51
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Söderström B, Ruda A, Widmalm G, Daley DO. An OregonGreen488-labelled d-amino acid for visualizing peptidoglycan by super-resolution STED nanoscopy. MICROBIOLOGY-SGM 2020; 166:1129-1135. [PMID: 33237852 DOI: 10.1099/mic.0.000996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorescent d-amino acids (FDAAs) are molecular probes that are widely used for labelling the peptidoglycan layer of bacteria. When added to growing cells they are incorporated into the stem peptide by a transpeptidase reaction, allowing the timing and localization of peptidoglycan synthesis to be determined by fluorescence microscopy. Herein we describe the chemical synthesis of an OregonGreen488-labelled FDAA (OGDA). We also demonstrate that OGDA can be efficiently incorporated into the PG of Gram-positive and some Gram-negative bacteria, and imaged by super-resolution stimulated emission depletion (STED) nanoscopy at a resolution well below 100 nm.
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Affiliation(s)
- Bill Söderström
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, Japan.,The iThree Institute, University of Technology Sydney, Australia
| | - Alessandro Ruda
- Department of Organic Chemistry, Stockholm University, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Stockholm University, Sweden
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
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52
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La Piana L, Viaggi V, Principe L, Di Bella S, Luzzaro F, Viale M, Bertola N, Vecchio G. Polypyridine ligands as potential metallo-β-lactamase inhibitors. J Inorg Biochem 2020; 215:111315. [PMID: 33285370 DOI: 10.1016/j.jinorgbio.2020.111315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 11/19/2022]
Abstract
Bacteria have developed multiple resistance mechanisms against the most used antibiotics. In particular, zinc-dependent metallo-β-lactamase producing bacteria are a growing threat, and therapeutic options are limited. Zinc chelators have recently been investigated as metallo-β-lactamase inhibitors, as they are often able to restore carbapenem susceptibility. We synthesized polypyridyl ligands, N,N'-bis(2-pyridylmethyl)-ethylenediamine, N,N,N'-tris(2-pyridylmethyl)-ethylenediamine, N,N'-bis(2-pyridylmethyl)-ethylenediamine-N-acetic acid (N,N,N'-tris(2-pyridylmethyl)-ethylenediamine-N'-acetic acid, which can form zinc(II) complexes. We tested their ability to restore the antibiotic activity of meropenem against three clinical strains isolated from blood and metallo-β-lactamase producers (Klebsiella pneumoniae, Enterobacter cloacae, and Stenotrophomonas maltophilia). We functionalized N,N,N'-tris(2-pyridylmethyl)-ethylenediamine with D-alanyl-D-alanyl-D-alanine methyl ester with the aim to increase bacterial uptake. We observed synergistic activity of four polypyridyl ligands with meropenem against all tested isolates, while the combination N,N'-bis(2-pyridylmethyl)-ethylenediamine and meropenem was synergistic only against New Delhi and Verona integron-encoded metallo-β-lactamase-producing bacteria. All synergistic interactions restored the antimicrobial activity of meropenem, providing a significant decrease of minimal inhibitory concentration value (by 8- to 128-fold). We also studied toxicity of the ligands in two normal peripheral blood lymphocytes.
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Affiliation(s)
- Luana La Piana
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Valentina Viaggi
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Via dell'Eremo 9/11, 23900 Lecco, Italy
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio Hospital, Largo Bologna, 88900 Crotone, Italy
| | - Stefano Di Bella
- Clinical Department of Medical, Surgical and Health Sciences, Trieste University, strada di Fiume 447, 34149 Trieste, Italy
| | - Francesco Luzzaro
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Via dell'Eremo 9/11, 23900 Lecco, Italy
| | - Maurizio Viale
- IRCCS Ospedale Policlinico San Martino, U.O. Bioterapie, L.go R. Benzi 10, 16132 Genova, Italy
| | - Nadia Bertola
- IRCCS Ospedale Policlinico San Martino, U.O. Bioterapie, L.go R. Benzi 10, 16132 Genova, Italy
| | - Graziella Vecchio
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy; Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Piazza Umberto I 1, 70121 Bari, Italy.
