1
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White MEH, Sinn LR, Jones DM, de Folter J, Aulakh SK, Wang Z, Flynn HR, Krüger L, Tober-Lau P, Demichev V, Kurth F, Mülleder M, Blanchard V, Messner CB, Ralser M. Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics. Nat Biomed Eng 2024; 8:233-247. [PMID: 37474612 DOI: 10.1038/s41551-023-01067-5] [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: 07/19/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
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Affiliation(s)
- Matthew E H White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ludwig R Sinn
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Marc Jones
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Joost de Folter
- Software Engineering and Artificial Intelligence Technology Platform, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ziyue Wang
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lynn Krüger
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility High-throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Véronique Blanchard
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Precision Proteomic Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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2
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Cervia-Hasler C, Brüningk SC, Hoch T, Fan B, Muzio G, Thompson RC, Ceglarek L, Meledin R, Westermann P, Emmenegger M, Taeschler P, Zurbuchen Y, Pons M, Menges D, Ballouz T, Cervia-Hasler S, Adamo S, Merad M, Charney AW, Puhan M, Brodin P, Nilsson J, Aguzzi A, Raeber ME, Messner CB, Beckmann ND, Borgwardt K, Boyman O. Persistent complement dysregulation with signs of thromboinflammation in active Long Covid. Science 2024; 383:eadg7942. [PMID: 38236961 DOI: 10.1126/science.adg7942] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/24/2023] [Indexed: 01/23/2024]
Abstract
Long Covid is a debilitating condition of unknown etiology. We performed multimodal proteomics analyses of blood serum from COVID-19 patients followed up to 12 months after confirmed severe acute respiratory syndrome coronavirus 2 infection. Analysis of >6500 proteins in 268 longitudinal samples revealed dysregulated activation of the complement system, an innate immune protection and homeostasis mechanism, in individuals experiencing Long Covid. Thus, active Long Covid was characterized by terminal complement system dysregulation and ongoing activation of the alternative and classical complement pathways, the latter associated with increased antibody titers against several herpesviruses possibly stimulating this pathway. Moreover, markers of hemolysis, tissue injury, platelet activation, and monocyte-platelet aggregates were increased in Long Covid. Machine learning confirmed complement and thromboinflammatory proteins as top biomarkers, warranting diagnostic and therapeutic interrogation of these systems.
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Affiliation(s)
- Carlo Cervia-Hasler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Sarah C Brüningk
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tobias Hoch
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Bowen Fan
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Giulia Muzio
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ryan C Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Ceglarek
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Roman Meledin
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Patrick Westermann
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research, University of Zurich, 7265 Davos, Switzerland
| | - Marc Emmenegger
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Patrick Taeschler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Michele Pons
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Dominik Menges
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Tala Ballouz
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Sara Cervia-Hasler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Sarah Adamo
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Miriam Merad
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander W Charney
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Milo Puhan
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Petter Brodin
- Unit for Clinical Pediatrics, Department of Women's and Children's Health, Karolinska Institute, 17165 Solna, Sweden
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research, University of Zurich, 7265 Davos, Switzerland
| | - Noam D Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Data Driven and Digital Medicine (D3M), Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karsten Borgwardt
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
- Faculty of Medicine and Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
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3
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Munro V, Kelly V, Messner CB, Kustatscher G. Cellular control of protein levels: A systems biology perspective. Proteomics 2023:e2200220. [PMID: 38012370 DOI: 10.1002/pmic.202200220] [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: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from transcription to protein degradation. Recent advances in transcriptomics and proteomics have complemented our understanding of these fundamental cellular processes with a quantitative, systems-level perspective. Multi-omic studies revealed significant quantitative, kinetic and functional differences between the genome, transcriptome and proteome. While protein levels often correlate with mRNA levels, quantitative investigations have demonstrated a substantial impact of translation and protein degradation on protein expression control. In addition, protein-level regulation appears to play a crucial role in buffering protein abundances against undesirable mRNA expression variation. These findings have practical implications for many fields, including gene function prediction and precision medicine.
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Affiliation(s)
- Victoria Munro
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Van Kelly
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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4
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Messner CB, Demichev V, Muenzner J, Aulakh SK, Barthel N, Röhl A, Herrera-Domínguez L, Egger AS, Kamrad S, Hou J, Tan G, Lemke O, Calvani E, Szyrwiel L, Mülleder M, Lilley KS, Boone C, Kustatscher G, Ralser M. The proteomic landscape of genome-wide genetic perturbations. Cell 2023; 186:2018-2034.e21. [PMID: 37080200 PMCID: PMC7615649 DOI: 10.1016/j.cell.2023.03.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 05/17/2022] [Revised: 01/20/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library in Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We find that global protein expression is driven by a complex interplay of (1) general biological properties, including translation rate, protein turnover, the formation of protein complexes, growth rate, and genome architecture, followed by (2) functional properties, such as the connectivity of a protein in genetic, metabolic, and physical interaction networks. Moreover, we show that functional proteomics complements current gene annotation strategies through the assessment of proteome profile similarity, protein covariation, and reverse proteome profiling. Thus, our study reveals principles that govern protein expression and provides a genome-spanning resource for functional annotation.
