1
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Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers KJ, Nickel M, Prevedel R, Musser JM, Savitski MM, Arendt D. Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response. Curr Biol 2024; 34:361-375.e9. [PMID: 38181793 DOI: 10.1016/j.cub.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/03/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024]
Abstract
A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling "contractions" that lead to canal closure and water expulsion. Here, we combine live 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate the sequence and detail of shape changes, the tissues and molecular physiology involved, and the control of these movements. Morphometric analysis and targeted perturbation suggest that the movement is driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent canal system. Thermal proteome profiling and quantitative phosphoproteomics confirm the control of cellular relaxation by an Akt/NO/PKG/PKA pathway. Agitation-induced deflation leads to differential phosphorylation of proteins forming epithelial cell junctions, implying their mechanosensitive role. Unexpectedly, untargeted metabolomics detect a concomitant decrease in antioxidant molecules during deflation, reflecting an increase in reactive oxygen species. Together with the secretion of proteinases, cytokines, and granulin, this indicates an inflammation-like state of the deflating sponge reminiscent of vascular endothelial cells experiencing oscillatory shear stress. These results suggest the conservation of an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals and offer a possible mechanism for whole-body coordination through diffusible paracrine signals and mechanotransduction.
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Affiliation(s)
- Fabian Ruperti
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Collaboration for joint Ph.D. degree between EMBL and Heidelberg University, Faculty of Biosciences 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Ling Wang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Nick Marschlich
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Clement Potel
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Emanuel Maus
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bernhard Drotleff
- Metabolomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Klaske J Schippers
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Michael Nickel
- Bionic consulting Dr. Michael Nickel, 71686 Remseck am Neckar, Germany
| | - Robert Prevedel
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jacob M Musser
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany.
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2
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Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A. Systematic analysis of drug combinations against Gram-positive bacteria. Nat Microbiol 2023; 8:2196-2212. [PMID: 37770760 PMCID: PMC10627819 DOI: 10.1038/s41564-023-01486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Drug combinations can expand options for antibacterial therapies but have not been systematically tested in Gram-positive species. We profiled ~8,000 combinations of 65 antibacterial drugs against the model species Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulated previously known drug interactions, but also identified ten times more novel interactions in the pathogen S. aureus, including 150 synergies. We showed that two synergies were equally effective against multidrug-resistant S. aureus clinical isolates in vitro and in vivo. Interactions were largely species-specific and synergies were distinct from those of Gram-negative species, owing to cell surface and drug uptake differences. We also tested 2,728 combinations of 44 commonly prescribed non-antibiotic drugs with 62 drugs with antibacterial activity against S. aureus and identified numerous antagonisms that might compromise the efficacy of antimicrobial therapies. We identified even more synergies and showed that the anti-aggregant ticagrelor synergized with cationic antibiotics by modifying the surface charge of S. aureus. All data can be browsed in an interactive interface ( https://apps.embl.de/combact/ ).
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Affiliation(s)
- Elisabetta Cacace
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vladislav Kim
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Vallo Varik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Michael Knopp
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuela Tietgen
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | | | - Kemal Inecik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Alessio Milanese
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Department of Biology, Institute of Microbiology, and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin Mitosch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Molecular Biology and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
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3
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Zijlmans DW, Hernández-Quiles M, Jansen PWTC, Becher I, Stein F, Savitski MM, Vermeulen M. STPP-UP: An alternative method for drug target identification using protein thermal stability. J Biol Chem 2023; 299:105279. [PMID: 37742922 PMCID: PMC10594562 DOI: 10.1016/j.jbc.2023.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/22/2023] [Accepted: 09/17/2023] [Indexed: 09/26/2023] Open
Abstract
Thermal proteome profiling (TPP) has significantly advanced the field of drug discovery by facilitating proteome-wide identification of drug targets and off-targets. However, TPP has not been widely applied for high-throughput drug screenings, since the method is labor intensive and requires a lot of measurement time on a mass spectrometer. Here, we present Single-tube TPP with Uniform Progression (STPP-UP), which significantly reduces both the amount of required input material and measurement time, while retaining the ability to identify drug targets for compounds of interest. By using incremental heating of a single sample, changes in protein thermal stability across a range of temperatures can be assessed, while alleviating the need to measure multiple samples heated to different temperatures. We demonstrate that STPP-UP is able to identify the direct interactors for anticancer drugs in both human and mice cells. In summary, the STPP-UP methodology represents a useful tool to advance drug discovery and drug repurposing efforts.
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Affiliation(s)
- Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Miguel Hernández-Quiles
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Isabelle Becher
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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4
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Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers K, Nickel M, Prevedel R, Musser JM, Savitski MM, Arendt D. Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response. bioRxiv 2023:2023.08.02.551666. [PMID: 37577507 PMCID: PMC10418225 DOI: 10.1101/2023.08.02.551666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling "contractions" that lead to canal closure and water expulsion. Here, we combine 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate anatomy, molecular physiology, and control of these movements. We find them driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent system, controlled by an Akt/NO/PKG/A pathway. A concomitant increase in reactive oxygen species and secretion of proteinases and cytokines indicate an inflammation-like state reminiscent of vascular endothelial cells experiencing oscillatory shear stress. This suggests an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals.
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Affiliation(s)
- Fabian Ruperti
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Collaboration for joint Ph.D. degree between EMBL and Heidelberg University, Faculty of Biosciences 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Ling Wang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nick Marschlich
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Clement Potel
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Emanuel Maus
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bernhard Drotleff
- Metabolomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Klaske Schippers
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Michael Nickel
- Bionic Consulting Dr. Michael Nickel, 71686 Remseck am Neckar, Germany
| | - Robert Prevedel
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jacob M Musser
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
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5
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Irazoki O, Ter Beek J, Alvarez L, Mateus A, Colin R, Typas A, Savitski MM, Sourjik V, Berntsson RPA, Cava F. D-amino acids signal a stress-dependent run-away response in Vibrio cholerae. Nat Microbiol 2023; 8:1549-1560. [PMID: 37365341 PMCID: PMC10390336 DOI: 10.1038/s41564-023-01419-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
To explore favourable niches while avoiding threats, many bacteria use a chemotaxis navigation system. Despite decades of studies on chemotaxis, most signals and sensory proteins are still unknown. Many bacterial species release D-amino acids to the environment; however, their function remains largely unrecognized. Here we reveal that D-arginine and D-lysine are chemotactic repellent signals for the cholera pathogen Vibrio cholerae. These D-amino acids are sensed by a single chemoreceptor MCPDRK co-transcribed with the racemase enzyme that synthesizes them under the control of the stress-response sigma factor RpoS. Structural characterization of this chemoreceptor bound to either D-arginine or D-lysine allowed us to pinpoint the residues defining its specificity. Interestingly, the specificity for these D-amino acids appears to be restricted to those MCPDRK orthologues transcriptionally linked to the racemase. Our results suggest that D-amino acids can shape the biodiversity and structure of complex microbial communities under adverse conditions.
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Affiliation(s)
- Oihane Irazoki
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Laura Alvarez
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology, and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden.
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6
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Groh C, Haberkant P, Stein F, Filbeck S, Pfeffer S, Savitski MM, Boos F, Herrmann JM. Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins. Life Sci Alliance 2023; 6:e202201805. [PMID: 36941057 PMCID: PMC10027898 DOI: 10.26508/lsa.202201805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Cellular functionality relies on a well-balanced, but highly dynamic proteome. Dysfunction of mitochondrial protein import leads to the cytosolic accumulation of mitochondrial precursor proteins which compromise cellular proteostasis and trigger a mitoprotein-induced stress response. To dissect the effects of mitochondrial dysfunction on the cellular proteome as a whole, we developed pre-post thermal proteome profiling. This multiplexed time-resolved proteome-wide thermal stability profiling approach with isobaric peptide tags in combination with a pulsed SILAC labelling elucidated dynamic proteostasis changes in several dimensions: In addition to adaptations in protein abundance, we observed rapid modulations of the thermal stability of individual cellular proteins. Different functional groups of proteins showed characteristic response patterns and reacted with group-specific kinetics, allowing the identification of functional modules that are relevant for mitoprotein-induced stress. Thus, our new pre-post thermal proteome profiling approach uncovered a complex response network that orchestrates proteome homeostasis in eukaryotic cells by time-controlled adaptations of the abundance and the conformation of proteins.
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Affiliation(s)
- Carina Groh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | | | | | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany;
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7
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Zhang X, Sridharan S, Zagoriy I, Eugster Oegema C, Ching C, Pflaesterer T, Fung HKH, Becher I, Poser I, Müller CW, Hyman AA, Savitski MM, Mahamid J. Molecular mechanisms of stress-induced reactivation in mumps virus condensates. Cell 2023; 186:1877-1894.e27. [PMID: 37116470 PMCID: PMC10156176 DOI: 10.1016/j.cell.2023.03.015] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 09/21/2022] [Accepted: 03/14/2023] [Indexed: 04/30/2023]
Abstract
Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular stress disrupts the metastable host-virus equilibrium in persistent infection and induces viral replication in a culture model of mumps virus. Using a combination of cell biology, whole-cell proteomics, and cryo-electron tomography, we show that persistent viral replication factories are dynamic condensates and identify the largely disordered viral phosphoprotein as a driver of their assembly. Upon stress, increased phosphorylation of the phosphoprotein at its interaction interface with the viral polymerase coincides with the formation of a stable replication complex. By obtaining atomic models for the authentic mumps virus nucleocapsid, we elucidate a concomitant conformational change that exposes the viral genome to its replication machinery. These events constitute a stress-mediated switch within viral condensates that provide an environment to support upregulation of viral replication.
