1
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Grigaitis P, van den Bogaard SL, Teusink B. Elevated energy costs of biomass production in mitochondrial respiration-deficient Saccharomyces cerevisia. FEMS Yeast Res 2023; 23:7000830. [PMID: 36694952 PMCID: PMC9949590 DOI: 10.1093/femsyr/foad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/10/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Microbial growth requires energy for maintaining the existing cells and producing components for the new ones. Microbes therefore invest a considerable amount of their resources into proteins needed for energy harvesting. Growth in different environments is associated with different energy demands for growth of yeast Saccharomyces cerevisiae, although the cross-condition differences remain poorly characterized. Furthermore, a direct comparison of the energy costs for the biosynthesis of the new biomass across conditions is not feasible experimentally; computational models, on the contrary, allow comparing the optimal metabolic strategies and quantify the respective costs of energy and nutrients. Thus in this study, we used a resource allocation model of S. cerevisiae to compare the optimal metabolic strategies between different conditions. We found that S. cerevisiae with respiratory-impaired mitochondria required additional energetic investments for growth, while growth on amino acid-rich media was not affected. Amino acid supplementation in anaerobic conditions also was predicted to rescue the growth reduction in mitochondrial respiratory shuttle-deficient mutants of S. cerevisiae. Collectively, these results point to elevated costs of resolving the redox imbalance caused by de novo biosynthesis of amino acids in mitochondria. To sum up, our study provides an example of how resource allocation modeling can be used to address and suggest explanations to open questions in microbial physiology.
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Affiliation(s)
- Pranas Grigaitis
- Corresponding author. Systems Biology Lab, A-Life/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands; E-mail:
| | - Samira L van den Bogaard
- Systems Biology Lab, A-Life/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, A-Life/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands
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2
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Manicki M, Aydin H, Abriata LA, Overmyer KA, Guerra RM, Coon JJ, Dal Peraro M, Frost A, Pagliarini DJ. Structure and functionality of a multimeric human COQ7:COQ9 complex. Mol Cell 2022; 82:4307-4323.e10. [PMID: 36306796 PMCID: PMC10058641 DOI: 10.1016/j.molcel.2022.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 07/01/2022] [Accepted: 10/04/2022] [Indexed: 11/18/2022]
Abstract
Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipid-, substrate-, and NADH-bound complex comprising two complex Q subunits: the hydroxylase COQ7 and the lipid-binding protein COQ9. We reveal that COQ7 adopts a ferritin-like fold with a hydrophobic channel whose substrate-binding capacity is enhanced by COQ9. Using molecular dynamics, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for the CoQ intermediates to translocate from the bilayer to the proteins' lipid-binding sites. Two such tetramers assemble into a soluble octamer with a pseudo-bilayer of lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors within the membrane and coordinate subsequent synthesis steps toward producing CoQ.
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Affiliation(s)
- Mateusz Manicki
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Halil Aydin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA
| | - Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53506, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub and Altos Labs Bay Area Institute of Science, San Francisco, CA, USA.
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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3
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Krause DJ, Hittinger CT. Functional Divergence in a Multi-gene Family Is a Key Evolutionary Innovation for Anaerobic Growth in Saccharomyces cerevisiae. Mol Biol Evol 2022; 39:6711080. [PMID: 36134526 PMCID: PMC9551191 DOI: 10.1093/molbev/msac202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The amplification and diversification of genes into large multi-gene families often mark key evolutionary innovations, but this process often creates genetic redundancy that hinders functional investigations. When the model budding yeast Saccharomyces cerevisiae transitions to anaerobic growth conditions, the cell massively induces the expression of seven serine/threonine-rich anaerobically-induced cell wall mannoproteins (anCWMPs): TIP1, TIR1, TIR2, TIR3, TIR4, DAN1, and DAN4. Here, we show that these genes likely derive evolutionarily from a single ancestral anCWMP locus, which was duplicated and translocated to new genomic contexts several times both prior to and following the budding yeast whole genome duplication (WGD) event. Based on synteny and their phylogeny, we separate the anCWMPs into four gene subfamilies. To resolve prior inconclusive genetic investigations of these genes, we constructed a set of combinatorial deletion mutants to determine their contributions toward anaerobic growth in S. cerevisiae. We found that two genes, TIR1 and TIR3, were together necessary and sufficient for the anCWMP contribution to anaerobic growth. Overexpressing either gene alone was insufficient for anaerobic growth, implying that they encode non-overlapping functional roles in the cell during anaerobic growth. We infer from the phylogeny of the anCWMP genes that these two important genes derive from an ancient duplication that predates the WGD event, whereas the TIR1 subfamily experienced gene family amplification after the WGD event. Taken together, the genetic and molecular evidence suggests that one key anCWMP gene duplication event, several auxiliary gene duplication events, and functional divergence underpin the evolution of anaerobic growth in budding yeasts.
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Affiliation(s)
- David J Krause
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI
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4
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Whole-Genome Transformation of Yeast Promotes Rare Host Mutations with a Single Causative SNP Enhancing Acetic Acid Tolerance. Mol Cell Biol 2022; 42:e0056021. [PMID: 35311587 PMCID: PMC9022575 DOI: 10.1128/mcb.00560-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Whole-genome (WG) transformation (WGT) with DNA from the same or another species has been used to obtain strains with superior traits. Very few examples have been reported in eukaryotes—most apparently involving integration of large fragments of foreign DNA into the host genome. We show that WGT of a haploid acetic acid-sensitive Saccharomyces cerevisiae strain with DNA from a tolerant strain, but not from nontolerant strains, generated many tolerant transformants, some of which were stable upon subculturing under nonselective conditions. The most tolerant stable transformant contained no foreign DNA but only seven nonsynonymous single nucleotide polymorphisms (SNPs), of which none was present in the donor genome. The SNF4 mutation c.[805G→T], generating Snf4E269*, was the main causative SNP. Allele exchange of SNF4E269* or snf4Δ in industrial strains with unrelated genetic backgrounds enhanced acetic acid tolerance during fermentation under industrially relevant conditions. Our work reveals a surprisingly small number of mutations introduced by WGT, which do not bear any sequence relatedness to the genomic DNA (gDNA) of the donor organism, including the causative mutation. Spontaneous mutagenesis under protection of a transient donor gDNA fragment, maintained as extrachromosomal circular DNA (eccDNA), might provide an explanation. Support for this mechanism was obtained by transformation with genomic DNA of a yeast strain containing NatMX and selection on medium with nourseothricin. Seven transformants were obtained that gradually lost their nourseothricin resistance upon subculturing in nonselective medium. Our work shows that WGT is an efficient strategy for rapidly generating and identifying superior alleles capable of improving selectable traits of interest in industrial yeast strains.
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5
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Horiuchi S, Namba S, Saeki N, Satoh A, Moriya H. Identification of uncharacterized proteins potentially localized to mitochondria (UPMs) in Saccharomyces cerevisiae using a fluorescent protein unstable in the cytoplasm. Yeast 2021; 39:303-311. [PMID: 34913195 DOI: 10.1002/yea.3685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/14/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic cells are composed of organelles, and each organelle contains proteins that play a role in its function. Therefore, the localization of a protein, especially to organelles, is a clue to infer the function of that protein. In this study, we attempted to identify novel mitochondrially localized proteins in the budding yeast Saccharomyces cerevisiae using a fluorescent protein (GFPdeg) that is rapidly degraded in the cytoplasm. Of the budding yeast proteins predicted to localize to mitochondria by the prediction tool Deeploc-1.0, those with known mitochondrial localization or functional relevance were eliminated, and 95 proteins of unknown function were selected as candidates for analysis. By forced expression of GFPdeg fusion proteins with these proteins and observation of their localization, we identified 35 uncharacterized proteins potentially localized to mitochondria (UPMs) including 8 previously identified proteins that localize to mitochondria. Most of these had no N-terminal mitochondrial localization signal and were evolutionarily young "emerging genes" that exist only in S. cerevisiae. Some of these genes were found to be upregulated during the postdiauxic shift phase when mitochondria are being developed, suggesting that they are actually involved in some mitochondrial function.