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Affiliation(s)
- Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland
| | - Vadim Demichev
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, UK
| | - Julia Muenzner
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Simran K Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Natalie Barthel
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Annika Röhl
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | | | - Anna-Sophia Egger
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Stephan Kamrad
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Jing Hou
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Guihong Tan
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Oliver Lemke
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Enrica Calvani
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, UK
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S3E1, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; RIKEN Center for Sustainable Resource Science, Wako, 351-0198 Saitama, Japan
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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5
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Messner CB, Demichev V, Wang Z, Hartl J, Kustatscher G, Mülleder M, Ralser M. Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology. Proteomics 2023; 23:e2200013. [PMID: 36349817 DOI: 10.1002/pmic.202200013] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [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: 07/07/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022]
Abstract
There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.
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Affiliation(s)
- Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Vadim Demichev
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ziyue Wang
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Hartl
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh, Scotland, UK
| | - Michael Mülleder
- Core Facility High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Ralser
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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6
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Correia-Melo C, Kamrad S, Tengölics R, Messner CB, Trebulle P, Townsend S, Jayasree Varma S, Freiwald A, Heineike BM, Campbell K, Herrera-Dominguez L, Kaur Aulakh S, Szyrwiel L, Yu JSL, Zelezniak A, Demichev V, Mülleder M, Papp B, Alam MT, Ralser M. Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan. Cell 2023; 186:63-79.e21. [PMID: 36608659 DOI: 10.1016/j.cell.2022.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 03/22/2022] [Revised: 09/07/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
Metabolism is deeply intertwined with aging. Effects of metabolic interventions on aging have been explained with intracellular metabolism, growth control, and signaling. Studying chronological aging in yeast, we reveal a so far overlooked metabolic property that influences aging via the exchange of metabolites. We observed that metabolites exported by young cells are re-imported by chronologically aging cells, resulting in cross-generational metabolic interactions. Then, we used self-establishing metabolically cooperating communities (SeMeCo) as a tool to increase metabolite exchange and observed significant lifespan extensions. The longevity of the SeMeCo was attributable to metabolic reconfigurations in methionine consumer cells. These obtained a more glycolytic metabolism and increased the export of protective metabolites that in turn extended the lifespan of cells that supplied them with methionine. Our results establish metabolite exchange interactions as a determinant of cellular aging and show that metabolically cooperating cells can shape the metabolic environment to extend their lifespan.
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Affiliation(s)
- Clara Correia-Melo
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.
| | - Stephan Kamrad
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Roland Tengölics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged 6726, Hungary; HCEMM-BRC Metabolic Systems Biology Lab, Szeged 6726, Hungary
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland
| | - Pauline Trebulle
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - StJohn Townsend
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | | | - Anja Freiwald
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Benjamin M Heineike
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Quantitative Gene Expression Research Group, MRC London Institute of Medical Sciences (LMS), London W12 0HS, UK; Quantitative Gene Expression Research Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW2 2AZ, UK
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Lucía Herrera-Dominguez
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Simran Kaur Aulakh
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Lukasz Szyrwiel
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Aleksej Zelezniak
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Vadim Demichev
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Michael Mülleder
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged 6726, Hungary; HCEMM-BRC Metabolic Systems Biology Lab, Szeged 6726, Hungary
| | - Mohammad Tauqeer Alam
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al-Ain, United Arab Emirates
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.
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7
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Yu JSL, Heineike BM, Hartl J, Aulakh SK, Correia-Melo C, Lehmann A, Lemke O, Agostini F, Lee CT, Demichev V, Messner CB, Mülleder M, Ralser M. Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy. PLoS Biol 2022; 20:e3001912. [PMID: 36455053 PMCID: PMC9757880 DOI: 10.1371/journal.pbio.3001912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/16/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which organosulfur auxotrophy caused by deletion of the homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. In combining the use of self-establishing metabolically cooperating (SeMeCo) communities with proteomic, genetic, and biochemical approaches, we discovered an uncharacterized gene product YLL058Wp, herein named Hydrogen Sulfide Utilizing-1 (HSU1). Hsu1p acts as a homocysteine synthase and allows the cells to substitute for Met17p by reassimilating hydrosulfide ions leaked from met17Δ cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity to overcome sulfur limitation.
