1
|
Nieto-Domínguez M, Sako A, Enemark-Rasmussen K, Gotfredsen CH, Rago D, Nikel PI. Enzymatic synthesis of mono- and trifluorinated alanine enantiomers expands the scope of fluorine biocatalysis. Commun Chem 2024; 7:104. [PMID: 38724655 PMCID: PMC11082193 DOI: 10.1038/s42004-024-01188-1] [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: 11/28/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
Fluorinated amino acids serve as an entry point for establishing new-to-Nature chemistries in biological systems, and novel methods are needed for the selective synthesis of these building blocks. In this study, we focused on the enzymatic synthesis of fluorinated alanine enantiomers to expand fluorine biocatalysis. The alanine dehydrogenase from Vibrio proteolyticus and the diaminopimelate dehydrogenase from Symbiobacterium thermophilum were selected for in vitro production of (R)-3-fluoroalanine and (S)-3-fluoroalanine, respectively, using 3-fluoropyruvate as the substrate. Additionally, we discovered that an alanine racemase from Streptomyces lavendulae, originally selected for setting an alternative enzymatic cascade leading to the production of these non-canonical amino acids, had an unprecedented catalytic efficiency in β-elimination of fluorine from the monosubstituted fluoroalanine. The in vitro enzymatic cascade based on the dehydrogenases of V. proteolyticus and S. thermophilum included a cofactor recycling system, whereby a formate dehydrogenase from Pseudomonas sp. 101 (either native or engineered) coupled formate oxidation to NAD(P)H formation. Under these conditions, the reaction yields for (R)-3-fluoroalanine and (S)-3-fluoroalanine reached >85% on the fluorinated substrate and proceeded with complete enantiomeric excess. The selected dehydrogenases also catalyzed the conversion of trifluoropyruvate into trifluorinated alanine as a first-case example of fluorine biocatalysis with amino acids carrying a trifluoromethyl group.
Collapse
Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aboubakar Sako
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| |
Collapse
|
2
|
Zheng Y, Zhu X, Jiang M, Cao F, You Q, Chen X. Development and Applications of D-Amino Acid Derivatives-based Metabolic Labeling of Bacterial Peptidoglycan. Angew Chem Int Ed Engl 2024; 63:e202319400. [PMID: 38284300 DOI: 10.1002/anie.202319400] [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: 12/18/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
Peptidoglycan, an essential component within the cell walls of virtually all bacteria, is composed of glycan strands linked by stem peptides that contain D-amino acids. The peptidoglycan biosynthesis machinery exhibits high tolerance to various D-amino acid derivatives. D-amino acid derivatives with different functionalities can thus be specifically incorporated into and label the peptidoglycan of bacteria, but not the host mammalian cells. This metabolic labeling strategy is highly selective, highly biocompatible, and broadly applicable, which has been utilized in various fields. This review introduces the metabolic labeling strategies of peptidoglycan by using D-amino acid derivatives, including one-step and two-step strategies. In addition, we emphasize the various applications of D-amino acid derivative-based metabolic labeling, including bacterial peptidoglycan visualization (existence, biosynthesis, and dynamics, etc.), bacterial visualization (including bacterial imaging and visualization of growth and division, metabolic activity, antibiotic susceptibility, etc.), pathogenic bacteria-targeted diagnostics and treatment (positron emission tomography (PET) imaging, photodynamic therapy, photothermal therapy, gas therapy, immunotherapy, etc.), and live bacteria-based therapy. Finally, a summary of this metabolic labeling and an outlook is provided.
Collapse
Affiliation(s)
- Yongfang Zheng
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Xinyu Zhu
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Mingyi Jiang
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Fangfang Cao
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Qing You
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| |
Collapse
|
3
|
Alanizi AA, Sorlin AM, Parker MFL, López-Álvarez M, Qin H, Lee SH, Blecha J, Rosenberg OS, Engel J, Ohliger MA, Flavell RR, Wilson DM. Bioorthogonal Radiolabeling of Azide-Modified Bacteria Using [ 18F]FB-sulfo-DBCO. Bioconjug Chem 2024; 35:517-527. [PMID: 38482815 PMCID: PMC11036355 DOI: 10.1021/acs.bioconjchem.4c00024] [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: 01/22/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 04/18/2024]
Abstract
Purpose: This study was motivated by the need for better positron emission tomography (PET)-compatible tools to image bacterial infection. Our previous efforts have targeted bacteria-specific metabolism via assimilation of carbon-11 labeled d-amino acids into the bacterial cell wall. Since the chemical determinants of this incorporation are not fully understood, we sought a high-throughput method to label d-amino acid derived structures with fluorine-18. Our strategy employed a chemical biology approach, whereby an azide (-N3) bearing d-amino acid is incorporated into peptidoglycan muropeptides, with subsequent "click" cycloaddition with an 18F-labeled strained cyclooctyne partner. Procedures: A water-soluble, 18F-labeled and dibenzocyclooctyne (DBCO)-derived radiotracer ([18F]FB-sulfo-DBCO) was synthesized. This tracer was incubated with pathogenic bacteria treated with azide-bearing d-amino acids, and incorporated 18F was determined via gamma counting. In vitro uptake in bacteria previously treated with azide-modified d-amino acids was compared to that in cultures treated with amino acid controls. The biodistribution of [18F]FB-sulfo-DBCO was studied in a cohort of healthy mice with implications for future in vivo imaging. Results: The new strain-promoted azide-alkyne cycloaddition (SPAAC) radiotracer [18F]FB-sulfo-DBCO was synthesized with high radiochemical yield and purity via N-succinimidyl 4-[18F]fluorobenzoate ([18F]SFB). Accumulation of [18F]FB-sulfo-DBCO was significantly higher in several bacteria treated with azide-modified d-amino acids than in controls; for example, we observed 7 times greater [18F]FB-sulfo-DBCO ligation in Staphylococcus aureus cultures incubated with 3-azido-d-alanine versus those incubated with d-alanine. Conclusions: The SPAAC radiotracer [18F]FB-sulfo-DBCO was validated in vitro via metabolic labeling of azide-bearing peptidoglycan muropeptides. d-Amino acid-derived PET radiotracers may be more efficiently screened via [18F]FB-sulfo-DBCO modification.