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Affiliation(s)
- Satoshi Horiuchi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Shotaro Namba
- Graduate School of Environmental and Life Sciences, Okayama University, Okayama, Japan
| | - Nozomu Saeki
- Graduate School of Environmental and Life Sciences, Okayama University, Okayama, Japan
| | - Ayano Satoh
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Hisao Moriya
- Graduate School of Environmental and Life Sciences, Okayama University, Okayama, Japan
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6
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Saccharomyces cerevisiae Gene Expression during Fermentation of Pinot Noir Wines at an Industrially Relevant Scale. Appl Environ Microbiol 2021; 87:AEM.00036-21. [PMID: 33741633 PMCID: PMC8208162 DOI: 10.1128/aem.00036-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to those observed under laboratory fermentation conditions but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., the presence of non-Saccharomyces microorganisms). Saccharomyces cerevisiae metabolism produces ethanol and other compounds during the fermentation of grape must into wine. Thousands of genes change expression over the course of a wine fermentation, allowing S. cerevisiae to adapt to and dominate the fermentation environment. Investigations into these gene expression patterns previously revealed genes that underlie cellular adaptation to the grape must and wine environments, involving metabolic specialization and ethanol tolerance. However, the majority of studies detailing gene expression patterns have occurred in controlled environments that may not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, an analysis of the S. cerevisiae RC212 gene expression program is presented, drawing from 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. A core gene expression program was observed across all fermentations irrespective of vintage, similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomyces microorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight into Saccharomyces cerevisiae biology critical to fermentation outcomes under industry-relevant conditions. IMPORTANCE This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to those observed under laboratory fermentation conditions but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., the presence of non-Saccharomyces microorganisms). Key genes and pathways highlighted by this work remain undercharacterized, indicating the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.
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7
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Tesnière C, Pradal M, Legras JL. Sterol uptake analysis in Saccharomyces and non-Saccharomyces wine yeast species. FEMS Yeast Res 2021; 21:6225805. [PMID: 33852000 DOI: 10.1093/femsyr/foab020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/09/2021] [Indexed: 01/18/2023] Open
Abstract
Sterols are essential components of the yeast membrane and their synthesis requires oxygen. Yet, Saccharomyces cerevisiae has developed the ability to take up sterols from the medium under anaerobiosis. Here we investigated sterol uptake efficiency and the expression of genes related to sterol import in Saccharomyces and non-Saccharomyces wine yeast species fermenting under anaerobic conditions. The sterol uptake efficiency of 39 strains was evaluated by flow cytometry (with 25-NBD Cholesterol, a fluorescent cholesterol probe introduced in the medium) and we found an important discrepancy between Saccharomyces and non-Saccharomyces wine yeast species that we correlated to a lower final cell population and a lower fermentation rate. A high uptake of sterol was observed in the various Saccharomyces strains. Spot tests performed on 13 of these strains confirmed the differences between Saccharomyces and non-Saccharomyces strains, suggesting that the presence of the sterol uptake transporters AUS1 and PDR11 could cause these discrepancies. Indeed, we could not find any homologue to these genes in the genome of Hanseniaspora uvarum, H. guillermondii, Lachancea thermotolerans, Torulaspora delbreueckii, Metschnikowia pulcherrima, or Starmarella bacillaris species. The specialization of sterol import function for post genome-duplication species may have favored growth under anaerobiosis.
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Affiliation(s)
- Catherine Tesnière
- SPO, Univ Montpellier, INRAE, Institut Agro, 2, place Pierre Viala, 34060 Montpellier, France
| | - Martine Pradal
- SPO, Univ Montpellier, INRAE, Institut Agro, 2, place Pierre Viala, 34060 Montpellier, France
| | - Jean-Luc Legras
- SPO, Univ Montpellier, INRAE, Institut Agro, 2, place Pierre Viala, 34060 Montpellier, France.,CIRM-Levures, SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
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8
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Nagy G, Kiss S, Varghese R, Bauer K, Szebenyi C, Kocsubé S, Homa M, Bodai L, Zsindely N, Nagy G, Vágvölgyi C, Papp T. Characterization of Three Pleiotropic Drug Resistance Transporter Genes and Their Participation in the Azole Resistance of Mucor circinelloides. Front Cell Infect Microbiol 2021; 11:660347. [PMID: 33937100 PMCID: PMC8079984 DOI: 10.3389/fcimb.2021.660347] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/19/2021] [Indexed: 02/04/2023] Open
Abstract
Mucormycosis is a life-threatening opportunistic infection caused by certain members of the fungal order Mucorales. This infection is associated with high mortality rate, which can reach nearly 100% depending on the underlying condition of the patient. Treatment of mucormycosis is challenging because these fungi are intrinsically resistant to most of the routinely used antifungal agents, such as most of the azoles. One possible mechanism of azole resistance is the drug efflux catalyzed by members of the ATP binding cassette (ABC) transporter superfamily. The pleiotropic drug resistance (PDR) transporter subfamily of ABC transporters is the most closely associated to drug resistance. The genome of Mucor circinelloides encodes eight putative PDR-type transporters. In this study, transcription of the eight pdr genes has been analyzed after azole treatment. Only the pdr1 showed increased transcript level in response to all tested azoles. Deletion of this gene caused increased susceptibility to posaconazole, ravuconazole and isavuconazole and altered growth ability of the mutant. In the pdr1 deletion mutant, transcript level of pdr2 and pdr6 significantly increased. Deletion of pdr2 and pdr6 was also done to create single and double knock out mutants for the three genes. After deletion of pdr2 and pdr6, growth ability of the mutant strains decreased, while deletion of pdr2 resulted in increased sensitivity against posaconazole, ravuconazole and isavuconazole. Our result suggests that the regulation of the eight pdr genes is interconnected and pdr1 and pdr2 participates in the resistance of the fungus to posaconazole, ravuconazole and isavuconazole.
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Affiliation(s)
- Gábor Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- MTA-SZTE “Lendület” Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Sándor Kiss
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Rakesh Varghese
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Kitti Bauer
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Csilla Szebenyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- MTA-SZTE “Lendület” Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Mónika Homa
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- MTA-SZTE “Lendület” Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Nóra Zsindely
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- MTA-SZTE “Lendület” Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Szeged, Hungary
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9
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Smith P, Owen DM, Lorenz CD, Makarova M. Asymmetric glycerophospholipids impart distinctive biophysical properties to lipid bilayers. Biophys J 2021; 120:1746-1754. [PMID: 33705758 DOI: 10.1016/j.bpj.2021.02.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 01/25/2023] Open
Abstract
Phospholipids are a diverse group of biomolecules consisting of a hydrophilic headgroup and two hydrophobic acyl tails. The nature of the head and length and saturation of the acyl tails are important for defining the biophysical properties of lipid bilayers. It has recently been shown that the membranes of certain yeast species contain high levels of unusual asymmetric phospholipids consisting of one long and one medium-chain acyl moiety, a configuration not common in mammalian cells or other well-studied model yeast species. This raises the possibility that structurally asymmetric glycerophospholipids impart distinctive biophysical properties to the yeast membranes. Previously, it has been shown that lipids with asymmetric length tails form a mixed interdigitated gel phase and exhibit unusual endotherm behavior upon heating and cooling. Here, however, we address physiologically relevant temperature conditions and, using atomistic molecular dynamics simulations and environmentally sensitive fluorescent membrane probes, characterize key biophysical parameters (such as lipid packing, diffusion coefficient, membrane thickness, and area per lipid) in membranes composed of both length-asymmetric glycerophospholipids and ergosterol. Interestingly, we show that saturated but asymmetric glycerophospholipids maintain membrane lipid order across a wide range of temperatures. We also show that these asymmetric lipids can substiture of unsaturated symmetric lipids in the phase behaviour of ternary lipid bilayers. This may allow cells to maintain membrane fluidity, even in environments that lack oxygen, which is required for the synthesis of unsaturated lipids and sterols.
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Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London, United Kingdom
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences and School of Mathematics, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | - Maria Makarova
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
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10
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Stanchev LD, Marek M, Xian F, Klöhn M, Silvestro D, Dittmar G, López-Marqués RL, Günther Pomorski T. Functional Significance of Conserved Cysteines in the Extracellular Loops of the ATP Binding Cassette Transporter Pdr11p. J Fungi (Basel) 2020; 7:jof7010002. [PMID: 33375075 PMCID: PMC7822014 DOI: 10.3390/jof7010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
The pleiotropic drug resistance (PDR) transporter Pdr11p is expressed under anaerobic growth conditions at the plasma membrane of the yeast Saccharomyces cerevisiae, where it facilitates the uptake of exogenous sterols. Members of the fungal PDR family contain six conserved cysteines in their extracellular loops (ECL). For the functional analysis of these cysteine residues in Pdr11p, we generated a series of single cysteine-to-serine mutants. All mutant proteins expressed well and displayed robust ATPase activity upon purification. Mass-spectrometry analysis identified two cysteine residues (C582 and C603) in ECL3 forming a disulfide bond. Further characterization by cell-based assays showed that all mutants are compromised in facilitating sterol uptake, protein stability, and trafficking to the plasma membrane. Our data highlight the fundamental importance of all six extracellular cysteine residues for the functional integrity of Pdr11p and provide new structural insights into the PDR family of transporters.
