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Byeon CH, Hansen KH, DePas W, Akbey Ü. High-resolution 2D solid-state NMR provides insights into nontuberculous mycobacteria. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 134:101970. [PMID: 39312837 DOI: 10.1016/j.ssnmr.2024.101970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 09/05/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024]
Abstract
We present a high-resolution magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize nontuberculous mycobacteria (NTM). We studied two different NTM strains, Mycobacterium smegmatis, a model, non-pathogenic strain, and Mycobacterium abscessus, an emerging and important human pathogen. Hydrated NTM samples were studied at natural abundance without isotope-labelling, as whole-cells versus cell envelope isolates, and native versus fixed sample preparations. We utilized 1D13C and 2D 1H-13C ssNMR spectra and peak deconvolution to identify NTM cell-wall chemical sites. More than ∼100 distinct 13C signals were identified in the ssNMR spectra. We provide tentative assignments for ∼30 polysaccharides by using well resolved 1H/13C chemical shifts from the 2D INEPT-based 1H-13C ssNMR spectrum. The signals originating from both the flexible and rigid fractions of the whole-cell bacteria samples were selectively analyzed by utilizing either CP or INEPT based 13C ssNMR spectra. CP buildup curves provide insights into the dynamical similarity of the cell-wall components for NTM strains. Signals from peptidoglycan, arabinogalactan and mycolic acid were identified. The majority of the 13C signals were not affected by fixation of the whole cell samples. The isolated cell envelope NMR spectrum overlap with the whole-cell spectrum to a large extent, where the latter has more signals. As an orthogonal way of characterizing these bacteria, electron microscopy (EM) was used to provide spatial information. ssNMR and EM data suggest that the M. abscessus cell-wall is composed of a smaller peptidoglycan layer which is more flexible compared to M. smegmatis, which may be related to its higher pathogenicity. Here in this work, we used high-resolution 2D ssNMR first time to characterize NTM strains and identify chemical sites. These results will aid the development of structure-based approaches to combat NTM infections.
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Affiliation(s)
| | | | - William DePas
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15261, United States
| | - Ümit Akbey
- Department of Structural Biology, United States.
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2
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Byeon CH, Kinney T, Saricayir H, Srinivasa S, Wells MK, Kim W, Akbey Ü. Tapping into the native Pseudomonas bacterial biofilm structure by high-resolution multidimensional solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 357:107587. [PMID: 37984030 PMCID: PMC10913148 DOI: 10.1016/j.jmr.2023.107587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
We present a multidimensional magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize native Pseudomonas fluorescens colony biofilms at natural abundance without isotope-labelling. By using a high-resolution INEPT-based 2D 1H-13C ssNMR spectrum and thorough peak deconvolution at the 1D ssNMR spectra, approximately 80/134 (in 1D/2D) distinct biofilm chemical sites were identified. We compared CP and INEPT 13C ssNMR spectra to differentiate signals originating from the mobile and rigid fractions of the biofilm, and qualitatively determined dynamical changes by comparing CP buildup behaviors. Protein and polysaccharide signals were differentiated and identified by utilizing FapC protein signals as a template, a biofilm forming functional amyloid from Pseudomonas. We identified several biofilm polysaccharide species such as glucose, mannan, galactose, heptose, rhamnan, fucose and N-acylated mannuronic acid by using 1H and 13C chemical shifts obtained from the 2D spectrum. To our knowledge, this study marks the first high-resolution multidimensional ssNMR characterization of a native bacterial biofilm. Our experimental pipeline can be readily applied to other in vitro biofilm model systems and natural biofilms and holds the promise of making a substantial impact on biofilm research, fostering new ideas and breakthroughs to aid in the development of strategic approaches to combat infections caused by biofilm-forming bacteria.
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Affiliation(s)
- Chang-Hyeock Byeon
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Ted Kinney
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Hakan Saricayir
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Sadhana Srinivasa
- Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Meghan K Wells
- Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Wook Kim
- Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States.
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Byeon CH, Kinney T, Saricayir H, Srinivasa S, Wells MK, Kim W, Akbey Ü. Tapping into the native Pseudomonas Bacterial Biofilm Structure by High-Resolution 1D and 2D MAS solid-state NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560490. [PMID: 37873242 PMCID: PMC10592892 DOI: 10.1101/2023.10.02.560490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
We present a high-resolution 1D and 2D magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize native Pseudomonas fluorescens colony biofilms at natural abundance without isotope-labelling. By using a high-resolution INEPT-based 2D 1 H- 13 C ssNMR spectrum and thorough peak deconvolution approach at the 1D ssNMR spectra, approximately 80/134 (in 1D/2D) distinct biofilm chemical sites were identified. We compared CP and INEPT 13 C ssNMR spectra to different signals originating from the mobile and rigid fractions of the biofilm, and qualitative determined dynamical changes by comparing CP buildup behaviors. Protein and polysaccharide signals were differentiated and identified by utilizing FapC signals as a template, a biofilm forming functional amyloid from Pseudomonas . We also attempted to identify biofilm polysaccharide species by using 1 H/ 13 C chemical shifts obtained from the 2D spectrum. This study marks the first demonstration of high-resolution 2D ssNMR spectroscopy for characterizing native bacterial biofilms and expands the scope of ssNMR in studying biofilms. Our experimental pipeline can be readily applied to other in vitro biofilm model systems and natural biofilms and holds the promise of making a substantial impact on biofilm research, fostering new ideas and breakthroughs to aid in the development of strategic approaches to combat infections caused by biofilm-forming bacteria.
