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Miguel-Ruano V, Acebrón I, Lee M, Martín-Galiano AJ, Freton C, de José UP, Ramachandran B, Gago F, Kjos M, Hesek D, Grangeasse C, Håvarstein LS, Straume D, Mobashery S, Hermoso JA. Characterization of VldE (Spr1875), a Pneumococcal Two-State l,d-Endopeptidase with a Four-Zinc Cluster in the Active Site. ACS Catal 2024; 14:18786-18798. [PMID: 39722888 PMCID: PMC11667670 DOI: 10.1021/acscatal.4c05090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 11/27/2024] [Accepted: 12/02/2024] [Indexed: 12/28/2024]
Abstract
Remodeling of the pneumococcal cell wall, carried out by peptidoglycan (PG) hydrolases, is imperative for maintaining bacterial cell shape and ensuring survival, particularly during cell division or stress response. The Streptococcus pneumoniae protein Spr1875 plays a role in stress response, both regulated by the VicRK two-component system (analogous to the WalRK TCS found in Firmicutes). Modular Spr1875 presents a putative cell-wall binding module at the N-terminus and a catalytic C-terminal module (Spr1875MT3) connected by a long linker. Assays of the full-length protein and Spr1875MT3 with PG-based synthetic substrates by liquid chromatography/mass spectrometry revealed Spr1875 as an l,d-endopeptidase, renamed VldE (for VicRK-regulated l,d-endopeptidase), which hydrolyzed the cross-linked stem peptide in the PG. Remarkably, we observed asymmetric turnover with specific recognition of the acceptor peptide strand. Localization experiments showed that the protein is directed to the septum, which suggests that muralytic activity could be required for pneumococcal growth under stress conditions. Our findings, based on six high-resolution X-ray crystallographic structures and molecular-dynamics simulations, reveal two states for VldEMT3. The protein transitions between a noncatalytic state that binds up to four zinc ions, thus behaving as a Zn2+ reservoir, and a catalytic state that performs the hydrolytic reaction with a single zinc ion. Furthermore, computational studies provide insight into the mechanism of catalytic-water activation and nucleophilic attack on the specific scissile peptide bond of the asymmetric cross-linked PG.
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Affiliation(s)
- Vega Miguel-Ruano
- Department
of Crystallography and Structural Biology, Consejo Superior de Investigaciones
Científicas, Instituto de Química-Física
“Blas Cabrera”, Madrid 28006, Spain
| | - Iván Acebrón
- Department
of Crystallography and Structural Biology, Consejo Superior de Investigaciones
Científicas, Instituto de Química-Física
“Blas Cabrera”, Madrid 28006, Spain
| | - Mijoon Lee
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | | | - Celine Freton
- Molecular
Microbiology and Structural Biochemistry, CNRS UMR, Université de Lyon, Lyon 69367, France
| | - Uxía P. de José
- Department
of Crystallography and Structural Biology, Consejo Superior de Investigaciones
Científicas, Instituto de Química-Física
“Blas Cabrera”, Madrid 28006, Spain
| | - Balajee Ramachandran
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Federico Gago
- Department
of Biomedical Sciences and IQM-CSIC Associate Unit, School of Medicine
and Health Sciences, University of Alcalá, Alcalá de Henares 28805, Spain
| | - Morten Kjos
- Department
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1430, Norway
| | - Dusan Hesek
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Christophe Grangeasse
- Molecular
Microbiology and Structural Biochemistry, CNRS UMR, Université de Lyon, Lyon 69367, France
| | - Leiv Sigve Håvarstein
- Department
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1430, Norway
| | - Daniel Straume
- Department
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1430, Norway
