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Rebnegger C, Coltman BL, Kowarz V, Peña DA, Mentler A, Troyer C, Hann S, Schöny H, Koellensperger G, Mattanovich D, Gasser B. Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates. Microb Cell Fact 2024; 23:43. [PMID: 38331812 PMCID: PMC10851509 DOI: 10.1186/s12934-024-02314-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Specific productivity (qP) in yeast correlates with growth, typically peaking at intermediate or maximum specific growth rates (μ). Understanding the factors limiting productivity at extremely low μ might reveal decoupling strategies, but knowledge of production dynamics and physiology in such conditions is scarce. Retentostats, a type of continuous cultivation, enable the well-controlled transition to near-zero µ through the combined retention of biomass and limited substrate supply. Recombinant Komagataella phaffii (syn Pichia pastoris) secreting a bivalent single domain antibody (VHH) was cultivated in aerobic, glucose-limited retentostats to investigate recombinant protein production dynamics and broaden our understanding of relevant physiological adaptations at near-zero growth conditions. RESULTS By the end of the retentostat cultivation, doubling times of approx. two months were reached, corresponding to µ = 0.00047 h-1. Despite these extremely slow growth rates, the proportion of viable cells remained high, and de novo synthesis and secretion of the VHH were observed. The average qP at the end of the retentostat was estimated at 0.019 mg g-1 h-1. Transcriptomics indicated that genes involved in protein biosynthesis were only moderately downregulated towards zero growth, while secretory pathway genes were mostly regulated in a manner seemingly detrimental to protein secretion. Adaptation to near-zero growth conditions of recombinant K. phaffii resulted in significant changes in the total protein, RNA, DNA and lipid content, and lipidomics revealed a complex adaptation pattern regarding the lipid class composition. The higher abundance of storage lipids as well as storage carbohydrates indicates that the cells are preparing for long-term survival. CONCLUSIONS In conclusion, retentostat cultivation proved to be a valuable tool to identify potential engineering targets to decouple growth and protein production and gain important insights into the physiological adaptation of K. phaffii to near-zero growth conditions.
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Affiliation(s)
- Corinna Rebnegger
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Benjamin L Coltman
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Viktoria Kowarz
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - David A Peña
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Axel Mentler
- Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Harald Schöny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Diethard Mattanovich
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Brigitte Gasser
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria.
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2
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Radkohl A, Schusterbauer V, Bernauer L, Rechberger GN, Wolinski H, Schittmayer M, Birner-Gruenberger R, Thallinger GG, Leitner E, Baeck M, Pichler H, Emmerstorfer-Augustin A. Human Sterols Are Overproduced, Stored and Excreted in Yeasts. Int J Mol Sci 2024; 25:781. [PMID: 38255855 PMCID: PMC10815178 DOI: 10.3390/ijms25020781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Sterols exert a profound influence on numerous cellular processes, playing a crucial role in both health and disease. However, comprehending the effects of sterol dysfunction on cellular physiology is challenging. Consequently, numerous processes affected by impaired sterol biosynthesis still elude our complete understanding. In this study, we made use of yeast strains that produce cholesterol instead of ergosterol and investigated the cellular response mechanisms on the transcriptome as well as the lipid level. The exchange of ergosterol for cholesterol caused the downregulation of phosphatidylethanolamine and phosphatidylserine and upregulation of phosphatidylinositol and phosphatidylcholine biosynthesis. Additionally, a shift towards polyunsaturated fatty acids was observed. While the sphingolipid levels dropped, the total amounts of sterols and triacylglycerol increased, which resulted in 1.7-fold enlarged lipid droplets in cholesterol-producing yeast cells. In addition to internal storage, cholesterol and its precursors were excreted into the culture supernatant, most likely by the action of ABC transporters Snq2, Pdr12 and Pdr15. Overall, our results demonstrate that, similarly to mammalian cells, the production of non-native sterols and sterol precursors causes lipotoxicity in K. phaffii, mainly due to upregulated sterol biosynthesis, and they highlight the different survival and stress response mechanisms on multiple, integrative levels.
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Affiliation(s)
- Astrid Radkohl
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Veronika Schusterbauer
- Bisy GmbH, 8200 Hofstaetten an der Raab, Austria
- Institute of Biomedical Informatics, Graz University of Technology, 8010 Graz, Austria
| | - Lukas Bernauer
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Gerald N. Rechberger
- Department of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
| | - Heimo Wolinski
- Department of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Matthias Schittmayer
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, 1040 Vienna, Austria (R.B.-G.)
| | - Ruth Birner-Gruenberger
- Institute of Chemical Technologies and Analytics, Technische Universität Wien, 1040 Vienna, Austria (R.B.-G.)
| | - Gerhard G. Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, 8010 Graz, Austria
| | - Erich Leitner
- Institute of Analytical Chemistry and Food Chemistry, University of Graz, NAWI Graz, 8010 Graz, Austria;
| | - Melanie Baeck
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, 8010 Graz, Austria
| | - Harald Pichler
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Acib—Austrian Centre of Industrial Biotechnology, 8010 Graz, Austria
| | - Anita Emmerstorfer-Augustin
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Acib—Austrian Centre of Industrial Biotechnology, 8010 Graz, Austria
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3
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Yu D, Boughton BA, Rupasinghe TWT, Hill CB, Herrfurth C, Scholz P, Feussner I, Roessner U. Discovery of novel neutral glycosphingolipids in cereal crops: rapid profiling using reversed-phased HPLC-ESI-QqTOF with parallel reaction monitoring. Sci Rep 2023; 13:22560. [PMID: 38110595 PMCID: PMC10728066 DOI: 10.1038/s41598-023-49981-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
This study explores the sphingolipid class of oligohexosylceramides (OHCs), a rarely studied group, in barley (Hordeum vulgare L.) through a new lipidomics approach. Profiling identified 45 OHCs in barley (Hordeum vulgare L.), elucidating their fatty acid (FA), long-chain base (LCB) and sugar residue compositions; and was accomplished by monophasic extraction followed by reverse-phased high performance liquid chromatography electrospray ionisation quadrupole-time-of-flight tandem mass spectrometry (HPLC-ESI-QqTOF-MS/MS) employing parallel reaction monitoring (PRM). Results revealed unknown ceramide species and highlighted distinctive FA and LCB compositions when compared to other sphingolipid classes. Structurally, the OHCs featured predominantly trihydroxy LCBs associated with hydroxylated FAs and oligohexosyl residues consisting of two-five glucose units in a linear 1 → 4 linkage. A survey found OHCs in tissues of major cereal crops while noting their absence in conventional dicot model plants. This study found salinity stress had only minor effects on the OHC profile in barley roots, leaving questions about their precise functions in plant biology unanswered.
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Affiliation(s)
- Dingyi Yu
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Mass Spectrometry Facility, St Vincent Institute of Medical Research, Fitzroy, VIC, 3065, Australia
| | - Berin A Boughton
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia.
- Australian National Phenome Centre, Murdoch University, Murdoch, WA, 6157, Australia.
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Thusitha W T Rupasinghe
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
- AbSciex, 2 Gilda Court, Mulgrave, VIC, 3170, Australia
| | - Camilla B Hill
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6157, Australia
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-Von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-Von-Liebig Weg 11, 37077, Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-Von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Patricia Scholz
- Department of Plant Biochemistry, Albrecht-Von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-Von-Liebig Weg 11, 37077, Goettingen, Germany
- ENS Lyon-Laboratoire Reproduction et Développement des Plantes, Equipe Signalisation Cellulaire (SICE), 46, Allée d'Italie, 69364, Lyon Cedex 07, France
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-Von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-Von-Liebig Weg 11, 37077, Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-Von-Liebig Weg 11, 37077, Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-Von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
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4
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Corucci G, Batchu KC, Luchini A, Santamaria A, Frewein MPK, Laux V, Haertlein M, Yamaryo-Botté Y, Botté CY, Sheridan T, Tully M, Maestro A, Martel A, Porcar L, Fragneto G. Developing advanced models of biological membranes with hydrogenous and deuterated natural glycerophospholipid mixtures. J Colloid Interface Sci 2023; 645:870-881. [PMID: 37178564 DOI: 10.1016/j.jcis.2023.04.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Cellular membranes are complex systems that consist of hundreds of different lipid species. Their investigation often relies on simple bilayer models including few synthetic lipid species. Glycerophospholipids (GPLs) extracted from cells are a valuable resource to produce advanced models of biological membranes. Here, we present the optimisation of a method previously reported by our team for the extraction and purification of various GPL mixtures from Pichia pastoris. The implementation of an additional purification step by High Performance Liquid Chromatography-Evaporative Light Scattering Detector (HPLC-ELSD) enabled for a better separation of the GPL mixtures from the neutral lipid fraction that includes sterols, and also allowed for the GPLs to be purified according to their different polar headgroups. Pure GPL mixtures at significantly high yields were produced through this approach. For this study, we utilised phoshatidylcholine (PC), phosphatidylserine (PS) and phosphatidylglycerol (PG) mixtures. These exhibit a single composition of the polar head, i.e., PC, PS or PG, but contain several molecular species consisting of acyl chains of varying length and unsaturation, which were determined by Gas Chromatography (GC). The lipid mixtures were produced both in their hydrogenous (H) and deuterated (D) versions and were used to form lipid bilayers both on solid substrates and as vesicles in solution. The supported lipid bilayers were characterised by quartz crystal microbalance with dissipation monitoring (QCM-D) and neutron reflectometry (NR), whereas the vesicles by small angle X-ray (SAXS) and neutron scattering (SANS). Our results show that despite differences in the acyl chain composition, the hydrogenous and deuterated extracts produced bilayers with very comparable structures, which makes them valuable to design experiments involving selective deuteration with techniques such as NMR, neutron scattering or infrared spectroscopy.
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Affiliation(s)
- Giacomo Corucci
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; École doctorale de Physique, Université Grenoble Alpes, 38400 Saint-Martin-d'Héres, France
| | | | - Alessandra Luchini
- European Spallation Source ERIC, P.O. Box 176, SE-221 00 Lund, Sweden; Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andreas Santamaria
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; Departamento de Química Física, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Moritz Paul Karl Frewein
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, 8010, Austria
| | - Valèrie Laux
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Yoshiki Yamaryo-Botté
- ApicoLipid Team & GEMELI Lipidomics Platform, Institute for Advanced Biosciences, CNRS UMR5309, INSERM (-National Institute for Health and Medical Research) U1209, Université Grenoble Alpes, 38000 Grenoble, France
| | - Cyrille Y Botté
- ApicoLipid Team & GEMELI Lipidomics Platform, Institute for Advanced Biosciences, CNRS UMR5309, INSERM (-National Institute for Health and Medical Research) U1209, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thomas Sheridan
- University College Dublin, Belfield, Dublin 4, Dublin, Ireland; AbbVie, Clonshaugh, Dublin 7, Co. Dublin, Ireland
| | - Mark Tully
- European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, CS 40220, 38043, Grenoble, France
| | - Armando Maestro
- Centro de Física de Materiales (CSIC, UPV/EHU) - Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; IKERBASQUE - Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Giovanna Fragneto
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; École doctorale de Physique, Université Grenoble Alpes, 38400 Saint-Martin-d'Héres, France; European Spallation Source ERIC, P.O. Box 176, SE-221 00 Lund, Sweden.