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Toke O. Three Decades of REDOR in Protein Science: A Solid-State NMR Technique for Distance Measurement and Spectral Editing. Int J Mol Sci 2023; 24:13637. [PMID: 37686450 PMCID: PMC10487747 DOI: 10.3390/ijms241713637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Solid-state NMR (ss-NMR) is a powerful tool to investigate noncrystallizable, poorly soluble molecular systems, such as membrane proteins, amyloids, and cell walls, in environments that closely resemble their physical sites of action. Rotational-echo double resonance (REDOR) is an ss-NMR methodology, which by reintroducing heteronuclear dipolar coupling under magic angle spinning conditions provides intramolecular and intermolecular distance restraints at the atomic level. In addition, REDOR can be exploited as a selection tool to filter spectra based on dipolar couplings. Used extensively as a spectroscopic ruler between isolated spins in site-specifically labeled systems and more recently as a building block in multidimensional ss-NMR pulse sequences allowing the simultaneous measurement of multiple distances, REDOR yields atomic-scale information on the structure and interaction of proteins. By extending REDOR to the determination of 1H-X dipolar couplings in recent years, the limit of measurable distances has reached ~15-20 Å, making it an attractive method of choice for the study of complex biomolecular assemblies. Following a methodological introduction including the most recent implementations, examples are discussed to illustrate the versatility of REDOR in the study of biological systems.
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Affiliation(s)
- Orsolya Toke
- Laboratory for NMR Spectroscopy, Structural Research Centre, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
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Rimal B, Chang J, Liu C, Rashid R, Singh M, Kim SJ. The effects of daptomycin on cell wall biosynthesis in Enterococcal faecalis. Sci Rep 2023; 13:12227. [PMID: 37507537 PMCID: PMC10382475 DOI: 10.1038/s41598-023-39486-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
Daptomycin is a cyclic lipodepsipeptide antibiotic reserved for the treatment of serious infections by multidrug-resistant Gram-positive pathogens. Its mode of action is considered to be multifaceted, encompassing the targeting and depolarization of bacterial cell membranes, alongside the inhibition of cell wall biosynthesis. To characterize the daptomycin mode of action, 15N cross-polarization at magic-angle spinning NMR measurements were performed on intact whole cells of Staphylococcus aureus grown in the presence of a sub-inhibitory concentration of daptomycin in a chemically defined media containing L-[ϵ-15N]Lys. Daptomycin-treated cells showed a reduction in the lysyl-ε-amide intensity that was consistent with cell wall thinning. However, the reduced lysyl-ε-amine intensity at 10 ppm indicated that the daptomycin-treated cells did not accumulate in Park's nucleotide, the cytoplasmic peptidoglycan (PG) precursor. Consequently, daptomycin did not inhibit the transglycosylation step of PG biosynthesis. To further elucidate the daptomycin mode of action, the PG composition of daptomycin-susceptible Enterococcus faecalis grown in the presence of daptomycin was analyzed using liquid chromatography-mass spectrometry. Sixty-nine muropeptide ions correspond to PG with varying degrees of modifications including crosslinking, acetylation, alanylation, and 1,6-anhydrous ring formation at MurNAc were quantified. Analysis showed that the cell walls of daptomycin-treated E. faecalis had a significant reduction in PG crosslinking which was accompanied by an increase in lytic transglycosylase activities and a decrease in PG-stem modifications by the carboxypeptidases. The changes in PG composition suggest that daptomycin inhibits cell wall biosynthesis by impeding the incorporation of nascent PG into the cell walls by transpeptidases and maturation by carboxypeptidases. As a result, the newly formed cell walls become highly susceptible to degradation by the autolysins, resulting in thinning of the cell wall.
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Affiliation(s)
- Binayak Rimal
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - James Chang
- Department of Chemistry One Bear Place #97046, Baylor University, Waco, TX, 76798, USA
| | - Chengyin Liu
- Department of Chemistry, Howard University, Washington, DC, 20059, USA
| | - Raiyan Rashid
- Department of Chemistry, Howard University, Washington, DC, 20059, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO, 63110, USA
| | - Sung Joon Kim
- Department of Chemistry, Howard University, Washington, DC, 20059, USA.
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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7
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Espinosa J, Lin TY, Estrella Y, Kim B, Molina H, Hang HC. Enterococcus NlpC/p60 Peptidoglycan Hydrolase SagA Localizes to Sites of Cell Division and Requires Only a Catalytic Dyad for Protease Activity. Biochemistry 2020; 59:4470-4480. [PMID: 33136372 DOI: 10.1021/acs.biochem.0c00755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptidoglycan is a vital component of the bacterial cell wall, and its dynamic remodeling by NlpC/p60 hydrolases is crucial for proper cell division and survival. Beyond these essential functions, we previously discovered that Enterococcus species express and secrete the NlpC/p60 hydrolase-secreted antigen A (SagA), whose catalytic activity can modulate host immune responses in animal models. However, the localization and peptidoglycan hydrolase activity of SagA in Enterococcus was still unclear. In this study, we show that SagA contributes to a triseptal structure in dividing cells of enterococci and localizes to sites of cell division through its N-terminal coiled-coil domain. Using molecular modeling and site-directed mutagenesis, we identify amino acid residues within the SagA-NlpC/p60 domain that are crucial for catalytic activity and potential substrate binding. Notably, these studies revealed that SagA may function via a catalytic Cys-His dyad instead of the predicted Cys-His-His triad, which is conserved in SagA orthologs from other Enterococcus species. Our results provide key additional insight into peptidoglycan remodeling in Enterococcus by SagA NlpC/p60 hydrolases.
