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Tan J, Zhu C, Li L, Wang J, Xia XH, Wang C. Engineering Cell Membranes: From Extraction Strategies to Emerging Biosensing Applications. Anal Chem 2024; 96:7880-7894. [PMID: 38272835 DOI: 10.1021/acs.analchem.3c01746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Affiliation(s)
- Jing Tan
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Chengcheng Zhu
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Lulu Li
- College of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212000, P.R. China
| | - Jin Wang
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, P.R. China
| | - Chen Wang
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, P.R. China
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2
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Liu Z, Lepori I, Chordia MD, Dalesandro BE, Guo T, Dong J, Siegrist MS, Pires MM. A Metabolic-Tag-Based Method for Assessing the Permeation of Small Molecules Across the Mycomembrane in Live Mycobacteria. Angew Chem Int Ed Engl 2023; 62:e202217777. [PMID: 36700874 PMCID: PMC10159989 DOI: 10.1002/anie.202217777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023]
Abstract
The general lack of permeability of small molecules observed for Mycobacterium tuberculosis (Mtb) is most ascribed to its unique cell envelope. More specifically, the outer mycomembrane is hypothesized to be the principal determinant for access of antibiotics to their molecular targets. We describe a novel assay that combines metabolic tagging of the peptidoglycan, which sits directly beneath the mycomembrane, click chemistry of test molecules, and a fluorescent labeling chase step, to measure the permeation of small molecules. We showed that the assay workflow was robust and compatible with high-throughput analysis in mycobacteria by testing a small panel of azide-tagged molecules. The general trend is similar across the two types of mycobacteria with some notable exceptions. We anticipate that this assay platform will lay the foundation for medicinal chemistry efforts to understand and improve uptake of both existing drugs and newly-discovered compounds into mycobacteria.
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Affiliation(s)
- Zichen Liu
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - Irene Lepori
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States
- Department of Microbiology, University of Massachusetts, Amherst, United States
| | - Mahendra D. Chordia
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | | | - Taijie Guo
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200232, China
| | - Jiajia Dong
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200232, China
| | - M. Sloan Siegrist
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States
- Department of Microbiology, University of Massachusetts, Amherst, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, United States
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3
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Chen D, Guo J, Li A, Sun C, Lin H, Lin H, Yang C, Wang W, Gao J. Metabolic fluorine labeling and hotspot imaging of dynamic gut microbiota in mice. SCIENCE ADVANCES 2023; 9:eabg6808. [PMID: 36706178 PMCID: PMC9882976 DOI: 10.1126/sciadv.abg6808] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Real-time localization and microbial activity information of indigenous gut microbiota over an extended period of time remains a challenge with existing visualizing methods. Here, we report a metabolic fluorine labeling (MEFLA)-based strategy for monitoring the dynamic gut microbiota via 19F magnetic resonance imaging (19F MRI). In situ labeling of different microbiota subgroups is achieved by using a panel of peptidoglycan-targeting MEFLA probes containing 19F atoms of different chemical shifts, and subsequent real-time in vivo imaging is accomplished by multiplexed hotspot 19F MRI with high sensitivity and unlimited penetration. Using this method, we realize extended visualization (>24 hours) of native gut microbes located at different intestinal sections and semiquantitative analysis of their metabolic dynamics modulated by various conditions, such as the host death and different β-lactam antibiotics. Our strategy holds great potential for noninvasive and real-time assessing of the metabolic activities and locations of the highly dynamic gut microbiota.
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Affiliation(s)
- Dongxia Chen
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Junnan Guo
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ao Li
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chengjie Sun
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Huibin Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Hongyu Lin
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Wei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Jinhao Gao
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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4
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Apostolos AJ, Chordia MD, Kolli SH, Dalesandro BE, Rutkowski MR, Pires MM. Real-time non-invasive fluorescence imaging of gut commensal bacteria to detect dynamic changes in the microbiome of live mice. Cell Chem Biol 2022; 29:S2451-9456(22)00416-0. [PMID: 36516833 PMCID: PMC10239791 DOI: 10.1016/j.chembiol.2022.11.010] [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: 05/27/2022] [Revised: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
In mammals, gut commensal microbiota interact extensively with the host, and the same interactions can be dysregulated in diseased states. Animal imaging is a powerful technique that is widely used to diagnose, measure, and track biological changes in model organisms such as laboratory mice. Several imaging techniques have been discovered and adopted by the research community that provide dynamic, non-invasive assessment of live animals, but these gains have not been universal across all fields of biology. Herein, we describe a method to non-invasively image commensal bacteria based on the specific metabolic labeling of bacterial cell walls to illuminate the gut bacteria of live mice. This tagging strategy may additionally provide unprecedented insight into cell wall turnover of gut commensals, which has implications for bacterial cellular growth and division, in a live animal.
