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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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2
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Chen MM, Kopittke PM, Zhao FJ, Wang P. Applications and opportunities of click chemistry in plant science. TRENDS IN PLANT SCIENCE 2024; 29:167-178. [PMID: 37612212 DOI: 10.1016/j.tplants.2023.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.
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Affiliation(s)
- Ming-Ming Chen
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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3
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Wright MH. Chemical biology tools for protein labelling: insights into cell-cell communication. Biochem J 2023; 480:1445-1457. [PMID: 37732646 PMCID: PMC10586760 DOI: 10.1042/bcj20220309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Multicellular organisms require carefully orchestrated communication between and within cell types and tissues, and many unicellular organisms also sense their context and environment, sometimes coordinating their responses. This review highlights contributions from chemical biology in discovering and probing mechanisms of cell-cell communication. We focus on chemical tools for labelling proteins in a cellular context and how these can be applied to decipher the target receptor of a signalling molecule, label a receptor of interest in situ to understand its biology, provide a read-out of protein activity or interactions in downstream signalling pathways, or discover protein-protein interactions across cell-cell interfaces.
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Affiliation(s)
- Megan H. Wright
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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Interrogating Plant-Microbe Interactions with Chemical Tools: Click Chemistry Reagents for Metabolic Labeling and Activity-Based Probes. Molecules 2021; 26:molecules26010243. [PMID: 33466477 PMCID: PMC7796436 DOI: 10.3390/molecules26010243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 01/01/2021] [Indexed: 01/22/2023] Open
Abstract
Continued expansion of the chemical biology toolbox presents many new and diverse opportunities to interrogate the fundamental molecular mechanisms driving complex plant-microbe interactions. This review will examine metabolic labeling with click chemistry reagents and activity-based probes for investigating the impacts of plant-associated microbes on plant growth, metabolism, and immune responses. While the majority of the studies reviewed here used chemical biology approaches to examine the effects of pathogens on plants, chemical biology will also be invaluable in future efforts to investigate mutualistic associations between beneficial microbes and their plant hosts.
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Fisher JF, Mobashery S. Constructing and deconstructing the bacterial cell wall. Protein Sci 2020; 29:629-646. [PMID: 31747090 PMCID: PMC7021008 DOI: 10.1002/pro.3737] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
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Jayaprada T, Hu J, Zhang Y, Feng H, Shen D, Geekiyanage S, Yao Y, Wang M. The interference of nonylphenol with bacterial cell-to-cell communication. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 257:113352. [PMID: 31672371 DOI: 10.1016/j.envpol.2019.113352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
The interference of nonylphenol (NP) with humans and animals, especially in hormone systems, has been well-studied. There is rarely any record of its effect on bacteria, which dominate in various environments. In our study, we employed Pseudomonas aeruginosa PAO1 as a model microorganism and took its common lifestyle biofilm, mainly regulated by quorum sensing (QS), as a cut-in point to investigate the effect of NP (1, 5, 10 mg L-1) on bacteria. The results showed that more than 5 mg L-1 of NP did interfere with biofilm formation and affected bacterial QS. In detail, the LasI/R circuit, but not the RhlI/R circuit, was considerably obstructed. The decrease in lasI and lasR expression resulted in a significant reduction in N-3-oxo-dodecanoyl homoserine lactone (3OC12-HSL) signals and the downstream production of elastases. Docking results indicated the binding of NP with LasR protein, simulating the binding of 3OC12-HSL with LasR protein, which explained the obstruction of the LasIR circuit. We concluded that NP competed with 3OC12-HSL and blocked 3OC12-HSL binding with the LasR protein, resulting in a direct interference in bacterial biofilm formation. This is the first report of NP interference with bacterial signaling, which is not only helpful to understand the effect of NP on various ecosystems, but is also beneficial to enrich our knowledge of inter-kingdom communication.
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Affiliation(s)
- Thilini Jayaprada
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Jingming Hu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yunyun Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Huajun Feng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Dongsheng Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Sudarshanee Geekiyanage
- Department of Agricultural Biology, University of Ruhuna, Mapalana, Kamburupitiya, 81100, Sri Lanka
| | - Yanlai Yao
- Institute of Environment Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China.
