1
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Takagi S, Suzuki N, Ishihama Y. Revisiting Protein Reversed-Phase Chromatography for Bottom-Up Proteomics. J Proteome Res 2024. [PMID: 39293027 DOI: 10.1021/acs.jproteome.4c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
We revisited protein reversed-phase chromatography (RP), using state-of-the-art RP columns developed for biopharmaceuticals, such as monoclonal antibodies, in order to evaluate the suitability of this methodology as a prefractionation step for bottom-up proteomics. The protein RP prefractionation (Prot-RP) method was compared with two other widely used prefractionation methods, SDS-PAGE and high-pH peptide RP (Pept-RP) by using cell lysates as samples. The overlap between fractions of Prot-RP was comparable to that of SDS-PAGE, and the protein recovery was approximately 2-fold higher. On the other hand, the overlap between fractions of Prot-RP was slightly larger than that of Pept-RP, but Prot-RP was able to identify more protein termini and more isoform-specific peptides than Pept-RP. Our results indicate that the combination of highly efficient protein prefractionation with modern mass spectrometers is particularly effective for proteoform profiling from cellular samples.
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Affiliation(s)
- Shunsuke Takagi
- Department of Molecular Systems BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Analytical and Quality Evaluation Research Laboratories, Daiichi Sankyo Co., Ltd., Hiratsuka, Kanagawa 254-0014, Japan
| | - Nobuyuki Suzuki
- Analytical and Quality Evaluation Research Laboratories, Daiichi Sankyo Co., Ltd., Hiratsuka, Kanagawa 254-0014, Japan
| | - Yasushi Ishihama
- Department of Molecular Systems BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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2
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Oeckl J, Janovska P, Adamcova K, Bardova K, Brunner S, Dieckmann S, Ecker J, Fromme T, Funda J, Gantert T, Giansanti P, Hidrobo MS, Kuda O, Kuster B, Li Y, Pohl R, Schmitt S, Schweizer S, Zischka H, Zouhar P, Kopecky J, Klingenspor M. Loss of UCP1 function augments recruitment of futile lipid cycling for thermogenesis in murine brown fat. Mol Metab 2022; 61:101499. [PMID: 35470094 PMCID: PMC9097615 DOI: 10.1016/j.molmet.2022.101499] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Josef Oeckl
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Petra Janovska
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Katerina Adamcova
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Kristina Bardova
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Sarah Brunner
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Sebastian Dieckmann
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Josef Ecker
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Tobias Fromme
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Jiri Funda
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Thomas Gantert
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Piero Giansanti
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Maria Soledad Hidrobo
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Ondrej Kuda
- Laboratory of Metabolism of Bioactive Lipids, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Yongguo Li
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Radek Pohl
- NMR spectroscopy, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Czech Republic
| | - Sabine Schmitt
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sabine Schweizer
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Hans Zischka
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, Munich, Germany
| | - Petr Zouhar
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic
| | - Jan Kopecky
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Czech Republic.
| | - Martin Klingenspor
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
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3
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Baasch S, Giansanti P, Kolter J, Riedl A, Forde AJ, Runge S, Zenke S, Elling R, Halenius A, Brabletz S, Hengel H, Kuster B, Brabletz T, Cicin-Sain L, Arens R, Vlachos A, Rohr JC, Stemmler MP, Kopf M, Ruzsics Z, Henneke P. Cytomegalovirus subverts macrophage identity. Cell 2021; 184:3774-3793.e25. [PMID: 34115982 DOI: 10.1016/j.cell.2021.05.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/26/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022]
Abstract
Cytomegaloviruses (CMVs) have co-evolved with their mammalian hosts for millions of years, leading to remarkable host specificity and high infection prevalence. Macrophages, which already populate barrier tissues in the embryo, are the predominant immune cells at potential CMV entry sites. Here we show that, upon CMV infection, macrophages undergo a morphological, immunophenotypic, and metabolic transformation process with features of stemness, altered migration, enhanced invasiveness, and provision of the cell cycle machinery for viral proliferation. This complex process depends on Wnt signaling and the transcription factor ZEB1. In pulmonary infection, mouse CMV primarily targets and reprograms alveolar macrophages, which alters lung physiology and facilitates primary CMV and secondary bacterial infection by attenuating the inflammatory response. Thus, CMV profoundly perturbs macrophage identity beyond established limits of plasticity and rewires specific differentiation processes, allowing viral spread and impairing innate tissue immunity.