Collapse
Affiliation(s)
- Aryn A. Alanizi
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
| | - Alexandre M. Sorlin
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
| | - Matthew F. L. Parker
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
- Department
of Psychiatry, Renaissance School of Medicine
at Stony Brook University, Stony
Brook, New York 11794, United States
| | - Marina López-Álvarez
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
| | - Hecong Qin
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
| | - Sang Hee Lee
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
| | - Joseph Blecha
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
| | - Oren S. Rosenberg
- Department
of Medicine, University of California, San
Francisco, San Francisco, California 94158, United States
| | - Joanne Engel
- Department
of Medicine, University of California, San
Francisco, San Francisco, California 94158, United States
| | - Michael A. Ohliger
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
- Department
of Radiology, Zuckerberg San Francisco General
Hospital, San Francisco, California 94110, United States
| | - Robert R. Flavell
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
| | - David M. Wilson
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
4
|
Sorlin A, López-Álvarez M, Biboy J, Gray J, Rabbitt SJ, Rahim JU, Lee SH, Bobba KN, Blecha J, Parker MF, Flavell RR, Engel J, Ohliger M, Vollmer W, Wilson DM. Peptidoglycan-Targeted [ 18F]3,3,3-Trifluoro-d-alanine Tracer for Imaging Bacterial Infection. JACS AU 2024; 4:1039-1047. [PMID: 38559735 PMCID: PMC10976610 DOI: 10.1021/jacsau.3c00776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 04/04/2024]
Abstract
Imaging is increasingly used to detect and monitor bacterial infection. Both anatomic (X-rays, computed tomography, ultrasound, and MRI) and nuclear medicine ([111In]-WBC SPECT, [18F]FDG PET) techniques are used in clinical practice but lack specificity for the causative microorganisms themselves. To meet this challenge, many groups have developed imaging methods that target pathogen-specific metabolism, including PET tracers integrated into the bacterial cell wall. We have previously reported the d-amino acid derived PET radiotracers d-methyl-[11C]-methionine, d-[3-11C]-alanine, and d-[3-11C]-alanine-d-alanine, which showed robust bacterial accumulation in vitro and in vivo. Given the clinical importance of radionuclide half-life, in the current study, we developed [18F]3,3,3-trifluoro-d-alanine (d-[18F]-CF3-ala), a fluorine-18 labeled tracer. We tested the hypothesis that d-[18F]-CF3-ala would be incorporated into bacterial peptidoglycan given its structural similarity to d-alanine itself. NMR analysis showed that the fluorine-19 parent amino acid d-[19F]-CF3-ala was stable in human and mouse serum. d-[19F]-CF3-ala was also a poor substrate for d-amino acid oxidase, the enzyme largely responsible for mammalian d-amino acid metabolism and a likely contributor to background signals using d-amino acid derived PET tracers. In addition, d-[19F]-CF3-ala showed robust incorporation into Escherichia coli peptidoglycan, as detected by HPLC/mass spectrometry. Based on these promising results, we developed a radiosynthesis of d-[18F]-CF3-ala via displacement of a bromo-precursor with [18F]fluoride followed by chiral stationary phase HPLC. Unexpectedly, the accumulation of d-[18F]-CF3-ala by bacteria in vitro was highest for Gram-negative pathogens in particular E. coli. In a murine model of acute bacterial infection, d-[18F]-CF3-ala could distinguish live from heat-killed E. coli, with low background signals. These results indicate the viability of [18F]-modified d-amino acids for infection imaging and indicate that improved specificity for bacterial metabolism can improve tracer performance.
Collapse
Affiliation(s)
- Alexandre
M. Sorlin
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
| | - Marina López-Álvarez
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
| | - Jacob Biboy
- The
Centre for Bacterial Cell Biology, Newcastle
University Newcastle, Newcastle
upon Tyne NE2 4AX, United Kingdom
| | - Joe Gray
- The
Centre for Bacterial Cell Biology, Newcastle
University Newcastle, Newcastle
upon Tyne NE2 4AX, United Kingdom
| | - Sarah J. Rabbitt
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
| | - Junaid Ur Rahim
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
| | - Sang Hee Lee
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
| | - Kondapa Naidu Bobba
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
| | - Joseph Blecha
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
| | - Mathew F.L. Parker
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
- Department
of Psychiatry, Renaissance School of Medicine
at Stony Brook University, Stony Brook, New York 11794, United States
| | - Robert R. Flavell
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
- UCSF
Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Joanne Engel
- Department
of Medicine, University of California, San
Francisco, San Francisco, California 94158, United States
- Department
of Microbiology and Immunology, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Michael Ohliger
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
- Department
of Radiology, Zuckerberg San Francisco General
Hospital, San Francisco, California 94110, United States
| | - Waldemar Vollmer
- The
Centre for Bacterial Cell Biology, Newcastle
University Newcastle, Newcastle
upon Tyne NE2 4AX, United Kingdom
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane 4072, Australia
| | - David M. Wilson
- Department
of Radiology, Biomedical Imaging University
of California, San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
5
|
Koatale P, Welling MM, Ndlovu H, Kgatle M, Mdanda S, Mdlophane A, Okem A, Takyi-Williams J, Sathekge MM, Ebenhan T. Insights into Peptidoglycan-Targeting Radiotracers for Imaging Bacterial Infections: Updates, Challenges, and Future Perspectives. ACS Infect Dis 2024; 10:270-286. [PMID: 38290525 PMCID: PMC10862554 DOI: 10.1021/acsinfecdis.3c00443] [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: 08/28/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 02/01/2024]
Abstract
The unique structural architecture of the peptidoglycan allows for the stratification of bacteria as either Gram-negative or Gram-positive, which makes bacterial cells distinguishable from mammalian cells. This classification has received attention as a potential target for diagnostic and therapeutic purposes. Bacteria's ability to metabolically integrate peptidoglycan precursors during cell wall biosynthesis and recycling offers an opportunity to target and image pathogens in their biological state. This Review explores the peptidoglycan biosynthesis for bacteria-specific targeting for infection imaging. Current and potential radiolabeled peptidoglycan precursors for bacterial infection imaging, their development status, and their performance in vitro and/or in vivo are highlighted. We conclude by providing our thoughts on how to shape this area of research for future clinical translation.
Collapse
Affiliation(s)
- Palesa
C. Koatale
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mick M. Welling
- Interventional
Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Honest Ndlovu
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mankgopo Kgatle
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Sipho Mdanda
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Amanda Mdlophane
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Ambrose Okem
- Department
of Anaesthesia, School of Clinical Medicine, University of Witwatersrand, 2050 Johannesburg, South Africa
| | - John Takyi-Williams
- Pharmacokinetic
and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mike M. Sathekge
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Thomas Ebenhan
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
- DSI/NWU Pre-clinical
Drug Development Platform, North West University, 2520 Potchefstroom, South Africa
| |
Collapse
|
6
|
Tan X, Zhang M, Liu S, Xiao X, Zhang Y, Jian H. Prophage enhances the ability of deep-sea bacterium Shewanella psychrophila WP2 to utilize D-amino acid. Microbiol Spectr 2024; 12:e0326323. [PMID: 38170979 PMCID: PMC10845958 DOI: 10.1128/spectrum.03263-23] [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: 09/01/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Prophages are prevalent in the marine bacterial genomes and reshape the physiology and metabolism of their hosts. However, whether and how prophages influence the microbial degradation of D-amino acids (D-AAs), which is one of the widely distributed recalcitrant dissolved organic matters (RDOMs) in the ocean, remain to be explored. In this study, we addressed this issue in a representative marine bacterium, Shewanella psychrophila WP2 (WP2), and its integrated prophage SP1. Notably, compared to the WP2 wild-type strain, the SP1 deletion mutant of WP2 (WP2ΔSP1) exhibited a significantly lower D-glutamate (D-Glu) consumption rate and longer lag phase when D-Glu was used as the sole nitrogen source. The subsequent transcriptome analysis identified 1,523 differentially expressed genes involved in diverse cellular processes, especially that multiple genes related to inorganic nitrogen metabolism were highly upregulated. In addition, the dynamic profiles of ammonium, nitrate, and nitrite were distinct between the culture media of WP2 and WP2ΔSP1. Finally, we provide evidence that SP1 conferred a competitive advantage to WP2 when D-Glu was used as the sole nitrogen source and SP1-like phages may be widely distributed in the global ocean. Taken together, these findings offer novel insight into the influences of prophages on host metabolism and RDOM cycling in marine environments.IMPORTANCEThis work represents the first exploration of the impact of prophages on the D-amino acid (D-AA) metabolism of deep-sea bacteria. By using S. psychrophila WP2 and its integrated prophage SP1 as a representative system, we found that SP1 can significantly increase the catabolism rate of WP2 to D-glutamate and produce higher concentrations of ammonium, resulting in faster growth and competitive advantages. Our findings not only deepen our understanding of the interaction between deep-sea prophages and hosts but also provide new insights into the ecological role of prophages in refractory dissolved organic matter and the nitrogen cycle in deep oceans.
