1
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Bon CG, Grigg JC, Lee J, Robb CS, Caveney NA, Eltis LD, Strynadka NCJ. Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1. J Struct Biol 2024; 216:108086. [PMID: 38527711 DOI: 10.1016/j.jsb.2024.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024]
Abstract
Staphylococcus aureus, an ESKAPE pathogen, is a major clinical concern due to its pathogenicity and manifold antimicrobial resistance mechanisms. The commonly used β-lactam antibiotics target bacterial penicillin-binding proteins (PBPs) and inhibit crosslinking of peptidoglycan strands that comprise the bacterial cell wall mesh, initiating a cascade of effects leading to bacterial cell death. S. aureus PBP1 is involved in synthesis of the bacterial cell wall during division and its presence is essential for survival of both antibiotic susceptible and resistant S. aureus strains. Here, we present X-ray crystallographic data for S. aureus PBP1 in its apo form as well as acyl-enzyme structures with distinct classes of β-lactam antibiotics representing the penicillins, carbapenems, and cephalosporins, respectively: oxacillin, ertapenem and cephalexin. Our structural data suggest that the PBP1 active site is readily accessible for substrate, with little conformational change in key structural elements required for its covalent acylation of β-lactam inhibitors. Stopped-flow kinetic analysis and gel-based competition assays support the structural observations, with even the weakest performing β-lactams still having comparatively high acylation rates and affinities for PBP1. Our structural and kinetic analysis sheds insight into the ligand-PBP interactions that drive antibiotic efficacy against these historically useful antimicrobial targets and expands on current knowledge for future drug design and treatment of S. aureus infections.
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Affiliation(s)
- Christopher G Bon
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Craig S Robb
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nathanael A Caveney
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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2
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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.
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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
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3
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Ocius KL, Kolli SH, Ahmad SS, Dressler JM, Chordia MD, Jutras BL, Rutkowski MR, Pires MM. Noninvasive Analysis of Peptidoglycan from Living Animals. Bioconjug Chem 2024; 35:489-498. [PMID: 38591251 PMCID: PMC11036361 DOI: 10.1021/acs.bioconjchem.4c00007] [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: 01/09/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activates peptidoglycan sensors in human cells, including the nucleotide-binding oligomerization domain-containing protein 2. When present in the gastrointestinal tract, both the polymeric form (sacculi) and depolymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth. To utilize this growing area of biology toward therapeutic prescriptions, it will be critical to directly analyze a key feature of the host-microbiome interaction from living hosts in a reproducible and noninvasive way. Here we show that metabolically labeled peptidoglycan/sacculi can be readily isolated from fecal samples collected from both mice and humans. Analysis of fecal samples provided a noninvasive route to probe the gut commensal community including the metabolic synchronicity with the host circadian clock. Together, these results pave the way for noninvasive diagnostic tools to interrogate the causal nature of peptidoglycan in host health and disease.
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Affiliation(s)
- Karl L. Ocius
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Sree H. Kolli
- Department
of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Saadman S. Ahmad
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Fralin
Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jules M. Dressler
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Fralin
Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Mahendra D. Chordia
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Brandon L. Jutras
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Fralin
Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center
for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Melanie R. Rutkowski
- Department
of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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4
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Zhang XL, Báti G, Li C, Guo A, Yeo C, Ding H, Pal KB, Xu Y, Qiao Y, Liu XW. GlcNAc-1,6-anhydro-MurNAc Moiety Affords Unusual Glycosyl Acceptor that Terminates Peptidoglycan Elongation. J Am Chem Soc 2024; 146:7400-7407. [PMID: 38456799 DOI: 10.1021/jacs.3c12526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Peptidoglycan (PG), an essential exoskeletal polymer in bacteria, is a well-known antibiotic target. PG polymerization requires the action of bacterial transglycosylases (TGases), which couple the incoming glycosyl acceptor to the donor. Interfering with the TGase activity can interrupt the PG assembly. Existing TGase inhibitors like moenomycin and Lipid II analogues always occupy the TGase active sites; other strategies to interfere with proper PG elongation have not been widely exploited. Inspired by the natural 1,6-anhydro-MurNAc termini that mark the ends of PG strands in bacteria, we hypothesized that the incorporation of an anhydromuramyl-containing glycosyl acceptor by TGase into the growing PG may effectively inhibit PG elongation. To explore this possibility, we synthesized 4-O-(N-acetyl-β-d-glucosaminyl)-1,6-anhydro-N-acetyl-β-d-muramyl-l-Ala-γ-d-Glu-l-Lys-d-Ala-d-Ala, 1, within 15 steps, and demonstrated that this anhydromuropeptide and its analogue lacking the peptide, 1-deAA, were both utilized by bacterial TGase as noncanonical anhydro glycosyl acceptors in vitro. The incorporation of an anhydromuramyl moiety into PG strands by TGases afforded efficient termination of glycan chain extension. Moreover, the preliminary in vitro studies of 1-deAA against Staphylococcus aureus showed that 1-deAA served as a reasonable antimicrobial adjunct of vancomycin. These insights imply the potential application of such anhydromuropeptides as novel classes of PG-terminating inhibitors, pointing toward novel strategies in antibacterial agent development.
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Affiliation(s)
- Xiao-Lin Zhang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Gábor Báti
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Chenyu Li
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Aoxin Guo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Claresta Yeo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Han Ding
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Kumar Bhaskar Pal
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Yuan Xu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Xue-Wei Liu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
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5
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Hillman A, Hyland SN, Wodzanowski KA, Moore DL, Ratna S, Jemas A, Sandles LMD, Chaya T, Ghosh A, Fox JM, Grimes CL. Minimalist Tetrazine N-Acetyl Muramic Acid Probes for Rapid and Efficient Labeling of Commensal and Pathogenic Peptidoglycans in Living Bacterial Culture and During Macrophage Invasion. J Am Chem Soc 2024; 146:6817-6829. [PMID: 38427023 PMCID: PMC10941766 DOI: 10.1021/jacs.3c13644] [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: 12/04/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
N-Acetyl muramic acid (NAM) probes containing alkyne or azide groups are commonly used to investigate aspects of cell wall synthesis because of their small size and ability to incorporate into bacterial peptidoglycan (PG). However, copper-catalyzed alkyne-azide cycloaddition (CuAAC) reactions are not compatible with live cells, and strain-promoted alkyne-azide cycloaddition (SPAAC) reaction rates are modest and, therefore, not as desirable for tracking the temporal alterations of bacterial cell growth, remodeling, and division. Alternatively, the tetrazine-trans-cyclooctene ligation (Tz-TCO), which is the fastest known bioorthogonal reaction and not cytotoxic, allows for rapid live-cell labeling of PG at biologically relevant time scales and concentrations. Previous work to increase reaction kinetics on the PG surface by using tetrazine probes was limited because of low incorporation of the probe. Described here are new approaches to construct a minimalist tetrazine (Tz)-NAM probe utilizing recent advancements in asymmetric tetrazine synthesis. This minimalist Tz-NAM probe was successfully incorporated into pathogenic and commensal bacterial PG where fixed and rapid live-cell, no-wash labeling was successful in both free bacterial cultures and in coculture with human macrophages. Overall, this probe allows for expeditious labeling of bacterial PG, thereby making it an exceptional tool for monitoring PG biosynthesis for the development of new antibiotic screens. The versatility and selectivity of this probe will allow for real-time interrogation of the interactions of bacterial pathogens in a human host and will serve a broader utility for studying glycans in multiple complex biological systems.
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Affiliation(s)
- Ashlyn
S. Hillman
- 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
| | - Kimberly A. Wodzanowski
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - DeVonte L. Moore
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Sushanta Ratna
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Andrew Jemas
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Liam-Michael D. Sandles
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Timothy Chaya
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - Arit Ghosh
- Delaware
Biotechnology Institute, UDEL Flow Cytometry Core, University of Delaware, Newark, Delaware 19716, United States
| | - Joseph M. Fox
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Catherine L. 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
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6
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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.
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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
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7
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Sun L, Yu Q, Peng F, Sun C, Wang D, Pu L, Xiong F, Tian Y, Peng C, Zhou Q. The antibacterial activity of berberine against Cutibacterium acnes: its therapeutic potential in inflammatory acne. Front Microbiol 2024; 14:1276383. [PMID: 38249466 PMCID: PMC10797013 DOI: 10.3389/fmicb.2023.1276383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Cutibacterium acnes (C. acnes) is a major pathogen implicated in the evolution of acne inflammation. Inhibition of C. acnes-induced inflammation is a prospective acne therapy strategy. Berberine (BBR), a safe and effective natural ingredient, has been proven to exhibit powerful antimicrobial and anti-inflammatory properties. However, the antimicrobial effect of BBR against C. acnes and its role in C. acnes-mediated inflammatory acne have not been explored. The objective of this investigation was to assess the antibacterial activity of BBR against C. acnes and its inhibitory effect on the inflammatory response. The results of in vitro experiments showed that BBR exhibited significant inhibition zones against four C. acnes strains, with the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) in the range of 6.25-12.5 μg/mL and 12.5-25 μg/mL, respectively. On the bacterial growth curve, the BBR-treated C. acnes exhibited obvious growth inhibition. Transmission electron microscopy (TEM) images indicated that BBR treatment resulted in significant morphological changes in C. acnes. High-content imaging analysis further confirmed that BBR could effectively inhibit the proliferation of C. acnes. The disruption of cell wall and cell membrane structure by BBR treatment was preliminary confirmed according to the leakage of cellular contents such as potassium (K+), magnesium (Mg2+), and alkaline phosphatase (AKP). Furthermore, we found that BBR could reduce the transcript levels of genes associated with peptidoglycan synthesis (murC, murD, mraY, and murG). Meanwhile, we investigated the modulatory ability of BBR on C. acnes-induced skin inflammation in mice. The results showed that BBR effectively reduced the number of C. acnes colonized in mice's ears, thereby alleviating ear swelling and erythema and significantly decreasing ear thickness and weight. In addition, BBR significantly decreased the levels of pro-inflammatory cytokines IL-6, IL-1β, and TNF-α in auricular tissues. These results suggest that BBR has the potential to treat inflammatory acne induced by C. acnes.
