1
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Kollár L, Grabrijan K, Hrast Rambaher M, Bozovičar K, Imre T, Ferenczy GG, Gobec S, Keserű GM. Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents. J Enzyme Inhib Med Chem 2024; 39:2305833. [PMID: 38410950 PMCID: PMC10901194 DOI: 10.1080/14756366.2024.2305833] [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: 08/29/2023] [Accepted: 01/08/2024] [Indexed: 02/28/2024] Open
Abstract
Penicillin-binding proteins (PBPs) contribute to bacterial cell wall biosynthesis and are targets of antibacterial agents. Here, we investigated PBP1b inhibition by boronic acid derivatives. Chemical starting points were identified by structure-based virtual screening and aliphatic boronic acids were selected for further investigations. Structure-activity relationship studies focusing on the branching of the boron-connecting carbon and quantum mechanical/molecular mechanical simulations showed that reaction barrier free energies are compatible with fast reversible covalent binding and small or missing reaction free energies limit the inhibitory activity of the investigated boronic acid derivatives. Therefore, covalent labelling of the lysine residue of the catalytic dyad was also investigated. Compounds with a carbonyl warhead and an appropriately positioned boronic acid moiety were shown to inhibit and covalently label PBP1b. Reversible covalent labelling of the catalytic lysine by imine formation and the stabilisation of the imine by dative N-B bond is a new strategy for PBP1b inhibition.
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Affiliation(s)
- Levente Kollár
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | | | | | | | - Tímea Imre
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
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2
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Jang H, Kim CM, Hong E, Park HH. Fully closed conformation of penicillin-binding protein revealed by structure of PBP2 from Acinetobacter baumannii. Biochem Biophys Res Commun 2024; 729:150368. [PMID: 38986258 DOI: 10.1016/j.bbrc.2024.150368] [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: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Penicillin-binding protein 2 (PBP2), a vital protein involved in bacterial cell-wall synthesis, serves a target for β-lactam antibiotics. Acinetobacter baumannii is a pathogen notorious for multidrug resistance; therefore, exploration of PBPs is pivotal in the development of new antimicrobial strategies. In this study, the tertiary structure of PBP2 from A. baumannii (abPBP2) was elucidated using X-ray crystallography. The structural analysis demonstrated notable movement in the head domain, potentially critical for its glycosyltransferase function, suggesting that abPBP2 assumes a fully closed conformation. Our findings offer valuable information for developing novel antimicrobial agents targeting abPBP2 that are applicable in combating multidrug-resistant infections.
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Affiliation(s)
- Hyunseok Jang
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Chang Min Kim
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.
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3
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Wang X, Li H, Wu C, Yang J, Wang J, Yang T. Metabolism-triggered sensor array aided by machine learning for rapid identification of pathogens. Biosens Bioelectron 2024; 255:116264. [PMID: 38588629 DOI: 10.1016/j.bios.2024.116264] [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: 02/19/2024] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/10/2024]
Abstract
Chemical-nose strategy has achieved certain success in the discrimination and identification of pathogens. However, this strategy usually relies on non-specific interactions, which are prone to be significantly disturbed by the change of environment thus limiting its practical usefulness. Herein, we present a novel chemical-nose sensing approach leveraging the difference in the dynamic metabolic variation during peptidoglycan metabolism among different species for rapid pathogen discrimination. Pathogens were first tethered with clickable handles through metabolic labeling at two different acidities (pH = 5 and 7) for 20 and 60 min, respectively, followed by click reaction with fluorescence up-conversion nanoparticles to generate a four-dimensional signal output. This discriminative multi-dimensional signal allowed eight types of model bacteria to be successfully classified within the training set into strains, genera, and Gram phenotypes. As the difference in signals of the four sensing channels reflects the difference in the amount/activity of enzymes involved in metabolic labeling, this strategy has good anti-interference capability, which enables precise pathogen identification within 2 h with 100% accuracy in spiked urinary samples and allows classification of unknown species out of the training set into the right phenotype. The robustness of this approach holds significant promise for its widespread application in pathogen identification and surveillance.
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Affiliation(s)
- Xin Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Huida Li
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Chengxin Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jianyu Yang
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jianhua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Ting Yang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
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4
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Dorrazehi GM, Winkle M, Desmet M, Stroobant V, Tanriver G, Degand H, Evrard D, Desguin B, Morsomme P, Biboy J, Gray J, Mitusińska K, Góra A, Vollmer W, Soumillion P. PBP-A, a cyanobacterial DD-peptidase with high specificity for amidated muropeptides, exhibits pH-dependent promiscuous activity harmful to Escherichia coli. Sci Rep 2024; 14:13999. [PMID: 38890528 PMCID: PMC11189452 DOI: 10.1038/s41598-024-64806-x] [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: 02/22/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Penicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) in bacteria. PBP-A from Thermosynechococcus elongatus belongs to a cyanobacterial family of enzymes sharing close structural and phylogenetic proximity to class A β-lactamases. With the long-term aim of converting PBP-A into a β-lactamase by directed evolution, we simulated what may happen when an organism like Escherichia coli acquires such a new PBP and observed growth defect associated with the enzyme activity. To further explore the molecular origins of this harmful effect, we decided to characterize deeper the activity of PBP-A both in vitro and in vivo. We found that PBP-A is an enzyme endowed with DD-carboxypeptidase and DD-endopeptidase activities, featuring high specificity towards muropeptides amidated on the D-iso-glutamyl residue. We also show that a low promiscuous activity on non-amidated peptidoglycan deteriorates E. coli's envelope, which is much higher under acidic conditions where substrate discrimination is mitigated. Besides expanding our knowledge of the biochemical activity of PBP-A, this work also highlights that promiscuity may depend on environmental conditions and how it may hinder rather than promote enzyme evolution in nature or in the laboratory.
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Affiliation(s)
- Gol Mohammad Dorrazehi
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Matthias Winkle
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
- Benchmark Animal Health Ltd, 1 Pioneer Building, Edinburgh Technopole, Milton Bridge, Penicuik, EH26 0GB, UK
| | - Martin Desmet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Vincent Stroobant
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, UCLouvain, Brussels, Belgium
| | - Gamze Tanriver
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100, Gliwice, Poland
| | - Hervé Degand
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Damien Evrard
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Benoît Desguin
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Joe Gray
- Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100, Gliwice, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100, Gliwice, Poland
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium.
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5
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Di Gregorio S, Weltman G, Fabbri C, Fernández S, Zárate S, Smayevsky J, Power P, Campos J, Llarrull LI, Mollerach M. Genetic and Phenotypic Changes Related to the Development of mec-Independent Oxacillin Non-Susceptibility in ST8 Staphylococcus aureus Recovered after Antibiotic Therapy in a Patient with Bacteremia. Antibiotics (Basel) 2024; 13:554. [PMID: 38927220 PMCID: PMC11200602 DOI: 10.3390/antibiotics13060554] [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: 04/26/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The mec-independent oxacillin non-susceptible S. aureus (MIONSA) strains represent a great clinical challenge, as they are not easily detected and can lead to treatment failure. However, the responsible molecular mechanisms are still very little understood. Here, we studied four clinical ST8-MSSA-t024 isolates recovered during the course of antibiotic treatment from a patient suffering successive episodes of bacteremia. The first isolates (SAMS1, SAMS2, and SAMS3) were susceptible to cefoxitin and oxacillin. The last one (SA2) was susceptible to cefoxitin, resistant to oxacillin, lacked mec genes, and had reduced susceptibility to teicoplanin. SA2 showed higher β-lactamase activity than SAMS1. However, β-lactamase hyperproduction could not be linked to oxacillin resistance as it was not inhibited by clavulanic acid, and no genetic changes that could account for its hyperproduction were found. Importantly, we hereby report the in vivo acquisition and coexistence of different adaptive mutations in genes associated with peptidoglycan synthesis (pbp2, rodA, stp1, yjbH, and yvqF/vraT), which is possibly related with the development of oxacillin resistance and reduced susceptibility to teicoplanin in SA2. Using three-dimensional models and PBP binding assays, we demonstrated the high contribution of the SA2 PBP2 Ala450Asp mutation to the observed oxacillin resistance phenotype. Our results should be considered as a warning for physicians and microbiologists in the region, as MIONSA detection and treatment represent an important clinical challenge.
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Affiliation(s)
- Sabrina Di Gregorio
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
| | - Gabriela Weltman
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Carolina Fabbri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, Rosario 2000, Argentina
| | - Silvina Fernández
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Soledad Zárate
- Laboratorio de Bacteriología, Micología y Parasitología, Centro de Educación Médica e Investigaciones Clínicas “Norberto Quirno” (CEMIC), Ciudad Autónoma de Buenos Aires 1431, Argentina
| | - Jorgelina Smayevsky
- Laboratorio de Bacteriología, Micología y Parasitología, Centro de Educación Médica e Investigaciones Clínicas “Norberto Quirno” (CEMIC), Ciudad Autónoma de Buenos Aires 1431, Argentina
| | - Pablo Power
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
| | - Josefina Campos
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282, Argentina
| | - Leticia Irene Llarrull
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, Rosario 2000, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, Rosario 2000, Argentina
| | - Marta Mollerach
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
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6
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Bonardi A, Nocentini A, Giovannuzzi S, Paoletti N, Ammara A, Bua S, Abutaleb NS, Abdelsattar AS, Capasso C, Gratteri P, Flaherty DP, Seleem MN, Supuran CT. Development of Penicillin-Based Carbonic Anhydrase Inhibitors Targeting Multidrug-Resistant Neisseria gonorrhoeae. J Med Chem 2024; 67:9613-9627. [PMID: 38776401 DOI: 10.1021/acs.jmedchem.4c00740] [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: 05/25/2024]
Abstract
The development of antibacterial drugs with new mechanisms of action is crucial in combating the rise of antibiotic-resistant infections. Bacterial carbonic anhydrases (CAs, EC 4.2.1.1) have been validated as promising antibacterial targets against pathogens such as Helicobacter pylori, Neisseria gonorrhoeae, and vancomycin-resistant enterococci. A multitarget strategy is proposed to design penicillin-based CA inhibitor hybrids for tackling resistance by targeting multiple bacterial pathways, thereby resensitizing drug-resistant strains to clinical antibiotics. The sulfonamide derivatives potently inhibited the CAs from N. gonorrhoeae and Escherichia coli with KI values in the range of 7.1-617.2 nM. Computational simulations with the main penicillin-binding protein (PBP) of N. gonorrhoeae indicated that these hybrid derivatives maintained the mechanism of action of the lead β-lactams. A subset of derivatives showed potent PBP-related antigonococcal effects against multidrug-resistant N. gonorrhoeae strains, with several compounds significantly outperforming both the lead β-lactam and CA inhibitor drugs (MIC values in the range 0.25 to 0.5 μg/mL).
