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Claushuis B, Cordfunke RA, de Ru AH, van Angeren J, Baumann U, van Veelen PA, Wuhrer M, Corver J, Drijfhout JW, Hensbergen PJ. Non-prime- and prime-side profiling of Pro-Pro endopeptidase specificity using synthetic combinatorial peptide libraries and mass spectrometry. FEBS J 2024. [PMID: 38767318 DOI: 10.1111/febs.17160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
A group of bacterial proteases, the Pro-Pro endopeptidases (PPEPs), possess the unique ability to hydrolyze proline-proline bonds in proteins. Since a protease's function is largely determined by its substrate specificity, methods that can extensively characterize substrate specificity are valuable tools for protease research. Previously, we achieved an in-depth characterization of PPEP prime-side specificity. However, PPEP specificity is also determined by the non-prime-side residues in the substrate. To gain a more complete insight into the determinants of PPEP specificity, we characterized the non-prime- and prime-side specificity of various PPEPs using a combination of synthetic combinatorial peptide libraries and mass spectrometry. With this approach, we deepened our understanding of the P3-P3' specificities of PPEP-1 and PPEP-2, while identifying the endogenous substrate of PPEP-2 as the most optimal substrate in our library data. Furthermore, by employing the library approach, we investigated the altered specificity of mutants of PPEP-1 and PPEP-2. Additionally, we characterized a novel PPEP from Anoxybacillus tepidamans, which we termed PPEP-4. Based on structural comparisons, we hypothesized that PPEP-4 displays a PPEP-1-like prime-side specificity, which was substantiated by the experimental data. Intriguingly, another putative PPEP from Clostridioides difficile, CD1597, did not display Pro-Pro endoproteolytic activity. Collectively, we characterized PPEP specificity in detail using our robust peptide library method and, together with additional structural information, provide more insight into the intricate mechanisms that govern protease specificity.
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Affiliation(s)
- Bart Claushuis
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Robert A Cordfunke
- Department of Immunology, Leiden University Medical Center, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Jordy van Angeren
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Ulrich Baumann
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Germany
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Jeroen Corver
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, The Netherlands
| | - Jan W Drijfhout
- Department of Immunology, Leiden University Medical Center, The Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
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2
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Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Vuylsteke M, Stadler C, Eyckerman S, Spirohn K, Hao T, Calderwood MA, Gevaert K. N-terminal proteoforms may engage in different protein complexes. Life Sci Alliance 2023; 6:e202301972. [PMID: 37316325 PMCID: PMC10267514 DOI: 10.26508/lsa.202301972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
Alternative translation initiation and alternative splicing may give rise to N-terminal proteoforms, proteins that differ at their N-terminus compared with their canonical counterparts. Such proteoforms can have altered localizations, stabilities, and functions. Although proteoforms generated from splice variants can be engaged in different protein complexes, it remained to be studied to what extent this applies to N-terminal proteoforms. To address this, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. First, we generated a catalogue of N-terminal proteoforms found in the HEK293T cellular cytosol from which 22 pairs were selected for interactome profiling. In addition, we provide evidence for the expression of several N-terminal proteoforms, identified in our catalogue, across different human tissues, as well as tissue-specific expression, highlighting their biological relevance. Protein-protein interaction profiling revealed that the overlap of the interactomes for both proteoforms is generally high, showing their functional relation. We also showed that N-terminal proteoforms can be engaged in new interactions and/or lose several interactions compared with their canonical counterparts, thus further expanding the functional diversity of proteomes.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tessa Van de Steene
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Charlotte Stadler
- Department of Protein Science, KTH Royal Institute of Technology and Science for Life Laboratories, Stockholm, Sweden
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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3
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Schaefer K, Lui I, Byrnes JR, Kang E, Zhou J, Weeks AM, Wells JA. Direct Identification of Proteolytic Cleavages on Living Cells Using a Glycan-Tethered Peptide Ligase. ACS CENTRAL SCIENCE 2022; 8:1447-1456. [PMID: 36313159 PMCID: PMC9615116 DOI: 10.1021/acscentsci.2c00899] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 06/16/2023]
Abstract
Proteolytic cleavage of cell surface proteins triggers critical processes including cell-cell interactions, receptor activation, and shedding of signaling proteins. Consequently, dysregulated extracellular proteases contribute to malignant cell phenotypes including most cancers. To understand these effects, methods are needed that identify proteolyzed membrane proteins within diverse cellular contexts. Herein we report a proteomic approach, called cell surface N-terminomics, to broadly identify precise cleavage sites (neo-N-termini) on the surface of living cells. First, we functionalized the engineered peptide ligase, called stabiligase, with an N-terminal nucleophile that enables covalent attachment to naturally occurring glycans. Upon the addition of a biotinylated peptide ester, glycan-tethered stabiligase efficiently tags extracellular neo-N-termini for proteomic analysis. To demonstrate the versatility of this approach, we identified and characterized 1532 extracellular neo-N-termini across a panel of different cell types including primary immune cells. The vast majority of cleavages were not identified by previous proteomic studies. Lastly, we demonstrated that single oncogenes, KRAS(G12V) and HER2, induce extracellular proteolytic remodeling of proteins involved in cancerous cell growth, invasion, and migration. Cell surface N-terminomics is a generalizable platform that can reveal proteolyzed, neoepitopes to target using immunotherapies.