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Affiliation(s)
- Lyubomir Dimitrov Stanchev
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Magdalena Marek
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Feng Xian
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Rue Thomas Edison 1A-B, L-1445 Strassen, Luxembourg; (F.X.); (G.D.)
| | - Mara Klöhn
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
| | - Daniele Silvestro
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Rue Thomas Edison 1A-B, L-1445 Strassen, Luxembourg; (F.X.); (G.D.)
| | - Rosa Laura López-Marqués
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany; (L.D.S.); (M.K.)
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (M.M.); (D.S.); (R.L.L.-M.)
- Correspondence: ; Tel.: +49-234-322-4430
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11
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Pinheiro T, Lip KYF, García-Ríos E, Querol A, Teixeira J, van Gulik W, Guillamón JM, Domingues L. Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions. Sci Rep 2020; 10:22329. [PMID: 33339840 PMCID: PMC7749138 DOI: 10.1038/s41598-020-77846-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/20/2020] [Indexed: 12/28/2022] Open
Abstract
Elucidation of temperature tolerance mechanisms in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- and supra-optimal temperatures under chemostat conditions. We employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains in all conditions was performed by sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS), allowing the quantification of 997 proteins, data available via ProteomeXchange (PXD016567). Our analysis demonstrated that temperature responses differ between the strains; however, we also found some common responsive proteins, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome. The proteomic data evidenced that the cold response involves strong repression of translation-related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation while, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects the yeast proteome, which can be a step forward in the comprehension and improvement of yeast thermotolerance.
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Affiliation(s)
- Tânia Pinheiro
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Ka Ying Florence Lip
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Estéfani García-Ríos
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Amparo Querol
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - José Teixeira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - José Manuel Guillamón
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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Iranmanesh E, Asadollahi MA, Biria D. Improving l-phenylacetylcarbinol production in Saccharomyces cerevisiae by in silico aided metabolic engineering. J Biotechnol 2020; 308:27-34. [DOI: 10.1016/j.jbiotec.2019.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/13/2019] [Accepted: 11/11/2019] [Indexed: 01/05/2023]
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Faletrov YV, Efimova VS, Horetski MS, Tugaeva KV, Frolova NS, Lin Q, Isaeva LV, Rubtsov MA, Sluchanko NN, Novikova LA, Shkumatov VM. New 20-hydroxycholesterol-like compounds with fluorescent NBD or alkyne labels: Synthesis, in silico interactions with proteins and uptake by yeast cells. Chem Phys Lipids 2019; 227:104850. [PMID: 31836520 DOI: 10.1016/j.chemphyslip.2019.104850] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/07/2023]
Abstract
20-hydroxycholesterol is a signaling oxysterol with immunomodulating functions and, thus, structural analogues with reporter capabilities could be useful for studying and modulating the cellular processes concerned. We have synthesized three new 20-hydroxycholesterol-like pregn-5-en-3β-ol derivatives with fluorescent 7-nitrobenzofurazan (NBD) or Raman-sensitive alkyne labels in their side-chains. In silico computations demonstrated the compounds possess good membrane permeability and can bind within active sites of known 20-hydroxycholesterol targets (e.g. Smoothened and yeast Osh4) and some other sterol-binding proteins (human LXRβ and STARD1; yeast START-kins Lam4S2 and Lam2S2). Having found good predicted membrane permeability and binding to some yeast proteins, we tested the compounds on microorganisms. Fluorescent microscopy indicated the uptake of the steroids by both Saccharomyces cerevisiae and Yarrowia lipolytica, whereas only S. cerevisiae demonstrated conversion of the compounds into 3-O-acetates, likely because 3-O-acetyltransferase Atf2p is present only in its genome. The new compounds provide new options to study the uptake, intracellular distribution and metabolism of sterols in yeast cells as well as might be used as ligands for sterol-binding proteins.
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Affiliation(s)
- Yaroslav V Faletrov
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Vera S Efimova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Matvey S Horetski
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Pr. 33, Moscow, 119071, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Nina S Frolova
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Quingquing Lin
- Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Ludmila V Isaeva
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Mikhail A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia; Lomonosov Moscow State University, Laboratoire Franco-Russe de Recherches en Oncologie, Moscow, 119234, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Pr. 33, Moscow, 119071, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Ludmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Vladimir M Shkumatov
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus.
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Rizzo J, Stanchev LD, da Silva VK, Nimrichter L, Pomorski TG, Rodrigues ML. Role of lipid transporters in fungal physiology and pathogenicity. Comput Struct Biotechnol J 2019; 17:1278-1289. [PMID: 31921394 PMCID: PMC6944739 DOI: 10.1016/j.csbj.2019.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/20/2019] [Accepted: 09/02/2019] [Indexed: 02/08/2023] Open
Abstract
The fungal cell wall and membrane are the most common targets of antifungal agents, but the potential of membrane lipid organization in regulating drug-target interactions has yet to be investigated. Energy-dependent lipid transporters have been recently associated with virulence and drug resistance in many pathogenic fungi. To illustrate this view, we discuss (i) the structural and biological aspects of ATP-driven lipid transporters, comprising P-type ATPases and ATP-binding cassette transporters, (ii) the role of these transporters in fungal physiology and virulence, and (iii) the potential of lipid transporters as targets for the development of novel antifungals. These recent observations indicate that the lipid-trafficking machinery in fungi is a promising target for studies on physiology, pathogenesis and drug development.
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Affiliation(s)
- Juliana Rizzo
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lyubomir Dimitrov Stanchev
- Department of Molecular Biochemistry, Ruhr University Bochum, Faculty of Chemistry and Biochemistry, 44780 Bochum, Germany
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C,Denmark
| | - Vanessa K.A. da Silva
- Programa de Pós-Graduação em Biologia Parasitária do Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Ruhr University Bochum, Faculty of Chemistry and Biochemistry, 44780 Bochum, Germany
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C,Denmark
| | - Marcio L. Rodrigues
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
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15
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Steady state analysis of influx and transbilayer distribution of ergosterol in the yeast plasma membrane. Theor Biol Med Model 2019; 16:13. [PMID: 31412941 PMCID: PMC6694696 DOI: 10.1186/s12976-019-0108-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/15/2019] [Indexed: 01/05/2023] Open
Abstract
Background The transbilayer sterol distribution between both plasma membrane (PM) leaflets has long been debated. Recent studies in mammalian cells and in yeast show that the majority of sterol resides in the inner PM leaflet. Since sterol flip-flop in model membranes is rapid and energy-independent, a mechanistic understanding for net enrichment of sterol in one leaflet is lacking. Import of ergosterol in yeast can take place via the ABC transporters Aus1/Pdr11 under anaerobic growth conditions, eventually followed by rapid non-vesicular sterol transport to the endoplasmic reticulum (ER). Little is known about how these transport steps are dynamically coordinated. Methods Here, a kinetic steady state model is presented which considers sterol import via Aus1/Pdr11, sterol flip-flop across the PM, bi-molecular complex formation and intracellular sterol release followed by eventual transport to and esterification of sterol in the ER. The steady state flux is calculated, and a thermodynamic analysis of feasibility is presented. Results It is shown that the steady state sterol flux across the PM can be entirely controlled by irreversible sterol import via Aus1/Pdr11. The transbilayer sterol flux at steady state is a non-linear function of the chemical potential difference of sterol between both leaflets. Non-vesicular release of sterol on the cytoplasmic side of the PM lowers the attainable sterol enrichment in the inner leaflet. Including complex formation of sterol with phospholipids or proteins can explain several puzzling experimental observations; 1) rapid sterol flip-flop across the PM despite net sterol enrichment in one leaflet, 2) a pronounced steady state sterol gradient between PM and ER despite fast non-vesicular sterol exchange between both compartments and 3) a non-linear dependence of ER sterol on ergosterol abundance in the PM. Conclusions A steady state model is presented that can account for the observed sterol asymmetry in the yeast PM, the strong sterol gradient between PM and ER and threshold-like expansion of ER sterol for increasing sterol influx into the PM. The model also provides new insight into selective uptake of cholesterol and its homeostasis in mammalian cells, and it provides testable predictions for future experiments.