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Affiliation(s)
- Luyao Sun
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qian Yu
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fu Peng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Chen Sun
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Daibo Wang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lin Pu
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fang Xiong
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuncai Tian
- Shanghai Zhizhenzhichen Technologies Co., Ltd., Shanghai, China
| | - Cheng Peng
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qinmei Zhou
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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8
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Sun Z, Lin H, Hu L, Neetu N, Sankaran B, Wang J, Prasad BVV, Palzkill T. Klebsiella pneumoniae carbapenemase variant 44 acquires ceftazidime-avibactam resistance by altering the conformation of active-site loops. J Biol Chem 2024; 300:105493. [PMID: 38000656 PMCID: PMC10716778 DOI: 10.1016/j.jbc.2023.105493] [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: 08/18/2023] [Revised: 11/14/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
Klebsiella pneumoniae carbapenemase 2 (KPC-2) is an important source of drug resistance as it can hydrolyze and inactivate virtually all β-lactam antibiotics. KPC-2 is potently inhibited by avibactam via formation of a reversible carbamyl linkage of the inhibitor with the catalytic serine of the enzyme. However, the use of avibactam in combination with ceftazidime (CAZ-AVI) has led to the emergence of CAZ-AVI-resistant variants of KPC-2 in clinical settings. One such variant, KPC-44, bears a 15 amino acid duplication in one of the active-site loops (270-loop). Here, we show that the KPC-44 variant exhibits higher catalytic efficiency in hydrolyzing ceftazidime, lower efficiency toward imipenem and meropenem, and a similar efficiency in hydrolyzing ampicillin, than the WT KPC-2 enzyme. In addition, the KPC-44 variant enzyme exhibits 12-fold lower AVI carbamylation efficiency than the KPC-2 enzyme. An X-ray crystal structure of KPC-44 showed that the 15 amino acid duplication results in an extended and partially disordered 270-loop and also changes the conformation of the adjacent 240-loop, which in turn has altered interactions with the active-site omega loop. Furthermore, a structure of KPC-44 with avibactam revealed that formation of the covalent complex results in further disorder in the 270-loop, suggesting that rearrangement of the 270-loop of KPC-44 facilitates AVI carbamylation. These results suggest that the duplication of 15 amino acids in the KPC-44 enzyme leads to resistance to CAZ-AVI by modulating the stability and conformation of the 270-, 240-, and omega-loops.
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Affiliation(s)
- Zhizeng Sun
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Hanfeng Lin
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Neetu Neetu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jin Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA.
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9
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Li X, Ma Z, Tang Q, Gui Z, Zhang B, Sun G, Li J, Li J, Li M, Li X, Ma H, Ye X. 8-octyl berberine combats Staphylococcus aureus by preventing peptidoglycan synthesis. Eur J Pharm Sci 2023; 191:106602. [PMID: 37806408 DOI: 10.1016/j.ejps.2023.106602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
Staphylococcus aureus is an important pathogenic bacterium responsible for various organ infections. The serious side effects and the development of antibiotic resistance have rendered the antibiotic therapy against S. aureus increasingly challenging, emphasizing the pressing need for the exploration of novel therapeutic agents. Our research has uncovered the promising antimicrobial properties of 8-octyl berberine (OBBR), a novel compound derived from berberine (BBR), against S. aureus. OBBR exhibited a minimum inhibitory concentration (MIC) of 1.0 μg/mL, which closely approximated that of levofloxacin. Intriguingly, a multipassage resistance assay demonstrated that the MIC of OBBR against S. aureus remained relatively stable, while levofloxacin exhibited a 4-fold increase over 20 days, suggesting that OBBR was less prone to inducing resistance. Mechanistically, our investigation, employing Zeta potential measurements, flow cytometry, scanning electron microscopy, and transmission electron microscopy, unveiled that OBBR induced morphological alterations in the bacteria. Furthermore, it disrupted the bacterial cell wall and membrane by altering membrane potential and compromising membrane integrity. These actions culminated in bacterial disintegration and apoptosis. Transcriptomic analysis shed light on significant downregulation of gene ontology terms, predominantly associated with membranes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis implicated OBBR in disturbing peptidoglycan biosynthesis, with the membrane protein MraY emerging as a potential target for OBBR's action against S. aureus. Notably, experiments involving the overexpression of MraY confirmed OBBR's inhibitory effect on peptidoglycan synthesis. Furthermore, molecular docking and cellular thermal shift assay revealed OBBR's direct interaction with MraY, potentially leading to the inhibition of the enzymatic activity of MraY and, consequently, impeding peptidoglycan synthesis. In summary, OBBR, by targeting MraY and inhibiting peptidoglycan synthesis, emerges as a promising alternative antibiotic against S. aureus, offering potential advantages in terms of limited drug resistance development.
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Affiliation(s)
- Xiaoduo Li
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China; Department of Clinical Laboratory, AnShun City People's Hospital, Guizhou 561000, China
| | - Zhengcai Ma
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qin Tang
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400715, China
| | - Zhenwei Gui
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Biao Zhang
- Department of Clinical Laboratory, AnShun City People's Hospital, Guizhou 561000, China
| | - Guang Sun
- Department of Clinical Laboratory, AnShun City People's Hospital, Guizhou 561000, China
| | - Jingwei Li
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Juan Li
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400715, China
| | - Mengmeng Li
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xuegang Li
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400715, China
| | - Hang Ma
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 400715, China.
| | - Xiaoli Ye
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China.
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10
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Braun C, Wingen LM, Menche D. Strategies and tactics for the synthesis of lipid I and II and shortened analogues: functional building blocks of bacterial cell wall biosynthesis. Nat Prod Rep 2023; 40:1718-1734. [PMID: 37492928 DOI: 10.1039/d3np00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Covering: the literature up to 2022This study discusses various synthetic strategies for the synthesis of lipid II, the pivotal bacterial cell wall precursor. In detail, it examines different solution phase approaches, reviews various solid phase sequences, and evaluates enzymatic ventures. The underlying rationale, scope, limitations, and perspectives of these strategies are discussed. The focus is on the tactics and strategies towards the authentic peptidoglycan compound, as well as analogues thereof with shortened side chains, which are increasingly recognized as more beneficial surrogates with more favorable physicochemical properties.
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Affiliation(s)
- Christina Braun
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany.
| | - Lukas Martin Wingen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany.
| | - Dirk Menche
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany.
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11
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Ambade SS, Gupta VK, Bhole RP, Khedekar PB, Chikhale RV. A Review on Five and Six-Membered Heterocyclic Compounds Targeting the Penicillin-Binding Protein 2 (PBP2A) of Methicillin-Resistant Staphylococcus aureus (MRSA). Molecules 2023; 28:7008. [PMID: 37894491 PMCID: PMC10609489 DOI: 10.3390/molecules28207008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a common human pathogen. Methicillin-resistant Staphylococcus aureus (MRSA) infections pose significant and challenging therapeutic difficulties. MRSA often acquires the non-native gene PBP2a, which results in reduced susceptibility to β-lactam antibiotics, thus conferring resistance. PBP2a has a lower affinity for methicillin, allowing bacteria to maintain peptidoglycan biosynthesis, a core component of the bacterial cell wall. Consequently, even in the presence of methicillin or other antibiotics, bacteria can develop resistance. Due to genes responsible for resistance, S. aureus becomes MRSA. The fundamental premise of this resistance mechanism is well-understood. Given the therapeutic concerns posed by resistant microorganisms, there is a legitimate demand for novel antibiotics. This review primarily focuses on PBP2a scaffolds and the various screening approaches used to identify PBP2a inhibitors. The following classes of compounds and their biological activities are discussed: Penicillin, Cephalosporins, Pyrazole-Benzimidazole-based derivatives, Oxadiazole-containing derivatives, non-β-lactam allosteric inhibitors, 4-(3H)-Quinazolinones, Pyrrolylated chalcone, Bis-2-Oxoazetidinyl macrocycles (β-lactam antibiotics with 1,3-Bridges), Macrocycle-embedded β-lactams as novel inhibitors, Pyridine-Coupled Pyrimidinones, novel Naphthalimide corbelled aminothiazoximes, non-covalent inhibitors, Investigational-β-lactam antibiotics, Carbapenem, novel Benzoxazole derivatives, Pyrazolylpyridine analogues, and other miscellaneous classes of scaffolds for PBP2a. Additionally, we discuss the penicillin-binding protein, a crucial target in the MRSA cell wall. Various aspects of PBP2a, bacterial cell walls, peptidoglycans, different crystal structures of PBP2a, synthetic routes for PBP2a inhibitors, and future perspectives on MRSA inhibitors are also explored.
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Affiliation(s)
- Shraddha S. Ambade
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra 282004, UP, India
| | - Ritesh P. Bhole
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, MH, India
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, MH, India
| | - Pramod B. Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
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12
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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.
