characterize the role of GCY1 in the glycerol (GLY) catabolic pathway in Saccharomyces cerevisiae. METHODS AND RESULTS Strains with disrupted or overexpressing GLY catabolic genes such as GCY1, DAK1 and DAK2 were constructed. The strains were cultivated under different aeration conditions and quickly quenched using a novel rapid sampling port. IC concentrations of GLY, dihydroxyacetone (DHA), glycerol 3-phosphate and dihydroxyacetone phosphate were analysed in the strains by gas chromatography/mass spectrometry. DHA was not detected in the gcy1 gene-disrupted strain but accumulated 225.91 μmol g DCW(-1) in a DHA kinase gene-deficient strain under micro-aerobic conditions. Additionally, a 16.1% increase in DHA occurred by overexpressing GCY1 in the DHA kinase-deficient strain. CONCLUSIONS Metabolic profiling showed that the GCY1 gene product functions as a GLY dehydrogenase in S. cerevisiae, particularly under micro-aerobic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic profiling of the GLY dissimilation pathway was successfully demonstrated in S. cerevisiae, and the function of GCY1 was explained by the results.
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Affiliation(s)
- J-Y Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul, Korea
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14
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Tretyakov K, Laur S, Vilo J. G = MAT: linking transcription factor expression and DNA binding data. PLoS One 2011; 6:e14559. [PMID: 21297945 PMCID: PMC3031503 DOI: 10.1371/journal.pone.0014559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 12/03/2010] [Indexed: 12/02/2022] Open
Abstract
Transcription factors are proteins that bind to motifs on the DNA and thus affect gene expression regulation. The qualitative description of the corresponding processes is therefore important for a better understanding of essential biological mechanisms. However, wet lab experiments targeted at the discovery of the regulatory interplay between transcription factors and binding sites are expensive. We propose a new, purely computational method for finding putative associations between transcription factors and motifs. This method is based on a linear model that combines sequence information with expression data. We present various methods for model parameter estimation and show, via experiments on simulated data, that these methods are reliable. Finally, we examine the performance of this model on biological data and conclude that it can indeed be used to discover meaningful associations. The developed software is available as a web tool and Scilab source code at http://biit.cs.ut.ee/gmat/.
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Affiliation(s)
| | - Sven Laur
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Quretec, Tartu, Estonia
- * E-mail:
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15
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Ochoa-Estopier A, Lesage J, Gorret N, Guillouet SE. Kinetic analysis of a Saccharomyces cerevisiae strain adapted for improved growth on glycerol: Implications for the development of yeast bioprocesses on glycerol. BIORESOURCE TECHNOLOGY 2011; 102:1521-1527. [PMID: 20869237 DOI: 10.1016/j.biortech.2010.08.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 07/30/2010] [Accepted: 08/02/2010] [Indexed: 05/29/2023]
Abstract
Glycerol is an agro-industrial residue generated in high amounts during the biodiesel production. The growing production of biodiesel is creating a worldwide glycerol surplus. Therefore, replacing sugar-based feedstock in bioprocesses by glycerol could be potentially attractive. Saccharomyces cerevisiae is one of the most commonly used microorganisms in the agri-food industry and therefore currently produced in large quantities from sugar-based feedstock. Unfortunately, growth of S. cerevisiae strains on glycerol is very low with reported μmax around 0.01 h(-1). This study demonstrates that successive growth of the S. cerevisiae CBS 8066, CEN.PK 113-7 D and Ethanol Red on glycerol as sole carbon source considerably improved the μmax from 0.01 up to 0.2 h(-1). The "adapted strain" CBS 8066-FL20 was kinetically characterized during aerobic and oxygen-limited cultivation in bioreactor and the results discussed in terms of their implication for developing glycerol-based S. cerevisiae bioprocesses.
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Affiliation(s)
- A Ochoa-Estopier
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Av. de Rangueil, F-31077 Toulouse, France
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16
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Ge H, Wei M, Fabrizio P, Hu J, Cheng C, Longo VD, Li LM. Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant. Nucleic Acids Res 2009; 38:143-58. [PMID: 19880387 PMCID: PMC2800218 DOI: 10.1093/nar/gkp849] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
In an attempt to elucidate the underlying longevity-promoting mechanisms of mutants lacking SCH9, which live three times as long as wild type chronologically, we measured their time-course gene expression profiles. We interpreted their expression time differences by statistical inferences based on prior biological knowledge, and identified the following significant changes: (i) between 12 and 24 h, stress response genes were up-regulated by larger fold changes and ribosomal RNA (rRNA) processing genes were down-regulated more dramatically; (ii) mitochondrial ribosomal protein genes were not up-regulated between 12 and 60 h as wild type were; (iii) electron transport, oxidative phosphorylation and TCA genes were down-regulated early; (iv) the up-regulation of TCA and electron transport was accompanied by deep down-regulation of rRNA processing over time; and (v) rRNA processing genes were more volatile over time, and three associated cis-regulatory elements [rRNA processing element (rRPE), polymerase A and C (PAC) and glucose response element (GRE)] were identified. Deletion of AZF1, which encodes the transcriptional factor that binds to the GRE element, reversed the lifespan extension of sch9Δ. The significant alterations in these time-dependent expression profiles imply that the lack of SCH9 turns on the longevity programme that extends the lifespan through changes in metabolic pathways and protection mechanisms, particularly, the regulation of aerobic respiration and rRNA processing.