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Affiliation(s)
- Alessandro Bonardi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Simone Giovannuzzi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Niccolò Paoletti
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Ammara
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Silvia Bua
- Research Institute of the University of Bucharest (ICUB), Bucharest 050663, Romania
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Abdallah S Abdelsattar
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | | | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
- Center for One Health Research, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
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7
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Salpadoru T, Pinks KE, Lieberman JA, Cotton K, Wozniak KL, Gerasimchuk N, Patrauchan MA. Novel antimony-based antimicrobial drug targets membranes of Gram-positive and Gram-negative bacterial pathogens. Microbiol Spectr 2024; 12:e0423423. [PMID: 38651882 DOI: 10.1128/spectrum.04234-23] [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: 12/21/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a significant worldwide public health crisis that continues to threaten our ability to successfully treat bacterial infections. With the decline in effectiveness of conventional antimicrobial therapies and the lack of new antibiotic pipelines, there is a renewed interest in exploring the potential of metal-based antimicrobial compounds. Antimony-based compounds with a long history of use in medicine have re-emerged as potential antimicrobial agents. We previously synthesized a series of novel organoantimony(V) compounds complexed with cyanoximates with a strong potential of antimicrobial activity against several AMR bacterial and fungal pathogens. Here, five selected compounds were studied for their antibacterial efficacy against three important bacterial pathogens: Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. Among five tested compounds, SbPh4ACO showed antimicrobial activity against all three bacterial strains with the MIC of 50-100 µg/mL. The minimum bactericidal concentration/MIC values were less than or equal to 4 indicating that the effects of SbPh4ACO are bactericidal. Moreover, ultra-thin electron microscopy revealed that SbPh4ACO treatment caused membrane disruption in all three strains, which was further validated by increased membrane permeability. We also showed that SbPh4ACO acted synergistically with the antibiotics, polymyxin B and cefoxitin used to treat AMR strains of P. aeruginosa and S. aureus, respectively, and that at synergistic MIC concentration 12.5 µg/mL, its cytotoxicity against the cell lines, Hela, McCoy, and A549 dropped below the threshold. Overall, the results highlight the antimicrobial potential of novel antimony-based compound, SbPh4ACO, and its use as a potentiator of other antibiotics against both Gram-positive and Gram-negative bacterial pathogens. IMPORTANCE Antibiotic resistance presents a critical global public health crisis that threatens our ability to combat bacterial infections. In light of the declining efficacy of traditional antibiotics, the use of alternative solutions, such as metal-based antimicrobial compounds, has gained renewed interest. Based on the previously synthesized innovative organoantimony(V) compounds, we selected and further characterized the antibacterial efficacy of five of them against three important Gram-positive and Gram-negative bacterial pathogens. Among these compounds, SbPh4ACO showed broad-spectrum bactericidal activity, with membrane-disrupting effects against all three pathogens. Furthermore, we revealed the synergistic potential of SbPh4ACO when combined with antibiotics, such as cefoxitin, at concentrations that exert no cytotoxic effects tested on three mammalian cell lines. This study offers the first report on the mechanisms of action of novel antimony-based antimicrobial and presents the therapeutic potential of SbPh4ACO in combating both Gram-positive and Gram-negative bacterial pathogens while enhancing the efficacy of existing antibiotics.
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Affiliation(s)
- Tarosha Salpadoru
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kevin E Pinks
- Department of Chemistry and Biochemistry, Missouri State University, Springfield, Missouri, USA
| | - Jacob A Lieberman
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kaitlyn Cotton
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Karen L Wozniak
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Nikolay Gerasimchuk
- Department of Chemistry and Biochemistry, Missouri State University, Springfield, Missouri, USA
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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8
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Yang L, Lawhorn S, Bongrand C, Kosmopoulos JC, Kuwabara J, VanNieuwenhze M, Mandel MJ, McFall-Ngai M, Ruby E. Bacterial growth dynamics in a rhythmic symbiosis. Mol Biol Cell 2024; 35:ar79. [PMID: 38598294 DOI: 10.1091/mbc.e24-01-0044] [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: 04/12/2024] Open
Abstract
The symbiotic relationship between the bioluminescent bacterium Vibrio fischeri and the bobtail squid Euprymna scolopes serves as a valuable system to investigate bacterial growth and peptidoglycan (PG) synthesis within animal tissues. To better understand the growth dynamics of V. fischeri in the crypts of the light-emitting organ of its juvenile host, we showed that, after the daily dawn-triggered expulsion of most of the population, the remaining symbionts rapidly proliferate for ∼6 h. At that point the population enters a period of extremely slow growth that continues throughout the night until the next dawn. Further, we found that PG synthesis by the symbionts decreases as they enter the slow-growing stage. Surprisingly, in contrast to the most mature crypts (i.e., Crypt 1) of juvenile animals, most of the symbiont cells in the least mature crypts (i.e., Crypt 3) were not expelled and, instead, remained in the slow-growing state throughout the day, with almost no cell division. Consistent with this observation, the expression of the gene encoding the PG-remodeling enzyme, L,D-transpeptidase (LdtA), was greatest during the slowly growing stage of Crypt 1 but, in contrast, remained continuously high in Crypt 3. Finally, deletion of the ldtA gene resulted in a symbiont that grew and survived normally in culture, but was increasingly defective in competing against its parent strain in the crypts. This result suggests that remodeling of the PG to generate additional 3-3 linkages contributes to the bacterium's fitness in the symbiosis, possibly in response to stresses encountered during the very slow-growing stage.
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Affiliation(s)
- Liu Yang
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - Susannah Lawhorn
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - Clotilde Bongrand
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - James C Kosmopoulos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Jill Kuwabara
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | | | - Mark J Mandel
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706
| | - Margaret McFall-Ngai
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Edward Ruby
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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9
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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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10
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Kang SJ, Kim DH, Lee BJ. Metallo-β-lactamase inhibitors: A continuing challenge for combating antibiotic resistance. Biophys Chem 2024; 309:107228. [PMID: 38552402 DOI: 10.1016/j.bpc.2024.107228] [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: 12/29/2023] [Revised: 03/18/2024] [Accepted: 03/23/2024] [Indexed: 04/22/2024]
Abstract
β-lactam antibiotics are the most successful and commonly used antibacterial agents, but the emergence of resistance to these drugs has become a global health threat. The expression of β-lactamase enzymes produced by pathogens, which hydrolyze the amide bond of the β-lactam ring, is the major mechanism for bacterial resistance to β-lactams. In particular, among class A, B, C and D β-lactamases, metallo-β-lactamases (MBLs, class B β-lactamases) are considered crucial contributors to resistance in gram-negative bacteria. To combat β-lactamase-mediated resistance, great efforts have been made to develop β-lactamase inhibitors that restore the activity of β-lactams. Some β-lactamase inhibitors, such as diazabicyclooctanes (DBOs) and boronic acid derivatives, have also been approved by the FDA. Inhibitors used in the clinic can inactivate mostly serine-β-lactamases (SBLs, class A, C, and D β-lactamases) but have not been effective against MBLs until now. In order to develop new inhibitors particularly for MBLs, various attempts have been suggested. Based on structural and mechanical studies of MBL enzymes, several MBL inhibitor candidates, including taniborbactam in phase 3 and xeruborbactam in phase 1, have been introduced in recent years. However, designing potent inhibitors that are effective against all subclasses of MBLs is still extremely challenging. This review summarizes not only the types of β-lactamase and mechanisms by which β-lactam antibiotics are inactivated, but also the research finding on β-lactamase inhibitors targeting these enzymes. These detailed information on β-lactamases and their inhibitors could give valuable information for novel β-lactamase inhibitors design.
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Affiliation(s)
- Su-Jin Kang
- College of Pharmacy, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Do-Hee Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea; Mastermeditech Ltd., Seoul 07793, Republic of Korea.
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11
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Zhang T, Nickerson R, Zhang W, Peng X, Shang Y, Zhou Y, Luo Q, Wen G, Cheng Z. The impacts of animal agriculture on One Health-Bacterial zoonosis, antimicrobial resistance, and beyond. One Health 2024; 18:100748. [PMID: 38774301 PMCID: PMC11107239 DOI: 10.1016/j.onehlt.2024.100748] [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: 08/28/2023] [Accepted: 05/02/2024] [Indexed: 05/24/2024] Open
Abstract
The industrialization of animal agriculture has undoubtedly contributed to the improvement of human well-being by increasing the efficiency of food animal production. At the same time, it has also drastically impacted the natural environment and human society. The One Health initiative emphasizes the interdependency of the health of ecosystems, animals, and humans. In this paper, we discuss some of the most profound consequences of animal agriculture practices from a One Health perspective. More specifically, we focus on impacts to host-microbe interactions by elaborating on how modern animal agriculture affects zoonotic infections, specifically those of bacterial origin, and the concomitant emergence of antimicrobial resistance (AMR). A key question underlying these deeply interconnected issues is how to better prevent, monitor, and manage infections in animal agriculture. To address this, we outline approaches to mitigate the impacts of agricultural bacterial zoonoses and AMR, including the development of novel treatments as well as non-drug approaches comprising integrated surveillance programs and policy and education regarding agricultural practices and antimicrobial stewardship. Finally, we touch upon additional major environmental and health factors impacted by animal agriculture within the One Health context, including animal welfare, food security, food safety, and climate change. Charting how these issues are interwoven to comprise the complex web of animal agriculture's broad impacts on One Health will allow for the development of concerted, multidisciplinary interventions which are truly necessary to tackle these issues from a One Health perspective.
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Affiliation(s)
- Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Rhea Nickerson
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Wenting Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xitian Peng
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
- Hubei Key Laboratory of Nutritional Quality and Safety of Agro-products, Wuhan 430064, Hubei, China
- Ministry of Agriculture and Rural Affairs Laboratory of Quality and Safe Risk Assessment for Agro-products (Wuhan), Wuhan 430064, Hubei, China
| | - Yu Shang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Youxiang Zhou
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
- Hubei Key Laboratory of Nutritional Quality and Safety of Agro-products, Wuhan 430064, Hubei, China
- Ministry of Agriculture and Rural Affairs Laboratory of Quality and Safe Risk Assessment for Agro-products (Wuhan), Wuhan 430064, Hubei, China
| | - Qingping Luo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Hongshan Laboratory, Wuhan 430064, China
| | - Guoyuan Wen
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Zhenyu Cheng
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
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12
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Choi HJ, Ki DU, Yoon SI. Structural and biochemical analysis of penicillin-binding protein 2 from Campylobacter jejuni. Biochem Biophys Res Commun 2024; 710:149859. [PMID: 38581948 DOI: 10.1016/j.bbrc.2024.149859] [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: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
Penicillin-binding protein 2 (PBP2) plays a key role in the formation of peptidoglycans in bacterial cell walls by crosslinking glycan chains through transpeptidase activity. PBP2 is also found in Campylobacter jejuni, a pathogenic bacterium that causes food-borne enteritis in humans. To elucidate the essential structural features of C. jejuni PBP2 (cjPBP2) that mediate its biological function, we determined the crystal structure of cjPBP2 and assessed its protein stability under various conditions. cjPBP2 adopts an elongated two-domain structure, consisting of a transpeptidase domain and a pedestal domain, and contains typical active site residues necessary for transpeptidase activity, as observed in other PBP2 proteins. Moreover, cjPBP2 responds to β-lactam antibiotics, including ampicillin, cefaclor, and cefmetazole, suggesting that β-lactam antibiotics inactivate cjPBP2. In contrast to typical PBP2 proteins, cjPBP2 is a rare example of a Zn2+-binding PBP2 protein, as the terminal structure of its transpeptidase domain accommodates a Zn2+ ion via three cysteine residues and one histidine residue. Zn2+ binding helps improve the protein stability of cjPBP2, providing opportunities to develop new C. jejuni-specific antibacterial drugs that counteract the Zn2+-binding ability of cjPBP2.