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Affiliation(s)
- Jason S. L. Yu
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Benjamin M. Heineike
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Johannes Hartl
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Simran K. Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Clara Correia-Melo
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Lehmann
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Oliver Lemke
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Cory T. Lee
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Vadim Demichev
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B. Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Mülleder
- Core Facility—High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
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8
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Varma SJ, Calvani E, Grüning NM, Messner CB, Grayson N, Capuano F, Mülleder M, Ralser M. Global analysis of cytosine and adenine DNA modifications across the tree of life. eLife 2022; 11:81002. [PMID: 35900202 PMCID: PMC9333990 DOI: 10.7554/elife.81002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022] Open
Abstract
Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical methods for the global quantification of DNA modifications have thus far been applied mostly to individual problems. We established a mass spectrometric method for the sensitive and accurate quantification of multiple enzymatic DNA modifications. Then, we isolated DNA from 124 archean, bacterial, fungal, plant, and mammalian species, and several tissues and created a resource of global DNA modification quantities. Our dataset provides insights into the general nature of enzymatic DNA modifications, reveals unique biological cases, and provides complementary quantitative information to normalize and assess the accuracy of sequencing-based detection of DNA modifications. We report that only three of the studied DNA modifications, methylcytosine (5mdC), methyladenine (N6mdA) and hydroxymethylcytosine (5hmdC), were detected above a picomolar detection limit across species, and dominated in higher eukaryotes (5mdC), in bacteria (N6mdA), or the vertebrate central nervous systems (5hmdC). All three modifications were detected simultaneously in only one of the tested species, Raphanus sativus. In contrast, these modifications were either absent or detected only at trace quantities, across all yeasts and insect genomes studied. Further, we reveal interesting biological cases. For instance, in Allium cepa, Helianthus annuus, or Andropogon gerardi, more than 35% of cytosines were methylated. Additionally, next to the mammlian CNS, 5hmdC was also detected in plants like Lepidium sativum and was found on 8% of cytosines in the Garra barreimiae brain samples. Thus, identifying unexpected levels of DNA modifications in several wild species, our resource underscores the need to address biological diversity for studying DNA modifications.
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Affiliation(s)
| | - Enrica Calvani
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nana-Maria Grüning
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Grayson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Michael Mülleder
- Core Facility-High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany.,The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
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9
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Yu JSL, Correia-Melo C, Zorrilla F, Herrera-Dominguez L, Wu MY, Hartl J, Campbell K, Blasche S, Kreidl M, Egger AS, Messner CB, Demichev V, Freiwald A, Mülleder M, Howell M, Berman J, Patil KR, Alam MT, Ralser M. Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance. Nat Microbiol 2022; 7:542-555. [PMID: 35314781 PMCID: PMC8975748 DOI: 10.1038/s41564-022-01072-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [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: 03/16/2021] [Accepted: 01/28/2022] [Indexed: 12/30/2022]
Abstract
Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of auxotrophic–prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites and, in this way, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically. Using microbiome data analysis and a self-establishing metabolically cooperating yeast community model, the authors show that the presence of auxotrophs in a microbial community increases metabolic interactions between cells and fosters antimicrobial drug tolerance.
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Affiliation(s)
- Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Clara Correia-Melo
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Francisco Zorrilla
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lucia Herrera-Dominguez
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Mary Y Wu
- High-Throughput Screening, The Francis Crick Institute, London, UK
| | - Johannes Hartl
- Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sonja Blasche
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marco Kreidl
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anna-Sophia Egger
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vadim Demichev
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anja Freiwald
- Department of Biochemistry, Charité University Medicine, Berlin, Germany.,Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany
| | - Michael Mülleder
- Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany
| | - Michael Howell
- High-Throughput Screening, The Francis Crick Institute, London, UK
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Kiran R Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mohammad Tauqeer Alam
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, UAE. .,Warwick Medical School, University of Warwick, Coventry, UK.
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK. .,Department of Biochemistry, Charité University Medicine, Berlin, Germany. .,Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany.
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10
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Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, Kurth F, Ralser M. A proteomic survival predictor for COVID-19 patients in intensive care. PLOS Digit Health 2022; 1:e0000007. [PMID: 36812516 PMCID: PMC9931303 DOI: 10.1371/journal.pdig.0000007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023]
Abstract
Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.
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Affiliation(s)
- Vadim Demichev
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge, United Kingdom
| | - Pinkus Tober-Lau
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Tatiana Nazarenko
- University College London, Department of Mathematics, London, United Kingdom
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
| | - Oliver Lemke
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Simran Kaur Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod, Russia
- Imperial College London, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, London, United Kingdom
| | - Annika Röhl
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Anja Freiwald
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Mirja Mittermaier
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Daniela Ludwig
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Lena J. Lippert
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Elisa T. Helbig
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Paula Stubbemann
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Nadine Olk
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Charlotte Thibeault
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Nana-Maria Grüning
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Oleg Blyuss
- Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod, Russia
- University of Hertfordshire, School of Physics, Astronomy and Mathematics, Hatfield, United Kingdom
- Sechenov First Moscow State Medical University, Department of Paediatrics and Paediatric Infectious Diseases, Moscow, Russia
| | - Spyros Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Matthew White
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Christoph B. Messner
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Michael Joannidis
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Innsbruck, Austria
| | - Thomas Sonnweber
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Sebastian J. Klein
