1
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Pierro A, Bonucci A, Magalon A, Belle V, Mileo E. Impact of Cellular Crowding on Protein Structural Dynamics Investigated by EPR Spectroscopy. Chem Rev 2024. [PMID: 39213496 DOI: 10.1021/acs.chemrev.3c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The study of how the intracellular medium influences protein structural dynamics and protein-protein interactions is a captivating area of research for scientists aiming to comprehend biomolecules in their native environment. As the cellular environment can hardly be reproduced in vitro, direct investigation of biomolecules within cells has attracted growing interest in the past two decades. Among magnetic resonances, site-directed spin labeling coupled to electron paramagnetic resonance spectroscopy (SDSL-EPR) has emerged as a powerful tool for studying the structural properties of biomolecules directly in cells. Since the first in-cell EPR experiment was reported in 2010, substantial progress has been made, and this Review provides a detailed overview of the developments and applications of this spectroscopic technique. The strategies available for preparing a cellular sample and the EPR methods that can be applied to cells will be discussed. The array of spin labels available, along with their strengths and weaknesses in cellular contexts, will also be described. Several examples will illustrate how in-cell EPR can be applied to different biological systems and how the cellular environment affects the structural and dynamic properties of different proteins. Lastly, the Review will focus on the future developments expected to expand the capabilities of this promising technique.
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Affiliation(s)
- Annalisa Pierro
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Alessio Bonucci
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
| | - Axel Magalon
- Aix Marseille University, CNRS, Laboratoire de Chimie Bactérienne (LCB), IMM, IM2B, Marseille, France
| | - Valérie Belle
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
| | - Elisabetta Mileo
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
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2
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Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 PMCID: PMC11363022 DOI: 10.1021/acs.chemrev.4c00031] [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: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
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Affiliation(s)
- Nikolaj G. Koch
- Department
of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis
Group, Institute of Chemistry, Technische
Universität Berlin, 10623 Berlin, Germany
- Chemical
Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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3
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Majekodunmi T, Britton D, Montclare JK. Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation. Chem Rev 2024; 124:9113-9135. [PMID: 39008623 PMCID: PMC11327963 DOI: 10.1021/acs.chemrev.3c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.
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Affiliation(s)
- Temiloluwa Majekodunmi
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Biomedical Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States
- Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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4
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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5
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [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: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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6
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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7
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Porter A, Newcomb E, DiStefano S, Poplawski J, Kim J, Axe M, Lucas Lu X. Triamcinolone acetonide has minimal effect on short- and long-term metabolic activities of cartilage. J Orthop Res 2024. [PMID: 38860529 DOI: 10.1002/jor.25913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Intra-articular corticosteroid injections, such as triamcinolone acetonide (TA), are commonly used by clinicians to manage joint synovial inflammation. However, due to conflicting evidence in literature, there is a fear among clinicians that the injections may be harmful to otherwise healthy cartilage in young patients. The purpose of this study was to evaluate the effects of TA on young, healthy chondrocytes. Articular cartilage samples were harvested from bovine knee joints (1-2 months old). In both healthy and inflammatory (interleukin-1β) challenged cartilage, samples were treated with TA at doses ranging from 1 nM to 200 μM. Following a short- (2 days) or long-term (10-14 days) treatment, chondrocyte viability, proliferation, and extracellular matrix (ECM) synthesis and degradation were evaluated with a click chemistry-based technique. Chondrocyte viability, proliferation, and anabolic activity were all minimally affected by short-term and long-term TA treatment. After both acute and sustained inflammatory challenges, TA reduced the catabolic activities in cartilage, reducing nascent glycosaminoglycan loss and maintaining cartilage mechanical properties. Overall, at physiologically relevant doses, TA had minimal negative impact on chondrocytes when maintained within their native ECM. Clinical significance: The findings provide new insight for current clinical practices concerning the use of TA in intra-articular injections, especially in young patients, and established a foundation for future investigations into the impact of corticosteroids on joint homeostasis.
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Affiliation(s)
- Annie Porter
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
| | - Emily Newcomb
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
| | - Steven DiStefano
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
| | - Jacob Poplawski
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
| | - Jonathan Kim
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
| | - Michael Axe
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
| | - Xin Lucas Lu
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
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8
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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9
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Lou J, Ancajas CF, Zhou Y, Lane NS, Reynolds TB, Best MD. Probing Glycerolipid Metabolism using a Caged Clickable Glycerol-3-Phosphate Probe. Chembiochem 2024:e202300853. [PMID: 38705850 DOI: 10.1002/cbic.202300853] [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: 12/19/2023] [Revised: 04/25/2024] [Accepted: 05/05/2024] [Indexed: 05/07/2024]
Abstract
In this study, we present the probe SATE-G3P-N3 as a novel tool for metabolic labeling of glycerolipids (GLs) to investigate lipid metabolism in yeast cells. By introducing a clickable azide handle onto the glycerol backbone, this probe enables general labeling of glycerolipids. Additionally, this probe contains a caged phosphate moiety at the glycerol sn-3 position to not only facilitate probe uptake by masking negative charge but also to bypass the phosphorylation step crucial for initiating phospholipid synthesis, thereby enhancing phospholipid labeling. The metabolic labeling activity of the probe was thoroughly assessed through cellular fluorescence microscopy, mass spectrometry (MS), and thin-layer chromatography (TLC) experiments. Fluorescence microscopy analysis demonstrated successful incorporation of the probe into yeast cells, with labeling predominantly localized at the plasma membrane. LCMS analysis confirmed metabolic labeling of various phospholipid species (PC, PS, PA, PI, and PG) and neutral lipids (MAG, DAG, and TAG), and GL labeling was corroborated by TLC. These results showcased the potential of the SATE-G3P-N3 probe in studying GL metabolism, offering a versatile and valuable approach to explore the intricate dynamics of lipids in yeast cells.
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Affiliation(s)
- Jinchao Lou
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Christelle F Ancajas
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Yue Zhou
- Department of Microbiology, University of Tennessee, Knoxville, 1311 Cumberland Avenue, Knoxville, TN, 337996, USA
| | - Nicolas S Lane
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, 1311 Cumberland Avenue, Knoxville, TN, 337996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
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10
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Franz P, Fierz B. Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective. J Mol Biol 2024; 436:168442. [PMID: 38211893 DOI: 10.1016/j.jmb.2024.168442] [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] [Received: 11/09/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene transcription, the regulation of deposition and removal of histone post-translational modifications (PTMs), such as acetylation, methylation, and phosphorylation, have been implicated in many chromatin regulation pathways. However, large PTMs such as ubiquitylation challenge research on many levels due to their chemical complexity. In recent years, chemical tools have been developed to generate chromatin in defined ubiquitylation states in vitro. Chemical biology approaches are now used to link specific histone ubiquitylation marks with downstream chromatin regulation events on the molecular level. Here, we want to highlight how chemical biology approaches have empowered the mechanistic study of chromatin ubiquitylation in the context of gene regulation and DNA repair with attention to future challenges.
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Affiliation(s)
- Pauline Franz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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11
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Basier C, Nurse P. TOR regulates variability of protein synthesis rates. EMBO J 2024; 43:1618-1633. [PMID: 38499788 PMCID: PMC11021518 DOI: 10.1038/s44318-024-00075-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Cellular processes are subject to inherent variability, but the extent to which cells can regulate this variability has received little investigation. Here, we explore the characteristics of the rate of cellular protein synthesis in single cells of the eukaryote fission yeast. Strikingly, this rate is highly variable despite protein synthesis being dependent on hundreds of reactions which might be expected to average out at the overall cellular level. The rate is variable over short time scales, and exhibits homoeostatic behaviour at the population level. Cells can regulate the level of variability through processes involving the TOR pathway, suggesting there is an optimal level of variability conferring a selective advantage. While this could be an example of bet-hedging, but we propose an alternative explanation: regulated 'loose' control of complex processes of overall cellular metabolism such as protein synthesis, may lead to this variability. This could ensure cells are fluid in control and agile in response to changing conditions, and may constitute a novel organisational principle of complex metabolic cellular systems.