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Keller LJ, Babin BM, Lakemeyer M, Bogyo M. Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Curr Opin Chem Biol 2019; 54:45-53. [PMID: 31835131 DOI: 10.1016/j.cbpa.2019.10.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/09/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Activity-based protein profiling (ABPP) is a robust chemoproteomic technique that uses activity-based probes to globally measure endogenous enzymatic activity in complex proteomes. It has been utilized extensively to characterize human disease states and identify druggable targets in diverse disease conditions. ABPP has also recently found applications in microbiology. This includes using activity-based probes (ABPs) for functional studies of pathogenic bacteria as well as complex communities within a microbiome. This review will focus on recent advances in the use of ABPs to profile enzyme activity in disease models, screen for selective inhibitors of key enzymes, and develop imaging tools to better understand the host-bacterial interface.
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Affiliation(s)
- Laura J Keller
- Department of Chemical & Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Brett M Babin
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Markus Lakemeyer
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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Zaytseva YV, Sidorov AV, Marakaev OA, Khmel IA. Plant-Microbial Interactions Involving Quorum Sensing Regulation. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Craft KM, Nguyen JM, Berg LJ, Townsend SD. Methicillin-resistant Staphylococcus aureus (MRSA): antibiotic-resistance and the biofilm phenotype. MEDCHEMCOMM 2019; 10:1231-1241. [PMID: 31534648 PMCID: PMC6748282 DOI: 10.1039/c9md00044e] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/12/2019] [Indexed: 12/18/2022]
Abstract
Staphylococcus aureus (S. aureus) is an asymptomatic colonizer of 30% of all human beings. While generally benign, antibiotic resistance contributes to the success of S. aureus as a human pathogen. Resistance is rapidly evolved through a wide portfolio of mechanisms including horizontal gene transfer and chromosomal mutation. In addition to traditional resistance mechanisms, a special feature of S. aureus pathogenesis is its ability to survive on both biotic and abiotic surfaces in the biofilm state. Due to this characteristic, S. aureus is a leading cause of human infection. Methicillin-resistant S. aureus (MRSA) in particular has emerged as a widespread cause of both community- and hospital-acquired infections. Currently, MRSA is responsible for 10-fold more infections than all multi-drug resistant (MDR) Gram-negative pathogens combined. Recently, MRSA was classified by the World Health Organization (WHO) as one of twelve priority pathogens that threaten human health. In this targeted mini-review, we discuss MRSA biofilm production, the relationship of biofilm production to antibiotic resistance, and front-line techniques to defeat the biofilm-resistance system.
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Affiliation(s)
- Kelly M Craft
- Department of Chemistry , Vanderbilt University , 7300 Stevenson Science Center , Nashville , TN 37235 , USA .
| | - Johny M Nguyen
- Department of Chemistry , Vanderbilt University , 7300 Stevenson Science Center , Nashville , TN 37235 , USA .
| | - Lawrence J Berg
- Department of Chemistry , Vanderbilt University , 7300 Stevenson Science Center , Nashville , TN 37235 , USA .
| | - Steven D Townsend
- Department of Chemistry , Vanderbilt University , 7300 Stevenson Science Center , Nashville , TN 37235 , USA .
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Brown SP, Blackwell HE, Hammer BK. The State of the Union Is Strong: a Review of ASM's 6th Conference on Cell-Cell Communication in Bacteria. J Bacteriol 2018; 200:e00291-18. [PMID: 29760210 PMCID: PMC6018360 DOI: 10.1128/jb.00291-18] [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] [Indexed: 11/20/2022] Open
Abstract
The 6th American Society for Microbiology Conference on Cell-Cell Communication in Bacteria convened from 16 to 19 October 2017 in Athens, GA. In this minireview, we highlight some of the research presented at that meeting that addresses central questions emerging in the field, including the following questions. How are cell-cell communication circuits designed to generate responses? Where are bacteria communicating? Finally, why are bacteria engaging in such behaviors?
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Affiliation(s)
- Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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