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Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R. MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress. EMBO J 2024; 43:1653-1685. [PMID: 38491296 PMCID: PMC11021466 DOI: 10.1038/s44318-024-00063-y] [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: 09/14/2022] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
Biological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.
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Affiliation(s)
- John Reinhard
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Leonhard Starke
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | | | - Per Haberkant
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | | | - Frank Stein
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | - Ofir Klein
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Charlotte Berhorst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Heike Stumpf
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - James P Sáenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Jochen Hub
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | - Maya Schuldiner
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Robert Ernst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany.
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany.
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McQuail J, Matera G, Gräfenhan T, Bischler T, Haberkant P, Stein F, Vogel J, Wigneshweraraj S. Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery. Nucleic Acids Res 2024; 52:2323-2339. [PMID: 38142457 PMCID: PMC10954441 DOI: 10.1093/nar/gkad1211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/17/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023] Open
Abstract
The RNA binding protein Hfq has a central role in the post-transcription control of gene expression in many bacteria. Numerous studies have mapped the transcriptome-wide Hfq-mediated RNA-RNA interactions in growing bacteria or bacteria that have entered short-term growth-arrest. To what extent post-transcriptional regulation underpins gene expression in growth-arrested bacteria remains unknown. Here, we used nitrogen (N) starvation as a model to study the Hfq-mediated RNA interactome as Escherichia coli enter, experience, and exit long-term growth arrest. We observe that the Hfq-mediated RNA interactome undergoes extensive changes during N starvation, with the conserved SdsR sRNA making the most interactions with different mRNA targets exclusively in long-term N-starved E. coli. Taking a proteomics approach, we reveal that in growth-arrested cells SdsR influences gene expression far beyond its direct mRNA targets. We demonstrate that the absence of SdsR significantly compromises the ability of the mutant bacteria to recover growth competitively from the long-term N-starved state and uncover a conserved post-transcriptional regulatory axis which underpins this process.
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Affiliation(s)
- Josh McQuail
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
| | - Gianluca Matera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Tom Gräfenhan
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
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Farley S, Stein F, Haberkant P, Tafesse FG, Schultz C. Trifunctional Sphinganine: A New Tool to Dissect Sphingolipid Function. ACS Chem Biol 2024; 19:336-347. [PMID: 38284972 PMCID: PMC10878393 DOI: 10.1021/acschembio.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/30/2024]
Abstract
Functions and cell biology of the sphingolipids sphingosine and sphinganine in cells are not well understood. While some signaling roles for sphingosine have been elucidated, the closely related sphinganine has been described only insofar as it does not elicit many of the same signaling responses. Here, we prepared multifunctionalized derivatives of the two lipid species that differ only in a single double bond of the carbon backbone. Using these novel probes, we were able to define their spatiotemporal distributions within cells. Furthermore, we used these tools to systematically map the protein interactomes of both lipids. The lipid-protein conjugates, prepared through photo-crosslinking in live cells and extraction via click chemistry to azide beads, revealed significant differences in the captured proteins, highlighting their distinct roles in various cellular processes. This work elucidates mechanistic differences between these critical lipids and sets the foundation for further studies of the cellular functions of sphingosine and sphinganine.
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Affiliation(s)
- Scotland Farley
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
- Department
of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Frank Stein
- European
Molecular Biology Laboratory, Proteomics
Core Facility, Heidelberg 69117, Germany
| | - Per Haberkant
- European
Molecular Biology Laboratory, Proteomics
Core Facility, Heidelberg 69117, Germany
| | - Fikadu G. Tafesse
- Department
of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Carsten Schultz
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
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Cherubini M, Erickson S, Padmanaban P, Haberkant P, Stein F, Beltran-Sastre V, Haase K. Flow in fetoplacental-like microvessels in vitro enhances perfusion, barrier function, and matrix stability. Sci Adv 2023; 9:eadj8540. [PMID: 38134282 PMCID: PMC10745711 DOI: 10.1126/sciadv.adj8540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Proper placental vascularization is vital for pregnancy outcomes, but assessing it with animal models and human explants has limitations. We introduce a 3D in vitro model of human placenta terminal villi including fetal mesenchyme and vascular endothelium. By coculturing HUVEC, placental fibroblasts, and pericytes in a macrofluidic chip with a flow reservoir, we generate fully perfusable fetal microvessels. Pressure-driven flow facilitates microvessel growth and remodeling, resulting in early formation of interconnected and lasting placental-like vascular networks. Computational fluid dynamics simulations predict shear forces, which increase microtissue stiffness, decrease diffusivity, and enhance barrier function as shear stress rises. Mass spectrometry analysis reveals enhanced protein expression with flow, including matrix stability regulators, proteins associated with actin dynamics, and cytoskeleton organization. Our model provides a powerful tool for deducing complex in vivo parameters, such as shear stress on developing vascularized placental tissue, and holds promise for unraveling gestational disorders related to the vasculature.
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Affiliation(s)
- Marta Cherubini
- European Molecular Biology Laboratory (EMBL), Barcelona, Spain
| | - Scott Erickson
- European Molecular Biology Laboratory (EMBL), Barcelona, Spain
| | | | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | - Kristina Haase
- European Molecular Biology Laboratory (EMBL), Barcelona, Spain
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5
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Madel RJ, Börger V, Dittrich R, Bremer M, Tertel T, Phuong NNT, Baba HA, Kordelas L, Staubach S, Stein F, Haberkant P, Hackl M, Grillari R, Grillari J, Buer J, Horn PA, Westendorf AM, Brandau S, Kirschning CJ, Giebel B. Independent human mesenchymal stromal cell-derived extracellular vesicle preparations differentially attenuate symptoms in an advanced murine graft-versus-host disease model. Cytotherapy 2023; 25:821-836. [PMID: 37055321 DOI: 10.1016/j.jcyt.2023.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/21/2023] [Accepted: 03/15/2023] [Indexed: 04/15/2023]
Abstract
BACKGROUND AIMS Extracellular vesicles (EVs) harvested from conditioned media of human mesenchymal stromal cells (MSCs) suppress acute inflammation in various disease models and promote regeneration of damaged tissues. After successful treatment of a patient with acute steroid-refractory graft-versus-host disease (GVHD) using EVs prepared from conditioned media of human bone marrow-derived MSCs, this study focused on improving the MSC-EV production for clinical application. METHODS Independent MSC-EV preparations all produced according to a standardized procedure revealed broad immunomodulatory differences. Only a proportion of the MSC-EV products applied effectively modulated immune responses in a multi-donor mixed lymphocyte reaction (mdMLR) assay. To explore the relevance of such differences in vivo, at first a mouse GVHD model was optimized. RESULTS The functional testing of selected MSC-EV preparations demonstrated that MSC-EV preparations revealing immunomodulatory capabilities in the mdMLR assay also effectively suppress GVHD symptoms in this model. In contrast, MSC-EV preparations, lacking such in vitro activities, also failed to modulate GVHD symptoms in vivo. Searching for differences of the active and inactive MSC-EV preparations, no concrete proteins or miRNAs were identified that could serve as surrogate markers. CONCLUSIONS Standardized MSC-EV production strategies may not be sufficient to warrant manufacturing of MSC-EV products with reproducible qualities. Consequently, given this functional heterogeneity, every individual MSC-EV preparation considered for the clinical application should be evaluated for its therapeutic potency before administration to patients. Here, upon comparing immunomodulating capabilities of independent MSC-EV preparations in vivo and in vitro, we found that the mdMLR assay was qualified for such analyses.