Collapse
Affiliation(s)
- Xiaoli Tan
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| |
Collapse
|
7
|
Kelly JJ, Dalesandro BE, Liu Z, Chordia MD, Ongwae GM, Pires MM. Measurement of Accumulation of Antibiotics to Staphylococcus aureus in Phagosomes of Live Macrophages. Angew Chem Int Ed Engl 2024; 63:e202313870. [PMID: 38051128 PMCID: PMC10799677 DOI: 10.1002/anie.202313870] [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: 10/16/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
Staphylococcus aureus (S. aureus) has evolved the ability to persist after uptake into host immune cells. This intracellular niche enables S. aureus to potentially escape host immune responses and survive the lethal actions of antibiotics. While the elevated tolerance of S. aureus to small-molecule antibiotics is likely to be multifactorial, we pose that there may be contributions related to permeation of antibiotics into phagocytic vacuoles, which would require translocation across two mammalian bilayers. To empirically test this, we adapted our recently developed permeability assay to determine the accumulation of FDA-approved antibiotics into phagocytic vacuoles of live macrophages. Bioorthogonal reactive handles were metabolically anchored within the surface of S. aureus, and complementary tags were chemically added to antibiotics. Following phagocytosis of tagged S. aureus cells, we were able to specifically analyze the arrival of antibiotics within the phagosomes of infected macrophages. Our findings enabled the determination of permeability differences between extra- and intracellular S. aureus, thus providing a roadmap to dissect the contribution of antibiotic permeability to intracellular pathogens.
Collapse
Affiliation(s)
| | | | - Zichen Liu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Mahendra D. Chordia
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - George M. Ongwae
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| |
Collapse
|
8
|
Lee SH, Kim JM, López-Álvarez M, Wang C, Sorlin AM, Bobba KN, Pichardo-González PA, Blecha J, Seo Y, Flavell RR, Engel J, Ohliger MA, Wilson DM. Imaging the Bacterial Cell Wall Using N-Acetyl Muramic Acid-Derived Positron Emission Tomography Radiotracers. ACS Sens 2023; 8:4554-4565. [PMID: 37992233 PMCID: PMC10749472 DOI: 10.1021/acssensors.3c01477] [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: 07/18/2023] [Revised: 10/10/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023]
Abstract
Imaging infections in patients is challenging using conventional methods, motivating the development of positron emission tomography (PET) radiotracers targeting bacteria-specific metabolic pathways. Numerous techniques have focused on the bacterial cell wall, although peptidoglycan-targeted PET tracers have been generally limited to the short-lived carbon-11 radioisotope (t1/2 = 20.4 min). In this article, we developed and tested new tools for infection imaging using an amino sugar component of peptidoglycan, namely, derivatives of N-acetyl muramic acid (NAM) labeled with the longer-lived fluorine-18 (t1/2 = 109.6 min) radioisotope. Muramic acid was reacted directly with 4-nitrophenyl 2-[18F]fluoropropionate ([18F]NFP) to afford the enantiomeric NAM derivatives (S)-[18F]FMA and (R)-[18F]FMA. Both diastereomers were easily isolated and showed robust accumulation by human pathogens in vitro and in vivo, including Staphylococcus aureus. These results form the basis for future clinical studies using fluorine-18-labeled NAM-derived PET radiotracers.
Collapse
Affiliation(s)
- Sang Hee Lee
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Jung Min Kim
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Marina López-Álvarez
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Chao Wang
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Alexandre M. Sorlin
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Kondapa Naidu Bobba
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Priamo A. Pichardo-González
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Joseph Blecha
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Youngho Seo
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Robert R. Flavell
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
- UCSF
Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Joanne Engel
- Department
of Medicine, University of California, San
Francisco, San Francisco, California 94158, United States
- Department
of Microbiology and Immunology, University
of California, San Francisco, San
Francisco, California 94158, United States
| | - Michael A. Ohliger
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
- Department
of Radiology, Zuckerberg San Francisco General
Hospital, San Francisco, California 94110, United States
| | - David M. Wilson
- Department
of Radiology and Biomedical Imaging, University
of California, San Francisco, San
Francisco, California 94158, United States
| |
Collapse
|
9
|
Kelly JJ, Dalesandro BE, Liu Z, Chordia MD, Ongwae GM, Pires MM. Measurement of Accumulation of Antibiotics to Staphylococcus aureus in Phagosomes of Live Macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528196. [PMID: 36824967 PMCID: PMC9949086 DOI: 10.1101/2023.02.13.528196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Staphylococcus aureus ( S. aureus ) has evolved the ability to persist after uptake into host immune cells. This intracellular niche enables S. aureus to potentially escape host immune responses and survive the lethal actions of antibiotics. While the elevated tolerance of S. aureus to small-molecule antibiotics is likely to be multifactorial, we pose that there may be contributions related to permeation of antibiotics into phagocytic vacuoles, which would require translocation across two mammalian bilayers. To empirically test this, we adapted our recently developed permeability assay to determine the accumulation of FDA-approved antibiotics into phagocytic vacuoles of live macrophages. Bioorthogonal reactive handles were metabolically anchored within the surface of S. aureus, and complementary tags were chemically added to antibiotics. Following phagocytosis of tagged S. aureus cells, we were able to specifically analyze the arrival of antibiotics within the phagosomes of infected macrophages. Our findings enabled the determination of permeability differences between extra- and intracellular S. aureus , thus providing a roadmap to dissect the contribution of antibiotic permeability to intracellular pathogens.
Collapse
|
10
|
Finin P, Khan RMN, Oh S, Boshoff HIM, Barry CE. Chemical approaches to unraveling the biology of mycobacteria. Cell Chem Biol 2023; 30:420-435. [PMID: 37207631 PMCID: PMC10201459 DOI: 10.1016/j.chembiol.2023.04.014] [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: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/21/2023]
Abstract
Mycobacterium tuberculosis (Mtb), perhaps more than any other organism, is intrinsically appealing to chemical biologists. Not only does the cell envelope feature one of the most complex heteropolymers found in nature1 but many of the interactions between Mtb and its primary host (we humans) rely on lipid and not protein mediators.2,3 Many of the complex lipids, glycolipids, and carbohydrates biosynthesized by the bacterium still have unknown functions, and the complexity of the pathological processes by which tuberculosis (TB) disease progress offers many opportunities for these molecules to influence the human response. Because of the importance of TB in global public health, chemical biologists have applied a wide-ranging array of techniques to better understand the disease and improve interventions.
Collapse
Affiliation(s)
- Peter Finin
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - R M Naseer Khan
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Apostolos AJ, Ocius KL, Koyasseril-Yehiya TM, Santamaria C, Silva JRA, Lameira J, Alves CN, Siegrist MS, Pires MM. Metabolic Processing of Selenium-Based Bioisosteres of meso-Diaminopimelic Acid in Live Bacteria. Biochemistry 2022; 61:1404-1414. [PMID: 35687722 DOI: 10.1021/acs.biochem.2c00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A primary component of all known bacterial cell walls is the peptidoglycan (PG) layer, which is composed of repeating units of sugars connected to short and unusual peptides. The various steps within PG biosynthesis are targets of potent antibiotics as proper assembly of the PG is essential for cellular growth and survival. Synthetic mimics of PG have proven to be indispensable tools to study the bacterial cell structure, growth, and remodeling. Yet, a common component of PG, meso-diaminopimelic acid (m-DAP) at the third position of the stem peptide, remains challenging to access synthetically and is not commercially available. Here, we describe the synthesis and metabolic processing of a selenium-based bioisostere of m-DAP (selenolanthionine) and show that it is installed within the PG of live bacteria by the native cell wall crosslinking machinery in mycobacterial species. This PG probe has an orthogonal release mechanism that could be important for downstream proteomics studies. Finally, we describe a bead-based assay that is compatible with high-throughput screening of cell wall enzymes. We envision that this probe will supplement the current methods available for investigating PG crosslinking in m-DAP-containing organisms.