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Affiliation(s)
- Hong Joon Choi
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Dong Uk Ki
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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13
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Shirley JD, Nauta KM, Gillingham JR, Diwakar S, Carlson EE. kinact / KI Value Determination for Penicillin-Binding Proteins in Live Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592586. [PMID: 38746240 PMCID: PMC11092749 DOI: 10.1101/2024.05.05.592586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Penicillin-binding proteins (PBPs) are an essential family of bacterial enzymes that are inhibited by the β-lactam class of antibiotics. PBP inhibition disrupts cell wall biosynthesis, which results in deficient growth and proliferation, and ultimately leads to lysis. IC 50 values are often employed as descriptors of enzyme inhibition and inhibitor selectivity but can be misleading in the study of time-dependent, irreversible inhibitors. Due to this disconnect, the second order rate constant k inact / K I is a more appropriate metric of covalent inhibitor potency. Despite being the gold standard measurement of potency, k inact / K I values are typically obtained from in vitro assays, which limits assay throughput if investigating an enzyme family with multiple homologs (such as the PBPs). Therefore, we developed a whole-cell k inact / K I assay to define inhibitor potency for the PBPs in Streptococcus pneumoniae using the fluorescent activity-based probe Bocillin-FL. Our results align with in vitro k inact / K I data and show a comparable relationship to previously established IC 50 values. These results support the validity of our in vivo k inact / K I method as a means of obtaining a full picture of β-lactam potency for a suite of PBPs. Abstract Figure
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14
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Jiang W, Lin T, Pan J, Rivera CE, Tincher C, Wang Y, Zhang Y, Gao X, Wang Y, Tsui HCT, Winkler ME, Lynch M, Long H. Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:198-211. [PMID: 38827133 PMCID: PMC11136922 DOI: 10.1007/s42995-024-00220-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 03/04/2024] [Indexed: 06/04/2024]
Abstract
Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic stability. However, our study of the wild-type Streptococcus pneumoniae D39, a pathogen responsible for many common diseases, revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation (MA) lines. This rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T direction. The high mutation rate may have resulted from a reduction in the overall efficiency of selection, conferred by the tiny effective population size in nature. In line with this, S. pneumoniae D39 also exhibited the lowest DNA mismatch-repair (MMR) efficiency among bacteria. Treatment with the antibiotic penicillin did not elevate the mutation rate, as penicillin did not induce DNA damage and S. pneumoniae lacks a stress response pathway. Our findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00220-6.
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Affiliation(s)
- Wanyue Jiang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Caitlyn E. Rivera
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | - Clayton Tincher
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Yu Zhang
- School of Mathematics Science, Ocean University of China, Qingdao, 266000 China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, Qingdao, 266237 China
| | - Yan Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Ho-Ching T. Tsui
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | | | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
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15
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Wang X, Lee JC. Staphylococcus aureus membrane vesicles: an evolving story. Trends Microbiol 2024:S0966-842X(24)00088-X. [PMID: 38677977 DOI: 10.1016/j.tim.2024.04.003] [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: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/29/2024]
Abstract
Staphylococcus aureus is an important bacterial pathogen that causes a wide variety of human diseases in community and hospital settings. S. aureus employs a diverse array of virulence factors, both surface-associated and secreted, to promote colonization, infection, and immune evasion. Over the past decade, a growing body of research has shown that S. aureus generates extracellular membrane vesicles (MVs) that package a variety of bacterial components, many of which are virulence factors. In this review, we summarize recent advances in our understanding of S. aureus MVs and highlight their biogenesis, cargo, and potential role in the pathogenesis of staphylococcal infections. Lastly, we present some emerging questions in the field.
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Affiliation(s)
- Xiaogang Wang
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA.
| | - Jean C Lee
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
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16
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Hsu TW, Fang JM. Advances and prospects of analytic methods for bacterial transglycosylation and inhibitor discovery. Analyst 2024; 149:2204-2222. [PMID: 38517346 DOI: 10.1039/d3an01968c] [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: 03/23/2024]
Abstract
The cell wall is essential for bacteria to maintain structural rigidity and withstand external osmotic pressure. In bacteria, the cell wall is composed of peptidoglycan. Lipid II is the basic unit for constructing highly cross-linked peptidoglycan scaffolds. Transglycosylase (TGase) is the initiating enzyme in peptidoglycan synthesis that catalyzes the ligation of lipid II moieties into repeating GlcNAc-MurNAc polysaccharides, followed by transpeptidation to generate cross-linked structures. In addition to the transglycosylases in the class-A penicillin-binding proteins (aPBPs), SEDS (shape, elongation, division and sporulation) proteins are also present in most bacteria and play vital roles in cell wall renewal, elongation, and division. In this review, we focus on the latest analytical methods including the use of radioactive labeling, gel electrophoresis, mass spectrometry, fluorescence labeling, probing undecaprenyl pyrophosphate, fluorescence anisotropy, ligand-binding-induced tryptophan fluorescence quenching, and surface plasmon resonance to evaluate TGase activity in cell wall formation. This review also covers the discovery of TGase inhibitors as potential antibacterial agents. We hope that this review will give readers a better understanding of the chemistry and basic research for the development of novel antibiotics.
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Affiliation(s)
- Tse-Wei Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
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17
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Turner JM, Stratton CM, Bala S, Cardenas Alvarez M, Nicholas RA, Davies C. Ureidopenicillins Are Potent Inhibitors of Penicillin-Binding Protein 2 from Multidrug-Resistant Neisseria gonorrhoeae H041. ACS Infect Dis 2024; 10:1298-1311. [PMID: 38446051 DOI: 10.1021/acsinfecdis.3c00713] [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: 03/07/2024]
Abstract
Effective treatment of gonorrhea is threatened by the increasing prevalence of Neisseria gonorrhoeae strains resistant to the extended-spectrum cephalosporins (ESCs). Recently, we demonstrated the promise of the third-generation cephalosporin cefoperazone as an antigonococcal agent due to its rapid second-order rate of acylation against penicillin-binding protein 2 (PBP2) from the ESC-resistant strain H041 and robust antimicrobial activity against H041. Noting the presence of a ureido moiety in cefoperazone, we evaluated a subset of structurally similar ureido β-lactams, including piperacillin, azlocillin, and mezlocillin, for activity against PBP2 from H041 using biochemical and structural analyses. We found that the ureidopenicillin piperacillin has a second-order rate of acylation against PBP2 that is 12-fold higher than cefoperazone and 85-fold higher than ceftriaxone and a lower MIC against H041 than ceftriaxone. Surprisingly, the affinity of ureidopenicillins for PBP2 is minimal, indicating that their inhibitory potency is due to a higher rate of the acylation step of the reaction compared to cephalosporins. Enhanced acylation results from the combination of a penam scaffold with a 2,3-dioxopiperazine-containing R1 group. Crystal structures show that the ureido β-lactams overcome the effects of resistance mutations present in PBP2 from H041 by eliciting conformational changes that are hindered when PBP2 interacts with the weaker inhibitor ceftriaxone. Overall, our results support the potential of piperacillin as a treatment for gonorrhea and provide a framework for the future design of β-lactams with improved activity against ESC-resistant N. gonorrhoeae.
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Affiliation(s)
- Jonathan M Turner
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Caleb M Stratton
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama 36688, United States
| | - Sandeepchowdary Bala
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama 36688, United States
| | - Maria Cardenas Alvarez
- Departments of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Robert A Nicholas
- Departments of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Christopher Davies
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama 36688, United States
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18
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Razew A, Herail Q, Miyachiro M, Anoyatis-Pelé C, Bougault C, Dessen A, Arthur M, Simorre JP. Monitoring Drug-Protein Interactions in the Bacterial Periplasm by Solution Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2024; 146:9252-9260. [PMID: 38500259 DOI: 10.1021/jacs.4c00604] [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: 03/20/2024]
Abstract
The rapid spread of antimicrobial resistance across bacterial pathogens poses a serious risk to the efficacy and sustainability of available treatments. This puts pressure on research concerning the development of new drugs. Here, we present an in-cell NMR-based research strategy to monitor the activity of the enzymes located in the periplasmic space delineated by the inner and outer membranes of Gram-negative bacteria. We demonstrate its unprecedented analytical power in monitoring in situ and in real time (i) the hydrolysis of β-lactams by β-lactamases, (ii) the interaction of drugs belonging to the β-lactam family with their essential targets, and (iii) the binding of inhibitors to these enzymes. We show that in-cell NMR provides a powerful analytical tool for investigating new drugs targeting the molecular components of the bacterial periplasm.
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Affiliation(s)
- Alicja Razew
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Quentin Herail
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Mayara Miyachiro
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | | | - Catherine Bougault
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Andrea Dessen
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Michel Arthur
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Jean-Pierre Simorre
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
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19
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Marchant P, Vivanco E, Silva A, Nevermann J, Fuentes I, Barrera B, Otero C, Calderón IL, Gil F, Fuentes JA. β-lactam-induced OMV release promotes polymyxin tolerance in Salmonella enterica sv. Typhi. Front Microbiol 2024; 15:1389663. [PMID: 38591031 PMCID: PMC10999688 DOI: 10.3389/fmicb.2024.1389663] [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: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
The rise of multidrug-resistant bacteria is a global concern, leading to a renewed reliance on older antibiotics like polymyxins as a last resort. Polymyxins, cationic cyclic peptides synthesized nonribosomally, feature a hydrophobic acyl tail and positively charged residues. Their antimicrobial mechanism involves initial interaction with Gram-negative bacterial outer-membrane components through polar and hydrophobic interactions. Outer membrane vesicles (OMVs), nano-sized proteoliposomes secreted from the outer membrane of Gram-negative bacteria, play a crucial role in tolerating harmful molecules, including cationic peptides such as polymyxins. Existing literature has documented environmental changes' impact on modulating OMV properties in Salmonella Typhimurium. However, less information exists regarding OMV production and characteristics in Salmonella Typhi. A previous study in our laboratory showed that S. Typhi ΔmrcB, a mutant associated with penicillin-binding protein (PBP, a β-lactam antibiotic target), exhibited hypervesiculation. Consequently, this study investigated the potential impact of β-lactam antibiotics on promoting polymyxin tolerance via OMVs in S. Typhi. Our results demonstrated that sub-lethal doses of β-lactams increased bacterial survival against polymyxin B in S. Typhi. This phenomenon stems from β-lactam antibiotics inducing hypervesiculation of OMVs with higher affinity for polymyxin B, capturing and diminishing its biologically effective concentration. These findings suggest that β-lactam antibiotic use may inadvertently contribute to decreased polymyxin effectivity against S. Typhi or other Gram-negative bacteria, complicating the effective treatment of infections caused by these pathogens. This study emphasizes the importance of evaluating the influence of β-lactam antibiotics on the interaction between OMVs and other antimicrobial agents.