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Affiliation(s)
- Kaitlin Schaefer
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Irene Lui
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James R. Byrnes
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Emily Kang
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Jie Zhou
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Amy M. Weeks
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James A. Wells
- Department
of Pharmaceutical Chemistry, 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
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4
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Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Demol H, Gevaert K. Limited evidence for protein products of non-coding transcripts in the HEK293T cellular cytosol. Mol Cell Proteomics 2022; 21:100264. [PMID: 35788065 PMCID: PMC9396073 DOI: 10.1016/j.mcpro.2022.100264] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 10/25/2022] Open
Abstract
Ribosome profiling has revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream ORFs, long non-coding RNAs, overlapping ORFs, ORFs in UTRs or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling and CRISPR-based screens showed that hundreds of ORFs derived from non-coding transcripts produce (micro)proteins, while other studies failed to find evidence for such types of non-canonical translation products. Here, we attempted to discover translation products from non-coding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from non-coding regions, but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap based interactome analysis of two N-terminal proteoforms originating from non-coding regions finally showed the functional potential of these novel proteins.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Tessa Van de Steene
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Hans Demol
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium.
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5
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Fernández E, Bogaert A, Timmerman E, Staes A, Impens F, Gevaert K. A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms. Methods Mol Biol 2022; 2477:293-309. [PMID: 35524124 DOI: 10.1007/978-1-0716-2257-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Especially in eukaryotes, the N-terminal acetylation status of a protein reveals translation initiation sites and substrate specificities and activities of N-terminal acetyltransferases (NATs). Here, we discuss a bottom-up proteomics protocol for the enrichment of N-terminal peptides via strong cation exchange chromatography. This protocol is based on depleting internal tryptic peptides from proteome digests through their retention on strong cation exchangers, leaving N-terminally acetylated/blocked peptides enriched among the nonretained peptides. As such, one can identify novel N-terminal proteoforms and quantify the degree of N-terminal protein acetylation.
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Affiliation(s)
- Esperanza Fernández
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Bogaert
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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6
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Chen Y, Inzé D, Vanhaeren H. Post-translational modifications regulate the activity of the growth-restricting protease DA1. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3352-3366. [PMID: 33587751 DOI: 10.1093/jxb/erab062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Plants are a primary food source and can form the basis for renewable energy resources. The final size of their organs is by far the most important trait to consider when seeking increased plant productivity. Being multicellular organisms, plant organ size is mainly determined by the coordination between cell proliferation and cell expansion. The protease DA1 limits the duration of cell proliferation and thereby restricts final organ size. Since its initial identification as a negative regulator of organ growth, various transcriptional regulators of DA1, but also interacting proteins, have been identified. These interactors include cleavage substrates of DA1, and also proteins that modulate the activity of DA1 through post-translational modifications, such as ubiquitination, deubiquitination, and phosphorylation. In addition, many players in the DA1 pathway display conserved phenotypes in other dicot and even monocot species. In this review, we provide a timely overview of the complex, but intriguing, molecular mechanisms that fine-tune the activity of DA1 and therefore final organ size. Moreover, we lay out a roadmap to identify and characterize substrates of proteases and frame the substrate cleavage events in their biological context.
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Affiliation(s)
- Ying Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Hannes Vanhaeren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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7
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New strategies to identify protease substrates. Curr Opin Chem Biol 2020; 60:89-96. [PMID: 33220627 DOI: 10.1016/j.cbpa.2020.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/31/2022]
Abstract
Proteome dynamics is governed by transcription, translation, and post-translational modifications. Limited proteolysis is an irreversible post-translational modification that generates multiple but unique proteoforms from almost every native protein. Elucidating these proteoforms and understanding their dynamics at a system-wide level is of utmost importance because uncontrolled proteolytic cleavages correlate with many pathologies. Mass spectrometry-based degradomics has revolutionized protease research and invented workflows for global identification of protease substrates with resolution down to precise cleavage sites. In this review, we provide an overview of current strategies in protease substrate degradomics and introduce the concept of workflow, mass spectrometry-based and in silico enrichment of protein termini with the perspective of full deconvolution of digital proteome maps for precision medicine, and degradomics biomarker diagnostics.
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8
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Affiliation(s)
- Andreas O. Helbig
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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9
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Tanco S, Aviles FX, Gevaert K, Lorenzo J, Van Damme P. Identification of Carboxypeptidase Substrates by C-Terminal COFRADIC. Methods Mol Biol 2017; 1574:115-133. [PMID: 28315247 DOI: 10.1007/978-1-4939-6850-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We here present a detailed procedure for studying protein C-termini and their posttranslational modifications by C-terminal COFRADIC. In fact, this procedure can enrich for both C-terminal and N-terminal peptides through a combination of a strong cation exchange fractionation step at low pH, which removes the majority of nonterminal peptides in whole-proteome digests, while the actual COFRADIC step segregates C-terminal peptides from N-terminal peptides. When used in a differential mode, C-terminal COFRADIC allows for the identification of neo-C-termini generated by the action of proteases, which in turn leads to the identification of protease substrates. More specifically, this technology can be applied to determine the natural substrate repertoire of carboxypeptidases on a proteome-wide scale.
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Affiliation(s)
- Sebastian Tanco
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Francesc Xavier Aviles
- Institut de Biotecnologia i Biomedicina (IBB), Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, IBB-Campus de la UAB, Bellaterra, 08193, Barcelona, Spain
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Julia Lorenzo
- Institut de Biotecnologia i Biomedicina (IBB), Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, IBB-Campus de la UAB, Bellaterra, 08193, Barcelona, Spain.
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium.
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium.
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