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13
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Ameer A, Cheng Y, Saleem F, Uzma, McKenna A, Richmond A, Gundogdu O, Sloan WT, Javed S, Ijaz UZ. Temporal stability and community assembly mechanisms in healthy broiler cecum. Front Microbiol 2023; 14:1197838. [PMID: 37779716 PMCID: PMC10534011 DOI: 10.3389/fmicb.2023.1197838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
In recent years, there has been an unprecedented advancement in in situ analytical approaches that contribute to the mechanistic understanding of microbial communities by explicitly incorporating ecology and studying their assembly. In this study, we have analyzed the temporal profiles of the healthy broiler cecal microbiome from day 3 to day 35 to recover the stable and varying components of microbial communities. During this period, the broilers were fed three different diets chronologically, and therefore, we have recovered signature microbial species that dominate during each dietary regime. Since broilers were raised in multiple pens, we have also parameterized these as an environmental condition to explore microbial niches and their overlap. All of these analyses were performed in view of different parameters such as body weight (BW-mean), feed intake (FI), feed conversion ratio (FCR), and age (days) to link them to a subset of microbes that these parameters have a bearing upon. We found that gut microbial communities exhibited strong and statistically significant specificity for several environmental variables. Through regression models, genera that positively/negatively correlate with the bird's age were identified. Some short-chain fatty acids (SCFAs)-producing bacteria, including Izemoplasmatales, Gastranaerophilales, and Roseburia, have a positive correlation with age. Certain pathogens, such as Escherichia-Shigella, Sporomusa, Campylobacter, and Enterococcus, negatively correlated with the bird's age, which indicated a high disease risk in the initial days. Moreover, the majority of pathways involved in amino acid biosynthesis were also positively correlated with the bird's age. Some probiotic genera associated with improved performance included Oscillospirales; UCG-010, Shuttleworthia, Bifidobacterium, and Butyricicoccaceae; UCG-009. In general, predicted antimicrobial resistance genes (piARGs) contributed at a stable level, but there was a slight increase in abundance when the diet was changed. To the best of the authors' knowledge, this is one of the first studies looking at the stability, complexity, and ecology of natural broiler microbiota development in a temporal setting.
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Affiliation(s)
- Aqsa Ameer
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Youqi Cheng
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Farrukh Saleem
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Uzma
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - William T. Sloan
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Sundus Javed
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Umer Zeeshan Ijaz
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
- College of Science and Engineering, University of Galway, Galway, Ireland
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14
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Ocius KL, Kolli SH, Ahmad SS, Dressler JM, Chordia MD, Jutras BL, Rutkowski MR, Pires MM. Non-invasive Analysis of Peptidoglycan from Living Animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.549941. [PMID: 37693563 PMCID: PMC10491127 DOI: 10.1101/2023.07.21.549941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activate peptidoglycan sensors in human cells, including the Nucleotide-binding oligomerization domain containing protein 2 (NOD2). When present in the gastrointestinal tract, both the polymeric form (sacculi) and de-polymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth. To leverage this growing area of biology towards therapeutic prescriptions, it will be critical to directly analyze a key feature of the host-microbiome interaction from living hosts in a reproducible and non-invasive way. Here we show that metabolically labeled peptidoglycan/sacculi can be readily isolated from fecal samples collected from both mice and humans. Analysis of fecal samples provided a non-invasive route to probe the gut commensal community including the metabolic synchronicity with the host circadian clock. Together, these results pave the way for non-invasive diagnostic tools to interrogate the causal nature of peptidoglycan in host health and disease.
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15
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Kawai Y, Kawai M, Mackenzie ES, Dashti Y, Kepplinger B, Waldron KJ, Errington J. On the mechanisms of lysis triggered by perturbations of bacterial cell wall biosynthesis. Nat Commun 2023; 14:4123. [PMID: 37433811 DOI: 10.1038/s41467-023-39723-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/20/2023] [Indexed: 07/13/2023] Open
Abstract
Inhibition of bacterial cell wall synthesis by antibiotics such as β-lactams is thought to cause explosive lysis through loss of cell wall integrity. However, recent studies on a wide range of bacteria have suggested that these antibiotics also perturb central carbon metabolism, contributing to death via oxidative damage. Here, we genetically dissect this connection in Bacillus subtilis perturbed for cell wall synthesis, and identify key enzymatic steps in upstream and downstream pathways that stimulate the generation of reactive oxygen species through cellular respiration. Our results also reveal the critical role of iron homeostasis for the oxidative damage-mediated lethal effects. We show that protection of cells from oxygen radicals via a recently discovered siderophore-like compound uncouples changes in cell morphology normally associated with cell death, from lysis as usually judged by a phase pale microscopic appearance. Phase paling appears to be closely associated with lipid peroxidation.
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Affiliation(s)
- Yoshikazu Kawai
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Maki Kawai
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Eilidh Sohini Mackenzie
- Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Yousef Dashti
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Bernhard Kepplinger
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, 50-383, Wrocław, Poland
| | - Kevin John Waldron
- Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia.
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16
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Kawai Y, Errington J. Dissecting the roles of peptidoglycan synthetic and autolytic activities in the walled to L-form bacterial transition. Front Microbiol 2023; 14:1204979. [PMID: 37333659 PMCID: PMC10272550 DOI: 10.3389/fmicb.2023.1204979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023] Open
Abstract
Bacterial cells are surrounded by a peptidoglycan (PG) wall, which is a crucial target for antibiotics. It is well known that treatment with cell wall-active antibiotics occasionally converts bacteria to a non-walled "L-form" state that requires the loss of cell wall integrity. L-forms may have an important role in antibiotic resistance and recurrent infection. Recent work has revealed that inhibition of de novo PG precursor synthesis efficiently induces the L-form conversion in a wide range of bacteria, but the molecular mechanisms remain poorly understood. Growth of walled bacteria requires the orderly expansion of the PG layer, which involves the concerted action not just of synthases but also degradative enzymes called autolysins. Most rod-shaped bacteria have two complementary systems for PG insertion, the Rod and aPBP systems. Bacillus subtilis has two major autolysins, called LytE and CwlO, which are thought to have partially redundant functions. We have dissected the functions of autolysins, relative to the Rod and aPBP systems, during the switch to L-form state. Our results suggest that when de novo PG precursor synthesis is inhibited, residual PG synthesis occurs specifically via the aPBP pathway, and that this is required for continued autolytic activity by LytE/CwlO, resulting in cell bulging and efficient L-form emergence. The failure of L-form generation in cells lacking aPBPs was rescued by enhancing the Rod system and in this case, emergence specifically required LytE but was not associated with cell bulging. Our results suggest that two distinct pathways of L-form emergence exist depending on whether PG synthesis is being supported by the aPBP or RodA PG synthases. This work provides new insights into mechanisms of L-form generation, and specialisation in the roles of essential autolysins in relation to the recently recognised dual PG synthetic systems of bacteria.
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17
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Griffin ME, Klupt S, Espinosa J, Hang HC. Peptidoglycan NlpC/P60 peptidases in bacterial physiology and host interactions. Cell Chem Biol 2023; 30:436-456. [PMID: 36417916 PMCID: PMC10192474 DOI: 10.1016/j.chembiol.2022.11.001] [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: 05/18/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall is composed of a highly crosslinked matrix of glycopeptide polymers known as peptidoglycan that dictates bacterial cell morphology and protects against environmental stresses. Regulation of peptidoglycan turnover is therefore crucial for bacterial survival and growth and is mediated by key protein complexes and enzyme families. Here, we review the prevalence, structure, and activity of NlpC/P60 peptidases, a family of peptidoglycan hydrolases that are crucial for cell wall turnover and division as well as interactions with antibiotics and different hosts. Understanding the molecular functions of NlpC/P60 peptidases should provide important insight into bacterial physiology, their interactions with different kingdoms of life, and the development of new therapeutic approaches.
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Affiliation(s)
- Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Steven Klupt
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.
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18
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Keller MR, Dörr T. Bacterial metabolism and susceptibility to cell wall-active antibiotics. Adv Microb Physiol 2023; 83:181-219. [PMID: 37507159 PMCID: PMC11024984 DOI: 10.1016/bs.ampbs.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Bacterial infections are increasingly resistant to antimicrobial therapy. Intense research focus has thus been placed on identifying the mechanisms that bacteria use to resist killing or growth inhibition by antibiotics and the ways in which bacteria share these traits with one another. This work has led to the advancement of new drugs, combination therapy regimens, and a deeper appreciation for the adaptability seen in microorganisms. However, while the primary mechanisms of action of most antibiotics are well understood, the more subtle contributions of bacterial metabolic state to repairing or preventing damage caused by antimicrobials (thereby promoting survival) are still understudied. Here, we review a modern viewpoint on a classical system: examining bacterial metabolism's connection to antibiotic susceptibility. We dive into the relationship between metabolism and antibiotic efficacy through the lens of growth rate, energy state, resource allocation, and the infection environment, focusing on cell wall-active antibiotics.
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Affiliation(s)
- Megan Renee Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States; Department of Microbiology, Cornell University, Ithaca, NY, United States; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States.
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19
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Tandukar S, Kwon E, Kim DY. Structural insights into the regulation of peptidoglycan DL-endopeptidases by inhibitory protein IseA. Structure 2023; 31:619-628.e4. [PMID: 36963396 DOI: 10.1016/j.str.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/29/2023] [Accepted: 02/27/2023] [Indexed: 03/26/2023]
Abstract
Peptidoglycan, a physical barrier that protects bacteria from the environment, is constantly degraded and resynthesized for remodeling during cell growth and division. Because excessive or insufficient peptidoglycan hydrolysis affects bacterial homeostasis and viability, peptidoglycan degradation must be precisely regulated. In Bacillus subtilis, DL-endopeptidases play an essential role in peptidoglycan remodeling, and their activity is regulated by IseA. Here, we report the crystal structure of peptidoglycan DL-endopeptidase LytE complexed with IseA. In the crystal structure, the inhibitory loop connecting the two lobes of IseA blocks the active site of LytE by mimicking its substrate. Consistently, mutations in the inhibitory loop resulted in the loss of IseA activity. The structure also shows that conformational rearrangements in both LytE and IseA restrict access of the inhibitory loop to the LytE catalytic site. These results reveal an inhibition mechanism of peptidoglycan DL-endopeptidase in which the inhibitory protein mimics the substrate but is not degraded.
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Affiliation(s)
| | - Eunju Kwon
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, South Korea.
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, South Korea.