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Affiliation(s)
- Xiaojie Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Sindhuja Sridharan
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christina Eugster Oegema
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Cyan Ching
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tim Pflaesterer
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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8
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Etibor TA, Vale-Costa S, Sridharan S, Brás D, Becher I, Mello VH, Ferreira F, Alenquer M, Savitski MM, Amorim MJ. Defining basic rules for hardening influenza A virus liquid condensates. eLife 2023; 12:85182. [PMID: 37013374 PMCID: PMC10154025 DOI: 10.7554/elife.85182] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 11/25/2022] [Accepted: 03/16/2023] [Indexed: 04/05/2023] Open
Abstract
In biological systems, liquid and solid-like biomolecular condensates may contain the same molecules but their behaviour, including movement, elasticity and viscosity, is different on account of distinct physicochemical properties. As such, it is known that phase transitions affect the function of biological condensates and that material properties can be tuned by several factors including temperature, concentration and valency. It is, however, unclear if some factors are more efficient than others at regulating their behaviour. Viral infections are good systems to address this question as they form condensates de novo as part of their replication programmes. Here, we used influenza A virus liquid cytosolic condensates, A.K.A viral inclusions, to provide a proof of concept that liquid condensate hardening via changes in the valency of its components is more efficient than altering their concentration or the temperature of the cell. Liquid IAV inclusions may be hardened by targeting vRNP interactions via the known NP oligomerizing molecule, nucleozin, both in vitro and in vivo without affecting host proteome abundance nor solubility. This study is a starting point for understanding how to pharmacologically modulate the material properties of IAV inclusions and may offer opportunities for alternative antiviral strategies.
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Affiliation(s)
| | - Silvia Vale-Costa
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Daniela Brás
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Victor Hugo Mello
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Filipe Ferreira
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Marta Alenquer
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Maria-João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
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9
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Kurzawa N, Leo IR, Stahl M, Kunold E, Becher I, Audrey A, Mermelekas G, Huber W, Mateus A, Savitski MM, Jafari R. Deep thermal profiling for detection of functional proteoform groups. Nat Chem Biol 2023:10.1038/s41589-023-01284-8. [PMID: 36941476 PMCID: PMC10374440 DOI: 10.1038/s41589-023-01284-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/09/2023] [Indexed: 03/23/2023]
Abstract
The complexity of the functional proteome extends considerably beyond the coding genome, resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is important to understand cellular physiology and its deregulation in diseases but challenging to perform systematically. Here we applied thermal proteome profiling with deep peptide coverage to detect functional proteoform groups in acute lymphoblastic leukemia cell lines with different cytogenetic aberrations. We detected 15,846 proteoforms, capturing differently spliced, cleaved and post-translationally modified proteins expressed from 9,290 genes. We identified differential co-aggregation of proteoform pairs and established links to disease biology. Moreover, we systematically made use of measured biophysical proteoform states to find specific biomarkers of drug sensitivity. Our approach, thus, provides a powerful and unique tool for systematic detection and functional annotation of proteoform groups.
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Affiliation(s)
- Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Isabelle Rose Leo
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Matthias Stahl
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Elena Kunold
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anastasia Audrey
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Georgios Mermelekas
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Rozbeh Jafari
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology Karolinska Institutet, Science for Life Laboratory, Solna, Sweden.
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10
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Le Sueur C, Hammarén HM, Sridharan S, Savitski MM. Thermal proteome profiling: Insights into protein modifications, associations, and functions. Curr Opin Chem Biol 2022; 71:102225. [PMID: 36368297 DOI: 10.1016/j.cbpa.2022.102225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022]
Abstract
Tracking proteins' biophysical characteristics on a proteome-wide scale can provide valuable information on their functions and interactions. Thermal proteome profiling (TPP) is a multiplexed quantitative proteomics approach that measures changes in protein thermal stability-a key biophysical property-across different cellular states. Developed in 2014, as a target-deconvolution assay for drugs and other small molecules, TPP has since evolved to a system-level biochemical omics technique providing insights into context-dependent changes in protein states. In this review, we summarise key advances in the experimental and data analysis pipeline that have aided this transformation and discuss the recent developments and applications of TPP.
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Affiliation(s)
- Cecile Le Sueur
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Henrik M Hammarén
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Sindhuja Sridharan
- Barts Brain Tumour Center, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.
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11
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Ibarra IL, Ratnu VS, Gordillo L, Hwang IY, Mariani L, Weinand K, Hammarén HM, Heck J, Bulyk ML, Savitski MM, Zaugg JB, Noh KM. Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements. Mol Syst Biol 2022; 18:e10473. [PMID: 35996956 PMCID: PMC9396287 DOI: 10.15252/msb.202110473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 12/30/2022] Open
Abstract
Neuronal stimulation induced by the brain-derived neurotrophic factor (BDNF) triggers gene expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. However, its role in chromatin regulation is unclear. Here, using temporal profiling of chromatin accessibility and transcription in mouse primary cortical neurons upon either BDNF stimulation or depolarization (KCl), we identify features that define BDNF-specific chromatin-to-gene expression programs. Enhancer activation is an early event in the regulatory control of BDNF-treated neurons, where the bZIP motif-binding Fos protein pioneered chromatin opening and cooperated with co-regulatory transcription factors (Homeobox, EGRs, and CTCF) to induce transcription. Deleting cis-regulatory sequences affect BDNF-mediated Arc expression, a regulator of synaptic plasticity. BDNF-induced accessible regions are linked to preferential exon usage by neurodevelopmental disorder-related genes and the heritability of neuronal complex traits, which were validated in human iPSC-derived neurons. Thus, we provide a comprehensive view of BDNF-mediated genome regulatory features using comparative genomic approaches to dissect mammalian neuronal stimulation.
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Affiliation(s)
- Ignacio L Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany.,Institute of Computational Biology, Helmholtz Center Munich, Oberschleißheim, Germany
| | - Vikram S Ratnu
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Lucia Gordillo
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - In-Young Hwang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Luca Mariani
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kathryn Weinand
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Henrik M Hammarén
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jennifer Heck
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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12
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Sridharan S, Hernandez-Armendariz A, Kurzawa N, Potel CM, Memon D, Beltrao P, Bantscheff M, Huber W, Cuylen-Haering S, Savitski MM. Systematic discovery of biomolecular condensate-specific protein phosphorylation. Nat Chem Biol 2022; 18:1104-1114. [PMID: 35864335 PMCID: PMC9512703 DOI: 10.1038/s41589-022-01062-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 01/07/2022] [Accepted: 05/13/2022] [Indexed: 12/27/2022]
Abstract
Reversible protein phosphorylation is an important mechanism for regulating (dis)assembly of biomolecular condensates. However, condensate-specific phosphosites remain largely unknown, thereby limiting our understanding of the underlying mechanisms. Here, we combine solubility proteome profiling with phosphoproteomics to quantitatively map several hundred phosphosites enriched in either soluble or condensate-bound protein subpopulations, including a subset of phosphosites modulating protein–RNA interactions. We show that multi-phosphorylation of the C-terminal disordered segment of heteronuclear ribonucleoprotein A1 (HNRNPA1), a key RNA-splicing factor, reduces its ability to locate to nuclear clusters. For nucleophosmin 1 (NPM1), an essential nucleolar protein, we show that phosphorylation of S254 and S260 is crucial for lowering its partitioning to the nucleolus and additional phosphorylation of distal sites enhances its retention in the nucleoplasm. These phosphorylation events decrease RNA and protein interactions of NPM1 to regulate its condensation. Our dataset is a rich resource for systematically uncovering the phosphoregulation of biomolecular condensates. ![]()
A combination of solubility proteome profiling with phosphoproteomics enables systematic analysis of the phosphorylation status of proteins in soluble and condensate-bound pools.
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Affiliation(s)
- Sindhuja Sridharan
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Alberto Hernandez-Armendariz
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Clement M Potel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Danish Memon
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Pedro Beltrao
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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13
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Kallergi E, Daskalaki AD, Kolaxi A, Camus C, Ioannou E, Mercaldo V, Haberkant P, Stein F, Sidiropoulou K, Dalezios Y, Savitski MM, Bagni C, Choquet D, Hosy E, Nikoletopoulou V. Dendritic autophagy degrades postsynaptic proteins and is required for long-term synaptic depression in mice. Nat Commun 2022; 13:680. [PMID: 35115539 PMCID: PMC8814153 DOI: 10.1038/s41467-022-28301-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/14/2022] [Indexed: 01/18/2023] Open
Abstract
The pruning of dendritic spines during development requires autophagy. This process is facilitated by long-term depression (LTD)-like mechanisms, which has led to speculation that LTD, a fundamental form of synaptic plasticity, also requires autophagy. Here, we show that the induction of LTD via activation of NMDA receptors or metabotropic glutamate receptors initiates autophagy in the postsynaptic dendrites in mice. Dendritic autophagic vesicles (AVs) act in parallel with the endocytic machinery to remove AMPA receptor subunits from the membrane for degradation. During NMDAR-LTD, key postsynaptic proteins are sequestered for autophagic degradation, as revealed by quantitative proteomic profiling of purified AVs. Pharmacological inhibition of AV biogenesis, or conditional ablation of atg5 in pyramidal neurons abolishes LTD and triggers sustained potentiation in the hippocampus. These deficits in synaptic plasticity are recapitulated by knockdown of atg5 specifically in postsynaptic pyramidal neurons in the CA1 area. Conducive to the role of synaptic plasticity in behavioral flexibility, mice with autophagy deficiency in excitatory neurons exhibit altered response in reversal learning. Therefore, local assembly of the autophagic machinery in dendrites ensures the degradation of postsynaptic components and facilitates LTD expression.