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53
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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54
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Hira J, Uddin MJ, Haugland MM, Lentz CS. From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology. Molecules 2020; 25:E4949. [PMID: 33114655 PMCID: PMC7663024 DOI: 10.3390/molecules25214949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.
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Affiliation(s)
- Jonathan Hira
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Md. Jalal Uddin
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Marius M. Haugland
- Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
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55
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Qiao Y, Hayashi H, Chong Teo S. Chemical Toolbox to Decode the Microbiota Lexicon. Chem Asian J 2020; 15:2117-2128. [PMID: 32558250 DOI: 10.1002/asia.202000541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/14/2020] [Indexed: 12/15/2022]
Abstract
The human microbiota deploys a diverse range of molecules and metabolites to engage in chemical communications with the host, mediating fundamental aspects of host health. Studies of the structures and activities of bioactive molecules produced by the microbiota are imperative to address their implications in microbiota associated diseases in human. By drawing experiences from different research fields, chemists and chemical biologists, who are experts in dealing with chemical molecules, are uniquely positioned to contribute to the emerging knowledge of human microbiota. In this minireview, we discuss the current chemical tools and methods that are pertinent to the discovery of microbiota molecules and metabolites, characterizations of their protein targets, as well as evaluations of their biodistributions in hosts. These are key aspects in understanding the chemical underpinnings of the microbiota-host interactions that would enable future development of diagnostics and therapeutics targeting the human microbiota.
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Affiliation(s)
- Yuan Qiao
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
| | - Hirohito Hayashi
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
| | - Seng Chong Teo
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
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56
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Wodzanowski KA, Cassel SE, Grimes CL, Kloxin AM. Tools for probing host-bacteria interactions in the gut microenvironment: From molecular to cellular levels. Bioorg Med Chem Lett 2020; 30:127116. [PMID: 32223923 PMCID: PMC7476074 DOI: 10.1016/j.bmcl.2020.127116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/28/2020] [Accepted: 03/15/2020] [Indexed: 12/31/2022]
Abstract
Healthy function of the gut microenvironment is dependent on complex interactions between the bacteria of the microbiome, epithelial and immune (host) cells, and the surrounding tissue. Misregulation of these interactions is implicated in disease. A range of tools have been developed to study these interactions, from mechanistic studies to therapeutic evaluation. In this Digest, we highlight select tools at the cellular and molecular level for probing specific cell-microenvironment interactions. Approaches are overviewed for controlling and probing cell-cell interactions, from transwell and microfluidic devices to engineered bacterial peptidoglycan fragments, and cell-matrix interactions, from three-dimensional scaffolds to chemical handles for in situ modifications.
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Affiliation(s)
| | - Samantha E Cassel
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Catherine L Grimes
- Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Biological Sciences, University of Delaware, Newark, DE 19716, United States.
| | - April M Kloxin
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States; Materials Science and Engineering, University of Delaware, Newark, DE 19716, United States.
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57
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Fluorescent amino acids as versatile building blocks for chemical biology. Nat Rev Chem 2020; 4:275-290. [PMID: 37127957 DOI: 10.1038/s41570-020-0186-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
Fluorophores have transformed the way we study biological systems, enabling non-invasive studies in cells and intact organisms, which increase our understanding of complex processes at the molecular level. Fluorescent amino acids have become an essential chemical tool because they can be used to construct fluorescent macromolecules, such as peptides and proteins, without disrupting their native biomolecular properties. Fluorescent and fluorogenic amino acids with unique photophysical properties have been designed for tracking protein-protein interactions in situ or imaging nanoscopic events in real time with high spatial resolution. In this Review, we discuss advances in the design and synthesis of fluorescent amino acids and how they have contributed to the field of chemical biology in the past 10 years. Important areas of research that we review include novel methodologies to synthesize building blocks with tunable spectral properties, their integration into peptide and protein scaffolds using site-specific genetic encoding and bioorthogonal approaches, and their application to design novel artificial proteins, as well as to investigate biological processes in cells by means of optical imaging.