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5
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Eigenfeld M, Wittmann L, Kerpes R, Schwaminger S, Becker T. Quantification methods of determining brewer's and pharmaceutical yeast cell viability: accuracy and impact of nanoparticles. Anal Bioanal Chem 2023:10.1007/s00216-023-04676-w. [PMID: 37083758 DOI: 10.1007/s00216-023-04676-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/22/2023]
Abstract
For industrial processes, a fast, precise, and reliable method of determining the physiological state of yeast cells, especially viability, is essential. However, an increasing number of processes use magnetic nanoparticles (MNPs) for yeast cell manipulation, but their impact on yeast cell viability and the assay itself is unclear. This study tested the viability of Saccharomyces pastorianus ssp. carlsbergensis and Pichia pastoris by comparing traditional colourimetric, high-throughput, and growth assays with membrane fluidity. Results showed that methylene blue staining is only reliable for S. pastorianus cells with good viability, being erroneous in low viability (R2 = 0.945; [Formula: see text] = 5.78%). In comparison, the fluorescence microscopy-based assay of S. pastorianus demonstrated a coefficient of determination of R2 = 0.991 at [Formula: see text] ([Formula: see text] = 2.50%) and flow cytometric viability determination using carboxyfluorescein diacetate (CFDA), enabling high-throughput analysis of representative cell numbers; R2 = 0.972 ([Formula: see text]; [Formula: see text] = 3.89%). Membrane fluidity resulted in a non-linear relationship with the viability of the yeast cells ([Formula: see text]). We also determined similar results using P. pastoris yeast. In addition, we demonstrated that MNPs affected methylene blue staining by overestimating viability. The random forest model has been shown to be a precise method for classifying nanoparticles and yeast cells and viability differentiation in flow cytometry by using CFDA. Moreover, CFDA and membrane fluidity revealed precise results for both yeasts, also in the presence of nanoparticles, enabling fast and reliable determination of viability in many experiments using MNPs for yeast cell manipulation or separation.
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Affiliation(s)
- Marco Eigenfeld
- Chair of Brewing and Beverage Technology, Technical University of Munich, TUM School of Life Science, Weihenstephaner Steig 20, 85354, Freising, Germany
| | - Leonie Wittmann
- Chair of Bioseparation Engineering, Technical University of Munich, TUM School of Engineering and Design, Boltzmannstr. 15, 85748, Garching, Germany
| | - Roland Kerpes
- Chair of Brewing and Beverage Technology, Technical University of Munich, TUM School of Life Science, Weihenstephaner Steig 20, 85354, Freising, Germany.
| | - Sebastian Schwaminger
- Chair of Bioseparation Engineering, Technical University of Munich, TUM School of Engineering and Design, Boltzmannstr. 15, 85748, Garching, Germany
- Division of Medicinal Chemistry, Medical University of Graz, Otto-Loewi Research Center, Neue Stiftingtalstr. 6, 8010, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Thomas Becker
- Chair of Brewing and Beverage Technology, Technical University of Munich, TUM School of Life Science, Weihenstephaner Steig 20, 85354, Freising, Germany
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6
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Lehmayer L, Bernauer L, Emmerstorfer-Augustin A. ‘Applying the auxin-based degron system for the inducible, reversible and complete protein degradation in Komagataella phaffii’. iScience 2022; 25:104888. [PMID: 36043049 PMCID: PMC9420516 DOI: 10.1016/j.isci.2022.104888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 06/10/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
The auxin-inducible degron (AID) system is a useful technique to rapidly deplete any protein of interest “on-demand.” In this study, we successfully established the AID system for the “biotech” yeast Komagataella phaffii. First, we tested different expression levels of TIR1 for auxin-induced degradation of the glycerol kinase Gut1. Moderate expression of TIR1 resulted in complete degradation of the target protein within several minutes. Second, we show that the absence of all three Wsc type sensors is detrimental to cell growth, which indicates that these are the dominant cell wall sensors this yeast. Third, down-regulation of Erg1, an essential enzyme of the ergosterol biosynthetic pathway, resulted in quick and efficient accumulation of squalene, a pharmaceutically relevant reagent. We conclude that AID is an extremely powerful tool that, for the first time, enables the analysis of gene essentiality and function in K. phaffii. Conditional AID mutants are generated in Komagataella phaffii expressing OsTIR1 Target proteins fused to AID are depleted rapidly on the addition of auxin The deletion of all three Wsc-type severely reduces the growth of K. phaffii Cells degrading Erg1 quickly and efficiently accumulated squalene
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Affiliation(s)
- Leonie Lehmayer
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/II, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Lukas Bernauer
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/II, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Anita Emmerstorfer-Augustin
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/II, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- acib - Austrian Centre of Industrial Biotechnology, 8010 Graz, Austria
- Corresponding author
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7
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Liu Z, Yu K, Wu S, Weng X, Luo S, Zeng M, Wang X, Hu X. Comparative lipidomics of methanol induced Pichia pastoris cells at different culture phases uncovers the diversity and variability of lipids. Enzyme Microb Technol 2022; 160:110090. [DOI: 10.1016/j.enzmictec.2022.110090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/26/2022]
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8
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Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183896. [PMID: 35217000 DOI: 10.1016/j.bbamem.2022.183896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]
Abstract
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
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Affiliation(s)
- Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S Brown
- University of Guelph, Department of Physics, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany.
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9
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König S, Gömann J, Zienkiewicz A, Zienkiewicz K, Meldau D, Herrfurth C, Feussner I. Sphingolipid-Induced Programmed Cell Death is a Salicylic Acid and EDS1-Dependent Phenotype in Arabidopsis Fatty Acid Hydroxylase (Fah1, Fah2) and Ceramide Synthase (Loh2) Triple Mutants. PLANT & CELL PHYSIOLOGY 2022; 63:317-325. [PMID: 34910213 PMCID: PMC8917834 DOI: 10.1093/pcp/pcab174] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Ceramides (Cers) and long-chain bases (LCBs) are plant sphingolipids involved in the induction of plant programmed cell death (PCD). The fatty acid hydroxylase mutant fah1 fah2 exhibits high Cer levels and moderately elevated LCB levels. Salicylic acid glucoside level is increased in this mutant, but no cell death can be detected by trypan blue staining. To determine the effect of Cers with different chain lengths, fah1 fah2 was crossed with ceramide synthase mutants longevity assurance gene one homologue1-3 (loh1, loh2 and loh3). Surprisingly, only triple mutants with loh2 show cell death detected by trypan blue staining under the selected conditions. Sphingolipid profiling revealed that the greatest differences between the triple mutant plants are in the LCB and LCB-phosphate (LCB-P) fraction. fah1 fah2 loh2 plants accumulate LCB d18:0, LCB t18:0 and LCB-P d18:0. Crossing fah1 fah2 loh2 with the salicylic acid (SA) synthesis mutant sid2-2 and with the SA signaling mutants enhanced disease susceptibility 1-2 (eds1-2) and phytoalexin deficient 4-1 (pad4-1) revealed that lesions are SA- and EDS1-dependent. These quadruple mutants also confirm that there may be a feedback loop between SA and sphingolipid metabolism as they accumulated less Cers and LCBs. In conclusion, PCD in fah1 fah2 loh2 is a SA- and EDS1-dependent phenotype, which is likely due to accumulation of LCBs.
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Affiliation(s)
- Stefanie König
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
| | - Jasmin Gömann
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
| | | | | | - Dorothea Meldau
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
| | - Cornelia Herrfurth
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
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10
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Schoeny H, Rampler E, Binh Chu D, Schoeberl A, Galvez L, Blaukopf M, Kosma P, Koellensperger G. Achieving Absolute Molar Lipid Concentrations: A Phospholipidomics Cross-Validation Study. Anal Chem 2022; 94:1618-1625. [PMID: 35025205 PMCID: PMC8792901 DOI: 10.1021/acs.analchem.1c03743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/05/2022] [Indexed: 01/28/2023]
Abstract
Standardization is essential in lipidomics and part of a huge community effort. However, with the still ongoing lack of reference materials, benchmarking quantification is hampered. Here, we propose traceable lipid class quantification as an important layer for the validation of quantitative lipidomics workflows. 31P nuclear magnetic resonance (NMR) and inductively coupled plasma (ICP)-mass spectrometry (MS) can use certified species-unspecific standards to validate shotgun or liquid chromatography (LC)-MS-based lipidomics approaches. We further introduce a novel lipid class quantification strategy based on lipid class separation and mass spectrometry using an all ion fragmentation (AIF) approach. Class-specific fragments, measured over a mass range typical for the lipid classes, are integrated to assess the lipid class concentration. The concept proved particularly interesting as low absolute limits of detection in the fmol range were achieved and LC-MS platforms are widely used in the field of lipidomics, while the accessibility of NMR and ICP-MS is limited. Using completely independent calibration strategies, the introduced validation scheme comprised the quantitative assessment of the complete phospholipid sub-ome, next to the individual lipid classes. Komagataella phaffii served as a prime example, showcasing mass balances and supporting the value of benchmarks for quantification at the lipid species level.
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Affiliation(s)
- Harald Schoeny
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Evelyn Rampler
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
- Vienna
Metabolomics Center (VIME), University of
Vienna, Althanstraße
14, 1090 Vienna, Austria
- Chemistry
Meets Microbiology, Althanstraße
14, 1090 Vienna, Austria
| | - Dinh Binh Chu
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
- School
of Chemical Engineering, Hanoi University
of Science and Technology, 1 Dai Co Viet, Hai Ba Trung, Hanoi 100000, Vietnam
| | - Anna Schoeberl
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Luis Galvez
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Markus Blaukopf
- Department
of Chemistry, University of Natural Resources
and Life Sciences Vienna, 1190 Vienna, Austria
| | - Paul Kosma
- Department
of Chemistry, University of Natural Resources
and Life Sciences Vienna, 1190 Vienna, Austria
| | - Gunda Koellensperger
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
- Vienna
Metabolomics Center (VIME), University of
Vienna, Althanstraße
14, 1090 Vienna, Austria
- Chemistry
Meets Microbiology, Althanstraße
14, 1090 Vienna, Austria
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11
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A Gas Chromatography-Mass Spectrometry Method for the Determination of Fatty Acids and Sterols in Yeast and Grape Juice. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11115152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lipids are essential components of all living cells. In an oenological context, the supply of unsaturated lipids in grape juice allows the yeasts to grow and ferment, despite very low levels of oxygen. The current study proposes a systematic optimization procedure for the analysis of fatty acids and sterols relevant to the grape fermentation process, including both extracellular and intracellular (i.e., yeast cells) lipids. Even though it was extensive, the sample preparation yielded reproducible results for all compounds of interest. The stability of the analyzed compounds was also tested to offer some implementation flexibility for the extensive procedure. The performance parameters (i.e., selectivity, linearity, limit of detection and quantitation, accuracy, and precision) indicated that the method was suitable for future practical implementation. The proof of concept also suggests that the list of compounds of interest can be expanded if additional peaks are identified. Given the large variation in concentrations, the dilution of the matrix needs to be carefully considered in order to ensure that the lipids of interest are still within the dynamic range and not below the limit of detection and/or quantification.