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Affiliation(s)
- Emmanouela Kallergi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | | | - Angeliki Kolaxi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | - Come Camus
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Evangelia Ioannou
- School of Biological Sciences, University of Crete, Heraklion, 70013, Greece
| | - Valentina Mercaldo
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | - Per Haberkant
- Proteomic Core Facility (PCF), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- Proteomic Core Facility (PCF), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Yannis Dalezios
- School of Medicine, University of Crete, Heraklion, 71003, Greece
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Mikhail M Savitski
- Proteomic Core Facility (PCF), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), University of Rome Tor Vergata, Rome, 00133, Italy
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Daniel Choquet
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, F-33000, Bordeaux, France
| | - Eric Hosy
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
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14
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Zhang X, Sridharan S, Zagoriy I, Eugster Oegema C, Ching C, Pflaesterer T, Fung HK, Poser I, Müller CW, Hyman AA, Savitski MM, Mahamid J. Molecular mechanism of stress-induced reactivation in mumps virus condensates. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Kokot T, Hoermann B, Helm D, Chojnacki JE, Savitski MM, Köhn M. PLDMS: Phosphopeptide Library Dephosphorylation Followed by Mass Spectrometry Analysis to Determine the Specificity of Phosphatases for Dephosphorylation Site Sequences. Methods Mol Biol 2022; 2499:43-64. [PMID: 35696074 DOI: 10.1007/978-1-0716-2317-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A detailed understanding of the sequence preference surrounding phosphorylation sites is essential for deciphering the function of the human phosphoproteome . Whereas the mechanisms for substrate site recognition by kinases are relatively well understood, the selection mechanisms for the corresponding phosphatases pose several obstacles. However, multiple pieces of evidence point towards a role of the amino acid sequence in the direct vicinity of the phosphorylation site for recognition by phosphatase enzymes. Peptide library-based studies for enzymes attaching posttranslational modifications (PTMs) are relatively straight forward to carry out. However, studying enzymes removing PTMs pose a challenge in that libraries with a PTM attached are needed as a starting point. Here, we present our methodology using large synthetic phosphopeptide libraries to study the preferred sequence context of protein phosphatases. The approach, termed "phosphopeptide library dephosphorylation followed by mass spectrometry" (PLDMS), allows for the exact control of phosphorylation site incorporation and the synthetic route is capable of covering several thousand peptides in a single tube reaction. Furthermore, it enables the user to analyze MS data tailored to the needs of a specific library and thereby increase data quality. We therefore expect a wide applicability of this technique for a range of enzymes catalyzing the removal of PTMs.
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Affiliation(s)
- Thomas Kokot
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Bernhard Hoermann
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Dominic Helm
- Protein Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeremy E Chojnacki
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Proteomics Core Facility, Heidelberg, Germany
| | - Maja Köhn
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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16
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Abstract
Drug target deconvolution can accelerate the drug discovery process by identifying a drug's targets (facilitating medicinal chemistry efforts) and off-targets (anticipating toxicity effects or adverse drug reactions). Multiple mass spectrometry-based approaches have been developed for this purpose, but thermal proteome profiling (TPP) remains to date the only one that does not require compound modification and can be used to identify intracellular targets in living cells. TPP is based on the principle that the thermal stability of a protein can be affected by its interactions. Recent developments of this approach have expanded its applications beyond drugs and cell cultures to studying protein-drug interactions and biological phenomena in tissues. These developments open up the possibility of studying drug treatment or mechanisms of disease in a holistic fashion, which can result in the design of better drugs and lead to a better understanding of fundamental biology. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; .,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Jessica Perrin
- Cellzome GmbH, GlaxoSmithKline, 69117 Heidelberg, Germany
| | | | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
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17
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Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR. Bioaccumulation of therapeutic drugs by human gut bacteria. Nature 2021; 597:533-538. [PMID: 34497420 PMCID: PMC7614428 DOI: 10.1038/s41586-021-03891-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/10/2021] [Indexed: 02/08/2023]
Abstract
Bacteria in the gut can modulate the availability and efficacy of therapeutic drugs. However, the systematic mapping of the interactions between drugs and bacteria has only started recently1 and the main underlying mechanism proposed is the chemical transformation of drugs by microorganisms (biotransformation). Here we investigated the depletion of 15 structurally diverse drugs by 25 representative strains of gut bacteria. This revealed 70 bacteria-drug interactions, 29 of which had not to our knowledge been reported before. Over half of the new interactions can be ascribed to bioaccumulation; that is, bacteria storing the drug intracellularly without chemically modifying it, and in most cases without the growth of the bacteria being affected. As a case in point, we studied the molecular basis of bioaccumulation of the widely used antidepressant duloxetine by using click chemistry, thermal proteome profiling and metabolomics. We find that duloxetine binds to several metabolic enzymes and changes the metabolite secretion of the respective bacteria. When tested in a defined microbial community of accumulators and non-accumulators, duloxetine markedly altered the composition of the community through metabolic cross-feeding. We further validated our findings in an animal model, showing that bioaccumulating bacteria attenuate the behavioural response of Caenorhabditis elegans to duloxetine. Together, our results show that bioaccumulation by gut bacteria may be a common mechanism that alters drug availability and bacterial metabolism, with implications for microbiota composition, pharmacokinetics, side effects and drug responses, probably in an individual manner.
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Affiliation(s)
- Martina Klünemann
- European Molecular Biology Laboratory, Heidelberg, Germany.,Evonik Operations GmbH, Essen, Germany
| | - Sergej Andrejev
- European Molecular Biology Laboratory, Heidelberg, Germany.,German Cancer Research Center, Heidelberg, Germany
| | - Sonja Blasche
- European Molecular Biology Laboratory, Heidelberg, Germany.,Medical Research Council Toxicology Unit, Cambridge, UK
| | - Andre Mateus
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Prasad Phapale
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | - Bernd Simon
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Timothy A Scott
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Eleni Kafkia
- Medical Research Council Toxicology Unit, Cambridge, UK
| | | | - Katharina Zirngibl
- European Molecular Biology Laboratory, Heidelberg, Germany.,Medical Research Council Toxicology Unit, Cambridge, UK
| | | | - Manuel Banzhaf
- European Molecular Biology Laboratory, Heidelberg, Germany.,School of Biosciences, University of Birmingham, Birmingham, UK
| | - Marie-Therese Mackmull
- European Molecular Biology Laboratory, Heidelberg, Germany.,ETH Zürich, Zürich, Switzerland
| | | | - Leo Nesme
- European Molecular Biology Laboratory, Heidelberg, Germany.,Molecular Health GmbH, Heidelberg, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Heidelberg, Germany.,University of Würzburg, Würzburg, Germany
| | - Lisa Maier
- European Molecular Biology Laboratory, Heidelberg, Germany.,University of Tübingen, Tübingen, Germany
| | - Thomas Bock
- European Molecular Biology Laboratory, Heidelberg, Germany.,Biozentrum, University of Basel, Basel, Switzerland
| | - Vinita Periwal
- European Molecular Biology Laboratory, Heidelberg, Germany.,Medical Research Council Toxicology Unit, Cambridge, UK
| | - Manjeet Kumar
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yongkyu Kim
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Melanie Tramontano
- European Molecular Biology Laboratory, Heidelberg, Germany.,German Cancer Research Center, Heidelberg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory, Heidelberg, Germany.,Chemical Physiology and Biochemistry Department, Oregon Health & Science University, Portland, OR, USA
| | - Martin Beck
- European Molecular Biology Laboratory, Heidelberg, Germany.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Janosch Hennig
- European Molecular Biology Laboratory, Heidelberg, Germany.,Biophysical Chemistry Department, University of Bayreuth, Bayreuth, Germany
| | | | | | - Filipe Cabreiro
- Institute of Structural and Molecular Biology, University College London, London, UK.,Institute of Clinical Sciences, Imperial College London, London, UK.,CECAD, University of Cologne, Köln, Germany
| | | | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany. .,Max Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea. .,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
| | | | - Kiran R Patil
- European Molecular Biology Laboratory, Heidelberg, Germany. .,Medical Research Council Toxicology Unit, Cambridge, UK.
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18
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Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J. Structure and dynamics of the quaternary hunchback mRNA translation repression complex. Nucleic Acids Res 2021; 49:8866-8885. [PMID: 34329466 PMCID: PMC8421216 DOI: 10.1093/nar/gkab635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 01/02/2023] Open
Abstract
A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. This suppression is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins during RNA suppression remains a long-standing open question. Here, we characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos with hunchback mRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternary hunchback mRNA suppression complex comprising the RNA binding domains is flexible with unoccupied nucleotides functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, the presence of the Pum-HD/Nanos-ZnF complex has no effect on the equilibrium RNA binding affinity of the Brat RNA binding domain. This is in accordance with previous studies, which showed that Brat can suppress mRNA independently and is distributed uniformly throughout the embryo.
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Affiliation(s)
- Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Sophie L Winter
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jaelle Foot
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Kathryn Perez
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Miloš T Ivanović
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Inga Loedige
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Frank Gabel
- Institut Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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19
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Mateus A, Savitski MM, Piazza I. The rise of proteome-wide biophysics. Mol Syst Biol 2021; 17:e10442. [PMID: 34293219 PMCID: PMC8297615 DOI: 10.15252/msb.202110442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/26/2021] [Accepted: 06/04/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Andre Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
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20
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Walch P, Selkrig J, Knodler LA, Rettel M, Stein F, Fernandez K, Viéitez C, Potel CM, Scholzen K, Geyer M, Rottner K, Steele-Mortimer O, Savitski MM, Holden DW, Typas A. Global mapping of Salmonella enterica-host protein-protein interactions during infection. Cell Host Microbe 2021; 29:1316-1332.e12. [PMID: 34237247 DOI: 10.1016/j.chom.2021.06.004] [Citation(s) in RCA: 31] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 02/24/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022]
Abstract
Intracellular bacterial pathogens inject effector proteins to hijack host cellular processes and promote their survival and proliferation. To systematically map effector-host protein-protein interactions (PPIs) during infection, we generated a library of 32 Salmonella enterica serovar Typhimurium (STm) strains expressing chromosomally encoded affinity-tagged effectors and quantified PPIs in macrophages and epithelial cells. We identified 446 effector-host PPIs, 25 of which were previously described, and validated 13 by reciprocal co-immunoprecipitation. While effectors converged on the same host cellular processes, most had multiple targets, which often differed between cell types. We demonstrate that SseJ, SseL, and SifA modulate cholesterol accumulation at the Salmonella-containing vacuole (SCV) partially via the cholesterol transporter Niemann-Pick C1 protein. PipB recruits the organelle contact site protein PDZD8 to the SCV, and SteC promotes actin bundling by phosphorylating formin-like proteins. This study provides a method for probing host-pathogen PPIs during infection and a resource for interrogating STm effector mechanisms.
