1
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Frommelt F, Fossati A, Uliana F, Wendt F, Xue P, Heusel M, Wollscheid B, Aebersold R, Ciuffa R, Gstaiger M. DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nat Methods 2024; 21:635-647. [PMID: 38532014 PMCID: PMC11009110 DOI: 10.1038/s41592-024-02211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.
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Affiliation(s)
- Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Fabian Wendt
- Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Guangzhou National Laboratory, Guang Zhou, China
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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2
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Torres-Sangiao E, Happonen L, Heusel M, Palm F, Gueto-Tettay C, Malmström L, Shannon O, Malmström J. Quantification of adaptive immune responses against protein binding interfaces in the streptococcal M1 protein. Mol Cell Proteomics 2024:100753. [PMID: 38527648 DOI: 10.1016/j.mcpro.2024.100753] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024] Open
Abstract
Bacterial or viral antigens can contain subdominant protein regions that elicit weak antibody responses upon vaccination or infection although there is accumulating evidence that antibody responses against subdominant regions can enhance the protective immune response. One proposed mechanism for subdominant protein regions is binding of host proteins that prevent antibody production against epitopes hidden within the protein binding interfaces. Here, we used affinity-purification combined with quantitative mass spectrometry (AP-MS) to examine the level of competition between antigen-specific antibodies and host-pathogen protein interaction networks using the M1 protein from Streptococcus pyogenes as a model system. As most humans have circulating antibodies against the M1 protein, we first used AP-MS to show that the M1 protein interspecies protein network formed with human plasma proteins is largely conserved in naïve mice. Immunizing mice with the M1 protein generated a time-dependent increase of anti-M1 antibodies. AP-MS analysis comparing the composition of the M1-plasma protein network from naïve and immunized mice showed a significant enrichment of 292 IgG peptides associated with 56 IgG chains in the immune mice. Despite the significant increase of bound IgGs, the levels of interacting plasma proteins were not significantly reduced in the immune mice. The results indicate that the antigen-specific polyclonal IgG against the M1 protein primarily targets epitopes outside the other plasma protein binding interfaces. In conclusion, this study demonstrates that AP-MS is a promising strategy to determine the relationship between antigen-specific antibodies and host-pathogen interaction networks that could be used to define subdominant protein regions of relevance for vaccine development.
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Affiliation(s)
- E Torres-Sangiao
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden; Health Research Institute of Santiago de Compostela (IDIS), Escherichia coli group. 15706 Santiago de Compostela, Spain; University Hospital Complex of Santiago de Compostela, Clinical Microbiology Lab. 15706 Santiago de Compostela, Spain.
| | - L Happonen
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden
| | - M Heusel
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden; Evosep ApS, Buchwaldsgade 35, Odense, Denmark
| | - F Palm
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden
| | - C Gueto-Tettay
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden
| | - L Malmström
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden
| | - O Shannon
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden; Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, 20506 Malmö, Sweden
| | - J Malmström
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden.
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3
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Bludau I, Nicod C, Martelli C, Xue P, Heusel M, Fossati A, Uliana F, Frommelt F, Aebersold R, Collins BC. Rapid Profiling of Protein Complex Reorganization in Perturbed Systems. J Proteome Res 2023; 22:1520-1536. [PMID: 37058003 PMCID: PMC10167687 DOI: 10.1021/acs.jproteome.3c00125] [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] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Protein complexes constitute the primary functional modules of cellular activity. To respond to perturbations, complexes undergo changes in their abundance, subunit composition, or state of modification. Understanding the function of biological systems requires global strategies to capture this contextual state information. Methods based on cofractionation paired with mass spectrometry have demonstrated the capability for deep biological insight, but the scope of studies using this approach has been limited by the large measurement time per biological sample and challenges with data analysis. There has been little uptake of this strategy into the broader life science community despite its rich biological information content. We present a rapid integrated experimental and computational workflow to assess the reorganization of protein complexes across multiple cellular states. The workflow combines short gradient chromatography and DIA/SWATH mass spectrometry with a data analysis toolset to quantify changes in a complex organization. We applied the workflow to study the global protein complex rearrangements of THP-1 cells undergoing monocyte to macrophage differentiation and subsequent stimulation of macrophage cells with lipopolysaccharide. We observed substantial proteome reorganization on differentiation and less pronounced changes in macrophage stimulation. We establish our integrated differential pipeline for rapid and state-specific profiling of protein complex organization.