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12
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Yeast Cells in Microencapsulation. General Features and Controlling Factors of the Encapsulation Process. Molecules 2021; 26:molecules26113123. [PMID: 34073703 PMCID: PMC8197184 DOI: 10.3390/molecules26113123] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Besides their best-known uses in the food and fermentation industry, yeasts have also found application as microcapsules. In the encapsulation process, exogenous and most typically hydrophobic compounds diffuse and end up being passively entrapped in the cell body, and can be released upon application of appropriate stimuli. Yeast cells can be employed either living or dead, intact, permeabilized, or even emptied of all their original cytoplasmic contents. The main selling points of this set of encapsulation technologies, which to date has predominantly targeted food and-to a lesser extent-pharmaceutical applications, are the low cost, biodegradability and biocompatibility of the capsules, coupled to their sustainable origin (e.g., spent yeast from brewing). This review aims to provide a broad overview of the different kinds of yeast-based microcapsules and of the main physico-chemical characteristics that control the encapsulation process and its efficiency.
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13
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Valli M, Grillitsch K, Grünwald-Gruber C, Tatto NE, Hrobath B, Klug L, Ivashov V, Hauzmayer S, Koller M, Tir N, Leisch F, Gasser B, Graf AB, Altmann F, Daum G, Mattanovich D. A subcellular proteome atlas of the yeast Komagataella phaffii. FEMS Yeast Res 2021; 20:5700286. [PMID: 31922548 PMCID: PMC6981350 DOI: 10.1093/femsyr/foaa001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
The compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.
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Affiliation(s)
- Minoska Valli
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Karlheinz Grillitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Nadine E Tatto
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Bernhard Hrobath
- Institute of Statistics, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - Lisa Klug
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Vasyl Ivashov
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Sandra Hauzmayer
- School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Martina Koller
- School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Nora Tir
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Friedrich Leisch
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Statistics, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Günther Daum
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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14
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Heymich ML, Nißl L, Hahn D, Noll M, Pischetsrieder M. Antioxidative, Antifungal and Additive Activity of the Antimicrobial Peptides Leg1 and Leg2 from Chickpea. Foods 2021; 10:foods10030585. [PMID: 33799496 PMCID: PMC7998185 DOI: 10.3390/foods10030585] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 01/29/2023] Open
Abstract
The fight against food waste benefits from novel agents inhibiting spoilage. The present study investigated the preservative potential of the antimicrobial peptides Leg1 (RIKTVTSFDLPALRFLKL) and Leg2 (RIKTVTSFDLPALRWLKL) recently identified in chickpea legumin hydrolysates. Checkerboard assays revealed strong additive antimicrobial effects of Leg1/Leg2 with sodium benzoate against Escherichia coli and Bacillus subtilis with fractional inhibitory concentrations of 0.625 and 0.75. Additionally, Leg1/Leg2 displayed antifungal activity with minimum inhibitory concentrations of 500/250 µM against Saccharomyces cerevisiae and 250/125 µM against Zygosaccharomyces bailii. In contrast, no cytotoxic effects were observed against human Caco-2 cells at concentrations below 2000 µM (Leg1) and 1000 µM (Leg2). Particularly Leg2 showed antioxidative activity by radical scavenging and reducing mechanisms (maximally 91.5/86.3% compared to 91.2/94.7% for the control ascorbic acid). The present results demonstrate that Leg1/Leg2 have the potential to be applied as preservatives protecting food and other products against bacterial, fungal and oxidative spoilage.
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Affiliation(s)
- Marie-Louise Heymich
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany; (M.-L.H.); (D.H.)
| | - Laura Nißl
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, Friedrich-Streib-Str. 2, 96450 Coburg, Germany; (L.N.); (M.N.)
| | - Dominik Hahn
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany; (M.-L.H.); (D.H.)
| | - Matthias Noll
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, Friedrich-Streib-Str. 2, 96450 Coburg, Germany; (L.N.); (M.N.)
| | - Monika Pischetsrieder
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany; (M.-L.H.); (D.H.)
- Correspondence:
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15
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Rampler E, Hermann G, Grabmann G, El Abiead Y, Schoeny H, Baumgartinger C, Köcher T, Koellensperger G. Benchmarking Non-Targeted Metabolomics Using Yeast-Derived Libraries. Metabolites 2021; 11:metabo11030160. [PMID: 33802096 PMCID: PMC7998801 DOI: 10.3390/metabo11030160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/01/2021] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
Non-targeted analysis by high-resolution mass spectrometry (HRMS) is an essential discovery tool in metabolomics. To date, standardization and validation remain a challenge. Community-wide accepted cost-effective benchmark materials are lacking. In this work, we propose yeast (Pichia pastoris) extracts derived from fully controlled fermentations for this purpose. We established an open-source metabolite library of >200 identified metabolites based on compound identification by accurate mass, matching retention times, and MS/MS, as well as a comprehensive literature search. The library includes metabolites from the classes of (1) organic acids and derivatives (2) nucleosides, nucleotides, and analogs, (3) lipids and lipid-like molecules, (4) organic oxygen compounds, (5) organoheterocyclic compounds, (6) organic nitrogen compounds, and (7) benzoids at expected concentrations ranges of sub-nM to µM. As yeast is a eukaryotic organism, key regulatory elements are highly conserved between yeast and all annotated metabolites were also reported in the human metabolome database (HMDB). Orthogonal state-of-the-art reversed-phase (RP-) and hydrophilic interaction chromatography mass spectrometry (HILIC-MS) non-targeted analysis and authentic standards revealed that 104 out of the 206 confirmed metabolites were reproducibly recovered and stable over the course of three years when stored at −80 °C. Overall, 67 out of these 104 metabolites were identified with comparably stable areas over all three yeast fermentation and are the ideal starting point for benchmarking experiments. The provided yeast benchmark material enabled not only to test for the chemical space and coverage upon method implementation and developments but also allowed in-house routines for instrumental performance tests. Transferring the quality control strategy of proteomics workflows based on the number of protein identification in HeLa extracts, metabolite IDs in the yeast benchmarking material can be used as metabolomics quality control. Finally, the benchmark material opens new avenues for batch-to-batch corrections in large-scale non-targeted metabolomics studies.
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Affiliation(s)
- Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
- ISOtopic Solutions, Währinger Str. 38, 1090 Vienna, Austria
| | - Gerlinde Grabmann
- Metabolomics Core Facility, Vienna BioCenter Core Facilities, Dr.-Bohr-Gasse 3, 1030 Vienna, Austria; (G.G.); (T.K.)
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
| | - Christoph Baumgartinger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
| | - Thomas Köcher
- Metabolomics Core Facility, Vienna BioCenter Core Facilities, Dr.-Bohr-Gasse 3, 1030 Vienna, Austria; (G.G.); (T.K.)
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Correspondence:
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16
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Mbuyane LL, Bauer FF, Divol B. The metabolism of lipids in yeasts and applications in oenology. Food Res Int 2021; 141:110142. [PMID: 33642009 DOI: 10.1016/j.foodres.2021.110142] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/26/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
Abstract
Lipids are valuable compounds present in all living organisms, which display an array of functions related to compartmentalization, energy storage and enzyme activation. Furthermore, these compounds are an integral part of the plasma membrane which is responsible for maintaining structure, facilitating the transport of solutes in and out of the cell and cellular signalling necessary for cell survival. The lipid composition of the yeast Saccharomyces cerevisiae has been extensively investigated and the impact of lipids on S. cerevisiae cellular functions during wine alcoholic fermentation is well documented. Although other yeast species are currently used in various industries and are receiving increasing attention in winemaking, little is known about their lipid metabolism. This review article provides an extensive and critical evaluation of our knowledge on the biosynthesis, accumulation, metabolism and regulation of fatty acids and sterols in yeasts. The implications of the yeast lipid content on stress resistance as well as performance during alcoholic fermentation are discussed and a particular emphasis is given on non-Saccharomyces yeasts. Understanding lipid requirements and metabolism in non-Saccharomyces yeasts may lead to a better management of these yeast to enhance their contributions to wine properties.
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Affiliation(s)
- Lethiwe Lynett Mbuyane
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Florian Franz Bauer
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Benoit Divol
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa.
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17
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Bernauer L, Radkohl A, Lehmayer LGK, Emmerstorfer-Augustin A. Komagataella phaffii as Emerging Model Organism in Fundamental Research. Front Microbiol 2021; 11:607028. [PMID: 33505376 PMCID: PMC7829337 DOI: 10.3389/fmicb.2020.607028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/14/2020] [Indexed: 01/11/2023] Open
Abstract
Komagataella phaffii (Pichia pastoris) is one of the most extensively applied yeast species in pharmaceutical and biotechnological industries, and, therefore, also called the biotech yeast. However, thanks to more advanced strain engineering techniques, it recently started to gain attention as model organism in fundamental research. So far, the most studied model yeast is its distant cousin, Saccharomyces cerevisiae. While these data are of great importance, they limit our knowledge to one organism only. Since the divergence of the two species 250 million years ago, K. phaffii appears to have evolved less rapidly than S. cerevisiae, which is why it remains more characteristic of the common ancient yeast ancestors and shares more features with metazoan cells. This makes K. phaffii a valuable model organism for research on eukaryotic molecular cell biology, a potential we are only beginning to fully exploit. As methylotrophic yeast, K. phaffii has the intriguing property of being able to efficiently assimilate methanol as a sole source of carbon and energy. Therefore, major efforts have been made using K. phaffii as model organism to study methanol assimilation, peroxisome biogenesis and pexophagy. Other research topics covered in this review range from yeast genetics including mating and sporulation behavior to other cellular processes such as protein secretion, lipid biosynthesis and cell wall biogenesis. In this review article, we compare data obtained from K. phaffii with S. cerevisiae and other yeasts whenever relevant, elucidate major differences, and, most importantly, highlight the big potential of using K. phaffii in fundamental research.