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Affiliation(s)
- Rabea J Madel
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; Department of Infectious Diseases, West German Centre for Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Verena Börger
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robin Dittrich
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michel Bremer
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tobias Tertel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Nhi Ngo Thi Phuong
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Hideo A Baba
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lambros Kordelas
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Simon Staubach
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | | | - Johannes Grillari
- Evercyte GmbH, Vienna, Austria; University of Natural Resources and Life Science, Vienna, Austria
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Astrid M Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sven Brandau
- Department of Otorhinolaryngology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Carsten J Kirschning
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
| | - Bernd Giebel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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Groh C, Haberkant P, Stein F, Filbeck S, Pfeffer S, Savitski MM, Boos F, Herrmann JM. Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins. Life Sci Alliance 2023; 6:e202201805. [PMID: 36941057 PMCID: PMC10027898 DOI: 10.26508/lsa.202201805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Cellular functionality relies on a well-balanced, but highly dynamic proteome. Dysfunction of mitochondrial protein import leads to the cytosolic accumulation of mitochondrial precursor proteins which compromise cellular proteostasis and trigger a mitoprotein-induced stress response. To dissect the effects of mitochondrial dysfunction on the cellular proteome as a whole, we developed pre-post thermal proteome profiling. This multiplexed time-resolved proteome-wide thermal stability profiling approach with isobaric peptide tags in combination with a pulsed SILAC labelling elucidated dynamic proteostasis changes in several dimensions: In addition to adaptations in protein abundance, we observed rapid modulations of the thermal stability of individual cellular proteins. Different functional groups of proteins showed characteristic response patterns and reacted with group-specific kinetics, allowing the identification of functional modules that are relevant for mitoprotein-induced stress. Thus, our new pre-post thermal proteome profiling approach uncovered a complex response network that orchestrates proteome homeostasis in eukaryotic cells by time-controlled adaptations of the abundance and the conformation of proteins.
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Affiliation(s)
- Carina Groh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | | | | | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany;
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7
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Reinhardt L, Musacchio F, Bichmann M, Behrendt A, Ercan-Herbst E, Stein J, Becher I, Haberkant P, Mader J, Schöndorf DC, Schmitt M, Korffmann J, Reinhardt P, Pohl C, Savitski M, Klein C, Gasparini L, Fuhrmann M, Ehrnhoefer DE. Dual truncation of tau by caspase-2 accelerates its CHIP-mediated degradation. Neurobiol Dis 2023; 182:106126. [PMID: 37086756 DOI: 10.1016/j.nbd.2023.106126] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/24/2023] Open
Abstract
Intraneuronal aggregates of the microtubule binding protein Tau are a hallmark of different neurodegenerative diseases including Alzheimer's disease (AD). In these aggregates, Tau is modified by posttranslational modifications such as phosphorylation as well as by proteolytic cleavage. Here we identify a novel Tau cleavage site at aspartate 65 (D65) that is specific for caspase-2. In addition, we show that the previously described cleavage site at D421 is also efficiently processed by caspase-2, and both sites are cleaved in human brain samples. Caspase-2-generated Tau fragments show increased aggregation potential in vitro, but do not accumulate in vivo after AAV-mediated overexpression in mouse hippocampus. Interestingly, we observe that steady-state protein levels of caspase-2 generated Tau fragments are low in our in vivo model despite strong RNA expression, suggesting efficient clearance. Consistent with this hypothesis, we find that caspase-2 cleavage significantly improves the recognition of Tau by the ubiquitin E3 ligase CHIP, leading to increased ubiquitination and faster degradation of Tau fragments. Taken together our data thus suggest that CHIP-induced ubiquitination is of particular importance for the clearance of caspase-2 generated Tau fragments in vitro and in vivo.
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Affiliation(s)
- Lydia Reinhardt
- BioMed X Institute, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany; AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Fabrizio Musacchio
- Neuroimmunology and Imaging Group, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
| | - Maria Bichmann
- BioMed X Institute, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Annika Behrendt
- BioMed X Institute, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Ebru Ercan-Herbst
- BioMed X Institute, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Juliane Stein
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Isabelle Becher
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Per Haberkant
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Julia Mader
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - David C Schöndorf
- BioMed X Institute, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany; AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Melanie Schmitt
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Jürgen Korffmann
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Peter Reinhardt
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Christian Pohl
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Mikhail Savitski
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Corinna Klein
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Laura Gasparini
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany
| | - Martin Fuhrmann
- Neuroimmunology and Imaging Group, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
| | - Dagmar E Ehrnhoefer
- BioMed X Institute, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany; AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, 67061 Ludwigshafen am Rhein, Germany.
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Nemeikaitė-Čėnienė A, Haberkant P, Kučiauskas D, Stein F, Čėnas N. Redox Proteomic Profile of Tirapazamine-Resistant Murine Hepatoma Cells. Int J Mol Sci 2023; 24:ijms24076863. [PMID: 37047836 PMCID: PMC10094930 DOI: 10.3390/ijms24076863] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
3-Amino-1,2,4-benzotriazine-1,4-dioxide (tirapazamine, TPZ) and other heteroaromatic N-oxides (ArN→O) exhibit tumoricidal, antibacterial, and antiprotozoal activities. Their action is attributed to the enzymatic single-electron reduction to free radicals that initiate the prooxidant processes. In order to clarify the mechanisms of aerobic mammalian cytotoxicity of ArN→O, we derived a TPZ-resistant subline of murine hepatoma MH22a cells (resistance index, 5.64). The quantitative proteomic of wild-type and TPZ-resistant cells revealed 5818 proteins, of which 237 were up- and 184 down-regulated. The expression of the antioxidant enzymes aldehyde- and alcohol dehydrogenases, carbonyl reductases, catalase, and glutathione reductase was increased 1.6-5.2 times, whereas the changes in the expression of glutathione peroxidase, superoxide dismutase, thioredoxin reductase, and peroxiredoxins were less pronounced. The expression of xenobiotics conjugating glutathione-S-transferases was increased by 1.6-2.6 times. On the other hand, the expression of NADPH:cytochrome P450 reductase was responsible for the single-electron reduction in TPZ and for the 2.1-fold decrease. These data support the fact that the main mechanism of action of TPZ under aerobic conditions is oxidative stress. The unchanged expression of intranuclear antioxidant proteins peroxiredoxin, glutaredoxin, and glutathione peroxidase, and a modest increase in the expression of DNA damage repair proteins, tend to support non-site-specific but not intranuclear oxidative stress as a main factor of TPZ aerobic cytotoxicity.