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Innsbruck, Austria
| | - Alex Pizzini
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Yvonne Wohlfarter
- Medical University of Innsbruck, Institute of Human Genetics, Innsbruck, Austria
| | - Sabina Sahanic
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Richard Hilbe
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Benedikt Schaefer
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Sonja Wagner
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Felix Machleidt
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Carmen Garcia
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Christoph Ruwwe-Glösenkamp
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Tilman Lingscheid
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Laure Bosquillon de Jarcy
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Miriam S. Stegemann
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Moritz Pfeiffer
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Linda Jürgens
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Sophy Denker
- Charité–Universitätsmedizin Berlin, Medical Department of Hematology, Oncology & Tumor Immunology, Virchow Campus & Molekulares Krebsforschungszentrum, Berlin, Germany
| | - Daniel Zickler
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Claudia Spies
- Charité–Universitätsmedizin Berlin, Department of Anesthesiology and Intensive Care, Berlin, Germany
| | - Andreas Edel
- Charité–Universitätsmedizin Berlin, Department of Anesthesiology and Intensive Care, Berlin, Germany
| | - Nils B. Müller
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Philipp Enghard
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
- Chalmers University of Technology, Department of Biology and Biological Engineering, Gothenburg, Sweden
| | - Rosa Bellmann-Weiler
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Günter Weiss
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Archie Campbell
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
- University of Edinburgh, Usher Institute, Edinburgh, United Kingdom
| | - Caroline Hayward
- University of Edinburgh, MRC Human Genetics Unit, Institute of Genetics and Cancer, Edinburgh, United Kingdom
| | - David J. Porteous
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
- University of Edinburgh, Usher Institute, Edinburgh, United Kingdom
| | - Riccardo E. Marioni
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
| | - Alexander Uhrig
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Heinz Zoller
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Judith Löffler-Ragg
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Markus A. Keller
- Medical University of Innsbruck, Institute of Human Genetics, Innsbruck, Austria
| | - Ivan Tancevski
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - John F. Timms
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
| | - Alexey Zaikin
- University College London, Department of Mathematics, London, United Kingdom
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
- Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod, Russia
- Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Stefan Hippenstiel
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Michael Ramharter
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, Hamburg, Germany
| | - Holger Müller-Redetzky
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Martin Witzenrath
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Norbert Suttorp
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Kathryn Lilley
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge, United Kingdom
| | - Michael Mülleder
- Charité–Universitätsmedizin Berlin, Core Facility—High-Throughput Mass Spectrometry, Berlin, Germany
| | - Leif Erik Sander
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | | | - Florian Kurth
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, Hamburg, Germany
- * E-mail:
| | - Markus Ralser
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
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11
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Piedrafita G, Varma SJ, Castro C, Messner CB, Szyrwiel L, Griffin JL, Ralser M. Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure. PLoS Biol 2021; 19:e3001468. [PMID: 34860829 PMCID: PMC8673631 DOI: 10.1371/journal.pbio.3001468] [Citation(s) in RCA: 10] [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: 01/30/2021] [Revised: 12/15/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken–egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a “metabolism first” theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network. The evolutionary origins of metabolism are largely unknown. This study shows that the prebiotically available proteinogenic amino acid cysteine can promote the metabolism-like rate-limiting formation of ribose-5-phosphate, suggesting that early metabolic pathways could have emerged thought the stepwise enzymatization of non-enzymatic reaction sequences.
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Affiliation(s)
- Gabriel Piedrafita
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Sreejith J. Varma
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cecilia Castro
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Christoph B. Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lukasz Szyrwiel
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Julian L. Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- The Rowett Institute, The University of Aberdeen, Aberdeen, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
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12
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Demichev V, Tober-Lau P, Lemke O, Nazarenko T, Thibeault C, Whitwell H, Röhl A, Freiwald A, Szyrwiel L, Ludwig D, Correia-Melo C, Aulakh SK, Helbig ET, Stubbemann P, Lippert LJ, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Mittermaier M, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Enghard P, Zelezniak A, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Müller-Redetzky H, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, Ralser M, Kurth F. A time-resolved proteomic and prognostic map of COVID-19. Cell Syst 2021; 12:780-794.e7. [PMID: 34139154 PMCID: PMC8201874 DOI: 10.1016/j.cels.2021.05.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/24/2021] [Accepted: 05/07/2021] [Indexed: 12/14/2022]
Abstract
COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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Affiliation(s)
- Vadim Demichev
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge CB21GA, UK
| | - Pinkus Tober-Lau
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Oliver Lemke
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Tatiana Nazarenko
- University College London, Department of Mathematics, London WC1E 6BT, UK; University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK
| | - Charlotte Thibeault
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Harry Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW72AZ, UK; Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod 603105, Russia; Imperial College London, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, London SW7 2AZ, UK
| | - Annika Röhl
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Anja Freiwald
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Daniela Ludwig
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Simran Kaur Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Elisa T Helbig
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Paula Stubbemann
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Lena J Lippert
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Nana-Maria Grüning
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Oleg Blyuss
- Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod 603105, Russia; University of Hertfordshire, School of Physics, Astronomy and Mathematics, Hatfield AL10 9AB, UK; Sechenov First Moscow State Medical University, Department of Paediatrics and Paediatric Infectious Diseases, Moscow 119435, Russia
| | - Spyros Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Matthew White
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Christoph B Messner
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Michael Joannidis
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, 6020 Innsbruck, Austria
| | - Thomas Sonnweber
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Sebastian J Klein
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, 6020 Innsbruck, Austria