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Affiliation(s)
- Clovis Basier
- Cell Cycle Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, NY, 10065, USA
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12
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Weigert Muñoz A, Zhao W, Sieber SA. Monitoring host-pathogen interactions using chemical proteomics. RSC Chem Biol 2024; 5:73-89. [PMID: 38333198 PMCID: PMC10849124 DOI: 10.1039/d3cb00135k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/09/2023] [Indexed: 02/10/2024] Open
Abstract
With the rapid emergence and the dissemination of microbial resistance to conventional chemotherapy, the shortage of novel antimicrobial drugs has raised a global health threat. As molecular interactions between microbial pathogens and their mammalian hosts are crucial to establish virulence, pathogenicity, and infectivity, a detailed understanding of these interactions has the potential to reveal novel therapeutic targets and treatment strategies. Bidirectional molecular communication between microbes and eukaryotes is essential for both pathogenic and commensal organisms to colonise their host. In particular, several devastating pathogens exploit host signalling to adjust the expression of energetically costly virulent behaviours. Chemical proteomics has emerged as a powerful tool to interrogate the protein interaction partners of small molecules and has been successfully applied to advance host-pathogen communication studies. Here, we present recent significant progress made by this approach and provide a perspective for future studies.
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Affiliation(s)
- Angela Weigert Muñoz
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University Shenzhen 518118 China
| | - Stephan A Sieber
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Germany
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13
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Schauenburg D, Weil T. Chemical Reactions in Living Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303396. [PMID: 37679060 PMCID: PMC10885656 DOI: 10.1002/advs.202303396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/18/2023] [Indexed: 09/09/2023]
Abstract
The term "in vivo ("in the living") chemistry" refers to chemical reactions that take place in a complex living system such as cells, tissue, body liquids, or even in an entire organism. In contrast, reactions that occur generally outside living organisms in an artificial environment (e.g., in a test tube) are referred to as in vitro. Over the past decades, significant contributions have been made in this rapidly growing field of in vivo chemistry, but it is still not fully understood, which transformations proceed efficiently without the formation of by-products or how product formation in such complex environments can be characterized. Potential applications can be imagined that synthesize drug molecules directly within the cell or confer new cellular functions through controlled chemical transformations that will improve the understanding of living systems and develop new therapeutic strategies. The guiding principles of this contribution are twofold: 1) Which chemical reactions can be translated from the laboratory to the living system? 2) Which characterization methods are suitable for studying reactions and structure formation in complex living environments?
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Affiliation(s)
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
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14
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Immler F, Schneider T, Kovermann M. Targeted Preparation and NMR Spectroscopic Characterization of Lys11-Linked Ubiquitin Trimers. Chembiochem 2024; 25:e202300670. [PMID: 37983597 DOI: 10.1002/cbic.202300670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
Ubiquitylation refers to the attachment of mono- or poly-ubiquitin molecules to a substrate protein. To shield ubiquitin chains against potential hydrolysis, a facile, click-chemistry based approach was recently established for the generation of site-specifically conjugated ubiquitin dimers relying on triazole-linkage. Here, the preparation of such ubiquitin chains was advanced by the generation of homotypic Lys11-linked ubiquitin trimers considering an isotopic labeling scheme in a moiety-wise manner. The structural and dynamical impact on the ubiquitin unit at proximal, central, or distal position that is potentially invoked by the respective other two moieties was systematically probed by heteronuclear high-resolution NMR spectroscopic approaches. As a result, conjugating a third ubiquitin moiety to the proximal or distal site of a ubiquitin dimer does not alter structural and dynamical characteristics as it has been seen for ubiquitin dimers. This observation suggests that recognition of a homotypically assembled ubiquitin chain by a potential substrate is primarily done by screening the length of a ubiquitin chain rather than relying on subtle changes in structure or dynamic properties of single ubiquitin moieties composing the chain.
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Affiliation(s)
- Fabian Immler
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| | - Tobias Schneider
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
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15
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Pagliuca S, Ferraro F. Immune-driven clonal cell selection at the intersection among cancer, infections, autoimmunity and senescence. Semin Hematol 2024; 61:22-34. [PMID: 38341340 DOI: 10.1053/j.seminhematol.2024.01.002] [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] [Received: 11/25/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Immune surveillance mechanisms play a crucial role in maintaining lifelong immune homeostasis in response to pathologic stimuli and aberrant cell states. However, their persistence, especially in the context of chronic antigenic exposure, can create a fertile ground for immune evasion. These escaping cell phenotypes, harboring a variety of genomic and transcriptomic aberrances, chiefly in human leukocyte antigen (HLA) and antigen presentation machinery genes, may survive and proliferate, featuring a scenario of clonal cell expansion with immune failure characteristics. While well characterized in solid and, to some extent, hematological malignancies, little is known about their occurrence and significance in other disease contexts. Historical literature highlights the role for escaping HLA-mediated recognition as a strategy adopted by virus to evade from the immune system, hinting at the potential for immune aberrant cell expansion in the context of chronic infections. Additionally, unmasked in idiopathic aplastic anemia as a mechanism able to rescue failing hematopoiesis, HLA clonal escape may operate in autoimmune disorders, particularly in tissues targeted by aberrant immune responses. Furthermore, senescent cell status emerging as immunogenic phenotypes stimulating T cell responses, may act as a bottleneck for the selection of such immune escaping clones, blurring the boundaries between neoplastic transformation, aging and inflammation. Here we provide a fresh overview and perspective on this immune-driven clonal cell expansion, linking pathophysiological features of neoplastic, autoimmune, infectious and senescence processes exposed to immune surveillance.
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Affiliation(s)
- Simona Pagliuca
- Hematology Department, Nancy University Hospital and UMR7365, IMoPA, University of Lorraine, Vandoeuvre-lès-Nancy, France.
| | - Francesca Ferraro
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
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16
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Zhang Q, Kuang G, Wang L, Duan P, Sun W, Ye F. Designing Bioorthogonal Reactions for Biomedical Applications. RESEARCH (WASHINGTON, D.C.) 2023; 6:0251. [PMID: 38107023 PMCID: PMC10723801 DOI: 10.34133/research.0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 12/19/2023]
Abstract
Bioorthogonal reactions are a class of chemical reactions that can be carried out in living organisms without interfering with other reactions, possessing high yield, high selectivity, and high efficiency. Since the first proposal of the conception by Professor Carolyn Bertozzi in 2003, bioorthogonal chemistry has attracted great attention and has been quickly developed. As an important chemical biology tool, bioorthogonal reactions have been applied broadly in biomedicine, including bio-labeling, nucleic acid functionalization, drug discovery, drug activation, synthesis of antibody-drug conjugates, and proteolysis-targeting chimeras. Given this, we summarized the basic knowledge, development history, research status, and prospects of bioorthogonal reactions and their biomedical applications. The main purpose of this paper is to furnish an overview of the intriguing bioorthogonal reactions in a variety of biomedical applications and to provide guidance for the design of novel reactions to enrich bioorthogonal chemistry toolkits.