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Affiliation(s)
- Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Ti-Yu Lin
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Yadyvic Estrella
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Byungchul Kim
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States.,Departments of Immunology & Microbiology and Chemistry, Scripps Research, La Jolla, California 92037, United States
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8
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Apostolos AJ, Pidgeon SE, Pires MM. Remodeling of Cross-bridges Controls Peptidoglycan Cross-linking Levels in Bacterial Cell Walls. ACS Chem Biol 2020; 15:1261-1267. [PMID: 32167281 DOI: 10.1021/acschembio.0c00002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cell walls are barriers found in almost all known bacterial cells. These structures establish a controlled interface between the external environment and vital cellular components. A primary component of cell wall is a highly cross-linked matrix called peptidoglycan (PG). PG cross-linking, carried out by transglycosylases and transpeptidases, is necessary for proper cell wall assembly. Transpeptidases, targets of β-lactam antibiotics, stitch together two neighboring PG stem peptides (acyl-donor and acyl-acceptor strands). We recently described a novel class of cellular PG probes that were processed exclusively as acyl-donor strands. Herein, we have accessed the other half of the transpeptidase reaction by developing probes that are processed exclusively as acyl-acceptor strands. The critical nature of the cross-bridge on the PG peptide was demonstrated in live bacterial cells, and surprising promiscuity in cross-bridge primary sequence was found in various bacterial species. Additionally, acyl-acceptor probes provided insight into how chemical remodeling of the PG cross-bridge (e.g., amidation) can modulate cross-linking levels, thus establishing a physiological role of PG structural variations. Together, the acyl-donor and -acceptor probes will provide a versatile platform to interrogate PG cross-linking in physiologically relevant settings.
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Affiliation(s)
- Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlotesville, Virginia 22904, United States
| | - Sean E. Pidgeon
- Department of Chemistry, University of Virginia, Charlotesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlotesville, Virginia 22904, United States
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9
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Porfírio S, Carlson RW, Azadi P. Elucidating Peptidoglycan Structure: An Analytical Toolset. Trends Microbiol 2019; 27:607-622. [DOI: 10.1016/j.tim.2019.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 01/04/2023]
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10
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Kim B, Wang YC, Hespen CW, Espinosa J, Salje J, Rangan KJ, Oren DA, Kang JY, Pedicord VA, Hang HC. Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis. eLife 2019; 8:e45343. [PMID: 30969170 PMCID: PMC6483599 DOI: 10.7554/elife.45343] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
We discovered that Enterococcus faecium (E. faecium), a ubiquitous commensal bacterium, and its secreted peptidoglycan hydrolase (SagA) were sufficient to enhance intestinal barrier function and pathogen tolerance, but the precise biochemical mechanism was unknown. Here we show E. faecium has unique peptidoglycan composition and remodeling activity through SagA, which generates smaller muropeptides that more effectively activates nucleotide-binding oligomerization domain-containing protein 2 (NOD2) in mammalian cells. Our structural and biochemical studies show that SagA is a NlpC/p60-endopeptidase that preferentially hydrolyzes crosslinked Lys-type peptidoglycan fragments. SagA secretion and NlpC/p60-endopeptidase activity was required for enhancing probiotic bacteria activity against Clostridium difficile pathogenesis in vivo. Our results demonstrate that the peptidoglycan composition and hydrolase activity of specific microbiota species can activate host immune pathways and enhance tolerance to pathogens.
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Affiliation(s)
- Byungchul Kim
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Yen-Chih Wang
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Charles W Hespen
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Jeanne Salje
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Kavita J Rangan
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Deena A Oren
- Structural Biology Resource CenterThe Rockefeller UniversityNew YorkUnited States
| | - Jin Young Kang
- Laboratory of Molecular BiophysicsThe Rockefeller UniversityNew YorkUnited States
| | - Virginia A Pedicord
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUnited Kingdom
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
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11
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Design, synthesis and biological activity of novel demethylvancomycin dimers against vancomycin-resistant enterococcus faecalis. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.04.091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Bowden S, Joseph C, Tang S, Cannon J, Francis E, Zhou M, Baker JR, Choi SK. Oritavancin Retains a High Affinity for a Vancomycin-Resistant Cell-Wall Precursor via Its Bivalent Motifs of Interaction. Biochemistry 2018; 57:2723-2732. [PMID: 29651842 DOI: 10.1021/acs.biochem.8b00187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite its potent antibacterial activities against drug-resistant Gram-positive pathogens, oritavancin remains partially understood with respect to its primary mode of hydrogen bond interaction with a cell-wall peptide regarding the role of its lipophilic 4'-chlorobiphenyl moiety. Here we report a surface plasmon resonance (SPR) study performed in two cell-wall model surfaces, each prepared by immobilization with a vancomycin-susceptible Lys-d-Ala-d-Ala or vancomycin-resistant Lys-d-Ala-d-Lac peptide. Analysis of binding kinetics performed on the peptide surface showed that oritavancin bound ∼100-1000-fold more tightly than vancomycin on each model surface. Ligand competition experiments conducted by SPR and fluorescence spectroscopy provided evidence that such affinity enhancement can be attributed to its 4'-chlorobiphenyl moiety, possibly through a hydrophobic interaction that led to a gain of free energy with a contribution from enthalpy as suggested by a variable-temperature SPR experiment. On the basis of these findings, we propose a model for the bivalent motifs of interaction of oritavancin with cell-wall peptides, by which the drug molecule can retain a strong interaction even with the vancomycin-resistant peptide. In summary, this study advances our understanding of oritavancin and offers new insight into the significance of bivalent motifs in the design of glycopeptide antibiotics.