| | - Alex Pizzini
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Yvonne Wohlfarter
- Medical University of Innsbruck, Institute of Human Genetics, 6020 Innsbruck, Austria
| | - Sabina Sahanic
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Richard Hilbe
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Benedikt Schaefer
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Sonja Wagner
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Mirja Mittermaier
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany
| | - Felix Machleidt
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Carmen Garcia
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Christoph Ruwwe-Glösenkamp
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Tilman Lingscheid
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Laure Bosquillon de Jarcy
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Miriam S Stegemann
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Moritz Pfeiffer
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Linda Jürgens
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Sophy Denker
- Charité Universitätsmedizin Berlin, Medical Department of Hematology, Oncology & Tumor Immunology, Virchow Campus & Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany
| | - Daniel Zickler
- Charité Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, 10117 Berlin, Germany
| | - Philipp Enghard
- Charité Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, 10117 Berlin, Germany
| | - Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; Chalmers Tekniska Högskola, Department of Biology and Biological Engineering, SE-412 96 Gothenburg, Sweden
| | - Archie Campbell
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK; University of Edinburgh, Usher Institute, Edinburgh EH16 4UX, UK
| | - Caroline Hayward
- University of Edinburgh, MRC Human Genetics Unit, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK
| | - David J Porteous
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK; University of Edinburgh, Usher Institute, Edinburgh EH16 4UX, UK
| | - Riccardo E Marioni
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK
| | - Alexander Uhrig
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Holger Müller-Redetzky
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Heinz Zoller
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Judith Löffler-Ragg
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Markus A Keller
- Medical University of Innsbruck, Institute of Human Genetics, 6020 Innsbruck, Austria
| | - Ivan Tancevski
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - John F Timms
- University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK
| | - Alexey Zaikin
- University College London, Department of Mathematics, London WC1E 6BT, UK; University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK; Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod 603105, Russia
| | - Stefan Hippenstiel
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Michael Ramharter
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, 20359 Hamburg, Germany
| | - Martin Witzenrath
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Norbert Suttorp
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Kathryn Lilley
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge CB21GA, UK
| | - Michael Mülleder
- Charité - Universitätsmedizin Berlin, Core Facility - High-Throughput Mass Spectrometry, 10117 Berlin, Germany
| | - Leif Erik Sander
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Markus Ralser
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK.
| | - Florian Kurth
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, 20359 Hamburg, Germany
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13
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Messner CB, Demichev V, Bloomfield N, Yu JSL, White M, Kreidl M, Egger AS, Freiwald A, Ivosev G, Wasim F, Zelezniak A, Jürgens L, Suttorp N, Sander LE, Kurth F, Lilley KS, Mülleder M, Tate S, Ralser M. Ultra-fast proteomics with Scanning SWATH. Nat Biotechnol 2021; 39:846-854. [PMID: 33767396 PMCID: PMC7611254 DOI: 10.1038/s41587-021-00860-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [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: 10/26/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.
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Affiliation(s)
- Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | | | - Jason S L Yu
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Matthew White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Marco Kreidl
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anna-Sophia Egger
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anja Freiwald
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Linda Jürgens
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Michael Mülleder
- Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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14
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Messner CB, Demichev V, Wendisch D, Michalick L, White M, Freiwald A, Textoris-Taube K, Vernardis SI, Egger AS, Kreidl M, Ludwig D, Kilian C, Agostini F, Zelezniak A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, von Kalle C, Campbell A, Hayward C, Porteous DJ, Marioni RE, Langenberg C, Lilley KS, Kuebler WM, Mülleder M, Drosten C, Suttorp N, Witzenrath M, Kurth F, Sander LE, Ralser M. Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection. Cell Syst 2020; 11:11-24.e4. [PMID: 32619549 PMCID: PMC7264033 DOI: 10.1016/j.cels.2020.05.012] [Citation(s) in RCA: 336] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.
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Affiliation(s)
- Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Vadim Demichev
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; Department of Biochemistry, The University of Cambridge, Cambridge CB21GA, UK
| | - Daniel Wendisch
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Laura Michalick
- Charité Universitätsmedizin, Institute of Physiology, 10117 Berlin, Germany
| | - Matthew White
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Anja Freiwald
- Charité Universitätsmedizin, Core Facility - High-Throughput Mass Spectrometry, 10117 Berlin, Germany; Charité Universitätsmedizin, Department of Biochemistry, 10117 Berlin, Germany
| | - Kathrin Textoris-Taube
- Charité Universitätsmedizin, Core Facility - High-Throughput Mass Spectrometry, 10117 Berlin, Germany
| | - Spyros I Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Anna-Sophia Egger
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Marco Kreidl
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Daniela Ludwig
- Charité Universitätsmedizin, Department of Biochemistry, 10117 Berlin, Germany
| | - Christiane Kilian
- Charité Universitätsmedizin, Department of Biochemistry, 10117 Berlin, Germany
| | - Federica Agostini
- Charité Universitätsmedizin, Department of Biochemistry, 10117 Berlin, Germany
| | - Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Charlotte Thibeault
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Moritz Pfeiffer
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Stefan Hippenstiel
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Andreas Hocke
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Christof von Kalle
- Berlin Institute of Health (BIH) and Charité Universitätsmedizin, Clinical Study Center (CSC), 10117 Berlin, Germany
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; Usher Institute, University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh EH16 4UX, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Claudia Langenberg
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Kathryn S Lilley
- Department of Biochemistry, The University of Cambridge, Cambridge CB21GA, UK
| | - Wolfgang M Kuebler
- Charité Universitätsmedizin, Institute of Physiology, 10117 Berlin, Germany
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility - High-Throughput Mass Spectrometry, 10117 Berlin, Germany
| | - Christian Drosten
- Charité Universitätsmedizin, Department of Virology, 10117 Berlin, Germany
| | - Norbert Suttorp
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Martin Witzenrath
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Florian Kurth
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Leif Erik Sander
- Charité Universitätsmedizin, Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; Charité Universitätsmedizin, Department of Biochemistry, 10117 Berlin, Germany.
