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Meyer T, Knittelfelder O, Smolnig M, Rockenfeller P. Quantifying yeast lipidomics by high-performance thin-layer chromatography (HPTLC) and comparison to mass spectrometry-based shotgun lipidomics. Microb Cell 2024; 11:57-68. [PMID: 38384676 PMCID: PMC10879857 DOI: 10.15698/mic2024.02.815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/23/2024]
Abstract
Lipidomic analysis in diverse biological settings has become a frequent tool to increase our understanding of the processes of life. Cellular lipids play important roles not only as being the main components of cellular membranes, but also in the regulation of cell homeostasis as lipid signaling molecules. Yeast has been harnessed for biomedical research based on its good conservation of genetics and fundamental cell organisation principles and molecular pathways. Further application in so-called humanised yeast models have been developed which take advantage of yeast as providing the basics of a living cell with full control over heterologous expression. Here we present evidence that high-performance thin-layer chromatography (HPTLC) represents an effective alternative to replace cost intensive mass spectrometry-based lipidomic analyses. We provide statistical comparison of identical samples by both methods, which support the use of HPTLC for quantitative analysis of the main yeast lipid classes.
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Affiliation(s)
- Thorsten Meyer
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Martin Smolnig
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Patrick Rockenfeller
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
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Davis J, Meyer T, Smolnig M, Smethurst DG, Neuhaus L, Heyden J, Broeskamp F, Edrich ES, Knittelfelder O, Kolb D, Haar TVD, Gourlay CW, Rockenfeller P. A dynamic actin cytoskeleton is required to prevent constitutive VDAC-dependent MAPK signalling and aberrant lipid homeostasis. iScience 2023; 26:107539. [PMID: 37636069 PMCID: PMC10450525 DOI: 10.1016/j.isci.2023.107539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/14/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
The dynamic nature of the actin cytoskeleton is required to coordinate many cellular processes, and a loss of its plasticity has been linked to accelerated cell aging and attenuation of adaptive response mechanisms. Cofilin is an actin-binding protein that controls actin dynamics and has been linked to mitochondrial signaling pathways that control drug resistance and cell death. Here we show that cofilin-driven chronic depolarization of the actin cytoskeleton activates cell wall integrity mitogen-activated protein kinase (MAPK) signalling and disrupts lipid homeostasis in a voltage-dependent anion channel (VDAC)-dependent manner. Expression of the cof1-5 mutation, which reduces the dynamic nature of actin, triggers loss of cell wall integrity, vacuole fragmentation, disruption of lipid homeostasis, lipid droplet (LD) accumulation, and the promotion of cell death. The integrity of the actin cytoskeleton is therefore essential to maintain the fidelity of MAPK signaling, lipid homeostasis, and cell health in S. cerevisiae.
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Affiliation(s)
- Jack Davis
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Thorsten Meyer
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Martin Smolnig
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | | | - Lisa Neuhaus
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Jonas Heyden
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Filomena Broeskamp
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | | | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Dagmar Kolb
- Medical University of Graz, Core Facility Ultrastructure Analysis, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Campbell W. Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Patrick Rockenfeller
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
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Smolnig M, Fasching S, Stelzl U. De Novo Linear Phosphorylation Site Motifs for BCR-ABL Kinase Revealed by Phospho-Proteomics in Yeast. J Proteome Res 2023; 22:1790-1799. [PMID: 37053475 PMCID: PMC10243146 DOI: 10.1021/acs.jproteome.2c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Indexed: 04/15/2023]
Abstract
BCR-ABL is the oncogenic fusion product of tyrosine kinase ABL1 and a highly frequent driver of acute lymphocytic leukemia (ALL) and chronic myeloid leukemia (CML). The kinase activity of BCR-ABL is strongly elevated; however, changes of substrate specificity in comparison to wild-type ABL1 kinase are less well characterized. Here, we heterologously expressed full-length BCR-ABL kinases in yeast. We exploited the proteome of living yeast as an in vivo phospho-tyrosine substrate for assaying human kinase specificity. Phospho-proteomic analysis of ABL1 and BCR-ABL isoforms p190 and p210 yielded a high-confidence data set of 1127 phospho-tyrosine sites on 821 yeast proteins. We used this data set to generate linear phosphorylation site motifs for ABL1 and the oncogenic ABL1 fusion proteins. The oncogenic kinases yielded a substantially different linear motif when compared to ABL1. Kinase set enrichment analysis with human pY-sites that have high linear motif scores well-recalled BCR-ABL driven cancer cell lines from human phospho-proteome data sets.