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Affiliation(s)
- Qingfei Zhang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
| | - Gaizhen Kuang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Li Wang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Ping Duan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Weijian Sun
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Fangfu Ye
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
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17
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Borteçen T, Müller T, Krijgsveld J. An integrated workflow for quantitative analysis of the newly synthesized proteome. Nat Commun 2023; 14:8237. [PMID: 38086798 PMCID: PMC10716174 DOI: 10.1038/s41467-023-43919-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
The analysis of proteins that are newly synthesized upon a cellular perturbation can provide detailed insight into the proteomic response that is elicited by specific cues. This can be investigated by pulse-labeling of cells with clickable and stable-isotope-coded amino acids for the enrichment and mass spectrometric characterization of newly synthesized proteins (NSPs), however convoluted protocols prohibit their routine application. Here we report the optimization of multiple steps in sample preparation, mass spectrometry and data analysis, and we integrate them into a semi-automated workflow for the quantitative analysis of the newly synthesized proteome (QuaNPA). Reduced input requirements and data-independent acquisition (DIA) enable the analysis of triple-SILAC-labeled NSP samples, with enhanced throughput while featuring high quantitative accuracy. We apply QuaNPA to investigate the time-resolved cellular response to interferon-gamma (IFNg), observing rapid induction of targets 2 h after IFNg treatment. QuaNPA provides a powerful approach for large-scale investigation of NSPs to gain insight into complex cellular processes.
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Affiliation(s)
- Toman Borteçen
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Heidelberg University, Faculty of Biosciences, Im Neuenheimer Feld 581, Heidelberg, Germany
| | - Torsten Müller
- Heidelberg University, Medical Faculty, Im Neuenheimer Feld 581, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany.
- Heidelberg University, Medical Faculty, Im Neuenheimer Feld 581, Heidelberg, Germany.
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18
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Oeller M, Kang RJD, Bolt HL, Gomes Dos Santos AL, Weinmann AL, Nikitidis A, Zlatoidsky P, Su W, Czechtizky W, De Maria L, Sormanni P, Vendruscolo M. Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids. Nat Commun 2023; 14:7475. [PMID: 37978172 PMCID: PMC10656490 DOI: 10.1038/s41467-023-42940-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) such as residues containing post-translational modifications (PTMs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the intrinsic solubility of mAA-containing peptides in aqueous solution at room temperature. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different small-size mAAs for a total number of 37 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides and confirm that our method can accurately assess the solubility of peptides containing mAAs. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm .
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ryan J D Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Bolt
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ana L Gomes Dos Santos
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Annika Langborg Weinmann
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Antonios Nikitidis
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pavol Zlatoidsky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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19
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Lyu HN, Fu C, Chai X, Gong Z, Zhang J, Wang J, Wang J, Dai L, Xu C. Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution. Cell Syst 2023; 14:883-894.e4. [PMID: 37734376 DOI: 10.1016/j.cels.2023.08.003] [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] [Received: 05/27/2022] [Revised: 05/29/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023]
Abstract
Understanding the thermal stability of the plant proteome in the context of the native cellular environment would aid the design of crops with high thermal tolerance, but only limited such data are available. Here, we applied quantitative mass spectrometry to profile the thermal stability of the Arabidopsis proteome and identify thermo-sensitive and thermo-resilient protein networks in Arabidopsis, providing a basis for understanding heat-induced damage. We also show that the similarities of the protein-melting curves can be used as a proxy to evaluate system-wide protein-protein interactions in non-engineered plants and enable the identification of transient interactions exhibited by metabolons in the context of the cellular environment. Finally, we report a systematic comparison of the thermal stability of paralogs in Arabidopsis to aid the investigation and understanding of gene duplication and protein evolution. Taken together, our results could have broad implications for the fields of plant thermal tolerance, plant protein assemblies, and evolution.
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Affiliation(s)
- Hai-Ning Lyu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chunjin Fu
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, China
| | - Xin Chai
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zipeng Gong
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang 550004, China
| | - Junzhe Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiaqi Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Jigang Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, China; School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Lingyun Dai
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, China.
| | - Chengchao Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, China.
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20
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Pasieka A, Diamanti E, Uliassi E, Laura Bolognesi M. Click Chemistry and Targeted Degradation: A Winning Combination for Medicinal Chemists? ChemMedChem 2023; 18:e202300422. [PMID: 37706617 DOI: 10.1002/cmdc.202300422] [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] [Revised: 09/01/2023] [Indexed: 09/15/2023]
Abstract
Click chemistry is universally recognized as a powerful strategy for the fast and precise assembly of diverse building blocks. Targeted Protein Degradation (TPD) is a new therapeutic modality based on heterobifunctional small-molecule degraders that provides new opportunities to medicinal chemists dealing with undruggable targets and incurable diseases. Here, we highlight how very recently the TPD field and that of click chemistry have merged, opening up the possibility for fine-tuning the properties of a degrader, chemically assembled through a "click" synthesis. By reviewing concrete examples, we want to provide the reader with the insight that the application of click and bioorthogonal chemistry in the TDP field may be a winning combination.
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Affiliation(s)
- Anna Pasieka
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Eleonora Diamanti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Elisa Uliassi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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21
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Quintana ILL, Paul A, Chowdhury A, Moulton KD, Kulkarni SS, Dube DH. Thioglycosides Act as Metabolic Inhibitors of Bacterial Glycan Biosynthesis. ACS Infect Dis 2023; 9:2025-2035. [PMID: 37698279 PMCID: PMC10580310 DOI: 10.1021/acsinfecdis.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 09/13/2023]
Abstract
Glycans that coat the surface of bacteria are compelling antibiotic targets because they contain distinct monosaccharides that are linked to pathogenesis and are absent in human cells. Disrupting glycan biosynthesis presents a path to inhibiting the ability of a bacterium to infect the host. We previously demonstrated that O-glycosides act as metabolic inhibitors and disrupt bacterial glycan biosynthesis. Inspired by a recent study which showed that thioglycosides (S-glycosides) are 10 times more effective than O-glycosides at inhibiting glycan biosynthesis in mammalian cells, we crafted a panel of S-glycosides based on rare bacterial monosaccharides. The novel thioglycosides altered glycan biosynthesis and fitness in pathogenic bacteria but had no notable effect on glycosylation or growth in beneficial bacteria or mammalian cells. In contrast to findings in mammalian cells, S-glycosides and O-glycosides exhibited comparable potency in bacteria. However, S-glycosides exhibited enhanced selectivity relative to O-glycosides. These novel metabolic inhibitors will allow selective perturbation of the bacterial glycocalyx for functional studies and set the stage to expand our antibiotic arsenal.
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Affiliation(s)
- Isabella
de la Luz Quintana
- Department
of Chemistry & Biochemistry, Bowdoin
College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Ankita Paul
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400-076, India
| | - Aniqa Chowdhury
- Department
of Chemistry & Biochemistry, Bowdoin
College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Karen D. Moulton
- Department
of Chemistry & Biochemistry, Bowdoin
College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Suvarn S. Kulkarni
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400-076, India
| | - Danielle H. Dube
- Department
of Chemistry & Biochemistry, Bowdoin
College, 6600 College Station, Brunswick, Maine 04011, United States
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22
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Tang Q, Chen X. Nascent Proteomics: Chemical Tools for Monitoring Newly Synthesized Proteins. Angew Chem Int Ed Engl 2023; 62:e202305866. [PMID: 37309018 DOI: 10.1002/anie.202305866] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Cellular proteins are dynamically regulated in response to environmental stimuli. Conventional proteomics compares the entire proteome in different cellular states to identify differentially expressed proteins, which suffers from limited sensitivity for analyzing acute and subtle changes. To address this challenge, nascent proteomics has been developed, which selectively analyzes the newly synthesized proteins, thus offering a more sensitive and timely insight into the dynamic changes of the proteome. In this Minireview, we discuss recent advancements in nascent proteomics, with an emphasis on methodological developments. Also, we delve into the current challenges and provide an outlook on the future prospects of this exciting field.