| | - Shahriar Mobashery
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Juan A. Hermoso
- Department
of Crystallography and Structural Biology, Consejo Superior de Investigaciones
Científicas, Instituto de Química-Física
“Blas Cabrera”, Madrid 28006, Spain
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2
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Maday SDM, Kingsbury JM, Weaver L, Pantos O, Wallbank JA, Doake F, Masterton H, Hopkins M, Dunlop R, Gaw S, Theobald B, Risani R, Abbel R, Smith D, Handley KM, Lear G. Taxonomic variation, plastic degradation, and antibiotic resistance traits of plastisphere communities in the maturation pond of a wastewater treatment plant. Appl Environ Microbiol 2024; 90:e0071524. [PMID: 39329490 PMCID: PMC11497791 DOI: 10.1128/aem.00715-24] [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: 04/15/2024] [Accepted: 09/04/2024] [Indexed: 09/28/2024] Open
Abstract
Wastewater treatment facilities can filter out some plastics before they reach the open environment, yet microplastics often persist throughout these systems. As they age, microplastics in wastewater may both leach and sorb pollutants and fragment to provide an increased surface area for bacterial attachment and conjugation, possibly impacting antimicrobial resistance (AMR) traits. Despite this, little is known about the effects of persistent plastic pollution on microbial functioning. To address this knowledge gap, we deployed five different artificially weathered plastic types and a glass control into the final maturation pond of a municipal wastewater treatment plant in Ōtautahi-Christchurch, Aotearoa/New Zealand. We sampled the plastic-associated biofilms (plastisphere) at 2, 6, 26, and 52 weeks, along with the ambient pond water, at three different depths (20, 40, and 60 cm from the pond water surface). We investigated the changes in plastisphere microbial diversity and functional potential through metagenomic sequencing. Bacterial 16S ribosomal RNA genes composition did not vary among plastic types and glass controls (P = 0.997) but varied among sampling times [permutational multivariate analysis of variance (PERMANOVA), P = 0.001] and depths (PERMANOVA, P = 0.011). Overall, there was no polymer-substrate specificity evident in the total composition of genes (PERMANOVA, P = 0.67), but sampling time (PERMANOVA, P = 0.002) and depth were significant factors (PERMANOVA, P = 0.001). The plastisphere housed diverse AMR gene families, potentially influenced by biofilm-meditated conjugation. The plastisphere also harbored an increased abundance of genes associated with the biodegradation of nylon, or nylon-associated substances, including nylon oligomer-degrading enzymes and hydrolases.IMPORTANCEPlastic pollution is pervasive and ubiquitous. Occurrences of plastics causing entanglement or ingestion, the leaching of toxic additives and persistent organic pollutants from environmental plastics, and their consequences for marine macrofauna are widely reported. However, little is known about the effects of persistent plastic pollution on microbial functioning. Shotgun metagenomics sequencing provides us with the necessary tools to examine broad-scale community functioning to further investigate how plastics influence microbial communities. This study provides insight into the functional consequence of continued exposure to waste plastic by comparing the prokaryotic functional potential of biofilms on five types of plastic [linear low-density polyethylene (LLDPE), nylon-6, polyethylene terephthalate, polylactic acid, and oxygen-degradable LLDPE], glass, and ambient pond water over 12 months and at different depths (20, 40, and 60 cm) within a tertiary maturation pond of a municipal wastewater treatment plant.