Collapse
Affiliation(s)
- Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Karl L Ocius
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | | | - Carolina Santamaria
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States
| | - José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Cláudio N Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - M Sloan Siegrist
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| |
Collapse
|
14
|
Impact of crossbridge structure on peptidoglycan crosslinking: A synthetic stem peptide approach. Methods Enzymol 2022; 665:259-279. [PMID: 35379437 DOI: 10.1016/bs.mie.2021.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall, whose main component is peptidoglycan (PG), provides cellular rigidity and prevents lysis from osmotic pressure. Moreover, the cell wall is the main interface between the external environment and internal cellular components. Given its essentiality, many antibiotics target enzymes related to the biosynthesis of cell wall. Of these enzymes, transpeptidases (TPs) are central to proper cell wall assembly and their inactivation is the mechanism of action of many antibiotics including β-lactams. TPs are responsible for stitching together strands of PG to make the crosslinked meshwork of the cell wall. This chapter focuses on the use of solid-phase peptide synthesis to build PG analogs that become site-selectively incorporated into the cell wall of live bacterial cells. This method allows for the design of fluorescent handles on PG probes that will enable the interrogation of substrate preferences of TPs (e.g., amidation at the glutamic acid residue, crossbridge presence) by analyzing the level of probe incorporation within the native cell wall of live bacterial cells.
Collapse
|
15
|
Banahene N, Kavunja HW, Swarts BM. Chemical Reporters for Bacterial Glycans: Development and Applications. Chem Rev 2022; 122:3336-3413. [PMID: 34905344 PMCID: PMC8958928 DOI: 10.1021/acs.chemrev.1c00729] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species─including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.
Collapse
Affiliation(s)
- Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, United States
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, United States
| | - Herbert W. Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, United States
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, United States
| | | |
Collapse
|
16
|
Ferraro NJ, Kim S, Im W, Pires MM. Systematic Assessment of Accessibility to the Surface of Staphylococcus aureus. ACS Chem Biol 2021; 16:2527-2536. [PMID: 34609132 DOI: 10.1021/acschembio.1c00604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proteins from bacterial foes, antimicrobial peptides, and host immune proteins must navigate past a dense layer of bacterial surface biomacromolecules to reach the peptidoglycan (PG) layer of Gram-positive bacteria. A subclass of molecules (e.g., antibiotics with intracellular targets) also must permeate through the PG (in a molecular sieving manner) to reach the cytoplasmic membrane. Despite the biological and therapeutic importance of surface accessibility, systematic analyses in live bacterial cells have been lacking. We describe a live cell fluorescence assay that is robust, shows a high level of reproducibility, and reports on the permeability of molecules to and within the PG scaffold. Moreover, our study shows that teichoic acids impede the permeability of molecules of a wide range of sizes and chemical composition.
Collapse
Affiliation(s)
- Noel J. Ferraro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Seonghoon Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| |
Collapse
|
17
|
Brown AR, Wodzanowski KA, Santiago CC, Hyland SN, Follmar JL, Asare-Okai P, Grimes CL. Protected N-Acetyl Muramic Acid Probes Improve Bacterial Peptidoglycan Incorporation via Metabolic Labeling. ACS Chem Biol 2021; 16:1908-1916. [PMID: 34506714 DOI: 10.1021/acschembio.1c00268] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Metabolic glycan probes have emerged as an excellent tool to investigate vital questions in biology. Recently, methodology to incorporate metabolic bacterial glycan probes into the cell wall of a variety of bacterial species has been developed. In order to improve this method, a scalable synthesis of the peptidoglycan precursors is developed here, allowing for access to essential peptidoglycan immunological fragments and cell wall building blocks. The question was asked if masking polar groups of the glycan probe would increase overall incorporation, a common strategy exploited in mammalian glycobiology. Here, we show, through cellular assays, that E. coli do not utilize peracetylated peptidoglycan substrates but do employ methyl esters. The 10-fold improvement of probe utilization indicates that (i) masking the carboxylic acid is favorable for transport and (ii) bacterial esterases are capable of removing the methyl ester for use in peptidoglycan biosynthesis. This investigation advances bacterial cell wall biology, offering a prescription on how to best deliver and utilize bacterial metabolic glycan probes.
Collapse
Affiliation(s)
- Ashley R. Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Kimberly A. Wodzanowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Cintia C. Santiago
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Stephen N. Hyland
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Julianna L. Follmar
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - PapaNii Asare-Okai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
| |
Collapse
|
18
|
Apostolos AJ, Ferraro NJ, Dalesandro BE, Pires MM. SaccuFlow: A High-Throughput Analysis Platform to Investigate Bacterial Cell Wall Interactions. ACS Infect Dis 2021; 7:2483-2491. [PMID: 34291914 DOI: 10.1021/acsinfecdis.1c00255] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Bacterial cell walls are formidable barriers that protect bacterial cells against external insults and oppose internal turgor pressure. While cell wall composition is variable across species, peptidoglycan is the principal component of all cell walls. Peptidoglycan is a mesh-like scaffold composed of cross-linked strands that can be heavily decorated with anchored proteins. The biosynthesis and remodeling of peptidoglycan must be tightly regulated by cells because disruption to this biomacromolecule is lethal. This essentiality is exploited by the human innate immune system in resisting colonization and by a number of clinically relevant antibiotics that target peptidoglycan biosynthesis. Evaluation of molecules or proteins that interact with peptidoglycan can be a complicated and, typically, qualitative effort. We have developed a novel assay platform (SaccuFlow) that preserves the native structure of bacterial peptidoglycan and is compatible with high-throughput flow cytometry analysis. We show that the assay is facile and versatile as demonstrated by its compatibility with sacculi from Gram-positive bacteria, Gram-negative bacteria, and mycobacteria. Finally, we highlight the utility of this assay to assess the activity of sortase A from Staphylococcus aureus against potential antivirulence agents.
Collapse
Affiliation(s)
- Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Noel J. Ferraro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Brianna E. Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| |
Collapse
|
19
|
Luong P, Dube DH. Dismantling the bacterial glycocalyx: Chemical tools to probe, perturb, and image bacterial glycans. Bioorg Med Chem 2021; 42:116268. [PMID: 34130219 DOI: 10.1016/j.bmc.2021.116268] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
The bacterial glycocalyx is a quintessential drug target comprised of structurally distinct glycans. Bacterial glycans bear unusual monosaccharide building blocks whose proper construction is critical for bacterial fitness, survival, and colonization in the human host. Despite their appeal as therapeutic targets, bacterial glycans are difficult to study due to the presence of rare bacterial monosaccharides that are linked and modified in atypical manners. Their structural complexity ultimately hampers their analytical characterization. This review highlights recent advances in bacterial chemical glycobiology and focuses on the development of chemical tools to probe, perturb, and image bacterial glycans and their biosynthesis. Current technologies have enabled the study of bacterial glycosylation machinery even in the absence of detailed structural information.