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Affiliation(s)
- Qi Tang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Science, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
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23
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Knecht S, Eberl HC, Kreisz N, Ugwu UJ, Starikova T, Kuster B, Wilhelm S. An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics. Mol Cell Proteomics 2023; 22:100636. [PMID: 37597723 PMCID: PMC10518356 DOI: 10.1016/j.mcpro.2023.100636] [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] [Received: 02/27/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS-based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry-based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science.
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Affiliation(s)
- Sascha Knecht
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - H Christian Eberl
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany
| | - Norbert Kreisz
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Ukamaka Juliet Ugwu
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tatiana Starikova
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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24
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Pelgrom LR, Davis GM, O'Shaughnessy S, Wezenberg EJM, Van Kasteren SI, Finlay DK, Sinclair LV. QUAS-R: An SLC1A5-mediated glutamine uptake assay with single-cell resolution reveals metabolic heterogeneity with immune populations. Cell Rep 2023; 42:112828. [PMID: 37478011 DOI: 10.1016/j.celrep.2023.112828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/26/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023] Open
Abstract
System-level analysis of single-cell data is rapidly transforming the field of immunometabolism. Given the competitive demand for nutrients in immune microenvironments, there is a need to understand how and when immune cells access these nutrients. Here, we describe a new approach for single-cell analysis of nutrient uptake where we use in-cell biorthogonal labeling of a functionalized amino acid after transport into the cell. In this manner, the bona fide active uptake of glutamine via SLC1A5/ASCT2 could be quantified. We used this assay to interrogate the transport capacity of complex immune subpopulations, both in vitro and in vivo. Taken together, our findings provide an easy sensitive single-cell assay to assess which cells support their function via SLC1A5-mediated uptake. This is a significant addition to the single-cell metabolic toolbox required to decode the metabolic landscape of complex immune microenvironments.
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Affiliation(s)
- Leonard R Pelgrom
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Gavin M Davis
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland
| | - Simon O'Shaughnessy
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland
| | - Emilie J M Wezenberg
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Sander I Van Kasteren
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
| | - David K Finlay
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland; School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland.
| | - Linda V Sinclair
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.
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25
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Mishra PK, Sharma N, Kim H, Lee C, Rhee HW. GEN-Click: Genetically Encodable Click Reactions for Spatially Restricted Metabolite Labeling. ACS CENTRAL SCIENCE 2023; 9:1650-1657. [PMID: 37637744 PMCID: PMC10450880 DOI: 10.1021/acscentsci.3c00511] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 08/29/2023]
Abstract
Chemical reactions for the in situ modification of biomolecules within living cells are under development. Among these reactions, bio-orthogonal reactions such as click chemistry using copper(I) and Staudinger ligation are widely used for specific biomolecule tracking in live systems. However, currently available live cell copper(I)-catalyzed azide/alkyne cycloaddition reactions are not designed in a spatially resolved manner. Therefore, we developed the "GEN-Click" system, which can target the copper(I)-catalyzed azide/alkyne cycloaddition reaction catalysts proximal to the protein of interest and can be genetically expressed in a live cell. The genetically controlled, spatially restricted, metal-catalyzed biorthogonal reaction can be used for proximity biotin labeling of various azido-bearing biomolecules (e.g., protein, phospholipid, oligosaccharides) in living cell systems. Using GEN-Click, we successfully detected local metabolite-transferring events at cell-cell contact sites.
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Affiliation(s)
| | - Nirmali Sharma
- Department
of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyunwoo Kim
- Department
of Biological Sciences, Ulsan National Institute
of Science and Technology, Ulsan 44919, Republic
of Korea
| | - Changwook Lee
- Department
of Biological Sciences, Ulsan National Institute
of Science and Technology, Ulsan 44919, Republic
of Korea
| | - Hyun-Woo Rhee
- Department
of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- School
of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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26
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Jordan VN, Ordureau A, An H. Identifying E3 Ligase Substrates With Quantitative Degradation Proteomics. Chembiochem 2023; 24:e202300108. [PMID: 37166757 PMCID: PMC10548883 DOI: 10.1002/cbic.202300108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/12/2023]
Abstract
Controlled protein degradation by the ubiquitin-proteasome pathway is critical for almost all cellular processes. E3 ubiquitin ligases are responsible for targeting proteins for ubiquitylation and subsequent proteasomal degradation with spatial and temporal precision. While studies have revealed various E3-substrate pairs involved in distinct biological processes, the complete substrate profiles of individual E3 ligases are largely unknown. Here we report a new approach to identify substrates of an E3 ligase for proteasomal degradation using unnatural amino acid incorporation pulse-chase proteomics (degradomics). Applying this approach, we determine the steady-state substrates of the C-terminal to LisH (CTLH) E3 ligase, a multi-component complex with poorly defined substrates. By comparing the proteome degradation profiles of active and inactive CTLH-expressing cells, we successfully identify previously known and new potential substrates of CTLH ligase. Altogether, degradomics can comprehensively identify degradation substrates of an E3 ligase, which can be adapted for other E3 ligases in various cellular contexts.
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Affiliation(s)
- Victoria N Jordan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alban Ordureau
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Heeseon An
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10065, USA
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27
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Jecmen T, Tuzhilkin R, Sulc M. Photo-Methionine, Azidohomoalanine and Homopropargylglycine Are Incorporated into Newly Synthesized Proteins at Different Rates and Differentially Affect the Growth and Protein Expression Levels of Auxotrophic and Prototrophic E. coli in Minimal Medium. Int J Mol Sci 2023; 24:11779. [PMID: 37511538 PMCID: PMC10380393 DOI: 10.3390/ijms241411779] [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: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Residue-specific incorporation of non-canonical amino acids (ncAAs) introduces bio-orthogonal functionalities into proteins. As such, this technique is applied in protein characterization and quantification. Here, we studied protein expression with three methionine analogs, namely photo-methionine (pMet), azidohomoalanine (Aha) and homopropargylglycine (Hpg), in prototrophic E. coli BL-21 and auxotrophic E. coli B834 to maximize ncAA content, thereby assessing the effect of ncAAs on bacterial growth and the expression of cytochrome b5 (b5M46), green fluorescence protein (MBP-GFP) and phage shock protein A. In auxotrophic E. coli, ncAA incorporation ranged from 50 to 70% for pMet and reached approximately 50% for Aha, after 26 h expression, with medium and low expression levels of MBP-GFP and b5M46, respectively. In the prototrophic strain, by contrast, the protein expression levels were higher, albeit with a sharp decrease in the ncAA content after the first hours of expression. Similar expression levels and 70-80% incorporation rates were achieved in both bacterial strains with Hpg. Our findings provide guidance for expressing proteins with a high content of ncAAs, highlight pitfalls in determining the levels of methionine replacement by ncAAs by MALDI-TOF mass spectrometry and indicate a possible systematic bias in metabolic labeling techniques using Aha or Hpg.