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Affiliation(s)
- Stefan D. M. Maday
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Olga Pantos
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Jessica A. Wallbank
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Fraser Doake
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Hayden Masterton
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Maisie Hopkins
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rosa Dunlop
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sally Gaw
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | | | | | | | | | - Kim M. Handley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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3
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Buddle JE, Thompson LM, Williams AS, Wright RCT, Durham WM, Turner CE, Chaudhuri RR, Brockhurst MA, Fagan RP. Identification of pathways to high-level vancomycin resistance in Clostridioides difficile that incur high fitness costs in key pathogenicity traits. PLoS Biol 2024; 22:e3002741. [PMID: 39146240 PMCID: PMC11326576 DOI: 10.1371/journal.pbio.3002741] [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: 10/13/2023] [Accepted: 07/09/2024] [Indexed: 08/17/2024] Open
Abstract
Clostridioides difficile is an important human pathogen, for which there are very limited treatment options, primarily the glycopeptide antibiotic vancomycin. In recent years, vancomycin resistance has emerged as a serious problem in several gram-positive pathogens, but high-level resistance has yet to be reported for C. difficile, although it is not known if this is due to constraints upon resistance evolution in this species. Here, we show that resistance to vancomycin can evolve rapidly under ramping selection but is accompanied by fitness costs and pleiotropic trade-offs, including sporulation defects that would be expected to severely impact transmission. We identified 2 distinct pathways to resistance, both of which are predicted to result in changes to the muropeptide terminal D-Ala-D-Ala that is the primary target of vancomycin. One of these pathways involves a previously uncharacterised D,D-carboxypeptidase, expression of which is controlled by a dedicated two-component signal transduction system. Our findings suggest that while C. difficile is capable of evolving high-level vancomycin resistance, this outcome may be limited clinically due to pleiotropic effects on key pathogenicity traits. Moreover, our data identify potential mutational routes to resistance that should be considered in genomic surveillance.
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Affiliation(s)
- Jessica E Buddle
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Lucy M Thompson
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Anne S Williams
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Rosanna C T Wright
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - William M Durham
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Claire E Turner
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Roy R Chaudhuri
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Robert P Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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4
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Hu J, Han X, Ma X, Chen X, Zhou Z, Peng P, Yu Z, Hou Y, Han P, Pang L, Yang Y, Xu J, Wu W. Comparative proteomic analysis of vancomycin-sensitive and vancomycin-intermediate resistant Staphylococcus aureus. Eur J Clin Microbiol Infect Dis 2024; 43:139-153. [PMID: 37985551 DOI: 10.1007/s10096-023-04709-3] [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: 05/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
PURPOSE The extensive use of vancomycin has led to the development of Staphylococcus aureus strains with varying degrees of resistance to vancomycin. The present study aimed to explore the molecular causes of vancomycin resistance by conducting a proteomics analysis of subcellular fractions isolated from vancomycin-intermediate resistant S. aureus (VISA) and vancomycin-sensitive S. aureus (VSSA) strains. METHODS We conducted proteomics analysis of subcellular fractions isolated from 2 isogenic S. aureus strains: strain 11 (VSSA) and strain 11Y (VISA). We used an integrated quantitative proteomics approach assisted by bioinformatics analysis, and comprehensively investigated the proteome profile. Intensive bioinformatics analysis, including protein annotation, functional classification, functional enrichment, and functional enrichment-based cluster analysis, was used to annotate quantifiable targets. RESULTS We identified 128 upregulated proteins and 21 downregulated proteins in strain 11Y as compared to strain 11. The largest group of differentially expressed proteins was composed of enzymatic proteins associated with metabolic and catalytic activity, which accounted for 32.1% and 50% of the total proteins, respectively. Some proteins were indispensable parts of the regulatory networks of S. aureus that were altered with vancomycin treatment, and these proteins were related to cell wall metabolism, cell adhesion, proteolysis, and pressure response. CONCLUSION Our proteomics study revealed regulatory proteins associated with vancomycin resistance in S. aureus. Some of these proteins were involved in the regulation of cell metabolism and function, which provides potential targets for the development of strategies to manage vancomycin resistance in S. aureus.