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Affiliation(s)
- Aušra Nemeikaitė-Čėnienė
- State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08406 Vilnius, Lithuania
| | - Per Haberkant
- Proteomics Core Facility EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Dalius Kučiauskas
- Department of Xenobiotics Biochemistry, Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Frank Stein
- Proteomics Core Facility EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Narimantas Čėnas
- Department of Xenobiotics Biochemistry, Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
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9
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Altuzar J, Notbohm J, Stein F, Haberkant P, Hempelmann P, Heybrock S, Worsch J, Saftig P, Höglinger D. Lysosome-targeted multifunctional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor. Proc Natl Acad Sci U S A 2023; 120:e2213886120. [PMID: 36893262 PMCID: PMC10089177 DOI: 10.1073/pnas.2213886120] [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: 08/12/2022] [Accepted: 01/31/2023] [Indexed: 03/11/2023] Open
Abstract
Lysosomes are catabolic organelles involved in macromolecular digestion, and their dysfunction is associated with pathologies ranging from lysosomal storage disorders to common neurodegenerative diseases, many of which have lipid accumulation phenotypes. The mechanism of lipid efflux from lysosomes is well understood for cholesterol, while the export of other lipids, particularly sphingosine, is less well studied. To overcome this knowledge gap, we have developed functionalized sphingosine and cholesterol probes that allow us to follow their metabolism, protein interactions, and their subcellular localization. These probes feature a modified cage group for lysosomal targeting and controlled release of the active lipids with high temporal precision. An additional photocrosslinkable group allowed for the discovery of lysosomal interactors for both sphingosine and cholesterol. In this way, we found that two lysosomal cholesterol transporters, NPC1 and to a lesser extent LIMP-2/SCARB2, bind to sphingosine and showed that their absence leads to lysosomal sphingosine accumulation which hints at a sphingosine transport role of both proteins. Furthermore, artificial elevation of lysosomal sphingosine levels impaired cholesterol efflux, consistent with sphingosine and cholesterol sharing a common export mechanism.
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Affiliation(s)
- Janathan Altuzar
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
| | - Judith Notbohm
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, 69117Heidelberg, Germany
| | - Per Haberkant
- European Molecular Biology Laboratory, 69117Heidelberg, Germany
| | - Pia Hempelmann
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
| | - Saskia Heybrock
- Institute of Biochemistry, Christian-Albrechts-Universität Kiel, 24118Kiel, Germany
| | - Jutta Worsch
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
| | - Paul Saftig
- Institute of Biochemistry, Christian-Albrechts-Universität Kiel, 24118Kiel, Germany
| | - Doris Höglinger
- Heidelberg University Biochemistry Center, Ruprecht-Karls-Universität Heidelberg, 69120Heidelberg, Germany
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10
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Weidenhausen J, Kopp J, Ruger-Herreros C, Stein F, Haberkant P, Lapouge K, Sinning I. Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity. Int J Mol Sci 2022; 23:ijms231810805. [PMID: 36142717 PMCID: PMC9500918 DOI: 10.3390/ijms231810805] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Most eukaryotic proteins are N-terminally acetylated by a set of Nα acetyltransferases (NATs). This ancient and ubiquitous modification plays a fundamental role in protein homeostasis, while mutations are linked to human diseases and phenotypic defects. In particular, Naa50 features species-specific differences, as it is inactive in yeast but active in higher eukaryotes. Together with NatA, it engages in NatE complex formation for cotranslational acetylation. Here, we report Naa50 homologs from the filamentous fungi Chaetomium thermophilum and Neurospora crassa with significant N- and C-terminal extensions to the conserved GNAT domain. Structural and biochemical analyses show that CtNaa50 shares the GNAT structure and substrate specificity with other homologs. However, in contrast to previously analyzed Naa50 proteins, it does not form NatE. The elongated N-terminus increases Naa50 thermostability and binds to dynein light chain protein 1, while our data suggest that conserved positive patches in the C-terminus allow for ribosome binding independent of NatA. Our study provides new insights into the many facets of Naa50 and highlights the diversification of NATs during evolution.
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Affiliation(s)
- Jonas Weidenhausen
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Carmen Ruger-Herreros
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Center for Molecular Biology of the University of Heidelberg (ZMBH), 69120 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Protein Expression and Purification Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Correspondence:
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11
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Kallergi E, Daskalaki AD, Kolaxi A, Camus C, Ioannou E, Mercaldo V, Haberkant P, Stein F, Sidiropoulou K, Dalezios Y, Savitski MM, Bagni C, Choquet D, Hosy E, Nikoletopoulou V. Dendritic autophagy degrades postsynaptic proteins and is required for long-term synaptic depression in mice. Nat Commun 2022; 13:680. [PMID: 35115539 PMCID: PMC8814153 DOI: 10.1038/s41467-022-28301-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/14/2022] [Indexed: 01/18/2023] Open
Abstract
The pruning of dendritic spines during development requires autophagy. This process is facilitated by long-term depression (LTD)-like mechanisms, which has led to speculation that LTD, a fundamental form of synaptic plasticity, also requires autophagy. Here, we show that the induction of LTD via activation of NMDA receptors or metabotropic glutamate receptors initiates autophagy in the postsynaptic dendrites in mice. Dendritic autophagic vesicles (AVs) act in parallel with the endocytic machinery to remove AMPA receptor subunits from the membrane for degradation. During NMDAR-LTD, key postsynaptic proteins are sequestered for autophagic degradation, as revealed by quantitative proteomic profiling of purified AVs. Pharmacological inhibition of AV biogenesis, or conditional ablation of atg5 in pyramidal neurons abolishes LTD and triggers sustained potentiation in the hippocampus. These deficits in synaptic plasticity are recapitulated by knockdown of atg5 specifically in postsynaptic pyramidal neurons in the CA1 area. Conducive to the role of synaptic plasticity in behavioral flexibility, mice with autophagy deficiency in excitatory neurons exhibit altered response in reversal learning. Therefore, local assembly of the autophagic machinery in dendrites ensures the degradation of postsynaptic components and facilitates LTD expression.