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Affiliation(s)
- Philipp Walch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Leigh A Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, USA; Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Mandy Rettel
- EMBL, Proteomics Core Facility, Heidelberg, Germany
| | - Frank Stein
- EMBL, Proteomics Core Facility, Heidelberg, Germany
| | - Keith Fernandez
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Cristina Viéitez
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany; EMBL European Bioinformatics Institute, (EMBL-EBI), Hinxton, UK
| | - Clément M Potel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Karoline Scholzen
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Klemens Rottner
- Division of Molecular Cell Biology, Zoological Institute, TU Braunschweig, Braunschweig, Germany; Molecular Cell Biology Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Olivia Steele-Mortimer
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Mikhail M Savitski
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany; EMBL, Proteomics Core Facility, Heidelberg, Germany
| | - David W Holden
- MRC Centre for Molecular Bacteriology and Infection, Imperial College, London, UK
| | - Athanasios Typas
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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21
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Beckham KSH, Ritter C, Chojnowski G, Ziemianowicz DS, Mullapudi E, Rettel M, Savitski MM, Mortensen SA, Kosinski J, Wilmanns M. Structure of the mycobacterial ESX-5 type VII secretion system pore complex. Sci Adv 2021; 7:7/26/eabg9923. [PMID: 34172453 PMCID: PMC8232910 DOI: 10.1126/sciadv.abg9923] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/10/2021] [Indexed: 05/28/2023]
Abstract
The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation machinery and the composition of the central secretion pore have remained unknown. Here, we present the high-resolution structure of the 2.1-megadalton ESX-5 core complex. Our structure captured a dynamic, secretion-competent conformation of the pore within a well-defined transmembrane section, sandwiched between two flexible protein layers at the cytosolic entrance and the periplasmic exit. We propose that this flexibility endows the ESX-5 machinery with large conformational plasticity required to accommodate targeted protein secretion. Compared to known secretion systems, a highly dynamic state of the pore may represent a fundamental principle of bacterial secretion machineries.
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Affiliation(s)
- Katherine S H Beckham
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christina Ritter
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel S Ziemianowicz
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Edukondalu Mullapudi
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Simon A Mortensen
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.
- University Hamburg Clinical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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22
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Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Mooijman D, Benes V, Savitski MM, Gebauer F, Hennig J. Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. Cell Rep 2021; 32:107930. [PMID: 32697992 PMCID: PMC7383231 DOI: 10.1016/j.celrep.2020.107930] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs), which provide these proteins with a modular architecture. Accumulating evidence supports that RBP architectural modularity and adaptability define the specificity of their interactions with RNA. However, how multiple RBDs recognize their cognate single-stranded RNA (ssRNA) sequences in concert remains poorly understood. Here, we use Upstream of N-Ras (Unr) as a model system to address this question. Although reported to contain five ssRNA-binding cold-shock domains (CSDs), we demonstrate that Unr includes an additional four CSDs that do not bind RNA (pseudo-RBDs) but are involved in mediating RNA tertiary structure specificity by reducing the conformational heterogeneity of Unr. Disrupting the interactions between canonical and non-canonical CSDs impacts RNA binding, Unr-mediated translation regulation, and the Unr-dependent RNA interactome. Taken together, our studies reveal a new paradigm in protein-RNA recognition, where interactions between RBDs and pseudo-RBDs select RNA tertiary structures, influence RNP assembly, and define target specificity. Discovery of non-canonical cold-shock domains Non-canonical cold-shock domains do not bind RNA independently Interdomain contacts mediate RNA structure specificity and impact translation Determination of an Unr-dependent ribonucleoprotein (RNP) interactome
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Provaznik
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lara Jayne Sweetapple
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Laura Villacorta
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Dylan Mooijman
- Developmental Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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23
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Kurzawa N, Mateus A, Savitski MM. Rtpca: an R package for differential thermal proximity coaggregation analysis. Bioinformatics 2021; 37:431-433. [PMID: 32717044 PMCID: PMC8058776 DOI: 10.1093/bioinformatics/btaa682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
Summary Rtpca is an R package implementing methods for inferring protein–protein interactions (PPIs) based on thermal proteome profiling experiments of a single condition or in a differential setting via an approach called thermal proximity coaggregation. It offers user-friendly tools to explore datasets for their PPI predictive performance and easily integrates with available R packages. Availability and implementation Rtpca is available from Bioconductor (https://bioconductor.org/packages/Rtpca). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nils Kurzawa
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.,Candidate for Joint PhD Between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
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24
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Mateus A, Kurzawa N, Becher I, Sridharan S, Helm D, Stein F, Typas A, Savitski MM. Thermal proteome profiling for interrogating protein interactions. Mol Syst Biol 2021; 16:e9232. [PMID: 32133759 PMCID: PMC7057112 DOI: 10.15252/msb.20199232] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [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: 09/13/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
Thermal proteome profiling (TPP) is based on the principle that, when subjected to heat, proteins denature and become insoluble. Proteins can change their thermal stability upon interactions with small molecules (such as drugs or metabolites), nucleic acids or other proteins, or upon post-translational modifications. TPP uses multiplexed quantitative mass spectrometry-based proteomics to monitor the melting profile of thousands of expressed proteins. Importantly, this approach can be performed in vitro, in situ, or in vivo. It has been successfully applied to identify targets and off-targets of drugs, or to study protein-metabolite and protein-protein interactions. Therefore, TPP provides a unique insight into protein state and interactions in their native context and at a proteome-wide level, allowing to study basic biological processes and their underlying mechanisms.
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Affiliation(s)
- André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sindhuja Sridharan
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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25
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Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio‐Hernandez I, Rettel M, Kim H, Voogdt CGP, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski MM. SARS-CoV-2 infection remodels the host protein thermal stability landscape. Mol Syst Biol 2021; 17:e10188. [PMID: 33590968 PMCID: PMC7885171 DOI: 10.15252/msb.202010188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health and has compromised economic stability. In addition to the development of an effective vaccine, it is imperative to understand how SARS-CoV-2 hijacks host cellular machineries on a system-wide scale so that potential host-directed therapies can be developed. In situ proteome-wide abundance and thermal stability measurements using thermal proteome profiling (TPP) can inform on global changes in protein activity. Here we adapted TPP to high biosafety conditions amenable to SARS-CoV-2 handling. We discovered pronounced temporal alterations in host protein thermostability during infection, which converged on cellular processes including cell cycle, microtubule and RNA splicing regulation. Pharmacological inhibition of host proteins displaying altered thermal stability or abundance during infection suppressed SARS-CoV-2 replication. Overall, this work serves as a framework for expanding TPP workflows to globally important human pathogens that require high biosafety containment and provides deeper resolution into the molecular changes induced by SARS-CoV-2 infection.
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Affiliation(s)
- Joel Selkrig
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Megan Stanifer
- Department of Infectious DiseasesMolecular VirologyHeidelberg University HospitalHeidelbergGermany
| | - André Mateus
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Karin Mitosch
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | | | - Mandy Rettel
- Proteomics Core FacilityEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Heeyoung Kim
- Department of Infectious DiseasesMolecular VirologyHeidelberg University HospitalHeidelbergGermany
| | - Carlos G P Voogdt
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Philipp Walch
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Faculty of BiosciencesEMBL and Heidelberg UniversityHeidelbergGermany
| | - Carmon Kee
- Department of Infectious DiseasesMolecular VirologyHeidelberg University HospitalHeidelbergGermany
| | - Nils Kurzawa
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Faculty of BiosciencesEMBL and Heidelberg UniversityHeidelbergGermany
| | - Frank Stein
- Proteomics Core FacilityEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Clément Potel
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Anna Jarzab
- Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Bernhard Kuster
- Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Ralf Bartenschlager
- Department of Infectious DiseasesMolecular VirologyHeidelberg University HospitalHeidelbergGermany
- Division “Virus‐associated Carcinogenesis”German Cancer Research Center (DKFZ)HeidelbergGermany
- German Center for Infection ResearchHeidelberg Partner siteHeidelbergGermany
| | - Steeve Boulant
- Department of Infectious Diseases, VirologyHeidelberg University HospitalHeidelbergGermany
- Research Group “Cellular Polarity and Viral Infection”German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Pedro Beltrao
- European Bioinformatics Institute (EMBL‐EBI)HinxtonUK
| | - Athanasios Typas
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Mikhail M Savitski
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
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26
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Nimgaonkar I, Archer NF, Becher I, Shahrad M, LeDesma RA, Mateus A, Caballero-Gómez J, Berneshawi AR, Ding Q, Douam F, Gaska JM, Savitski MM, Kim H, Ploss A. Isocotoin suppresses hepatitis E virus replication through inhibition of heat shock protein 90. Antiviral Res 2021; 185:104997. [PMID: 33326835 PMCID: PMC8649941 DOI: 10.1016/j.antiviral.2020.104997] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 07/14/2020] [Revised: 11/21/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
Hepatitis E virus (HEV) causes 14 million infections and 60,000 deaths per year globally, with immunocompromised persons and pregnant women experiencing severe symptoms. Although ribavirin can be used to treat chronic hepatitis E, toxicity in pregnant patients and the emergence of resistant strains are major concerns. Therefore there is an imminent need for effective HEV antiviral agents. The aims of this study were to develop a drug screening platform and to discover novel approaches to targeting steps within the viral life cycle. We developed a screening platform for molecules inhibiting HEV replication and selected a candidate, isocotoin. Isocotoin inhibits HEV replication through interference with heat shock protein 90 (HSP90), a host factor not previously known to be involved in HEV replication. Additional work is required to understand the compound's translational potential, however this suggests that HSP90-modulating molecules, which are in clinical development as anti-cancer agents, may be promising therapies against HEV.