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Affiliation(s)
- Lukas Bernauer
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
| | - Astrid Radkohl
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
| | | | - Anita Emmerstorfer-Augustin
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
- acib—Austrian Centre of Industrial Biotechnology, Graz, Austria
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18
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Abstract
The plant lipidome is highly complex and changes dynamically under the influence of various biotic and abiotic stresses. Targeted analyses based on mass spectrometry enable the detection and characterization of the plant lipidome. It can be analyzed in plant tissues of different developmental stages and from isolated cellular organelles and membranes. Here, we describe a sensitive method to establish the relative abundance of molecular lipid species belonging to three lipid categories: glycerolipids, sphingolipids, and sterol lipids. The method is based on a monophasic lipid extraction and includes the derivatization of a few rare and low-abundant lipid classes. The molecular lipid species are resolved by lipid class-specific reverse-phase liquid chromatography and detected by nanoelectrospray ionization coupled with tandem mass spectrometry. The triple quadrupole analyzer is used for detection with multiple reaction monitoring (MRM). Mass transition lists are constructed based on the knowledge of organism-specific lipid building blocks. They are initially determined by classical lipid analytical methods and then used for combinative assembly of all possible lipid structures. The targeted analysis enables detailed and comprehensive profiling of the entire lipid content and composition of plants.
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19
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Luchini A, Vitiello G. Mimicking the Mammalian Plasma Membrane: An Overview of Lipid Membrane Models for Biophysical Studies. Biomimetics (Basel) 2020; 6:biomimetics6010003. [PMID: 33396534 PMCID: PMC7838988 DOI: 10.3390/biomimetics6010003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023] Open
Abstract
Cell membranes are very complex biological systems including a large variety of lipids and proteins. Therefore, they are difficult to extract and directly investigate with biophysical methods. For many decades, the characterization of simpler biomimetic lipid membranes, which contain only a few lipid species, provided important physico-chemical information on the most abundant lipid species in cell membranes. These studies described physical and chemical properties that are most likely similar to those of real cell membranes. Indeed, biomimetic lipid membranes can be easily prepared in the lab and are compatible with multiple biophysical techniques. Lipid phase transitions, the bilayer structure, the impact of cholesterol on the structure and dynamics of lipid bilayers, and the selective recognition of target lipids by proteins, peptides, and drugs are all examples of the detailed information about cell membranes obtained by the investigation of biomimetic lipid membranes. This review focuses specifically on the advances that were achieved during the last decade in the field of biomimetic lipid membranes mimicking the mammalian plasma membrane. In particular, we provide a description of the most common types of lipid membrane models used for biophysical characterization, i.e., lipid membranes in solution and on surfaces, as well as recent examples of their applications for the investigation of protein-lipid and drug-lipid interactions. Altogether, promising directions for future developments of biomimetic lipid membranes are the further implementation of natural lipid mixtures for the development of more biologically relevant lipid membranes, as well as the development of sample preparation protocols that enable the incorporation of membrane proteins in the biomimetic lipid membranes.
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Affiliation(s)
- Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark;
| | - Giuseppe Vitiello
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
- CSGI-Center for Colloid and Surface Science, via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
- Correspondence:
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20
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Luchini A, Sebastiani F, Tidemand FG, Batchu KC, Campana M, Fragneto G, Cárdenas M, Arleth L. Peptide discs as precursors of biologically relevant supported lipid bilayers. J Colloid Interface Sci 2020; 585:376-385. [PMID: 33307306 DOI: 10.1016/j.jcis.2020.11.086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022]
Abstract
Supported lipid bilayers (SLBs) are commonly used to investigate the structure and dynamics of biological membranes. Vesicle fusion is a widely exploited method to produce SLBs. However, this process becomes less favoured when the vesicles contain complex lipid mixtures, e.g. natural lipid extracts. In these cases, it is often necessary to change experimental parameters, such as temperature, to unphysiological values to trigger the SLB formation. This may induce lipid degradation and is also not compatible with including membrane proteins or other biomolecules into the bilayers. Here, we show that the peptide discs, ~10 nm discoidal lipid bilayers stabilized in solution by a self-assembled 18A peptide belt, can be used as precursors for SLBs. The characterizations by means of neutron reflectometry and attenuated total reflectance-FTIR spectroscopy show that SLBs were successfully formed both from synthetic lipid mixtures (surface coverage 90-95%) and from natural lipid mixtures (surface coverage ~85%). Traces of 18A peptide (below 0.02 M ratio) left at the support surface after the bilayer formation do not affect the SLB structure. Altogether, we demonstrate that peptide disc formation of SLBs is much faster than the SLB formation by vesicle fusion and without the need of altering any experimental variable from physiologically relevant values.
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Affiliation(s)
- Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
| | - Federica Sebastiani
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, Per Albin Hanssons Väg 35, 21432 Malmö, Sweden
| | | | | | - Mario Campana
- ISIS-STFC, Rutherford Appleton Laboratory, Chilton, Oxon OX11 0QX, United Kingdom
| | - Giovanna Fragneto
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Marité Cárdenas
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, Per Albin Hanssons Väg 35, 21432 Malmö, Sweden
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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21
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Križanović S, Stanzer D, Mrvčić J, Hanousek-Čiča K, Kralj E, Čanadi Jurešić G. Lipid Composition of Sheffersomyces stipitis M12 Strain Grown on Glycerol as a Carbon Source. Food Technol Biotechnol 2020; 58:203-213. [PMID: 32831572 PMCID: PMC7416122 DOI: 10.17113/ftb.58.02.20.6540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Research background In this study the content and composition of lipids in ergosterol-reduced Sheffersomyces stipitis M12 strain grown on glycerol as a carbon source is determined. Blocking the ergosterol synthesis route in yeast cells is a recently proposed method for increasing S-adenosyl-l-methionine (SAM) production. Experimental approach The batch cultivation of M12 yeast was carried out under aerobic conditions in a laboratory bioreactor with glycerol as carbon source, and with pulsed addition of methionine. Glycerol and SAM content were monitored by high-performance liquid chromatography, while fatty acid composition of different lipid classes, separated by solid phase extraction, was determined by gas chromatography. Results and conclusion Despite the reduced amount of ergosterol in yeast cells, thanks to the reorganized lipid metabolism, M12 strain achieved high biomass yield and SAM production. Neutral lipids prevailed (making more than 75% of total lipids), but their content and composition differed significantly in the two tested types of yeast. Unsaturated and C18 fatty acids prevailed in both the M12 strain and wild type. In all fractions except free fatty acids, the index of unsaturation in M12 strain was lower than in the wild strain. Our tested strain adjusts itself by changing the content of lipids (mainly phospholipids, sterols and sterol esters), and with desaturation adjustments, to maintain proper functioning and fulfil increased energy needs. Novelty and scientific contribution Reorganization of S. stipitis lipid composition caused by blocking the metabolic pathway of ergosterol synthesis was presented. A simple scheme of actual lipid metabolism during active SAM production in S. stipitis, grown on glycerol was constructed and shown. This fundamental knowledge of lipid metabolic pathways will be a helpful tool in improving S. stipitis as an expression host and a model organism, opening new perspectives for its applied research.
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Affiliation(s)
- Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Damir Stanzer
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jasna Mrvčić
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Karla Hanousek-Čiča
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Elizabeta Kralj
- Karlovac University of Applied Science, Trg Josipa Jurja Strossmayera 9, 47000 Karlovac, Croatia
| | - Gordana Čanadi Jurešić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia
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22
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CD81 extracted in SMALP nanodiscs comprises two distinct protein populations within a lipid environment enriched with negatively charged headgroups. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183419. [PMID: 32735789 PMCID: PMC7456796 DOI: 10.1016/j.bbamem.2020.183419] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/05/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Tetraspanins exert a wide range of cellular functions of broad medical importance. Despite this, their biophysical characteristics are incompletely understood. Only two high-resolution structures of full-length tetraspanins have been solved. One is that of human CD81, which is involved in the infectivity of human pathogens including influenza, HIV, the malarial Plasmodium parasite and hepatitis C virus (HCV). The CD81 crystal structure identifies a cholesterol-binding pocket, which has been suggested to be important in the regulation of tetraspanin function. Here we investigate the use of styrene-maleic anhydride co-polymers (SMA) for the solubilisation and purification of CD81 within a lipid environment. When CD81 was expressed in the yeast Pichia pastoris, it could be solubilised and purified using SMA2000. This SMALP-encapsulated CD81 retained its native folded structure, as determined by the binding of two conformation-sensitive anti-CD81 antibodies. Analysis by size exclusion chromatography revealed two distinct populations of CD81, only one of which bound the HCV glycoprotein, E2. Optimization of expression and buffer conditions increased the proportion of E2-binding competent CD81 protein. Mass spectrometry analysis indicated that the lipid environment surrounding CD81 is enriched with negatively charged lipids. These results establish a platform to study the influence of protein-lipid interactions in tetraspanin biology. CD81 expressed in Pichia pastoris can be solubilised and purified using SMA polymer. SMALP-encapsulated CD81 retains native folded structure. Expression and buffer conditions can be optimized to improve protein quality. The lipid environment surrounding CD81 is enriched with negatively charged lipids.
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23
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Knittelfelder O, Prince E, Sales S, Fritzsche E, Wöhner T, Brankatschk M, Shevchenko A. Sterols as dietary markers for Drosophila melanogaster. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158683. [DOI: 10.1016/j.bbalip.2020.158683] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 11/16/2022]
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24
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Schoeny H, Rampler E, Hermann G, Grienke U, Rollinger JM, Koellensperger G. Preparative supercritical fluid chromatography for lipid class fractionation-a novel strategy in high-resolution mass spectrometry based lipidomics. Anal Bioanal Chem 2020; 412:2365-2374. [PMID: 32130438 PMCID: PMC7118041 DOI: 10.1007/s00216-020-02463-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/08/2020] [Accepted: 01/28/2020] [Indexed: 01/01/2023]
Abstract
In this work, a lipidomics workflow based on offline semi-preparative lipid class-specific fractionation by supercritical fluid chromatography (SFC) followed by high-resolution mass spectrometry was introduced. The powerful SFC approach offered separation of a wide polarity range for lipids, enabled enrichment (up to 3 orders of magnitude) of lipids, selective fractionation of 14 lipid classes/subclasses, and increased dynamic range enabling in-depth characterization. A significantly increased coverage of low abundant lipids improving lipid identification by numbers and degree (species and molecular level) was obtained in Pichia pastoris when comparing high-resolution mass spectrometry based lipidomics with and without prior fractionation. Proof-of-principle experiments using a standard reference material (SRM 1950, NIST) for human plasma showed that the proposed strategy enabled quantitative lipidomics. Indeed, for 70 lipids, the consensus values available for this sample could be met. Thus, the novel workflow is ideally suited for lipid class-specific purification/isolation from milligram amounts of sample while not compromising on omics type of analysis (identification and quantification). Finally, compared with established fractionation/pre-concentration approaches, semi-preparative SFC is superior in terms of versatility, as it involved only volatile modifiers and salt additives facilitating any follow-up use such as qualitative or quantitate analysis or further purification down to the single lipid species level. Graphical Abstract.