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13
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Chang JD, Wallace AG, Foster EE, Kim SJ. Peptidoglycan Compositional Analysis of Enterococcus faecalis Biofilm by Stable Isotope Labeling by Amino Acids in a Bacterial Culture. Biochemistry 2018; 57:1274-1283. [PMID: 29368511 DOI: 10.1021/acs.biochem.7b01207] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptidoglycan (PG) is a major component of the cell wall in Enterococcus faecalis. Accurate analysis of PG composition provides crucial insights into the bacterium's cellular functions and responses to external stimuli, but this analysis remains challenging because of various chemical modifications to PG-repeat subunits. We characterized changes to the PG composition of E. faecalis grown as planktonic bacteria and biofilm by developing "stable isotope labeling by amino acids in bacterial culture" (SILAB), optimized for bacterial cultures with incomplete amino acid labeling. This comparative analysis by mass spectrometry was performed by labeling E. faecalis in biofilm with heavy Lys (l-[13C6,2D9,15N2]Lys) and planktonic bacteria with natural abundance l-Lys, then mixing equal amounts of bacteria from each condition, and performing cell wall isolation and mutanolysin digestion necessary for liquid chromatography and mass spectrometry. An analytical method was developed to determine muropeptide abundances using correction factors to compensate for incomplete heavy Lys isotopic enrichment (98.33 ± 0.05%) and incorporation (83.23 ± 1.16%). Forty-seven pairs of PG fragment ions from isolated cell walls of planktonic and biofilm samples were selected for SILAB analysis. We found that the PG in biofilm showed an increased level of PG cross-linking, an increased level of N-deacetylation of GlcNAc, a decreased level of O-acetylation of MurNAc, and an increased number of stem modifications by d,d- and l,d-carboxypeptidases.
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Affiliation(s)
- James D Chang
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Ashley G Wallace
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Erin E Foster
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
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14
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Yang H, Singh M, Kim SJ, Schaefer J. Characterization of the tertiary structure of the peptidoglycan of Enterococcus faecalis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2017; 1859:2171-2180. [PMID: 28784459 PMCID: PMC5610627 DOI: 10.1016/j.bbamem.2017.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/29/2022]
Abstract
Solid-state NMR spectra of whole cells and isolated cell walls of Enterococcus faecalis grown in media containing combinations of 13C and 15N specific labels in d- and l-alanine and l-lysine (in the presence of an alanine racemase inhibitor alaphosphin) have been used to determine the composition and architecture of the cell-wall peptidoglycan. The compositional variables include the concentrations of (i) peptidoglycan stems without bridges, (ii) d-alanylated wall teichoic acid, (iii) cross-links, and (iv) uncross-linked tripeptide and tetra/pentapeptide stems. Connectivities of l-alanyl carbonyl‑carbon bridge labels to d-[3-13C]alanyl and l-[ε-15N]lysyl stem labels prove that the peptidoglycan of E. faecalis has the same hybrid short-bridge architecture (with a mix of parallel and perpendicular stems) as the FemA mutant of Staphylococcus aureus, in which the cross-linked stems are perpendicular to one another and the cross-linking is close to the ideal 50% value. This is the first determination of the cell-wall chemical and geometrical architecture of whole cells of E. faecalis, a major source of nosocomial infections worldwide.
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Affiliation(s)
- Hao Yang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA.
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15
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Chang JD, Foster EE, Yang H, Kim SJ. Quantification of the d-Ala-d-Lac-Terminated Peptidoglycan Structure in Vancomycin-Resistant Enterococcus faecalis Using a Combined Solid-State Nuclear Magnetic Resonance and Mass Spectrometry Analysis. Biochemistry 2017; 56:612-622. [PMID: 28040891 PMCID: PMC6906607 DOI: 10.1021/acs.biochem.6b00774] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Induction of vancomycin resistance in vancomycin-resistant enterococci (VRE) involves replacement of the d-Ala-d-Ala terminus of peptidoglycan (PG) stems with d-Ala-d-Lac, dramatically reducing the binding affinity of vancomycin for lipid II. Effects from vancomycin resistance induction in Enterococcus faecalis (ATCC 51299) were characterized using a combined solid-state nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS) analysis. Solid-state NMR directly measured the total amounts of d-Lac and l,d-Ala metabolized from [2-13C]pyruvate, accumulated Park's nucleotide, and changes to the PG bridge-linking density during the early exponential growth phase (OD660 = 0.4) in intact whole cells of VRE. A high level of accumulation of depsipeptide-substituted Park's nucleotide consistent with the inhibition of the transglycosylation step of PG biosynthesis during the initial phase of vancomycin resistance was observed, while no changes to the PG bridge-linking density following the induction of vancomycin resistance were detected. This indicated that the attachment of the PG bridge to lipid II by the peptidyl transferases was not inhibited by the d-Ala-d-Lac-substituted PG stem structure in VRE. Compositions of mutanolysin-digested isolated cell walls of VRE grown with and without vancomycin resistance induction were determined by LC-MS. Muropeptides with PG stems terminating in d-Ala-d-Lac were found only in VRE grown in the presence of vancomycin. Percentages of muropeptides with a pentapeptide stem terminating in d-Ala-d-Lac for VRE grown in the presence of vancomycin were 26% for the midexponential phase (OD660 = 0.6) and 57% for the stationary growth phase (OD660 = 1.0). These high percentages indicate that d-Ala-d-Lac-substituted lipid II was efficiently utilized for PG biosynthesis in VRE.