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Affiliation(s)
- Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany 82152
| | - Charlotte Nicod
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
- Division of Infection Medicine (BMC), Department of Clinical Sciences, Lund University, Lund, Sweden 22184
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- J. David Gladstone Institutes, San Francisco, California 94158, United States
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland 8052
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland 8092
| | - Ben C Collins
- School of Biological Sciences, Queen's University of Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, U.K
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4
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Tanner L, Single AB, Bhongir RKV, Heusel M, Mohanty T, Karlsson CAQ, Pan L, Clausson CM, Bergwik J, Wang K, Andersson CK, Oommen RM, Erjefält JS, Malmström J, Wallner O, Boldogh I, Helleday T, Kalderén C, Egesten A. Small-molecule-mediated OGG1 inhibition attenuates pulmonary inflammation and lung fibrosis in a murine lung fibrosis model. Nat Commun 2023; 14:643. [PMID: 36746968 PMCID: PMC9902543 DOI: 10.1038/s41467-023-36314-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Interstitial lung diseases such as idiopathic pulmonary fibrosis (IPF) are caused by persistent micro-injuries to alveolar epithelial tissues accompanied by aberrant repair processes. IPF is currently treated with pirfenidone and nintedanib, compounds which slow the rate of disease progression but fail to target underlying pathophysiological mechanisms. The DNA repair protein 8-oxoguanine DNA glycosylase-1 (OGG1) has significant roles in the modulation of inflammation and metabolic syndromes. Currently, no pharmaceutical solutions targeting OGG1 have been utilized in the treatment of IPF. In this study we show Ogg1-targeting siRNA mitigates bleomycin-induced pulmonary fibrosis in male mice, highlighting OGG1 as a tractable target in lung fibrosis. The small molecule OGG1 inhibitor, TH5487, decreases myofibroblast transition and associated pro-fibrotic gene expressions in fibroblast cells. In addition, TH5487 decreases levels of pro-inflammatory mediators, inflammatory cell infiltration, and lung remodeling in a murine model of bleomycin-induced pulmonary fibrosis conducted in male C57BL6/J mice. OGG1 and SMAD7 interact to induce fibroblast proliferation and differentiation and display roles in fibrotic murine and IPF patient lung tissue. Taken together, these data suggest that TH5487 is a potentially clinically relevant treatment for IPF but further study in human trials is required.
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Affiliation(s)
- L Tanner
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden.
| | - A B Single
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden
| | - R K V Bhongir
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden
| | - M Heusel
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - T Mohanty
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - C A Q Karlsson
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - L Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - C-M Clausson
- Division of Airway Inflammation, Department of Experimental Medical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - J Bergwik
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden
| | - K Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - C K Andersson
- Respiratory Cell Biology, Department of Experimental Medical Sciences Lund, Lund University, SE-221 84, Lund, Sweden
| | - R M Oommen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - J S Erjefält
- Division of Airway Inflammation, Department of Experimental Medical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - J Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84, Lund, Sweden
| | - O Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - I Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - T Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Oxcia AB, Norrbackagatan 70C, SE-113 34, Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - C Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Oxcia AB, Norrbackagatan 70C, SE-113 34, Stockholm, Sweden
| | - A Egesten
- Respiratory Medicine, Allergology, & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 84, Lund, Sweden
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5
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Abstract
![]()
Data-independent
acquisition-mass spectrometry (DIA-MS) is the
method of choice for deep, consistent, and accurate single-shot profiling
in bottom-up proteomics. While classic workflows for targeted quantification
from DIA-MS data require auxiliary data-dependent acquisition (DDA)
MS analysis of subject samples to derive prior-knowledge spectral
libraries, library-free approaches based on in silico prediction promise deep DIA-MS profiling with reduced experimental
effort and cost. Coverage and sensitivity in such analyses are however
limited, in part, by the large library size and persistent deviations
from the experimental data. We present MSLibrarian, a new workflow
and tool to obtain optimized predicted spectral libraries by the integrated
usage of spectrum-centric DIA data interpretation via the DIA-Umpire
approach to inform and calibrate the in silico predicted
library and analysis approach. Predicted-vs-observed comparisons enabled
optimization of intensity prediction parameters, calibration of retention
time prediction for deviating chromatographic setups, and optimization
of the library scope and sample representativeness. Benchmarking via
a dedicated ground-truth-embedded experiment of species-mixed proteins
and quantitative ratio-validation confirmed gains of up to 13% on
peptide and 8% on protein level at equivalent FDR control and validation
criteria. MSLibrarian is made available as an open-source R software
package, including step-by-step user instructions, at https://github.com/MarcIsak/MSLibrarian.