Collapse
Affiliation(s)
- Phuong Luong
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Danielle H Dube
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA.
| |
Collapse
|
20
|
Dalesandro BE, Pires MM. Induction of Endogenous Antibody Recruitment to the Surface of the Pathogen Enterococcus faecium. ACS Infect Dis 2021; 7:1116-1125. [PMID: 33179504 DOI: 10.1021/acsinfecdis.0c00547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the foreseeable future, conventional small molecule antibiotics will continue to be the predominant treatment option due to wide patient coverage and low costs. Today, however, there is already a significant portion of patients that fail to respond to small molecule antibiotics and, according to the Centers for Disease Control and Prevention, this number is poised to increase in the coming years. Therefore, this rise in drug resistant bacteria must be countered with the development of nontraditional therapies. We propose a measure based on the re-engagement of the immune system toward pathogenic bacteria by grafting bacterial cell surfaces with immunogenic agents. Herein, we describe a class of cell wall analogues that selectively graft bacterial cell surfaces with epitopes that promote their opsonization. More specifically, synthetic analogues of peptidoglycan conjugated to haptens were designed to be incorporated by the cell wall biosynthetic machinery into live Enterococcus faecium. E. faecium is a formidable human pathogen that poses a considerable burden to healthcare and often results in fatalities. We showed that treatment of E. faecium and vancomycin-resistant strains with the cell wall analogues led to the display of haptens on the cell surface, which induced the recruitment of antibodies existing in the serum of humans. These results demonstrate the feasibility in using cell wall analogues as the basis of a class of bacterial immunotherapies against dangerous pathogens.
Collapse
Affiliation(s)
- Brianna E. Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| |
Collapse
|
21
|
Dyakin VV, Wisniewski TM, Lajtha A. Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg. Symmetry (Basel) 2021; 13:455. [PMID: 34350031 PMCID: PMC8330555 DOI: 10.3390/sym13030455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and racemization originated from the studies of fossils and cataract disease. Under the pressure of new results, this concept has a broader significance linking protein folding, aggregation, and disfunction to an organism's cognitive and behavioral functions. The integrity of cognitive function is provided by a delicate balance between the evolutionarily imposed molecular homo-chirality and the epigenetic/developmental impact of spontaneous and enzymatic racemization. The chirality of amino acids is the crucial player in the modulation the structure and function of proteins, lipids, and DNA. The collapse of homochirality by racemization is the result of the conformational phase transition. The racemization of protein-bound amino acids (spontaneous and enzymatic) occurs through thermal activation over the energy barrier or by the tunnel transfer effect under the energy barrier. The phase transition is achieved through the intermediate state, where the chirality of alpha carbon vanished. From a thermodynamic consideration, the system in the homo-chiral (single enantiomeric) state is characterized by a decreased level of entropy. The oscillating protein chirality is suggesting its distinct significance in the neurotransmission and flow of perceptual information, adaptive associative learning, and cognitive laterality. The common pathological hallmarks of neurodegenerative disorders include protein misfolding, aging, and the deposition of protease-resistant protein aggregates. Each of the landmarks is influenced by racemization. The brain region, cell type, and age-dependent racemization critically influence the functions of many intracellular, membrane-bound, and extracellular proteins including amyloid precursor protein (APP), TAU, PrP, Huntingtin, α-synuclein, myelin basic protein (MBP), and collagen. The amyloid cascade hypothesis in Alzheimer's disease (AD) coexists with the failure of amyloid beta (Aβ) targeting drug therapy. According to our view, racemization should be considered as a critical factor of protein conformation with the potential for inducing order, disorder, misfolding, aggregation, toxicity, and malfunctions.
Collapse
Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Center for Neurochemistry, The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| |
Collapse
|
22
|
Emerging trends in aggregation induced emissive luminogens as bacterial theranostics. J Drug Target 2021; 29:793-807. [PMID: 33583291 DOI: 10.1080/1061186x.2021.1888111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The emergence and spread of pathogenic bacteria, particularly antibiotic-resistant strains pose grave global concerns worldwide, which demand for the rapid development of highly selective and sensitive strategies for specific bacterial detection, identification, imaging and therapy. The fascinating feature of aggregation-induced emissive molecules (AIEgens) to display fluorescence in aggregate form can be suitably coupled with nanotechnology for developing theranostic AIE dots that can offer convenient and customised functions such as sensing, imaging, detection, discrimination and cell kill of different bacterial types. The initial section of the article reveals the necessity for incorporating diagnostic imaging with antibacterial therapy, while the latter part delivers mechanistic insights on the benefits of AIE fluorophores in theranostic applications. Further, the review illustrates the recent advancements of AIEgens as theranostic nanolights in bacterial detection, identification and eradication. The review is organised according to the different classes of AIE-active bacterial theranostics such as carrier-free nanoprodrugs, nanomachines for synergistic imaging-guided cancer treatment and bacterial kill, AIE polymers, bioconjugates and nanoparticle carriers. By elucidating their design principles and applications, as well as highlighting the recent trends and perspectives that can be further explored, we hope to instill more research interest in AIE bacterial theranostics for future translational research.HighlightsCombination of aggregation induced emissive fluorophores and nanotechnology for developing bacterial theranostics.AIE theranostics with customised functions for bacterial imaging, detection, discrimination and cell kill.
Collapse
|
23
|
Marshall AP, Shirley JD, Carlson EE. Enzyme-targeted fluorescent small-molecule probes for bacterial imaging. Curr Opin Chem Biol 2020; 57:155-165. [PMID: 32799037 DOI: 10.1016/j.cbpa.2020.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Abstract
Molecular imaging methods to visualize myriad biochemical processes in bacteria have traditionally been dependent upon molecular biology techniques to incorporate fluorescent biomolecules (e.g., fusion proteins). Such methods have been instrumental in our understanding of how bacteria function but are not without drawbacks, including potential perturbation to native protein expression and function. To overcome these limitations, the use of fluorescent small-molecule probes has gained much attention. Here, we highlight examples from the recent literature that showcase the utility of small-molecule probes for the fluorescence imaging of bacterial cells, including electrophilic, metabolic, and enzyme-activated probes. Although the use of these types of compounds for bacterial imaging is still relatively new, the selected examples demonstrate the exciting potential of these critical tools in the exploration of bacterial physiology.
Collapse
Affiliation(s)
- Andrew P Marshall
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
| |
Collapse
|
24
|
Fluorescent probes for investigating peptidoglycan biosynthesis in mycobacteria. Curr Opin Chem Biol 2020; 57:50-57. [DOI: 10.1016/j.cbpa.2020.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 02/02/2023]
|
25
|
Parker MFL, Flavell RR, Luu JM, Rosenberg OS, Ohliger MA, Wilson DM. Small Molecule Sensors Targeting the Bacterial Cell Wall. ACS Infect Dis 2020; 6:1587-1598. [PMID: 32433879 DOI: 10.1021/acsinfecdis.9b00515] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This review highlights recent efforts to detect bacteria using engineered small molecules that are processed and incorporated similarly to their natural counterparts. There are both scientific and clinical justifications for these endeavors. The use of detectable, cell-wall targeted chemical probes has elucidated microbial behavior, with several fluorescent labeling methods in widespread laboratory use. Furthermore, many existing efforts including ours, focus on developing new imaging tools to study infection in clinical practice. The bacterial cell wall, a remarkably rich and complex structure, is an outstanding target for bacteria-specific detection. Several cell wall components are found in bacteria but not mammals, especially peptidoglycan, lipopolysaccharide, and teichoic acids. As this review highlights, the development of laboratory tools for fluorescence microscopy has vastly outstripped related positron emission tomography (PET) or single photon emission computed tomography (SPECT) radiotracer development. However, there is great synergy between these chemical strategies, which both employ mimicry of endogenous substrates to incorporate detectable structures. As the field of bacteria-specific imaging grows, it will be important to understand the mechanisms involved in microbial incorporation of radionuclides. Additionally, we will highlight the clinical challenges motivating this imaging effort.