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Affiliation(s)
- Ila Nimgaonkar
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Nicholas F Archer
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mohammad Shahrad
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Robert A LeDesma
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Javier Caballero-Gómez
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Andrew R Berneshawi
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Qiang Ding
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Florian Douam
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Jenna M Gaska
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hahn Kim
- Princeton University Small Molecule Screening Center, Frick Laboratory, Princeton University, Princeton, NJ, USA; Department of Chemistry, Frick Laboratory, Princeton University, Princeton, NJ, USA
| | - Alexander Ploss
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
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27
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Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM. A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nat Commun 2020; 11:5783. [PMID: 33188197 PMCID: PMC7666118 DOI: 10.1038/s41467-020-19529-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. However, current data analysis strategies use preset thresholds that can lead to suboptimal sensitivity/specificity tradeoffs and limited comparability across datasets. Here, we present a method based on statistical hypothesis testing on curves, which provides control of the false discovery rate. We apply it to several datasets probing epigenetic drugs and a metabolite. This leads us to detect off-target drug engagement, including the finding that the HDAC8 inhibitor PCI-34051 and its analog BRD-3811 bind to and inhibit leucine aminopeptidase 3. An implementation is available as an R package from Bioconductor (https://bioconductor.org/packages/TPP2D). We hope that our method will facilitate prioritizing targets from thermal profiling experiments. 2D-thermal proteome profiling (2D-TPP) is a powerful assay for probing interactions of proteins with small molecules in their native context. Here the authors provide a statistical method for false discovery rate controlled analysis for 2D-TPP applications.
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Affiliation(s)
- Nils Kurzawa
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, 69120, Germany
| | - Isabelle Becher
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Sindhuja Sridharan
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, Heidelberg, 69120, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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28
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Määttä TA, Rettel M, Sridharan S, Helm D, Kurzawa N, Stein F, Savitski MM. Aggregation and disaggregation features of the human proteome. Mol Syst Biol 2020; 16:e9500. [PMID: 33022891 PMCID: PMC7538195 DOI: 10.15252/msb.20209500] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/25/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022] Open
Abstract
Protein aggregates have negative implications in disease. While reductionist experiments have increased our understanding of aggregation processes, the systemic view in biological context is still limited. To extend this understanding, we used mass spectrometry-based proteomics to characterize aggregation and disaggregation in human cells after non-lethal heat shock. Aggregation-prone proteins were enriched in nuclear proteins, high proportion of intrinsically disordered regions, high molecular mass, high isoelectric point, and hydrophilic amino acids. During recovery, most aggregating proteins disaggregated with a rate proportional to the aggregation propensity: larger loss in solubility was counteracted by faster disaggregation. High amount of intrinsically disordered regions were associated with faster disaggregation. However, other characteristics enriched in aggregating proteins did not correlate with the disaggregation rates. In addition, we analyzed changes in protein thermal stability after heat shock. Soluble remnants of aggregated proteins were more thermally stable compared with control condition. Therefore, our results provide a rich resource of heat stress-related protein solubility data and can foster further studies related to protein aggregation diseases.
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Affiliation(s)
- Tomi A Määttä
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
| | - Mandy Rettel
- Proteomics Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Sindhuja Sridharan
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Dominic Helm
- Proteomics Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Nils Kurzawa
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
| | - Frank Stein
- Proteomics Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Mikhail M Savitski
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Proteomics Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
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29
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Jacobs Cachá C, Puig Gay N, Helm D, Rettel M, Sellares J, Meseguer A, Savitski MM, Moreso F, Soler MJ, Seron Micas D, López Hellín J. P0349A MISSPROCESSED FORM OF APOLIPOPROTEIN A-I IS SPECIFICALLY ASSOCIATED TO RECURRENT FOCAL SEGMENTAL GLOMERULOSCLEROSIS. Nephrol Dial Transplant 2020. [DOI: 10.1093/ndt/gfaa142.p0349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background and Aims
Recurrence of idiopathic FSGS, a glomerular disease of unknown aetiology, is a serious complication after kidney transplantation. There are no accurate means to diagnose the relapses or to detect the patients at risk. In an exploratory study we detected Apolipoprotein A-Ib (ApoA-Ib), a high molecular weight form of ApoA-I, specifically in urine of kidney transplanted patients that relapsed of FSGS. The diagnostic performance of ApoA-Ib has been assessed in two independent cohorts obtaining high specificity (94,1 %) and sensitivity (87,5 %) to detect FSGS relapses. It has also a potential to detect patients at risk of relapse as ApoA-Ib predates the recurrence episodes in most of the cases. As urinary ApoA-Ib is strongly associated to primary FSGS we aimed to unravel the nature of the modification present in ApoA-Ib.
Method
The whole APOA1 gene was sequenced in ApoA-Ib positive and negative patients and the protein structure was studied using 2D electrophoresis followed by mass spectrometry.
Results
No genetic variations in the APOA1 gene were found in the ApoA-Ib positive patients that could explain the increase in the molecular mass. The mass spectrometry analysis revealed three extra amino acids at the N-Terminal end of ApoA-Ib that were not present in the standard plasmatic form of ApoA-I. These amino acids corresponded to half of the propeptide sequence of the immature form of ApoA-I (proApoA-I). These results suggest that proApoA-I is miss-cleaved producing ApoA-Ib probably due to an altered protease activity in recurrent FSGS patients
Conclusion
ApoA-Ib, found specifically in urine of recurrent FSGS patients, is a misprocessed form of ApoA-I that retains three aminoacids of the six-aminoacid N-terminal propeptide of proApoA-I. The description of ApoA-Ib could be relevant not only to allow the automated analysis of this biomarker in the clinical laboratory but also to shed light into the molecular mechanism of idiopathic FSGS.
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Affiliation(s)
- Conxita Jacobs Cachá
- Vall d'Hebrón Institut de Recerca (VHIR), Nephrology research group, Barcelona, Spain
- Hospital Universitari Vall d'Hebrón, Nephrology department, Barcelona, Spain
| | - Natàlia Puig Gay
- Vall d'Hebrón Institut de Recerca (VHIR), Renal Pathophysiology Group, Barcelona, Spain
| | - Dominic Helm
- European molecular biology laboratory, Proteomics core facility, Heidelberg, Germany
| | - Mandy Rettel
- European molecular biology laboratory, Proteomics core facility, Heidelberg, Germany
| | - Joana Sellares
- Vall d'Hebrón Institut de Recerca (VHIR), Nephrology research group, Barcelona, Spain
- Hospital Universitari Vall d'Hebrón, Nephrology department, Barcelona, Spain
| | - Anna Meseguer
- Vall d'Hebrón Institut de Recerca (VHIR), Renal Pathophysiology Group, Barcelona, Spain
| | - Mikhail M Savitski
- European molecular biology laboratory, Proteomics core facility, Heidelberg, Germany
- European molecular biology laboratory, Genome Biology, Heidelberg, Germany
| | - Francesc Moreso
- Vall d'Hebrón Institut de Recerca (VHIR), Nephrology research group, Barcelona, Spain
- Hospital Universitari Vall d'Hebrón, Nephrology department, Barcelona, Spain
| | - María José Soler
- Vall d'Hebrón Institut de Recerca (VHIR), Nephrology research group, Barcelona, Spain
- Hospital Universitari Vall d'Hebrón, Nephrology department, Barcelona, Spain
| | - Daniel Seron Micas
- Hospital Universitari Vall d'Hebrón, Biochemistry department, Barcelona, Spain
- Vall d'Hebrón Institut de Recerca (VHIR), Biochemistry Research Group, Barcelona, Spain
| | - Joan López Hellín
- Hospital Universitari Vall d'Hebrón, Biochemistry department, Barcelona, Spain
- Vall d'Hebrón Institut de Recerca (VHIR), Biochemistry Research Group, Barcelona, Spain
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30
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Viéitez C, Martínez-Cebrián G, Solé C, Böttcher R, Potel CM, Savitski MM, Onnebo S, Fabregat M, Shilatifard A, Posas F, de Nadal E. A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress. Nucleic Acids Res 2020; 48:3455-3475. [PMID: 32064518 PMCID: PMC7144942 DOI: 10.1093/nar/gkaa081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 06/08/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Cells have the ability to sense, respond and adapt to environmental fluctuations. Stress causes a massive reorganization of the transcriptional program. Many examples of histone post-translational modifications (PTMs) have been associated with transcriptional activation or repression under steady-state growth conditions. Comparatively less is known about the role of histone PTMs in the cellular adaptive response to stress. Here, we performed high-throughput genetic screenings that provide a novel global map of the histone residues required for transcriptional reprogramming in response to heat and osmotic stress. Of note, we observed that the histone residues needed depend on the type of gene and/or stress, thereby suggesting a 'personalized', rather than general, subset of histone requirements for each chromatin context. In addition, we identified a number of new residues that unexpectedly serve to regulate transcription. As a proof of concept, we characterized the function of the histone residues H4-S47 and H4-T30 in response to osmotic and heat stress, respectively. Our results uncover novel roles for the kinases Cla4 and Ste20, yeast homologs of the mammalian PAK2 family, and the Ste11 MAPK as regulators of H4-S47 and H4-T30, respectively. This study provides new insights into the role of histone residues in transcriptional regulation under stress conditions.
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Affiliation(s)
- Cristina Viéitez
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Gerard Martínez-Cebrián
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carme Solé
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - René Böttcher
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Clement M Potel
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Sara Onnebo
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
| | - Marc Fabregat
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, IL 60611, USA
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
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31
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Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B. Meltome atlas-thermal proteome stability across the tree of life. Nat Methods 2020; 17:495-503. [PMID: 32284610 DOI: 10.1038/s41592-020-0801-4] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic proteins show a nonlinear relationship between the degree of disordered protein structure and thermal stability. The data indicate that evolutionary conservation of protein complexes is reflected by similar thermal stability of their proteins, and we show examples in which genomic alterations can affect thermal stability. Proteins of the respiratory chain were found to be very stable in many organisms, and human mitochondria showed close to normal respiration at 46 °C. We also noted cell-type-specific effects that can affect protein stability or the efficacy of drugs. This meltome atlas broadly defines the proteome amenable to thermal profiling in biology and drug discovery and can be explored online at http://meltomeatlas.proteomics.wzw.tum.de:5003/ and http://www.proteomicsdb.org.