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Affiliation(s)
- Pedro Marchant
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Erika Vivanco
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Andrés Silva
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jan Nevermann
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Ignacio Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Boris Barrera
- Escuela de Tecnología Médica, Facultad de Salud, Universidad Santo Tomás, Santiago, Chile
| | - Carolina Otero
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Iván L. Calderón
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Fernando Gil
- Microbiota-Host Interactions and Clostridia Research Group, Universidad Andres Bello, Santiago, Chile
| | - Juan A. Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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20
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Lee C, Han SI, Na H, Kim Z, Ahn JW, Oh B, Kim HS. Comprehensive understanding of the mutant 'giant' Arthrospira platensis developed via ultraviolet mutagenesis. FRONTIERS IN PLANT SCIENCE 2024; 15:1369976. [PMID: 38567133 PMCID: PMC10985164 DOI: 10.3389/fpls.2024.1369976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Introduction Cyanobacteria are typically of a size that can be observed under a microscope. Here, we present cyanobacteria of a size that can be observed with the naked eye. Arthrospira platensis NCB002 strain showed differentiated morphological characteristics compared to previously reported Arthrospira spp. Methods Arthrospira platensis NCB002 was obtained by the UV irradiation of Arthrospira sp. NCB001, which was isolated from freshwater and owned by NCell Co., Ltd. A. platensis NIES-39 was obtained from the National Institute for Environmental Studies (Tsukuba, Japan). We used various analytical techniques to determine its overall characteristics. Results and discussion The draft genome of strain NCB002 consists of five contigs comprising 6,864,973 bp with a G+C content of 44.3 mol%. The strain NCB002 had an average length of 11.69 ± 1.35 mm and a maximum of 15.15 mm, which is 23.4-50.5 times longer than the length (0.3-0.5 mm) of previously known Arthrospira spp., allowing it to be harvested using a thin sieve. Transcriptome analysis revealed that these morphological differences resulted from changes in cell wall formation mechanisms and increased cell division. Our results show that NCB002 has outstanding industrial value and provides a comprehensive understanding of it.
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Affiliation(s)
- Changsu Lee
- Bio Division, NCell. Co., Ltd., Seoul, Republic of Korea
| | - Sang-Il Han
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Ho Na
- Bio Division, NCell. Co., Ltd., Seoul, Republic of Korea
| | - Zun Kim
- Bio Division, NCell. Co., Ltd., Seoul, Republic of Korea
| | - Joon Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Byeolnim Oh
- Department of Electronic Engineering, Kwangwoon University, Seoul, Republic of Korea
| | - Hyun Soo Kim
- Department of Electronic Engineering, Kwangwoon University, Seoul, Republic of Korea
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21
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Zhang S, Liao X, Ding T, Ahn J. Role of β-Lactamase Inhibitors as Potentiators in Antimicrobial Chemotherapy Targeting Gram-Negative Bacteria. Antibiotics (Basel) 2024; 13:260. [PMID: 38534695 DOI: 10.3390/antibiotics13030260] [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: 02/25/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
Since the discovery of penicillin, β-lactam antibiotics have commonly been used to treat bacterial infections. Unfortunately, at the same time, pathogens can develop resistance to β-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems by producing β-lactamases. Therefore, a combination of β-lactam antibiotics with β-lactamase inhibitors has been a promising approach to controlling β-lactam-resistant bacteria. The discovery of novel β-lactamase inhibitors (BLIs) is essential for effectively treating antibiotic-resistant bacterial infections. Therefore, this review discusses the development of innovative inhibitors meant to enhance the activity of β-lactam antibiotics. Specifically, this review describes the classification and characteristics of different classes of β-lactamases and the synergistic mechanisms of β-lactams and BLIs. In addition, we introduce potential sources of compounds for use as novel BLIs. This provides insights into overcoming current challenges in β-lactamase-producing bacteria and designing effective treatment options in combination with BLIs.
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Affiliation(s)
- Song Zhang
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Xinyu Liao
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
| | - Tian Ding
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
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22
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Bollinger KW, Müh U, Ocius KL, Apostolos AJ, Pires MM, Helm RF, Popham DL, Weiss DS, Ellermeier CD. Identification of a new family of peptidoglycan transpeptidases reveals atypical crosslinking is essential for viability in Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.584917. [PMID: 38559057 PMCID: PMC10980060 DOI: 10.1101/2024.03.14.584917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Clostridioides difficile, the leading cause of antibiotic-associated diarrhea, relies primarily on 3-3 crosslinks created by L,D-transpeptidases (LDTs) to fortify its peptidoglycan (PG) cell wall. This is unusual, as in most bacteria the vast majority of PG crosslinks are 4-3 crosslinks, which are created by penicillin-binding proteins (PBPs). Here we report the unprecedented observation that 3-3 crosslinking is essential for viability in C. difficile. We also report the discovery of a new family of LDTs that use a VanW domain to catalyze 3-3 crosslinking rather than a YkuD domain as in all previously known LDTs. Bioinformatic analyses indicate VanW domain LDTs are less common than YkuD domain LDTs and are largely restricted to Gram-positive bacteria. Our findings suggest that LDTs might be exploited as targets for antibiotics that kill C. difficile without disrupting the intestinal microbiota that is important for keeping C. difficile in check.
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Affiliation(s)
- Kevin W. Bollinger
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ute Müh
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Karl L. Ocius
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
- Present address: Haleon, 1211 Sherwood Ave, Richmond, VA 23220
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Richard F. Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - David S. Weiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Graduate Program in Genetics, University of Iowa, Iowa City, IA USA
| | - Craig D. Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Graduate Program in Genetics, University of Iowa, Iowa City, IA USA
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23
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Araten AH, Brooks RS, Choi SDW, Esguerra LL, Savchyn D, Wu EJ, Leon G, Sniezek KJ, Brynildsen MP. Cephalosporin resistance, tolerance, and approaches to improve their activities. J Antibiot (Tokyo) 2024; 77:135-146. [PMID: 38114565 DOI: 10.1038/s41429-023-00687-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/23/2023] [Accepted: 11/05/2023] [Indexed: 12/21/2023]
Abstract
Cephalosporins comprise a β-lactam antibiotic class whose first members were discovered in 1945 from the fungus Cephalosporium acremonium. Their clinical use for Gram-negative bacterial infections is widespread due to their ability to traverse outer membranes through porins to gain access to the periplasm and disrupt peptidoglycan synthesis. More recent members of the cephalosporin class are administered as last resort treatments for complicated urinary tract infections, MRSA, and other multi-drug resistant pathogens, such as Neisseria gonorrhoeae. Unfortunately, there has been a global increase in cephalosporin-resistant strains, heteroresistance to this drug class has been a topic of increasing concern, and tolerance and persistence are recognized as potential causes of cephalosporin treatment failure. In this review, we summarize the cephalosporin antibiotic class from discovery to their mechanisms of action, and discuss the causes of cephalosporin treatment failure, which include resistance, tolerance, and phenomena when those qualities are exhibited by only small subpopulations of bacterial cultures (heteroresistance and persistence). Further, we discuss how recent efforts with cephalosporin conjugates and combination treatments aim to reinvigorate this antibiotic class.
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Affiliation(s)
- Alison H Araten
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Rachel S Brooks
- Department of English, Princeton University, Princeton, NJ, USA
| | - Sarah D W Choi
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Laura L Esguerra
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Diana Savchyn
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Emily J Wu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Gabrielle Leon
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Katherine J Sniezek
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
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24
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Djorić D, Atkinson SN, Kristich CJ. Reciprocal regulation of enterococcal cephalosporin resistance by products of the autoregulated yvcJ-glmR-yvcL operon enhances fitness during cephalosporin exposure. PLoS Genet 2024; 20:e1011215. [PMID: 38512984 PMCID: PMC10986989 DOI: 10.1371/journal.pgen.1011215] [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: 08/18/2023] [Revised: 04/02/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Enterococci are commensal members of the gastrointestinal tract and also major nosocomial pathogens. They possess both intrinsic and acquired resistance to many antibiotics, including intrinsic resistance to cephalosporins that target bacterial cell wall synthesis. These antimicrobial resistance traits make enterococcal infections challenging to treat. Moreover, prior therapy with antibiotics, including broad-spectrum cephalosporins, promotes enterococcal proliferation in the gut, resulting in dissemination to other sites of the body and subsequent infection. As a result, a better understanding of mechanisms of cephalosporin resistance is needed to enable development of new therapies to treat or prevent enterococcal infections. We previously reported that flow of metabolites through the peptidoglycan biosynthesis pathway is one determinant of enterococcal cephalosporin resistance. One factor that has been implicated in regulating flow of metabolites into cell wall biosynthesis pathways of other Gram-positive bacteria is GlmR. In enterococci, GlmR is encoded as the middle gene of a predicted 3-gene operon along with YvcJ and YvcL, whose functions are poorly understood. Here we use genetics and biochemistry to investigate the function of the enterococcal yvcJ-glmR-yvcL gene cluster. Our results reveal that YvcL is a DNA-binding protein that regulates expression of the yvcJ-glmR-yvcL operon in response to cell wall stress. YvcJ and GlmR bind UDP-GlcNAc and reciprocally regulate cephalosporin resistance in E. faecalis, and binding of UDP-GlcNAc by YvcJ appears essential for its activity. Reciprocal regulation by YvcJ/GlmR is essential for fitness during exposure to cephalosporin stress. Additionally, our results indicate that enterococcal GlmR likely acts by a different mechanism than the previously studied GlmR of Bacillus subtilis, suggesting that the YvcJ/GlmR regulatory module has evolved unique targets in different species of bacteria.
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Affiliation(s)
- Dušanka Djorić
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Samantha N. Atkinson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Center for Microbiome Research, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Christopher J. Kristich
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
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25
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George JL, Agbavor C, Cabo LF, Cahoon LA. Streptococcus pneumoniae secretion chaperones PrsA, SlrA, and HtrA are required for competence, antibiotic resistance, colonization, and invasive disease. Infect Immun 2024; 92:e0049023. [PMID: 38226817 PMCID: PMC10863415 DOI: 10.1128/iai.00490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Streptococcus pneumoniae is a Gram-positive bacterium and a significant health threat with the populations most at risk being children, the elderly, and the immuno-compromised. To colonize and transition into an invasive infectious organism, S. pneumoniae secretes virulence factors that are translocated across the bacterial membrane and destined for surface exposure, attachment to the cell wall, or secretion into the host. The surface exposed protein chaperones PrsA, SlrA, and HtrA facilitate S. pneumoniae protein secretion; however, the distinct roles contributed by each of these secretion chaperones have not been well defined. Tandem Mass-Tagged Mass Spectrometry and virulence, adhesion, competence, and cell wall integrity assays were used to interrogate the individual and collective contributions of PrsA, SlrA, and HtrA to multiple aspects of S. pneumoniae physiology and virulence. PrsA, SlrA, and HtrA were found to play critical roles in S. pneumoniae host cell infection and competence, and the absence of each of these secretion chaperones significantly altered the S. pneumoniae secretome in distinct ways. PrsA and SlrA were additionally found to contribute to cell wall assembly and resistance to cell wall-active antimicrobials and were important for enabling S. pneumoniae host cell adhesion during colonization and invasive infection. These findings serve to further illustrate the pivotal contributions of PrsA, SlrA, and HtrA to S. pneumoniae protein secretion and virulence.