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Affiliation(s)
- Sebastian Baasch
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Piero Giansanti
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Julia Kolter
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - André Riedl
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Aaron James Forde
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Solveig Runge
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Simon Zenke
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Roland Elling
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106 Freiburg, Germany
| | - Anne Halenius
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Simone Brabletz
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hartmut Hengel
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University Munich, 85354 Freising, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Luka Cicin-Sain
- Immune Aging and Chronic Infections Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hanover Medical School (MHH), 30625 Hanover, Germany
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Jan Christopher Rohr
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106 Freiburg, Germany
| | - Marc Philippe Stemmler
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Zsolt Ruzsics
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Philipp Henneke
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106 Freiburg, Germany.
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4
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A mass spectrometry-based proteome map of drug action in lung cancer cell lines. Nat Chem Biol 2020; 16:1111-1119. [PMID: 32690943 DOI: 10.1038/s41589-020-0572-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 05/22/2020] [Indexed: 11/08/2022]
Abstract
Mass spectrometry-based discovery proteomics is an essential tool for the proximal readout of cellular drug action. Here, we apply a robust proteomic workflow to rapidly profile the proteomes of five lung cancer cell lines in response to more than 50 drugs. Integration of millions of quantitative protein-drug associations substantially improved the mechanism of action (MoA) deconvolution of single compounds. For example, MoA specificity increased after removal of proteins that frequently responded to drugs and the aggregation of proteome changes across cell lines resolved compound effects on proteostasis. We leveraged these findings to demonstrate efficient target identification of chemical protein degraders. Aggregating drug response across cell lines also revealed that one-quarter of compounds modulated the abundance of one of their known protein targets. Finally, the proteomic data led us to discover that inhibition of mitochondrial function is an off-target mechanism of the MAP2K1/2 inhibitor PD184352 and that the ALK inhibitor ceritinib modulates autophagy.
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5
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Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B. Meltome atlas-thermal proteome stability across the tree of life. Nat Methods 2020; 17:495-503. [PMID: 32284610 DOI: 10.1038/s41592-020-0801-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic proteins show a nonlinear relationship between the degree of disordered protein structure and thermal stability. The data indicate that evolutionary conservation of protein complexes is reflected by similar thermal stability of their proteins, and we show examples in which genomic alterations can affect thermal stability. Proteins of the respiratory chain were found to be very stable in many organisms, and human mitochondria showed close to normal respiration at 46 °C. We also noted cell-type-specific effects that can affect protein stability or the efficacy of drugs. This meltome atlas broadly defines the proteome amenable to thermal profiling in biology and drug discovery and can be explored online at http://meltomeatlas.proteomics.wzw.tum.de:5003/ and http://www.proteomicsdb.org.
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Affiliation(s)
- Anna Jarzab
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Nils Kurzawa
- Genome Biology Unit, EMBL, Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | | | - Matthias Moerch
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Niels Leijten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Yangyang Bian
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Eva Musiol
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | | | | | | | - Charlotte Daly
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Britta Spanier
- Chair of Nutritional Physiology, Technical University of Munich, Freising, Germany
| | - Angel Angelov
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Wolfgang Liebl
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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6
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Wang D, Eraslan B, Wieland T, Hallström B, Hopf T, Zolg DP, Zecha J, Asplund A, Li LH, Meng C, Frejno M, Schmidt T, Schnatbaum K, Wilhelm M, Ponten F, Uhlen M, Gagneur J, Hahne H, Kuster B. A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. Mol Syst Biol 2019; 15:e8503. [PMID: 30777892 PMCID: PMC6379049 DOI: 10.15252/msb.20188503] [Citation(s) in RCA: 426] [Impact Index Per Article: 85.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 01/01/2019] [Accepted: 01/08/2019] [Indexed: 11/28/2022] Open
Abstract
Genome-, transcriptome- and proteome-wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein-level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue-specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.
