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Abu Sammour D, Cairns JL, Boskamp T, Marsching C, Kessler T, Ramallo Guevara C, Panitz V, Sadik A, Cordes J, Schmidt S, Mohammed SA, Rittel MF, Friedrich M, Platten M, Wolf I, von Deimling A, Opitz CA, Wick W, Hopf C. Spatial probabilistic mapping of metabolite ensembles in mass spectrometry imaging. Nat Commun 2023; 14:1823. [PMID: 37005414 PMCID: PMC10067847 DOI: 10.1038/s41467-023-37394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Mass spectrometry imaging vows to enable simultaneous spatially resolved investigation of hundreds of metabolites in tissues, but it primarily relies on traditional ion images for non-data-driven metabolite visualization and analysis. The rendering and interpretation of ion images neither considers nonlinearities in the resolving power of mass spectrometers nor does it yet evaluate the statistical significance of differential spatial metabolite abundance. Here, we outline the computational framework moleculaR ( https://github.com/CeMOS-Mannheim/moleculaR ) that is expected to improve signal reliability by data-dependent Gaussian-weighting of ion intensities and that introduces probabilistic molecular mapping of statistically significant nonrandom patterns of relative spatial abundance of metabolites-of-interest in tissue. moleculaR also enables cross-tissue statistical comparisons and collective molecular projections of entire biomolecular ensembles followed by their spatial statistical significance evaluation on a single tissue plane. It thereby fosters the spatially resolved investigation of ion milieus, lipid remodeling pathways, or complex scores like the adenylate energy charge within the same image.
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Affiliation(s)
- Denis Abu Sammour
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - James L Cairns
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Tobias Boskamp
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany
| | - Christian Marsching
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carina Ramallo Guevara
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Verena Panitz
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Ahmed Sadik
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Bioscience, Heidelberg University, Heidelberg, Germany
| | - Jonas Cordes
- Faculty of Computer Science, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Shad A Mohammed
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Miriam F Rittel
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Mirco Friedrich
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Platten
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivo Wolf
- Faculty of Computer Science, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- DKTK Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christiane A Opitz
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany.
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
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Kampa JM, Kellner U, Marsching C, Ramallo Guevara C, Knappe UJ, Sahin M, Giampà M, Niehaus K, Bednarz H. Glioblastoma multiforme: Metabolic differences to peritumoral tissue and
IDH
‐mutated gliomas revealed by mass spectrometry imaging. Neuropathology 2020; 40:546-558. [DOI: 10.1111/neup.12671] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 01/19/2023]
Affiliation(s)
- Judith M. Kampa
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Udo Kellner
- Institut für Pathologie, Johannes Wesling Klinikum Minden Germany
| | - Christian Marsching
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS) Mannheim University of Applied Sciences Mannheim Germany
| | - Carina Ramallo Guevara
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS) Mannheim University of Applied Sciences Mannheim Germany
| | - Ulrich J. Knappe
- Klinik für Neurochirurgie, Johannes Wesling Klinikum Minden Germany
| | - Mikail Sahin
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Marco Giampà
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
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Cerletti M, Paggi R, Troetschel C, Ferrari MC, Guevara CR, Albaum S, Poetsch A, De Castro R. LonB Protease Is a Novel Regulator of Carotenogenesis Controlling Degradation of Phytoene Synthase in Haloferax volcanii. J Proteome Res 2018; 17:1158-1171. [PMID: 29411617 DOI: 10.1021/acs.jproteome.7b00809] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The membrane protease LonB is an essential protein in the archaeon Haloferax volcanii and globally impacts its physiology. However, natural substrates of the archaeal Lon protease have not been identified. The whole proteome turnover was examined in a H. volcanii LonB mutant under reduced and physiological protease levels. LC-MS/MS combined with stable isotope labeling was applied for the identification/quantitation of membrane and cytoplasm proteins. Differential synthesis and degradation rates were evidenced for 414 proteins in response to Lon expression. A total of 58 proteins involved in diverse cellular processes showed a degradation pattern (none/very little degradation in the absence of Lon and increased degradation in the presence of Lon) consistent with a LonB substrate, which was further substantiated for several of these candidates by pull-down assays. The most notable was phytoene synthase (PSY), the rate-limiting enzyme in carotenoid biosynthesis. The rapid degradation of PSY upon LonB induction in addition to the remarkable stabilization of this protein and hyperpigmentation phenotype in the Lon mutant strongly suggest that PSY is a LonB substrate. This work identifies for the first time candidate targets of the archaeal Lon protease and establishes proteolysis by Lon as a novel post-translational regulatory mechanism of carotenogenesis.