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Affiliation(s)
- Jian Hu
- Department of Laboratory Medicine, Yixing Hospital of Traditional Chinese Medicine, Yixing, No. 128 East Yangquan Road, Yicheng Subdistrict, Yixing, 214200, Jiangsu, People's Republic of China
| | - Xinjun Han
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Xiaoxue Ma
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Xutao Chen
- Department of Laboratory Medicine, Yixing Hospital of Traditional Chinese Medicine, Yixing, No. 128 East Yangquan Road, Yicheng Subdistrict, Yixing, 214200, Jiangsu, People's Republic of China
| | - Zhenping Zhou
- Department of Laboratory Medicine, Yixing Hospital of Traditional Chinese Medicine, Yixing, No. 128 East Yangquan Road, Yicheng Subdistrict, Yixing, 214200, Jiangsu, People's Republic of China
| | - Peilan Peng
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Zhao Yu
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Yongzhi Hou
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Peiru Han
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Long Pang
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Yali Yang
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Jia Xu
- Department of Medical Microbiology, Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, 110034, People's Republic of China.
| | - Wenhui Wu
- Department of Laboratory Medicine, Yixing Hospital of Traditional Chinese Medicine, Yixing, No. 128 East Yangquan Road, Yicheng Subdistrict, Yixing, 214200, Jiangsu, People's Republic of China.
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Xia R, Sun M, Balcázar JL, Yu P, Hu F, Alvarez PJJ. Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes. THE ISME JOURNAL 2023:10.1038/s41396-023-01408-x. [PMID: 37069233 DOI: 10.1038/s41396-023-01408-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023]
Abstract
The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg-1) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg-1) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.
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Affiliation(s)
- Rong Xia
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China
| | - Mingming Sun
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China.
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), 17003, Girona, Spain
- University of Girona, 17004, Girona, Spain
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310085, China.
| | - Feng Hu
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China
| | - Pedro J J Alvarez
- Civil and Environmental Engineering Department, Rice University, Houston, TX, 77005, USA
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Li G, Walker MJ, De Oliveira DMP. Vancomycin Resistance in Enterococcus and Staphylococcus aureus. Microorganisms 2022; 11:microorganisms11010024. [PMID: 36677316 PMCID: PMC9866002 DOI: 10.3390/microorganisms11010024] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.
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7
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Sionov RV, Steinberg D. Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:1239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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Affiliation(s)
- Ronit Vogt Sionov
- The Biofilm Research Laboratory, The Institute of Biomedical and Oral Research, The Faculty of Dental Medicine, Hadassah Medical School, The Hebrew University, Jerusalem 9112102, Israel;
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8
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Olademehin OP, Shuford KL, Kim SJ. Molecular dynamics simulations of the secondary-binding site in disaccharide-modified glycopeptide antibiotics. Sci Rep 2022; 12:7087. [PMID: 35490171 PMCID: PMC9056522 DOI: 10.1038/s41598-022-10735-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
Oritavancin is a semisynthetic glycopeptide antibiotic used to treat severe infections by multidrug-resistant Gram-positive pathogens. Oritavancin is known to be a thousand times more potent than vancomycin against Gram-positive bacteria due to the additional interactions with bacterial peptidoglycan (PG) facilitated by a secondary-binding site. The presence of this secondary-binding site is evident in desleucyl-oritavancin, an Edman degradation product of oritavancin, still retaining its potency against Gram-positive bacteria, whereas desleucyl-vancomycin is devoid of any antimicrobial activities. Herein, using explicit solvent molecular dynamics (MD) simulations, steered MD simulations, and umbrella sampling, we show evidence of a secondary-binding site mediated by the disaccharide-modified hydrophobic sidechain of oritavancin interactions with the pentaglycyl-bridge segment of the PG. The interactions were characterized through comparison to the interaction of PG with chloroeremomycin, vancomycin, and the desleucyl analogs of the glycopeptides. Our results show that the enhanced binding of oritavancin to PG over the binding of the other complexes studied is due to an increase in the hydrophobic effect, electrostatic and van der Waals interactions, and not the average number of hydrogen bonds. Our ranking of the binding interactions of the biomolecular complexes directly correlates with the order based on their experimental minimum inhibitory concentrations. The results of our simulations provide insight into the modification of glycopeptides to increase their antimicrobial activities or the design of novel antibiotics against pathogenic Gram-positive bacteria.