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Affiliation(s)
- Emmanouela Kallergi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | | | - Angeliki Kolaxi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | - Come Camus
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Evangelia Ioannou
- School of Biological Sciences, University of Crete, Heraklion, 70013, Greece
| | - Valentina Mercaldo
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | - Per Haberkant
- Proteomic Core Facility (PCF), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- Proteomic Core Facility (PCF), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Yannis Dalezios
- School of Medicine, University of Crete, Heraklion, 71003, Greece
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Mikhail M Savitski
- Proteomic Core Facility (PCF), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), University of Rome Tor Vergata, Rome, 00133, Italy
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Daniel Choquet
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, F-33000, Bordeaux, France
| | - Eric Hosy
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
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12
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Bichmann M, Prat Oriol N, Ercan-Herbst E, Schöndorf DC, Gomez Ramos B, Schwärzler V, Neu M, Schlüter A, Wang X, Jin L, Hu C, Tian Y, Ried JS, Haberkant P, Gasparini L, Ehrnhoefer DE. SETD7-mediated monomethylation is enriched on soluble Tau in Alzheimer's disease. Mol Neurodegener 2021; 16:46. [PMID: 34215303 PMCID: PMC8254302 DOI: 10.1186/s13024-021-00468-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Human tauopathies including Alzheimer's disease (AD) are characterized by alterations in the post-translational modification (PTM) pattern of Tau, which parallel the formation of insoluble Tau aggregates, neuronal dysfunction and degeneration. While PTMs on aggregated Tau have been studied in detail, much less is known about the modification patterns of soluble Tau. Furthermore, PTMs other than phosphorylation have only come into focus recently and are still understudied. Soluble Tau species are likely responsible for the spreading of pathology during disease progression and are currently being investigated as targets for immunotherapies. A better understanding of their biochemical properties is thus of high importance. METHODS We used a mass spectrometry approach to characterize Tau PTMs on a detergent-soluble fraction of human AD and control brain tissue, which led to the discovery of novel lysine methylation events. We developed specific antibodies against Tau methylated at these sites and biochemically characterized methylated Tau species in extracts from human brain, the rTg4510 mouse model and in hiPSC-derived neurons. RESULTS Our study demonstrates that methylated Tau levels increase with Tau pathology stage in human AD samples as well as in a mouse model of Tauopathy. Methylated Tau is enriched in soluble brain extracts and is not associated with hyperphosphorylated, high molecular weight Tau species. We also show that in hiPSC-derived neurons and mouse brain, methylated Tau preferentially localizes to the cell soma and nuclear fractions and is absent from neurites. Knock down and inhibitor studies supported by proteomics data led to the identification of SETD7 as a novel lysine methyltransferase for Tau. SETD7 specifically methylates Tau at K132, an event that facilitates subsequent methylation at K130. CONCLUSIONS Our findings indicate that methylated Tau has a specific somatic and nuclear localization, suggesting that the methylation of soluble Tau species may provide a signal for their translocation to different subcellular compartments. Since the mislocalization and depletion of Tau from axons is associated with tauopathies, our findings may shed light onto this disease-associated phenomenon.
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Affiliation(s)
- Maria Bichmann
- BioMed X Institute, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
| | - Nuria Prat Oriol
- BioMed X Institute, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
- Present address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ebru Ercan-Herbst
- BioMed X Institute, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
| | - David C Schöndorf
- BioMed X Institute, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstr. 50, 67061, Ludwigshafen am Rhein, Germany
| | - Borja Gomez Ramos
- BioMed X Institute, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
- Present address: Life Sciences Research Unit, University of Luxembourg, L-4367, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Vera Schwärzler
- BioMed X Institute, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
| | - Marie Neu
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstr. 50, 67061, Ludwigshafen am Rhein, Germany
| | - Annabelle Schlüter
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstr. 50, 67061, Ludwigshafen am Rhein, Germany
| | - Xue Wang
- AbbVie Bioresearch Center (ABC), 100 Research Dr, Worcester, MA, 01605, USA
| | - Liang Jin
- AbbVie Bioresearch Center (ABC), 100 Research Dr, Worcester, MA, 01605, USA
| | - Chenqi Hu
- AbbVie Bioresearch Center (ABC), 100 Research Dr, Worcester, MA, 01605, USA
| | - Yu Tian
- AbbVie Bioresearch Center (ABC), 100 Research Dr, Worcester, MA, 01605, USA
| | - Janina S Ried
- AbbVie Deutschland GmbH & Co. KG, Genomics Research Center, Knollstr. 50, 67061, Ludwigshafen am Rhein, Germany
| | - Per Haberkant
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Laura Gasparini
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstr. 50, 67061, Ludwigshafen am Rhein, Germany
| | - Dagmar E Ehrnhoefer
- BioMed X Institute, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany.
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstr. 50, 67061, Ludwigshafen am Rhein, Germany.
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13
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Schlagowski AM, Knöringer K, Morlot S, Sánchez Vicente A, Flohr T, Krämer L, Boos F, Khalid N, Ahmed S, Schramm J, Murschall LM, Haberkant P, Stein F, Riemer J, Westermann B, Braun RJ, Winklhofer KF, Charvin G, Herrmann JM. Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol. EMBO J 2021; 40:e107913. [PMID: 34191328 PMCID: PMC8365258 DOI: 10.15252/embj.2021107913] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 02/02/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
The formation of protein aggregates is a hallmark of neurodegenerative diseases. Observations on patient samples and model systems demonstrated links between aggregate formation and declining mitochondrial functionality, but causalities remain unclear. We used Saccharomyces cerevisiae to analyze how mitochondrial processes regulate the behavior of aggregation‐prone polyQ protein derived from human huntingtin. Expression of Q97‐GFP rapidly led to insoluble cytosolic aggregates and cell death. Although aggregation impaired mitochondrial respiration only slightly, it considerably interfered with the import of mitochondrial precursor proteins. Mutants in the import component Mia40 were hypersensitive to Q97‐GFP, whereas Mia40 overexpression strongly suppressed the formation of toxic Q97‐GFP aggregates both in yeast and in human cells. Based on these observations, we propose that the post‐translational import of mitochondrial precursor proteins into mitochondria competes with aggregation‐prone cytosolic proteins for chaperones and proteasome capacity. Mia40 regulates this competition as it has a rate‐limiting role in mitochondrial protein import. Therefore, Mia40 is a dynamic regulator in mitochondrial biogenesis that can be exploited to stabilize cytosolic proteostasis.
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Affiliation(s)
| | | | - Sandrine Morlot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Ana Sánchez Vicente
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Tamara Flohr
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Lena Krämer
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Nabeel Khalid
- German Research Center for Artificial Intelligence DFKI, Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence DFKI, Kaiserslautern, Germany
| | - Jana Schramm
- Cell Biology, University of Bayreuth, Bayreuth, Germany
| | | | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Jan Riemer
- Biochemistry, University of Cologne, Cologne, Germany
| | | | - Ralf J Braun
- Cell Biology, University of Bayreuth, Bayreuth, Germany.,Neurodegeneration, Danube Private University, Krems/Donau, Austria
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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14
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Karkampouna S, De Filippo MR, Ng CKY, Klima I, Zoni E, Spahn M, Stein F, Haberkant P, Thalmann GN, Kruithof-de Julio M. Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures. Cancers (Basel) 2020; 12:cancers12123786. [PMID: 33334054 PMCID: PMC7768471 DOI: 10.3390/cancers12123786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/01/2020] [Accepted: 12/10/2020] [Indexed: 01/08/2023] Open
Abstract
Resistance acquisition to androgen deprivation treatment and metastasis progression are a major clinical issue associated with prostate cancer (PCa). The role of stroma during disease progression is insufficiently defined. Using transcriptomic and proteomic analyses on differentially aggressive patient-derived xenografts (PDXs), we investigated whether PCa tumors predispose their microenvironment (stroma) to a metastatic gene expression pattern. RNA sequencing was performed on the PCa PDXs BM18 (castration-sensitive) and LAPC9 (castration-resistant), representing different disease stages. Using organism-specific reference databases, the human-specific transcriptome (tumor) was identified and separated from the mouse-specific transcriptome (stroma). To identify proteomic changes in the tumor (human) versus the stroma (mouse), we performed human/mouse cell separation and subjected protein lysates to quantitative Tandem Mass Tag labeling and mass spectrometry. Tenascin C (TNC) was among the most abundant stromal genes, modulated by androgen levels in vivo and highly expressed in castration-resistant LAPC9 PDX. The tissue microarray of primary PCa samples (n = 210) showed that TNC is a negative prognostic marker of the clinical progression to recurrence or metastasis. Stroma markers of osteoblastic PCa bone metastases seven-up signature were induced in the stroma by the host organism in metastatic xenografts, indicating conserved mechanisms of tumor cells to induce a stromal premetastatic signature. A 50-gene list stroma signature was identified based on androgen-dependent responses, which shows a linear association with the Gleason score, metastasis progression and progression-free survival. Our data show that metastatic PCa PDXs, which differ in androgen sensitivity, trigger differential stroma responses, which show the metastasis risk stratification and prognostic biomarker potential.