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15
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Demichev V, Messner CB, Vernardis SI, Lilley KS, Ralser M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods 2020; 17:41-44. [PMID: 31768060 PMCID: PMC6949130 DOI: 10.1038/s41592-019-0638-x] [Citation(s) in RCA: 619] [Impact Index Per Article: 154.8] [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: 08/15/2018] [Accepted: 10/09/2019] [Indexed: 01/12/2023]
Abstract
We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA proteomic applications, and is particularly beneficial for high-throughput applications, as it is fast and enables deep and confident proteome coverage when used in combination with fast chromatographic methods.
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Affiliation(s)
- Vadim Demichev
- Department of Biochemistry and The Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Spyros I Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Kathryn S Lilley
- Department of Biochemistry and The Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK.
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
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16
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Zelezniak A, Vowinckel J, Capuano F, Messner CB, Demichev V, Polowsky N, Mülleder M, Kamrad S, Klaus B, Keller MA, Ralser M. Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts. Cell Syst 2018; 7:269-283.e6. [PMID: 30195436 PMCID: PMC6167078 DOI: 10.1016/j.cels.2018.08.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [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: 12/20/2017] [Revised: 05/29/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]
Abstract
A challenge in solving the genotype-to-phenotype relationship is to predict a cell’s metabolome, believed to correlate poorly with gene expression. Using comparative quantitative proteomics, we found that differential protein expression in 97 Saccharomyces cerevisiae kinase deletion strains is non-redundant and dominated by abundance changes in metabolic enzymes. Associating differential enzyme expression landscapes to corresponding metabolomes using network models provided reasoning for poor proteome-metabolome correlations; differential protein expression redistributes flux control between many enzymes acting in concert, a mechanism not captured by one-to-one correlation statistics. Mapping these regulatory patterns using machine learning enabled the prediction of metabolite concentrations, as well as identification of candidate genes important for the regulation of metabolism. Overall, our study reveals that a large part of metabolism regulation is explained through coordinated enzyme expression changes. Our quantitative data indicate that this mechanism explains more than half of metabolism regulation and underlies the interdependency between enzyme levels and metabolism, which renders the metabolome a predictable phenotype. The proteome of kinase knockouts is dominated by enzyme abundance changes The enzyme expression profiles of kinase knockouts are non-redundant Metabolism is regulated by many expression changes acting in concert Machine learning accurately predicts the metabolome from enzyme abundance
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Affiliation(s)
- Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Biognosys AG, Schlieren, Switzerland
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Vadim Demichev
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Nicole Polowsky
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Michael Mülleder
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Stephan Kamrad
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Bernd Klaus
- Centre for Statistical Data Analysis, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Department of Biochemistry, Charité Universitaetsmedizin Berlin, Berlin, Germany.
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17
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Keller MA, Driscoll PC, Messner CB, Ralser M. 1H-NMR as implemented in several origin of life studies artificially implies the absence of metabolism-like non-enzymatic reactions by being signal-suppressed. Wellcome Open Res 2018. [DOI: 10.12688/wellcomeopenres.12103.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Background. Life depends on small subsets of chemically possible reactions. A chemical process can hence be prebiotically plausible, yet be unrelated to the origins of life. An example is the synthesis of nucleotides from hydrogen cyanide, considered prebiotically plausible, but incompatible with metabolic evolution. In contrast, only few metabolism-compatible prebiotic reactions were known until recently. Here, we question whether technical limitations may have contributed to the situation. Methods: Enzymes evolved to accelerate and control biochemical reactions. This situation dictates that compared to modern metabolic pathways, precursors to enzymatic reactions have been slower and less efficient, yielding lower metabolite quantities. This situation demands for the application of highly sensitive analytical techniques for studying ‘proto-metabolism’. We noticed that a set of proto-metabolism studies derive conclusions from the absence of metabolism-like signals, yet do not report detection limits. We here benchmark the respective 1H-NMR implementation for the ability to detect Krebs cycle intermediates, considered examples of plausible metabolic precursors. Results: Compared to metabolomics ‘gold-standard’ methods, 1H-NMR as implemented is i) at least one hundred- to thousand-fold less sensitive, ii) prone to selective metabolite loss, and iii) subject to signal suppression by Fe(II) concentrations as extrapolated from Archean sediment. In sum these restrictions mount to huge sensitivity deficits, so that even highly concentrated Krebs cycle intermediates are rendered undetectable unless the method is altered to boost sensitivity. Conclusions 1H-NMR as implemented in several origin of life studies does not achieve the sensitivity to detect cellular metabolite concentrations, let alone evolutionary precursors at even lower concentration. These studies can hence not serve as proof-of-absence for metabolism-like reactions. Origin of life theories that essentially depend on this assumption, i.e. those that consider proto-metabolism to consist of non-metabolism-like reactions derived from non-metabolic precursors like hydrogen cyanide, may have been derived from a misinterpretation of negative analytical results.