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Affiliation(s)
| | - Kevin L Shuford
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA.
| | - Sung J Kim
- Department of Chemistry, Howard University, Washington, DC, 20059, USA.
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9
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Bottalico L, Charitos IA, Potenza MA, Montagnani M, Santacroce L. The war against bacteria, from the past to present and beyond. Expert Rev Anti Infect Ther 2021; 20:681-706. [PMID: 34874223 DOI: 10.1080/14787210.2022.2013809] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION The human defense against microorganisms dates back to the ancient civilizations, with attempts to use substances from vegetal, animal, or inorganic origin to fight infections. Today, the emerging threat of multidrug-resistant bacteria highlights the consequences of antibiotics inappropriate use, and the urgent need for novel effective molecules. METHODS AND MATERIALS We extensively researched on more recent data within PubMed, Medline, Web of Science, Elsevier's EMBASE, Cochrane Review for the modern pharmacology in between 1987 - 2021. The historical evolution included a detailed analysis of past studies on the significance of medical applications in the ancient therapeutic field. AREAS COVERED We examined the history of antibiotics development and discovery, the most relevant biochemical aspects of their mode of action, and the biomolecular mechanisms conferring bacterial resistance to antibiotics. EXPERT OPINION The list of pathogens showing low sensitivity or full resistance to most currently available antibiotics is growing worldwide. Long after the 'golden age' of antibiotic discovery, the most novel molecules should be carefully reserved to treat serious bacterial infections of susceptible bacteria. A correct diagnostic and therapeutic procedure can slow down the spreading of nosocomial and community infections sustained by multidrug-resistant bacterial strains.
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Affiliation(s)
- Lucrezia Bottalico
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (Cediclo), University of Bari, Bari, Italy
| | - Ioannis Alexandros Charitos
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (Cediclo), University of Bari, Bari, Italy.,Emergency/Urgent Department, National Poisoning Center, Riuniti University Hospital of Foggia, Foggia, Italy
| | - Maria Assunta Potenza
- Department of Biomedical Sciences and Human Oncology - Section of Pharmacology, School of Medicine, University of Bari "Aldo Moro," Policlinico University Hospital of Bari, Bari, Italy
| | - Monica Montagnani
- Department of Biomedical Sciences and Human Oncology - Section of Pharmacology, School of Medicine, University of Bari "Aldo Moro," Policlinico University Hospital of Bari, Bari, Italy
| | - Luigi Santacroce
- Department of Interdisciplinary Medicine, Microbiology and Virology Unit, School of Medicine,University of Bari "Aldo Moro", Bari, Italy
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10
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Andreo-Vidal A, Binda E, Fedorenko V, Marinelli F, Yushchuk O. Genomic Insights into the Distribution and Phylogeny of Glycopeptide Resistance Determinants within the Actinobacteria Phylum. Antibiotics (Basel) 2021; 10:1533. [PMID: 34943745 PMCID: PMC8698665 DOI: 10.3390/antibiotics10121533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/26/2022] Open
Abstract
The spread of antimicrobial resistance (AMR) creates a challenge for global health security, rendering many previously successful classes of antibiotics useless. Unfortunately, this also includes glycopeptide antibiotics (GPAs), such as vancomycin and teicoplanin, which are currently being considered last-resort drugs. Emerging resistance towards GPAs risks limiting the clinical use of this class of antibiotics-our ultimate line of defense against multidrug-resistant (MDR) Gram-positive pathogens. But where does this resistance come from? It is widely recognized that the GPA resistance determinants-van genes-might have originated from GPA producers, such as soil-dwelling Gram-positive actinobacteria, that use them for self-protection. In the current work, we present a comprehensive bioinformatics study on the distribution and phylogeny of GPA resistance determinants within the Actinobacteria phylum. Interestingly, van-like genes (vlgs) were found distributed in different arrangements not only among GPA-producing actinobacteria but also in the non-producers: more than 10% of the screened actinobacterial genomes contained one or multiple vlgs, while less than 1% encoded for a biosynthetic gene cluster (BGC). By phylogenetic reconstructions, our results highlight the co-evolution of the different vlgs, indicating that the most diffused are the ones coding for putative VanY carboxypeptidases, which can be found alone in the genomes or associated with a vanS/R regulatory pair.