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Affiliation(s)
- Anna Jarzab
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Nils Kurzawa
- Genome Biology Unit, EMBL, Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | | | - Matthias Moerch
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Niels Leijten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Yangyang Bian
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Eva Musiol
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | | | | | | | - Charlotte Daly
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Britta Spanier
- Chair of Nutritional Physiology, Technical University of Munich, Freising, Germany
| | - Angel Angelov
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Wolfgang Liebl
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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32
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Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo JJ, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Typas A, Savitski MM, Espinoza JL, O'Rourke A, Nelson KE, Hiller S, Noinaj N, Schäberle TF, D'Onofrio A, Lewis K. Author Correction: A new antibiotic selectively kills Gram-negative pathogens. Nature 2020; 580:E3. [PMID: 32269338 DOI: 10.1038/s41586-020-2063-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Yu Imai
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Kirsten J Meyer
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Akira Iinishi
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Quentin Favre-Godal
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Robert Green
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Sylvie Manuse
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Mariaelena Caboni
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Miho Mori
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Samantha Niles
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Meghan Ghiglieri
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Chandrashekhar Honrao
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Xiaoyu Ma
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Jason J Guo
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.,Barnett Institute for Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Alexandros Makriyannis
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Luis Linares-Otoya
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Zerlina G Wuisan
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Hundeep Kaur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Runrun Wu
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.,Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Josh L Espinoza
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Aubrie O'Rourke
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Karen E Nelson
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Human Biology, J. Craig Venter Institute, Rockville, MD, USA.,Department of Genomic Medicine, J. Craig Venter Institute, Rockville, MD, USA
| | | | - Nicholas Noinaj
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.,Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany.,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Anthony D'Onofrio
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA.
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33
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Sueki A, Stein F, Savitski MM, Selkrig J, Typas A. Systematic Localization of Escherichia coli Membrane Proteins. mSystems 2020; 5:e00808-19. [PMID: 32127419 PMCID: PMC7055658 DOI: 10.1128/msystems.00808-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 11/27/2019] [Accepted: 02/14/2020] [Indexed: 11/20/2022] Open
Abstract
The molecular architecture and function of the Gram-negative bacterial cell envelope are dictated by protein composition and localization. Proteins that localize to the inner membranes (IM) and outer membranes (OM) of Gram-negative bacteria play critical and distinct roles in cellular physiology; however, approaches to systematically interrogate their distribution across both membranes and the soluble cell fraction are lacking. Here, we employed multiplexed quantitative mass spectrometry using tandem mass tag (TMT) labeling to assess membrane protein localization in a proteome-wide fashion by separating IM and OM vesicles from exponentially growing Escherichia coli K-12 cells on a sucrose density gradient. The migration patterns for >1,600 proteins were classified in an unbiased manner, accurately recapitulating decades of knowledge in membrane protein localization in E. coli For 559 proteins that are currently annotated as peripherally associated with the IM (G. Orfanoudaki and A. Economou, Mol Cell Proteomics 13:3674-3687, 2014, https://doi.org/10.1074/mcp.O114.041137) and that display potential for dual localization to either the IM or cytoplasm, we could allocate 110 proteins to the IM and 206 proteins to the soluble cell fraction based on their fractionation patterns. In addition, we uncovered 63 cases, in which our data disagreed with current localization annotation in protein databases. For 42 of these cases, we were able to find supportive evidence for our localization findings in the literature. We anticipate that our systems-level analysis of the E. coli membrane proteome will serve as a useful reference data set to query membrane protein localization, as well as to provide a novel methodology to rapidly and systematically map membrane protein localization in more poorly characterized Gram-negative species.IMPORTANCE Current knowledge of protein localization, particularly outer membrane proteins, is highly dependent on bioinformatic predictions. To date, no systematic experimental studies have directly compared protein localization spanning the inner and outer membranes of E. coli By combining sucrose density gradient fractionation of inner membrane (IM) and outer membrane (OM) proteins with multiplex quantitative proteomics, we systematically quantified localization patterns for >1,600 proteins, providing high-confidence localization annotations for 1,368 proteins. Of these proteins, we resolve the predominant localization of 316 proteins that currently have dual annotation (cytoplasmic and IM) in protein databases and identify new annotations for 42 additional proteins. Overall, we present a novel quantitative methodology to systematically map membrane proteins in Gram-negative bacteria and use it to unravel the biological complexity of the membrane proteome architecture in E. coli.
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Affiliation(s)
- Anna Sueki
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
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34
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Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P. The functional landscape of the human phosphoproteome. Nat Biotechnol 2020; 38:365-373. [PMID: 31819260 PMCID: PMC7100915 DOI: 10.1038/s41587-019-0344-3] [Citation(s) in RCA: 202] [Impact Index Per Article: 50.5] [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: 02/28/2019] [Accepted: 11/05/2019] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. Although tens of thousands of phosphorylation sites have been identified in human cells, approaches to determine the functional importance of each phosphosite are lacking. Here, we manually curated 112 datasets of phospho-enriched proteins, generated from 104 different human cell types or tissues. We re-analyzed the 6,801 proteomics experiments that passed our quality control criteria, creating a reference phosphoproteome containing 119,809 human phosphosites. To prioritize functional sites, we used machine learning to identify 59 features indicative of proteomic, structural, regulatory or evolutionary relevance and integrate them into a single functional score. Our approach identifies regulatory phosphosites across different molecular mechanisms, processes and diseases, and reveals genetic susceptibilities at a genomic scale. Several regulatory phosphosites were experimentally validated, including identifying a role in neuronal differentiation for phosphosites in SMARCC2, a member of the SWI/SNF chromatin-remodeling complex.
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Affiliation(s)
- David Ochoa
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Andrew F Jarnuczak
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cristina Viéitez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maja Gehre
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Margaret Soucheray
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Askar A Kleefeldt
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anthony Hill
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luz Garcia-Alonso
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frank Stein
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nevan J Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Danielle L Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology and the Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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35
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Banzhaf M, Yau HC, Verheul J, Lodge A, Kritikos G, Mateus A, Cordier B, Hov AK, Stein F, Wartel M, Pazos M, Solovyova AS, Breukink E, van Teeffelen S, Savitski MM, den Blaauwen T, Typas A, Vollmer W. Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli. EMBO J 2020; 39:e102246. [PMID: 32009249 PMCID: PMC7049810 DOI: 10.15252/embj.2019102246] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 04/15/2019] [Revised: 12/20/2019] [Accepted: 01/14/2020] [Indexed: 12/16/2022] Open
Abstract
The peptidoglycan (PG) sacculus provides bacteria with the mechanical strength to maintain cell shape and resist osmotic stress. Enlargement of the mesh‐like sacculus requires the combined activity of peptidoglycan synthases and hydrolases. In Escherichia coli, the activity of two PG synthases is driven by lipoproteins anchored in the outer membrane (OM). However, the regulation of PG hydrolases is less well understood, with only regulators for PG amidases having been described. Here, we identify the OM lipoprotein NlpI as a general adaptor protein for PG hydrolases. NlpI binds to different classes of hydrolases and can specifically form complexes with various PG endopeptidases. In addition, NlpI seems to contribute both to PG elongation and division biosynthetic complexes based on its localization and genetic interactions. Consistent with such a role, we reconstitute PG multi‐enzyme complexes containing NlpI, the PG synthesis regulator LpoA, its cognate bifunctional synthase, PBP1A, and different endopeptidases. Our results indicate that peptidoglycan regulators and adaptors are part of PG biosynthetic multi‐enzyme complexes, regulating and potentially coordinating the spatiotemporal action of PG synthases and hydrolases.
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Affiliation(s)
- Manuel Banzhaf
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Hamish Cl Yau
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Jolanda Verheul
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Adam Lodge
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - George Kritikos
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Baptiste Cordier
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Ann Kristin Hov
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Morgane Wartel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuel Pazos
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | | | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | | | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,European Molecular Biology Laboratory, Structural & Computational Unit, Heidelberg, Germany
| | - Tanneke den Blaauwen
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,European Molecular Biology Laboratory, Structural & Computational Unit, Heidelberg, Germany
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
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36
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Jacobs-Cachá C, Puig-Gay N, Helm D, Rettel M, Sellarès J, Meseguer A, Savitski MM, Moreso FJ, Soler MJ, Seron D, Lopez-Hellin J. A misprocessed form of Apolipoprotein A-I is specifically associated with recurrent Focal Segmental Glomerulosclerosis. Sci Rep 2020; 10:1159. [PMID: 31980684 PMCID: PMC6981185 DOI: 10.1038/s41598-020-58197-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/10/2020] [Indexed: 12/29/2022] Open
Abstract
Apolipoprotein A-Ib (ApoA-Ib) is a high molecular weight form of Apolipoprotein A-I (ApoA-I) found specifically in the urine of kidney-transplanted patients with recurrent idiopathic focal segmental glomerulosclerosis (FSGS). To determine the nature of the modification present in ApoA-Ib, we sequenced the whole APOA1 gene in ApoA-Ib positive and negative patients, and we also studied the protein primary structure using mass spectrometry. No genetic variations in the APOA1 gene were found in the ApoA-Ib positive patients that could explain the increase in its molecular mass. The mass spectrometry analysis revealed three extra amino acids at the N-Terminal end of ApoA-Ib that were not present in the standard plasmatic form of ApoA-I. These amino acids corresponded to half of the propeptide sequence of the immature form of ApoA-I (proApoA-I) indicating that ApoA-Ib is a misprocessed form of proApoA-I. The description of ApoA-Ib could be relevant not only because it can allow the automated analysis of this biomarker in the clinical practice but also because it has the potential to shed light into the molecular mechanisms that cause idiopathic FSGS, which is currently unknown.
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Affiliation(s)
- Conxita Jacobs-Cachá
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain. .,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain.
| | - Natàlia Puig-Gay
- Renal Physiopathology Group-CIBBIM. Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joana Sellarès
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Anna Meseguer
- Renal Physiopathology Group-CIBBIM. Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Mikhail M Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.,Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Francesc J Moreso
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Maria José Soler
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Daniel Seron
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Joan Lopez-Hellin
- Renal Physiopathology Group-CIBBIM. Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain. .,Biochemistry Department, Hospital Vall d'Hebrón, Barcelona, Spain.