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Affiliation(s)
- Tomas Jecmen
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 43 Prague, Czech Republic
| | - Roman Tuzhilkin
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 43 Prague, Czech Republic
| | - Miroslav Sulc
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 43 Prague, Czech Republic
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Kirschner F, Arnold-Schild D, Leps C, Łącki MK, Klein M, Chen Y, Ludt A, Marini F, Kücük C, Stein L, Distler U, Sielaff M, Michna T, Riegel K, Rajalingam K, Bopp T, Tenzer S, Schild H. Modulation of cellular transcriptome and proteome composition by azidohomoalanine-implications on click chemistry-based secretome analysis. J Mol Med (Berl) 2023; 101:855-867. [PMID: 37231147 PMCID: PMC10300158 DOI: 10.1007/s00109-023-02333-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15-39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale. KEY MESSAGES: Azide-containing amino acid analogs affect gene expression profiles. Azide-containing amino acid analogs influence cellular proteome. Azidohomoalanine labeling induces cellular stress and apoptotic pathways. Secretome consists of proteins with dysregulated expression profiles.
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Affiliation(s)
- Friederike Kirschner
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Christian Leps
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Matthias Klein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yannic Chen
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Annekathrin Ludt
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Can Kücük
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Lara Stein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Malte Sielaff
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Thomas Michna
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Kristina Riegel
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Bopp
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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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] [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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30
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Peng Y, Wei X, Yang K. Synthesis and Excision Repair of Site-Specific 3'-End DNA-Histone Cross-Links Derived from Abasic Sites. Bioconjug Chem 2023. [PMID: 37184979 DOI: 10.1021/acs.bioconjchem.3c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Histones catalyze the DNA strand incision at apurinic/apyrimidinic (AP) sites accompanied by formation of reversible but long-lived DNA-protein cross-links (DPCs) at 3'-DNA termini within single-strand breaks. These DPCs need to be removed because 3'-hydroxyl is required for gap-filling DNA repair synthesis but are challenging to study because of their reversible nature. Here we report a chemical approach to synthesize stable and site-specific 3'-histone-DPCs and their repair by three nucleases, human AP endonuclease 1, tyrosyl-DNA phosphodiesterase 1, and three-prime repair exonuclease 1. Our method employs oxime ligation to install an alkyne to 3'-DNA terminus, genetic incorporation of an azidohomoalanine to histone H4 at a defined position, and click reaction to conjugate DNA to H4 site-specifically. Using these model DPC substrates, we demonstrated that the DPC repair efficiency is highly affected by the local protein environment, and prior DPC proteolysis facilitates the repair.
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Affiliation(s)
- Ying Peng
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Xiaoying Wei
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kun Yang
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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31
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Ban Ž, Barišić A, Crnolatac I, Kazazić S, Škulj S, Savini F, Bertoša B, Barišić I, Piantanida I. Highly selective preparation of N-terminus Horseradish peroxidase-DNA conjugate with fully retained enzymatic activity: HRP-DNA structure - activity relation. Enzyme Microb Technol 2023; 168:110257. [PMID: 37209508 DOI: 10.1016/j.enzmictec.2023.110257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Within the last decade, the field of bio-nanoengineering has achieved significant advances allowing us to generate, e.g., nanoscaled molecular machineries with arbitrary shapes. To unleash the full potential of novel methods such as DNA origami technology, it is important to functionalise complex molecules and nanostructures precisely. Thus, considerable attention has been given to site-selective modifications of proteins allowing further incorporation of various functionalities. Here, we describe a method for the covalent attachment of oligonucleotides to the glycosylated horseradish peroxidase protein (HRP) with high N-terminus selectivity and significant yield while conserving the enzymatic activity. This two-step process includes a pH-controlled metal-free diazotransfer reaction using imidazole-1-sulfonyl azide hydrogen sulfate, which at pH 8.5 results in an N-terminal azide-functionalized protein, followed by the Cu-free click SPAAC reaction to dibenzocyclooctyne- (DBCO) modified oligonucleotides. The reaction conditions were optimised to achieve maximum yield and the best performance. The resulting protein-oligonucleotide conjugates (HRP-DNA) were characterised by electrophoresis and mass spectrometry (MS). Native-PAGE experiments demonstrated different migration patterns for HRP-DNA and the azido-modified protein allowing zymogram experiments. Structure-activity relationships of novel HRP-DNA conjugates were assessed using molecular dynamics simulations, characterising the molecular interactions that define the structural and dynamical properties of the obtained protein-oligonucleotide conjugates (POC).
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Affiliation(s)
- Željka Ban
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Saša Kazazić
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.
| | - Ivan Barišić
- AIT Austrian Institute of Technology,Vienna, Austria.
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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32
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Case M, Navaratna T, Vinh J, Thurber G. Rapid Evaluation of Staple Placement in Stabilized α Helices Using Bacterial Surface Display. ACS Chem Biol 2023; 18:905-914. [PMID: 37039514 PMCID: PMC10773984 DOI: 10.1021/acschembio.3c00048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
There are a wealth of proteins involved in disease that cannot be targeted by current therapeutics because they are inside cells, inaccessible to most macromolecules, and lack small-molecule binding pockets. Stapled peptides, where two amino acids are covalently linked, form a class of macrocycles that have the potential to penetrate cell membranes and disrupt intracellular protein-protein interactions. However, their discovery relies on solid-phase synthesis, greatly limiting queries into their complex design space involving amino acid sequence, staple location, and staple chemistry. Here, we use stabilized peptide engineering by Escherichia coli display (SPEED), which utilizes noncanonical amino acids and click chemistry for stabilization, to rapidly screen staple location and linker structure to accelerate peptide design. After using SPEED to confirm hotspots in the mdm2-p53 interaction, we evaluated different staple locations and staple chemistry to identify several novel nanomolar and sub-nanomolar antagonists. Next, we evaluated SPEED in the B cell lymphoma 2 (Bcl-2) protein family, which is responsible for regulating apoptosis. We report that novel staple locations modified in the context of BIM, a high affinity but nonspecific naturally occurring peptide, improve its specificity against the highly homologous proteins in the Bcl-2 family. These compounds demonstrate the importance of screening linker location and chemistry in identifying high affinity and specific peptide antagonists. Therefore, SPEED can be used as a versatile platform to evaluate multiple design criteria for stabilized peptide engineering.
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33
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Steinert ND, Jorgenson KW, Lin KH, Hermanson JB, Lemens JL, Hornberger TA. A novel method for visualizing in-vivo rates of protein degradation provides insight into how TRIM28 regulates muscle size. iScience 2023; 26:106526. [PMID: 37070069 PMCID: PMC10105291 DOI: 10.1016/j.isci.2023.106526] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/27/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
Skeletal muscle size is controlled by the balance between protein synthesis and protein degradation. Given the essential role of skeletal muscle in maintaining a high quality of life, understanding the mechanisms that modulate this balance are of critical importance. Previously, we demonstrated that muscle-specific knockout of TRIM28 reduces muscle size and function and in the current study, we discovered that this effect is associated with an increase in protein degradation and a dramatic reduction in the expression of Mettl21c. Importantly, we also determined that overexpression of Mettl21c is sufficient to induce hypertrophy in both control and TRIM28 knockout muscles. Moreover, we developed a simple pulse-chase biorthogonal non-canonical amino acid tagging technique that enabled us to visualize the in vivo rate of protein degradation, and with this technique were able to conclude that the hypertrophic effect of Mettl21c is due, at least in part, to an inhibition of protein degradation.