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20
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Antimicrobial peptides for combating drug-resistant bacterial infections. Drug Resist Updat 2023; 68:100954. [PMID: 36905712 DOI: 10.1016/j.drup.2023.100954] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023]
Abstract
The problem of drug resistance due to long-term use of antibiotics has been a concern for years. As this problem grows worse, infections caused by multiple bacteria are expanding rapidly and are extremely detrimental to human health. Antimicrobial peptides (AMPs) are a good alternative to current antimicrobials with potent antimicrobial activity and unique antimicrobial mechanisms, which have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Currently, researchers have conducted clinical investigations on AMPs for drug-resistant bacterial infections while integrating new technologies in the development of AMPs, such as changing amino acid structure of AMPs and using different delivery methods for AMPs. This article introduces the basic properties of AMPs, deliberates the mechanism of drug resistance in bacteria and the therapeutic mechanism of AMPs. The current disadvantages and advances of AMPs in combating drug-resistant bacterial infections are also discussed. This article provides important insights into the research and clinical application of new AMPs for drug-resistant bacterial infections.
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21
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Sloan DB, Warren JM, Williams AM, Kuster SA, Forsythe ES. Incompatibility and Interchangeability in Molecular Evolution. Genome Biol Evol 2023; 15:evac184. [PMID: 36583227 PMCID: PMC9839398 DOI: 10.1093/gbe/evac184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Jessica M Warren
- Center for Mechanisms of Evolution, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Alissa M Williams
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Shady A Kuster
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, Colorado
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22
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Nirwan S, Chahal V, Kakkar R. A comparative study of different docking methodologies to assess the protein-ligand interaction for the E. coli MurB enzyme. J Biomol Struct Dyn 2022; 40:11229-11238. [PMID: 34323658 DOI: 10.1080/07391102.2021.1957019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We have investigated the active site of E. coli MurB using the Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The docking of three novel series of 4-thiazolidinone derivatives has been performed using two methods: rigid docking and flexible docking (Induced Fit Docking: IFD). The results have been compared to understand the conformational aspects of the enzyme. The docking results from rigid docking show that the ligands with highly negative ΔGbind have poor docking scores. In addition, the value of the regression coefficient (R) obtained on correlating the ΔGbind and the experimental pMIC values is insignificant. On keeping the protein flexible, there is a remarkable improvement in both the docking score and ΔGbind, along with a good value of R (0.64). Two important residues, Tyr254 and Try190 are found to be highly displaced during the flexible docking and hence their role in effective ligand binding has been confirmed. Thus, comparing the two methodologies, IFD has emerged as the more appropriate one for studying the E. coli MurB enzyme. To further substantiate the findings, MD studies over a time period of 20 ns have been performed on the IFD-LIII j and Rigid/XP-LIII j complexes and the results shows the former complex to be more stable, with lower average RMSD and higher average ΔGbind.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonam Nirwan
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Varun Chahal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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23
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Lund V, Gangotra H, Zhao Z, Sutton JAF, Wacnik K, DeMeester K, Liang H, Santiago C, Leimkuhler Grimes C, Jones S, Foster SJ. Coupling Novel Probes with Molecular Localization Microscopy Reveals Cell Wall Homeostatic Mechanisms in Staphylococcus aureus. ACS Chem Biol 2022; 17:3298-3305. [PMID: 36414253 PMCID: PMC9764285 DOI: 10.1021/acschembio.2c00741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Bacterial cell wall peptidoglycan is essential for viability, and its synthesis is targeted by antibiotics, including penicillin. To determine how peptidoglycan homeostasis controls cell architecture, growth, and division, we have developed novel labeling approaches. These are compatible with super-resolution fluorescence microscopy to examine peptidoglycan synthesis, hydrolysis, and the localization of the enzymes required for its biosynthesis (penicillin binding proteins (PBPs)). Synthesis of a cephalosporin-based fluorescent probe revealed a pattern of PBPs at the septum during division, supporting a model of dispersed peptidoglycan synthesis. Metabolic and hydroxylamine-based probes respectively enabled the synthesis of glycan strands and associated reducing termini of the peptidoglycan to be mapped. Foci and arcs of reducing termini appear as a result of both synthesis of glycan strands and glucosaminidase activity of the major peptidoglycan hydrolase, SagB. Our studies provide molecular level details of how essential peptidoglycan dynamics are controlled during growth and division.
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Affiliation(s)
- Victoria
A. Lund
- School
of Biosciences, University of Sheffield, Sheffield S10 2TN, United Kingdom,The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Haneesh Gangotra
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom,The
Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Zhen Zhao
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom,The
Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Joshua A. F. Sutton
- School
of Biosciences, University of Sheffield, Sheffield S10 2TN, United Kingdom,The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Katarzyna Wacnik
- School
of Biosciences, University of Sheffield, Sheffield S10 2TN, United Kingdom,The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Kristen DeMeester
- Department
of Chemistry and Biochemistry and Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
| | - Hai Liang
- Department
of Chemistry and Biochemistry and Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
| | - Cintia Santiago
- Department
of Chemistry and Biochemistry and Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
| | - Catherine Leimkuhler Grimes
- Department
of Chemistry and Biochemistry and Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
| | - Simon Jones
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom,The
Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom,E-mail:
| | - Simon J. Foster
- School
of Biosciences, University of Sheffield, Sheffield S10 2TN, United Kingdom,The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom,E-mail:
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24
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Apostolos AJ, Chordia MD, Kolli SH, Dalesandro BE, Rutkowski MR, Pires MM. Real-time non-invasive fluorescence imaging of gut commensal bacteria to detect dynamic changes in the microbiome of live mice. Cell Chem Biol 2022; 29:S2451-9456(22)00416-0. [PMID: 36516833 PMCID: PMC10239791 DOI: 10.1016/j.chembiol.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
In mammals, gut commensal microbiota interact extensively with the host, and the same interactions can be dysregulated in diseased states. Animal imaging is a powerful technique that is widely used to diagnose, measure, and track biological changes in model organisms such as laboratory mice. Several imaging techniques have been discovered and adopted by the research community that provide dynamic, non-invasive assessment of live animals, but these gains have not been universal across all fields of biology. Herein, we describe a method to non-invasively image commensal bacteria based on the specific metabolic labeling of bacterial cell walls to illuminate the gut bacteria of live mice. This tagging strategy may additionally provide unprecedented insight into cell wall turnover of gut commensals, which has implications for bacterial cellular growth and division, in a live animal.
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Affiliation(s)
- Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Mahendra D Chordia
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Sree H Kolli
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Melanie R Rutkowski
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
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25
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Fathalla RK, Fröhner W, Bader CD, Fischer PD, Dahlem C, Chatterjee D, Mathea S, Kiemer AK, Arthanari H, Müller R, Abdel-Halim M, Ducho C, Engel M. Identification and Biochemical Characterization of Pyrrolidinediones as Novel Inhibitors of the Bacterial Enzyme MurA. J Med Chem 2022; 65:14740-14763. [PMID: 36269107 PMCID: PMC9989942 DOI: 10.1021/acs.jmedchem.2c01275] [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] [Indexed: 11/28/2022]
Abstract
To develop novel antibiotics, targeting the early steps of cell wall peptidoglycan biosynthesis seems to be a promising strategy that is still underutilized. MurA, the first enzyme in this pathway, is targeted by the clinically used irreversible inhibitor fosfomycin. However, mutations in its binding site can cause bacterial resistance. We herein report a series of novel reversible pyrrolidinedione-based MurA inhibitors that equally inhibit wild type (WT) MurA and the fosfomycin-resistant MurA C115D mutant, showing an additive effect with fosfomycin for the inhibition of WT MurA. For the most potent inhibitor 46 (IC50 = 4.5 μM), the mode of inhibition was analyzed using native mass spectrometry and protein NMR spectroscopy. The compound class was nontoxic against human cells and highly stable in human S9 fraction, human plasma, and bacterial cell lysate. Taken together, this novel compound class might be further developed toward antibiotic drug candidates that inhibit cell wall synthesis.
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Affiliation(s)
- Reem K. Fathalla
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Wolfgang Fröhner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Chantal D. Bader
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Patrick D. Fischer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
- Department of Cancer Biology, Dana-Farber Cancer Institute, 02215, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 02115, Boston, MA, USA
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Alexandra K. Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, 02215, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 02115, Boston, MA, USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Helmholtz International Lab for Antiinfectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Matthias Engel
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
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26
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Wang Y, Wang J, Yu D, Zou J, Zhang C, Yan H, Ye X, Chen Y. Microbial Community Structure of Colostrum in Women with Antibiotic Exposure Immediately After Delivery. Breastfeed Med 2022; 17:940-946. [PMID: 36378822 DOI: 10.1089/bfm.2022.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: The microbial community in human milk is associated with many maternal and neonatal factors. This study aimed to investigate the effect of antibiotic exposure on the microbial community structure of colostrum. Methods: Twenty women with antibiotic treatment immediately after delivery and 10 age-matched control women were enrolled at the Guangdong Women and Children Hospital. Colostrum samples were collected within postpartum 30 hours. The V4 variable region of the bacterial 16S rRNA gene was sequenced to characterize the microbial profile using Illumina MiSeq platform. Results: Phyla Proteobacteria and Firmicutes were the predominant bacteria in colostrum samples. The core and abundant genera in colostrum included Streptococcus, Staphylococcus, and Pseudomonas. Compared with the control group, principal coordinate analysis based on the Bray-Curtis distance showed a significant difference in milk microbial community in women with antibiotic exposure, accompanied by a significantly lower alpha diversity and a different microbial ecological network. Furthermore, the relative abundances of genera Actinomyces, Anaerobacter, and Clostridium_sensu_stricto significantly decreased after antibiotic treatment. Conclusions: This study provided evidence of alterations in the colostrum microbial community with antibiotic exposure, improving our understanding of the effects of antibiotic treatment on the milk microbiome.