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Affiliation(s)
- James D. Chang
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Erin E. Foster
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Hao Yang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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16
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Romaniuk JAH, Cegelski L. Bacterial cell wall composition and the influence of antibiotics by cell-wall and whole-cell NMR. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0024. [PMID: 26370936 DOI: 10.1098/rstb.2015.0024] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The ability to characterize bacterial cell-wall composition and structure is crucial to understanding the function of the bacterial cell wall, determining drug modes of action and developing new-generation therapeutics. Solid-state NMR has emerged as a powerful tool to quantify chemical composition and to map cell-wall architecture in bacteria and plants, even in the context of unperturbed intact whole cells. In this review, we discuss solid-state NMR approaches to define peptidoglycan composition and to characterize the modes of action of old and new antibiotics, focusing on examples in Staphylococcus aureus. We provide perspectives regarding the selected NMR strategies as we describe the exciting and still-developing cell-wall and whole-cell NMR toolkit. We also discuss specific discoveries regarding the modes of action of vancomycin analogues, including oritavancin, and briefly address the reconsideration of the killing action of β-lactam antibiotics. In such chemical genetics approaches, there is still much to be learned from perturbations enacted by cell-wall assembly inhibitors, and solid-state NMR approaches are poised to address questions of cell-wall composition and assembly in S. aureus and other organisms.
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Affiliation(s)
- Joseph A H Romaniuk
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, CA 94305, USA
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, CA 94305, USA
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17
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Yao CH, Fowle-Grider R, Mahieu NG, Liu GY, Chen YJ, Wang R, Singh M, Potter GS, Gross RW, Schaefer J, Johnson SL, Patti GJ. Exogenous Fatty Acids Are the Preferred Source of Membrane Lipids in Proliferating Fibroblasts. Cell Chem Biol 2016; 23:483-93. [PMID: 27049668 PMCID: PMC5510604 DOI: 10.1016/j.chembiol.2016.03.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/11/2016] [Accepted: 03/11/2016] [Indexed: 12/11/2022]
Abstract
Cellular proliferation requires the formation of new membranes. It is often assumed that the lipids needed for these membranes are synthesized mostly de novo. Here, we show that proliferating fibroblasts prefer to take up palmitate from the extracellular environment over synthesizing it de novo. Relative to quiescent fibroblasts, proliferating fibroblasts increase their uptake of palmitate, decrease fatty acid degradation, and instead direct more palmitate to membrane lipids. When exogenous palmitate is provided in the culture media at physiological concentrations, de novo synthesis accounts for only a minor fraction of intracellular palmitate in proliferating fibroblasts as well as proliferating HeLa and H460 cells. Blocking fatty acid uptake decreased the proliferation rate of fibroblasts, HeLa, and H460 cells, while supplementing media with exogenous palmitate resulted in decreased glucose uptake and rendered cells less sensitive to glycolytic inhibition. Our results suggest that cells scavenging exogenous lipids may be less susceptible to drugs targeting glycolysis and de novo lipid synthesis.
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Affiliation(s)
- Cong-Hui Yao
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA; Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Ronald Fowle-Grider
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA; Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Nathanial G Mahieu
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA; Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Gao-Yuan Liu
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA; Division of Bioorganic and Molecular Pharmacology, Department of Internal Medicine, Washington University, St. Louis, MO 63110, USA
| | - Ying-Jr Chen
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA; Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Rencheng Wang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA; Department of Medicine, Washington University, St. Louis, MO 63110, USA; Department of Genetics, Washington University, St. Louis, MO 63110, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Gregory S Potter
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Richard W Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA; Division of Bioorganic and Molecular Pharmacology, Department of Internal Medicine, Washington University, St. Louis, MO 63110, USA
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Stephen L Johnson
- Department of Genetics, Washington University, St. Louis, MO 63110, USA
| | - Gary J Patti
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA; Department of Medicine, Washington University, St. Louis, MO 63110, USA.