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Affiliation(s)
- Andrés Andreo-Vidal
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.A.-V.); (E.B.); (O.Y.)
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.A.-V.); (E.B.); (O.Y.)
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine;
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.A.-V.); (E.B.); (O.Y.)
| | - Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.A.-V.); (E.B.); (O.Y.)
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine;
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Structural Characterization of EnpA D,L-Endopeptidase from Enterococcus faecalis Prophage Provides Insights into Substrate Specificity of M23 Peptidases. Int J Mol Sci 2021; 22:ijms22137136. [PMID: 34281200 PMCID: PMC8269130 DOI: 10.3390/ijms22137136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/18/2021] [Accepted: 06/29/2021] [Indexed: 01/28/2023] Open
Abstract
The best-characterized members of the M23 family are glycyl-glycine hydrolases, such as lysostaphin (Lss) from Staphylococcus simulans or LytM from Staphylococcus aureus. Recently, enzymes with broad specificities were reported, such as EnpACD from Enterococcus faecalis, that cleaves D,L peptide bond between the stem peptide and a cross-bridge. Previously, the activity of EnpACD was demonstrated only on isolated peptidoglycan fragments. Herein we report conditions in which EnpACD lyses bacterial cells live with very high efficiency demonstrating great bacteriolytic potential, though limited to a low ionic strength environment. We have solved the structure of the EnpACD H109A inactive variant and analyzed it in the context of related peptidoglycan hydrolases structures to reveal the bases for the specificity determination. All M23 structures share a very conserved β-sheet core which constitutes the rigid bottom of the substrate-binding groove and active site, while variable loops create the walls of the deep and narrow binding cleft. A detailed analysis of the binding groove architecture, specificity of M23 enzymes and D,L peptidases demonstrates that the substrate groove, which is particularly deep and narrow, is accessible preferably for peptides composed of amino acids with short side chains or subsequent L and D-isomers. As a result, the bottom of the groove is involved in interactions with the main chain of the substrate while the side chains are protruding in one plane towards the groove opening. We concluded that the selectivity of the substrates is based on their conformations allowed only for polyglycine chains and alternating chirality of the amino acids.
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Moon K, Jeon JH, Kang I, Park KS, Lee K, Cha CJ, Lee SH, Cho JC. Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes. MICROBIOME 2020; 8:75. [PMID: 32482165 PMCID: PMC7265639 DOI: 10.1186/s40168-020-00863-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/11/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate. RESULTS We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1 × e-5 and query coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases blaHRV-1 and blaHRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages. CONCLUSION Our results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions. Video abstract.