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Affiliation(s)
- Jada L. George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah F. Cabo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Laty A. Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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26
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Koatale P, Welling MM, Ndlovu H, Kgatle M, Mdanda S, Mdlophane A, Okem A, Takyi-Williams J, Sathekge MM, Ebenhan T. Insights into Peptidoglycan-Targeting Radiotracers for Imaging Bacterial Infections: Updates, Challenges, and Future Perspectives. ACS Infect Dis 2024; 10:270-286. [PMID: 38290525 PMCID: PMC10862554 DOI: 10.1021/acsinfecdis.3c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 02/01/2024]
Abstract
The unique structural architecture of the peptidoglycan allows for the stratification of bacteria as either Gram-negative or Gram-positive, which makes bacterial cells distinguishable from mammalian cells. This classification has received attention as a potential target for diagnostic and therapeutic purposes. Bacteria's ability to metabolically integrate peptidoglycan precursors during cell wall biosynthesis and recycling offers an opportunity to target and image pathogens in their biological state. This Review explores the peptidoglycan biosynthesis for bacteria-specific targeting for infection imaging. Current and potential radiolabeled peptidoglycan precursors for bacterial infection imaging, their development status, and their performance in vitro and/or in vivo are highlighted. We conclude by providing our thoughts on how to shape this area of research for future clinical translation.
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Affiliation(s)
- Palesa
C. Koatale
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mick M. Welling
- Interventional
Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Honest Ndlovu
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mankgopo Kgatle
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Sipho Mdanda
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Amanda Mdlophane
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Ambrose Okem
- Department
of Anaesthesia, School of Clinical Medicine, University of Witwatersrand, 2050 Johannesburg, South Africa
| | - John Takyi-Williams
- Pharmacokinetic
and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mike M. Sathekge
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Thomas Ebenhan
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
- DSI/NWU Pre-clinical
Drug Development Platform, North West University, 2520 Potchefstroom, South Africa
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27
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Wu XY, Zhao ZY, Osman EEA, Wang XJ, Choo YM, Benjamin MM, Xiong J, Hamann MT, Luo C, Hu JF. Platanosides from Platanus × acerifolia: New molecules, SAR, and target validation of a strong lead for drug-resistant bacterial infections and the associated sepsis. Bioorg Chem 2024; 143:107103. [PMID: 38211549 DOI: 10.1016/j.bioorg.2024.107103] [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: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
Three undescribed (1-3) and nine known (4-12) platanosides were isolated and characterized from a bioactive extract of the May leaves of Platanus × acerifolia that initially showed inhibition against Staphylococcus aureus. Targeted compound mining was guided by an LC-MS/MS-based molecular ion networking (MoIN) strategy combined with conventional isolation procedures from a unique geographic location. The novel structures were mainly determined by 2D NMR and computational (NMR/ECD calculations) methods. Compound 1 is a rare acylated kaempferol rhamnoside possessing a truxinate unit. 6 (Z,E-platanoside) and 7 (E,E-platanoside) were confirmed to have remarkable inhibitory effects against both methicillin-resistant S. aureus (MIC: ≤ 16 μg/mL) and glycopeptide-resistant Enterococcus faecium (MIC: ≤ 1 μg/mL). These platanosides were subjected to docking analyses against FabI (enoyl-ACP reductase) and PBP1/2 (penicillin binding protein), both of which are pivotal enzymes governing bacterial growth but not found in the human host. The results showed that 6 and 7 displayed superior binding affinities towards FabI and PBP2. Moreover, surface plasmon resonance studies on the interaction of 1/7 and FabI revealed that 7 has a higher affinity (KD = 1.72 μM), which further supports the above in vitro data and is thus expected to be a novel anti-antibacterial drug lead.
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Affiliation(s)
- Xi-Ying Wu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China; Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, PR China
| | - Ze-Yu Zhao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Ezzat E A Osman
- Department of Medicinal Chemistry, Theodor Bilharz Research Institute, Kornaish El-Nile St., Giza 12411, Egypt
| | - Xiao-Juan Wang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, Gansu, PR China; Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA
| | - Yeun-Mun Choo
- Chemistry Department, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Menny M Benjamin
- Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Mark T Hamann
- Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA.
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, PR China
| | - Jin-Feng Hu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China; Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA.
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28
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Kang SM, Kim DH. Structural Insights into the Penicillin-Binding Protein 4 (DacB) from Mycobacterium tuberculosis. Int J Mol Sci 2024; 25:983. [PMID: 38256057 PMCID: PMC10815838 DOI: 10.3390/ijms25020983] [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: 12/19/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Mycobacterium tuberculosis, a major cause of mortality from a single infectious agent, possesses a remarkable mycobacterial cell envelope. Penicillin-Binding Proteins (PBPs) are a family of bacterial enzymes involved in the biosynthesis of peptidoglycan. PBP4 (DacB) from M. tuberculosis (MtbPBP4) has been known to function as a carboxypeptidase, and the role and significance of carboxypeptidases as targets for anti-tuberculosis drugs or antibiotics have been extensively investigated over the past decade. However, their precise involvement remains incompletely understood. In this study, we employed predictive modeling and analyzed the three-dimensional structure of MtbPBP4. Interestingly, MtbPBP4 displayed a distinct domain structure compared to its homologs. Docking studies with meropenem verified the presence of active site residues conserved in PBPs. These findings establish a structural foundation for comprehending the molecular function of MtbPBP4 and offer a platform for the exploration of novel antibiotics.
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Affiliation(s)
- Sung-Min Kang
- College of Pharmacy, Duksung Women’s University, Seoul 01369, Republic of Korea
| | - Do-Hee Kim
- Jeju Research Institute of Pharmaceutical Sciences, College of Pharmacy, Jeju National University, Jeju 63243, Republic of Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Republic of Korea
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29
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Park S, Fan J, Chamakuri S, Palaniappan M, Sharma K, Qin X, Wang J, Tan Z, Judge A, Hu L, Sankaran B, Li F, Prasad BVV, Matzuk MM, Palzkill T. Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. J Med Chem 2024; 67:620-642. [PMID: 38117688 DOI: 10.1021/acs.jmedchem.3c01834] [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: 12/22/2023]
Abstract
β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.
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Affiliation(s)
- Suhyeorn Park
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kiran Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Martin M Matzuk
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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30
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Conti P, Lazzaro LM, Longo F, Lenzo F, Giardina A, Fortuna SA, Stefani S, Campanile F. Unveiling the Relationship between Ceftobiprole and High-Molecular-Mass (HMM) Penicillin-Binding Proteins (PBPs) in Enterococcus faecalis. Antibiotics (Basel) 2024; 13:65. [PMID: 38247624 PMCID: PMC10812503 DOI: 10.3390/antibiotics13010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/30/2023] [Accepted: 01/06/2024] [Indexed: 01/23/2024] Open
Abstract
Low-affinity PBP4, historically linked to penicillin resistance in Enterococcus faecalis, may still have affinity for novel cephalosporins. Ceftobiprole (BPR) is a common therapeutic choice, even with PBP4-related overexpression and amino acid substitution due to mutations. Our study aims to explore the interaction between BPR and High-Molecular-Mass (HMM) low-reactive PBPs in Penicillin-Resistant-Ampicillin-Susceptible/Ceftobiprole Non-Susceptible (PRAS/BPR-NS) E. faecalis clinical isolates. We conducted competition assays examining class A and B HMM PBPs from four PRAS/BPR-NS E. faecalis strains using purified membrane proteins and fluorescent penicillin (Bocillin FL), in treated and untreated conditions. Interaction strength was assessed calculating the 50% inhibitory concentration (IC50) values for ceftobiprole, by analyzing fluorescence intensity trends. Due to its low affinity, PBP4 did not display significant acylation among all strains. Moreover, both PBP1a and PBP1b showed a similar insensitivity trend. Conversely, other PBPs showed IC50 values ranging from 1/2-fold to 4-fold MICs. Upon higher BPR concentrations, increased percentages of PBP4 inhibition were observed in all strains. Our results support the hypothesis that PBP4 is necessary but not sufficient for BPR resistance, changing the paradigm for enterococcal cephalosporin resistance. We hypothesize that cooperation between class B PBP4 and at least one bifunctional class A PBP could be required to synthesize peptidoglycan and promote growth.
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Affiliation(s)
- Paola Conti
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lorenzo Mattia Lazzaro
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Fabio Longo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
- Department of Public Health and Pediatrics, University of Torino, 10126 Turin, Italy
| | - Federica Lenzo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Alessandra Giardina
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Sebastiano Alberto Fortuna
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
| | - Floriana Campanile
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section of Microbiology, University of Catania, 95123 Catania, Italy; (P.C.); (L.M.L.); (F.L.); (F.L.); (A.G.); (S.A.F.); (S.S.)
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31
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Vazulka S, Schiavinato M, Tauer C, Wagenknecht M, Cserjan-Puschmann M, Striedner G. RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling. Microb Cell Fact 2024; 23:14. [PMID: 38183013 PMCID: PMC10768439 DOI: 10.1186/s12934-023-02278-w] [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: 10/12/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Escherichia coli is a cost-effective expression system for production of antibody fragments like Fabs. Various yield improvement strategies have been applied, however, Fabs remain challenging to produce. This study aimed to characterize the gene expression response of commonly used E. coli strains BL21(DE3) and HMS174(DE3) to periplasmic Fab expression using RNA sequencing (RNA-seq). Two Fabs, Fabx and FTN2, fused to a post-translational translocation signal sequence, were produced in carbon-limited fed-batch cultivations. RESULTS Production of Fabx impeded cell growth substantially stronger than FTN2 and yields of both Fabs differed considerably. The most noticeable, common changes in Fab-producing cells suggested by our RNA-seq data concern the cell envelope. The Cpx and Psp stress responses, both connected to inner membrane integrity, were activated, presumably by recombinant protein aggregation and impairment of the Sec translocon. The data additionally suggest changes in lipopolysaccharide synthesis, adjustment of membrane permeability, and peptidoglycan maturation and remodeling. Moreover, all Fab-producing strains showed depletion of Mg2+, indicated by activation of the PhoQP two-component signal transduction system during the early stage and sulfur and phosphate starvation during the later stage of the process. Furthermore, our data revealed ribosome stalling, caused by the Fabx amino acid sequence, as a contributor to low Fabx yields. Increased Fabx yields were obtained by a site-specific amino acid exchange replacing the stalling sequence. Contrary to expectations, cell growth was not impacted by presence or removal of the stalling sequence. Considering ribosome rescue is a conserved mechanism, the substantial differences observed in gene expression between BL21(DE3) and HMS174(DE3) in response to ribosome stalling on the recombinant mRNA were surprising. CONCLUSIONS Through characterization of the gene expression response to Fab production under industrially relevant cultivation conditions, we identified potential cell engineering targets. Thereby, we hope to enable rational approaches to improve cell fitness and Fab yields. Furthermore, we highlight ribosome stalling caused by the amino acid sequence of the recombinant protein as a possible challenge during recombinant protein production.