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Affiliation(s)
- Sofia Karkampouna
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
| | - Maria R. De Filippo
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
| | - Charlotte K. Y. Ng
- Oncogenomics Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 40, 3008 Bern, Switzerland;
| | - Irena Klima
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
| | - Eugenio Zoni
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
| | - Martin Spahn
- Lindenhofspital Bern, Prostate Center Bern, 3012 Bern, Switzerland;
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; (F.S.); (P.H.)
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; (F.S.); (P.H.)
| | - George N. Thalmann
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
- Department of Urology, Inselspital, Anna Seiler Haus, Bern University Hospital, 3010 Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
- Department of Urology, Inselspital, Anna Seiler Haus, Bern University Hospital, 3010 Bern, Switzerland
- Correspondence:
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15
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Perner J, Helm D, Haberkant P, Hatalova T, Kropackova S, Ribeiro JM, Kopacek P. The Central Role of Salivary Metalloproteases in Host Acquired Resistance to Tick Feeding. Front Cell Infect Microbiol 2020; 10:563349. [PMID: 33312963 PMCID: PMC7708348 DOI: 10.3389/fcimb.2020.563349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/18/2020] [Accepted: 10/20/2020] [Indexed: 01/07/2023] Open
Abstract
During feeding on vertebrate hosts, ticks secrete saliva composed of a rich cocktail of bioactive molecules modulating host immune responses. Although most of the proteinaceous fraction of tick saliva is of little immunogenicity, repeated feeding of ticks on mammalian hosts may lead to impairment of tick feeding, preventing full engorgement. Here, we challenged rabbits with repeated feeding of both Ixodes ricinus nymphs and adults and observed the formation of specific antibodies against several tick salivary proteins. Repeated feeding of both I. ricinus stages led to a gradual decrease in engorged weights. To identify the salivary antigens, isolated immunoglobulins from repeatedly infested rabbits were utilized for a protein pull-down from the saliva of pilocarpine-treated ticks. Eluted antigens were first identified by peptide mass fingerprinting with the aid of available I. ricinus salivary gland transcriptomes originating from early phases of tick feeding. To increase the authenticity of immunogens identified, we also performed, for the first time, de novo assembly of the sialome from I. ricinus females fed for six days, a timepoint used for pilocarpine-salivation. The most dominant I. ricinus salivary immunogens identified in our study were zinc-dependent metalloproteases of three different families. To corroborate the role of metalloproteases at the tick/host interface, we fed ticks micro-injected with a zinc metalloprotease inhibitor, phosphoramidon, on a rabbit. These ticks clearly failed to initiate feeding and to engorge. However, neither feeding to ticks immune blood of repeatedly infested rabbits, nor phosphoramidon injection into ticks, prevented their engorgement when fed in vitro on an artificial membrane system. These data show that Zn metalloproteases play a decisive role in the success of tick feeding, mediated by complex molecular interactions between the host immune, inflammatory, and hemostatic processes, which are absent in in vitro feeding. This basic concept warrants further investigation and reconsideration of the current strategies towards the development of an effective “anti-tick” vaccine.
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Affiliation(s)
- Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Dominic Helm
- Proteomics Core Facility, The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tereza Hatalova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Sara Kropackova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Jose M Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Petr Kopacek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
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16
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Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Mooijman D, Benes V, Savitski MM, Gebauer F, Hennig J. Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. Cell Rep 2020; 32:107930. [PMID: 32697992 PMCID: PMC7383231 DOI: 10.1016/j.celrep.2020.107930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs), which provide these proteins with a modular architecture. Accumulating evidence supports that RBP architectural modularity and adaptability define the specificity of their interactions with RNA. However, how multiple RBDs recognize their cognate single-stranded RNA (ssRNA) sequences in concert remains poorly understood. Here, we use Upstream of N-Ras (Unr) as a model system to address this question. Although reported to contain five ssRNA-binding cold-shock domains (CSDs), we demonstrate that Unr includes an additional four CSDs that do not bind RNA (pseudo-RBDs) but are involved in mediating RNA tertiary structure specificity by reducing the conformational heterogeneity of Unr. Disrupting the interactions between canonical and non-canonical CSDs impacts RNA binding, Unr-mediated translation regulation, and the Unr-dependent RNA interactome. Taken together, our studies reveal a new paradigm in protein-RNA recognition, where interactions between RBDs and pseudo-RBDs select RNA tertiary structures, influence RNP assembly, and define target specificity.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Provaznik
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lara Jayne Sweetapple
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Laura Villacorta
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Dylan Mooijman
- Developmental Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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17
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Girstmair H, Tippel F, Lopez A, Tych K, Stein F, Haberkant P, Schmid PWN, Helm D, Rief M, Sattler M, Buchner J. The Hsp90 isoforms from S. cerevisiae differ in structure, function and client range. Nat Commun 2019; 10:3626. [PMID: 31399574 PMCID: PMC6689086 DOI: 10.1038/s41467-019-11518-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/19/2019] [Indexed: 12/24/2022] Open
Abstract
The molecular chaperone Hsp90 is an important regulator of proteostasis. It has remained unclear why S. cerevisiae possesses two Hsp90 isoforms, the constitutively expressed Hsc82 and the stress-inducible Hsp82. Here, we report distinct differences despite a sequence identity of 97%. Consistent with its function under stress conditions, Hsp82 is more stable and refolds more efficiently than Hsc82. The two isoforms also differ in their ATPases and conformational cycles. Hsc82 is more processive and populates closed states to a greater extent. Variations in the N-terminal ATP-binding domain modulate its dynamics and conformational cycle. Despite these differences, the client interactomes are largely identical, but isoform-specific interactors exist both under physiological and heat shock conditions. Taken together, changes mainly in the N-domain create a stress-specific, more resilient protein with a shifted activity profile. Thus, the precise tuning of the Hsp90 isoforms preserves the basic mechanism but adapts it to specific needs. S. cerevisiae encodes two Hsp90 isoforms, the constitutively expressed Hsc82 and stress-inducible Hsp82 that are 97% identical. Here, the authors combine a range of biophysical methods and show that they differ in their enzymatic properties, resilience to stress and client range, which suggests that they evolved to provide fine-tuned chaperone assistance under physiological and stress conditions.