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Affiliation(s)
- Nathaniel D. Steinert
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Kent W. Jorgenson
- Department of Molecular and Cellular Pharmacology, University of Wisconsin - Madison, Madison, WI, USA
- School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, USA
| | - Kuan-Hung Lin
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Jake B. Hermanson
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Jake L. Lemens
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Troy A. Hornberger
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
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34
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Bose P, Jaiswal MK, Singh SK, Singh RK, Tiwari VK. Growing impact of sialic acid-containing glycans in future drug discovery. Carbohydr Res 2023; 527:108804. [PMID: 37031650 DOI: 10.1016/j.carres.2023.108804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023]
Abstract
In nature, almost all cells are covered with a complex array of glycan chain namely sialic acids or nuraminic acids, a negatively charged nine carbon sugars which is considered for their great therapeutic importance since long back. Owing to its presence at the terminal end of lipid bilayer (commonly known as terminal sugars), the well-defined sialosides or sialoconjugates have served pivotal role on the cell surfaces and thus, the sialic acid-containing glycans can modulate and mediate a number of imperative cellular interactions. Understanding of the sialo-protein interaction and their roles in vertebrates in regard of normal physiology, pathological variance, and evolution has indeed a noteworthy journey in medicine. In this tutorial review, we present a concise overview about the structure, linkages in chemical diversity, biological significance followed by chemical and enzymatic modification/synthesis of sialic acid containing glycans. A more focus is attempted about the recent advances, opportunity, and more over growing impact of sialosides and sialoconjugates in future drug discovery and development.
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Saleh AM, VanDyk TG, Jacobson KR, Khan SA, Calve S, Kinzer-Ursem TL. An Integrative Biology Approach to Quantify the Biodistribution of Azidohomoalanine In Vivo. Cell Mol Bioeng 2023; 16:99-115. [PMID: 37096070 PMCID: PMC10121978 DOI: 10.1007/s12195-023-00760-4] [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: 11/01/2022] [Accepted: 02/22/2023] [Indexed: 04/26/2023] Open
Abstract
Background Identification and quantitation of newly synthesized proteins (NSPs) are critical to understanding protein dynamics in development and disease. Probing the nascent proteome can be achieved using non-canonical amino acids (ncAAs) to selectively label the NSPs utilizing endogenous translation machinery, which can then be quantitated with mass spectrometry. We have previously demonstrated that labeling the in vivo murine proteome is feasible via injection of azidohomoalanine (Aha), an ncAA and methionine (Met) analog, without the need for Met depletion. Aha labeling can address biological questions wherein temporal protein dynamics are significant. However, accessing this temporal resolution requires a more complete understanding of Aha distribution kinetics in tissues. Results To address these gaps, we created a deterministic, compartmental model of the kinetic transport and incorporation of Aha in mice. Model results demonstrate the ability to predict Aha distribution and protein labeling in a variety of tissues and dosing paradigms. To establish the suitability of the method for in vivo studies, we investigated the impact of Aha administration on normal physiology by analyzing plasma and liver metabolomes following various Aha dosing regimens. We show that Aha administration induces minimal metabolic alterations in mice. Conclusions Our results demonstrate that we can reproducibly predict protein labeling and that the administration of this analog does not significantly alter in vivo physiology over the course of our experimental study. We expect this model to be a useful tool to guide future experiments utilizing this technique to study proteomic responses to stimuli. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-023-00760-4.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Tyler G. VanDyk
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Kathryn R. Jacobson
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
| | - Shaheryar A. Khan
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
- Paul M. Rady Department of Mechanical Engineering, University of Colorado – Boulder, 1111 Engineering Center, 427 UCB, Boulder, CO 80309 USA
| | - Tamara L. Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
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Reemst K, Shahin H, Shahar OD. Learning and memory formation in zebrafish: Protein dynamics and molecular tools. Front Cell Dev Biol 2023; 11:1120984. [PMID: 36968211 PMCID: PMC10034119 DOI: 10.3389/fcell.2023.1120984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Research on learning and memory formation at the level of neural networks, as well as at the molecular level, is challenging due to the immense complexity of the brain. The zebrafish as a genetically tractable model organism can overcome many of the current challenges of studying molecular mechanisms of learning and memory formation. Zebrafish have a translucent, smaller and more accessible brain than that of mammals, allowing imaging of the entire brain during behavioral manipulations. Recent years have seen an extensive increase in published brain research describing the use of zebrafish for the study of learning and memory. Nevertheless, due to the complexity of the brain comprising many neural cell types that are difficult to isolate, it has been difficult to elucidate neural networks and molecular mechanisms involved in memory formation in an unbiased manner, even in zebrafish larvae. Therefore, data regarding the identity, location, and intensity of nascent proteins during memory formation is still sparse and our understanding of the molecular networks remains limited, indicating a need for new techniques. Here, we review recent progress in establishing learning paradigms for zebrafish and the development of methods to elucidate neural and molecular networks of learning. We describe various types of learning and highlight directions for future studies, focusing on molecular mechanisms of long-term memory formation and promising state-of-the-art techniques such as cell-type-specific metabolic labeling.
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Affiliation(s)
- Kitty Reemst
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
| | - Heba Shahin
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
| | - Or David Shahar
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
- *Correspondence: Or David Shahar,
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37
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van Kasteren S, Rozen DE. Using click chemistry to study microbial ecology and evolution. ISME COMMUNICATIONS 2023; 3:9. [PMID: 36721064 PMCID: PMC9889756 DOI: 10.1038/s43705-022-00205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 02/01/2023]
Abstract
Technological advances have largely driven the revolution in our understanding of the structure and function of microbial communities. Culturing, long the primary tool to probe microbial life, was supplanted by sequencing and other -omics approaches, which allowed detailed quantitative insights into species composition, metabolic potential, transcriptional activity, secretory responses and more. Although the ability to characterize "who's there" has never been easier or cheaper, it remains technically challenging and expensive to understand what the diverse species and strains that comprise microbial communities are doing in situ, and how these behaviors change through time. Our aim in this brief review is to introduce a developing toolkit based on click chemistry that can accelerate and reduce the expense of functional analyses of the ecology and evolution of microbial communities. After first outlining the history of technological development in this field, we will discuss key applications to date using diverse labels, including BONCAT, and then end with a selective (biased) view of areas where click-chemistry and BONCAT-based approaches stand to have a significant impact on our understanding of microbial communities.
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Affiliation(s)
- Sander van Kasteren
- Leiden Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden, 2300 RA, The Netherlands.
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2300 RA, The Netherlands.
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Shanbhag K, Sharma K, Kamat SS. Photoreactive bioorthogonal lipid probes and their applications in mammalian biology. RSC Chem Biol 2023; 4:37-46. [PMID: 36685253 PMCID: PMC9811504 DOI: 10.1039/d2cb00174h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
Lipids are an important class of biological molecules that possess many critical physiological functions, which enable the optimal survival of all organisms, including humans. While the role of lipids in the formation of biological cellular membranes and as a source of energy is fairly well understood, the cellular signalling pathways that lipids modulate in mammals are, in comparison, poorly characterized mechanistically and/or largely unknown. In an effort to dissect these mammalian cellular pathways regulated by signalling lipids and map hitherto unknown protein-lipid interactions, the last two decades have seen tremendous progress in the development of multifunctional lipid probes that, in conjunction with well-established bioorthogonal chemistries and chemoproteomics platforms, has almost exponentially expanded our knowledge in this field. In this review, we focus on the various photoreactive bioorthogonal lipid probes described in the literature, and briefly summarize the different photo-crosslinking groups and bioorthogonal chemistries used by them. Furthermore, we report specific case examples of such photoreactive bioorthogonal lipid probes, and discuss the new biological pathways and insights that have emerged from their use through chemoproteomics in mammalian cells. Finally, we highlight the challenges associated with the use of lipid probes in biological systems, and highlight their importance in the discovery and mechanistic understanding of lipid signalling pathways in the years to come.