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18
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Kim SJ, Chang J, Singh M. Peptidoglycan architecture of Gram-positive bacteria by solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1848:350-62. [PMID: 24915020 PMCID: PMC4258515 DOI: 10.1016/j.bbamem.2014.05.031] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/30/2014] [Accepted: 05/31/2014] [Indexed: 10/25/2022]
Abstract
Peptidoglycan is an essential component of cell wall in Gram-positive bacteria with unknown architecture. In this review, we summarize solid-state NMR approaches to address some of the unknowns in the Gram-positive bacteria peptidoglycan architecture: 1) peptidoglycan backbone conformation, 2) PG-lattice structure, 3) variations in the peptidoglycan architecture and composition, 4) the effects of peptidoglycan bridge-length on the peptidoglycan architecture in Fem mutants, 5) the orientation of glycan strands with respect to the membrane, and 6) the relationship between the peptidoglycan structure and the glycopeptide antibiotic mode of action. Solid-state NMR analyses of Staphylococcus aureus cell wall show that peptidoglycan chains are surprisingly ordered and densely packed. The peptidoglycan disaccharide backbone adopts 4-fold screw helical symmetry with the disaccharide unit periodicity of 40Å. Peptidoglycan lattice in the S. aureus cell wall is formed by cross-linked PG stems that have parallel orientations. The structural characterization of Fem-mutants of S. aureus with varying lengths of bridge structures suggests that the PG-bridge length is an important determining factor for the PG architecture.
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Affiliation(s)
- Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA.
| | - James Chang
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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19
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Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre JP. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. J Am Chem Soc 2014; 136:17852-60. [PMID: 25429710 PMCID: PMC4544747 DOI: 10.1021/ja5105987] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains-the catalytic domain as well as the proposed peptidoglycan recognition domain-are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein-peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.
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Affiliation(s)
- Paul Schanda
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Sébastien Triboulet
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Univ. Pierre et Marie Curie-Paris 6, UMR S 1138, 75006 Paris (France)
- Université Paris Descartes, Sorbonne, UMR S 1138, 75006 Paris (France); INSERM, U1138, 75006 Paris (France)
| | - Cédric Laguri
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Catherine M. Bougault
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Morgane Callon
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Univ. Pierre et Marie Curie-Paris 6, UMR S 1138, 75006 Paris (France)
- Université Paris Descartes, Sorbonne, UMR S 1138, 75006 Paris (France); INSERM, U1138, 75006 Paris (France)
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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20
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Kim SJ, Singh M, Sharif S, Schaefer J. Cross-link formation and peptidoglycan lattice assembly in the FemA mutant of Staphylococcus aureus. Biochemistry 2014; 53:1420-7. [PMID: 24517508 PMCID: PMC3985804 DOI: 10.1021/bi4016742] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/09/2014] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus FemA mutant grown in the presence of an alanine-racemase inhibitor was labeled with d-[1-(13)C]alanine, l-[3-(13)C]alanine, [2-(13)C]glycine, and l-[5-(19)F]lysine to characterize some details of the peptidoglycan tertiary structure. Rotational-echo double-resonance (REDOR) NMR of isolated cell walls was used to measure internuclear distances between (13)C-labeled alanines and (19)F-labeled lysine incorporated in the peptidoglycan. The alanyl (13)C labels were preselected for REDOR measurement by their proximity to the glycine label using (13)C-(13)C spin diffusion. The observed (13)C-(13)C and (13)C-(19)F distances are consistent with a tightly packed, hybrid architecture containing both parallel and perpendicular stems in a repeating structural motif within the peptidoglycan.
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Affiliation(s)
- Sung Joon Kim
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Manmilan Singh
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
| | - Shasad Sharif
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
| | - Jacob Schaefer
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
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21
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Škedelj V, Perdih A, Brvar M, Kroflič A, Dubbée V, Savage V, O'Neill AJ, Solmajer T, Bešter-Rogač M, Blanot D, Hugonnet JE, Magnet S, Arthur M, Mainardi JL, Stojan J, Zega A. Discovery of the first inhibitors of bacterial enzyme d-aspartate ligase from Enterococcus faecium (Aslfm). Eur J Med Chem 2013; 67:208-20. [DOI: 10.1016/j.ejmech.2013.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 06/01/2013] [Accepted: 06/02/2013] [Indexed: 01/24/2023]
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22
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Gullion T, Yu TY, Singh M, Patti GJ, Potter GS, Schaefer J. Oxygen-17 appears only in protein in water-stressed soybean leaves labeled by (17)O2. J Am Chem Soc 2010; 132:10802-7. [PMID: 20681713 DOI: 10.1021/ja102264w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used a rotational-echo adiabatic-passage double-resonance (13)C{(17)O} solid-state NMR experiment to prove that the glycine produced in the oxygenase reaction of ribulose bisphosphate carboxylase-oxygenase is incorporated exclusively into protein (or protein precursors) of intact, water-stressed soybean leaves exposed to (13)CO(2) and (17)O(2). The water stress increased stomatal resistance and decreased gas exchange so that the Calvin cycle in the leaf chloroplasts was no more than 35% (13)C isotopically enriched. Labeled O(2) levels were sufficient, however, to increase the (17)O isotopic concentration of oxygenase products 20-fold over the natural-abundance level of 0.04%. The observed direct incorporation of glycine into protein shows that water stress suppresses photorespiration in soybean leaves.
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Affiliation(s)
- Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, USA
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23
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Reid CW, Fulton KM, Twine SM. Never take candy from a stranger: the role of the bacterial glycome in host–pathogen interactions. Future Microbiol 2010; 5:267-88. [DOI: 10.2217/fmb.09.103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
With the comprehensive study and complete sequencing of the Haemophilus influenzae genome in 1995 came the term ‘genomics’ and the beginning of the ‘omics’ era. Since this time, several analogous fields, such as transcriptomics and proteomics, have emerged. While growth and advancement in these fields have increased understanding of microbial virulence, the study of bacterial glycomes is still in its infancy and little is known concerning their role in host–pathogen interactions. Bacterial glycomics is challenging owing to the diversity of glyco-conjugate molecules, vast array of unusual sugars and limited number of analytical approaches available. However, recent advances in glycomics technologies offer the potential for exploration and characterization of both the structures and functions of components of bacterial glycomes in a systematic manner. Such characterization is a prerequisite for discerning the role of bacterial glycans in the interaction between host defences and bacterial virulence factors.