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Affiliation(s)
- Yanli Wang
- Neonatal Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Junping Wang
- Neonatal Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Dongling Yu
- Neonatal Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jingjing Zou
- Neonatal Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Chunyi Zhang
- Neonatal Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Huiheng Yan
- Neonatal Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiuzhen Ye
- Neonatal Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yunbin Chen
- Neonatal Department, Guangdong Women and Children Hospital, Guangzhou, China
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27
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Development of Whole-Cell Biosensors for Screening of Peptidoglycan-Targeting Antibiotics in a Gram-Negative Bacterium. Appl Environ Microbiol 2022; 88:e0084622. [PMID: 36040151 PMCID: PMC9499016 DOI: 10.1128/aem.00846-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is an urgent need to develop novel antibiotics since antibiotic resistance is an increasingly serious threat to global public health. Whole-cell biosensors are one of the promising strategies for new antibiotic discovery. The peptidoglycan (PG) of the bacterial cell wall is one of the most important targets for antibiotics. However, the biosensors for the detection of PG-targeting antibiotics in Gram-negative bacteria have not been developed, mainly because of the lack of the regulatory systems that sense and respond to PG stress. Recently, we identified a novel two-component signal transduction system (PghKR) that is responsible for sensing and responding to PG damage in the Gram-negative bacterium Shewanella oneidensis. Based on this system, we developed biosensors for the detection of PG-targeting antibiotics. Using ampicillin as an inducer for PG stress and the bacterial luciferase LuxCDABE as the reporter, we found that the PghKR biosensors are specific to antibiotics targeting PG synthesis, including β-lactams, vancomycin, and d-cycloserine. Deletion of genes encoding PG permease AmpG and β-lactamase BlaA improves the sensitivity of the biosensors substantially. The PghKR biosensor in the background of ΔblaA is also functional on agar plates, providing a simple method for screening bacteria that produce PG-targeting antibiotics. IMPORTANCE The growing problem of antibiotic resistance in Gram-negative bacteria urgently needs new strategies so that researchers can develop novel antibiotics. Microbial whole-cell biosensors are capable of sensing various stimuli with a quantifiable output and show tremendous potential for the discovery of novel antibiotics. As the Achilles' heel of bacteria, the synthesis of the peptidoglycan (PG) is targeted by many antibiotics. However, the regulatory systems that sense and respond to PG-targeting stress in Gram-negative bacteria are reported rarely, restricting the development of biosensors for the detection of PG-targeting antibiotics. In this study, we developed a highly sensitive and specific biosensor based on a novel two-component system in the Gram-negative bacterium Shewanella oneidensis that is responsible for the sensing and responding to PG stress. Our biosensors have great potential for discovering novel antibiotics and determining the mode of action of antibiotics.
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28
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Ansari S, Yamaoka Y. Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance. Clin Microbiol Rev 2022; 35:e0025821. [PMID: 35404105 PMCID: PMC9491184 DOI: 10.1128/cmr.00258-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.
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Affiliation(s)
- Shamshul Ansari
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, USA
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
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29
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Biological Features and In Planta Transcriptomic Analyses of a Microviridae Phage (CLasMV1) in " Candidatus Liberibacter asiaticus". Int J Mol Sci 2022; 23:ijms231710024. [PMID: 36077424 PMCID: PMC9456138 DOI: 10.3390/ijms231710024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022] Open
Abstract
“Candidatus Liberibacter asiaticus” (CLas) is the causal agent of citrus Huanglongbing (HLB, also called citrus greening disease), a highly destructive disease threatening citrus production worldwide. A novel Microviridae phage (named CLasMV1) has been found to infect CLas, providing a potential therapeutic strategy for CLas/HLB control. However, little is known about the CLasMV1 biology. In this study, we analyzed the population dynamics of CLasMV1 between the insect vector of CLas, the Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) and the holoparasitic dodder plant (Cuscuta campestris Yunck.); both acquired CLasMV1-infected CLas from an HLB citrus. All CLas-positive dodder samples were CLasMV1-positive, whereas only 32% of CLas-positive ACP samples were identified as CLasMV1-positive. Quantitative analyses showed a similar distribution pattern of CLasMV1 phage and CLas among eight citrus cultivars by presenting at highest abundance in the fruit pith and/or the center axis of the fruit. Transcriptome analyses revealed the possible lytic activity of CLasMV1 on CLas in fruit pith as evidenced by high-level expressions of CLasMV1 genes, and CLas genes related to cell wall biogenesis and remodeling to maintain the CLas cell envelope integrity. The up-regulation of CLas genes were involved in restriction–modification system that could involve possible phage resistance for CLas during CLasMV1 infection. In addition, the regulation of CLas genes involved in cell surface components and Sec pathway by CLasMV1 phage could be beneficial for phage infection. This study expanded our knowledge of CLasMV1 phage that will benefit further CLas phage research and HLB control.
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30
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Lorente Cobo N, Sibinelli-Sousa S, Biboy J, Vollmer W, Bayer-Santos E, Prehna G. Molecular characterization of the type VI secretion system effector Tlde1a reveals a structurally altered LD-transpeptidase fold. J Biol Chem 2022; 298:102556. [PMID: 36183829 PMCID: PMC9638812 DOI: 10.1016/j.jbc.2022.102556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/01/2022] Open
Abstract
The type VI secretion system (T6SS) is a molecular machine that Gram-negative bacteria have adapted for multiple functions, including interbacterial competition. Bacteria use the T6SS to deliver protein effectors into adjacent cells to kill rivals and establish niche dominance. Central to T6SS-mediated bacterial competition is an arms race to acquire diverse effectors to attack and neutralize target cells. The peptidoglycan has a central role in bacterial cell physiology, and effectors that biochemically modify peptidoglycan structure effectively induce cell death. One such T6SS effector is Tlde1a from Salmonella Typhimurium. Tlde1a functions as an LD-carboxypeptidase to cleave tetrapeptide stems and as an LD-transpeptidase to exchange the terminal D-alanine of a tetrapeptide stem with a noncanonical D-amino acid. To understand how Tlde1a exhibits toxicity at the molecular level, we determined the X-ray crystal structure of Tlde1a alone and in complex with D-amino acids. Our structural data revealed that Tlde1a possesses a unique LD-transpeptidase fold consisting of a dual pocket active site with a capping subdomain. This includes an exchange pocket to bind a D-amino acid for exchange and a catalytic pocket to position the D-alanine of a tetrapeptide stem for cleavage. Our toxicity assays in Escherichia coli and in vitro peptidoglycan biochemical assays with Tlde1a variants correlate Tlde1a molecular features directly to its biochemical functions. We observe that the LD-carboxypeptidase and LD-transpeptidase activities of Tlde1a are both structurally and functionally linked. Overall, our data highlight how an LD-transpeptidase fold has been structurally altered to create a toxic effector in the T6SS arms race.
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Affiliation(s)
- Neil Lorente Cobo
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Stephanie Sibinelli-Sousa
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ethel Bayer-Santos
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Canada.
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31
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Subedi BP, Schofield LR, Carbone V, Wolf M, Martin WF, Ronimus RS, Sutherland-Smith AJ. Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36178458 DOI: 10.1099/mic.0.001235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Archaea have diverse cell wall types, yet none are identical to bacterial peptidoglycan (murein). Methanogens Methanobacteria and Methanopyrus possess cell walls of pseudomurein, a structural analogue of murein. Pseudomurein differs from murein in containing the unique archaeal sugar N-acetyltalosaminuronic acid instead of N-acetylmuramic acid, β-1,3 glycosidic bonds in place of β-1,4 bonds and only l-amino acids in the peptide cross-links. We have determined crystal structures of methanogen pseudomurein peptide ligases (termed pMurE) from Methanothermus fervidus (Mfer762) and Methanothermobacter thermautotrophicus (Mth734) that are structurally most closely related to bacterial MurE peptide ligases. The homology of the archaeal pMurE and bacterial MurE enzymes is clear both in the overall structure and at the level of each of the three domains. In addition, we identified two UDP-binding sites in Mfer762 pMurE, one at the exterior surface of the interface of the N-terminal and middle domains, and a second site at an inner surface continuous with the highly conserved interface of the three domains. Residues involved in ATP binding in MurE are conserved in pMurE, suggesting that a similar ATP-binding pocket is present at the interface of the middle and the C-terminal domains of pMurE. The presence of pMurE ligases in members of the Methanobacteriales and Methanopyrales, that are structurally related to bacterial MurE ligases, supports the idea that the biosynthetic origins of archaeal pseudomurein and bacterial peptidoglycan cell walls are evolutionarily related.
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Affiliation(s)
- Bishwa P Subedi
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand.,Present address: Faculty of Medicine, Nursing and Health Sciences, Monash Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Linley R Schofield
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Vincenzo Carbone
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Maximilian Wolf
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,Present address: Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ron S Ronimus
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
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32
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Dinarvand M, Koch FC, Al Mouiee D, Vuong K, Vijayan A, Tanzim AF, Azad AKM, Penesyan A, Castaño-Rodríguez N, Vafaee F. dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data. Microb Genom 2022; 8. [PMID: 36136078 DOI: 10.1099/mgen.0.000862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Infection triggers a dynamic cascade of reciprocal events between host and pathogen wherein the host activates complex mechanisms to recognise and kill pathogens while the pathogen often adjusts its virulence and fitness to avoid eradication by the host. The interaction between the pathogen and the host results in large-scale changes in gene expression in both organisms. Dual RNA-seq, the simultaneous detection of host and pathogen transcripts, has become a leading approach to unravelling complex molecular interactions between the host and the pathogen and is particularly informative for intracellular organisms. The amount of in vitro and in vivo dual RNA-seq data is rapidly growing, which demands computational pipelines to effectively analyse such data. In particular, holistic, systems-level, and temporal analyses of dual RNA-seq data are essential to enable further insights into the host-pathogen transcriptional dynamics and potential interactions. Here, we developed an integrative network-driven bioinformatics pipeline, dRNASb, a systems biology-based computational pipeline to analyse temporal transcriptional clusters, incorporate molecular interaction networks (e.g. protein-protein interactions), identify topologically and functionally key transcripts in host and pathogen, and associate host and pathogen temporal transcriptome to decipher potential between-species interactions. The pipeline is applicable to various dual RNA-seq data from different species and experimental conditions. As a case study, we applied dRNASb to analyse temporal dual RNA-seq data of Salmonella-infected human cells, which enabled us to uncover genes contributing to the infection process and their potential functions and to identify putative associations between host and pathogen genes during infection. Overall, dRNASb has the potential to identify key genes involved in bacterial growth or host defence mechanisms for future uses as therapeutic targets.