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Affiliation(s)
- Dongxue Wang
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Basak Eraslan
- Computational Biology, Department of Informatics, Technical University of Munich, Garching bei München, Germany
- Department of Biochemistry, Quantitative Biosciences Munich, Gene Center, Ludwig Maximilian Universität, München, Germany
| | | | - Björn Hallström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | | | - Daniel Paul Zolg
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Anna Asplund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Li-Hua Li
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | | | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Frederik Ponten
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Julien Gagneur
- Computational Biology, Department of Informatics, Technical University of Munich, Garching bei München, Germany
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
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7
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Kindt A, Liebisch G, Clavel T, Haller D, Hörmannsperger G, Yoon H, Kolmeder D, Sigruener A, Krautbauer S, Seeliger C, Ganzha A, Schweizer S, Morisset R, Strowig T, Daniel H, Helm D, Küster B, Krumsiek J, Ecker J. The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice. Nat Commun 2018; 9:3760. [PMID: 30218046 PMCID: PMC6138742 DOI: 10.1038/s41467-018-05767-4] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 07/05/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Interactions between the gut microbial ecosystem and host lipid homeostasis are highly relevant to host physiology and metabolic diseases. We present a comprehensive multi-omics view of the effect of intestinal microbial colonization on hepatic lipid metabolism, integrating transcriptomic, proteomic, phosphoproteomic, and lipidomic analyses of liver and plasma samples from germfree and specific pathogen-free mice. Microbes induce monounsaturated fatty acid generation by stearoyl-CoA desaturase 1 and polyunsaturated fatty acid elongation by fatty acid elongase 5, leading to significant alterations in glycerophospholipid acyl-chain profiles. A composite classification score calculated from the observed alterations in fatty acid profiles in germfree mice clearly differentiates antibiotic-treated mice from untreated controls with high sensitivity. Mechanistic investigations reveal that acetate originating from gut microbial degradation of dietary fiber serves as precursor for hepatic synthesis of C16 and C18 fatty acids and their related glycerophospholipid species that are also released into the circulation.
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Affiliation(s)
- Alida Kindt
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Department of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333, Netherlands
| | - Gerhard Liebisch
- Institute of Clinical Chemistry, Universitätsklinikum Regensburg, Regensburg, 93053, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, Universitätsklinikum Aachen, Aachen, 52074, Germany.,ZIEL Institute for Food and Health, Technische Universität München (TUM), Freising, 85354, Germany
| | - Dirk Haller
- ZIEL Institute for Food and Health, Technische Universität München (TUM), Freising, 85354, Germany.,Ernährung und Immunologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Gabriele Hörmannsperger
- ZIEL Institute for Food and Health, Technische Universität München (TUM), Freising, 85354, Germany.,Ernährung und Immunologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Hongsup Yoon
- ZIEL Institute for Food and Health, Technische Universität München (TUM), Freising, 85354, Germany.,Ernährung und Immunologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Daniela Kolmeder
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Alexander Sigruener
- Institute of Clinical Chemistry, Universitätsklinikum Regensburg, Regensburg, 93053, Germany
| | - Sabrina Krautbauer
- Institute of Clinical Chemistry, Universitätsklinikum Regensburg, Regensburg, 93053, Germany
| | - Claudine Seeliger
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Alexandra Ganzha
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Sabine Schweizer
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Rosalie Morisset
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Till Strowig
- Research Group Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Hannelore Daniel
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Dominic Helm
- Proteomics and Bioanalytics, Technische Universität München (TUM), Freising, 85354, Germany
| | - Bernhard Küster
- Proteomics and Bioanalytics, Technische Universität München (TUM), Freising, 85354, Germany
| | - Jan Krumsiek
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany. .,German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany. .,Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, 10021, USA.
| | - Josef Ecker
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany.