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37
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Childs D, Bach K, Franken H, Anders S, Kurzawa N, Bantscheff M, Savitski MM, Huber W. Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins. Mol Cell Proteomics 2019; 18:2506-2515. [PMID: 31582558 PMCID: PMC6885700 DOI: 10.1074/mcp.tir119.001481] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/01/2019] [Indexed: 12/19/2022] Open
Abstract
Detecting the targets of drugs and other molecules in intact cellular contexts is a major objective in drug discovery and in biology more broadly. Thermal proteome profiling (TPP) pursues this aim at proteome-wide scale by inferring target engagement from its effects on temperature-dependent protein denaturation. However, a key challenge of TPP is the statistical analysis of the measured melting curves with controlled false discovery rates at high proteome coverage and detection power. We present nonparametric analysis of response curves (NPARC), a statistical method for TPP based on functional data analysis and nonlinear regression. We evaluate NPARC on five independent TPP data sets and observe that it is able to detect subtle changes in any region of the melting curves, reliably detects the known targets, and outperforms a melting point-centric, single-parameter fitting approach in terms of specificity and sensitivity. NPARC can be combined with established analysis of variance (ANOVA) statistics and enables flexible, factorial experimental designs and replication levels. An open source software implementation of NPARC is provided.
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Affiliation(s)
- Dorothee Childs
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany; Cellzome GmbH, GlaxoSmithKline, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Karsten Bach
- Department of Pharmacology, University of Cambridge, CB2 1PD, Cambridge, UK; Cancer Research UK Cambridge Cancer Centre, CB2 0RE, Cambridge, UK
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Nils Kurzawa
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany.
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38
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Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo JJ, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Typas A, Savitski MM, Espinoza JL, O'Rourke A, Nelson KE, Hiller S, Noinaj N, Schäberle TF, D'Onofrio A, Lewis K. A new antibiotic selectively kills Gram-negative pathogens. Nature 2019; 576:459-464. [PMID: 31747680 PMCID: PMC7188312 DOI: 10.1038/s41586-019-1791-1] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [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: 04/03/2019] [Accepted: 11/08/2019] [Indexed: 11/16/2022]
Abstract
The current need for novel antibiotics is especially acute for
drug-resistant Gram-negative pathogens1,2. These
microorganisms have a highly restrictive permeability barrier, which limits
penetration of most compounds3,4. As a result, the last class of
antibiotics acting against Gram-negative bacteria was developed in the
60s2. We reason that
useful compounds can be found in bacteria that share similar requirements for
antibiotics with humans, and focus on Photorhabdus symbionts of
entomopathogenic nematode microbiomes. Here we report a new antibiotic that we
name darobactin, from a screen of Photorhabdus isolates.
Darobactin is coded by a silent operon with little production under laboratory
conditions, and is ribosomally synthesized. Darobactin has an unusual structure
with two fused rings that form post-translationally. The compound is active
against important Gram-negative pathogens both in vitro and in
animal models of infection. Mutants resistant to darobactin map to BamA, an
essential chaperone and translocator that folds outer membrane proteins. Our
study suggests that bacterial symbionts of animals harbor antibiotics that are
particularly suitable for development into therapeutics.
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Affiliation(s)
- Yu Imai
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Kirsten J Meyer
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Akira Iinishi
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Quentin Favre-Godal
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Robert Green
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Sylvie Manuse
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Mariaelena Caboni
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Miho Mori
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Samantha Niles
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Meghan Ghiglieri
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Chandrashekhar Honrao
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Xiaoyu Ma
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Jason J Guo
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA.,Barnett Institute for Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Alexandros Makriyannis
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Luis Linares-Otoya
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Zerlina G Wuisan
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Hundeep Kaur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Runrun Wu
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.,Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Josh L Espinoza
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Aubrie O'Rourke
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Karen E Nelson
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Human Biology, J. Craig Venter Institute, Rockville, MD, USA.,Department of Genomic Medicine, J. Craig Venter Institute, Rockville, MD, USA
| | | | - Nicholas Noinaj
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.,Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany.,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Anthony D'Onofrio
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA.
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39
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Sridharan S, Kurzawa N, Werner T, Günthner I, Helm D, Huber W, Bantscheff M, Savitski MM. Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP. Nat Commun 2019; 10:1155. [PMID: 30858367 PMCID: PMC6411743 DOI: 10.1038/s41467-019-09107-y] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/22/2019] [Indexed: 02/03/2023] Open
Abstract
Adenosine triphosphate (ATP) plays fundamental roles in cellular biochemistry and was recently discovered to function as a biological hydrotrope. Here, we use mass spectrometry to interrogate ATP-mediated regulation of protein thermal stability and protein solubility on a proteome-wide scale. Thermal proteome profiling reveals high affinity interactions of ATP as a substrate and as an allosteric modulator that has widespread influence on protein complexes and their stability. Further, we develop a strategy for proteome-wide solubility profiling, and discover ATP-dependent solubilization of at least 25% of the insoluble proteome. ATP increases the solubility of positively charged, intrinsically disordered proteins, and their susceptibility for solubilization varies depending on their localization to different membrane-less organelles. Moreover, a few proteins, exhibit an ATP-dependent decrease in solubility, likely reflecting polymer formation. Our data provides a proteome-wide, quantitative insight into how ATP influences protein structure and solubility across the spectrum of physiologically relevant concentrations. ATP can function as a biological hydrotrope, but its global effects on protein solubility have not yet been characterized. Here, the authors quantify the effect of ATP on the thermal stability and solubility of the cellular proteome, providing insights into protein solubility regulation by ATP.
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Affiliation(s)
- Sindhuja Sridharan
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Candidate for joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, 69120, Heidelberg, Germany
| | - Thilo Werner
- Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Ina Günthner
- Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | | | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
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40
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Pereira F, Rettel M, Stein F, Savitski MM, Collinson I, Römisch K. Effect of Sec61 interaction with Mpd1 on endoplasmic reticulum-associated degradation. PLoS One 2019; 14:e0211180. [PMID: 30682149 PMCID: PMC6347170 DOI: 10.1371/journal.pone.0211180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 10/10/2018] [Accepted: 01/08/2019] [Indexed: 01/16/2023] Open
Abstract
Proteins that misfold in the endoplasmic reticulum (ER) are transported back to the cytosol for ER-associated degradation (ERAD). The Sec61 channel is one of the candidates for the retrograde transport conduit. Channel opening from the ER lumen must be triggered by ERAD factors and substrates. Here we aimed to identify new lumenal interaction partners of the Sec61 channel by chemical crosslinking and mass spectrometry. In addition to known Sec61 interactors we detected ERAD factors including Cue1, Ubc6, Ubc7, Asi3, and Mpd1. We show that the CPY* ERAD factor Mpd1 binds to the lumenal Sec61 hinge region. Deletion of the Mpd1 binding site reduced the interaction between both proteins and caused an ERAD defect specific for CPY* without affecting protein import into the ER or ERAD of other substrates. Our data suggest that Mpd1 binding to Sec61 is a prerequisite for CPY* ERAD and confirm a role of Sec61 in ERAD of misfolded secretory proteins.
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Affiliation(s)
- Fabio Pereira
- Faculty of Natural Sciences and Technology, Saarland University, Saarbruecken, Germany
| | - Mandy Rettel
- Proteomics Core Facility, EMBL, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL, Heidelberg, Germany
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Karin Römisch
- Faculty of Natural Sciences and Technology, Saarland University, Saarbruecken, Germany
- * E-mail:
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41
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Abstract
Increasing antibiotic resistance urges for new technologies for studying microbes and antimicrobial mechanism of action. We adapted thermal proteome profiling (TPP) to probe the thermostability of Escherichia coli proteins in vivoE. coli had a more thermostable proteome than human cells, with protein thermostability depending on subcellular location-forming a high-to-low gradient from the cell surface to the cytoplasm. While subunits of protein complexes residing in one compartment melted similarly, protein complexes spanning compartments often had their subunits melting in a location-wise manner. Monitoring the E. coli meltome and proteome at different growth phases captured changes in metabolism. Cells lacking TolC, a component of multiple efflux pumps, exhibited major physiological changes, including differential thermostability and levels of its interaction partners, signaling cascades, and periplasmic quality control. Finally, we combined in vitro and in vivo TPP to identify targets of known antimicrobial drugs and to map their downstream effects. In conclusion, we demonstrate that TPP can be used in bacteria to probe protein complex architecture, metabolic pathways, and intracellular drug target engagement.
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Affiliation(s)
- André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jacob Bobonis
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Johannes Hevler
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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42
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Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Savitski MM, Bork P, Göttig S, Typas A. Species-specific activity of antibacterial drug combinations. Nature 2018; 559:259-263. [PMID: 29973719 DOI: 10.1038/s41586-018-0278-9] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/24/2018] [Indexed: 12/12/2022]
Abstract
The spread of antimicrobial resistance has become a serious public health concern, making once-treatable diseases deadly again and undermining the achievements of modern medicine1,2. Drug combinations can help to fight multi-drug-resistant bacterial infections, yet they are largely unexplored and rarely used in clinics. Here we profile almost 3,000 dose-resolved combinations of antibiotics, human-targeted drugs and food additives in six strains from three Gram-negative pathogens-Escherichia coli, Salmonella enterica serovar Typhimurium and Pseudomonas aeruginosa-to identify general principles for antibacterial drug combinations and understand their potential. Despite the phylogenetic relatedness of the three species, more than 70% of the drug-drug interactions that we detected are species-specific and 20% display strain specificity, revealing a large potential for narrow-spectrum therapies. Overall, antagonisms are more common than synergies and occur almost exclusively between drugs that target different cellular processes, whereas synergies are more conserved and are enriched in drugs that target the same process. We provide mechanistic insights into this dichotomy and further dissect the interactions of the food additive vanillin. Finally, we demonstrate that several synergies are effective against multi-drug-resistant clinical isolates in vitro and during infections of the larvae of the greater wax moth Galleria mellonella, with one reverting resistance to the last-resort antibiotic colistin.