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Affiliation(s)
- Hannah Girstmair
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, 85748, Garching, Germany
| | - Franziska Tippel
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, 85748, Garching, Germany
| | - Abraham Lopez
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Katarzyna Tych
- Center for Integrated Protein Science at the Department of Physics, Technische Universität München, 85748 Garching, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, 69117, Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, 69117, Heidelberg, Germany
| | - Philipp Werner Norbert Schmid
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, 85748, Garching, Germany
| | - Dominic Helm
- Proteomics Core Facility, EMBL Heidelberg, 69117, Heidelberg, Germany
| | - Matthias Rief
- Center for Integrated Protein Science at the Department of Physics, Technische Universität München, 85748 Garching, Germany
| | - Michael Sattler
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, 85748, Garching, Germany.
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18
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Wheeler S, Haberkant P, Bhardwaj M, Tongue P, Ferraz MJ, Halter D, Sprong H, Schmid R, Aerts JM, Sullo N, Sillence DJ. Cytosolic glucosylceramide regulates endolysosomal function in Niemann-Pick type C disease. Neurobiol Dis 2019; 127:242-252. [DOI: 10.1016/j.nbd.2019.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/06/2019] [Accepted: 03/09/2019] [Indexed: 12/22/2022] Open
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19
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Behrendt A, Bichmann M, Ercan-Herbst E, Haberkant P, Schöndorf DC, Wolf M, Fahim SA, Murolo E, Ehrnhoefer DE. Asparagine endopeptidase cleaves tau at N167 after uptake into microglia. Neurobiol Dis 2019; 130:104518. [PMID: 31229689 DOI: 10.1016/j.nbd.2019.104518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/08/2019] [Accepted: 06/19/2019] [Indexed: 01/03/2023] Open
Abstract
Tau cleavage by different proteolytic enzymes generates short, aggregation-prone fragments that have been implicated in the pathogenesis of Alzheimer's disease (AD). Asparagine endopeptidase (AEP) activity in particular has been associated with tau dysfunction and aggregation, and the activity of the protease is increased in both aging and AD. Using a mass spectrometry approach, we identified a novel tau cleavage site at N167 and confirmed its processing by AEP. In combination with the previously known site at N368, we show that AEP cleavage yields a tau fragment that is present in both control and AD brains at similar levels. AEP is a lysosomal enzyme, and our data suggest that it is expressed in microglia rather than in neurons. Accordingly, we observe tau cleavage at N167 and N368 after endocytotic uptake into microglia, but not neurons. However, tau168-368 does not accumulate in microglia and we thus conclude that the fragment is part of a proteolytic cascade leading to tau degradation. While we confirm previous studies showing increased overall AEP activity in AD brains, our data suggests that AEP-mediated cleavage of tau is a physiological event occurring during microglial degradation of the secreted neuronal protein. As a consequence, we caution against preventing AEP-mediated tau cleavage as a therapeutic approach in AD.
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Affiliation(s)
- Annika Behrendt
- BioMed X Innovation Center, Im Neuenheimer Feld 515, Heidelberg 69120, Germany
| | - Maria Bichmann
- BioMed X Innovation Center, Im Neuenheimer Feld 515, Heidelberg 69120, Germany
| | - Ebru Ercan-Herbst
- BioMed X Innovation Center, Im Neuenheimer Feld 515, Heidelberg 69120, Germany
| | - Per Haberkant
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg 69117, Germany
| | - David C Schöndorf
- BioMed X Innovation Center, Im Neuenheimer Feld 515, Heidelberg 69120, Germany
| | - Michael Wolf
- BioMed X Innovation Center, Im Neuenheimer Feld 515, Heidelberg 69120, Germany
| | - Salma A Fahim
- BioMed X Innovation Center, Im Neuenheimer Feld 515, Heidelberg 69120, Germany
| | - Enrico Murolo
- BioMed X Innovation Center, Im Neuenheimer Feld 515, Heidelberg 69120, Germany
| | - Dagmar E Ehrnhoefer
- BioMed X Innovation Center, Im Neuenheimer Feld 515, Heidelberg 69120, Germany.
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20
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Bockelmann S, Mina JGM, Korneev S, Hassan DG, Müller D, Hilderink A, Vlieg HC, Raijmakers R, Heck AJR, Haberkant P, Holthuis JCM. A search for ceramide binding proteins using bifunctional lipid analogs yields CERT-related protein StarD7. J Lipid Res 2018; 59:515-530. [PMID: 29343537 DOI: 10.1194/jlr.m082354] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/12/2018] [Indexed: 12/21/2022] Open
Abstract
Ceramides are central intermediates of sphingolipid metabolism with dual roles as mediators of cellular stress signaling and mitochondrial apoptosis. How ceramides exert their cytotoxic effects is unclear and their poor solubility in water hampers a search for specific protein interaction partners. Here, we report the application of a photoactivatable and clickable ceramide analog, pacCer, to identify ceramide binding proteins and unravel the structural basis by which these proteins recognize ceramide. Besides capturing ceramide transfer protein (CERT) from a complex proteome, our approach yielded CERT-related steroidogenic acute regulatory protein D7 (StarD7) as novel ceramide binding protein. Previous work revealed that StarD7 is required for efficient mitochondrial import of phosphatidylcholine (PC) and serves a critical role in mitochondrial function and morphology. Combining site-directed mutagenesis and photoaffinity labeling experiments, we demonstrate that the steroidogenic acute regulatory transfer domain of StarD7 harbors a common binding site for PC and ceramide. While StarD7 lacks robust ceramide transfer activity in vitro, we find that its ability to shuttle PC between model membranes is specifically affected by ceramides. Besides demonstrating the suitability of pacCer as a tool to hunt for ceramide binding proteins, our data point at StarD7 as a candidate effector protein by which ceramides may exert part of their mitochondria-mediated cytotoxic effects.
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Affiliation(s)
- Svenja Bockelmann
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany
| | - John G M Mina
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany.,School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Sergei Korneev
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Dina G Hassan
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Dagmar Müller
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Angelika Hilderink
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Hedwich C Vlieg
- Membrane Biochemistry and Biophysics Division , Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Reinout Raijmakers
- Biomoleular Mass Spectrometry and Proteomics Division, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomoleular Mass Spectrometry and Proteomics Division, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Per Haberkant
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Joost C M Holthuis
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany .,Membrane Biochemistry and Biophysics Division , Utrecht University, 3584 CH Utrecht, The Netherlands
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21
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Schonauer S, Körschen HG, Penno A, Rennhack A, Breiden B, Sandhoff K, Gutbrod K, Dörmann P, Raju DN, Haberkant P, Gerl MJ, Brügger B, Zigdon H, Vardi A, Futerman AH, Thiele C, Wachten D. Identification of a feedback loop involving β-glucosidase 2 and its product sphingosine sheds light on the molecular mechanisms in Gaucher disease. J Biol Chem 2017; 292:6177-6189. [PMID: 28258214 DOI: 10.1074/jbc.m116.762831] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/03/2017] [Indexed: 11/06/2022] Open
Abstract
The lysosomal acid β-glucosidase GBA1 and the non-lysosomal β-glucosidase GBA2 degrade glucosylceramide (GlcCer) to glucose and ceramide in different cellular compartments. Loss of GBA2 activity and the resulting accumulation of GlcCer results in male infertility, whereas mutations in the GBA1 gene and loss of GBA1 activity cause the lipid-storage disorder Gaucher disease. However, the role of GBA2 in Gaucher disease pathology and its relationship to GBA1 is not well understood. Here, we report a GBA1-dependent down-regulation of GBA2 activity in patients with Gaucher disease. Using an experimental approach combining cell biology, biochemistry, and mass spectrometry, we show that sphingosine, the cytotoxic metabolite accumulating in Gaucher cells through the action of GBA2, directly binds to GBA2 and inhibits its activity. We propose a negative feedback loop, in which sphingosine inhibits GBA2 activity in Gaucher cells, preventing further sphingosine accumulation and, thereby, cytotoxicity. Our findings add a new chapter to the understanding of the complex molecular mechanism underlying Gaucher disease and the regulation of β-glucosidase activity in general.