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Affiliation(s)
- Marc Isaksson
- Department of Biomedical Engineering, Lund University, 22100 Lund, Sweden.,Department of Experimental Medical Science and Wallenberg Center for Molecular Medicine, Lund University, 22100 Lund, Sweden
| | - Christofer Karlsson
- Infection Medicine Proteomics Lab, Division of Infection Medicine (BMC), Faculty of Medicine, Lund University, 22100 Lund, Sweden
| | - Thomas Laurell
- Department of Biomedical Engineering, Lund University, 22100 Lund, Sweden
| | - Agnete Kirkeby
- Department of Experimental Medical Science and Wallenberg Center for Molecular Medicine, Lund University, 22100 Lund, Sweden.,Department of Neuroscience, University of Copenhagen, DK-2200 Copenhagen, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Moritz Heusel
- Infection Medicine Proteomics Lab, Division of Infection Medicine (BMC), Faculty of Medicine, Lund University, 22100 Lund, Sweden
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6
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Bludau I, Frank M, Dörig C, Cai Y, Heusel M, Rosenberger G, Picotti P, Collins BC, Röst H, Aebersold R. Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nat Commun 2021; 12:3810. [PMID: 34155216 PMCID: PMC8217233 DOI: 10.1038/s41467-021-24030-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 12/08/2020] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
To a large extent functional diversity in cells is achieved by the expansion of molecular complexity beyond that of the coding genome. Various processes create multiple distinct but related proteins per coding gene - so-called proteoforms - that expand the functional capacity of a cell. Evaluating proteoforms from classical bottom-up proteomics datasets, where peptides instead of intact proteoforms are measured, has remained difficult. Here we present COPF, a tool for COrrelation-based functional ProteoForm assessment in bottom-up proteomics data. It leverages the concept of peptide correlation analysis to systematically assign peptides to co-varying proteoform groups. We show applications of COPF to protein complex co-fractionation data as well as to more typical protein abundance vs. sample data matrices, demonstrating the systematic detection of assembly- and tissue-specific proteoform groups, respectively, in either dataset. We envision that the presented approach lays the foundation for a systematic assessment of proteoforms and their functional implications directly from bottom-up proteomic datasets.
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Affiliation(s)
- Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Max Frank
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christian Dörig
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Yujia Cai
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Division of Infection Medicine (BMC), Department of Clinical Sciences, Lund University, Lund, Sweden
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Columbia University, New York, NY, USA
| | - Paola Picotti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Hannes Röst
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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7
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Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Syst 2020; 11:589-607.e8. [PMID: 33333029 PMCID: PMC8034988 DOI: 10.1016/j.cels.2020.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 04/30/2020] [Revised: 08/25/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions (PPIs) play critical functional and regulatory roles in cellular processes. They are essential for macromolecular complex formation, which in turn constitutes the basis for protein interaction networks that determine the functional state of a cell. We and others have previously shown that chromatographic fractionation of native protein complexes in combination with bottom-up mass spectrometric analysis of consecutive fractions supports the multiplexed characterization and detection of state-specific changes of protein complexes. In this study, we extend co-fractionation and mass spectrometric data analysis to perform quantitative, network-based studies of proteome organization, via the size-exclusion chromatography algorithmic toolkit (SECAT). This framework explicitly accounts for the dynamic nature and rewiring of protein complexes across multiple cell states and samples, thus, elucidating molecular mechanisms that are differentially implemented across different experimental settings. Systematic analysis of multiple datasets shows that SECAT represents a highly scalable and effective methodology to assess condition/state-specific protein-network state. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven CT, USA; Department of Pharmacology, Yale University School of Medicine, New Haven CT, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland.