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Affiliation(s)
- Christopher W Reid
- National Research Council – Institute for Biological Science, Ottawa, Ontario, K1A 0R6, Canada
| | - Kelly M Fulton
- National Research Council – Institute for Biological Science, Ottawa, Ontario, K1A 0R6, Canada
| | - Susan M Twine
- National Research Council – Institute for Biological Science, Ottawa, Ontario, K1A 0R6, Canada
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24
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Architecture of peptidoglycan: more data and more models. Trends Microbiol 2010; 18:59-66. [DOI: 10.1016/j.tim.2009.12.004] [Citation(s) in RCA: 244] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 10/28/2009] [Accepted: 12/08/2009] [Indexed: 01/09/2023]
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25
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Garimella R, Halye JL, Harrison W, Klebba PE, Rice CV. Conformation of the phosphate D-alanine zwitterion in bacterial teichoic acid from nuclear magnetic resonance spectroscopy. Biochemistry 2009; 48:9242-9. [PMID: 19746945 PMCID: PMC4196936 DOI: 10.1021/bi900503k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformation of d-alanine (d-Ala) groups of bacterial teichoic acid is a central, yet untested, paradigm of microbiology. The d-Ala binds via the C-terminus, thereby allowing the amine to exist as a free cationic NH(3)(+) group with the ability to form a contact ion pair with the nearby anionic phosphate group. This conformation hinders metal chelation by the phosphate because the zwitterion pair is charge neutral. To the contrary, the repulsion of cationic antimicrobial peptides (CAMPs) is attributed to the presence of the d-Ala cation; thus the ion pair does not form in this model. Solid-state nuclear magnetic resonance (NMR) spectroscopy has been used to measure the distance between amine and phosphate groups within cell wall fragments of Bacillus subtilis. The bacteria were grown on media containing (15)N d-Ala and beta-chloroalanine racemase inhibitor. The rotational-echo double-resonance (REDOR) pulse sequence was used to measure the internuclear dipolar coupling, and the results demonstrate (1) the metal-free amine-to-phosphate distance is 4.4 A and (2) the amine-to-phosphate distance increases to 5.4 A in the presence of Mg(2+) ions. As a result, the zwitterion exists in a nitrogen-oxygen ion pair configuration providing teichoic acid with a positive charge to repel CAMPs. Additionally, the amine of d-Ala does not prevent magnesium chelation in contradiction to the prevailing view of teichoic acids in metal binding. Thus, the NMR-based description of teichoic acid structure resolves the contradictory models, advances the basic understanding of cell wall biochemistry, and provides possible insight into the creation of new antibiotic therapies.
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Affiliation(s)
- Ravindranath Garimella
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| | - Jeffrey L. Halye
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| | - William Harrison
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| | - Phillip E. Klebba
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| | - Charles V. Rice
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
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26
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Patti GJ, Kim SJ, Yu TY, Dietrich E, Tanaka KSE, Parr TR, Far AR, Schaefer J. Vancomycin and oritavancin have different modes of action in Enterococcus faecium. J Mol Biol 2009; 392:1178-91. [PMID: 19576226 DOI: 10.1016/j.jmb.2009.06.064] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 06/20/2009] [Accepted: 06/24/2009] [Indexed: 02/03/2023]
Abstract
The increasing frequency of Enterococcus faecium isolates with multidrug resistance is a serious clinical problem given the severely limited number of therapeutic options available to treat these infections. Oritavancin is a promising new alternative in clinical development that has potent antimicrobial activity against both staphylococcal and enterococcal vancomycin-resistant pathogens. Using solid-state NMR to detect changes in the cell-wall structure and peptidoglycan precursors of whole cells after antibiotic-induced stress, we report that vancomycin and oritavancin have different modes of action in E. faecium. Our results show the accumulation of peptidoglycan precursors after vancomycin treatment, consistent with transglycosylase inhibition, but no measurable difference in cross-linking. In contrast, after oritavancin exposure, we did not observe the accumulation of peptidoglycan precursors. Instead, the number of cross-links is significantly reduced, showing that oritavancin primarily inhibits transpeptidation. We propose that the activity of oritavancin is the result of a secondary binding interaction with the E. faecium peptidoglycan. The hypothesis is supported by results from (13)C{(19)F} rotational-echo double-resonance (REDOR) experiments on whole cells enriched with l-[1-(13)C]lysine and complexed with desleucyl [(19)F]oritavancin. These experiments establish that an oritavancin derivative with a damaged d-Ala-d-Ala binding pocket still binds to E. faecium peptidoglycan. The (13)C{(19)F} REDOR dephasing maximum indicates that the secondary binding site of oritavancin is specific to nascent and template peptidoglycan. We conclude that the inhibition of transpeptidation by oritavancin in E. faecium is the result of the large number of secondary binding sites relative to the number of primary binding sites.