Collapse
Affiliation(s)
- Matthew F. L. Parker
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Robert R. Flavell
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Justin M. Luu
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Oren S. Rosenberg
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
| | - Michael A. Ohliger
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
- Department of Radiology, Zuckerberg San Francisco General Hospital, San Francisco, California 94110, United States
| | - David M. Wilson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
26
|
Sharifzadeh S, Dempwolff F, Kearns DB, Carlson EE. Harnessing β-Lactam Antibiotics for Illumination of the Activity of Penicillin-Binding Proteins in Bacillus subtilis. ACS Chem Biol 2020; 15:1242-1251. [PMID: 32155044 DOI: 10.1021/acschembio.9b00977] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Selective chemical probes enable individual investigation of penicillin-binding proteins (PBPs) and provide critical information about their enzymatic activity with spatial and temporal resolution. To identify scaffolds for novel probes to study peptidoglycan biosynthesis in Bacillus subtilis, we evaluated the PBP inhibition profiles of 21 β-lactam antibiotics from different structural subclasses using a fluorescence-based assay. Most compounds readily labeled PBP1, PBP2a, PBP2b, or PBP4. Almost all penicillin scaffolds were coselective for all or combinations of PBP2a, 2b, and 4. Cephalosporins, on the other hand, possessed the lowest IC50 values for PBP1 alone or along with PBP4 (ceftriaxone, cefoxitin) and 2b (cefotaxime) or 2a, 2b, and 4 (cephalothin). Overall, five selective inhibitors for PBP1 (aztreonam, faropenem, piperacillin, cefuroxime, and cefsulodin), one selective inhibitor for PBP5 (6-aminopenicillanic acid), and various coselective inhibitors for other PBPs in B. subtilis were discovered. Surprisingly, carbapenems strongly inhibited PBP3, formerly shown to have low affinity for β-lactams and speculated to be involved in β-lactam resistance in B. subtilis. To investigate the specific roles of PBP3, we developed activity-based probes based on the meropenem core and utilized them to monitor the activity of PBP3 in living cells. We showed that PBP3 activity localizes as patches in single cells and concentrates as a ring at the septum and the division site during the cell growth cycle. Our activity-based approach enabled spatial resolution of the transpeptidation activity of individual PBPs in this model microorganism, which was not possible with previous chemical and biological approaches.
Collapse
Affiliation(s)
| | - Felix Dempwolff
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | | |
Collapse
|
27
|
Sharifzadeh S, Brown NW, Shirley JD, Bruce KE, Winkler ME, Carlson EE. Chemical tools for selective activity profiling of bacterial penicillin-binding proteins. Methods Enzymol 2020; 638:27-55. [PMID: 32416917 DOI: 10.1016/bs.mie.2020.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Penicillin-binding proteins (PBPs) are membrane-associated proteins involved in the biosynthesis of peptidoglycan (PG), the main component of bacterial cell walls. These proteins were discovered and named for their affinity to bind the β-lactam antibiotic penicillin. The importance of the PBPs has long been appreciated; however, specific roles of individual family members in each bacterial strain, as well as their protein-protein interactions, are yet to be understood. The apparent functional redundancy of the 4-18 PBPs that most eubacteria possess makes determination of their individual roles difficult. Existing techniques to study PBPs are not ideal because they do not directly visualize protein activity and can suffer from artifacts and perturbations of native PBP function. Therefore, development of new methods for studying the roles of individual PBPs in cell wall synthesis is required. We recently generated a library of fluorescent chemical probes containing a β-lactone scaffold that specifically targets the PBPs, enabling the visualization of their catalytic activity. Herein, we describe a general protocol to label and detect the activity of individual PBPs in Streptococcus pneumoniae using our fluorescent β-lactone probes.
Collapse
Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Nathaniel W Brown
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Kevin E Bruce
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Malcolm E Winkler
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
| |
Collapse
|
28
|
d-Methionine and d-Phenylalanine Improve Lactococcus lactis F44 Acid Resistance and Nisin Yield by Governing Cell Wall Remodeling. Appl Environ Microbiol 2020; 86:AEM.02981-19. [PMID: 32111594 DOI: 10.1128/aem.02981-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/22/2020] [Indexed: 12/30/2022] Open
Abstract
Lactococcus lactis encounters various environmental challenges, especially acid stress, during its growth. The cell wall can maintain the integrity and shape of the cell under environmental stress, and d-amino acids play an important role in cell wall synthesis. Here, by analyzing the effects of 19 different d-amino acids on the physiology of L. lactis F44, we found that exogenously supplied d-methionine and d-phenylalanine increased the nisin yield by 93.22% and 101.29%, respectively, as well as significantly increasing the acid resistance of L. lactis F44. The composition of the cell wall in L. lactis F44 with exogenously supplied d-Met or d-Phe was further investigated via a vancomycin fluorescence experiment and a liquid chromatography-mass spectrometry assay, which demonstrated that d-Met could be incorporated into the fifth position of peptidoglycan (PG) muropeptides and d-Phe could be added to the fourth and fifth positions. Moreover, overexpression of the PG synthesis gene murF further enhanced the levels of d-Met and d-Phe involved in PG and increased the survival rate under acid stress and the nisin yield of the strain. This study reveals that the exogenous supply of d-Met or d-Phe can change the composition of the cell wall and influence acid tolerance as well as nisin yield in L. lactis IMPORTANCE As d-amino acids play an important role in cell wall synthesis, we analyzed the effects of 19 different d-amino acids on L. lactis F44, demonstrating that d-Met and d-Phe can participate in peptidoglycan (PG) synthesis and improve the acid resistance and nisin yield of this strain. murF overexpression further increased the levels of d-Met and d-Phe incorporated into PG and contributed to the acid resistance of the strain. These findings suggest that d-Met and d-Phe can be incorporated into PG to improve the acid resistance and nisin yield of L. lactis, and this study provides new ideas for the enhancement of nisin production.
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Melzer ES, Sein CE, Chambers JJ, Siegrist MS. DivIVA concentrates mycobacterial cell envelope assembly for initiation and stabilization of polar growth. Cytoskeleton (Hoboken) 2018; 75:498-507. [PMID: 30160378 PMCID: PMC6644302 DOI: 10.1002/cm.21490] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/07/2018] [Accepted: 06/27/2018] [Indexed: 12/31/2022]
Abstract
In many model organisms, diffuse patterning of cell wall peptidoglycan synthesis by the actin homolog MreB enables the bacteria to maintain their characteristic rod shape. In Caulobacter crescentus and Escherichia coli, MreB is also required to sculpt this morphology de novo. Mycobacteria are rod-shaped but expand their cell wall from discrete polar or subpolar zones. In this genus, the tropomyosin-like protein DivIVA is required for the maintenance of cell morphology. DivIVA has also been proposed to direct peptidoglycan synthesis to the tips of the mycobacterial cell. The precise nature of this regulation is unclear, as is its role in creating rod shape from scratch. We find that DivIVA localizes nascent cell wall and covalently associated mycomembrane but is dispensable for the assembly process itself. Mycobacterium smegmatis rendered spherical by peptidoglycan digestion or by DivIVA depletion are able to regain rod shape at the population level in the presence of DivIVA. At the single cell level, there is a close spatiotemporal correlation between DivIVA foci, rod extrusion and concentrated cell wall synthesis. Thus, although the precise mechanistic details differ from other organisms, M. smegmatis also establish and propagate rod shape by cytoskeleton-controlled patterning of peptidoglycan. Our data further support the emerging notion that morphology is a hardwired trait of bacterial cells.