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Affiliation(s)
- Huanying Ge
- Andrus Gerontology Center, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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17
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Roberts GG, Hudson AP. Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S. cerevisiae. Yeast 2009; 26:95-110. [PMID: 19235764 DOI: 10.1002/yea.1655] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Previous studies from this laboratory indicated that the product of the RSF1 gene of S. cerevisiae is present in both nucleus and mitochondria, and they suggested that Rsf1p acts as a transcriptional modulator. To investigate this latter question, we performed transcriptome profiling of an rsf1 mutant strain and its wild-type parent during a shift from glucose-based fermentative to glycerol-based respiratory growth to identify genes whose expression is regulated by Rsf1p. Loss of Rsf1p engendered a decrease in transcript levels from many genes encoding components of the electron transport chain and various other mitochondrially-localized products. The earlier studies further showed that rsf1 cells exhibit a growth defect on medium containing glycerol, but not ethanol, as sole carbon source. Importantly, transcriptome profiling of the rsf1 mutant during shift from glucose- to glycerol-based medium revealed that the product of this gene plays a major role in both orchestration of the transition to, and maintenance of, efficient growth on glycerol as sole carbon source. An increase in transcript levels from genes encoding products that function in the stress response, and an imbalance between expression of genes encoding glycerol anabolic and catabolic enzymes, was observed in the rsf1 mutant during steady-state growth on glycerol- but not ethanol-based medium; this suggests the presence of partially separate transcriptional regulatory systems for transition to respiratory growth on each of these two carbon sources. Genes whose expression is affected by loss of Rsf1p, which lacks a known DNA-binding motif, lack a common DNA sequence motif in their upstream regions. These and other data presented here strongly suggest that the transcriptional effects exerted by Rsf1p are mediated via interaction with other transcription factors.
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Affiliation(s)
- George G Roberts
- Department of Immunology and Microbiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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18
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Roberts GG, Di Loreto MJ, Marshall M, Wang J, DeGracia DJ. Hippocampal cellular stress responses after global brain ischemia and reperfusion. Antioxid Redox Signal 2007; 9:2265-75. [PMID: 17715997 DOI: 10.1089/ars.2007.1786] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Brain ischemia and reperfusion (I/R) induce neuronal intracellular stress responses, including the heat-shock response (HSR) and the unfolded protein response (UPR), but the roles of each in neuronal survival or death are not well understood. We assessed the relative expression of UPR (ATF4, CHOP, GRP78, XBP-1) and HSR-related (HSP70 and HSC70) mRNAs and proteins after brain I/R. We evaluated these in hippocampal CA1 and CA3 after normothermic, transient global forebrain ischemia and up to 42 h of reperfusion. In CA1, chop and xbp-1 mRNA showed maximal 14- and 12-fold increases, and the only protein increase observed was for 30-kDa XBP-1. CA3 showed induction of only xbp-1. GRP78 protein declined in CA1, but increased twofold and then declined in CA3. Transcription of hsp70 was an order of magnitude greater than that of any UPR-induced transcript in either CA1 or CA3. HSP70 translation in CA1 lagged CA3 by approximately 24 h. We conclude that (a) in terms of functional end products, the ER stress response after brain ischemia and reperfusion more closely resembles the integrated stress response than the UPR; and (b) the HSR leads to quantitatively greater mRNA production in postischemic neurons, suggesting that cytoplasmic stress predominates over ER stress in reperfused neurons.
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Affiliation(s)
- George G Roberts
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
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19
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Roberts GG, Hudson AP. Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling. Mol Genet Genomics 2006; 276:170-86. [PMID: 16741729 DOI: 10.1007/s00438-006-0133-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Accepted: 04/19/2006] [Indexed: 10/24/2022]
Abstract
Transcriptome analyses using a wild-type strain of Saccharomyces cerevisiae were performed to assess the overall pattern of gene expression during the transition from glucose-based fermentative to glycerol-based respiratory growth. These experiments revealed a complex suite of metabolic and structural changes associated with the adaptation process. Alterations in gene expression leading to remodeling of various membrane transport systems and the cortical actin cytoskeleton were observed. Transition to respiratory growth was accompanied by alterations in transcript patterns demonstrating not only a general stress response, as seen in earlier studies, but also the oxidative and osmotic stress responses. In some contrast to earlier studies, these experiments identified modulation of expression for many genes specifying transcription factors during the transition to glycerol-based growth. Importantly and unexpectedly, an ordered series of changes was seen in transcript levels from genes encoding components of the TFIID, SAGA (Spt-Ada-Gcn5-Acetyltransferase), and SLIK (Saga LIKe) complexes and all three RNA polymerases, suggesting a modulation of structure for the basal transcriptional machinery during adaptation to respiratory growth. In concert with data given in earlier studies, the results presented here highlight important aspects of metabolic and other adaptations to respiratory growth in yeast that are common to utilization of multiple carbon sources. Importantly, they also identify aspects specific to adaptation of this organism to growth on glycerol as sole carbon source.
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Affiliation(s)
- George G Roberts
- Department Immunology and Microbiology, Wayne State University School of Medicine, Gordon H. Scott Hall, 540 East Canfield Ave., Detroit, MI 48201, USA
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20
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John Wiley & Sons, Ltd.. Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1315] [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] Open
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