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Affiliation(s)
- Gary J Patti
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130, USA
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27
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Sharif S, Kim SJ, Labischinski H, Schaefer J. Characterization of peptidoglycan in fem-deletion mutants of methicillin-resistant Staphylococcus aureus by solid-state NMR. Biochemistry 2009; 48:3100-8. [PMID: 19309106 PMCID: PMC2785074 DOI: 10.1021/bi801750u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compositional analysis of the peptidoglycan (PG) of a wild-type methicillin-resistant Staphylococcus aureus and its fem-deletion mutants has been performed on whole cells and cell walls using stable-isotope labeling and rotational-echo double-resonance NMR. The labels included [1-(13)C,(15)N]glycine and l-[epsilon-(15)N]lysine (for a direct measure of the number of glycyl residues in the bridging segment), [1-(13)C]glycine and l-[epsilon-(15)N]lysine (concentration of bridge links), and d-[1-(13)C]alanine and [(15)N]glycine (concentrations of cross-links and wall teichoic acids). The bridging segment length changed from 5.0 glycyl residues (wild-type strain) to 2.5 +/- 0.1 (FemB) with modest changes in cross-link and bridge-link concentrations. This accurate in situ measurement for the FemB mutant indicates a heterogeneous PG structure with 25% monoglycyl and 75% triglycyl bridges. When the bridging segment was reduced to a single glycyl residue 1.0 +/- 0.1 (FemA), the level of cross-linking decreased by more than 20%, resulting in a high concentration of open N-terminal glycyl segments.
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Affiliation(s)
- Shasad Sharif
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| | - Sung Joon Kim
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| | - Harald Labischinski
- MerLion Pharmaceuticals GmbH, Robert-Rössle-Straβe 10, 13125 Berlin, Germany
| | - Jacob Schaefer
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
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28
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Patti GJ, Chen J, Gross ML. Method revealing bacterial cell-wall architecture by time-dependent isotope labeling and quantitative liquid chromatography/mass spectrometry. Anal Chem 2009; 81:2437-45. [PMID: 19281243 PMCID: PMC2715431 DOI: 10.1021/ac802587r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular details of the biosynthesis and resulting architecture of the bacterial cell wall remain unclear but are essential to understanding the activity of glycopeptide antibiotics, the recognition of pathogens by hosts, and the processes of bacterial growth and division. Here we report a new strategy to elucidate bacterial cell-wall architecture based on time-dependent isotope labeling of bacterial cells quantified by liquid chromatography/accurate mass measurement mass spectrometry. The results allow us to track the fate of cell-wall precursors (which contain the vancomycin-binding site) in Enterococcus faecium, a leading antibiotic-resistant pathogen. By comparing isotopic enrichments of postinsertionally modified cell-wall precursors, we find that tripeptides and species without aspartic acid/asparagine (Asp/Asn, Asx) bridges are specific to mature cell wall. Additionally, we find that the sequence of cell-wall maturation varies throughout a cell cycle. We suggest that actively dividing E. faecium cells have three zones of unique peptidoglycan processing. Our results reveal new organizational characteristics of the bacterial cell wall that are important to understanding tertiary structure and designing novel drugs for antibiotic-resistant pathogens.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
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Vaidyanathan S, Fletcher JS, Jarvis RM, Henderson A, Lockyer NP, Goodacre R, Vickerman JC. Explanatory multivariate analysis of ToF-SIMS spectra for the discrimination of bacterial isolates. Analyst 2009; 134:2352-60. [DOI: 10.1039/b907570d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Patti GJ, Chen J, Schaefer J, Gross ML. Characterization of structural variations in the peptidoglycan of vancomycin-susceptible Enterococcus faecium: understanding glycopeptide-antibiotic binding sites using mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1467-75. [PMID: 18692403 PMCID: PMC2613859 DOI: 10.1016/j.jasms.2008.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/20/2008] [Accepted: 06/21/2008] [Indexed: 05/23/2023]
Abstract
Enterococcus faecium, an opportunistic pathogen that causes a significant number of hospital-acquired infections each year, presents a serious clinical challenge because an increasing number of infections are resistant to the so-called antibiotic of last resort, vancomycin. Vancomycin and other new glycopeptide derivatives target the bacterial cell wall, thereby perturbing its biosynthesis. To help determine the modes of action of glycopeptide antibiotics, we have developed a bottom-up mass spectrometry approach complemented by solid-state nuclear magnetic resonance (NMR) to elucidate important structural characteristics of vancomycin-susceptible E. faecium peptidoglycan. Using accurate-mass measurements and integrating ion-current chromatographic peaks of digested peptidoglycan, we identified individual muropeptide species and approximated the relative amount of each. Even though the organism investigated is susceptible to vancomycin, only 3% of the digested peptidoglycan has the well-known D-Ala-D-Ala vancomycin-binding site. The data are consistent with a previously proposed template model of cell-wall biosynthesis where D-Ala-D-Ala stems that are not cross-linked are cleaved in mature peptidoglycan. Additionally, our mass-spectrometry approach allowed differentiation and quantification of muropeptide species seen as unresolved chromatographic peaks. Our method provides an estimate of the extent of muropeptides containing O-acetylation, amidation, hydroxylation, and the number of species forming cyclic imides. The varieties of muropeptides on which the modifications are detected suggest that significant processing occurs in mature peptidoglycan where several enzymes are active in editing cell-wall structure.
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Affiliation(s)
- Gary J Patti
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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