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Affiliation(s)
- Mojdeh Dinarvand
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Forrest C Koch
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Al Mouiee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW, Australia
| | - Kaylee Vuong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Abhishek Vijayan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Afia Fariha Tanzim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - A K M Azad
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Natalia Castaño-Rodríguez
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW, Australia
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33
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Zhang J, Zhu B, Xu X, Liu Y, Li Q, Li Y, Lu F. Remodeling Bacillus amyloliquefaciens Cell Wall Rigidity to Reduce Cell Lysis and Increase the Yield of Heterologous Proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10552-10562. [PMID: 35984403 DOI: 10.1021/acs.jafc.2c04454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacillus amyloliquefaciens has great potential as a host for heterologous protein production, but its severe autolytic behavior has precluded its industrial application to date. Because d,l-endopeptidase activity-guided cell wall rigidity is considered essential for autolysis resistance, we investigated the effects of d,l-endopeptidase genes lytE, lytF, cwlO, and cwlS play on the growth, lysis, and morphology remodeling of B. amyloliquefaciens strain TCCC11018. Individual and combinatorial deletion of lytE, lytF, and cwlS enhanced the cell growth and delayed cell lysis. For the best mutant with the lytF and cwlS double deletion, the viable cell number at 24 h increased by 11.90% and the cell wall thickness at 6 h increased by 25.87%. Transcriptomic and proteomic analyses indicated that the improvement was caused by enhanced peptidoglycan synthesis. With the lytF and cwlS double deletion, the extracellular green fluorescent protein and phospholipase D expression levels increased by 113 and 55.89%, respectively. This work broadens our understanding of the relationship between d,l-endopeptidases and B. amyloliquefaciens cell characteristics, which provides an effective strategy to improve the heterologous protein expression in B. amyloliquefaciens-based cell factories.
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Affiliation(s)
- Jinfang Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Baoyue Zhu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Xiaojian Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Qinggang Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
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34
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Vacariu CM, Tanner ME. Recent Advances in the Synthesis and Biological Applications of Peptidoglycan Fragments. Chemistry 2022; 28:e202200788. [PMID: 35560956 DOI: 10.1002/chem.202200788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 11/09/2022]
Abstract
The biosynthesis, breakdown, and modification of peptidoglycan (PG) play vital roles in both bacterial viability and in the response of human physiology to bacterial infection. Studies on PG biochemistry are hampered by the fact that PG is an inhomogeneous insoluble macromolecule. Chemical synthesis is therefore an important means to obtain PG fragments that may serve as enzyme substrates and elicitors of the human immune response. This review outlines the recent advances in the synthesis and biochemical studies of PG fragments, PG biosynthetic intermediates (such as Park's nucleotides and PG lipids), and PG breakdown products (such as muramyl dipeptides and anhydro-muramic acid-containing fragments). A rich variety of synthetic approaches has been applied to preparing such compounds since carbohydrate, peptide, and phospholipid chemical methodologies must all be applied.
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Affiliation(s)
- Condurache M Vacariu
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
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The Role of Mre Factors and Cell Division in Peptidoglycan Growth in the Multicellular Cyanobacterium Anabaena. mBio 2022; 13:e0116522. [PMID: 35876506 PMCID: PMC9426583 DOI: 10.1128/mbio.01165-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacteria in general serve two main tasks: cell growth and division. Both processes include peptidoglycan extension to allow cell expansion and to form the poles of the daughter cells, respectively. The cyanobacterium Anabaena forms filaments of communicated cells in which the outer membrane and the peptidoglycan sacculus, which is engrossed in the intercellular regions between contiguous cells, are continuous along the filament. During the growth of Anabaena, peptidoglycan incorporation was weak at the cell periphery. During cell division, midcell peptidoglycan incorporation matched the localization of the divisome, and incorporation persisted in the intercellular septa, even after the division was completed. MreB, MreC, and MreD were located throughout the cell periphery and, in contrast to other bacteria, also to the divisome all along midcell peptidoglycan growth. In Anabaena mutants bearing inactivated mreB, mreC, or mreD genes, which showed conspicuous alterations in the filament morphology, consecutive septal bands of peptidoglycan growth were frequently not parallel to each other and were irregularly spaced along the filament, reproducing the disposition of the Z-ring. Both lateral and septal growth was impaired in strains down-expressing Z-ring components, and MreB and MreD appeared to directly interact with some divisome components. We propose that, in Anabaena, association with the divisome is a way for localization of MreB, MreC, and MreD at the cell poles, where they regulate lateral, midcell, and septal peptidoglycan growth with the latter being involved in localization and maintenance of the intercellular septal-junction protein structures that mediate cell-cell communication along the filament.
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36
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Vahdati SN, Behboudi H, Navasatli SA, Tavakoli S, Safavi M. New insights into the inhibitory roles and mechanisms of D-amino acids in bacterial biofilms in medicine, industry, and agriculture. Microbiol Res 2022; 263:127107. [PMID: 35843196 DOI: 10.1016/j.micres.2022.127107] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022]
Abstract
Biofilms are complex aggregates of microbes that are tightly protected by an extracellular matrix (ECM) and may attach to a surface or adhere together. A higher persistence of bacteria on biofilms makes them resistant not only to harsh conditions but also to various antibiotics which led to the emergence of problems in different applications. Recently, it has been discovered that many bacteria produce and release various D-amino acids (D-AAs) to inhibit biofilm formation, which made a great deal of interest in research into the control of bacterial biofilms in diverse fields, such as human health, industrial settings, and medical devices. D-AAs have various mechanisms to inhibit bacterial biofilms such as: (i) interfering with protein synthesis (ii) Inhibition of extracellular polymeric materials (EPS) productions (protein, eDNA, and polysaccharide) (iii) Inhibition of quorum sensing (autoinducers), and (iv) interfere with peptidoglycan synthesis, these various modes of action, enables these small molecules to inhibit both Gram-negative and Gram-positive bacterial biofilms. Since most biofilms are multi-species, D-AAs in combination with other antimicrobial agents are good choices to combat a variety of bacterial biofilms without displaying toxicity on human cells. This review article addressed the role of D-AAs in controlling several bacterial biofilms and described the possible or definite mechanisms involved in this process.
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Affiliation(s)
- Saeed Niazi Vahdati
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Hossein Behboudi
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran.
| | - Sepideh Aliniaye Navasatli
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Sara Tavakoli
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Maliheh Safavi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
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Qie X, Zan M, Gui P, Chen H, Wang J, Lin K, Mei Q, Ge M, Zhang Z, Tang Y, Dong WF, Song Y. Design, Synthesis, and Application of Carbon Dots With Synergistic Antibacterial Activity. Front Bioeng Biotechnol 2022; 10:894100. [PMID: 35757804 PMCID: PMC9213729 DOI: 10.3389/fbioe.2022.894100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
The diversity of bacteria and their ability to acquire drug resistance lead to many challenges in traditional antibacterial methods. Photothermal therapies that convert light energy into localized physical heat to kill target microorganisms do not induce resistance and provide an alternative for antibacterial treatment. However, many photothermal materials cannot specifically target bacteria, which can lead to thermal damage to normal tissues, thus seriously affecting their biological applications. Here, we designed and synthesized bacteria-affinitive photothermal carbon dots (BAPTCDs) targeting MurD ligase that catalyzes the synthesis of peptidoglycan (PG) in bacteria. BAPTCDs presented specific recognition ability and excellent photothermal properties. BAPTCDs can bind to bacteria very tightly due to their chiral structure and inhibit enzyme activity by competing with D-glutamic acid to bind to MurD ligases, thus inhibiting the synthesis of bacterial walls. It also improves the accuracy of bacteria treatment by laser irradiation. Through the synergy of biochemical and physical effects, the material offers outstanding antibacterial effects and potentially contributes to tackling the spread of antibiotic resistance and facilitation of antibiotic stewardship.
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Affiliation(s)
- Xingwang Qie
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Minghui Zan
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Ping Gui
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Hongyi Chen
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,University of Science and Technology of China, Hefei, China
| | - Jingkai Wang
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,University of Science and Technology of China, Hefei, China
| | - Kaicheng Lin
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Qian Mei
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Mingfeng Ge
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhiqiang Zhang
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yuguo Tang
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Wen-Fei Dong
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,University of Science and Technology of China, Hefei, China
| | - Yizhi Song
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,University of Science and Technology of China, Hefei, China
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38
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Wang M, Buist G, van Dijl JM. Staphylococcus aureus cell wall maintenance - the multifaceted roles of peptidoglycan hydrolases in bacterial growth, fitness, and virulence. FEMS Microbiol Rev 2022; 46:6604383. [PMID: 35675307 PMCID: PMC9616470 DOI: 10.1093/femsre/fuac025] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/22/2022] [Accepted: 05/25/2022] [Indexed: 01/07/2023] Open
Abstract
Staphylococcus aureus is an important human and livestock pathogen that is well-protected against environmental insults by a thick cell wall. Accordingly, the wall is a major target of present-day antimicrobial therapy. Unfortunately, S. aureus has mastered the art of antimicrobial resistance, as underscored by the global spread of methicillin-resistant S. aureus (MRSA). The major cell wall component is peptidoglycan. Importantly, the peptidoglycan network is not only vital for cell wall function, but it also represents a bacterial Achilles' heel. In particular, this network is continuously opened by no less than 18 different peptidoglycan hydrolases (PGHs) encoded by the S. aureus core genome, which facilitate bacterial growth and division. This focuses attention on the specific functions executed by these enzymes, their subcellular localization, their control at the transcriptional and post-transcriptional levels, their contributions to staphylococcal virulence and their overall importance in bacterial homeostasis. As highlighted in the present review, our understanding of the different aspects of PGH function in S. aureus has been substantially increased over recent years. This is important because it opens up new possibilities to exploit PGHs as innovative targets for next-generation antimicrobials, passive or active immunization strategies, or even to engineer them into effective antimicrobial agents.