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Affiliation(s)
- Kira Moon
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jeong Ho Jeon
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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13
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Stogios PJ, Savchenko A. Molecular mechanisms of vancomycin resistance. Protein Sci 2020; 29:654-669. [PMID: 31899563 DOI: 10.1002/pro.3819] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022]
Abstract
Vancomycin and related glycopeptides are drugs of last resort for the treatment of severe infections caused by Gram-positive bacteria such as Enterococcus species, Staphylococcus aureus, and Clostridium difficile. Vancomycin was long considered immune to resistance due to its bactericidal activity based on binding to the bacterial cell envelope rather than to a protein target as is the case for most antibiotics. However, two types of complex resistance mechanisms, each comprised of a multi-enzyme pathway, emerged and are now widely disseminated in pathogenic species, thus threatening the clinical efficiency of vancomycin. Vancomycin forms an intricate network of hydrogen bonds with the d-Ala-d-Ala region of Lipid II, interfering with the peptidoglycan layer maturation process. Resistance to vancomycin involves degradation of this natural precursor and its replacement with d-Ala-d-lac or d-Ala-d-Ser alternatives to which vancomycin has low affinity. Through extensive research over 30 years after the initial discovery of vancomycin resistance, remarkable progress has been made in molecular understanding of the enzymatic cascades responsible. Progress has been driven by structural studies of the key components of the resistance mechanisms which provided important molecular understanding such as, for example, the ability of this cascade to discriminate between vancomycin sensitive and resistant peptidoglycan precursors. Important structural insights have been also made into the molecular evolution of vancomycin resistance enzymes. Altogether this molecular data can accelerate inhibitor discovery and optimization efforts to reverse vancomycin resistance. Here, we overview our current understanding of this complex resistance mechanism with a focus on the structural and molecular aspects.
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Affiliation(s)
- Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID).,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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Vermassen A, Leroy S, Talon R, Provot C, Popowska M, Desvaux M. Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan. Front Microbiol 2019; 10:331. [PMID: 30873139 PMCID: PMC6403190 DOI: 10.3389/fmicb.2019.00331] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/08/2019] [Indexed: 11/13/2022] Open
Abstract
The cell wall (CW) of bacteria is an intricate arrangement of macromolecules, at least constituted of peptidoglycan (PG) but also of (lipo)teichoic acids, various polysaccharides, polyglutamate and/or proteins. During bacterial growth and division, there is a constant balance between CW degradation and biosynthesis. The CW is remodeled by bacterial hydrolases, whose activities are carefully regulated to maintain cell integrity or lead to bacterial death. Each cell wall hydrolase (CWH) has a specific role regarding the PG: (i) cell wall amidase (CWA) cleaves the amide bond between N-acetylmuramic acid and L-alanine residue at the N-terminal of the stem peptide, (ii) cell wall glycosidase (CWG) catalyses the hydrolysis of the glycosidic linkages, whereas (iii) cell wall peptidase (CWP) cleaves amide bonds between amino acids within the PG chain. After an exhaustive overview of all known conserved catalytic domains responsible for CWA, CWG, and CWP activities, this review stresses that the CWHs frequently display a modular architecture combining multiple and/or different catalytic domains, including some lytic transglycosylases as well as CW binding domains. From there, direct physiological and collateral roles of CWHs in bacterial cells are further discussed.
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Affiliation(s)
- Aurore Vermassen
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Régine Talon
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | | | - Magdalena Popowska
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
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15
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Kim HS, Hahn H, Kim J, Jang DM, Lee JY, Back JM, Im HN, Kim H, Han BW, Suh SW. Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanY B. Int J Biol Macromol 2018; 119:335-344. [PMID: 30016658 DOI: 10.1016/j.ijbiomac.2018.07.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/15/2018] [Accepted: 07/12/2018] [Indexed: 11/19/2022]
Abstract
Vancomycin resistance in Enterococci and its transfer to methicillin-resistant Staphylococcus aureus are challenging problems in health care institutions worldwide. High-level vancomycin resistance is conferred by acquiring either transposable elements of the VanA or VanB type. Enterococcus faecalis VanYB in the VanB-type operon is a d,d-carboxypeptidase that recognizes the peptidyl-d-Ala4-d-Ala5 extremity of peptidoglycan and hydrolyses the terminal d-Ala on the extracellular side of the cell wall, thereby increasing the level of glycopeptide antibiotics resistance. However, at the molecular level, it remains unclear how VanYB manipulates peptidoglycan peptides for vancomycin resistance. In this study, we have determined the crystal structures of E. faecalis VanYB in the d-Ala-d-Ala-bound, d-Ala-bound, and -unbound states. The interactions between VanYB and d-Ala-d-Ala observed in the crystal provide the molecular basis for the recognition of peptidoglycan substrates by VanYB. Moreover, comparisons with the related VanX and VanXY enzymes reveal distinct structural features of E. faecalis VanYB around the active-site cleft, thus shedding light on its unique substrate specificity. Our results could serve as the foundation for unravelling the molecular mechanism of vancomycin resistance and for developing novel antibiotics against the vancomycin-resistant Enterococcus species.