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Affiliation(s)
- Karthik Shanbhag
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, PashanPune411008MaharashtraIndia
| | - Kavita Sharma
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, PashanPune411008MaharashtraIndia
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, PashanPune411008MaharashtraIndia
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Jakob J, Kröger A, Klawonn F, Bruder D, Jänsch L. Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes. Front Immunol 2023; 14:1091837. [PMID: 36875139 PMCID: PMC9977998 DOI: 10.3389/fimmu.2023.1091837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
MAIT cells are multifunctional innate-like effector cells recognizing bacterial-derived vitamin B metabolites presented by the non-polymorphic MHC class I related protein 1 (MR1). However, our understanding of MR1-mediated responses of MAIT cells upon their interaction with other immune cells is still incomplete. Here, we performed the first translatome study of primary human MAIT cells interacting with THP-1 monocytes in a bicellular system. We analyzed the interaction between MAIT and THP-1 cells in the presence of the activating 5-OP-RU or the inhibitory Ac-6-FP MR1-ligand. Using bio-orthogonal non-canonical amino acid tagging (BONCAT) we were able to enrich selectively those proteins that were newly translated during MR1-dependent cellular interaction. Subsequently, newly translated proteins were measured cell-type-specifically by ultrasensitive proteomics to decipher the coinciding immune responses in both cell types. This strategy identified over 2,000 MAIT and 3,000 THP-1 active protein translations following MR1 ligand stimulations. Translation in both cell types was found to be increased by 5-OP-RU, which correlated with their conjugation frequency and CD3 polarization at MAIT cell immunological synapses in the presence of 5-OP-RU. In contrast, Ac-6-FP only regulated a few protein translations, including GSK3B, indicating an anergic phenotype. In addition to known effector responses, 5-OP-RU-induced protein translations uncovered type I and type II Interferon-driven protein expression profiles in both MAIT and THP-1 cells. Interestingly, the translatome of THP-1 cells suggested that activated MAIT cells can impact M1/M2 polarization in these cells. Indeed, gene and surface expression of CXCL10, IL-1β, CD80, and CD206 confirmed an M1-like phenotype of macrophages being induced in the presence of 5-OP-RU-activated MAIT cells. Furthermore, we validated that the Interferon-driven translatome was accompanied by the induction of an antiviral phenotype in THP-1 cells, which were found able to suppress viral replication following conjugation with MR1-activated MAIT cells. In conclusion, BONCAT translatomics extended our knowledge of MAIT cell immune responses at the protein level and discovered that MR1-activated MAIT cells are sufficient to induce M1 polarization and an anti-viral program of macrophages.
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Affiliation(s)
- Josefine Jakob
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Hygiene, Infection Immunology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andrea Kröger
- Innate Immunity and Infection, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Hygiene, Molecular Microbiology, Health Campus Immunology, Infectiology and Inflammation, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Frank Klawonn
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dunja Bruder
- Institute of Medical Microbiology and Hospital Hygiene, Infection Immunology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
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40
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Shin J, Lee C. Profiling of Secreted Proteins in Serum-Containing Media Using BONCAT and Pulsed SILAC. Methods Mol Biol 2023; 2603:235-243. [PMID: 36370284 DOI: 10.1007/978-1-0716-2863-8_19] [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: 06/16/2023]
Abstract
Secreted proteins play pivotal roles in signal transduction and cell-to-cell communication. Despite increasing interest in secretome analysis over the past decade, most studies on this topic have utilized serum-free medium (SFM). However, fetal bovine serum (FBS) is the most widely used serum supplement for cell culture, and secretome analysis using serum-containing medium (SCM) is important to identify proteins secreted under realistic conditions and to understand their physiological roles. In this chapter, we describe a simple and robust protocol based on bioorthogonal non-canonical amino acid tagging (BONCAT) and pulsed stable isotope labeling by amino acids in cell culture (pSILAC), for identification and quantitation of the cell secretome in SCM. In this protocol, the secretome of SFM is compared with that of SCM to confirm the effect of FBS. Additionally, for mass spectrometric data processing, we provide parameters that increase true positives and decrease both false positives and false negatives.
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Affiliation(s)
- Jihye Shin
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan.
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Korea.
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, Korea.
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41
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Wang W, Jiang Y, Huang Z, Nguyen HVT, Liu B, Hartweg M, Shirakura M, Qin KP, Johnson JA. Discrete, Chiral Polymer-Insulin Conjugates. J Am Chem Soc 2022; 144:23332-23339. [PMID: 36126328 PMCID: PMC10440729 DOI: 10.1021/jacs.2c07382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polymer conjugation has been widely used to improve the stability and pharmacokinetics of therapeutic biomacromolecules; however, conventional methods to generate such conjugates often use disperse and/or achiral polymers with limited functionality. The heterogeneity of such conjugates may lead to manufacturing variability, poorly controlled biological performance, and limited ability to optimize structure-property relationships. Here, using insulin as a model therapeutic polypeptide, we introduce a strategy for the synthesis of polymer-protein conjugates based on discrete, chiral polymers synthesized through iterative exponential growth (IEG). These conjugates eliminate manufacturing variables originating from polymer dispersity and poorly controlled absolute configuration. Moreover, they offer tunable molecular features, such as conformational rigidity, that can be modulated to impact protein function, enabling faster or longer-lasting blood glucose responses in diabetic mice when compared to PEGylated insulin and the commercial insulin variant Lantus. Furthermore, IEG-insulin conjugates showed no signs of decreased activity, immunogenicity, or toxicity following repeat dosing. This work represents a significant step toward the synthesis of precise synthetic polymer-biopolymer conjugates and reveals that fine tuning of synthetic polymer structure may be used to optimize such conjugates in the future.
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Affiliation(s)
- Wencong Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yivan Jiang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zhihao Huang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Hung V.-T. Nguyen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bin Liu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Manuel Hartweg
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Masamichi Shirakura
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - K. Peter Qin
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremiah A. Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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42
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Dorn RS, Prescher JA. Bioorthogonal Phosphines: Then and Now. Isr J Chem 2022. [DOI: 10.1002/ijch.202200070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert S. Dorn
- Departments of Chemistry University of California Irvine California 92697 United States
| | - Jennifer A. Prescher
- Departments of Chemistry University of California Irvine California 92697 United States
- Molecular Biology & Biochemistry University of California Irvine California 92697 United States
- Pharmaceutical Sciences University of California Irvine California 92697 United States
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43
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Yi W, Xiao P, Liu X, Zhao Z, Sun X, Wang J, Zhou L, Wang G, Cao H, Wang D, Li Y. Recent advances in developing active targeting and multi-functional drug delivery systems via bioorthogonal chemistry. Signal Transduct Target Ther 2022; 7:386. [PMID: 36460660 PMCID: PMC9716178 DOI: 10.1038/s41392-022-01250-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Bioorthogonal chemistry reactions occur in physiological conditions without interfering with normal physiological processes. Through metabolic engineering, bioorthogonal groups can be tagged onto cell membranes, which selectively attach to cargos with paired groups via bioorthogonal reactions. Due to its simplicity, high efficiency, and specificity, bioorthogonal chemistry has demonstrated great application potential in drug delivery. On the one hand, bioorthogonal reactions improve therapeutic agent delivery to target sites, overcoming off-target distribution. On the other hand, nanoparticles and biomolecules can be linked to cell membranes by bioorthogonal reactions, providing approaches to developing multi-functional drug delivery systems (DDSs). In this review, we first describe the principle of labeling cells or pathogenic microorganisms with bioorthogonal groups. We then highlight recent breakthroughs in developing active targeting DDSs to tumors, immune systems, or bacteria by bioorthogonal chemistry, as well as applications of bioorthogonal chemistry in developing functional bio-inspired DDSs (biomimetic DDSs, cell-based DDSs, bacteria-based and phage-based DDSs) and hydrogels. Finally, we discuss the difficulties and prospective direction of bioorthogonal chemistry in drug delivery. We expect this review will help us understand the latest advances in the development of active targeting and multi-functional DDSs using bioorthogonal chemistry and inspire innovative applications of bioorthogonal chemistry in developing smart DDSs for disease treatment.