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8
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Zecha J, Meng C, Zolg DP, Samaras P, Wilhelm M, Kuster B. Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics. Mol Cell Proteomics 2018; 17:974-992. [PMID: 29414762 PMCID: PMC5930408 DOI: 10.1074/mcp.ra118.000583] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/31/2018] [Indexed: 11/06/2022] Open
Abstract
The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass spectrometry-based technologies allow determination of endogenous protein turnover on a proteome-wide scale. However, standard dynamic SILAC (Stable Isotope Labeling in Cell Culture) approaches can suffer from missing data across pulse time-points limiting the accuracy of such analysis. This issue is of particular relevance when studying protein stability at the level of proteoforms because often only single peptides distinguish between different protein products of the same gene. To address this shortcoming, we evaluated the merits of combining dynamic SILAC and tandem mass tag (TMT)-labeling of ten pulse time-points in a single experiment. Although the comparison to the standard dynamic SILAC method showed a high concordance of protein turnover rates, the pulsed SILAC-TMT approach yielded more comprehensive data (6000 proteins on average) without missing values. Replicate analysis further established that the same reproducibility of turnover rate determination can be obtained for peptides and proteins facilitating proteoform resolved investigation of protein stability. We provide several examples of differentially turned over splice variants and show that post-translational modifications can affect cellular protein half-lives. For example, N-terminally processed peptides exhibited both faster and slower turnover behavior compared with other peptides of the same protein. In addition, the suspected proteolytic processing of the fusion protein FAU was substantiated by measuring vastly different stabilities of the cleavage products. Furthermore, differential peptide turnover suggested a previously unknown mechanism of activity regulation by post-translational destabilization of cathepsin D as well as the DNA helicase BLM. Finally, our comprehensive data set facilitated a detailed evaluation of the impact of protein properties and functions on protein stability in steady-state cells and uncovered that the high turnover of respiratory chain complex I proteins might be explained by oxidative stress.
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Affiliation(s)
- Jana Zecha
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- §German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- ¶German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Chen Meng
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Daniel Paul Zolg
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Patroklos Samaras
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Bernhard Kuster
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany;
- §German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- ¶German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- ‖Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, 85354 Freising, Germany
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9
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Lee CY, Wang D, Wilhelm M, Zolg DP, Schmidt T, Schnatbaum K, Reimer U, Pontén F, Uhlén M, Hahne H, Kuster B. Mining the Human Tissue Proteome for Protein Citrullination. Mol Cell Proteomics 2018; 17:1378-1391. [PMID: 29610271 DOI: 10.1074/mcp.ra118.000696] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/28/2018] [Indexed: 11/06/2022] Open
Abstract
Citrullination is a posttranslational modification of arginine catalyzed by five peptidylarginine deiminases (PADs) in humans. The loss of a positive charge may cause structural or functional alterations, and while the modification has been linked to several diseases, including rheumatoid arthritis (RA) and cancer, its physiological or pathophysiological roles remain largely unclear. In part, this is owing to limitations in available methodology to robustly enrich, detect, and localize the modification. As a result, only a few citrullination sites have been identified on human proteins with high confidence. In this study, we mined data from mass-spectrometry-based deep proteomic profiling of 30 human tissues to identify citrullination sites on endogenous proteins. Database searching of ∼70 million tandem mass spectra yielded ∼13,000 candidate spectra, which were further triaged by spectrum quality metrics and the detection of the specific neutral loss of isocyanic acid from citrullinated peptides to reduce false positives. Because citrullination is easily confused with deamidation, we synthetized ∼2,200 citrullinated and 1,300 deamidated peptides to build a library of reference spectra. This led to the validation of 375 citrullination sites on 209 human proteins. Further analysis showed that >80% of the identified modifications sites were new, and for 56% of the proteins, citrullination was detected for the first time. Sequence motif analysis revealed a strong preference for Asp and Gly, residues around the citrullination site. Interestingly, while the modification was detected in 26 human tissues with the highest levels found in the brain and lung, citrullination levels did not correlate well with protein expression of the PAD enzymes. Even though the current work represents the largest survey of protein citrullination to date, the modification was mostly detected on high abundant proteins, arguing that the development of specific enrichment methods would be required in order to study the full extent of cellular protein citrullination.