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58
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Hong S, Zheng DW, Zhang QL, Deng WW, Song WF, Cheng SX, Sun ZJ, Zhang XZ. An RGB-emitting molecular cocktail for the detection of bacterial fingerprints. Chem Sci 2020; 11:4403-4409. [PMID: 33209242 PMCID: PMC7643548 DOI: 10.1039/d0sc01704c] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 01/27/2023] Open
Abstract
Accumulating evidence indicates that colonized microbes play a crucial role in regulating health and disease in the human body. Detecting microbes should be essential for understanding the relationship between microbes and diseases, as well as increasing our ability to detect diseases. Here, a combined metabolic labeling strategy was developed to identify different bacterial species and microbiota by the use of three different fluorescent metabolite derivatives emitting red, green, and blue (RGB) fluorescence. Upon co-incubation with microbes, these fluorescent metabolite derivatives are incorporated into bacteria, generating unique true-color fingerprints for different bacterial species and different microbiota. A portable spectrometer was also fabricated to automate the colorimetric analysis in combination with a smartphone to conveniently identify different bacterial species and microbiota. Herein, the effectiveness of this system was demonstrated by the identification of certain bacterial species and microbiota in mice with different diseases, such as skin infections and bacteremia. By analyzing the microbiota fingerprints of saliva samples from clinical patients and healthy people, this system was proved to precisely distinguish oral squamous cell carcinoma (OSCC, n = 29) samples from precancerous (n = 10) and healthy (n = 5) samples.
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Affiliation(s)
- Sheng Hong
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Di-Wei Zheng
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Qiu-Ling Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Wei-Wei Deng
- Department of Oral Maxillofacial Head Neck Oncology , School and Hospital of Stomatology , Wuhan University , Wuhan 430072 , P. R. China
| | - Wen-Fang Song
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Si-Xue Cheng
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
| | - Zhi-Jun Sun
- Department of Oral Maxillofacial Head Neck Oncology , School and Hospital of Stomatology , Wuhan University , Wuhan 430072 , P. R. China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China .
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59
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Cochrane SA, Lohans CT. Breaking down the cell wall: Strategies for antibiotic discovery targeting bacterial transpeptidases. Eur J Med Chem 2020; 194:112262. [PMID: 32248005 DOI: 10.1016/j.ejmech.2020.112262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022]
Abstract
The enzymes involved in bacterial cell wall synthesis are established antibiotic targets, and continue to be a central focus for antibiotic development. Bacterial penicillin-binding proteins (and, in some bacteria, l,d-transpeptidases) form essential peptide cross-links in the cell wall. Although the β-lactam class of antibiotics target these enzymes, bacterial resistance threatens their clinical use, and there is an urgent unmet need for new antibiotics. However, the search for new antibiotics targeting the bacterial cell wall is hindered by a number of obstacles associated with screening the enzymes involved in peptidoglycan synthesis. This review describes recent approaches for measuring the activity and inhibition of penicillin-binding proteins and l,d-transpeptidases, highlighting strategies that are poised to serve as valuable tools for high-throughput screening of transpeptidase inhibitors, supporting the development of new antibiotics.
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Affiliation(s)
- Stephen A Cochrane
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen's University Belfast, Belfast, BT9 5AG, UK.
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada.