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Affiliation(s)
- Wenzhe Yi
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Ping Xiao
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Xiaochen Liu
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Zitong Zhao
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Xiangshi Sun
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Jue Wang
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Lei Zhou
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Guanru Wang
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Haiqiang Cao
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Dangge Wang
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, Yantai, 264000 China
| | - Yaping Li
- grid.9227.e0000000119573309State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, 264000 China
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Wang KL, Zhang JX, Min D, Lv JL, Liu DF, Yu HQ. Detection and Quantification of Antimicrobial-Resistant Cells in Aquatic Environments by Bioorthogonal Noncanonical Amino Acid Tagging. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15685-15694. [PMID: 36251006 DOI: 10.1021/acs.est.2c05024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aquatic environments are important reservoirs of antibiotic wastes, antibiotic resistance genes, and bacteria, enabling the persistence and proliferation of antibiotic resistance in different bacterial populations. To prevent the spread of antibiotic resistance, effective approaches to detect antimicrobial susceptibility in aquatic environments are highly desired. In this work, we adopt a metabolism-based bioorthogonal noncanonical amino acid tagging (BONCAT) method to detect, visualize, and quantify active antimicrobial-resistant bacteria in water samples by exploiting the differences in bacterial metabolic responses to antibiotics. The BONCAT approach can be applied to rapidly detect bacterial resistance to multiple antibiotics within 20 min of incubation, regardless of whether they act on proteins or DNA. In addition, the combination of BONCAT with the microscope enables the intuitive characterization of antibiotic-resistant bacteria in mixed systems at single-cell resolution. Furthermore, BONCAT coupled with flow cytometry exhibits good performance in determining bacterial resistance ratios to chloramphenicol and population heterogeneity in hospital wastewater samples. In addition, this approach is also effective in detecting antibiotic-resistant bacteria in natural water samples. Therefore, such a simple, fast, and efficient BONCAT-based approach will be valuable in monitoring the increase and spread of antibiotic resistance within natural and engineered aquatic environments.
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Affiliation(s)
- Kai-Li Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jia-Xin Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jun-Lu Lv
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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45
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Ortho-Phosphinoarenesulfonamide-Mediated Staudinger Reduction of Aryl and Alkyl Azides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27175707. [PMID: 36080474 PMCID: PMC9458194 DOI: 10.3390/molecules27175707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022]
Abstract
Conventional Staudinger reductions of organic azides are sluggish with aryl or bulky aliphatic azides. In addition, Staudinger reduction usually requires a large excess of water to promote the decomposition of the aza-ylide intermediate into phosphine oxide and amine products. To overcome the challenges above, we designed a novel triaryl phosphine reagent 2c with an ortho-SO2NH2 substituent. Herein, we report that such phosphine reagents are able to mediate the Staudinger reduction of both aryl and alkyl azides in either anhydrous or wet solvents. Good to excellent yields were obtained in all cases (even at a diluted concentration of 0.01 M). The formation of B-TAP, a cyclic aza-ylide, instead of phosphine oxide, eliminates the requirement of water in the Staudinger reduction. In addition, computational studies disclose that the intramolecular protonation of the aza-ylide by the ortho-SO2NH2 group is kinetically favorable and responsible for the acceleration of Staudinger reduction of the aryl azides.
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46
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Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022; 61:e202200648. [PMID: 35226765 PMCID: PMC9401566 DOI: 10.1002/anie.202200648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 11/10/2022]
Abstract
Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.
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Affiliation(s)
- Jan G. Löffler
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Erhan Deniz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Carolin Feid
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Valentin G. Franz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Jens Bredenbeck
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
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47
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Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
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48
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Luong P, Ghosh A, Moulton KD, Kulkarni SS, Dube DH. Synthesis and Application of Rare Deoxy Amino l-Sugar Analogues to Probe Glycans in Pathogenic Bacteria. ACS Infect Dis 2022; 8:889-900. [PMID: 35302355 PMCID: PMC9445936 DOI: 10.1021/acsinfecdis.2c00060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacterial cell envelope glycans are compelling antibiotic targets as they are critical for strain fitness and pathogenesis yet are virtually absent from human cells. However, systematic study and perturbation of bacterial glycans remains challenging due to their utilization of rare deoxy amino l-sugars, which impede traditional glycan analysis and are not readily available from natural sources. The development of chemical tools to study bacterial glycans is a crucial step toward understanding and altering these biomolecules. Here we report an expedient methodology to access azide-containing analogues of a variety of unusual deoxy amino l-sugars starting from readily available l-rhamnose and l-fucose. Azide-containing l-sugar analogues facilitated metabolic profiling of bacterial glycans in a range of Gram-negative bacteria and revealed differential utilization of l-sugars in symbiotic versus pathogenic bacteria. Further application of these probes will refine our knowledge of the glycan repertoire in diverse bacteria and aid in the design of novel antibiotics.
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Affiliation(s)
- Phuong Luong
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Antara Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400-076, India
| | - Karen D. Moulton
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Suvarn S. Kulkarni
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400-076, India
| | - Danielle H. Dube
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011, United States
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49
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Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jan G. Löffler
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Erhan Deniz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Carolin Feid
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Valentin G. Franz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Jens Bredenbeck
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
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50
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Abdelkader EH, Qianzhu H, George J, Frkic RL, Jackson CJ, Nitsche C, Otting G, Huber T. Genetic Encoding of Cyanopyridylalanine for In‐Cell Protein Macrocyclization by the Nitrile–Aminothiol Click Reaction. Angew Chem Int Ed Engl 2022; 61:e202114154. [PMID: 35102680 PMCID: PMC9304162 DOI: 10.1002/anie.202114154] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Indexed: 12/04/2022]
Abstract
Cyanopyridylalanines are non‐canonical amino acids that react with aminothiol compounds under physiological conditions in a biocompatible manner without requiring added catalyst. Here we present newly developed aminoacyl‐tRNA synthetases for genetic encoding of meta‐ and para‐cyanopyridylalanine to enable the site‐specific attachment of a wide range of different functionalities. The outstanding utility of the cyanopyridine moiety is demonstrated by examples of i) post‐translational functionalization of proteins, ii) in‐cell macrocyclization of peptides and proteins, and iii) protein stapling. The biocompatible nature of the protein ligation chemistry enabled by the cyanopyridylalanine amino acid opens a new path to specific in vivo protein modifications in complex biological environments.
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Affiliation(s)
- Elwy H. Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Haocheng Qianzhu
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Josemon George
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Rebecca L. Frkic
- ARC Centre of Excellence for Innovations in Peptide & Protein Science Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Colin J. Jackson
- ARC Centre of Excellence for Innovations in Peptide & Protein Science Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Christoph Nitsche
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Thomas Huber
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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