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16
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Tulha J, Lucas C. Saccharomyces cerevisiae mitochondrial Por1/yVDAC1 (voltage-dependent anion channel 1) interacts physically with the MBOAT O-acyltransferase Gup1/HHATL in the control of cell wall integrity and programmed cell death. FEMS Yeast Res 2019; 18:5089977. [PMID: 30184078 DOI: 10.1093/femsyr/foy097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/31/2018] [Indexed: 02/06/2023] Open
Abstract
Gup1 is the yeast counterpart of the high eukaryotes HHATL. This and the close homologue Gup2/HHAT regulate the Hedgehog morphogenic, developmental pathway. In yeasts, a similar paracrine pathway is not known though the Δgup1 mutant is associated with morphology and proliferation/death processes. As a first step toward identifying the actual molecular/enzymatic function of Gup1, this work identified by co-immunoprecipitation the yeast mitochondria membrane VDAC1/Por1 as a physical partner of Gup1. Gup1 locates in the ER and the plasma membrane. It was now confirmed to further locate, as Por1, in the mitochondrial sub-cellular fraction. The yeast Por1-Gup1 association was found important for (i) the sensitivity to cell wall perturbing agents and high temperature, (ii) the differentiation into structured colonies, (iii) the size achieved by multicellular aggregates/mats and (iv) acetic-acid-induced Programmed Cell Death. Moreover, the absence of Gup1 increased the levels of POR1 mRNA, while decreasing the amounts of intracellular Por1, which was concomitantly previously known to be secreted by the mutant but not by wt. Additionally, Por1 patchy distribution in the mitochondrial membrane was evened. Results suggest that Por1 and Gup1 collaborate in the control of colony morphology and mat development, but more importantly of cellular integrity and death.
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Affiliation(s)
- Joana Tulha
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-054 Braga, Portugal
| | - Cândida Lucas
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-054 Braga, Portugal.,Institute of Science and Innovation on Bio-sustainability (IB-S), University of Minho, 4710-054 Braga, Portugal
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17
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Solanko LM, Sullivan DP, Sere YY, Szomek M, Lunding A, Solanko KA, Pizovic A, Stanchev LD, Pomorski TG, Menon AK, Wüstner D. Ergosterol is mainly located in the cytoplasmic leaflet of the yeast plasma membrane. Traffic 2018; 19:198-214. [DOI: 10.1111/tra.12545] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 12/22/2017] [Accepted: 12/22/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Lukasz M. Solanko
- Department of Biochemistry and Molecular BiologyUniversity of Southern Denmark Odense M Denmark
| | - David P. Sullivan
- Department of BiochemistryWeill Cornell Medical College New York, New York
| | - Yves Y. Sere
- Department of BiochemistryWeill Cornell Medical College New York, New York
| | - Maria Szomek
- Department of Biochemistry and Molecular BiologyUniversity of Southern Denmark Odense M Denmark
| | - Anita Lunding
- Department of Biochemistry and Molecular BiologyUniversity of Southern Denmark Odense M Denmark
| | - Katarzyna A. Solanko
- Department of Biochemistry and Molecular BiologyUniversity of Southern Denmark Odense M Denmark
| | - Azra Pizovic
- Department of Biochemistry and Molecular BiologyUniversity of Southern Denmark Odense M Denmark
| | - Lyubomir D. Stanchev
- Department of Plant and Environmental SciencesUniversity of Copenhagen Frederiksberg C Denmark
- Department of Molecular BiochemistryRuhr‐University Bochum Bochum Germany
| | - Thomas Günther Pomorski
- Department of Plant and Environmental SciencesUniversity of Copenhagen Frederiksberg C Denmark
- Department of Molecular BiochemistryRuhr‐University Bochum Bochum Germany
| | - Anant K. Menon
- Department of BiochemistryWeill Cornell Medical College New York, New York
| | - Daniel Wüstner
- Department of Biochemistry and Molecular BiologyUniversity of Southern Denmark Odense M Denmark
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18
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Peter JJ, Watson TL, Walker ME, Gardner JM, Lang TA, Borneman A, Forgan A, Tran T, Jiranek V. Use of a wine yeast deletion collection reveals genes that influence fermentation performance under low-nitrogen conditions. FEMS Yeast Res 2018; 18:4841842. [DOI: 10.1093/femsyr/foy009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 02/05/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Josephine J Peter
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tommaso L Watson
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Michelle E Walker
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Jennifer M Gardner
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tom A Lang
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Anthony Borneman
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Angus Forgan
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tina Tran
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Vladimir Jiranek
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
- Australian Research Council Training Centre for Innovative Wine Production, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
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19
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Nielson JR, Fredrickson EK, Waller TC, Rendón OZ, Schubert HL, Lin Z, Hill CP, Rutter J. Sterol Oxidation Mediates Stress-Responsive Vms1 Translocation to Mitochondria. Mol Cell 2017; 68:673-685.e6. [PMID: 29149595 PMCID: PMC5837041 DOI: 10.1016/j.molcel.2017.10.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/03/2017] [Accepted: 10/17/2017] [Indexed: 12/25/2022]
Abstract
Vms1 translocates to damaged mitochondria in response to stress, whereupon its binding partner, Cdc48, contributes to mitochondrial protein homeostasis. Mitochondrial targeting of Vms1 is mediated by its conserved mitochondrial targeting domain (MTD), which, in unstressed conditions, is inhibited by intramolecular binding to the Vms1 leucine-rich sequence (LRS). Here, we report a 2.7 Å crystal structure of Vms1 that reveals that the LRS lies in a hydrophobic groove in the autoinhibited MTD. We also demonstrate that the oxidized sterol, ergosterol peroxide, is necessary and sufficient for Vms1 localization to mitochondria, through binding the MTD in an interaction that is competitive with binding to the LRS. These data support a model in which stressed mitochondria generate an oxidized sterol receptor that recruits Vms1 to support mitochondrial protein homeostasis.
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Affiliation(s)
- Jason R Nielson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Eric K Fredrickson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - T Cameron Waller
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Olga Zurita Rendón
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah College of Pharmacy, Salt Lake City, UT 84112, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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20
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Laub KR, Marek M, Stanchev LD, Herrera SA, Kanashova T, Bourmaud A, Dittmar G, Günther Pomorski T. Purification and characterisation of the yeast plasma membrane ATP binding cassette transporter Pdr11p. PLoS One 2017; 12:e0184236. [PMID: 28922409 PMCID: PMC5602531 DOI: 10.1371/journal.pone.0184236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/21/2017] [Indexed: 12/27/2022] Open
Abstract
The ATP binding cassette (ABC) transporters Pdr11p and its paralog Aus1p are expressed under anaerobic growth conditions at the plasma membrane of the yeast Saccharomyces cerevisiae and are required for sterol uptake. However, the precise mechanism by which these ABC transporters facilitate sterol movement is unknown. In this study, an overexpression and purification procedure was developed with the aim to characterise the Pdr11p transporter. Engineering of Pdr11p variants fused at the C terminus with green fluorescent protein (Pdr11p-GFP) and containing a FLAG tag at the N terminus facilitated expression analysis and one-step purification, respectively. The detergent-solubilised and purified protein displayed a stable ATPase activity with a broad pH optimum near 7.4. Mutagenesis of the conserved lysine to methionine (K788M) in the Walker A motif abolished ATP hydrolysis. Remarkably, and in contrast to Aus1p, ATPase activity of Pdr11p was insensitive to orthovanadate and not specifically stimulated by phosphatidylserine upon reconstitution into liposomes. Our results highlight distinct differences between Pdr11p and Aus1p and create an experimental basis for further biochemical studies of both ABC transporters to elucidate their function.
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Affiliation(s)
- Katrine Rude Laub
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Magdalena Marek
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lyubomir Dimitrov Stanchev
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Department of Molecular Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Sara Abad Herrera
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Department of Molecular Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Tamara Kanashova
- Mass spectrometry core unit, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Adèle Bourmaud
- Proteome and Genome research laboratory, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Gunnar Dittmar
- Mass spectrometry core unit, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Proteome and Genome research laboratory, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Thomas Günther Pomorski
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Department of Molecular Biochemistry, Ruhr University Bochum, Bochum, Germany
- * E-mail:
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21
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Lucas C, Ferreira C, Cazzanelli G, Franco-Duarte R, Tulha J, Roelink H, Conway SJ. Yeast Gup1(2) Proteins Are Homologues of the Hedgehog Morphogens Acyltransferases HHAT(L): Facts and Implications. J Dev Biol 2016; 4:E33. [PMID: 29615596 PMCID: PMC5831804 DOI: 10.3390/jdb4040033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/16/2022] Open
Abstract
In multiple tissues, the Hedgehog secreted morphogen activates in the receiving cells a pathway involved in cell fate, proliferation and differentiation in the receiving cells. This pathway is particularly important during embryogenesis. The protein HHAT (Hedgehog O-acyltransferase) modifies Hh morphogens prior to their secretion, while HHATL (Hh O-acyltransferase-like) negatively regulates the pathway. HHAT and HHATL are homologous to Saccharomyces cerevisiae Gup2 and Gup1, respectively. In yeast, Gup1 is associated with a high number and diversity of biological functions, namely polarity establishment, secretory/endocytic pathway functionality, vacuole morphology and wall and membrane composition, structure and maintenance. Phenotypes underlying death, morphogenesis and differentiation are also included. Paracrine signalling, like the one promoted by the Hh pathway, has not been shown to occur in microbial communities, despite the fact that large aggregates of cells like biofilms or colonies behave as proto-tissues. Instead, these have been suggested to sense the population density through the secretion of quorum-sensing chemicals. This review focuses on Gup1/HHATL and Gup2/HHAT proteins. We review the functions and physiology associated with these proteins in yeasts and higher eukaryotes. We suggest standardisation of the presently chaotic Gup-related nomenclature, which includes KIAA117, c3orf3, RASP, Skinny, Sightless and Central Missing, in order to avoid the disclosure of otherwise unnoticed information.