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Affiliation(s)
- Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO Box 30001, 9700 RB Groningen, the Netherlands
| | | | - Jan Maarten van Dijl
- Corresponding author: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. box 30001, HPC EB80, 9700 RB Groningen, the Netherlands, Tel. +31-50-3615187; Fax. +31-50-3619105; E-mail:
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39
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Adam J, Del Sorbo MR, Kaur J, Romano R, Singh M, Valadan M, Altucci C. Surface Interactions Studies of Novel Two-Dimensional Molybdenum Disulfide with Gram-Negative and Gram-Positive Bacteria. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2070186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Jaber Adam
- Laboratory of Bio-Nano-Photonics, Department of Physics “Ettore Pancini”, University of Naples “Federico II”, Naples, Italy
| | | | - Jasneet Kaur
- Laboratory of Bio-Nano-Photonics, Department of Physics “Ettore Pancini”, University of Naples “Federico II”, Naples, Italy
| | - Rocco Romano
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | - Manjot Singh
- Laboratory of Bio-Nano-Photonics, Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Mohammadhassan Valadan
- Laboratory of Bio-Nano-Photonics, Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
- Istituto Nazionale di Fisica Nucleare, Naples, Italy
| | - Carlo Altucci
- Laboratory of Bio-Nano-Photonics, Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
- Istituto Nazionale di Fisica Nucleare, Naples, Italy
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40
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Ahmadvand P, Avillan JJ, Lewis JA, Call DR, Kang C. Characterization of Interactions between CTX-M-15 and Clavulanic Acid, Desfuroylceftiofur, Ceftiofur, Ampicillin, and Nitrocefin. Int J Mol Sci 2022; 23:ijms23095229. [PMID: 35563620 PMCID: PMC9100253 DOI: 10.3390/ijms23095229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamases (ESBLs) are commonly associated with Gram-negative, hospital-acquired infections worldwide. Several beta-lactamase inhibitors, such as clavulanate, are used to inhibit the activity of these enzymes. To understand the mechanism of CTX-M-15 activity, we have determined the crystal structures of CTX-M-15 in complex with two specific classes of beta-lactam compounds, desfuroylceftiofur (DFC) and ampicillin, and an inhibitor, clavulanic acid. The crystal structures revealed that Ser70 and five other residues (Lys73, Tyr105, Glu166, Ser130, and Ser237) participate in catalysis and binding of those compounds. Based on analysis of steady-state kinetics, thermodynamic data, and molecular docking to both wild-type and S70A mutant structures, we determined that CTX-M-15 has a similar affinity for all beta-lactam compounds (ceftiofur, nitrocefin, DFC, and ampicillin), but with lower affinity for clavulanic acid. A catalytic mechanism for tested β-lactams and two-step inhibition mechanism of clavulanic acid were proposed. CTX-M-15 showed a higher activity toward DFC and nitrocefin, but significantly lower activity toward ampicillin and ceftiofur. The interaction between CTX-M-15 and both ampicillin and ceftiofur displayed a higher entropic but lower enthalpic effect, compared with DFC and nitrocefin. DFC, a metabolite of ceftiofur, displayed lower entropy and higher enthalpy than ceftiofur. This finding suggests that compounds containing amine moiety (e.g., ampicillin) and the furfural moiety (e.g., ceftiofur) could hinder the hydrolytic activity of CTX-M-15.
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Affiliation(s)
- Parvaneh Ahmadvand
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (P.A.); (J.A.L.)
| | - Johannetsy J. Avillan
- Paul G Allen School for Global Health, Washington State University, Pullman, WA 99164, USA; (J.J.A.); (D.R.C.)
| | - Jacob A. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (P.A.); (J.A.L.)
| | - Douglas R. Call
- Paul G Allen School for Global Health, Washington State University, Pullman, WA 99164, USA; (J.J.A.); (D.R.C.)
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (P.A.); (J.A.L.)
- Correspondence:
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41
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β-Lactam Resistance in Azospirillum baldaniorum Sp245 Is Mediated by Lytic Transglycosylase and β-Lactamase and Regulated by a Cascade of RpoE7→RpoH3 Sigma Factors. J Bacteriol 2022; 204:e0001022. [PMID: 35352964 DOI: 10.1128/jb.00010-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Bacterial resistance to β-lactam antibiotics is often mediated by β-lactamases and lytic transglycosylases. Azospirillum baldaniorum Sp245 is a plant-growth-promoting rhizobacterium that shows high levels of resistance to ampicillin. Investigating the molecular basis of ampicillin resistance and its regulation in A. baldaniorum Sp245, we found that a gene encoding lytic transglycosylase (Ltg1) is organized divergently from a gene encoding an extracytoplasmic function (ECF) σ factor (RpoE7) in its genome. Inactivation of rpoE7 in A. baldaniorum Sp245 led to increased ability to form cell-cell aggregates and produce exopolysaccharides and biofilm, suggesting that rpoE7 might contribute to antibiotic resistance. Inactivation of ltg1 in A. baldaniorum Sp245, however, adversely affected its growth, indicating a requirement of Ltg1 for optimal growth. The expression of rpoE7, as well that of as ltg1, was positively regulated by RpoE7, and overexpression of RpoE7 conferred ampicillin sensitivity to both the rpoE7::km mutant and its parent. In addition, RpoE7 negatively regulated the expression of a gene encoding a β-lactamase (bla1). Out of the 5 paralogs of RpoH encoded in the genome of A. baldaniorum Sp245, RpoH3 played major roles in conferring ampicillin sensitivity and in the downregulation of bla1. The expression of rpoH3 was positively regulated by RpoE7. Collectively, these observations reveal a novel regulatory cascade of RpoE7-RpoH3 σ factors that negatively regulates ampicillin resistance in A. baldaniorum Sp245 by controlling the expression of a β-lactamase and a lytic transglycosylase. In the absence of a cognate anti-sigma factor, addressing how the activity of RpoE7 is regulated by β-lactams will unravel new mechanisms of regulation of β-lactam resistance in bacteria. IMPORTANCE Antimicrobial resistance is a global health problem that requires a better understanding of the mechanisms that bacteria use to resist antibiotics. Bacteria inhabiting the plant rhizosphere are a potential source of antibiotic resistance, but their mechanisms controlling antibiotic resistance are poorly understood. A. baldaniorum Sp245 is a rhizobacterium that is known for its characteristic resistance to ampicillin. Here, we show that an AmpC-type β-lactamase and a lytic transglycosylase mediate resistance to ampicillin in A. baldaniorum Sp245. While the gene encoding lytic transglycosylase is positively regulated by an ECF σ-factor (RpoE7), a cascade of RpoE7 and RpoH3 σ factors negatively regulates the expression of β-lactamase. This is the first evidence showing involvement of a regulatory cascade of σ factors in the regulation of ampicillin resistance in a rhizobacterium.
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Kumar S, Mollo A, Kahne D, Ruiz N. The Bacterial Cell Wall: From Lipid II Flipping to Polymerization. Chem Rev 2022; 122:8884-8910. [PMID: 35274942 PMCID: PMC9098691 DOI: 10.1021/acs.chemrev.1c00773] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to the PG matrix during cell elongation and division. The lipid-linked precursor for PG biogenesis, Lipid II, is synthesized in the inner leaflet of the cytoplasmic membrane and is subsequently translocated across the bilayer so that the PG building block can be polymerized and cross-linked by complex multiprotein machines. This review focuses on major discoveries that have significantly changed our understanding of PG biogenesis in the past decade. In particular, we highlight progress made toward understanding the translocation of Lipid II across the cytoplasmic membrane by the MurJ flippase, as well as the recent discovery of a novel class of PG polymerases, the SEDS (shape, elongation, division, and sporulation) glycosyltransferases RodA and FtsW. Since PG biogenesis is an effective target of antibiotics, these recent developments may lead to the discovery of much-needed new classes of antibiotics to fight bacterial resistance.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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43
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Gottstein J, Zaschke-Kriesche J, Unsleber S, Voitsekhovskaia I, Kulik A, Behrmann LV, Overbeck N, Stühler K, Stegmann E, Smits SHJ. New insights into the resistance mechanism for the BceAB-type transporter SaNsrFP. Sci Rep 2022; 12:4232. [PMID: 35273305 PMCID: PMC8913810 DOI: 10.1038/s41598-022-08095-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
Treatment of bacterial infections is one of the major challenges of our time due to the evolved resistance mechanisms of pathogens against antibiotics. To circumvent this problem, it is necessary to understand the mode of action of the drug and the mechanism of resistance of the pathogen. One of the most potent antibiotic targets is peptidoglycan (PGN) biosynthesis, as this is an exclusively occurring and critical feature of bacteria. Lipid II is an essential PGN precursor synthesized in the cytosol and flipped into the outer leaflet of the membrane prior to its incorporation into nascent PGN. Antimicrobial peptides (AMPs), such as nisin and colistin, targeting PGN synthesis are considered promising weapons against multidrug-resistant bacteria. However, human pathogenic bacteria that were also resistant to these compounds evolved by the expression of an ATP-binding cassette transporter of the bacitracin efflux (BceAB) type localized in the membrane. In the human pathogen Streptococcus agalactiae, the BceAB transporter SaNsrFP is known to confer resistance to the antimicrobial peptide nisin. The exact mechanism of action for SaNsrFP is poorly understood. For a detailed characterization of the resistance mechanism, we heterologously expressed SaNsrFP in Lactococcus lactis. We demonstrated that SaNsrFP conferred resistance not only to nisin but also to a structurally diverse group of antimicrobial PGN-targeting compounds such as ramoplanin, lysobactin, or bacitracin/(Zn)-bacitracin. Growth experiments revealed that SaNsrFP-producing cells exhibited normal behavior when treated with nisin and/or bacitracin, in contrast to the nonproducing cells, for which growth was significantly reduced. We further detected the accumulation of PGN precursors in the cytoplasm after treating the cells with bacitracin. This did not appear when SaNsrFP was produced. Whole-cell proteomic protein experiments verified that the presence of SaNsrFP in L. lactis resulted in higher production of several proteins associated with cell wall modification. These included, for example, the N-acetylmuramic acid-6-phosphate etherase MurQ and UDP-glucose 4-epimerase. Analysis of components of the cell wall of SaNsrFP-producing cells implied that the transporter is involved in cell wall modification. Since we used an ATP-deficient mutant of the transporter as a comparison, we can show that SaNsrFP and its inactive mutant do not show the same phenotype, albeit expressed at similar levels, which demonstrates the ATP dependency of the mediated resistance processes. Taken together, our data agree to a target protection mechanism and imply a direct involvement of SaNsrFP in resistance by shielding the membrane-localized target of these antimicrobial peptides, resulting in modification of the cell wall.