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Affiliation(s)
- Sophie Schonauer
- From the Minerva Max Planck Research Group, Molecular Physiology, and
| | - Heinz G Körschen
- the Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), 53175 Bonn, Germany
| | - Anke Penno
- the Department of Cell Biology of Lipids, LIMES Institute, University of Bonn, Bonn, Germany
| | - Andreas Rennhack
- the Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), 53175 Bonn, Germany
| | - Bernadette Breiden
- the LIMES Institute, c/o Kekulé-Institute, University of Bonn, 53115 Bonn, Germany
| | - Konrad Sandhoff
- the LIMES Institute, c/o Kekulé-Institute, University of Bonn, 53115 Bonn, Germany
| | - Katharina Gutbrod
- the Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53115 Bonn, Germany
| | - Peter Dörmann
- the Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53115 Bonn, Germany
| | - Diana N Raju
- From the Minerva Max Planck Research Group, Molecular Physiology, and
| | - Per Haberkant
- the Proteomic Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Mathias J Gerl
- the Biochemie-Zentrum (BZH), Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Britta Brügger
- the Biochemie-Zentrum (BZH), Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Hila Zigdon
- the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel, and
| | - Ayelet Vardi
- the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel, and
| | - Anthony H Futerman
- the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel, and
| | - Christoph Thiele
- the Department of Cell Biology of Lipids, LIMES Institute, University of Bonn, Bonn, Germany
| | - Dagmar Wachten
- From the Minerva Max Planck Research Group, Molecular Physiology, and .,the Institute of Innate Immunity, University Hospital, University of Bonn, 53127 Bonn, Germany
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22
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Gerl MJ, Bittl V, Kirchner S, Sachsenheimer T, Brunner HL, Lüchtenborg C, Özbalci C, Wiedemann H, Wegehingel S, Nickel W, Haberkant P, Schultz C, Krüger M, Brügger B. Sphingosine-1-Phosphate Lyase Deficient Cells as a Tool to Study Protein Lipid Interactions. PLoS One 2016; 11:e0153009. [PMID: 27100999 PMCID: PMC4839656 DOI: 10.1371/journal.pone.0153009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 11/03/2015] [Accepted: 03/21/2016] [Indexed: 12/11/2022] Open
Abstract
Cell membranes contain hundreds to thousands of individual lipid species that are of structural importance but also specifically interact with proteins. Due to their highly controlled synthesis and role in signaling events sphingolipids are an intensely studied class of lipids. In order to investigate their metabolism and to study proteins interacting with sphingolipids, metabolic labeling based on photoactivatable sphingoid bases is the most straightforward approach. In order to monitor protein-lipid-crosslink products, sphingosine derivatives containing a reporter moiety, such as a radiolabel or a clickable group, are used. In normal cells, degradation of sphingoid bases via action of the checkpoint enzyme sphingosine-1-phosphate lyase occurs at position C2-C3 of the sphingoid base and channels the resulting hexadecenal into the glycerolipid biosynthesis pathway. In case the functionalized sphingosine looses the reporter moiety during its degradation, specificity towards sphingolipid labeling is maintained. In case degradation of a sphingosine derivative does not remove either the photoactivatable or reporter group from the resulting hexadecenal, specificity towards sphingolipid labeling can be achieved by blocking sphingosine-1-phosphate lyase activity and thus preventing sphingosine derivatives to be channeled into the sphingolipid-to-glycerolipid metabolic pathway. Here we report an approach using clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated nuclease Cas9 to create a sphingosine-1-phosphate lyase (SGPL1) HeLa knockout cell line to disrupt the sphingolipid-to-glycerolipid metabolic pathway. We found that the lipid and protein compositions as well as sphingolipid metabolism of SGPL1 knock-out HeLa cells only show little adaptations, which validates these cells as model systems to study transient protein-sphingolipid interactions.
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Affiliation(s)
- Mathias J. Gerl
- Heidelberg University Biochemistry Center, Heidelberg, Germany
- * E-mail: (MJG); (BB)
| | - Verena Bittl
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | | | | | | | | | - Cagakan Özbalci
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | | | | | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Per Haberkant
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
- * E-mail: (MJG); (BB)
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23
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Haberkant P, Stein F, Höglinger D, Gerl MJ, Brügger B, Van Veldhoven PP, Krijgsveld J, Gavin AC, Schultz C. Bifunctional Sphingosine for Cell-Based Analysis of Protein-Sphingolipid Interactions. ACS Chem Biol 2016; 11:222-30. [PMID: 26555438 DOI: 10.1021/acschembio.5b00810] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sphingolipids are essential structural components of cellular membranes and are crucial regulators of cellular processes. While current high-throughput approaches allow for the systematic mapping of interactions of soluble proteins with their lipid-binding partners, photo-cross-linking is the only technique that enables for the proteome-wide mapping of integral membrane proteins with their direct lipid environment. Here, we report the synthesis of a photoactivatable and clickable analog of sphingosine (pacSph). When administered to sphingosine-1-phosphate lyase deficient cells, pacSph allows its metabolic fate and the subcellular flux of de novo synthesized sphingolipids to be followed in a time-resolved manner. The chemoproteomic profiling yielded over 180 novel sphingolipid-binding proteins, of which we validated a number, demonstrating the unique value of this technique as a discovery tool. This work provides an important resource for the understanding of the global cellular interplay between sphingolipids and their interacting proteins.
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Affiliation(s)
- Per Haberkant
- European Molecular Biology Laboratory, Cell Biology
and Biophysics Unit, Meyerhofstr.
1, 69117 Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, Cell Biology
and Biophysics Unit, Meyerhofstr.
1, 69117 Heidelberg, Germany
| | - Doris Höglinger
- European Molecular Biology Laboratory, Cell Biology
and Biophysics Unit, Meyerhofstr.
1, 69117 Heidelberg, Germany
| | - Mathias J. Gerl
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Paul P. Van Veldhoven
- Laboratory
for Lipid Biochemistry and Protein Interactions, Department of Cellular
and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural
and Computational Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory, Cell Biology
and Biophysics Unit, Meyerhofstr.