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Affiliation(s)
- Cândida Lucas
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Célia Ferreira
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK;
| | - Giulia Cazzanelli
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Ricardo Franco-Duarte
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Joana Tulha
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
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22
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Pomorski TG, Menon AK. Lipid somersaults: Uncovering the mechanisms of protein-mediated lipid flipping. Prog Lipid Res 2016; 64:69-84. [PMID: 27528189 DOI: 10.1016/j.plipres.2016.08.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/10/2016] [Indexed: 12/22/2022]
Abstract
Membrane lipids diffuse rapidly in the plane of the membrane but their ability to flip spontaneously across a membrane bilayer is hampered by a significant energy barrier. Thus spontaneous flip-flop of polar lipids across membranes is very slow, even though it must occur rapidly to support diverse aspects of cellular life. Here we discuss the mechanisms by which rapid flip-flop occurs, and what role lipid flipping plays in membrane homeostasis and cell growth. We focus on conceptual aspects, highlighting mechanistic insights from biochemical and in silico experiments, and the recent, ground-breaking identification of a number of lipid scramblases.
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Affiliation(s)
- Thomas Günther Pomorski
- Faculty of Chemistry and Biochemistry, Molecular Biochemistry, Ruhr University Bochum, Universitätstrasse 150, D-44780 Bochum, Germany; Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
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23
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Solanko KA, Modzel M, Solanko LM, Wüstner D. Fluorescent Sterols and Cholesteryl Esters as Probes for Intracellular Cholesterol Transport. Lipid Insights 2016; 8:95-114. [PMID: 27330304 PMCID: PMC4902042 DOI: 10.4137/lpi.s31617] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/04/2016] [Accepted: 04/07/2016] [Indexed: 12/20/2022] Open
Abstract
Cholesterol transport between cellular organelles comprised vesicular trafficking and nonvesicular exchange; these processes are often studied by quantitative fluorescence microscopy. A major challenge for using this approach is producing analogs of cholesterol with suitable brightness and structural and chemical properties comparable with those of cholesterol. This review surveys currently used fluorescent sterols with respect to their behavior in model membranes, their photophysical properties, as well as their transport and metabolism in cells. In the first part, several intrinsically fluorescent sterols, such as dehydroergosterol or cholestatrienol, are discussed. These polyene sterols (P-sterols) contain three conjugated double bonds in the steroid ring system, giving them slight fluorescence in ultraviolet light. We discuss the properties of P-sterols relative to cholesterol, outline their chemical synthesis, and explain how to image them in living cells and organisms. In particular, we show that P-sterol esters inserted into low-density lipoprotein can be tracked in the fibroblasts of Niemann–Pick disease using high-resolution deconvolution microscopy. We also describe fluorophore-tagged cholesterol probes, such as BODIPY-, NBD-, Dansyl-, or Pyrene-tagged cholesterol, and eventual esters of these analogs. Finally, we survey the latest developments in the synthesis and use of alkyne cholesterol analogs to be labeled with fluorophores by click chemistry and discuss the potential of all approaches for future applications.
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Affiliation(s)
- Katarzyna A Solanko
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Lukasz M Solanko
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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Dickinson Q, Bottoms S, Hinchman L, McIlwain S, Li S, Myers CL, Boone C, Coon JJ, Hebert A, Sato TK, Landick R, Piotrowski JS. Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain. Microb Cell Fact 2016; 15:17. [PMID: 26790958 PMCID: PMC4721058 DOI: 10.1186/s12934-016-0417-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/08/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Imidazolium ionic liquids (IILs) underpin promising technologies that generate fermentable sugars from lignocellulose for future biorefineries. However, residual IILs are toxic to fermentative microbes such as Saccharomyces cerevisiae, making IIL-tolerance a key property for strain engineering. To enable rational engineering, we used chemical genomic profiling to understand the effects of IILs on S. cerevisiae. RESULTS We found that IILs likely target mitochondria as their chemical genomic profiles closely resembled that of the mitochondrial membrane disrupting agent valinomycin. Further, several deletions of genes encoding mitochondrial proteins exhibited increased sensitivity to IIL. High-throughput chemical proteomics confirmed effects of IILs on mitochondrial protein levels. IILs induced abnormal mitochondrial morphology, as well as altered polarization of mitochondrial membrane potential similar to valinomycin. Deletion of the putative serine/threonine kinase PTK2 thought to activate the plasma-membrane proton efflux pump Pma1p conferred a significant IIL-fitness advantage. Conversely, overexpression of PMA1 conferred sensitivity to IILs, suggesting that hydrogen ion efflux may be coupled to influx of the toxic imidazolium cation. PTK2 deletion conferred resistance to multiple IILs, including [EMIM]Cl, [BMIM]Cl, and [EMIM]Ac. An engineered, xylose-converting ptk2∆ S. cerevisiae (Y133-IIL) strain consumed glucose and xylose faster and produced more ethanol in the presence of 1 % [BMIM]Cl than the wild-type PTK2 strain. We propose a model of IIL toxicity and resistance. CONCLUSIONS This work demonstrates the utility of chemical genomics-guided biodesign for development of superior microbial biocatalysts for the ever-changing landscape of fermentation inhibitors.
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Affiliation(s)
- Quinn Dickinson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Scott Bottoms
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Li Hinchman
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Sean McIlwain
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Sheena Li
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
| | - Charles Boone
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Joshua J Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Alexander Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, WI, USA.
| | - Jeff S Piotrowski
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
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Graham A. Mitochondrial regulation of macrophage cholesterol homeostasis. Free Radic Biol Med 2015; 89:982-92. [PMID: 26416507 DOI: 10.1016/j.freeradbiomed.2015.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/28/2015] [Accepted: 08/11/2015] [Indexed: 12/19/2022]
Abstract
This review explores the relationship between mitochondrial structure and function in the regulation of macrophage cholesterol metabolism and proposes that mitochondrial dysfunction contributes to loss of the elegant homeostatic mechanisms which normally maintain cellular sterol levels within defined limits. Mitochondrial sterol 27-hydroxylase (CYP27A1) can generate oxysterol activators of liver X receptors which heterodimerise with retinoid X receptors, enhancing the transcription of ATP binding cassette transporters (ABCA1, ABCG1, and ABCG4), that can remove excess cholesterol via efflux to apolipoproteins A-1, E, and high density lipoprotein, and inhibit inflammation. The activity of CYP27A1 is regulated by the rate of supply of cholesterol substrate to the inner mitochondrial membrane, mediated by a complex of proteins. The precise identity of this dynamic complex remains controversial, even in steroidogenic tissues, but may include steroidogenic acute regulatory protein and the 18 kDa translocator protein, together with voltage-dependent anion channels, ATPase AAA domain containing protein 3A, and optic atrophy type 1 proteins. Certainly, overexpression of StAR and TSPO proteins can enhance macrophage cholesterol efflux to apoA-I and/or HDL, while perturbations in mitochondrial function, or changes in the expression of mitochondrial fusion proteins, alter the efficiency of cholesterol efflux. Molecules which can sustain or improve mitochondrial function or increase the activity of the protein complex involved in cholesterol transfer may have utility in resolving the problem of dysregulated macrophage cholesterol homeostasis, a condition which may contribute to inflammation, atherosclerosis, nonalcoholic steatohepatitis, osteoblastic bone resorption, and some disorders of the central nervous system.
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Affiliation(s)
- Annette Graham
- Department of Life Sciences, School of Health and Life Sciences, and Institute for Applied Health Research, Glasgow Caledonian University, 70 Cowcaddens Road, Glasgow G4 0BA, United Kingdom.