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Affiliation(s)
- Julia Gottstein
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Julia Zaschke-Kriesche
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Sandra Unsleber
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Irina Voitsekhovskaia
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Lara V Behrmann
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Nina Overbeck
- Molecular Proteomics Laboratory, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
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44
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Sharan D, Carlson EE. Expanded profiling of β-lactam selectivity for penicillin-binding proteins in Streptococcus pneumoniae D39. Biol Chem 2022; 403:433-443. [PMID: 35218689 DOI: 10.1515/hsz-2021-0386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022]
Abstract
Penicillin-binding proteins (PBPs) are integral to bacterial cell division as they mediate the final steps of cell wall maturation. Selective fluorescent probes are useful for understanding the role of individual PBPs, including their localization and activity during growth and division of bacteria. For the development of new selective probes for PBP imaging, several β-lactam antibiotics were screened, as they are known to covalently bind PBP in vivo. The PBP inhibition profiles of 16 commercially available β-lactam antibiotics were evaluated in an unencapsulated derivative of the D39 strain of Streptococcus pneumoniae, IU1945. These β-lactams have not previously been characterized for their PBP inhibition profiles in S. pneumoniae and these data augment those obtained from a library of 20 compounds that we previously reported. We investigated seven penicillins, three carbapenems, and six cephalosporins. Most of these β-lactams were found to be co-selective for PBP2x and PBP3, as was noted in our previous studies. Six out of 16 antibiotics were selective for PBP3 and one molecule was co-selective for PBP1a and PBP3. Overall, this work expands the chemical space available for development of future β-lactam-based probes for specific pneumococcal PBP labeling and these methods can be used for the development of probes for PBP labelling in other bacterial species.
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Affiliation(s)
- Deepti Sharan
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA.,Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, MN 55454, USA.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, USA.,Department of Pharmacology, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, USA
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45
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Acebrón-García-de-Eulate M, Mayol-Llinàs J, Holland MTO, Kim SY, Brown KP, Marchetti C, Hess J, Di Pietro O, Mendes V, Abell C, Floto RA, Coyne AG, Blundell TL. Discovery of Novel Inhibitors of Uridine Diphosphate- N-Acetylenolpyruvylglucosamine Reductase (MurB) from Pseudomonas aeruginosa, an Opportunistic Infectious Agent Causing Death in Cystic Fibrosis Patients. J Med Chem 2022; 65:2149-2173. [PMID: 35080396 PMCID: PMC7614804 DOI: 10.1021/acs.jmedchem.1c01684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is of major concern for cystic fibrosis patients where this infection can be fatal. With the emergence of drug-resistant strains, there is an urgent need to develop novel antibiotics against P. aeruginosa. MurB is a promising target for novel antibiotic development as it is involved in the cell wall biosynthesis. MurB has been shown to be essential in P. aeruginosa, and importantly, no MurB homologue exists in eukaryotic cells. A fragment-based drug discovery approach was used to target Pa MurB. This led to the identification of a number of fragments, which were shown to bind to MurB. One fragment, a phenylpyrazole scaffold, was shown by ITC to bind with an affinity of Kd = 2.88 mM (LE 0.23). Using a structure guided approach, different substitutions were synthesized and the initial fragment was optimized to obtain a small molecule with Kd = 3.57 μM (LE 0.35).
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Affiliation(s)
| | - Joan Mayol-Llinàs
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Matthew T O Holland
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Karen P Brown
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Chiara Marchetti
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeannine Hess
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Ornella Di Pietro
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
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46
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Liu Y, Liu S, Zhi Q, Zhuang P, Zhang R, Zhang Z, Zhang K, Sun Y. Arginine-induced metabolomic perturbation in Streptococcus mutans. J Oral Microbiol 2022; 14:2015166. [PMID: 35024088 PMCID: PMC8745357 DOI: 10.1080/20002297.2021.2015166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Streptococcus mutans is a major pathogen responsible for dental caries. Arginine is a promising potential caries preventive agent which can inhibit the growth of S. mutans. However, the mechanism whereby arginine inhibits S. mutans growth remains unclear. Aim To assess the impact of arginine-induced metabolomic perturbations on S. mutans under biofilm conditions. Methods We identified 5,933 and 7,413 ions in positive (ESI+) and negative (ESI-) electrospray ion modes, respectively, with a total of 11.05% and 11.58% differential ions subsequently detected in two respective modes. Further analyses of these metabolites led to identification of 8 and 22 metabolic pathways that were affected by arginine treatment in ESI+ and ESI- modes., Results Once or twice daily treatments of S. mutans biofilms with arginine resulted in reductions in biofilm biomass. Significant reductions in EPS production were observed following twice daily arginine treatments. Identified metabolites that were significantly differentially abundant following arginine treatment were associated with glycolysis metabolism, amino sugar and nucleotide sugar metabolism, and peptidoglycan synthesis. Conclusions Arginine can reduce S. mutans biofilm growth and acid production by inhibiting glycolysis, amino sugar and nucleotide sugar metabolism, and peptidoglycan synthesis.
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Affiliation(s)
- Yudong Liu
- Department of Histology and Embryology, Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Shanshan Liu
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China.,Department of Stomatology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Qinghui Zhi
- Department of Preventive Dentistry, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Peilin Zhuang
- Department of Stomatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Rongxiu Zhang
- Department of Stomatology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Zhenzhen Zhang
- Department of Stomatology, Bengbu Medical College, Bengbu, China
| | - Kai Zhang
- Department of Stomatology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Yu Sun
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, China
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47
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Yussif BM, Checco JW. Evaluation of endogenous peptide stereochemistry using liquid chromatography-mass spectrometry-based spiking experiments. Methods Enzymol 2022; 663:205-234. [DOI: 10.1016/bs.mie.2021.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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48
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Sassine J, Pazos M, Breukink E, Vollmer W. Lytic transglycosylase MltG cleaves in nascent peptidoglycan and produces short glycan strands. Cell Surf 2021; 7:100053. [PMID: 34036206 PMCID: PMC8135044 DOI: 10.1016/j.tcsw.2021.100053] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/17/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria encase their cytoplasmic membrane with peptidoglycan (PG) to maintain the shape of the cell and protect it from bursting. The enlargement of the PG layer is facilitated by the coordinated activities of PG synthesising and -cleaving enzymes. In Escherichia coli, the cytoplasmic membrane-bound lytic transglycosylase MltG associates with PG synthases and was suggested to terminate the polymerisation of PG glycan strands. Using pull-down and surface plasmon resonance, we detected interactions between MltG from Bacillus subtilis and two PG synthases; the class A PBP1 and the class B PBP2B. Using in vitro PG synthesis assays with radio-labelled or fluorophore-labelled B. subtilis-type and/or E. coli-type lipid II, we showed that both, BsMltG and EcMltG, are lytic tranglycosylases and that their activity is higher during ongoing glycan strand polymerisation. MltG competed with the transpeptidase activity of class A PBPs, but had no effect on their glycosyltransferase activity, and produced glycan strands with a length of 7 disaccharide units from cleavage in the nascent strands. We hypothesize that MltG cleaves the nascent strands to produce short glycan strands that are used in the cell for a yet unknown process.
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Affiliation(s)
- Jad Sassine
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Manuel Pazos
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre of Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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49
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Abstract
Most bacteria are protected from environmental offenses by a cell wall consisting of strong yet elastic peptidoglycan. The cell wall is essential for preserving bacterial morphology and viability, and thus the enzymes involved in the production and turnover of peptidoglycan have become preferred targets for many of our most successful antibiotics. In the past decades, Vibrio cholerae, the gram-negative pathogen causing the diarrheal disease cholera, has become a major model for understanding cell wall genetics, biochemistry, and physiology. More than 100 articles have shed light on novel cell wall genetic determinants, regulatory links, and adaptive mechanisms. Here we provide the first comprehensive review of V. cholerae's cell wall biology and genetics. Special emphasis is placed on the similarities and differences with Escherichia coli, the paradigm for understanding cell wall metabolism and chemical structure in gram-negative bacteria.
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Affiliation(s)
- Laura Alvarez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
| | - Sara B Hernandez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
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50
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Belliveau NM, Chure G, Hueschen CL, Garcia HG, Kondev J, Fisher DS, Theriot JA, Phillips R. Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. Cell Syst 2021; 12:924-944.e2. [PMID: 34214468 PMCID: PMC8460600 DOI: 10.1016/j.cels.2021.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/12/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022]
Abstract
Despite abundant measurements of bacterial growth rate, cell size, and protein content, we lack a rigorous understanding of what sets the scale of these quantities and when protein abundances should (or should not) depend on growth rate. Here, we estimate the basic requirements and physical constraints on steady-state growth by considering key processes in cellular physiology across a collection of Escherichia coli proteomic data covering ≈4,000 proteins and 36 growth rates. Our analysis suggests that cells are predominantly tuned for the task of cell doubling across a continuum of growth rates; specific processes do not limit growth rate or dictate cell size. We present a model of proteomic regulation as a function of nutrient supply that reconciles observed interdependences between protein synthesis, cell size, and growth rate and propose that a theoretical inability to parallelize ribosomal synthesis places a firm limit on the achievable growth rate. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Nathan M Belliveau
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Griffin Chure
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina L Hueschen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Hernan G Garcia
- Department of Molecular Cell Biology and Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Daniel S Fisher
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Julie A Theriot
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA.
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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