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Affiliation(s)
- Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Chemistry Meets Microbiology, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
- ISOtopic Solutions, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Ulrike Grienke
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Pharmacognosy, Faculty of Life Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Judith M Rollinger
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Pharmacognosy, Faculty of Life Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Chemistry Meets Microbiology, Althanstrasse 14, 1090, Vienna, Austria.
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25
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Zienkiewicz A, Gömann J, König S, Herrfurth C, Liu YT, Meldau D, Feussner I. Disruption of Arabidopsis neutral ceramidases 1 and 2 results in specific sphingolipid imbalances triggering different phytohormone-dependent plant cell death programmes. THE NEW PHYTOLOGIST 2020; 226:170-188. [PMID: 31758808 DOI: 10.1111/nph.16336] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/18/2019] [Indexed: 05/05/2023]
Abstract
Sphingolipids act as regulators of programmed cell death (PCD) and the plant defence response. The homeostasis between long-chain base (LCB) and ceramide (Cer) seems to play an important role in executions of PCD. Therefore, deciphering the role of neutral ceramidases (NCER) is crucial to identify the sphingolipid compounds that trigger and execute PCD. We performed comprehensive sphingolipid and phytohormone analyses of Arabidopsis ncer mutants, combined with gene expression profiling and microscopic analyses. While ncer1 exhibited early leaf senescence (developmentally controlled PCD - dPCD) and an increase in hydroxyceramides, ncer2 showed spontaneous cell death (pathogen-triggered PCD-like - pPCD) accompanied by an increase in LCB t18:0 at 35 d, respectively. Loss of NCER1 function resulted in accumulation of jasmonoyl-isoleucine (JA-Ile) in the leaves, whereas disruption of NCER2 was accompanied by higher levels of salicylic acid (SA) and increased sensitivity to Fumonisin B1 (FB1 ). All mutants were also found to activate plant defence pathways. These data strongly suggest that NCER1 hydrolyses ceramides whereas NCER2 functions as a ceramide synthase. Our results reveal an important role of NCER in the regulation of both dPCD and pPCD via a tight connection between the phytohormone and sphingolipid levels in these two processes.
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Affiliation(s)
- Agnieszka Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100, Toruń, Poland
| | - Jasmin Gömann
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
| | - Stefanie König
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077, Goettingen, Germany
| | - Yi-Tse Liu
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
| | - Dorothea Meldau
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077, Goettingen, Germany
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26
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Luchini A, Delhom R, Cristiglio V, Knecht W, Wacklin-Knecht H, Fragneto G. Effect of ergosterol on the interlamellar spacing of deuterated yeast phospholipid multilayers. Chem Phys Lipids 2020; 227:104873. [PMID: 31926858 DOI: 10.1016/j.chemphyslip.2020.104873] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/14/2019] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
Sterols regulate several physico-chemical properties of biological membranes that are considered to be linked to function. Ergosterol is the main sterol molecule found in the cell membranes of yeasts and other fungi. Like the cholesterol found in mammalian cells, ergosterol has been proposed to have an ordering and condensing effect on saturated phospholipid membranes. The effects of cholesterol have been investigated extensively and result in an increase in the membrane thickness and the lipid acyl chain order. Less information is available on the effects of ergosterol on phospholipid membranes. Neutron Diffraction (ND) was used to characterize the effect of ergosterol on lipid multilayers prepared with deuterated natural phospholipids extracted from the yeast Pichia pastoris. The data show that the effect of ergosterol on membranes prepared from the natural phospholipid extract rich in unsaturated acyl chains, differs from what has been observed previously in membranes rich in saturated phospholipids. In contrast to cholesterol in synthetic phospholipid membranes, the presence of ergosterol up to 30 mol % in yeast phospholipid membranes only slightly altered the multilayer structure. In particular, only a small decrease in the multilayer d-spacing was observed as function of increasing ergosterol concentrations. This result highlights the need for further investigation to elucidate the effects of ergosterol in biological lipid mixtures.
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Affiliation(s)
- Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, UniversiteTsparken 5, 2100 Copenhagen, Denmark.
| | - Robin Delhom
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | | | - Wolfgang Knecht
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden; Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Hanna Wacklin-Knecht
- European Spallation Source ERIC, P.O. Box 176, 22100 Lund, Sweden; Division of Physical Chemistry, Lund University, P.O.Box 124, 22100 Lund, Sweden
| | - Giovanna Fragneto
- Institut Laue-Langevin, 71 Avenue Des Martyrs, 38000, Grenoble, France.
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27
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Bui TT, Suga K, Kuhl TL, Umakoshi H. Melting-Temperature-Dependent Interactions of Ergosterol with Unsaturated and Saturated Lipids in Model Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:10640-10647. [PMID: 31310548 DOI: 10.1021/acs.langmuir.9b01538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sterols such as cholesterol (Chol) and ergosterol (Erg) are known to regulate membrane properties in higher eukaryotes and in lower eukaryotes, respectively. To better understand the modulation of membrane properties by Erg, binary lipid membranes composed of Erg and diacylglycerophosphocholine (PC) were studied in Langmuir monolayer and bilayer vesicle systems. From the excess area measured by pressure-area isotherms, attractive interactions between Erg and saturated PC were significant above the melting temperature (Tm) of PC. Conversely, repulsive interactions were observed at temperatures below Tm. From the analyses of membrane fluidity and polarity using fluorescence probes, similar trends were observed for bilayer systems where Erg had an ordering effect on saturated PC vesicles in the fluid state. However, Chol had a stronger ordering effect than Erg. In unsaturated PC systems, Erg did not alter membrane ordering. These findings demonstrate that the interaction of Erg with the fluid-state PC lipids will maintain lower-eukaryote membranes in a more ordered state, similar to the effect of cholesterol in higher eukaryotes.
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Affiliation(s)
- Tham Thi Bui
- Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama-cho , Toyonaka , Osaka 560-8531 , Japan
| | - Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama-cho , Toyonaka , Osaka 560-8531 , Japan
| | | | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama-cho , Toyonaka , Osaka 560-8531 , Japan
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28
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Fabri JHTM, Godoy NL, Rocha MC, Munshi M, Cocio TA, von Zeska Kress MR, Fill TP, da Cunha AF, Del Poeta M, Malavazi I. The AGC Kinase YpkA Regulates Sphingolipids Biosynthesis and Physically Interacts With SakA MAP Kinase in Aspergillus fumigatus. Front Microbiol 2019; 9:3347. [PMID: 30692984 PMCID: PMC6339957 DOI: 10.3389/fmicb.2018.03347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/28/2018] [Indexed: 12/12/2022] Open
Abstract
Sphingolipids (SL) are complex lipids and components of the plasma membrane which are involved in numerous cellular processes, as well as important for virulence of different fungal pathogens. In yeast, SL biosynthesis is regulated by the "AGC kinases" Ypk1 and Ypk2, which also seem to connect the SL biosynthesis with the cell wall integrity (CWI) and the High Osmolarity Glycerol (HOG) pathways. Here, we investigate the role of ypkA Y PK1 in SL biosynthesis and its relationship with the CWI and the HOG pathways in the opportunistic human pathogen Aspergillus fumigatus. We found that ypkA is important for fungal viability, since the ΔypkA strain presented a drastically sick phenotype and complete absence of conidiation. We observed that under repressive condition, the conditional mutant niiA::ypkA exhibited vegetative growth defects, impaired germination and thermosensitivity. In addition, the ypkA loss of function caused a decrease in glycosphingolipid (GSL) levels, especially the metabolic intermediates belonging to the neutral GSL branch including dihydroceramide (DHC), ceramide (Cer), and glucosylceramide (GlcCer), but interestingly a small increase in ergosterol content. Genetic analyzes showed that ypkA genetically interacts with the MAP kinases of CWI and HOG pathways, mpkA and sakA, respectively, while only SakA physically interacts with YpkA. Our results suggest that YpkA is important for fungal survival through the regulation of GSL biosynthesis and cross talks with A. fumigatus MAP kinase pathways.
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Affiliation(s)
| | - Naiane Lima Godoy
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marina Campos Rocha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Mansa Munshi
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, United States
| | - Tiago Alexandre Cocio
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marcia Regina von Zeska Kress
- Departamento de Análises Clínicas Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - Anderson Ferreira da Cunha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, United States.,Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, NY, United States.,Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States.,Veterans Administration Medical Center, Northport, NY, United States
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
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29
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Yu D, Rupasinghe TW, Boughton BA, Natera SH, Hill CB, Tarazona P, Feussner I, Roessner U. A high-resolution HPLC-QqTOF platform using parallel reaction monitoring for in-depth lipid discovery and rapid profiling. Anal Chim Acta 2018; 1026:87-100. [DOI: 10.1016/j.aca.2018.03.062] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 02/07/2023]
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30
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Rampler E, Schoeny H, Mitic BM, El Abiead Y, Schwaiger M, Koellensperger G. Simultaneous non-polar and polar lipid analysis by on-line combination of HILIC, RP and high resolution MS. Analyst 2018; 143:1250-1258. [PMID: 29431763 DOI: 10.1039/c7an01984j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Given the chemical diversity of lipids and their biological relevance, suitable methods for lipid profiling and quantification are demanded to reduce sample complexity and analysis times. In this work, we present a novel on-line chromatographic method coupling hydrophilic interaction liquid chromatography (HILIC) dedicated to class-specific separation of polar lipid to reversed-phase chromatography (RP) for non-polar lipid analysis. More specifically, the void volume of the HILIC separation-consisting of non-polar lipids- is transferred to the orthogonal RP column enabling the on-line combination of HILIC with RP without any dilution in the second dimension. In this setup the orthogonal HILIC and RP separations were performed in parallel and the effluents of both columns were combined prior to high-resolution MS detection, offering the full separation space in one analytical run. Rapid separation for both polar and non-polar lipids within only 15 min (including reequilibration time) was enabled using sub-2 μm particles and UHPLC. The method proved to be robust with excellent retention time stability (RSDs < 1%) and LODs in the fmol to pmol (absolute on column) range even in the presence of complex biological matrix such as human plasma. The presented high-resolution LC-MS/MS method leads to class-specific separation of polar lipids and separation of non-polar lipids which is lost in conventional HILIC separations. HILIC-RP-MS is a promising tool for targeted and untargeted lipidomics workflows as three interesting features are combined namely (1) the decreased run time of state of the art shotgun MS methods, (2) the elevated linear dynamic range inherent to chromatographic separation and (3) increased level of identification by separation of polar and non-polar lipid classes.