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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28
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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29
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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30
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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31
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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32
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Marek M, Silvestro D, Fredslund MD, Andersen TG, Pomorski TG. Serum albumin promotes ATP-binding cassette transporter-dependent sterol uptake in yeast. FEMS Yeast Res 2014; 14:1223-33. [DOI: 10.1111/1567-1364.12219] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/21/2014] [Accepted: 10/08/2014] [Indexed: 12/23/2022] Open
Affiliation(s)
- Magdalena Marek
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN; Department of Plant and Environmental Sciences; University of Copenhagen; Frederiksberg C Denmark
| | - Daniele Silvestro
- Copenhagen Plant Science Center and the VILLUM Research Center ‘Plant Plasticity’; Department of Plant and Environmental Sciences; University of Copenhagen; Frederiksberg C, Copenhagen Denmark
| | - Maria D. Fredslund
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN; Department of Plant and Environmental Sciences; University of Copenhagen; Frederiksberg C Denmark
| | - Tonni G. Andersen
- Department of Plant Molecular Biology, Biophore, UNIL-Sorge; University of Lausanne; Lausanne Switzerland
| | - Thomas G. Pomorski
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN; Department of Plant and Environmental Sciences; University of Copenhagen; Frederiksberg C Denmark
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Della-Bianca BE, de Hulster E, Pronk JT, van Maris AJ, Gombert AK. Physiology of the fuel ethanol strainSaccharomyces cerevisiaePE-2 at low pH indicates a context-dependent performance relevant for industrial applications. FEMS Yeast Res 2014; 14:1196-205. [DOI: 10.1111/1567-1364.12217] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/04/2014] [Accepted: 09/23/2014] [Indexed: 12/27/2022] Open
Affiliation(s)
| | - Erik de Hulster
- Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | - Jack T. Pronk
- Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | | | - Andreas K. Gombert
- Department of Chemical Engineering; University of Sao Paulo; São Paulo-SP Brazil
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Binai NA, Bisschops MMM, van Breukelen B, Mohammed S, Loeff L, Pronk JT, Heck AJR, Daran-Lapujade P, Slijper M. Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures. J Proteome Res 2014; 13:3542-53. [PMID: 25000127 DOI: 10.1021/pr5003388] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Stationary-phase, carbon-starved shake-flask cultures of Saccharomyces cerevisiae are popular models for studying eukaryotic chronological aging. However, their nutrient-starved physiological status differs substantially from that of postmitotic metazoan cells. Retentostat cultures offer an attractive alternative model system in which yeast cells, maintained under continuous calorie restriction, hardly divide but retain high metabolic activity and viability for prolonged periods of time. Using TMT labeling and UHPLC-MS/MS, the present study explores the proteome of yeast cultures during transition from exponential growth to near-zero growth in severely calorie-restricted retentostats. This transition elicited protein level changes in 20% of the yeast proteome. Increased abundance of heat shock-related proteins correlated with increased transcript levels of the corresponding genes and was consistent with a strongly increased heat shock tolerance of retentostat-grown cells. A sizable fraction (43%) of the proteins with increased abundance under calorie restriction was involved in oxidative phosphorylation and in various mitochondrial functions that, under the anaerobic, nongrowing conditions used, have a very limited role. Although it may seem surprising that yeast cells confronted with severe calorie restriction invest in the synthesis of proteins that, under those conditions, do not contribute to fitness, these responses may confer metabolic flexibility and thereby a selective advantage in fluctuating natural habitats.
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Affiliation(s)
- Nadine A Binai
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014; 15:552. [PMID: 24993029 PMCID: PMC4099481 DOI: 10.1186/1471-2164-15-552] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 06/27/2014] [Indexed: 12/21/2022] Open
Abstract
Background Wine fermentation is a harsh ecological niche to which wine yeast are well adapted. The initial high osmotic pressure and acidity of grape juice is followed by nutrient depletion and increasing concentrations of ethanol as the fermentation progresses. Yeast’s adaptation to these and many other environmental stresses, enables successful completion of high-sugar fermentations. Earlier transcriptomic and growth studies have tentatively identified genes important for high-sugar fermentation. Whilst useful, such studies did not consider extended growth (>5 days) in a temporally dynamic multi-stressor environment such as that found in many industrial fermentation processes. Here, we identify genes whose deletion has minimal or no effect on growth, but results in failure to achieve timely completion of the fermentation of a chemically defined grape juice with 200 g L−1 total sugar. Results Micro- and laboratory-scale experimental fermentations were conducted to identify 72 clones from ~5,100 homozygous diploid single-gene yeast deletants, which exhibited protracted fermentation in a high-sugar medium. Another 21 clones (related by gene function, but initially eliminated from the screen because of possible growth defects) were also included. Clustering and numerical enrichment of genes annotated to specific Gene Ontology (GO) terms highlighted the vacuole’s role in ion homeostasis and pH regulation, through vacuole acidification. Conclusion We have identified 93 genes whose deletion resulted in the duration of fermentation being at least 20% longer than the wild type. An extreme phenotype, ‘stuck’ fermentation, was also observed when DOA4, NPT1, PLC1, PTK2, SIN3, SSQ1, TPS1, TPS2 or ZAP1 were deleted. These 93 Fermentation Essential Genes (FEG) are required to complete an extended high-sugar (wine-like) fermentation. Their importance is highlighted in our Fermentation Relevant Yeast Genes (FRYG) database, generated from literature and the fermentation-relevant phenotypic characteristics of null mutants described in the Saccharomyces Genome Database. The 93-gene set is collectively referred to as the ‘Fermentome’. The fact that 10 genes highlighted in this study have not previously been linked to fermentation-related stresses, supports our experimental rationale. These findings, together with investigations of the genetic diversity of industrial strains, are crucial for understanding the mechanisms behind yeast’s response and adaptation to stresses imposed during high-sugar fermentations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-552) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Vladimir Jiranek
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA 5064, Australia.
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Coffey N, Hinde J, Holian E. Clustering longitudinal profiles using P-splines and mixed effects models applied to time-course gene expression data. Comput Stat Data Anal 2014. [DOI: 10.1016/j.csda.2013.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wriessnegger T, Pichler H. Yeast metabolic engineering – Targeting sterol metabolism and terpenoid formation. Prog Lipid Res 2013; 52:277-93. [DOI: 10.1016/j.plipres.2013.03.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 12/28/2022]
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Nagi M, Tanabe K, Ueno K, Nakayama H, Aoyama T, Chibana H, Yamagoe S, Umeyama T, Oura T, Ohno H, Kajiwara S, Miyazaki Y. The Candida glabrata sterol scavenging mechanism, mediated by the ATP-binding cassette transporter Aus1p, is regulated by iron limitation. Mol Microbiol 2013; 88:371-81. [PMID: 23448689 DOI: 10.1111/mmi.12189] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2013] [Indexed: 11/26/2022]
Abstract
During disseminated infection by the opportunistic pathogen Candida glabrata, uptake of sterols such as serum cholesterol may play a significant role during pathogenesis. The ATP-binding cassette transporter Aus1p is thought to function as a sterol importer and in this study, we show that uptake of exogenous sterols occurred under anaerobic conditions in wild-type cells of C. glabrata but not in AUS1-deleted mutant (aus1Δ) cells. In aerobic cultures, growth inhibition by fluconazole was prevented in the presence of serum, and AUS1 expression was upregulated. Uptake of sterol by azole treated cells required the presence of serum, and sterol alone did not reverse FLC inhibition of growth. However, if iron availability in the growth medium was limited by addition of the iron chelators ferrozine or apo-transferrin, growth of wild-type cells, but not aus1Δ cells, was rescued. In a mouse model of disseminated infection, the C. glabrata aus1Δ strain caused a significantly decreased kidney fungal burden than the wild-type strain or a strain in which AUS1 was restored. We conclude that sterol uptake in C. glabrata can occur in iron poor environment of host tissues and thus may contribute to C. glabrata pathogenesis.