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Affiliation(s)
- Martin Smolnig
- Institute
of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Sandra Fasching
- Institute
of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
| | - Ulrich Stelzl
- Institute
of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Field
of Excellence BioHealth - University of Graz, 8010 Graz, Austria
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Rockenfeller P, Smolnig M, Diessl J, Bashir M, Schmiedhofer V, Knittelfelder O, Ring J, Franz J, Foessl I, Khan MJ, Rost R, Graier WF, Kroemer G, Zimmermann A, Carmona-Gutierrez D, Eisenberg T, Büttner S, Sigrist SJ, Kühnlein RP, Kohlwein SD, Gourlay CW, Madeo F. Diacylglycerol triggers Rim101 pathway-dependent necrosis in yeast: a model for lipotoxicity. Cell Death Differ 2018; 25:767-783. [PMID: 29230001 PMCID: PMC5864183 DOI: 10.1038/s41418-017-0014-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/18/2017] [Accepted: 10/16/2017] [Indexed: 02/03/2023] Open
Abstract
The loss of lipid homeostasis can lead to lipid overload and is associated with a variety of disease states. However, little is known as to how the disruption of lipid regulation or lipid overload affects cell survival. In this study we investigated how excess diacylglycerol (DG), a cardinal metabolite suspected to mediate lipotoxicity, compromises the survival of yeast cells. We reveal that increased DG achieved by either genetic manipulation or pharmacological administration of 1,2-dioctanoyl-sn-glycerol (DOG) triggers necrotic cell death. The toxic effects of DG are linked to glucose metabolism and require a functional Rim101 signaling cascade involving the Rim21-dependent sensing complex and the activation of a calpain-like protease. The Rim101 cascade is an established pathway that triggers a transcriptional response to alkaline or lipid stress. We propose that the Rim101 pathway senses DG-induced lipid perturbation and conducts a signaling response that either facilitates cellular adaptation or triggers lipotoxic cell death. Using established models of lipotoxicity, i.e., high-fat diet in Drosophila and palmitic acid administration in cultured human endothelial cells, we present evidence that the core mechanism underlying this calpain-dependent lipotoxic cell death pathway is phylogenetically conserved.
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Affiliation(s)
- Patrick Rockenfeller
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria.
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Martin Smolnig
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Jutta Diessl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Mina Bashir
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Division of Endocrinology and Diabetology, Medical University of Graz, Graz, 8010, Austria
| | - Vera Schmiedhofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Oskar Knittelfelder
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | - Julia Ring
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Joakim Franz
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Ines Foessl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Division of Endocrinology and Diabetology, Medical University of Graz, Graz, 8010, Austria
| | - Muhammad J Khan
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, 8010, Austria
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Islamabad, 44000, Pakistan
| | - René Rost
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, 8010, Austria
| | - Wolfgang F Graier
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, 8010, Austria
| | - Guido Kroemer
- INSERM U848, Villejuif, 94805, France
- Metabolomics Platform, Institut Gustave Roussy, Paris, 94805, France
- Centre de Recherche des Cordeliers, Paris, 75006, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, Paris, 75015, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, 75270, France
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | | | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- BioTechMed-Graz, Graz, 8010, Austria
| | - Sabrina Büttner
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Stephan J Sigrist
- Institute for Biology, Freie Universität Berlin, Berlin, 14195, Germany
- NeuroCure Charité, Berlin, 10117, Germany
| | - Ronald P Kühnlein
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- BioTechMed-Graz, Graz, 8010, Austria
- Max Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany
| | - Sepp D Kohlwein
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- BioTechMed-Graz, Graz, 8010, Austria
| | - Campbell W Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria.
- BioTechMed-Graz, Graz, 8010, Austria.
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