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Affiliation(s)
- Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Mahendra D Chordia
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Sree H Kolli
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Melanie R Rutkowski
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
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5
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Apostolos AJ, Kelly JJ, Ongwae GM, Pires MM. Structure Activity Relationship of the Stem Peptide in Sortase A Mediated Ligation from Staphylococcus aureus. Chembiochem 2022; 23:e202200412. [PMID: 36018606 PMCID: PMC9632411 DOI: 10.1002/cbic.202200412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/24/2022] [Indexed: 01/11/2023]
Abstract
The surfaces of most Gram-positive bacterial cells, including that of Staphylococcus aureus (S. aureus), are heavily decorated with proteins that coordinate cellular interactions with the extracellular space. In S. aureus, sortase A is the principal enzyme responsible for covalently anchoring proteins, which display the sorting signal LPXTG, onto the peptidoglycan (PG) matrix. Considerable efforts have been made to understand the role of this signal peptide in the sortase-mediated reaction. In contrast, much less is known about how the primary structure of the other substrate involved in the reaction (PG stem peptide) could impact sortase activity. To assess the sortase activity, a library of synthetic analogs of the stem peptide that mimic naturally existing variations found in the S. aureus PG primary sequence were evaluated. Using a combination of two unique assays, we showed that there is broad tolerability of substrate variations that are effectively processed by sortase A. While some of these stem peptide derivatives are naturally found in mature PG, they are not known to be present in the PG precursor, lipid II. These results suggest that sortase A could process both lipid II and mature PG as acyl-acceptor strands that might reside near the membrane, which has not been previously described.
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Affiliation(s)
| | - Joey J. Kelly
- Department of ChemistryUniversity of VirginiaCharlottesville, VA22904USA
| | - George M. Ongwae
- Department of ChemistryUniversity of VirginiaCharlottesville, VA22904USA
| | - Marcos M. Pires
- Department of ChemistryUniversity of VirginiaCharlottesville, VA22904USA
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6
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Lin H, Yang C, Wang W. Imitate to illuminate: labeling of bacterial peptidoglycan with fluorescent and bio-orthogonal stem peptide-mimicking probes. RSC Chem Biol 2022; 3:1198-1208. [PMID: 36320889 PMCID: PMC9533424 DOI: 10.1039/d2cb00086e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
Because of its high involvement in antibiotic therapy and the emergence of drug-resistance, the chemical structure and biosynthesis of bacterial peptidoglycan (PGN) have been some of the key topics in bacteriology for several decades. Recent advances in the development of fluorescent or bio-orthogonal stem peptide-mimicking probes for PGN-labeling have rekindled the interest of chemical biologists and microbiologists in this area. The structural designs, bio-orthogonal features and flexible uses of these peptide-based probes allow directly assessing, not only the presence of PGN in different biological systems, but also specific steps in PGN biosynthesis. In this review, we summarize the design rationales, functioning mechanisms, and microbial processes/questions involved in these PGN-targeting probes. Our perspectives on the limitations and future development of these tools are also presented. By imitating the structures of stem peptide, many fluorescent and bio-orthogonal labeling probes have been designed and used in illuminating the peptidoglycan biosynthesis processes.![]()
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Affiliation(s)
- Huibin Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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Coullon H, Candela T. Clostridioides difficile peptidoglycan modifications. Curr Opin Microbiol 2021; 65:156-161. [PMID: 34883390 DOI: 10.1016/j.mib.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
The cortex and peptidoglycan of Clostridioides difficile have been poorly investigated. This last decade, the interest increased because these two structures are highly modified and these modifications may be involved in antimicrobial resistance. For example, C. difficile peptidoglycan deacetylation was recently reported to be involved in lysozyme resistance. Modifications may also be important for spore cortex synthesis or spore germination, which is essential in C. difficile pathogenesis. As such, the enzymes responsible for modifications of the peptidoglycan and/or cortex could be new drug target candidates or used as anti-C. difficile agents, as seen for the CD11 autolysin. In this review, we focus on C. difficile peptidoglycan and cortex and compare their structures with those of other well studied bacteria.
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Affiliation(s)
- Héloise Coullon
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France; Division of Infectious Diseases, Dept. of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas Candela
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
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