Collapse
Affiliation(s)
- Emily S Melzer
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Caralyn E Sein
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - James J Chambers
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts.,Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts
| |
Collapse
|
32
|
Feigman MJS, Pires MM. Synthetic Immunobiotics: A Future Success Story in Small Molecule-Based Immunotherapy? ACS Infect Dis 2018; 4:664-672. [PMID: 29431421 DOI: 10.1021/acsinfecdis.7b00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Drug resistance to our current stock of antibiotics is projected to increase to levels that threaten our ability to reduce and eliminate bacterial infections, which is now considered one of the primary health care crises of the 21st century. Traditional antibiotic agents (e.g., penicillin) paved the way for massive advances in human health, but we need novel strategies to maintain the upper hand in the battle against pathogenic bacteria. Nontraditional strategies, such as targeted immunotherapies, could prove fruitful in complementing our antibiotic arsenal.
Collapse
Affiliation(s)
- Mary J. Sabulski Feigman
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
33
|
Abstract
Peptidoglycan is an essential component of the cell wall that protects bacteria from environmental stress. A carefully coordinated biosynthesis of peptidoglycan during cell elongation and division is required for cell viability. This biosynthesis involves sophisticated enzyme machineries that dynamically synthesize, remodel, and degrade peptidoglycan. However, when and where bacteria build peptidoglycan, and how this is coordinated with cell growth, have been long-standing questions in the field. The improvement of microscopy techniques has provided powerful approaches to study peptidoglycan biosynthesis with high spatiotemporal resolution. Recent development of molecular probes further accelerated the growth of the field, which has advanced our knowledge of peptidoglycan biosynthesis dynamics and mechanisms. Here, we review the technologies for imaging the bacterial cell wall and its biosynthesis activity. We focus on the applications of fluorescent d-amino acids, a newly developed type of probe, to visualize and study peptidoglycan synthesis and dynamics, and we provide direction for prospective research.
Collapse
Affiliation(s)
- Atanas D Radkov
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.,Current affiliation: Biophysics and Biochemistry Department, University of California, San Francisco, California 94158, USA;
| | - Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
| | - Garrett Booher
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
| | - Michael S VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
| |
Collapse
|
34
|
Mandel MJ. D-fining DarR: a LysR-type transcriptional regulator that responds to D-aspartate. J Bacteriol 2018; 200:e00121-18. [PMID: 29555693 PMCID: PMC6040187 DOI: 10.1128/jb.00121-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Work from Jones, Stabb, et al. describes a D-aspartate sensing system in Proteobacteria. D-amino acids are critical components of peptidoglycan and other structures. The new study identifies the LysR-type transcriptional regulator, DarR, which activates the aspartate racemase RacD. Overexpression of RacD enables it to synthesize D-glutamate and restore normal peptidoglycan in a Vibrio fischeri murI mutant. This study contributes to emerging roles for D-amino acids and how they are synthesized under distinct conditions.
Collapse
Affiliation(s)
- Mark J Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
| |
Collapse
|
35
|
Dockerty P, Edens JG, Tol MB, Morales Angeles D, Domenech A, Liu Y, Hirsch AKH, Veening JW, Scheffers DJ, Witte MD. Bicyclic enol cyclocarbamates inhibit penicillin-binding proteins. Org Biomol Chem 2018; 15:894-910. [PMID: 28045164 DOI: 10.1039/c6ob01664b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural products form attractive leads for the development of chemical probes and drugs. The antibacterial lipopeptide Brabantamide A contains an unusual enol cyclocarbamate and we used this scaffold as inspiration for the synthesis of a panel of enol cyclocarbamate containing compounds. By equipping the scaffold with different groups, we identified structural features that are essential for antibacterial activity. Some of the derivatives block incorporation of hydroxycoumarin carboxylic acid-amino d-alanine into the newly synthesized peptidoglycan. Activity-based protein-profiling experiments revealed that the enol carbamates inhibit a specific subset of penicillin-binding proteins in B. subtilis and S. pneumoniae.
Collapse
Affiliation(s)
- Paul Dockerty
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| | - Jerre G Edens
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| | - Menno B Tol
- Molecular Microbiology, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Danae Morales Angeles
- Molecular Microbiology, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Arnau Domenech
- Molecular Genetics, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Yun Liu
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| | - Anna K H Hirsch
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| | - Jan-Willem Veening
- Molecular Genetics, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Dirk-Jan Scheffers
- Molecular Microbiology, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Martin D Witte
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| |
Collapse
|
36
|
Welsh MA, Taguchi A, Schaefer K, Van Tyne D, Lebre-ton F, Gilmore MS, Kahne D, Walker S. Identification of a Functionally Unique Family of Penicillin-Binding Proteins. J Am Chem Soc 2017; 139:17727-17730. [PMID: 29182854 PMCID: PMC5729098 DOI: 10.1021/jacs.7b10170] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Penicillin-binding proteins (PBPs) are enzymes involved in the assembly of the bacterial cell wall, a major target for antibiotics. These proteins are classified by mass into high-molecular-weight PBPs, which are transpeptidases that form peptidoglycan cross-links, and low-molecular-weight PBPs, which are typically hydrolases. We report a functionally unique family of low-molecular-weight PBPs that act as transpeptidases rather than hydrolases, but they do not cross-link peptidoglycan. We show that these PBPs can exchange d-amino acids bearing chemical tags or affinity handles into peptidoglycan precursors, including Lipid II, enabling biochemical studies of proteins involved in cell wall assembly. We report that, in two organisms, the PBPs incorporate lysine into cellular peptidoglycan and that, further, the PBPs have the unprecedented ability to transfer the primary ε-amine of lysine to peptidoglycan.
Collapse
Affiliation(s)
- Michael A. Welsh
- Dept. of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Atsushi Taguchi
- Dept. of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Kaitlin Schaefer
- Dept. of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Daria Van Tyne
- Dept. of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, 02114
| | - François Lebre-ton
- Dept. of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, 02114
| | - Michael S. Gilmore
- Dept. of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
- Dept. of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, 02114
| | - Daniel Kahne
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Suzanne Walker
- Dept. of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| |
Collapse
|
37
|
Fluorescent D-amino-acids reveal bi-cellular cell wall modifications important for Bdellovibrio bacteriovorus predation. Nat Microbiol 2017; 2:1648-1657. [PMID: 28974693 PMCID: PMC5705579 DOI: 10.1038/s41564-017-0029-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/11/2017] [Indexed: 01/05/2023]
Abstract
Modification of essential bacterial peptidoglycan (PG) containing cell
walls can lead to antibiotic resistance, for example β-lactam resistance
by L,D-transpeptidase activities. Predatory Bdellovibrio
bacteriovorus are naturally antibacterial and combat infections by
traversing, modifying and finally destroying walls of Gram-negative prey
bacteria, modifying their own PG as they grow inside prey. Historically, these
multi-enzymatic processes on two similar PG walls have proved challenging to
elucidate. Here, with a PG labelling approach utilizing timed pulses of multiple
fluorescent D-amino acids (FDAAs), we illuminate dynamic changes that predator
and prey walls go through during the different phases of bacteria:bacteria
invasion. We show formation of a reinforced circular port-hole in the prey wall;
L,D-transpeptidaseBd mediated D-amino acid modifications
strengthening prey PG during Bdellovibrio invasion and a zonal
mode of predator-elongation. This process is followed by unconventional,
multi-point and synchronous septation of the intracellular
Bdellovibrio, accommodating odd- and even-numbered progeny
formation by non-binary division.