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Affiliation(s)
- Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anja Telzerow
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jacob Bobonis
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuel Banzhaf
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Emily Huth
- Institute of Medical Microbiology and Infection Control, Hospital of Goethe University, Frankfurt am Main, Germany
| | - Stefan Bassler
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jordi Zamarreño Beas
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Matylda Zietek
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Natalie Ng
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sunniva Foerster
- Institute of Social & Preventive Medicine, Institute of Infectious Diseases, University of Bern, Bern, Switzerland
| | - Benjamin Ezraty
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Frédéric Barras
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France.,Institut Pasteur, Paris, France
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural & Computational Biology Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Stephan Göttig
- Institute of Medical Microbiology and Infection Control, Hospital of Goethe University, Frankfurt am Main, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,European Molecular Biology Laboratory, Structural & Computational Biology Unit, Heidelberg, Germany.
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43
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Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M. Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis. Cell 2018; 173:260-274.e25. [PMID: 29551266 PMCID: PMC5871718 DOI: 10.1016/j.cell.2018.02.030] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 12/01/2017] [Accepted: 02/09/2018] [Indexed: 02/07/2023]
Abstract
Protein degradation plays important roles in biological processes and is tightly regulated. Further, targeted proteolysis is an emerging research tool and therapeutic strategy. However, proteome-wide technologies to investigate the causes and consequences of protein degradation in biological systems are lacking. We developed “multiplexed proteome dynamics profiling” (mPDP), a mass-spectrometry-based approach combining dynamic-SILAC labeling with isobaric mass tagging for multiplexed analysis of protein degradation and synthesis. In three proof-of-concept studies, we uncover different responses induced by the bromodomain inhibitor JQ1 versus a JQ1 proteolysis targeting chimera; we elucidate distinct modes of action of estrogen receptor modulators; and we comprehensively classify HSP90 clients based on their requirement for HSP90 constitutively or during synthesis, demonstrating that constitutive HSP90 clients have lower thermal stability than non-clients, have higher affinity for the chaperone, vary between cell types, and change upon external stimuli. These findings highlight the potential of mPDP to identify dynamically controlled degradation mechanisms in cellular systems. Multiplexed proteome dynamics profiling, mPDP, measures changes in proteostasis JQ1-PROTAC degrades a key mRNA export factor and blocks protein synthesis Raloxifene induces TMEM97 degradation dysregulating cholesterol homeostasis Characterization of proteins dependent on HSP90 constitutively or during synthesis
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Affiliation(s)
- Mikhail M Savitski
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Nico Zinn
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Daniel Poeckel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Gade
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anne J Wagner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Katrin Strohmer
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephanie Melchert
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Massimo Petretich
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anna Rutkowska
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Johanna Vappiani
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Michael Steidel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gavain M Sweetman
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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Mateus A, Määttä TA, Savitski MM. Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes. Proteome Sci 2017; 15:13. [PMID: 28652855 PMCID: PMC5482948 DOI: 10.1186/s12953-017-0122-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [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: 04/14/2017] [Accepted: 06/15/2017] [Indexed: 12/31/2022] Open
Abstract
In recent years, phenotypic-based screens have become increasingly popular in drug discovery. A major challenge of this approach is that it does not provide information about the mechanism of action of the hits. This has led to the development of multiple strategies for target deconvolution. Thermal proteome profiling (TPP) allows for an unbiased search of drug targets and can be applied in living cells without requiring compound labeling. TPP is based on the principle that proteins become more resistant to heat-induced unfolding when complexed with a ligand, e.g., the hit compound from a phenotypic screen. The melting proteome is also sensitive to other intracellular events, such as levels of metabolites, post-translational modifications and protein-protein interactions. In this review, we describe the principles of this approach, review the method and its developments, and discuss its current and future applications. While proteomics has generally focused on measuring relative protein concentrations, TPP provides a novel approach to gather complementary information on protein stability not present in expression datasets. Therefore, this strategy has great potential not only for drug discovery, but also for answering fundamental biological questions.
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Affiliation(s)
- André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Tomi A Määttä
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
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45
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Beckham KSH, Ciccarelli L, Bunduc CM, Mertens HDT, Ummels R, Lugmayr W, Mayr J, Rettel M, Savitski MM, Svergun DI, Bitter W, Wilmanns M, Marlovits TC, Parret AHA, Houben ENG. Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis. Nat Microbiol 2017; 2:17047. [DOI: 10.1038/nmicrobiol.2017.47] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/03/2017] [Indexed: 12/21/2022]
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46
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Becher I, Werner T, Doce C, Zaal EA, Tögel I, Khan CA, Rueger A, Muelbaier M, Salzer E, Berkers CR, Fitzpatrick PF, Bantscheff M, Savitski MM. Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat. Nat Chem Biol 2016; 12:908-910. [DOI: 10.1038/nchembio.2185] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/20/2016] [Indexed: 02/07/2023]
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47
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Klaeger S, Gohlke B, Perrin J, Gupta V, Heinzlmeir S, Helm D, Qiao H, Bergamini G, Handa H, Savitski MM, Bantscheff M, Médard G, Preissner R, Kuster B. Chemical Proteomics Reveals Ferrochelatase as a Common Off-target of Kinase Inhibitors. ACS Chem Biol 2016; 11:1245-54. [PMID: 26863403 DOI: 10.1021/acschembio.5b01063] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many protein kinases are valid drug targets in oncology because they are key components of signal transduction pathways. The number of clinical kinase inhibitors is on the rise, but these molecules often exhibit polypharmacology, potentially eliciting desired and toxic effects. Therefore, a comprehensive assessment of a compound's target space is desirable for a better understanding of its biological effects. The enzyme ferrochelatase (FECH) catalyzes the conversion of protoporphyrin IX into heme and was recently found to be an off-target of the BRAF inhibitor Vemurafenib, likely explaining the phototoxicity associated with this drug in melanoma patients. This raises the question of whether FECH binding is a more general feature of kinase inhibitors. To address this, we applied a chemical proteomics approach using kinobeads to evaluate 226 clinical kinase inhibitors for their ability to bind FECH. Surprisingly, low or submicromolar FECH binding was detected for 29 of all compounds tested and isothermal dose response measurements confirmed target engagement in cells. We also show that Vemurafenib, Linsitinib, Neratinib, and MK-2461 reduce heme levels in K562 cells, verifying that drug binding leads to a loss of FECH activity. Further biochemical and docking experiments identified the protoporphyrin pocket in FECH as one major drug binding site. Since the genetic loss of FECH activity leads to photosensitivity in humans, our data strongly suggest that FECH inhibition by kinase inhibitors is the molecular mechanism triggering photosensitivity in patients. We therefore suggest that a FECH assay should generally be part of the preclinical molecular toxicology package for the development of kinase inhibitors.
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Affiliation(s)
- Susan Klaeger
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bjoern Gohlke
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Structural
Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
| | | | - Vipul Gupta
- Department
of Nanoparticle Translational Research, Tokyo Medical University, Tokyo, Japan
| | - Stephanie Heinzlmeir
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Helm
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Huichao Qiao
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Hiroshi Handa
- Department
of Nanoparticle Translational Research, Tokyo Medical University, Tokyo, Japan
| | | | | | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Robert Preissner
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Structural
Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bavarian
Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
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Reinhard FBM, Eberhard D, Werner T, Franken H, Childs D, Doce C, Savitski MF, Huber W, Bantscheff M, Savitski MM, Drewes G. Thermal proteome profiling monitors ligand interactions with cellular membrane proteins. Nat Methods 2015; 12:1129-31. [PMID: 26524241 DOI: 10.1038/nmeth.3652] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/06/2015] [Indexed: 12/15/2022]
Abstract
We extended thermal proteome profiling to detect transmembrane protein-small molecule interactions in cultured human cells. When we assessed the effects of detergents on ATP-binding profiles, we observed shifts in denaturation temperature for ATP-binding transmembrane proteins. We also observed cellular thermal shifts in pervanadate-induced T cell-receptor signaling, delineating the membrane target CD45 and components of the downstream pathway, and with drugs affecting the transmembrane transporters ATP1A1 and MDR1.
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Affiliation(s)
| | - Dirk Eberhard
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Holger Franken
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Dorothee Childs
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carola Doce
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Maria Fälth Savitski
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Mikhail M Savitski
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
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49
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Savitski MM, Wilhelm M, Hahne H, Kuster B, Bantscheff M. A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets. Mol Cell Proteomics 2015; 14:2394-404. [PMID: 25987413 DOI: 10.1074/mcp.m114.046995] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Indexed: 02/06/2023] Open
Abstract
Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target-decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target-decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The "picked" protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The "picked" target-decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used "classic" protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in proteomics analysis software.
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Affiliation(s)
| | - Mathias Wilhelm
- §Chair for Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany; ¶SAP SE, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany
| | - Hannes Hahne
- §Chair for Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- §Chair for Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany; ‖Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Marcus Bantscheff
- From the ‡Cellzome GmbH, Meyerhofstrasse 1, 69117 Heidelberg, Germany;
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50
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Savitski MM, Reinhard FBM, Franken H, Werner T, Savitski MF, Eberhard D, Molina DM, Jafari R, Dovega RB, Klaeger S, Kuster B, Nordlund P, Bantscheff M, Drewes G. Tracking cancer drugs in living cells by thermal profiling of the proteome. Science 2014; 346:1255784. [DOI: 10.1126/science.1255784] [Citation(s) in RCA: 594] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The thermal stability of proteins can be used to assess ligand binding in living cells. We have generalized this concept by determining the thermal profiles of more than 7000 proteins in human cells by means of mass spectrometry. Monitoring the effects of small-molecule ligands on the profiles delineated more than 50 targets for the kinase inhibitor staurosporine. We identified the heme biosynthesis enzyme ferrochelatase as a target of kinase inhibitors and suggest that its inhibition causes the phototoxicity observed with vemurafenib and alectinib. Thermal shifts were also observed for downstream effectors of drug treatment. In live cells, dasatinib induced shifts in BCR-ABL pathway proteins, including CRK/CRKL. Thermal proteome profiling provides an unbiased measure of drug-target engagement and facilitates identification of markers for drug efficacy and toxicity.
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