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18
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Keller MA, Driscoll PC, Messner CB, Ralser M. Primordial Krebs-cycle-like non-enzymatic reactions detected by mass spectrometry and nuclear magnetic resonance. Wellcome Open Res 2017. [DOI: 10.12688/wellcomeopenres.12103.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Metabolism is the process of nutrient uptake and conversion, and executed by the metabolic network. Its evolutionary precursors most likely originated in non-enzymatic chemistry. To be exploitable in a Darwinian process that forms a metabolic pathway, non-enzymatic reactions need to form a chemical network that produces advantage-providing metabolites in a single, life compatible condition. In a hypothesis-generating, large-scale experiment, we recently screened iron and sulfur-rich solutions, and report that upon the formation of sulfate radicals, Krebs cycle intermediates establish metabolism-like non-enzymatic reactivity. A challenge to our results claims that the results obtained by liquid chromatography-selective reaction monitoring (LC-SRM) would not be reproducible by nuclear magnetic resonance spectroscopy (1H-NMR). Methods: This study compared the application of the two techniques to the relevant samples. Results: We detect hundred- to thousand-fold differences in the specific limits of detection between LC-SRM and 1H-NMR to detect Krebs cycle intermediates. Further, the use of 1H-NMR was found generally problematic to characterize early metabolic reactions, as Archean-sediment typical iron concentrations cause paramagnetic signal suppression. Consequently, we selected non-enzymatic Krebs cycle reactions that fall within the determined technical limits. We confirm that these proceed unequivocally as evidenced by both LC-SRM and 1H-NMR. Conclusions: These results strengthen our previous conclusions about the existence of unifying reaction conditions that enables a series of co-occurring metabolism-like non-enzymatic Krebs cycle reactions. We further discuss why constraints applying to metabolism disentangle concentration from importance of any reaction intermediates, and why evolutionary precursors to metabolic pathways must have had much lower metabolite concentrations compared to modern metabolic networks. Research into the chemical origins of life will hence miss out on the chemistry relevant for metabolism if its focus is restricted solely to highly abundant and unreactive metabolites, including when it ignores life-compatibility of the reaction conditions as an essential constraint in enzyme evolution.
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Güzel Y, Rainer M, Messner CB, Hussain S, Meischl F, Sasse M, Tessadri R, Bonn GK. Development of erbium phosphate doped poly(glycidyl methacrylate/ethylene dimethacrylate) spin columns for selective enrichment of phosphopeptides. J Sep Sci 2015; 38:1334-43. [DOI: 10.1002/jssc.201401409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/15/2015] [Accepted: 01/15/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Yüksel Güzel
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
- ADSI-Austrian Drug Screening Institute; Innsbruck Austria
| | - Matthias Rainer
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Christoph B. Messner
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Shah Hussain
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Florian Meischl
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Michael Sasse
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Richard Tessadri
- Institute of Mineralogy and Petrography; Leopold-Franzens University; Innsbruck Austria
| | - Günther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
- ADSI-Austrian Drug Screening Institute; Innsbruck Austria
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Abstract
Hybrid quantum mechanical/molecular mechanical simulations have been used to study the structural and dynamical properties of a La(iii)–phosphopeptide complex.
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Affiliation(s)
- Christoph B. Messner
- Institute of Analytical Chemistry and Radiochemistry
- Leopold-Franzens University
- 6020 Innsbruck
- Austria
| | - Günther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry
- Leopold-Franzens University
- 6020 Innsbruck
- Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Leopold-Franzens University
- 6020 Innsbruck
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Messner CB, Lutz OMD, Rainer M, Huck CW, Hofer TS, Rode BM, Bonn GK. Structure and dynamics of chromatographically relevant Fe(III)-chelates. J Phys Chem B 2014; 118:12232-8. [PMID: 25301257 DOI: 10.1021/jp505193y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Immobilized metal ion affinity chromatography (IMAC) is an important chromatographic technique for biomolecules. In order to get a detailed understanding of the hydration of immobilized Fe(III), complexes of Fe(III) with methyl substituted iminodiacetate ([Fe(MSIDA)(H2O)3](+)) as well as with methyl substituted nitrilotriacetate ([Fe(MSNTA)(H2O)2]) were simulated in aqueous solutions with the quantum mechanical charge field molecular dynamics (QMCF MD) approach. The simulations were carried out at the Hartree-Fock (HF) level of theory, since cluster calculations at the HF, MP2, and B3LYP levels of theory showed that this method results in a good compromise between computational effort and accuracy. None of the coordinating water molecules were exchanged during the simulation period of 15 ps. The Fe-OH2O bond distances as well as the Fe-OH2O stretching motions differed among the coordinating water molecules, indicating different bond strengths. For the water molecules in the second hydration layer, mean residence times of 2.7 and 1.9 ps were obtained for [Fe(MSIDA)(H2O)3](+) and [Fe(MSNTA)(H2O)2], respectively. Furthermore, infrared measurements were carried out to characterize the most prominent bond features of aqueous Fe(III)-NTA and to discuss these results in conjunction with the computationally derived frequencies.