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Affiliation(s)
- Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria.
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31
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Rampler E, Criscuolo A, Zeller M, El Abiead Y, Schoeny H, Hermann G, Sokol E, Cook K, Peake DA, Delanghe B, Koellensperger G. A Novel Lipidomics Workflow for Improved Human Plasma Identification and Quantification Using RPLC-MSn Methods and Isotope Dilution Strategies. Anal Chem 2018; 90:6494-6501. [PMID: 29708737 DOI: 10.1021/acs.analchem.7b05382] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lipid identification and quantification are essential objectives in comprehensive lipidomics studies challenged by the high number of lipids, their chemical diversity, and their dynamic range. In this work, we developed a tailored method for profiling and quantification combining (1) isotope dilution, (2) enhanced isomer separation by C30 fused-core reversed-phase material, and (3) parallel Orbitrap and ion trap detection by the Orbitrap Fusion Lumos Tribid mass spectrometer. The combination of parallelizable ion analysis without time loss together with different fragmentation techniques (HCD/CID) and an inclusion list led to higher quality in lipid identifications exemplified in human plasma and yeast samples. Moreover, we used lipidome isotope-labeling of yeast (LILY)-a fast and efficient in vivo labeling strategy in Pichia pastoris-to produce (nonradioactive) isotopically labeled eukaryotic lipid standards in yeast. We integrated the 13C lipids in the LC-MS workflow to enable relative and absolute compound-specific quantification in yeast and human plasma samples by isotope dilution. Label-free and compound-specific quantification was validated by comparison against a recent international interlaboratory study on human plasma SRM 1950. In this way, we were able to prove that LILY enabled quantification leads to accurate results, even in complex matrices. Excellent analytical figures of merit with enhanced trueness, precision and linearity over 4-5 orders of magnitude were observed applying compound-specific quantification with 13C-labeled lipids. We strongly believe that lipidomics studies will benefit from incorporating isotope dilution and LC-MSn strategies.
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Affiliation(s)
- Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,Vienna Metabolomics Center (VIME) , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria.,Chemistry Meets Microbiology , Althanstraße 14 , 1090 Vienna , Austria
| | - Angela Criscuolo
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany.,Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy , Universität Leipzig , Leipzig , Germany
| | - Martin Zeller
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,ISOtopic solutions , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Elena Sokol
- Thermo Fisher Scientific , 1 Boundary Park , Hemel Hempstead HP2 7GE , United Kingdom
| | - Ken Cook
- Thermo Fisher Scientific , 1 Boundary Park , Hemel Hempstead HP2 7GE , United Kingdom
| | - David A Peake
- Thermo Fisher Scientific , 355 River Oaks Parkway , 95134 San Jose , California United States
| | - Bernard Delanghe
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,Vienna Metabolomics Center (VIME) , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria.,Chemistry Meets Microbiology , Althanstraße 14 , 1090 Vienna , Austria
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Liu HY, Chen WL, Ober CK, Daniel S. Biologically Complex Planar Cell Plasma Membranes Supported on Polyelectrolyte Cushions Enhance Transmembrane Protein Mobility and Retain Native Orientation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1061-1072. [PMID: 29020444 DOI: 10.1021/acs.langmuir.7b02945] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Reconstituted supported lipid bilayers (SLB) are widely used as in vitro cell-surface models because they are compatible with a variety of surface-based analytical techniques. However, one of the challenges of using SLBs as a model of the cell surface is the limited complexity in membrane composition, including the incorporation of transmembrane proteins and lipid diversity that may impact the activity of those proteins. Additionally, it is challenging to preserve the transmembrane protein native orientation, function, and mobility in SLBs. Here, we leverage the interaction between cell plasma membrane vesicles and polyelectrolyte brushes to create planar bilayers from cell plasma membrane vesicles that have budded from the cell surface. This approach promotes the direct incorporation of membrane proteins and other species into the planar bilayer without using detergent or reconstitution and preserves membrane constituents. Furthermore, the structure of the polyelectrolyte brush serves as a cushion between the planar bilayer and rigid supporting surface, limiting the interaction of the cytosolic domains of membrane proteins with this surface. Single particle tracking was used to analyze the motion of GPI-linked yellow fluorescent proteins (GPI-YFP) and neon-green fused transmembrane P2X2 receptors (P2X2-neon) and shows that this platform retains over 75% mobility of multipass transmembrane proteins in its native membrane environment. An enzyme accessibility assay confirmed that the protein orientation is preserved and results in the extracellular domain facing toward the bulk phase and the cytosolic side facing the support. Because the platform presented here retains the complexity of the cell plasma membrane and preserves protein orientation and mobility, it is a better representative mimic of native cell surfaces, which may find many applications in biological assays aimed at understanding cell membrane phenomena.
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Affiliation(s)
- Han-Yuan Liu
- Robert F. Smith School of Chemical and Biomolecular Engineering, ‡Department of Material Science and Engineering, Cornell University , Ithaca, New York 14853, United States
| | - Wei-Liang Chen
- Robert F. Smith School of Chemical and Biomolecular Engineering, ‡Department of Material Science and Engineering, Cornell University , Ithaca, New York 14853, United States
| | - Christopher K Ober
- Robert F. Smith School of Chemical and Biomolecular Engineering, ‡Department of Material Science and Engineering, Cornell University , Ithaca, New York 14853, United States
| | - Susan Daniel
- Robert F. Smith School of Chemical and Biomolecular Engineering, ‡Department of Material Science and Engineering, Cornell University , Ithaca, New York 14853, United States
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Lenarčič T, Albert I, Böhm H, Hodnik V, Pirc K, Zavec AB, Podobnik M, Pahovnik D, Žagar E, Pruitt R, Greimel P, Yamaji-Hasegawa A, Kobayashi T, Zienkiewicz A, Gömann J, Mortimer JC, Fang L, Mamode-Cassim A, Deleu M, Lins L, Oecking C, Feussner I, Mongrand S, Anderluh G, Nürnberger T. Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins. Science 2018; 358:1431-1434. [PMID: 29242345 DOI: 10.1126/science.aan6874] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/31/2017] [Indexed: 01/05/2023]
Abstract
Necrosis and ethylene-inducing peptide 1-like (NLP) proteins constitute a superfamily of proteins produced by plant pathogenic bacteria, fungi, and oomycetes. Many NLPs are cytotoxins that facilitate microbial infection of eudicot, but not of monocot plants. Here, we report glycosylinositol phosphorylceramide (GIPC) sphingolipids as NLP toxin receptors. Plant mutants with altered GIPC composition were more resistant to NLP toxins. Binding studies and x-ray crystallography showed that NLPs form complexes with terminal monomeric hexose moieties of GIPCs that result in conformational changes within the toxin. Insensitivity to NLP cytolysins of monocot plants may be explained by the length of the GIPC head group and the architecture of the NLP sugar-binding site. We unveil early steps in NLP cytolysin action that determine plant clade-specific toxin selectivity.
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Affiliation(s)
- Tea Lenarčič
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Isabell Albert
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Hannah Böhm
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Vesna Hodnik
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Katja Pirc
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Apolonija B Zavec
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ema Žagar
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Rory Pruitt
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Peter Greimel
- Lipid Biology Laboratory, RIKEN, Wako Saitama 351-0198, Japan.,Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN Institute, Wako, Saitama 351-0198, Japan
| | - Akiko Yamaji-Hasegawa
- Lipid Biology Laboratory, RIKEN, Wako Saitama 351-0198, Japan.,Molecular Membrane Neuroscience, Brain Science Institute, RIKEN Institute, Wako, Saitama 351-0198, Japan
| | - Toshihide Kobayashi
- Lipid Biology Laboratory, RIKEN, Wako Saitama 351-0198, Japan.,UMR 7213 CNRS, University of Strasbourg, 67401 Illkirch, France
| | - Agnieszka Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Germany.,Göttingen Center for Molecular Biosciences, University of Göttingen, Germany
| | - Jasmin Gömann
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Germany.,Göttingen Center for Molecular Biosciences, University of Göttingen, Germany
| | - Jenny C Mortimer
- Joint Bioenergy Institute, Emeryville, CA 94608, USA.,Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lin Fang
- Joint Bioenergy Institute, Emeryville, CA 94608, USA.,Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Adiilah Mamode-Cassim
- Laboratoire de Biogenèse Membranaire, UMR 5200 CNRS-Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave-d'Ornon Cedex, France
| | - Magali Deleu
- Laboratory of Molecular Biophysics at Interfaces, University of Liège, Gembloux, Belgium
| | - Laurence Lins
- Laboratory of Molecular Biophysics at Interfaces, University of Liège, Gembloux, Belgium
| | - Claudia Oecking
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Germany.,Göttingen Center for Molecular Biosciences, University of Göttingen, Germany
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire, UMR 5200 CNRS-Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave-d'Ornon Cedex, France
| | - Gregor Anderluh
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Thorsten Nürnberger
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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Adelantado N, Tarazona P, Grillitsch K, García-Ortega X, Monforte S, Valero F, Feussner I, Daum G, Ferrer P. The effect of hypoxia on the lipidome of recombinant Pichia pastoris. Microb Cell Fact 2017; 16:86. [PMID: 28526017 PMCID: PMC5437588 DOI: 10.1186/s12934-017-0699-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 05/10/2017] [Indexed: 01/17/2023] Open
Abstract
Background Cultivation of recombinant Pichia pastoris (Komagataella sp.) under hypoxic conditions has a strong positive effect on specific productivity when the glycolytic GAP promoter is used for recombinant protein expression, mainly due to upregulation of glycolytic conditions. In addition, transcriptomic analyses of hypoxic P. pastoris pointed out important regulation of lipid metabolism and unfolded protein response (UPR). Notably, UPR that plays a role in the regulation of lipid metabolism, amino acid metabolism and protein secretion, was found to be upregulated under hypoxia. Results To improve our understanding of the interplay between lipid metabolism, UPR and protein secretion, the lipidome of a P. pastoris strain producing an antibody fragment was studied under hypoxic conditions. Furthermore, lipid composition analyses were combined with previously available transcriptomic datasets to further understand the impact of hypoxia on lipid metabolism. Chemostat cultures operated under glucose-limiting conditions under normoxic and hypoxic conditions were analyzed in terms of intra/extracellular product distribution and lipid composition. Integrated analysis of lipidome and transcriptome datasets allowed us to demonstrate an important remodeling of the lipid metabolism under limited oxygen availability. Additionally, cells with reduced amounts of ergosterol through fluconazole treatment were also included in the study to observe the impact on protein secretion and its lipid composition. Conclusions Our results show that cells adjust their membrane composition in response to oxygen limitation mainly by changing their sterol and sphingolipid composition. Although fluconazole treatment results a different lipidome profile than hypoxia, both conditions result in higher recombinant protein secretion levels. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0699-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Núria Adelantado
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain.,Evonik Nutrition & Care GmbH, Hanau, Germany
| | - Pablo Tarazona
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Karlheinz Grillitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Xavier García-Ortega
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Sergi Monforte
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Günther Daum
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria. .,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria.