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York NY, USA; Department of Biomedical Informatics, Columbia University, New York NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York NY, USA; J.P. Sulzberger Columbia Genome Center, Columbia University, New York NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York NY, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York NY, USA.
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8
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Helleboid P, Heusel M, Duc J, Piot C, Thorball CW, Coluccio A, Pontis J, Imbeault M, Turelli P, Aebersold R, Trono D. The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. EMBO J 2019; 38:e101220. [PMID: 31403225 PMCID: PMC6745500 DOI: 10.15252/embj.2018101220] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [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: 11/23/2018] [Revised: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 01/24/2023] Open
Abstract
Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin-inducing KAP1 as repressors of transposable elements (TEs) during early embryogenesis. Yet, their widespread expression in adult tissues and enrichment at other genetic loci indicate additional roles. Here, we characterized the protein interactome of 101 of the ~350 human KZFPs. Consistent with their targeting of TEs, most KZFPs conserved up to placental mammals essentially recruit KAP1 and associated effectors. In contrast, a subset of more ancient KZFPs rather interacts with factors related to functions such as genome architecture or RNA processing. Nevertheless, KZFPs from coelacanth, our most distant KZFP-encoding relative, bind the cognate KAP1. These results support a hypothetical model whereby KZFPs first emerged as TE-controlling repressors, were continuously renewed by turnover of their hosts' TE loads, and occasionally produced derivatives that escaped this evolutionary flushing by development and exaptation of novel functions.
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Affiliation(s)
| | - Moritz Heusel
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Julien Duc
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Cécile Piot
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Christian W Thorball
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrea Coluccio
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Julien Pontis
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Michaël Imbeault
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Priscilla Turelli
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Faculty of ScienceUniversity of ZurichZurichSwitzerland
| | - Didier Trono
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
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9
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Heusel M, Bludau I, Rosenberger G, Hafen R, Frank M, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R. Complex-centric proteome profiling by SEC-SWATH-MS. Mol Syst Biol 2019; 15:e8438. [PMID: 30642884 PMCID: PMC6346213 DOI: 10.15252/msb.20188438] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Proteins are major effectors and regulators of biological processes that can elicit multiple functions depending on their interaction with other proteins. The organization of proteins into macromolecular complexes and their quantitative distribution across these complexes is, therefore, of great biological and clinical significance. In this paper, we describe an integrated experimental and computational technique to quantify hundreds of protein complexes in a single operation. The method consists of size exclusion chromatography (SEC) to fractionate native protein complexes, SWATH/DIA mass spectrometry to precisely quantify the proteins in each SEC fraction, and the computational framework CCprofiler to detect and quantify protein complexes by error‐controlled, complex‐centric analysis using prior information from generic protein interaction maps. Our analysis of the HEK293 cell line proteome delineates 462 complexes composed of 2,127 protein subunits. The technique identifies novel sub‐complexes and assembly intermediates of central regulatory complexes while assessing the quantitative subunit distribution across them. We make the toolset CCprofiler freely accessible and provide a web platform, SECexplorer, for custom exploration of the HEK293 proteome modularity.
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Affiliation(s)
- Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Molecular and Translational Biomedicine of the Competence Center Personalized Medicine UZH/ETH, Zurich, Switzerland
| | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Robin Hafen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Max Frank
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Audrey van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland .,Faculty of Science, University of Zurich, Zurich, Switzerland
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10
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Caron E, Roncagalli R, Hase T, Wolski WE, Choi M, Menoita MG, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins BC, Ghosh S, Kitano H, Aebersold R, Malissen B, Gstaiger M. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Rep 2017; 18:3219-3226. [PMID: 28355572 PMCID: PMC5382234 DOI: 10.1016/j.celrep.2017.03.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 11/02/2022] Open
Abstract
Spatiotemporal organization of protein interactions in cell signaling is a fundamental process that drives cellular functions. Given differential protein expression across tissues and developmental stages, the architecture and dynamics of signaling interaction proteomes is, likely, highly context dependent. However, current interaction information has been almost exclusively obtained from transformed cells. In this study, we applied an advanced and robust workflow combining mouse genetics and affinity purification (AP)-SWATH mass spectrometry to profile the dynamics of 53 high-confidence protein interactions in primary T cells, using the scaffold protein GRB2 as a model. The workflow also provided a sufficient level of robustness to pinpoint differential interaction dynamics between two similar, but functionally distinct, primary T cell populations. Altogether, we demonstrated that precise and reproducible quantitative measurements of protein interaction dynamics can be achieved in primary cells isolated from mammalian tissues, allowing resolution of the tissue-specific context of cell-signaling events.