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Affiliation(s)
- Christoph B Messner
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innsbruck , Innrain 80-82, 6020 Innsbruck, Austria
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Canaval LR, Sakwarathorn T, Rode BM, Messner CB, Lutz OMD, Bonn GK. Erbium(III) in aqueous solution: an ab initio molecular dynamics study. J Phys Chem B 2013; 117:15151-6. [PMID: 24251538 DOI: 10.1021/jp410284z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Structural and dynamical properties of the erbium(III) ion in water have been obtained by means of ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations for the ground state and an excited state. The quality of the simulations has been monitored by recording UV/vis and Raman spectra of dilute solutions of ErCl3 and Er(NO3)3 in water and by comparison with EXAFS data from literature. Slight deviations between these data can be mainly attributed to relativistic effects, which are not sufficiently considered by the methodological framework. In both simulations, a mixture of coordination numbers eight and nine and a ligand exchange on the picosecond range are observed. The strength of the Er-ligand bond is considerably lower than that of trivalent transition metal ions but higher than that for La(III) and Ce(III) in aqueous solution. The main difference between ground state and excited state is the ligand exchange rate of the first shell. The second hydration shell is stable in both cases but with significantly different properties.
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Affiliation(s)
- Lorenz R Canaval
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 80-82, A-6020 Innsbruck, Austria
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Schemeth D, Rainer M, Messner CB, Rode BM, Bonn GK. Lanthanide-IMAC enrichment of carbohydrates and polyols. Biomed Chromatogr 2013; 28:412-8. [DOI: 10.1002/bmc.3035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/07/2013] [Accepted: 08/20/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Dieter Schemeth
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innrain 80-82 6020 Innsbruck Austria
| | - Matthias Rainer
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innrain 80-82 6020 Innsbruck Austria
| | - Christoph B. Messner
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innrain 80-82 6020 Innsbruck Austria
- Institute of General, Inorganic and Theoretical Chemistry; Leopold-Franzens University of Innsbruck; Innrain 80-82 6020 Innsbruck Austria
| | - Bernd M. Rode
- Institute of General, Inorganic and Theoretical Chemistry; Leopold-Franzens University of Innsbruck; Innrain 80-82 6020 Innsbruck Austria
| | - Günther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innrain 80-82 6020 Innsbruck Austria
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Lutz OMD, Messner CB, Hofer TS, Glätzle M, Huck CW, Bonn GK, Rode BM. Combined Ab Initio Computational and Infrared Spectroscopic Study of the cis- and trans-Bis(glycinato)copper(II) Complexes in Aqueous Environment. J Phys Chem Lett 2013; 4:1502-1506. [PMID: 26282305 DOI: 10.1021/jz400288c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The cis- and trans-bis(glycinato)copper(II) complexes in aqueous solution have been investigated by means of a combined theoretical and experimental approach. The conducted quantum mechanical charge field molecular dynamics (QMCF-MD) studies, being the first quantum mechanical simulations of organometallic complexes by this method, yielded accurate structural details of the investigated isomers as well as novel dynamic data, which has successfully been confirmed and extended by subsequent mid-infrared measurements. The spectroscopic results, critically assessed by adjacent multivariate data analysis, indicate an isomeric stability at ambient conditions, vanishing at elevated temperatures.
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Affiliation(s)
- Oliver M D Lutz
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christoph B Messner
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Thomas S Hofer
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Matthias Glätzle
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian W Huck
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Günther K Bonn
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Bernd M Rode
- †Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, ‡Institute of Analytical Chemistry and Radiochemistry, and ⊥General and Inorganic Chemistry Divison, Institute of General, Inorganic and Theoretical Chemistry, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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Mirza MR, Rainer M, Messner CB, Güzel Y, Schemeth D, Stasyk T, Choudhary MI, Huber LA, Rode BM, Bonn GK. A new type of metal chelate affinity chromatography using trivalent lanthanide ions for phosphopeptide enrichment. Analyst 2013; 138:2995-3004. [DOI: 10.1039/c3an36853j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Güzel Y, Rainer M, Mirza MR, Messner CB, Bonn GK. Highly selective recovery of phosphopeptides using trypsin-assisted digestion of precipitated lanthanide–phosphoprotein complexes. Analyst 2013; 138:2897-905. [DOI: 10.1039/c3an00066d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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