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Affiliation(s)
- Sophie Vazulka
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV, GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1120, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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32
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Huang LD, Gou XY, Yang MJ, Li MJ, Chen SN, Yan J, Liu XX, Sun AH. Peptidoglycan biosynthesis-associated enzymatic kinetic characteristics and β-lactam antibiotic inhibitory effects of different Streptococcus pneumoniae penicillin-binding proteins. Int J Biol Macromol 2024; 254:127784. [PMID: 37949278 DOI: 10.1016/j.ijbiomac.2023.127784] [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: 05/24/2023] [Revised: 09/15/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023]
Abstract
Penicillin-binding proteins (PBPs) include transpeptidases, carboxypeptidases, and endopeptidases for biosynthesis of peptidoglycans in the cell wall to maintain bacterial morphology and survival in the environment. Streptococcus pneumoniae expresses six PBPs, but their enzymatic kinetic characteristics and inhibitory effects on different β-lactam antibiotics remain poorly understood. In this study, all the six recombinant PBPs of S. pneumoniae displayed transpeptidase activity with different substrate affinities (Km = 1.56-9.11 mM) in a concentration-dependent manner, and rPBP3 showed a greater catalytic efficiency (Kcat = 2.38 s-1) than the other rPBPs (Kcat = 3.20-7.49 × 10-2 s-1). However, only rPBP3 was identified as a carboxypeptidase (Km = 8.57 mM and Kcat = 2.57 s-1). None of the rPBPs exhibited endopeptidase activity. Penicillin and cefotaxime inhibited the transpeptidase and carboxypeptidase activity of all the rPBPs but imipenem did not inhibited the enzymatic activities of rPBP3. Except for the lack of binding of imipenem to rPBP3, penicillin, cefotaxime, and imipenem bound to all the other rPBPs (KD = 3.71-9.35 × 10-4 M). Sublethal concentrations of penicillin, cefotaxime, and imipenem induced a decrease of pneumococcal pbps-mRNA levels (p < 0.05). These results indicated that all six PBPs of S. pneumoniae are transpeptidases, while only PBP3 is a carboxypeptidase. Imipenem has no inhibitory effect on pneumococcal PBP3. The pneumococcal genes for encoding endopeptidases remain to be determined.
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Affiliation(s)
- Li-Dan Huang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China; Yiwu Central Blood Station, Yiwu, Zhejiang 322000, PR China
| | - Xiao-Yu Gou
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China
| | - Mei-Juan Yang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China; The First Hospital of Putian City, Putian, Fujian 351100, PR China
| | - Meng-Jie Li
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China
| | - Sui-Ning Chen
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China
| | - Jie Yan
- Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PR China
| | - Xiao-Xiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China.
| | - Ai-Hua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, PR China.
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Wattam AR, Bowers N, Brettin T, Conrad N, Cucinell C, Davis JJ, Dickerman AW, Dietrich EM, Kenyon RW, Machi D, Mao C, Nguyen M, Olson RD, Overbeek R, Parrello B, Pusch GD, Shukla M, Stevens RL, Vonstein V, Warren AS. Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance. Methods Mol Biol 2024; 2802:547-571. [PMID: 38819571 DOI: 10.1007/978-1-0716-3838-5_18] [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: 06/01/2024]
Abstract
As genomic and related data continue to expand, research biologists are often hampered by the computational hurdles required to analyze their data. The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Centers (BRC) to assist researchers with their analysis of genome sequence and other omics-related data. Recently, the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD), and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs merged to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) at https://www.bv-brc.org/ . The combined BV-BRC leverages the functionality of the original resources for bacterial and viral research communities with a unified data model, enhanced web-based visualization and analysis tools, and bioinformatics services. Here we demonstrate how antimicrobial resistance data can be analyzed in the new resource.
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Affiliation(s)
- Alice R Wattam
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA.
| | - Nicole Bowers
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Thomas Brettin
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA
| | - Neal Conrad
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Clark Cucinell
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Allan W Dickerman
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - Emily M Dietrich
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Ronald W Kenyon
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - Dustin Machi
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - Chunhong Mao
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Robert D Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Ross Overbeek
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA
| | - Bruce Parrello
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA
| | - Gordon D Pusch
- Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Rick L Stevens
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | | | - Andrew S Warren
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, USA
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34
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Manoil D, Cerit EE, Fang H, Durual S, Brundin M, Belibasakis GN. Profiling Antibiotic Susceptibility among Distinct Enterococcus faecalis Isolates from Dental Root Canals. Antibiotics (Basel) 2023; 13:18. [PMID: 38247577 PMCID: PMC10812444 DOI: 10.3390/antibiotics13010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Enterococcus faecalis, a leading multi-resistant nosocomial pathogen, is also the most frequently retrieved species from persistently infected dental root canals, suggesting that the oral cavity is a possible reservoir for resistant strains. However, antimicrobial susceptibility testing (AST) for oral enterococci remains scarce. Here, we examined the AST profiles of 37 E. faecalis strains, including thirty-four endodontic isolates, two vanA-type vancomycin-resistant isolates, and the reference strain ATCC-29212. Using Etest gradient strips and established EUCAST standards, we determined minimum inhibitory concentrations (MICs) for amoxicillin, vancomycin, clindamycin, tigecycline, linezolid, and daptomycin. Results revealed that most endodontic isolates were susceptible to amoxicillin and vancomycin, with varying levels of intrinsic resistance to clindamycin. Isolates exceeding the clindamycin MIC of the ATCC-29212 strain were further tested against last-resort antibiotics, with 7/27 exhibiting MICs matching the susceptibility breakpoint for tigecycline, and 1/27 reaching that of linezolid. Both vanA isolates confirmed vancomycin resistance and demonstrated resistance to tigecycline. In conclusion, while most endodontic isolates remained susceptible to first-line antibiotics, several displayed marked intrinsic clindamycin resistance, and MICs matched tigecycline's breakpoint. The discovery of tigecycline resistance in vanA isolates highlights the propensity of clinical clone clusters to acquire multidrug resistance. Our results emphasize the importance of implementing AST strategies in dental practices for continued resistance surveillance.
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Affiliation(s)
- Daniel Manoil
- Division of Cariology and Endodontics, University Clinics of Dental Medicine, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institute, Campus Huddinge, 141 52 Stockholm, Sweden;
| | - Ender Efe Cerit
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institute, Campus Huddinge, 141 52 Stockholm, Sweden;
| | - Hong Fang
- Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Karolinska Institute, Campus Huddinge, 141 52 Stockholm, Sweden;
| | - Stéphane Durual
- Biomaterials Laboratory, Division of Fixed Prosthodontics and Biomaterials, University Clinics of Dental Medicine, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland;
| | - Malin Brundin
- Division of Endodontics, Department of Odontology, Umeå University, 901 87 Umeå, Sweden;
| | - Georgios N. Belibasakis
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institute, Campus Huddinge, 141 52 Stockholm, Sweden;
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35
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Harris-Jones TN, Pérez Medina KM, Hackett KT, Schave MA, Klimowicz AK, Schaub RE, Dillard JP. Mutation of mltG increases peptidoglycan fragment release, cell size, and antibiotic susceptibility in Neisseria gonorrhoeae. J Bacteriol 2023; 205:e0027723. [PMID: 38038461 PMCID: PMC10729727 DOI: 10.1128/jb.00277-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Neisseria gonorrhoeae is unusual in that the bacteria release larger amounts of cell wall material as they grow as compared to related bacteria, and the released cell wall fragments induce inflammation that leads to tissue damage in infected people. The study of MltG revealed the importance of this enzyme for controlling cell wall growth, cell wall fragment production, and bacterial cell size and suggests a role for MltG in a cell wall synthesis and degradation complex. The increased antibiotic sensitivities of mltG mutants suggest that an antimicrobial drug inhibiting MltG would be useful in combination therapy to restore the sensitivity of the bacteria to cell wall targeting antibiotics to which the bacteria are currently resistant.
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Affiliation(s)
- Tiffany N. Harris-Jones
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Krizia M. Pérez Medina
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Kathleen T. Hackett
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Melanie A. Schave
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Amy K. Klimowicz
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Ryan E. Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Joseph P. Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
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36
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Jiao F, Bao Y, Li M, Zhang Y, Zhang F, Wang P, Tao J, Tong HHY, Guo J. Unraveling the mechanism of ceftaroline-induced allosteric regulation in penicillin-binding protein 2a: insights for novel antibiotic development against methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0089523. [PMID: 37971241 PMCID: PMC10720500 DOI: 10.1128/aac.00895-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) acquires high-level resistance against β-lactam antibiotics by expressing penicillin-binding protein 2a (PBP2a). PBP2a is a cell wall-synthesizing protein whose closed active site exhibits a reduced binding affinity toward β-lactam antibiotics. Ceftaroline (CFT), a fifth-generation cephalosporin, can effectively inhibit the PBP2a activity by binding to an allosteric site to trigger the active site opening, allowing a second CFT to access the active site. However, the essential mechanism behind the allosteric behavior of PBP2a remains unclear. Herein, computational simulations are employed to elucidate how CFT allosterically regulates the conformation and dynamics of the active site of PBP2a. While CFT stabilizes the allosteric domain surrounding it, it simultaneously enhances the dynamics of the catalytic domain. Specifically, the study successfully captured the opening process of the active pocket in the allosteric CFT-bound systems and discovered that CFT alters the potential signal-propagating pathways from the allosteric site to the active site. These findings reveal the implied mechanism of the CFT-mediated allostery in PBP2a and provide new insights into dual-site drug design or combination therapy against MRSA targeting PBP2a.
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Affiliation(s)
- Fangfang Jiao
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Yiqiong Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengrong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Zhang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Pinkai Wang
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Tao
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Henry H. Y. Tong
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
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37
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Proj M, Hrast M, Bajc G, Frlan R, Meden A, Butala M, Gobec S. Discovery of a fragment hit compound targeting D-Ala:D-Ala ligase of bacterial peptidoglycan biosynthesis. J Enzyme Inhib Med Chem 2023; 38:387-397. [PMID: 36446617 PMCID: PMC9718554 DOI: 10.1080/14756366.2022.2149745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bacterial resistance is an increasing threat to healthcare systems, highlighting the need for discovering new antibacterial agents. An established technique, fragment-based drug discovery, was used to target a bacterial enzyme Ddl involved in the biosynthesis of peptidoglycan. We assembled general and focused fragment libraries that were screened in a biochemical inhibition assay. Screening revealed a new fragment-hit inhibitor of DdlB with a Ki value of 20.7 ± 4.5 µM. Binding to the enzyme was confirmed by an orthogonal biophysical method, surface plasmon resonance, making the hit a promising starting point for fragment development.