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
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Rampler E, Coman C, Hermann G, Sickmann A, Ahrends R, Koellensperger G. LILY-lipidome isotope labeling of yeast: in vivo synthesis of 13C labeled reference lipids for quantification by mass spectrometry. Analyst 2017; 142:1891-1899. [PMID: 28475182 DOI: 10.1039/c7an00107j] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quantification is an essential task in comprehensive lipidomics studies challenged by the high number of lipids, their chemical diversity and their dynamic range of the lipidome. In this work, we introduce lipidome isotope labeling of yeast (LILY) in order to produce (non-radioactive) isotopically labeled eukaryotic lipid standards in yeast for normalization and quantification in mass spectrometric assays. More specifically, LILY is a fast and efficient in vivo labeling strategy in Pichia pastoris for the production of 13C labeled lipid library further paving the way to comprehensive compound-specific internal standardization in quantitative mass spectrometry based assays. More than 200 lipid species (from PA, PC, PE, PG, PI, PS, LysoGP, CL, DAG, TAG, DMPE, Cer, HexCer, IPC, MIPC) were obtained from yeast extracts with an excellent 13C enrichment >99.5%, as determined by complementary high resolution mass spectrometry based shotgun and high resolution LC-MS/MS analysis. In a first proof of principle study we tested the relative and absolute quantification capabilities of the 13C enriched lipids obtained by LILY using a parallel reaction monitoring based LC-MS approach. In relative quantification it could be shown that compound specific internal standardization was essential for the accuracy extending the linear dynamic range to four orders of magnitude. Excellent analytical figures of merit were observed for absolute quantification for a selected panel of 5 investigated glycerophospholipids (e.g. LOQs around 5 fmol absolute; typical concentrations ranging between 1 to 10 nmol per 108 yeast cell starting material; RSDs <10% (N = 4)).
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Affiliation(s)
- Evelyn Rampler
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiolgy, Althanstraße 14, 1090 Vienna, Austria
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Gerrit Hermann
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and ISOtopic Solutions, Währingerstr. 38, 1090 Vienna, Austria
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany and College of Physical Sciences, University of Aberdeen, Department of Chemistry, AB24 3UE Aberdeen, UK and Medizinische Fakultät, Medizinische Proteom-Center (MCP), Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiolgy, Althanstraße 14, 1090 Vienna, Austria
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36
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Cámara E, Landes N, Albiol J, Gasser B, Mattanovich D, Ferrer P. Increased dosage of AOX1 promoter-regulated expression cassettes leads to transcription attenuation of the methanol metabolism in Pichia pastoris. Sci Rep 2017; 7:44302. [PMID: 28295011 PMCID: PMC5353721 DOI: 10.1038/srep44302] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/07/2017] [Indexed: 12/11/2022] Open
Abstract
The methanol-regulated alcohol oxidase promoter (PAOX1) of Pichia pastoris is one of the strongest promoters for heterologous gene expression in this methylotrophic yeast. Although increasing gene dosage is one of the most common strategies to increase recombinant protein productivities, the increase of gene dosage of Rhizopus oryzae lipase (ROL) in P. pastoris has been previously shown to reduce cell growth, lipase production and substrate consumption in high-copy strains. To better assess that physiological response, transcriptomics analysis was performed of a subset of strains with 1 to 15 ROL copies. The macroscopic physiological parameters confirm that growth yield and carbon uptake rate are gene dosage dependent, and were supported by the transcriptomic data, showing the impact of increased dosage of AOX1 promoter-regulated expression cassettes on P. pastoris physiology under steady methanolic growth conditions. Remarkably, increased number of cassettes led to transcription attenuation of the methanol metabolism and peroxisome biogenesis in P. pastoris, concomitant with reduced secretion levels of the heterologous product. Moreover, our data also point to a block in ROL mRNA translation in the higher ROL-copies constructs, while the low productivities of multi-copy strains under steady growth conditions do not appear to be directly related to UPR and ERAD induction.
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Affiliation(s)
- Elena Cámara
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain
| | - Nils Landes
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190 Vienna, Austria
| | - Joan Albiol
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain
| | - Brigitte Gasser
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190 Vienna, Austria
| | - Pau Ferrer
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain
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Su L, Ji D, Tao X, Yu L, Wu J, Xia Y. Recombinant expression, characterization, and application of a phospholipase B from Fusarium oxysporum. J Biotechnol 2017; 242:92-100. [DOI: 10.1016/j.jbiotec.2016.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/20/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023]
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A single heterologously expressed plant cellulose synthase isoform is sufficient for cellulose microfibril formation in vitro. Proc Natl Acad Sci U S A 2016; 113:11360-11365. [PMID: 27647898 DOI: 10.1073/pnas.1606210113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant cell walls are a composite material of polysaccharides, proteins, and other noncarbohydrate polymers. In the majority of plant tissues, the most abundant polysaccharide is cellulose, a linear polymer of glucose molecules. As the load-bearing component of the cell wall, individual cellulose chains are frequently bundled into micro and macrofibrils and are wrapped around the cell. Cellulose is synthesized by membrane-integrated and processive glycosyltransferases that polymerize UDP-activated glucose and secrete the nascent polymer through a channel formed by their own transmembrane regions. Plants express several different cellulose synthase isoforms during primary and secondary cell wall formation; however, so far, none has been functionally reconstituted in vitro for detailed biochemical analyses. Here we report the heterologous expression, purification, and functional reconstitution of Populus tremula x tremuloides CesA8 (PttCesA8), implicated in secondary cell wall formation. The recombinant enzyme polymerizes UDP-activated glucose to cellulose, as determined by enzyme degradation, permethylation glycosyl linkage analysis, electron microscopy, and mutagenesis studies. Catalytic activity is dependent on the presence of a lipid bilayer environment and divalent manganese cations. Further, electron microscopy analyses reveal that PttCesA8 produces cellulose fibers several micrometers long that occasionally are capped by globular particles, likely representing PttCesA8 complexes. Deletion of the enzyme's N-terminal RING-finger domain almost completely abolishes fiber formation but not cellulose biosynthetic activity. Our results demonstrate that reconstituted PttCesA8 is not only sufficient for cellulose biosynthesis in vitro but also suffices to bundle individual glucan chains into cellulose microfibrils.
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A single active catalytic site is sufficient to promote transport in P-glycoprotein. Sci Rep 2016; 6:24810. [PMID: 27117502 PMCID: PMC4846820 DOI: 10.1038/srep24810] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/05/2016] [Indexed: 11/23/2022] Open
Abstract
P-glycoprotein (Pgp) is an ABC transporter responsible for the ATP-dependent efflux of chemotherapeutic compounds from multidrug resistant cancer cells. Better understanding of the molecular mechanism of Pgp-mediated transport could promote rational drug design to circumvent multidrug resistance. By measuring drug binding affinity and reactivity to a conformation-sensitive antibody we show here that nucleotide binding drives Pgp from a high to a low substrate-affinity state and this switch coincides with the flip from the inward- to the outward-facing conformation. Furthermore, the outward-facing conformation survives ATP hydrolysis: the post-hydrolytic complex is stabilized by vanadate, and the slow recovery from this state requires two functional catalytic sites. The catalytically inactive double Walker A mutant is stabilized in a high substrate affinity inward-open conformation, but mutants with one intact catalytic center preserve their ability to hydrolyze ATP and to promote drug transport, suggesting that the two catalytic sites are randomly recruited for ATP hydrolysis.
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40
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Tomàs-Gamisans M, Ferrer P, Albiol J. Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PLoS One 2016; 11:e0148031. [PMID: 26812499 PMCID: PMC4734642 DOI: 10.1371/journal.pone.0148031] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/12/2016] [Indexed: 01/21/2023] Open
Abstract
Motivation Genome-scale metabolic models (GEMs) are tools that allow predicting a phenotype from a genotype under certain environmental conditions. GEMs have been developed in the last ten years for a broad range of organisms, and are used for multiple purposes such as discovering new properties of metabolic networks, predicting new targets for metabolic engineering, as well as optimizing the cultivation conditions for biochemicals or recombinant protein production. Pichia pastoris is one of the most widely used organisms for heterologous protein expression. There are different GEMs for this methylotrophic yeast of which the most relevant and complete in the published literature are iPP668, PpaMBEL1254 and iLC915. However, these three models differ regarding certain pathways, terminology for metabolites and reactions and annotations. Moreover, GEMs for some species are typically built based on the reconstructed models of related model organisms. In these cases, some organism-specific pathways could be missing or misrepresented. Results In order to provide an updated and more comprehensive GEM for P. pastoris, we have reconstructed and validated a consensus model integrating and merging all three existing models. In this step a comprehensive review and integration of the metabolic pathways included in each one of these three versions was performed. In addition, the resulting iMT1026 model includes a new description of some metabolic processes. Particularly new information described in recently published literature is included, mainly related to fatty acid and sphingolipid metabolism, glycosylation and cell energetics. Finally the reconstructed model was tested and validated, by comparing the results of the simulations with available empirical physiological datasets results obtained from a wide range of experimental conditions, such as different carbon sources, distinct oxygen availability conditions, as well as producing of two different recombinant proteins. In these simulations, the iMT1026 model has shown a better performance than the previous existing models.