Collapse
|
38
|
Hsu YP, Rittichier J, Kuru E, Yablonowski J, Pasciak E, Tekkam S, Hall E, Murphy B, Lee TK, Garner EC, Huang KC, Brun YV, VanNieuwenhze MS. Full color palette of fluorescent d-amino acids for in situ labeling of bacterial cell walls. Chem Sci 2017; 8:6313-6321. [PMID: 28989665 PMCID: PMC5628581 DOI: 10.1039/c7sc01800b] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/06/2017] [Indexed: 01/01/2023] Open
Abstract
Fluorescent d-amino acids (FDAAs) enable efficient in situ labeling of peptidoglycan in diverse bacterial species. Conducted by enzymes involved in peptidoglycan biosynthesis, FDAA labeling allows specific probing of cell wall formation/remodeling activity, bacterial growth and cell morphology. Their broad application and high biocompatibility have made FDAAs an important and effective tool for studies of peptidoglycan synthesis and dynamics, which, in turn, has created a demand for the development of new FDAA probes. Here, we report the synthesis of new FDAAs, with emission wavelengths that span the entire visible spectrum. We also provide data to characterize their photochemical and physical properties, and we demonstrate their utility for visualizing peptidoglycan synthesis in Gram-negative and Gram-positive bacterial species. Finally, we show the permeability of FDAAs toward the outer-membrane of Gram-negative organisms, pinpointing the probes available for effective labeling in these species. This improved FDAA toolkit will enable numerous applications for the study of peptidoglycan biosynthesis and dynamics.
Collapse
Affiliation(s)
- Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | | | - Erkin Kuru
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | - Jacob Yablonowski
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | - Erick Pasciak
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Srinivas Tekkam
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Edward Hall
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Brennan Murphy
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Timothy K Lee
- Department of Bioengineering , Stanford University , Stanford , CA 94305 , USA
| | - Ethan C Garner
- Molecular and Cellular Biology (FAS) Center for Systems Biology , Harvard University , Cambridge , Massachusetts 02138 , USA
| | - Kerwyn Casey Huang
- Department of Bioengineering , Stanford University , Stanford , CA 94305 , USA
- Department of Microbiology and Immunology , Stanford University School of Medicine , Stanford , CA 94305 , USA
| | - Yves V Brun
- Department of Biology , Indiana University , Bloomington , IN 47405 , USA .
| | - Michael S VanNieuwenhze
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| |
Collapse
|
39
|
Pidgeon SE, Pires MM. Cell Wall Remodeling of Staphylococcus aureus in Live Caenorhabditis elegans. Bioconjug Chem 2017; 28:2310-2315. [DOI: 10.1021/acs.bioconjchem.7b00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sean E. Pidgeon
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
40
|
Morales Angeles D, Liu Y, Hartman AM, Borisova M, de Sousa Borges A, de Kok N, Beilharz K, Veening JW, Mayer C, Hirsch AKH, Scheffers DJ. Pentapeptide-rich peptidoglycan at the Bacillus subtilis cell-division site. Mol Microbiol 2017; 104:319-333. [PMID: 28118510 DOI: 10.1111/mmi.13629] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2017] [Indexed: 11/28/2022]
Abstract
Peptidoglycan (PG), the major component of the bacterial cell wall, is one large macromolecule. To allow for the different curvatures of PG at cell poles and division sites, there must be local differences in PG architecture and eventually also chemistry. Here we report such local differences in the Gram-positive rod-shaped model organism Bacillus subtilis. Single-cell analysis after antibiotic treatment and labeling of the cell wall with a fluorescent analogue of vancomycin or the fluorescent D-amino acid analogue (FDAA) HCC-amino-D-alanine revealed that PG at the septum contains muropeptides with unprocessed stem peptides (pentapeptides). Whereas these pentapeptides are normally shortened after incorporation into PG, this activity is reduced at division sites indicating either a lower local degree of PG crosslinking or a difference in PG composition, which could be a topological marker for other proteins. The pentapeptides remain partially unprocessed after division when they form the new pole of a cell. The accumulation of unprocessed PG at the division site is not caused by the activity of the cell division specific penicillin-binding protein 2B. To our knowledge, this is the first indication of local differences in the chemical composition of PG in Gram-positive bacteria.
Collapse
Affiliation(s)
- Danae Morales Angeles
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, The Netherlands
| | - Yun Liu
- Stratingh Institute for Chemistry, University of Groningen, The Netherlands
| | - Alwin M Hartman
- Stratingh Institute for Chemistry, University of Groningen, The Netherlands
| | - Marina Borisova
- Department of Biology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Anabela de Sousa Borges
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, The Netherlands
| | - Niels de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, The Netherlands
| | - Katrin Beilharz
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, The Netherlands
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, The Netherlands.,Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Christoph Mayer
- Department of Biology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Anna K H Hirsch
- Stratingh Institute for Chemistry, University of Groningen, The Netherlands
| | - Dirk-Jan Scheffers
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, The Netherlands
| |
Collapse
|
41
|
Bandyopadhyay A, Cambray S, Gao J. Fast Diazaborine Formation of Semicarbazide Enables Facile Labeling of Bacterial Pathogens. J Am Chem Soc 2017; 139:871-878. [PMID: 27992180 PMCID: PMC6191850 DOI: 10.1021/jacs.6b11115] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bioorthogonal conjugation chemistry has enabled the development of tools for the interrogation of complex biological systems. Although a number of bioorthogonal reactions have been documented in literature, they are less ideal for one or several reasons including slow kinetics, low stability of the conjugated product, requirement of toxic catalysts, and side reactions with unintended biomolecules. Herein we report a fast (>103 M-1 s-1) and bioorthogonal conjugation reaction that joins semicarbazide to an aryl ketone or aldehyde with an ortho-boronic acid substituent. The boronic acid moiety greatly accelerates the initial formation of a semicarbazone conjugate, which rearranges into a stable diazaborine. The diazaborine formation can be performed in blood serum or cell lysates with minimal interference from biomolecules. We further demonstrate that application of this conjugation chemistry enables facile labeling of bacteria. A synthetic amino acid D-AB3, which presents a 2-acetylphenylboronic acid moiety as its side chain, was found to incorporate into several bacterial species through cell wall remodeling, with particularly high efficiency for Escherichia coli. Subsequent D-AB3 conjugation to a fluorophore-labeled semicarbazide allows robust detection of this bacterial pathogen in blood serum.
Collapse
Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
| | - Samantha Cambray
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
| | - Jianmin Gao
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02461
| |
Collapse
|
42
|
Fura JM, Pidgeon SE, Birabaharan M, Pires MM. Dipeptide-Based Metabolic Labeling of Bacterial Cells for Endogenous Antibody Recruitment. ACS Infect Dis 2016; 2:302-309. [PMID: 27294199 PMCID: PMC4898660 DOI: 10.1021/acsinfecdis.6b00007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 02/06/2023]
Abstract
![]()
The number of antibiotic-resistant
bacterial infections has increased
dramatically over the past decade. To combat these pathogens, novel
antimicrobial strategies must be explored and developed. We previously
reported a strategy based on hapten-modified cell wall analogues to
induce recruitment of endogenous antibodies to bacterial cell surfaces.
Cell surface remodeling using unnatural single d-amino acid
cell wall analogues led to modification at the C-terminus of the peptidoglycan
stem peptide. During peptidoglycan processing, installed hapten-displaying
amino acids can be subsequently removed by cell wall enzymes. Herein,
we disclose a two-step dipeptide peptidoglycan remodeling strategy
aimed at introducing haptens at an alternative site within the stem
peptide to improve retention and diminish removal by cell wall enzymes.
Through this redesigned strategy, we determined size constraints of
peptidoglycan remodeling and applied these constraints to attain hapten–linker
conjugates that produced high levels of antibody recruitment to bacterial
cell surfaces.
Collapse
Affiliation(s)
- Jonathan M. Fura
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sean E. Pidgeon
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Morgan Birabaharan
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|