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Affiliation(s)
- Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata 7600, Argentina
| | - Roberto Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata 7600, Argentina
| | | | - María Celeste Ferrari
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata 7600, Argentina
| | | | - Stefan Albaum
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University , 33615 Bielefeld, Germany
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum , 44801 Bochum, Germany.,School of Biomedical and Healthcare Sciences, Plymouth University , Plymouth PL4 8AA, United Kingdom
| | - Rosana De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata 7600, Argentina
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Ramallo Guevara C, Philipp O, Hamann A, Werner A, Osiewacz HD, Rexroth S, Rögner M, Poetsch A. Global Protein Oxidation Profiling Suggests Efficient Mitochondrial Proteome Homeostasis During Aging. Mol Cell Proteomics 2016; 15:1692-709. [PMID: 26884511 DOI: 10.1074/mcp.m115.055616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Indexed: 11/06/2022] Open
Abstract
The free radical theory of aging is based on the idea that reactive oxygen species (ROS) may lead to the accumulation of age-related protein oxidation. Because themajority of cellular ROS is generated at the respiratory electron transport chain, this study focuses on the mitochondrial proteome of the aging model Podospora anserina as target for ROS-induced damage. To ensure the detection of even low abundant modified peptides, separation by long gradient nLC-ESI-MS/MS and an appropriate statistical workflow for iTRAQ quantification was developed. Artificial protein oxidation was minimized by establishing gel-free sample preparation in the presence of reducing and iron-chelating agents. This first large scale, oxidative modification-centric study for P. anserina allowed the comprehensive quantification of 22 different oxidative amino acid modifications, and notably the quantitative comparison of oxidized and nonoxidized protein species. In total 2341 proteins were quantified. For 746 both protein species (unmodified and oxidatively modified) were detected and the modification sites determined. The data revealed that methionine residues are preferably oxidized. Further prominent identified modifications in decreasing order of occurrence were carbonylation as well as formation of N-formylkynurenine and pyrrolidinone. Interestingly, for the majority of proteins a positive correlation of changes in protein amount and oxidative damage were noticed, and a general decrease in protein amounts at late age. However, it was discovered that few proteins changed in oxidative damage in accordance with former reports. Our data suggest that P. anserina is efficiently capable to counteract ROS-induced protein damage during aging as long as protein de novo synthesis is functioning, ultimately leading to an overall constant relationship between damaged and undamaged protein species. These findings contradict a massive increase in protein oxidation during aging and rather suggest a protein damage homeostasis mechanism even at late age.
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Affiliation(s)
- Carina Ramallo Guevara
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, Bochum-44801, Germany
| | - Oliver Philipp
- §Molecular Developmental Biology, Faculty of Biosciences and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60438, Germany; ¶Molecular Bioinformatics, Faculty of Computer Science and Mathematics and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60325, Germany
| | - Andrea Hamann
- §Molecular Developmental Biology, Faculty of Biosciences and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60438, Germany
| | - Alexandra Werner
- §Molecular Developmental Biology, Faculty of Biosciences and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60438, Germany
| | - Heinz D Osiewacz
- §Molecular Developmental Biology, Faculty of Biosciences and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main-60438, Germany
| | - Sascha Rexroth
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, Bochum-44801, Germany
| | - Matthias Rögner
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, Bochum-44801, Germany
| | - Ansgar Poetsch
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, Bochum-44801, Germany;
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Cerletti M, Paggi RA, Guevara CR, Poetsch A, De Castro RE. Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii. J Proteomics 2015; 121:1-14. [PMID: 25829260 DOI: 10.1016/j.jprot.2015.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 01/23/2015] [Revised: 03/04/2015] [Accepted: 03/12/2015] [Indexed: 02/07/2023]
Abstract
UNLABELLED The membrane-associated LonB protease is essential for viability in Haloferax volcanii, however, the cellular processes affected by this protease in archaea are unknown. In this study, the impact of a lon conditional mutation (down-regulation) on H. volcanii physiology was examined by comparing proteomes of parental and mutant cells using shotgun proteomics. A total of 1778 proteins were identified (44% of H. volcanii predicted proteome) and 142 changed significantly in amount (≥2 fold). Of these, 66 were augmented in response to Lon deficiency suggesting they could be Lon substrates. The "Lon subproteome" included soluble and predicted membrane proteins expected to participate in diverse cellular processes. The dramatic stabilization of phytoene synthase (57 fold) in concert with overpigmentation of lon mutant cells suggests that Lon controls carotenogenesis in H. volcanii. Several hypothetical proteins, which may reveal novel functions and/or be involved in adaptation to extreme environments, were notably increased (300 fold). This study, which represents the first proteome examination of a Lon deficient archaeal cell, shows that Lon has a strong impact on H. volcanii physiology evidencing the cellular processes controlled by this protease in Archaea. Additionally, this work provides a platform for the discovery of novel targets of Lon proteases. BIOLOGICAL SIGNIFICANCE The proteome of a Lon-deficient archaeal cell was examined for the first time showing that Lon has a strong impact on H. volcanii physiology and evidencing the proteins and cellular processes controlled by this protease in Archaea. This work will facilitate future investigations aiming to address Lon function in archaea and provides a platform for the discovery of endogenous targets of the archaeal-type Lon as well as novel targets/processes regulated by Lon proteases. This knowledge will advance the understanding on archaeal physiology and the biological function of membrane proteases in microorganisms.
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Affiliation(s)
- Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina
| | | | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Rosana E De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina.
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