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Affiliation(s)
- Matic Proj
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Martina Hrast
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Bajc
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Rok Frlan
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Anže Meden
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Butala
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia,CONTACT Stanislav Gobec Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, 1000Ljubljana, Slovenia
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38
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Soonthonsrima T, Htoo HH, Thiennimitr P, Srisuknimit V, Nonejuie P, Chaikeeratisak V. Phage-induced bacterial morphological changes reveal a phage-derived antimicrobial affecting cell wall integrity. Antimicrob Agents Chemother 2023; 67:e0076423. [PMID: 37843261 PMCID: PMC10648931 DOI: 10.1128/aac.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023] Open
Abstract
In a looming post-antibiotic era, antibiotic alternatives have become key players in the combat against pathogens. Although recent advances in genomic research allow scientists to fully explore an organism's genome in the search for novel antibacterial molecules, laborious work is still needed in order to dissect each individual gene product for its antibacterial activity. Here, we exploited phage-induced bacterial morphological changes as anchors to explore and discover a potential phage-derived antimicrobial embedded in the phage genome. We found that, upon vibriophage KVP40 infection, Vibrio parahaemolyticus exhibited morphological changes similar to those observed when treated with mecillinam, a cell wall synthesis inhibitor, suggesting the mechanism of pre-killing that KVP40 exerts inside the bacterial cell upon sieging the host. Genome analysis revealed that, of all the annotated gene products in the KVP40 genome that are involved in cell wall degradation, lytic transglycosylase (LT) is of particular interest for subsequent functional studies. A single-cell morphological analysis revealed that heterologous expression of wild-type KVP40-LT induced similar bacterial morphological changes to those treated with the whole phage or mecillinam, prior to cell burst. On the contrary, neither the morphology nor the viability of the bacteria expressing signal-peptide truncated- or catalytic mutant E80A- KVP40-LT was affected, suggesting the necessity of these domains for the antibacterial activities. Altogether, this research paves the way for the future development of the discovery of phage-derived antimicrobials that is guided through phage-induced morphological changes.
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Affiliation(s)
- Tanapon Soonthonsrima
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Veerasak Srisuknimit
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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39
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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40
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Giovagnorio F, De Vito A, Madeddu G, Parisi SG, Geremia N. Resistance in Pseudomonas aeruginosa: A Narrative Review of Antibiogram Interpretation and Emerging Treatments. Antibiotics (Basel) 2023; 12:1621. [PMID: 37998823 PMCID: PMC10669487 DOI: 10.3390/antibiotics12111621] [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: 10/15/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium renowned for its resilience and adaptability across diverse environments, including clinical settings, where it emerges as a formidable pathogen. Notorious for causing nosocomial infections, P. aeruginosa presents a significant challenge due to its intrinsic and acquired resistance mechanisms. This comprehensive review aims to delve into the intricate resistance mechanisms employed by P. aeruginosa and to discern how these mechanisms can be inferred by analyzing sensitivity patterns displayed in antibiograms, emphasizing the complexities encountered in clinical management. Traditional monotherapies are increasingly overshadowed by the emergence of multidrug-resistant strains, necessitating a paradigm shift towards innovative combination therapies and the exploration of novel antibiotics. The review accentuates the critical role of accurate antibiogram interpretation in guiding judicious antibiotic use, optimizing therapeutic outcomes, and mitigating the propagation of antibiotic resistance. Misinterpretations, it cautions, can inadvertently foster resistance, jeopardizing patient health and amplifying global antibiotic resistance challenges. This paper advocates for enhanced clinician proficiency in interpreting antibiograms, facilitating informed and strategic antibiotic deployment, thereby improving patient prognosis and contributing to global antibiotic stewardship efforts.
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Affiliation(s)
- Federico Giovagnorio
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (F.G.); (S.G.P.)
| | - Andrea De Vito
- Unit of Infectious Diseases, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy;
| | - Giordano Madeddu
- Unit of Infectious Diseases, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy;
| | | | - Nicholas Geremia
- Unit of Infectious Diseases, Department of Clinical Medicine, Ospedale “dell’Angelo”, 30174 Venice, Italy
- Unit of Infectious Diseases, Department of Clinical Medicine, Ospedale Civile “S.S. Giovanni e Paolo”, 30122 Venice, Italy
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41
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Murase LS, Perez de Souza JV, Meneguello JE, Palomo CT, Fernandes Herculano Ramos Milaré ÁC, Negri M, Dias Siqueira VL, Demarchi IG, Vieira Teixeira JJ, Cardoso RF. Antibacterial and immunological properties of piperine evidenced by preclinical studies: a systematic review. Future Microbiol 2023; 18:1279-1299. [PMID: 37882762 DOI: 10.2217/fmb-2023-0101] [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: 05/02/2023] [Accepted: 08/23/2023] [Indexed: 10/27/2023] Open
Abstract
Aim: To review in vitro, in vivo, and in silico studies examining the antibacterial and immunomodulatory properties of piperine (PPN). Methods: This systematic review followed PRISMA guidelines, and five databases were searched. Results: A total of 40 articles were included in this study. Six aspects of PPN activity were identified, including antibacterial spectrum, association with antibiotics, efflux pump inhibition, biofilm effects, protein target binding, and modulation of immune functions/virulence factors. Most studies focused on Mycobacterium spp. and Staphylococcus aureus. Cell lineages and in vivo models were employed to study PPN antibacterial effects. Conclusion: We highlight PPN as a potential adjuvant in the treatment of bacterial infections. PPN possesses several antibacterial properties that need further exploration to determine the mechanisms behind its pharmacological activity.
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Affiliation(s)
- Letícia Sayuri Murase
- Postgraduate Program in Health Sciences, State University of Maringa, Maringá, Paraná, 87020-900, Brazil
| | - João Vítor Perez de Souza
- Postgraduate Program in Biosciences and Physiopathology, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
| | - Jean Eduardo Meneguello
- Postgraduate Program in Biosciences and Physiopathology, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
| | - Carolina Trevisolli Palomo
- Postgraduate Program in Health Sciences, State University of Maringa, Maringá, Paraná, 87020-900, Brazil
| | | | - Melyssa Negri
- Postgraduate Program in Health Sciences, State University of Maringa, Maringá, Paraná, 87020-900, Brazil
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
| | - Vera Lúcia Dias Siqueira
- Postgraduate Program in Biosciences and Physiopathology, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
| | - Izabel Galhardo Demarchi
- Department of Clinical Analysis, Federal University of Santa Catarina, Florianopólis, Santa Catarina, 88040-900, Brazil
| | - Jorge Juarez Vieira Teixeira
- Postgraduate Program in Health Sciences, State University of Maringa, Maringá, Paraná, 87020-900, Brazil
- Postgraduate Program in Biosciences and Physiopathology, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
| | - Rosilene Fressatti Cardoso
- Postgraduate Program in Health Sciences, State University of Maringa, Maringá, Paraná, 87020-900, Brazil
- Postgraduate Program in Biosciences and Physiopathology, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, 87020-900, Brazil
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42
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Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A. Systematic analysis of drug combinations against Gram-positive bacteria. Nat Microbiol 2023; 8:2196-2212. [PMID: 37770760 PMCID: PMC10627819 DOI: 10.1038/s41564-023-01486-9] [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: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Drug combinations can expand options for antibacterial therapies but have not been systematically tested in Gram-positive species. We profiled ~8,000 combinations of 65 antibacterial drugs against the model species Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulated previously known drug interactions, but also identified ten times more novel interactions in the pathogen S. aureus, including 150 synergies. We showed that two synergies were equally effective against multidrug-resistant S. aureus clinical isolates in vitro and in vivo. Interactions were largely species-specific and synergies were distinct from those of Gram-negative species, owing to cell surface and drug uptake differences. We also tested 2,728 combinations of 44 commonly prescribed non-antibiotic drugs with 62 drugs with antibacterial activity against S. aureus and identified numerous antagonisms that might compromise the efficacy of antimicrobial therapies. We identified even more synergies and showed that the anti-aggregant ticagrelor synergized with cationic antibiotics by modifying the surface charge of S. aureus. All data can be browsed in an interactive interface ( https://apps.embl.de/combact/ ).
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Affiliation(s)
- Elisabetta Cacace
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vladislav Kim
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Vallo Varik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Michael Knopp
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuela Tietgen
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | | | - Kemal Inecik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Alessio Milanese
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Department of Biology, Institute of Microbiology, and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin Mitosch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Molecular Biology and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
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43
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Lenoir C, Pelletier A, Manuse S, Millat H, Ducret A, Galinier A, Doan T, Grangeasse C. The morphogenic protein CopD controls the spatio-temporal dynamics of PBP1a and PBP2b in Streptococcus pneumoniae. mBio 2023; 14:e0141123. [PMID: 37728370 PMCID: PMC10653890 DOI: 10.1128/mbio.01411-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Penicillin-binding proteins (PBPs) are essential for proper bacterial cell division and morphogenesis. The genome of Streptococcus pneumoniae encodes for two class B PBPs (PBP2x and 2b), which are required for the assembly of the peptidoglycan framework and three class A PBPs (PBP1a, 1b and 2a), which remodel the peptidoglycan mesh during cell division. Therefore, their activities should be finely regulated in space and time to generate the pneumococcal ovoid cell shape. To date, two proteins, CozE and MacP, are known to regulate the function of PBP1a and PBP2a, respectively. In this study, we describe a novel regulator (CopD) that acts on both PBP1a and PBP2b. These findings provide valuable information for understanding bacterial cell division. Furthermore, knowing that ß-lactam antibiotic resistance often arises from PBP mutations, the characterization of such a regulator represents a promising opportunity to develop new strategies to resensitize resistant strains.
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Affiliation(s)
- Cassandra Lenoir
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Sylvie Manuse
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Hugo Millat
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR, Aix-Marseille Université, CNRS, Marseille, France
| | - Thierry Doan
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, UMR, Aix-Marseille Université, Marseille, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
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Liu Y, Zhang Y, Kang C, Tian D, Lu H, Xu B, Xia Y, Kashiwagi A, Westermann M, Hoischen C, Xu J, Yomo T. Comparative genomics hints at dispensability of multiple essential genes in two Escherichia coli L-form strains. Biosci Rep 2023; 43:BSR20231227. [PMID: 37819245 PMCID: PMC10600066 DOI: 10.1042/bsr20231227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023] Open
Abstract
Despite the critical role of bacterial cell walls in maintaining cell shapes, certain environmental stressors can induce the transition of many bacterial species into a wall-deficient state called L-form. Long-term induced Escherichia coli L-forms lose their rod shape and usually hold significant mutations that affect cell division and growth. Besides this, the genetic background of L-form bacteria is still poorly understood. In the present study, the genomes of two stable L-form strains of E. coli (NC-7 and LWF+) were sequenced and their gene mutation status was determined and compared with their parental strains. Comparative genomic analysis between two L-forms reveals both unique adaptions and common mutated genes, many of which belong to essential gene categories not involved in cell wall biosynthesis, indicating that L-form genetic adaptation impacts crucial metabolic pathways. Missense variants from L-forms and Lenski's long-term evolution experiment (LTEE) were analyzed in parallel using an optimized DeepSequence pipeline to investigate predicted mutation effects (α) on protein functions. We report that the two L-form strains analyzed display a frequency of 6-10% (0% for LTEE) in mutated essential genes where the missense variants have substantial impact on protein functions (α<0.5). This indicates the emergence of different survival strategies in L-forms through changes in essential genes during adaptions to cell wall deficiency. Collectively, our results shed light on the detailed genetic background of two E. coli L-forms and pave the way for further investigations of the gene functions in L-form bacterial models.