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Affiliation(s)
- Màrius Tomàs-Gamisans
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Pau Ferrer
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Joan Albiol
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- * E-mail:
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41
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Ampah-Korsah H, Anderberg HI, Engfors A, Kirscht A, Norden K, Kjellstrom S, Kjellbom P, Johanson U. The Aquaporin Splice Variant NbXIP1;1α Is Permeable to Boric Acid and Is Phosphorylated in the N-terminal Domain. FRONTIERS IN PLANT SCIENCE 2016; 7:862. [PMID: 27379142 PMCID: PMC4909777 DOI: 10.3389/fpls.2016.00862] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/01/2016] [Indexed: 05/22/2023]
Abstract
Aquaporins (AQPs) are membrane channel proteins that transport water and uncharged solutes across different membranes in organisms in all kingdoms of life. In plants, the AQPs can be divided into seven different subfamilies and five of these are present in higher plants. The most recently characterized of these subfamilies is the XIP subfamily, which is found in most dicots but not in monocots. In this article, we present data on two different splice variants (α and β) of NbXIP1;1 from Nicotiana benthamiana. We describe the heterologous expression of NbXIP1;1α and β in the yeast Pichia pastoris, the subcellular localization of the protein in this system and the purification of the NbXIP1;1α protein. Furthermore, we investigated the functionality and the substrate specificity of the protein by stopped-flow spectrometry in P. pastoris spheroplasts and with the protein reconstituted in proteoliposomes. The phosphorylation status of the protein and localization of the phosphorylated amino acids were verified by mass spectrometry. Our results show that NbXIP1;1α is located in the plasma membrane when expressed in P. pastoris, that it is not permeable to water but to boric acid and that the protein is phosphorylated at several amino acids in the N-terminal cytoplasmic domain of the protein. A growth assay showed that the yeast cells expressing the N-terminally His-tagged NbXIP1;1α were more sensitive to boric acid as compared to the cells expressing the C-terminally His-tagged isoform. This might suggest that the N-terminal His-tag functionally mimics the phosphorylation of the N-terminal domain and that the N-terminal domain is involved in gating of the channel.
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Tarazona P, Feussner K, Feussner I. An enhanced plant lipidomics method based on multiplexed liquid chromatography-mass spectrometry reveals additional insights into cold- and drought-induced membrane remodeling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:621-33. [PMID: 26340975 DOI: 10.1111/tpj.13013] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/17/2015] [Accepted: 08/26/2015] [Indexed: 05/20/2023]
Abstract
Within the lipidome of plants a few bulk molecular species hamper the detection of the rest, which are present at relatively low levels. In addition, low-abundance species are often masked by numerous isobaric interferences, such as those caused by isoelemental species and isotopologues. This scenario not only means that minor species are underrepresented, but also leads to potential misidentifications and limits the structural information gathered by lipidomics approaches. In order to overcome these limitations we have developed a multiplexed liquid chromatography-mass spectrometry lipidomics platform able to achieve an enhanced coverage of plant lipidomes. The platform is based on a single extraction step followed by a series of ultra-performance liquid chromatography separations. Post-column flow is then directed to both a triple quadrupole analyzer for targeted profiling and a time-of-flight analyzer for accurate mass analysis. As a proof of concept, plants were subjected to cold or drought, which are known to trigger widespread remodeling events in plant cell membranes. Analysis of the leaf lipidome yielded 393 molecular species within 23 different lipid classes. This enhanced coverage allowed us to identify lipid molecular species and even classes that are altered upon stress, allowing hypotheses on role of glycosylinositolphosphoceramides (GIPC), steryl glycosides (SG) and acylated steryl glycosides (ASG) in drought stress to be addressed and confirming the findings from numerous previous studies with a single, wide-ranging lipidomics approach. This extended our knowledge on membrane remodeling during the drought response, integrating sphingolipids and sterol lipids into the current glycerolipid-based model.
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Affiliation(s)
- Pablo Tarazona
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
- Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
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Pace H, Simonsson Nyström L, Gunnarsson A, Eck E, Monson C, Geschwindner S, Snijder A, Höök F. Preserved transmembrane protein mobility in polymer-supported lipid bilayers derived from cell membranes. Anal Chem 2015; 87:9194-203. [PMID: 26268463 DOI: 10.1021/acs.analchem.5b01449] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supported lipid bilayers (SLBs) have contributed invaluable information about the physiochemical properties of cell membranes, but their compositional simplicity often limits the level of knowledge that can be gained about the structure and function of transmembrane proteins in their native environment. Herein, we demonstrate a generic protocol for producing polymer-supported lipid bilayers on glass surfaces that contain essentially all naturally occurring cell-membrane components of a cell line while still retaining transmembrane protein mobility and activity. This was achieved by merging vesicles made from synthetic lipids (PEGylated lipids and POPC lipids) with native cell-membrane vesicles to generate hybrid vesicles which readily rupture into a continuous polymer-supported lipid bilayer. To investigate the properties of these complex hybrid SLBs and particularly the behavior of their integral membrane-proteins, we used total internal reflection fluorescence imaging to study a transmembrane protease, β-secretase 1 (BACE1), whose ectoplasmic and cytoplasmic domains could both be specifically targeted with fluorescent reporters. By selectively probing the two different orientations of BACE1 in the resulting hybrid SLBs, the role of the PEG-cushion on transmembrane protein lateral mobility was investigated. The results reveal the necessity of having the PEGylated lipids present during vesicle adsorption to prevent immobilization of transmembrane proteins with protruding domains. The proteolytic activity of BACE1 was unadulterated by the sonication process used to merge the synthetic and native membrane vesicles; importantly it was also conserved in the SLB. The presented strategy could thus serve both fundamental studies of membrane biophysics and the production of surface-based bioanalytical sensor platforms.
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Affiliation(s)
- Hudson Pace
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Lisa Simonsson Nyström
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, AstraZeneca R&D Mölndal , SE-43183 Mölndal, Sweden
| | - Elizabeth Eck
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Christopher Monson
- Department of Physical Science, Southern Utah University , Cedar City, Utah 84720 United States
| | | | - Arjan Snijder
- Discovery Sciences, AstraZeneca R&D Mölndal , SE-43183 Mölndal, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
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Garcia-Ortega X, Reyes C, Montesinos JL, Valero F. Overall Key Performance Indicator to Optimizing Operation of High-Pressure Homogenizers for a Reliable Quantification of Intracellular Components in Pichia pastoris. Front Bioeng Biotechnol 2015; 3:107. [PMID: 26284241 PMCID: PMC4522904 DOI: 10.3389/fbioe.2015.00107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/10/2015] [Indexed: 11/13/2022] Open
Abstract
The most commonly used cell disruption procedures may present lack of reproducibility, which introduces significant errors in the quantification of intracellular components. In this work, an approach consisting in the definition of an overall key performance indicator (KPI) was implemented for a lab scale high-pressure homogenizer (HPH) in order to determine the disruption settings that allow the reliable quantification of a wide sort of intracellular components. This innovative KPI was based on the combination of three independent reporting indicators: decrease of absorbance, release of total protein, and release of alkaline phosphatase activity. The yeast Pichia pastoris growing on methanol was selected as model microorganism due to it presents an important widening of the cell wall needing more severe methods and operating conditions than Escherichia coli and Saccharomyces cerevisiae. From the outcome of the reporting indicators, the cell disruption efficiency achieved using HPH was about fourfold higher than other lab standard cell disruption methodologies, such bead milling cell permeabilization. This approach was also applied to a pilot plant scale HPH validating the methodology in a scale-up of the disruption process. This innovative non-complex approach developed to evaluate the efficacy of a disruption procedure or equipment can be easily applied to optimize the most common disruption processes, in order to reach not only reliable quantification but also recovery of intracellular components from cell factories of interest.
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Affiliation(s)
- Xavier Garcia-Ortega
- Bioprocess Engineering and Applied Biocatalysis Group, Departament d'Enginyeria Química, Escola d'Enginyeria, Universitat Autònoma de Barcelona , Bellaterra , Spain
| | - Cecilia Reyes
- Bioprocess Engineering and Applied Biocatalysis Group, Departament d'Enginyeria Química, Escola d'Enginyeria, Universitat Autònoma de Barcelona , Bellaterra , Spain
| | - José Luis Montesinos
- Bioprocess Engineering and Applied Biocatalysis Group, Departament d'Enginyeria Química, Escola d'Enginyeria, Universitat Autònoma de Barcelona , Bellaterra , Spain
| | - Francisco Valero
- Bioprocess Engineering and Applied Biocatalysis Group, Departament d'Enginyeria Química, Escola d'Enginyeria, Universitat Autònoma de Barcelona , Bellaterra , Spain
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de Ghellinck A, Fragneto G, Laux V, Haertlein M, Jouhet J, Sferrazza M, Wacklin H. Lipid polyunsaturation determines the extent of membrane structural changes induced by Amphotericin B in Pichia pastoris yeast. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2317-25. [PMID: 26055896 DOI: 10.1016/j.bbamem.2015.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/20/2015] [Accepted: 06/04/2015] [Indexed: 12/18/2022]
Abstract
The activity of the potent but highly toxic antifungal drug Amphotericin B (AmB), used intravenously to treat systemic fungal and parasitic infections, is widely accepted to result from its specific interaction with the fungal sterol ergosterol. While the effect of sterols on AmB activity has been intensely investigated, the role of membrane phospholipid composition has largely been ignored, and structural studies of native membranes have been hampered by their complex and disordered nature. We show for the first time that the structure of fungal membranes derived from Pichia pastoris yeast depends on the degree of lipid polyunsaturation, which has an impact on the structural consequences of AmB activity. AmB inserts in yeast membranes even in the absence of ergosterol, and forms an extra-membraneous layer whose thickness is resolved to be 4-5 nm. In ergosterol-containing membranes, AmB insertion is accompanied by ergosterol extraction into this layer. The AmB-sponge mediated depletion of ergosterol from P. pastoris membranes gives rise to a significant membrane thinning effect that depends on the degree of lipid polyunsaturation. The resulting hydrophobic mismatch is likely to interfere with a much broader range of membrane protein functions than those directly involving ergosterol, and suggests that polyunsaturated lipids could boost the efficiency of AmB. Furthermore, a low degree of lipid polyunsaturation leads to least AmB insertion and may protect host cells against the toxic effects of AmB. These results provide a new framework based on lipid composition and membrane structure through which we can understand its antifungal action and develop better treatments.
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Affiliation(s)
- Alexis de Ghellinck
- Institut Laue-Langevin, 71 av des Martyrs, P.O. Box 156, 38000 Grenoble, France; Departement de Physique, Faculté des Sciences, Université Libre de Bruxelles, Bd du Triomphe CP223, 1050 Bruxelles, Belgium
| | - Giovanna Fragneto
- Institut Laue-Langevin, 71 av des Martyrs, P.O. Box 156, 38000 Grenoble, France
| | - Valerie Laux
- Institut Laue-Langevin, 71 av des Martyrs, P.O. Box 156, 38000 Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 av des Martyrs, P.O. Box 156, 38000 Grenoble, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS/CEA/Univ. Grenoble Alpes/INRA, 38000 Grenoble, France
| | - Michele Sferrazza
- Departement de Physique, Faculté des Sciences, Université Libre de Bruxelles, Bd du Triomphe CP223, 1050 Bruxelles, Belgium
| | - Hanna Wacklin
- European Spallation Source ESS AB, P.O. Box 176, 22100 Lund, Sweden; Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
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