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Affiliation(s)
- Chien-Yun Lee
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,§Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.,¶Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
| | - Dongxue Wang
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Daniel P Zolg
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tobias Schmidt
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Ulf Reimer
- ‖JPT Peptide Technologies GmbH, Berlin, Germany
| | - Fredrik Pontén
- **Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- ‡‡Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Bernhard Kuster
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; .,¶¶Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
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10
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Recent trends and analytical challenges in plant bioactive peptide separation, identification and validation. Anal Bioanal Chem 2018; 410:3425-3444. [PMID: 29353433 DOI: 10.1007/s00216-018-0852-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/12/2017] [Accepted: 01/03/2018] [Indexed: 12/11/2022]
Abstract
Interest in research into bioactive peptides (BPs) is growing because of their health-promoting ability. Several bioactivities have been ascribed to peptides, including antioxidant, antihypertensive and antimicrobial properties. As they can be produced from precursor proteins, the investigation of BPs in foods is becoming increasingly popular. For the same reason, production of BPs from by-products has also emerged as a possible means of reducing waste and recovering value-added compounds suitable for functional food production and supplements. Milk, meat and fish are the most investigated sources of BPs, but vegetable-derived peptides are also of interest. Vegetables are commonly consumed, and agro-industrial wastes constitute a cheap, large and lower environmental impact source of proteins. The use of advanced analytical techniques for separation and identification of peptides would greatly benefit the discovery of new BPs. In this context, this review provides an overview of the most recent applications in BP investigations for vegetable food and by-products. The most important issues regarding peptide isolation and separation, by single or multiple chromatographic techniques, are discussed. Additionally, problems connected with peptide identification in plants and non-model plants are discussed regarding the particular case of BP identification. Finally, the issue of peptide validation to confirm sequence and bioactivity is presented. Graphical representation of the analytical workflow needed for investigation of bioactive peptides and applied to vegetables and vegetable wastes Graphical Abstract.
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11
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Yu P, Petzoldt S, Wilhelm M, Zolg DP, Zheng R, Sun X, Liu X, Schneider G, Huhmer A, Kuster B. Trimodal Mixed Mode Chromatography That Enables Efficient Offline Two-Dimensional Peptide Fractionation for Proteome Analysis. Anal Chem 2017; 89:8884-8891. [DOI: 10.1021/acs.analchem.7b01356] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peng Yu
- Technical University of Munich, D-85354 Freising, Germany
| | - Svenja Petzoldt
- Technical University of Munich, D-85354 Freising, Germany
- German Cancer Consortium (DKTK), 80336 Munich, Germany
- German Cancer Center (DKFZ), D-69120 Heidelberg, Germany
| | | | | | - Runsheng Zheng
- Technical University of Munich, D-85354 Freising, Germany
| | - Xuefei Sun
- Thermo Fisher Scientific, Sunnyvale, California 94085, United States
| | - Xiaodong Liu
- Thermo Fisher Scientific, Sunnyvale, California 94085, United States
| | - Günter Schneider
- Department
of Medicine II, Klinikum rechts der Isar, Technical University of Munich, D-81675 Munich, Germany
| | - Andreas Huhmer
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Bernhard Kuster
- Technical University of Munich, D-85354 Freising, Germany
- German Cancer Consortium (DKTK), 80336 Munich, Germany
- German Cancer Center (DKFZ), D-69120 Heidelberg, Germany
- Center for Integrated Protein Science Munich, 85354 Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, 85354 Freising, Germany
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