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Affiliation(s)
- Minoru Nagi
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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Comparison of sterol import under aerobic and anaerobic conditions in three fungal species, Candida albicans, Candida glabrata, and Saccharomyces cerevisiae. EUKARYOTIC CELL 2013; 12:725-38. [PMID: 23475705 DOI: 10.1128/ec.00345-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sterol import has been characterized under various conditions in three distinct fungal species, the model organism Saccharomyces cerevisiae and two human fungal pathogens Candida glabrata and Candida albicans, employing cholesterol, the sterol of higher eukaryotes, as well as its fungal equivalent, ergosterol. Import was confirmed by the detection of esterified cholesterol within the cells. Comparing the three fungal species, we observe sterol import under three different conditions. First, as previously well characterized, we observe sterol import under low oxygen levels in S. cerevisiae and C. glabrata, which is dependent on the transcription factor Upc2 and/or its orthologs or paralogs. Second, we observe sterol import under aerobic conditions exclusively in the two pathogenic fungi C. glabrata and C. albicans. Uptake emerges during post-exponential-growth phases, is independent of the characterized Upc2-pathway and is slower compared to the anaerobic uptake in S. cerevisiae and C. glabrata. Third, we observe under normoxic conditions in C. glabrata that Upc2-dependent sterol import can be induced in the presence of fetal bovine serum together with fluconazole. In summary, C. glabrata imports sterols both in aerobic and anaerobic conditions, and the limited aerobic uptake can be further stimulated by the presence of serum together with fluconazole. S. cerevisiae imports sterols only in anaerobic conditions, demonstrating aerobic sterol exclusion. Finally, C. albicans imports sterols exclusively aerobically in post-exponential-growth phases, independent of Upc2. For the first time, we provide direct evidence of sterol import into the human fungal pathogen C. albicans, which until now was believed to be incapable of active sterol import.
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Faletrov YV, Bialevich KI, Edimecheva IP, Kostsin DG, Rudaya EV, Slobozhanina EI, Shkumatov VM. 22-NBD-cholesterol as a novel fluorescent substrate for cholesterol-converting oxidoreductases. J Steroid Biochem Mol Biol 2013; 134:59-66. [PMID: 23124253 DOI: 10.1016/j.jsbmb.2012.09.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 09/12/2012] [Accepted: 09/23/2012] [Indexed: 01/26/2023]
Abstract
Docking simulations and experimental data indicate that 22-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-23,24-bisnor-5-cholen-3β-ol (22-NBD-cholesterol), a common fluorescent sterol analog, binds into active sites of bovine cytochrome P450scc and microbial cholesterol dehydrogenases (CHDHs) and then undergoes regiospecific oxidations by these enzymes. The P450scc-dependent system was established to realize N-dealkylation activity toward 22-NBD-cholesterol, resulting in 7-nitrobenz[c][1,2,5]oxadiazole-4-amine (NBD-NH(2)) formation as a dominant fluorescent product. Basing on LC-MS data of the probes derivatized with hydroxylamine or cholesterol oxidase, both pregnenolone and 20-formyl-pregn-5-en-3β-ol were deduced to be steroidal co-products of NBD-NH(2), indicating intricate character of the reaction. Products of CHDH-mediated conversions of 22-NBD-cholesterol were defined as 3-oxo-4-en and 3-oxo-5-en derivatives of the steroid. Moreover, the 3-oxo-4-en derivative was also found to be formed after 22-NBD-cholesterol incubation with pathogenic bacterium Pseudomonas aeruginosa, indicating a possible application of the reaction for a selective and sensitive detection of some microbes. The 3-keto-4-en derivative of 22-NBD-cholesterol may be also suitable as a new fluorescent probe for steroid hormone-binding enzymes or receptors.
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Affiliation(s)
- Yaroslav V Faletrov
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str 14, 220030 Minsk, Belarus.
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H3K4 methyltransferase Set1 is involved in maintenance of ergosterol homeostasis and resistance to Brefeldin A. Proc Natl Acad Sci U S A 2013; 110:E1016-25. [PMID: 23382196 DOI: 10.1073/pnas.1215768110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Set1 is a conserved histone H3 lysine 4 (H3K4) methyltransferase that exists as a multisubunit complex. Although H3K4 methylation is located on many actively transcribed genes, few studies have established a direct connection showing that loss of Set1 and H3K4 methylation results in a phenotype caused by disruption of gene expression. In this study, we determined that cells lacking Set1 or Set1 complex members that disrupt H3K4 methylation have a growth defect when grown in the presence of the antifungal drug Brefeldin A (BFA), indicating that H3K4 methylation is needed for BFA resistance. To determine the role of Set1 in BFA resistance, we discovered that Set1 is important for the expression of genes in the ergosterol biosynthetic pathway, including the rate-limiting enzyme HMG-CoA reductase. Consequently, deletion of SET1 leads to a reduction in HMG-CoA reductase protein and total cellular ergosterol. In addition, the lack of Set1 results in an increase in the expression of DAN1 and PDR11, two genes involved in ergosterol uptake. The increase in expression of uptake genes in set1Δ cells allows sterols such as cholesterol and ergosterol to be actively taken up under aerobic conditions. Interestingly, when grown in the presence of ergosterol set1Δ cells become resistant to BFA, indicating that proper ergosterol levels are needed for antifungal drug resistance. These data show that H3K4 methylation impacts gene expression and output of a biologically and medically relevant pathway and determines why cells lacking H3K4 methylation have antifungal drug sensitivity.
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Ta MT, Kapterian TS, Fei W, Du X, Brown AJ, Dawes IW, Yang H. Accumulation of squalene is associated with the clustering of lipid droplets. FEBS J 2012; 279:4231-44. [DOI: 10.1111/febs.12015] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/20/2012] [Accepted: 09/13/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Minh T. Ta
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; Australia
| | - Tamar S. Kapterian
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; Australia
| | - Weihua Fei
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; Australia
| | - Ximing Du
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; Australia
| | - Andrew J. Brown
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; Australia
| | - Ian W. Dawes
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; Australia
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; Australia
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44
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Pedroso N, Gomes-Alves P, Marinho HS, Brito VB, Boada C, Antunes F, Herrero E, Penque D, Cyrne L. The plasma membrane-enriched fraction proteome response during adaptation to hydrogen peroxide in Saccharomyces cerevisiae. Free Radic Res 2012; 46:1267-79. [PMID: 22712517 DOI: 10.3109/10715762.2012.704997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In Saccharomyces cerevisiae, adaptation to hydrogen peroxide (H₂O₂) decreases plasma membrane permeability to H₂O₂, changes its lipid composition and reorganizes ergosterol-rich microdomains by a still unknown mechanism. Here we show, by a quantitative analysis of the H₂O₂-induced adaptation effect on the S. cerevisiae plasma membrane-enriched fraction proteome, using two-dimensional gel electrophoresis, that 44 proteins are differentially expressed. Most of these proteins were regulated at a post-transcriptional level. Fourteen of these proteins contain redox-sensitive cysteine residues and nine proteins are associated with lipid and vesicle traffic. In particular, three proteins found in eisosomes and in the eisosome-associated membrane compartment occupied by Can1p were up-regulated (Pil1p, Rfs1p and Pst2p) during adaptation to H₂O₂. Survival studies after exposure to lethal H₂O₂ doses using yeast strains bearing a gene deletion corresponding to proteins associated to lipid and vesicle traffic demonstrated for the first time that down-regulation of Kes1p, Vps4p and Ynl010wp and up-regulation of Atp1 and Atp2 increases resistance to H₂O₂. Moreover, for the pil1Δ strain, H₂O₂ at low levels produces a hormetic effect by increasing proliferation. In conclusion, these data further confirms the plasma membrane as an active cellular site during adaptation to H₂O₂ and shows that proteins involved in lipid and vesicle traffic are important mediators of H₂O₂ adaptation.
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Affiliation(s)
- Nuno Pedroso
- Departamento de Química e Bioquímica & Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
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45
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Jacquier N, Schneiter R. Mechanisms of sterol uptake and transport in yeast. J Steroid Biochem Mol Biol 2012; 129:70-8. [PMID: 21145395 DOI: 10.1016/j.jsbmb.2010.11.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 11/12/2010] [Accepted: 11/30/2010] [Indexed: 11/21/2022]
Abstract
Sterols are essential lipid components of eukaryotic membranes. Here we summarize recent advances in understanding how sterols are transported between different membranes. Baker's yeast is a particularly attractive organism to dissect this lipid transport pathway, because cells can synthesize their own major sterol, ergosterol, in the membrane of the endoplasmic reticulum from where it is then transported to the plasma membrane. However, Saccharomyces cerevisiae is also a facultative anaerobic organism, which becomes sterol auxotroph in the absence of oxygen. Under these conditions, cells take up sterol from the environment and transport the lipid back into the membrane of the endoplasmic reticulum, where the free sterol becomes esterified and is then stored in lipid droplets. Steryl ester formation is thus a reliable readout to assess the back-transport of exogenously provided sterols from the plasma membrane to the endoplasmic reticulum. Structure/function analysis has revealed that the bulk membrane function of the fungal ergosterol can be provided by structurally related sterols, including the mammalian cholesterol. Foreign sterols, however, are subject to a lipid quality control cycle in which the sterol is reversibly acetylated. Because acetylated sterols are efficiently excreted from cells, the substrate specificity of the deacetylating enzymes determines which sterols are retained. Membrane-bound acetylated sterols are excreted by the secretory pathway, more soluble acetylated sterol derivatives such as the steroid precursor pregnenolone, on the other hand, are excreted by a pathway that is independent of vesicle formation and fusion. Further analysis of this lipid quality control cycle is likely to reveal novel insight into the mechanisms that ensure sterol homeostasis in eukaryotic cells. Article from a special issue on Steroids and Microorganisms.