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60
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Kuru E, Radkov A, Meng X, Egan A, Alvarez L, Dowson A, Booher G, Breukink E, Roper DI, Cava F, Vollmer W, Brun Y, VanNieuwenhze MS. Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis. ACS Chem Biol 2019; 14:2745-2756. [PMID: 31743648 PMCID: PMC6929685 DOI: 10.1021/acschembio.9b00664] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Bacteria exhibit a myriad of different morphologies,
through the
synthesis and modification of their essential peptidoglycan (PG) cell
wall. Our discovery of a fluorescent D-amino acid (FDAA)-based PG labeling approach provided a powerful method
for observing how these morphological changes occur. Given that PG
is unique to bacterial cells and a common target for antibiotics,
understanding the precise mechanism(s) for incorporation of (F)DAA-based
probes is a crucial determinant in understanding the role of PG synthesis
in bacterial cell biology and could provide a valuable tool in the
development of new antimicrobials to treat drug-resistant antibacterial
infections. Here, we systematically investigate the mechanisms of
FDAA probe incorporation into PG using two model organisms Escherichia coli (Gram-negative) and Bacillus subtilis (Gram-positive). Our in vitro and in vivo data unequivocally demonstrate
that these bacteria incorporate FDAAs using two extracytoplasmic pathways:
through activity of their D,D-transpeptidases, and,
if present, by their L,D-transpeptidases and not
via cytoplasmic incorporation into a D-Ala-D-Ala
dipeptide precursor. Our data also revealed the unprecedented finding
that the DAA-drug, D-cycloserine, can be incorporated into
peptide stems by each of these transpeptidases, in addition to its
known inhibitory activity against D-alanine racemase and D-Ala-D-Ala ligase. These mechanistic findings enabled
development of a new, FDAA-based, in vitro labeling approach that
reports on subcellular distribution of muropeptides, an especially
important attribute to enable the study of bacteria with poorly defined
growth modes. An improved understanding of the incorporation mechanisms
utilized by DAA-based probes is essential when interpreting results
from high resolution experiments and highlights the antimicrobial
potential of synthetic DAAs.
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Affiliation(s)
- Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Atanas Radkov
- Department of Biochemistry and Biophysics, UCSF School of Medicine, San Francisco, California 94158, United States
| | - Xin Meng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alexander Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Laura Alvarez
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Amanda Dowson
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Garrett Booher
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Eefjan Breukink
- Department of Chemistry, Utrecht University, 3584 CH, Utrecht, Netherlands
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Yves Brun
- Department of Microbiology, Infectious Diseases, and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Michael S. VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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61
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Taguchi A, Kahne D, Walker S. Chemical tools to characterize peptidoglycan synthases. Curr Opin Chem Biol 2019; 53:44-50. [PMID: 31466035 PMCID: PMC6926152 DOI: 10.1016/j.cbpa.2019.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 02/02/2023]
Abstract
The peptidoglycan cell wall is a unique macromolecular structure in bacteria that defines their shape and confers protection from the surrounding environment. Decades of research has focused on understanding the peptidoglycan synthesis pathway and exploiting its essentiality for antibiotic development. Recently, a new class of peptidoglycan polymerases known as the SEDS (shape, elongation, division and sporulation) proteins were identified; these polytopic membrane proteins function together with the better-known penicillin-binding proteins (PBPs) to build the cell wall. In this review, we will highlight recent developments in chemical tools and methods to label the bacterial cell wall and discuss how these developments are leading to a better understanding of peptidoglycan synthases and their cellular roles.
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Affiliation(s)
- Atsushi Taguchi
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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62
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Hu F, Qi G, Kenry, Mao D, Zhou S, Wu M, Wu W, Liu B. Visualization and In Situ Ablation of Intracellular Bacterial Pathogens through Metabolic Labeling. Angew Chem Int Ed Engl 2019; 59:9288-9292. [DOI: 10.1002/anie.201910187] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Fang Hu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Guobin Qi
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Kenry
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Duo Mao
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Shiwei Zhou
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Min Wu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Wenbo Wu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Bin Liu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
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63
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Hu F, Qi G, Kenry, Mao D, Zhou S, Wu M, Wu W, Liu B. Visualization and In Situ Ablation of Intracellular Bacterial Pathogens through Metabolic Labeling. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fang Hu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Guobin Qi
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Kenry
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Duo Mao
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Shiwei Zhou