1, 69117 Heidelberg, Germany
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24
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Höglinger D, Haberkant P, Aguilera-Romero A, Riezman H, Porter FD, Platt FM, Galione A, Schultz C. Intracellular sphingosine releases calcium from lysosomes. eLife 2015; 4:e10616. [PMID: 26613410 PMCID: PMC4744193 DOI: 10.7554/elife.10616] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/27/2015] [Indexed: 12/15/2022] Open
Abstract
To elucidate new functions of sphingosine (Sph), we demonstrate that the spontaneous elevation of intracellular Sph levels via caged Sph leads to a significant and transient calcium release from acidic stores that is independent of sphingosine 1-phosphate, extracellular and ER calcium levels. This photo-induced Sph-driven calcium release requires the two-pore channel 1 (TPC1) residing on endosomes and lysosomes. Further, uncaging of Sph leads to the translocation of the autophagy-relevant transcription factor EB (TFEB) to the nucleus specifically after lysosomal calcium release. We confirm that Sph accumulates in late endosomes and lysosomes of cells derived from Niemann-Pick disease type C (NPC) patients and demonstrate a greatly reduced calcium release upon Sph uncaging. We conclude that sphingosine is a positive regulator of calcium release from acidic stores and that understanding the interplay between Sph homeostasis, calcium signaling and autophagy will be crucial in developing new therapies for lipid storage disorders such as NPC.
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Affiliation(s)
- Doris Höglinger
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Per Haberkant
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Howard Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Forbes D Porter
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Antony Galione
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Carsten Schultz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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25
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Haberkant P, Holthuis JCM. Fat & fabulous: bifunctional lipids in the spotlight. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1022-30. [PMID: 24440797 DOI: 10.1016/j.bbalip.2014.01.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/02/2014] [Accepted: 01/05/2014] [Indexed: 01/25/2023]
Abstract
Understanding biological processes at the mechanistic level requires a systematic charting of the physical and functional links between all cellular components. While protein-protein and protein-nucleic acid networks have been subject to many global surveys, other critical cellular components such as membrane lipids have rarely been studied in large-scale interaction screens. Here, we review the development of photoactivatable and clickable lipid analogues-so-called bifunctional lipids-as novel chemical tools that enable a global profiling of lipid-protein interactions in biological membranes. Recent studies indicate that bifunctional lipids hold great promise in systematic efforts to dissect the elaborate crosstalk between proteins and lipids in live cells and organisms. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Per Haberkant
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Joost C M Holthuis
- Molecular Cell Biology, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany.
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26
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Haberkant P, Raijmakers R, Wildwater M, Sachsenheimer T, Brügger B, Maeda K, Houweling M, Gavin AC, Schultz C, van Meer G, Heck AJR, Holthuis JCM. Bifunktionalisierte Fettsäuren zur Visualisierung und Identifizierung von Protein-Lipid-Interaktionen in lebenden Zellen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210178] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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27
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Haberkant P, Raijmakers R, Wildwater M, Sachsenheimer T, Brügger B, Maeda K, Houweling M, Gavin AC, Schultz C, van Meer G, Heck AJR, Holthuis JCM. In Vivo Profiling and Visualization of Cellular Protein-Lipid Interactions Using Bifunctional Fatty Acids. Angew Chem Int Ed Engl 2013; 52:4033-8. [DOI: 10.1002/anie.201210178] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Indexed: 11/05/2022]
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28
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Abstract
Photoactivatable groups meeting the criterion of minimal perturbance allow the investigation of interactions in biological samples. Here, we review the application of photoactivatable groups in lipids enabling the study of protein-lipid interactions in (biological) membranes. The chemistry of various photoactivatable groups is summarized and the specificity of the interactions detected is discussed. The recent introduction of 'click chemistry' in photocrosslinking of membrane proteins by photo-activatable lipids opens new possibilities for the analysis of crosslinked products and will help to close the gap between proteomics and lipidomics.
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Affiliation(s)
- Per Haberkant
- Membrane Enzymology, Bijvoet Center and Institute of Biomembranes, Utrecht University, NL-3584 CH Utrecht, The Netherlands.
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29
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Haberkant P, Schmitt O, Contreras FX, Thiele C, Hanada K, Sprong H, Reinhard C, Wieland FT, Brügger B. Protein-sphingolipid interactions within cellular membranes. J Lipid Res 2007; 49:251-62. [PMID: 17906222 DOI: 10.1194/jlr.d700023-jlr200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Each intracellular organelle critically depends on maintaining its specific lipid composition that in turn contributes to the biophysical properties of the membrane. With our knowledge increasing about the organization of membranes with defined microdomains of different lipid compositions, questions arise regarding the molecular mechanisms that underlie the targeting to/segregation from microdomains of a given protein. In addition to specific lipid-transmembrane segment interactions as a basis for partitioning, the presence in a given microdomain may alter the conformation of proteins and, thus, the activity and availability for regulatory modifications. However, for most proteins, the specific lipid environment of transmembrane segments as well as its relevance to protein function and overall membrane organization are largely unknown. To help fill this gap, we have synthesized a novel photoactive sphingolipid precursor that, together with a precursor for phosphoglycerolipids and with photo-cholesterol, was investigated in vivo with regard to specific protein transmembrane span-lipid interactions. As a proof of principle, we show specific labeling of the ceramide transporter with the sphingolipid probe and describe specific in vivo interactions of lipids with caveolin-1, phosphatidylinositol transfer protein beta, and the mature form of nicastrin. This novel photolabile sphingolipid probe allows the detection of protein-sphingolipid interactions within the membrane bilayer of living cells.
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Affiliation(s)
- Per Haberkant
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
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Brügger B, Glass B, Haberkant P, Leibrecht I, Wieland FT, Kräusslich HG. The HIV lipidome: a raft with an unusual composition. Proc Natl Acad Sci U S A 2006; 103:2641-6. [PMID: 16481622 PMCID: PMC1413831 DOI: 10.1073/pnas.0511136103] [Citation(s) in RCA: 537] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lipids of enveloped viruses play critical roles in viral morphogenesis and infectivity. They are derived from the host membranes from which virus budding occurs, but the precise lipid composition has not been determined for any virus. Employing mass spectrometry, this study provides a quantitative analysis of the lipid constituents of HIV and a comprehensive comparison with its host membranes. Both a substantial enrichment of the unusual sphingolipid dihydrosphingomyelin and a loss of viral infectivity upon inhibition of sphingolipid biosynthesis in host cells are reported, establishing a critical role for this lipid class in the HIV replication cycle. Intriguingly, the overall lipid composition of native HIV membranes resembles detergent-resistant membrane microdomains and is strikingly different from that of host cell membranes. With this composition, the HIV lipidome provides strong evidence for the existence of lipid rafts in living cells.
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Affiliation(s)
- Britta Brügger
- *Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany; and
| | - Bärbel Glass
- Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
| | - Per Haberkant
- *Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany; and
| | - Iris Leibrecht
- *Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany; and
| | - Felix T. Wieland
- *Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany; and
- To whom correspondence may be addressed. E-mail:
or
| | - Hans-Georg Kräusslich
- Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
- To whom correspondence may be addressed. E-mail:
or
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