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Affiliation(s)
- Etienne Caron
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Romain Roncagalli
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Takeshi Hase
- The Systems Biology Institute, Tokyo 108-0071, Japan
| | - Witold E Wolski
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, 8057 Zurich, Switzerland
| | - Meena Choi
- College of Science, College of Computer and Information Science, Northeastern University, Boston, MA 02115, USA
| | - Marisa G Menoita
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Stephane Durand
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Antonio García-Blesa
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Ivo Fierro-Monti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tatjana Sajic
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology and Brain Tumor Center, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Marie Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, 8057 Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Samik Ghosh
- The Systems Biology Institute, Tokyo 108-0071, Japan
| | - Hiroaki Kitano
- The Systems Biology Institute, Tokyo 108-0071, Japan; Okinawa Institute of Science and Technology Garuda School, 904-0495 Okinawa, Japan
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France; Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France.
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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11
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Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat Methods 2017; 14:921-927. [PMID: 28825704 PMCID: PMC5581544 DOI: 10.1038/nmeth.4398] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [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: 09/12/2016] [Accepted: 07/07/2017] [Indexed: 12/18/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry is the main method for high-throughput identification and quantification of peptides and inferred proteins. Within this field, data-independent acquisition (DIA) combined with peptide-centric scoring, exemplified by SWATH-MS, emerged as a scalable method to achieve deep and consistent proteome coverage across large-scale datasets. Here we discuss the adaptation of statistical concepts developed for discovery proteomics based on spectrum-centric scoring to large-scale DIA experiments analyzed with peptide-centric scoring strategies and provide guidance on their application. We show that optimal tradeoffs between sensitivity and specificity require careful considerations of the relationship between proteins in the samples and proteins represented in the spectral library. We propose the application of a global analyte constraint to prevent accumulation of false positives across large-scale datasets. Furthermore, to increase the quality and reproducibility of published proteomic results, well-established confidence criteria should be reported for detected peptide queries, peptides and inferred proteins.
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Affiliation(s)
- George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Uwe Schmitt
- ID Scientific IT Services, ETH Zurich, Zurich, Switzerland
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD program in Molecular and Translational Biomedicine, Competence Center Personalized Medicine (CC-PM), ETH Zurich and University of Zurich, Zurich, Switzerland
| | | | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick G A Pedrioli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Hannes L Röst
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Ying S Ting
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
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12
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Blattmann P, Heusel M, Aebersold R. SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools. PLoS One 2016; 11:e0153160. [PMID: 27054327 PMCID: PMC4824525 DOI: 10.1371/journal.pone.0153160] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 03/24/2016] [Indexed: 11/19/2022] Open
Abstract
SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.
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Affiliation(s)
- Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
- * E-mail:
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
- PhD program in Molecular and Translational Biomedicine, Competence Center Personalized Medicine UZH/ETH & Life Science Zurich Graduate School, ETH Zurich and University of Zurich, 8044, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
- Faculty of Science, University of Zurich, 8057, Zurich, Switzerland
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13
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Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Sci Data 2014; 1:140031. [PMID: 25977788 PMCID: PMC4322573 DOI: 10.1038/sdata.2014.31] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/06/2014] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).