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Min Wu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Wenbo Wu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Bin Liu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
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64
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Hsu YP, Booher G, Egan A, Vollmer W, VanNieuwenhze MS. d-Amino Acid Derivatives as in Situ Probes for Visualizing Bacterial Peptidoglycan Biosynthesis. Acc Chem Res 2019; 52:2713-2722. [PMID: 31419110 DOI: 10.1021/acs.accounts.9b00311] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The bacterial cell wall is composed of membrane layers and a rigid yet flexible scaffold called peptidoglycan (PG). PG provides mechanical strength to enable bacteria to resist damage from the environment and lysis due to high internal turgor. PG also has a critical role in dictating bacterial cell morphology. The essential nature of PG for bacterial propagation, as well as its value as an antibiotic target, has led to renewed interest in the study of peptidoglycan biosynthesis. However, significant knowledge gaps remain that must be addressed before a clear understanding of peptidoglycan synthesis and dynamics is realized. For example, the enzymes involved in the PG biosynthesis pathway have not been fully characterized. Our understanding of PG biosynthesis has been frequently revamped by the discovery of novel enzymes or newly characterized functions of known enzymes. In addition, we do not clearly know how the respective activities of these enzymes are coordinated with each other and how they control the spatial and temporal dynamics of PG synthesis. The emergence of molecular probes and imaging techniques has significantly advanced the study PG synthesis and modification. Prior efforts utilized the specificity of PG-targeting antibiotics and proteins to develop PG-specific probes, such as fluorescent vancomycin and fluorescent wheat germ agglutinin. However, these probes suffer from limitations due to toxic effects toward bacterial cells and poor membrane permeability. To address these issues, we designed and introduced a family of novel molecular probes, fluorescent d-amino acids (FDAAs), which are covalently incorporated into PG through the activities of endogenous bacterial transpeptidases. Their high biocompatibility and PG specificity have made them powerful tools for labeling peptidoglycan. In addition, their enzyme-mediated incorporation faithfully reflects the activity of PG synthases, providing a direct in situ method for studying PG formation during the bacterial life cycle. In this Account, we describe our efforts directed at the development of FDAAs and their derivatives. These probes have enabled for the first time the ability to visualize PG synthesis in live bacterial cells and in real time. We summarize experimental evidence for FDAA incorporation into PG and the enzyme-mediated incorporation pathway. We demonstrate various applications of FDAAs, including bacterial morphology analyses, PG growth model studies, investigation of PG-enzyme correlation, in vitro PG synthase activity assays, and antibiotic inhibition tests. Finally, we discuss the current limitations of the probes and our ongoing efforts to improve them. We are confident that these probes will prove to be valuable tools that will enable the discovery of new antibiotic targets and expand the available arsenal directed at the public health threat posed by antibiotic resistance.
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Affiliation(s)
- Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Simon Hall 001, 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
| | - Garrett Booher
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Simon Hall 001, 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
| | - Alexander Egan
- The Centre for Bacterial Cell Biology, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Michael S. VanNieuwenhze
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Simon Hall 001, 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
- Department of Chemistry, Indiana University Bloomington, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Peters K, Pazos M, VanNieuwenhze MS, Vollmer W. Optimized Protocol for the Incorporation of FDAA (HADA Labeling) for in situ Labeling of Peptidoglycan. Bio Protoc 2019; 9:e3316. [PMID: 33654824 DOI: 10.21769/bioprotoc.3316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/02/2022] Open
Abstract
The essential peptidoglycan (PG) layer surrounds the cytoplasmic membrane in nearly all bacteria. It is needed to maintain the shape of the cell and protect it from lysis due to high turgor. Growth of the PG layer is a complex process that involves the activities of PG synthases and hydrolases during elongation and cell division. PG growth sites can be labeled by the recently developed fluorescent D-amino acid (FDAA) probes in a range of different bacteria. FDAAs are incorporated into PG by dd-transpeptidases (Penicillin-binding proteins, PBPs) or, if present, ld-transpeptidase (LDTs). Long-pulse in situ labeling of E. coli cells with the FDAA 7-hydroxycoumarincarbonylamino-D-alanine (HADA) is expected to result in a uniform label at the side wall of cells and enhanced label at cell division sites due to the intense PG synthesis. However, we observed reduced label at mid-cell when labeling E. coli cells with HADA. We reasoned that probe incorporated at cell division sites may be removed by PG hydrolases and modified the labeling protocol to better preserve PG-incorporated HADA for fluorescence microscopy. Here, we report the optimized HADA-labeling protocol by which cells retain an enhanced HADA signal at the division septum.
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Affiliation(s)
- Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom
| | - Manuel Pazos
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom
| | | | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom
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