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Affiliation(s)
- Nicolas Jacquier
- Department of Medicine, Division of Biochemistry, University of Fribourg, Fribourg, Switzerland
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46
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Beh CT, McMaster CR, Kozminski KG, Menon AK. A detour for yeast oxysterol binding proteins. J Biol Chem 2012; 287:11481-8. [PMID: 22334669 DOI: 10.1074/jbc.r111.338400] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxysterol binding protein-related proteins, including the yeast proteins encoded by the OSH gene family (OSH1-OSH7), are implicated in the non-vesicular transfer of sterols between intracellular membranes and the plasma membrane. In light of recent studies, we revisited the proposal that Osh proteins are sterol transfer proteins and present new models consistent with known Osh protein functions. These models focus on the role of Osh proteins as sterol-dependent regulators of phosphoinositide and sphingolipid pathways. In contrast to their posited role as non-vesicular sterol transfer proteins, we propose that Osh proteins coordinate lipid signaling and membrane reorganization with the assembly of tethering complexes to promote molecular exchanges at membrane contact sites.
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Affiliation(s)
- Christopher T Beh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
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47
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Spanova M, Zweytick D, Lohner K, Klug L, Leitner E, Hermetter A, Daum G. Influence of squalene on lipid particle/droplet and membrane organization in the yeast Saccharomyces cerevisiae. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1821:647-53. [PMID: 22342273 PMCID: PMC3790963 DOI: 10.1016/j.bbalip.2012.01.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 01/12/2012] [Accepted: 01/30/2012] [Indexed: 02/02/2023]
Abstract
In a previous study (Spanova et al., 2010, J. Biol. Chem., 285, 6127–6133) we demonstrated that squalene, an intermediate of sterol biosynthesis, accumulates in yeast strains bearing a deletion of the HEM1 gene. In such strains, the vast majority of squalene is stored in lipid particles/droplets together with triacylglycerols and steryl esters. In mutants lacking the ability to form lipid particles, however, substantial amounts of squalene accumulate in organelle membranes. In the present study, we investigated the effect of squalene on biophysical properties of lipid particles and biological membranes and compared these results to artificial membranes. Our experiments showed that squalene together with triacylglycerols forms the fluid core of lipid particles surrounded by only a few steryl ester shells which transform into a fluid phase below growth temperature. In the hem1∆ deletion mutant a slight disordering effect on steryl esters was observed indicated by loss of the high temperature transition. Also in biological membranes from the hem1∆ mutant strain the effect of squalene per se is difficult to pinpoint because multiple effects such as levels of sterols and unsaturated fatty acids contribute to physical membrane properties. Fluorescence spectroscopic studies using endoplasmic reticulum, plasma membrane and artificial membranes revealed that it is not the absolute squalene level in membranes but rather the squalene to sterol ratio which mainly affects membrane fluidity/rigidity. In a fluid membrane environment squalene induces rigidity of the membrane, whereas in rigid membranes there is almost no additive effect of squalene. In summary, our results demonstrate that squalene (i) can be well accommodated in yeast lipid particles and organelle membranes without causing deleterious effects; and (ii) although not being a typical membrane lipid may be regarded as a mild modulator of biophysical membrane properties.
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Affiliation(s)
- Miroslava Spanova
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Dagmar Zweytick
- Institute of Biophysics and Nanosystems Research, Austrian Academy of Sciences, Graz, Austria
| | - Karl Lohner
- Institute of Biophysics and Nanosystems Research, Austrian Academy of Sciences, Graz, Austria
| | - Lisa Klug
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Erich Leitner
- Institute of Analytical Chemistry and Food Technology, Graz University of Technology, Austria
| | - Albin Hermetter
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- Corresponding author at: Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, A-8010 Graz, Austria. Tel.: + 43 316 873 6462; fax: + 43 316 873 6952.
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48
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Boender LGM, Maris AJA, Hulster EAF, Almering MJH, Klei IJ, Veenhuis M, Winde JH, Pronk JT, Daran-Lapujade P. Cellular responses of Saccharomyces cerevisiae at near-zero growth rates: transcriptome analysis of anaerobic retentostat cultures. FEMS Yeast Res 2011; 11:603-20. [PMID: 22093745 PMCID: PMC3498732 DOI: 10.1111/j.1567-1364.2011.00750.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 07/09/2011] [Accepted: 08/16/2011] [Indexed: 11/30/2022] Open
Abstract
Extremely low specific growth rates (below 0.01 h(-1) ) represent a largely unexplored area of microbial physiology. In this study, anaerobic, glucose-limited retentostats were used to analyse physiological and genome-wide transcriptional responses of Saccharomyces cerevisiae to cultivation at near-zero specific growth rates. While quiescence is typically investigated as a result of carbon starvation, cells in retentostat are fed by small, but continuous carbon and energy supply. Yeast cells cultivated near-zero specific growth rates, while metabolically active, exhibited characteristics previously associated with quiescence, including accumulation of storage polymers and an increased expression of genes involved in exit from the cell cycle into G(0) . Unexpectedly, analysis of transcriptome data from retentostat and chemostat cultures showed, as specific growth rate was decreased, that quiescence-related transcriptional responses were already set in at specific growth rates above 0.025 h(-1) . These observations stress the need for systematic dissection of physiological responses to slow growth, quiescence, ageing and starvation and indicate that controlled cultivation systems such as retentostats can contribute to this goal. Furthermore, cells in retentostat do not (or hardly) divide while remaining metabolically active, which emulates the physiological status of metazoan post-mitotic cells. We propose retentostat as a powerful cultivation tool to investigate chronological ageing-related processes.
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Affiliation(s)
- Léonie GM Boender
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Antonius JA Maris
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Erik AF Hulster
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Marinka JH Almering
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Ida J Klei
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Molecular Cell Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenHaren, The Netherlands
| | - Marten Veenhuis
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Molecular Cell Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenHaren, The Netherlands
| | - Johannes H Winde
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Jack T Pronk
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
| | - Pascale Daran-Lapujade
- Kluyver Centre for Genomics of Industrial FermentationDelft, The Netherlands
- Department of Biotechnology, Delft University of Technology, DelftThe Netherlands
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49
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Marek M, Milles S, Schreiber G, Daleke DL, Dittmar G, Herrmann A, Müller P, Pomorski TG. The yeast plasma membrane ATP binding cassette (ABC) transporter Aus1: purification, characterization, and the effect of lipids on its activity. J Biol Chem 2011; 286:21835-43. [PMID: 21521689 DOI: 10.1074/jbc.m111.244525] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The ATP binding cassette (ABC) transporter Aus1 is expressed under anaerobic growth conditions at the plasma membrane of the yeast Saccharomyces cerevisiae and is required for sterol uptake. These observations suggest that Aus1 promotes the translocation of sterols across membranes, but the precise transport mechanism has yet to be identified. In this study, an extraction and purification procedure was developed to characterize the Aus1 transporter. The detergent-solubilized protein was able to bind and hydrolyze ATP. Mutagenesis of the conserved lysine to methionine in the Walker A motif abolished ATP hydrolysis. Likewise, ATP hydrolysis was inhibited by classical inhibitors of ABC transporters. Upon reconstitution into proteoliposomes, the ATPase activity of Aus1 was specifically stimulated by phosphatidylserine (PS) in a stereoselective manner. We also found that Aus1-dependent sterol uptake, but not Aus1 expression and trafficking to the plasma membrane, was affected by changes in cellular PS levels. These results suggest a direct interaction between Aus1 and PS that is critical for the activity of the transporter.
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Affiliation(s)
- Magdalena Marek
- Institute of Biology, Humboldt University of Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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50
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Marisco G, Saito ST, Ganda IS, Brendel M, Pungartnik C. Low ergosterol content in yeast adh1 mutant enhances chitin maldistribution and sensitivity to paraquat-induced oxidative stress. Yeast 2011; 28:363-73. [DOI: 10.1002/yea.1844] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 01/02/2011] [Indexed: 01/05/2023] Open
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