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Affiliation(s)
- George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Ching Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Ruprecht Karls University of Heidelberg , DE-69117 Heidelberg, Germany
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Hannes L Röst
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Petri Kouvonen
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Molecular and Translational Biomedicine, Competence Centre for Systems Physiology and Metabolic Diseases (CC-SPMD), University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Etienne Caron
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Anton Vichalkovski
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marco Faini
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Olga T Schubert
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Pouya Faridi
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, 71345-1583 Shiraz, Iran
| | - H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Mariette Matondo
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Henry Lam
- Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay , Hong Kong, China
| | - Samuel L Bader
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - David S Campbell
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - Robert L Moritz
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Faculty of Science, University of Zurich , CH-8057 Zurich, Switzerland
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14
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Hoelsch K, Sührer I, Heusel M, Weuster-Botz D. Engineering of formate dehydrogenase: synergistic effect of mutations affecting cofactor specificity and chemical stability. Appl Microbiol Biotechnol 2012; 97:2473-81. [PMID: 22588502 DOI: 10.1007/s00253-012-4142-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 12/01/2022]
Abstract
Formate dehydrogenases (FDHs) are frequently used for the regeneration of cofactors in biotransformations employing NAD(P)H-dependent oxidoreductases. Major drawbacks of most native FDHs are their strong preference for NAD(+) and their low operational stability in the presence of reactive organic compounds such as α-haloketones. In this study, the FDH from Mycobacterium vaccae N10 (MycFDH) was engineered in order to obtain an enzyme that is not only capable of regenerating NADPH but also stable toward the α-haloketone ethyl 4-chloroacetoacetate (ECAA). To change the cofactor specificity, amino acids in the conserved NAD(+) binding motif were mutated. Among these mutants, MycFDH A198G/D221Q had the highest catalytic efficiency (k cat/K m) with NADP(+). The additional replacement of two cysteines (C145S/C255V) not only conferred a high resistance to ECAA but also enhanced the catalytic efficiency 6-fold. The resulting quadruple mutant MycFDH C145S/A198G/D221Q/C255V had a specific activity of 4.00 ± 0.13 U mg(-1) and a K m, NADP(+) of 0.147 ± 0.020 mM at 30 °C, pH 7. The A198G replacement had a major impact on the kinetic constants of the enzyme. The corresponding triple mutant, MycFDH C145S/D221Q/C255V, showed the highest specific activity reported to date for a NADP(+)-accepting FDH (v max, 10.25 ± 1.63 U mg(-1)). However, the half-saturation constant for NADP(+) (K m, NADP(+) , 0.92 ± 0.10 mM) was about one order of magnitude higher than the one of the quadruple mutant. Depending on the reaction setup, both novel MycFDH variants could be useful for the production of the chiral synthon ethyl (S)-4-chloro-3-hydroxybutyrate [(S)-ECHB] by asymmetric reduction of ECAA with NADPH-dependent ketoreductases.
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Affiliation(s)
- Kathrin Hoelsch
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, 85748 Garching, Germany.
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15
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Abstract
Class A G protein-coupled receptors (GPCRs) are known to form dimers and/or oligomeric arrays in vitro and in vivo. These complexes are thought to play important roles in modulating class A GPCR function. Many studies suggest that residues located on the "outer" (lipid-facing) surface of the transmembrane (TM) receptor core are critically involved in the formation of class A receptor dimers (oligomers). However, no clear consensus has emerged regarding the identity of the TM helices or TM subsegments involved in this process. To shed light on this issue, we have used the M(3) muscarinic acetylcholine receptor (M3R), a prototypic class A GPCR, as a model system. Using a comprehensive and unbiased approach, we subjected all outward-facing residues (70 amino acids total) of the TM helical bundle (TM1-7) of the M3R to systematic alanine substitution mutagenesis. We then characterized the resulting mutant receptors in radioligand binding and functional studies and determined their ability to form dimers (oligomers) in bioluminescence resonance energy transfer saturation assays. We found that M3R/M3R interactions are not dependent on the presence of one specific structural motif but involve the outer surfaces of multiple TM subsegments (TM1-5 and -7) located within the central and endofacial portions of the TM receptor core. Moreover, we demonstrated that the outward-facing surfaces of most TM helices play critical roles in proper receptor folding and/or function. Guided by the bioluminescence resonance energy transfer data, molecular modeling studies suggested the existence of multiple dimeric/oligomeric M3R arrangements, which may exist in a dynamic equilibrium. Given the high structural homology found among all class A GPCRs, our results should be of considerable general relevance.
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Affiliation(s)
| | | | - Tong Liu
- From the Laboratory of Bioorganic Chemistry and
| | - Stefano Costanzi
- Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Jürgen Wess
- From the Laboratory of Bioorganic Chemistry and
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