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Affiliation(s)
- Yunfei Liu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Yueyue Zhang
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Chen Kang
- School of Software Engineering, East China Normal University, Shanghai 200062, PR China
| | - Di Tian
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Hui Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Boying Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yang Xia
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Akiko Kashiwagi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Martin Westermann
- Center for Electron Microscopy, Medical Faculty, Friedrich–Schiller–University Jena, Ziegelmühlenweg 1, D-07743 Jena, Germany
| | - Christian Hoischen
- CF Imaging, Leibniz Institute On Aging, Fritz–Lipmann–Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
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45
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Rousseau CJ, Fraikin N, Zedek S, Van Melderen L. Are envelope stress responses essential for persistence to β-lactams in Escherichia coli? Antimicrob Agents Chemother 2023; 67:e0032923. [PMID: 37787525 PMCID: PMC10583663 DOI: 10.1128/aac.00329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/05/2023] [Indexed: 10/04/2023] Open
Abstract
Bacterial persistence to antibiotics defines the ability of small sub-populations of sensitive cells within an isogenic population to survive high doses of bactericidal antibiotics. Here, we investigated the importance of the five main envelope stress responses (ESRs) of Escherichia coli in persistence to five bactericidal β-lactam antibiotics by combining classical time-kill curve experiments and single-cell analysis using time-lapse microscopy. We showed that the survival frequency of mutants for the Bae, Cpx, Psp, and Rcs systems treated with different β-lactams is comparable to that of the wild-type strain, indicating that these ESRs do not play a direct role in persistence to β-lactams. Since the σE-encoding gene is essential, we could not directly test its role. Using fluorescent reporters to monitor the activation of ESRs, we observed that σE is induced by high doses of meropenem. However, the dynamics of σE activation during meropenem treatment did not reveal any difference in persister cells compared to the bulk of the population, indicating that σE activation is not a hallmark of persistence. The Bae, Cpx, Psp, and Rcs responses were neither induced by ampicillin nor by meropenem. However, pre-induction of the Rcs system by polymyxin B increased survival to meropenem in an Rcs-dependent manner, suggesting that this ESR might confer some yet uncharacterized advantages during meropenem treatment or at the post-antibiotic recovery step. Altogether, our data suggest that ESRs are not key actors in E. coli persistence to β-lactams in the conditions we tested.
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Affiliation(s)
- Clothilde J. Rousseau
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Nathan Fraikin
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Safia Zedek
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Laurence Van Melderen
- Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
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46
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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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47
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Harpring M, Cox JV. Plasticity in the cell division processes of obligate intracellular bacteria. Front Cell Infect Microbiol 2023; 13:1205488. [PMID: 37876871 PMCID: PMC10591338 DOI: 10.3389/fcimb.2023.1205488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/07/2023] [Indexed: 10/26/2023] Open
Abstract
Most bacteria divide through a highly conserved process called binary fission, in which there is symmetric growth of daughter cells and the synthesis of peptidoglycan at the mid-cell to enable cytokinesis. During this process, the parental cell replicates its chromosomal DNA and segregates replicated chromosomes into the daughter cells. The mechanisms that regulate binary fission have been extensively studied in several model organisms, including Eschericia coli, Bacillus subtilis, and Caulobacter crescentus. These analyses have revealed that a multi-protein complex called the divisome forms at the mid-cell to enable peptidoglycan synthesis and septation during division. In addition, rod-shaped bacteria form a multi-protein complex called the elongasome that drives sidewall peptidoglycan synthesis necessary for the maintenance of rod shape and the lengthening of the cell prior to division. In adapting to their intracellular niche, the obligate intracellular bacteria discussed here have eliminated one to several of the divisome gene products essential for binary fission in E. coli. In addition, genes that encode components of the elongasome, which were mostly lost as rod-shaped bacteria evolved into coccoid organisms, have been retained during the reductive evolutionary process that some coccoid obligate intracellular bacteria have undergone. Although the precise molecular mechanisms that regulate the division of obligate intracellular bacteria remain undefined, the studies summarized here indicate that obligate intracellular bacteria exhibit remarkable plasticity in their cell division processes.
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Affiliation(s)
| | - John V. Cox
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
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48
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Xiao F, Li W, Wang Z, Xu Q, Song Y, Huang J, Bai X, Xu H. Smartphone-assisted biosensor based on broom-like bacteria-specific magnetic enrichment platform for colorimetric detection of Listeria monocytogenes. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132250. [PMID: 37567141 DOI: 10.1016/j.jhazmat.2023.132250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Pathogenic bacteria contamination poses a major threat to human health. The detection of low-abundance bacteria in complex samples has always been a knotty problem, and high-sensitivity bacterial detection remains challenging. In this work, a novel magnetic platform with high enrichment efficiency for L. monocytogenes was developed. The magnetic platform was designed by branched polyglutamic acid-mediated indirect coupling of cefepime on magnetic nanoparticles (Cefe-PGA-MNPs), and the specific enrichment of low-abundance L. monocytogenes in real samples was achieved by an external magnet, with a capture efficiency over 90%. A controllable and highly active platinum-palladium nanozyme was synthesized and further introduced in the magnetic nanoplatform for the construction of enzymatic colorimetric biosensor. The total detection time for L. monocytogenes was within 100 min. The colorimetric signals generated by labelled nanozyme were corresponding to different concentrations of L. monocytogenes, with a limit of detection (LOD) of 3.1 × 101 CFU/mL, and high reliability and accuracy (with a recovery rate ranging from 96.5% to 116.4%) in the test of real samples. The concept of the developed method is applicable to various fields of biosensing that rely on magnetic separation platforms.
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Affiliation(s)
- Fangbin Xiao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Weiqiang Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Zhixing Wang
- Zhejiang Rural Commercial Digital Technology Co., Ltd., Hangzhou 310016, PR China
| | - Qian Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Yang Song
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Jin Huang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Xuekun Bai
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China.
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49
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Avila‐Cobian LF, Hoshino H, Horsman ME, Nguyen VT, Qian Y, Feltzer R, Kim C, Hu DD, Champion MM, Fisher JF, Mobashery S. Amber-codon suppression for spatial localization and in vivo photoaffinity capture of the interactome of the Pseudomonas aeruginosa rare lipoprotein A lytic transglycosylase. Protein Sci 2023; 32:e4781. [PMID: 37703013 PMCID: PMC10536563 DOI: 10.1002/pro.4781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
The 11 lytic transglycosylases of Pseudomonas aeruginosa have overlapping activities in the turnover of the cell-wall peptidoglycan. Rare lipoprotein A (RlpA) is distinct among the 11 by its use of only peptidoglycan lacking peptide stems. The spatial localization of RlpA and its interactome within P. aeruginosa are unknown. We employed suppression of introduced amber codons at sites in the rlpA gene for the introduction of the unnatural-amino-acids Νζ -[(2-azidoethoxy)carbonyl]-l-lysine (compound 1) and Nζ -[[[3-(3-methyl-3H-diazirin-3-yl)propyl]amino]carbonyl]-l-lysine (compound 2). In live P. aeruginosa, full-length RlpA incorporating compound 1 into its sequence was fluorescently tagged using strained-promoted alkyne-azide cycloaddition and examined by fluorescence microscopy. RlpA is present at low levels along the sidewall length of the bacterium, and at higher levels at the nascent septa of replicating bacteria. In intact P. aeruginosa, UV photolysis of full-length RlpA having compound 2 within its sequence generated a transient reactive carbene, which engaged in photoaffinity capture of neighboring proteins. Thirteen proteins were identified. Three of these proteins-PBP1a, PBP5, and MreB-are members of the bacterial divisome. The use of the complementary methodologies of non-canonical amino-acid incorporation, photoaffinity proximity analysis, and fluorescent microscopy confirm a dominant septal location for the RlpA enzyme of P. aeruginosa, as a divisome-associated activity. This accomplishment adds to the emerging recognition of the value of these methodologies for identification of the intracellular localization of bacterial proteins.
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Affiliation(s)
- Luis F. Avila‐Cobian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Hidekazu Hoshino
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Mark E. Horsman
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Van T. Nguyen
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Yuanyuan Qian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Rhona Feltzer
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Choon Kim
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Daniel D. Hu
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew M. Champion
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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50
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Ago R, Tahara YO, Yamaguchi H, Saito M, Ito W, Yamasaki K, Kasai T, Okamoto S, Chikada T, Oshima T, Osaka I, Miyata M, Niki H, Shiomi D. Relationship between the Rod complex and peptidoglycan structure in Escherichia coli. Microbiologyopen 2023; 12:e1385. [PMID: 37877652 PMCID: PMC10561026 DOI: 10.1002/mbo3.1385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Peptidoglycan for elongation in Escherichia coli is synthesized by the Rod complex, which includes RodZ. Although various mutant strains of the Rod complex have been isolated, the relationship between the activity of the Rod complex and the overall physical and chemical structures of the peptidoglycan have not been reported. We constructed a RodZ mutant, termed RMR, and analyzed the growth rate, morphology, and other characteristics of cells producing the Rod complexes containing RMR. The growth and morphology of RMR cells were abnormal, and we isolated suppressor mutants from RMR cells. Most of the suppressor mutations were found in components of the Rod complex, suggesting that these suppressor mutations increase the integrity and/or the activity of the Rod complex. We purified peptidoglycan from wild-type, RMR, and suppressor mutant cells and observed their structures in detail. We found that the peptidoglycan purified from RMR cells had many large holes and different compositions of muropeptides from those of WT cells. The Rod complex may be a determinant not only for the whole shape of peptidoglycan but also for its highly dense structure to support the mechanical strength of the cell wall.
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Affiliation(s)
- Risa Ago
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Yuhei O. Tahara
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
- The OMU Advanced Research Center for Natural Science and TechnologyOsaka Metropolitan UniversityOsakaJapan
| | - Honoka Yamaguchi
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Motoya Saito
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Wakana Ito
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Kaito Yamasaki
- Department of Pharmaceutical Engineering, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Taishi Kasai
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Sho Okamoto
- Microbial Physiology Laboratory, Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
| | - Taiki Chikada
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Taku Oshima
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Issey Osaka
- Department of Pharmaceutical Engineering, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Makoto Miyata
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
- The OMU Advanced Research Center for Natural Science and TechnologyOsaka Metropolitan UniversityOsakaJapan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
- Department of GeneticsThe Graduate University for Advanced Studies, SOKENDAIMishimaShizuokaJapan
| | - Daisuke Shiomi
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
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