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Ignacio BJ, Dijkstra J, Mora N, Slot EFJ, van Weijsten MJ, Storkebaum E, Vermeulen M, Bonger KM. THRONCAT: metabolic labeling of newly synthesized proteins using a bioorthogonal threonine analog. Nat Commun 2023; 14:3367. [PMID: 37291115 PMCID: PMC10250548 DOI: 10.1038/s41467-023-39063-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Profiling the nascent cellular proteome and capturing early proteomic changes in response to external stimuli provides valuable insights into cellular physiology. Existing metabolic protein labeling approaches based on bioorthogonal methionine- or puromycin analogs allow for the selective visualization and enrichment of newly synthesized proteins. However, their applications are limited as they often require methionine-free conditions, auxotrophic cells and/or are toxic to cells. Here, we introduce THRONCAT, a threonine-derived non-canonical amino acid tagging method based on the bioorthogonal threonine analog β-ethynylserine (βES) that enables efficient labeling of the nascent proteome in complete growth media within minutes. We use THRONCAT for the visualization and enrichment of nascent proteins in bacteria, mammalian cells and Drosophila melanogaster. We profile immediate proteome dynamics of B-cells in response to B-cell receptor activation simply by adding βES to the culture medium, demonstrating the ease-of-use of the method and its potential to address diverse biological questions. In addition, using a Drosophila model of Charcot-Marie-Tooth peripheral neuropathy, we show that THRONCAT enables visualization and quantification of relative protein synthesis rates in specific cell types in vivo.
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Affiliation(s)
- Bob J Ignacio
- Department of Synthetic Organic Chemistry, Chemical Biology Lab, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Jelmer Dijkstra
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalia Mora
- Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Erik F J Slot
- Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Margot J van Weijsten
- Department of Synthetic Organic Chemistry, Chemical Biology Lab, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Erik Storkebaum
- Molecular Neurobiology Laboratory, Donders Center for Neuroscience, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kimberly M Bonger
- Department of Synthetic Organic Chemistry, Chemical Biology Lab, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands.
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Ignacio BJ, Bakkum T, Bonger KM, Martin NI, van Kasteren SI. Metabolic labeling probes for interrogation of the host-pathogen interaction. Org Biomol Chem 2021; 19:2856-2870. [PMID: 33725048 DOI: 10.1039/d0ob02517h] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial infections are still one of the leading causes of death worldwide; despite the near-ubiquitous availability of antibiotics. With antibiotic resistance on the rise, there is an urgent need for novel classes of antibiotic drugs. One particularly troublesome class of bacteria are those that have evolved highly efficacious mechanisms for surviving inside the host. These contribute to their virulence by immune evasion, and make them harder to treat with antibiotics due to their residence inside intracellular membrane-limited compartments. This has sparked the development of new chemical reporter molecules and bioorthogonal probes that can be metabolically incorporated into bacteria to provide insights into their activity status. In this review, we provide an overview of several classes of metabolic labeling probes capable of targeting either the peptidoglycan cell wall, the mycomembrane of mycobacteria and corynebacteria, or specific bacterial proteins. In addition, we highlight several important insights that have been made using these metabolic labeling probes.
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Affiliation(s)
- Bob J Ignacio
- Institute for Molecules and Materials, Radbout Universiteit, Nijmegen, Gelderland, Netherlands
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Abstract
Toll-like receptors (TLRs) are vital elements of the mammalian immune system that function by recognizing pathogen-associated molecular patterns (PAMPs), bridging innate and adaptive immunity. They have become a prominent therapeutic target for the treatment of infectious diseases, cancer, and allergies, with many TLR agonists currently in clinical trials or approved as immunostimulants. Numerous studies have shown that conjugation of TLR agonists to other molecules can beneficially influence their potency, toxicity, pharmacokinetics, or function. The functional properties of TLR agonist conjugates, however, are highly dependent on the ligation strategy employed. Here, we review the chemical structural requirements for effective functional TLR agonist conjugation. In addition, we provide similar analysis for those that have yet to be conjugated. Moreover, we discuss applications of covalent TLR agonist conjugation and their implications for clinical use.
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Affiliation(s)
- Bob J. Ignacio
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Tyler J. Albin
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Aaron P. Esser-Kahn
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Martijn Verdoes
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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