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Affiliation(s)
- Hyoun Sook Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea; Therapeutic Target Discovery Branch, Division of Precision Medicine, National Cancer Center, Goyang, Gyeonggi, Republic of Korea; Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Hyunggu Hahn
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Jieun Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Ji Yeon Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Jang Mi Back
- Therapeutic Target Discovery Branch, Division of Precision Medicine, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Ha Na Im
- Therapeutic Target Discovery Branch, Division of Precision Medicine, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Haelee Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.
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16
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Resistance to nonribosomal peptide antibiotics mediated by D-stereospecific peptidases. Nat Chem Biol 2018; 14:381-387. [PMID: 29483640 DOI: 10.1038/s41589-018-0009-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/27/2017] [Indexed: 12/26/2022]
Abstract
Nonribosomal peptide antibiotics, including polymyxin, vancomycin, and teixobactin, most of which contain D-amino acids, are highly effective against multidrug-resistant bacteria. However, overusing antibiotics while ignoring the risk of resistance arising has inexorably led to widespread emergence of resistant bacteria. Therefore, elucidation of the emerging mechanisms of resistance to nonribosomal peptide antibiotics is critical to their implementation. Here we describe a networking-associated genome-mining platform for linking biosynthetic building blocks to resistance components associated with biosynthetic gene clusters. By applying this approach to 5,585 complete bacterial genomes spanning the entire domain of bacteria, with subsequent chemical and enzymatic analyses, we demonstrate a mechanism of resistance toward nonribosomal peptide antibiotics that is based on hydrolytic cleavage by D-stereospecific peptidases. Our finding reveals both the widespread distribution and broad-spectrum resistance potential of D-stereospecific peptidases, providing a potential early indicator of antibiotic resistance to nonribosomal peptide antibiotics.
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17
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Chang JD, Wallace AG, Foster EE, Kim SJ. Peptidoglycan Compositional Analysis of Enterococcus faecalis Biofilm by Stable Isotope Labeling by Amino Acids in a Bacterial Culture. Biochemistry 2018; 57:1274-1283. [PMID: 29368511 DOI: 10.1021/acs.biochem.7b01207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptidoglycan (PG) is a major component of the cell wall in Enterococcus faecalis. Accurate analysis of PG composition provides crucial insights into the bacterium's cellular functions and responses to external stimuli, but this analysis remains challenging because of various chemical modifications to PG-repeat subunits. We characterized changes to the PG composition of E. faecalis grown as planktonic bacteria and biofilm by developing "stable isotope labeling by amino acids in bacterial culture" (SILAB), optimized for bacterial cultures with incomplete amino acid labeling. This comparative analysis by mass spectrometry was performed by labeling E. faecalis in biofilm with heavy Lys (l-[13C6,2D9,15N2]Lys) and planktonic bacteria with natural abundance l-Lys, then mixing equal amounts of bacteria from each condition, and performing cell wall isolation and mutanolysin digestion necessary for liquid chromatography and mass spectrometry. An analytical method was developed to determine muropeptide abundances using correction factors to compensate for incomplete heavy Lys isotopic enrichment (98.33 ± 0.05%) and incorporation (83.23 ± 1.16%). Forty-seven pairs of PG fragment ions from isolated cell walls of planktonic and biofilm samples were selected for SILAB analysis. We found that the PG in biofilm showed an increased level of PG cross-linking, an increased level of N-deacetylation of GlcNAc, a decreased level of O-acetylation of MurNAc, and an increased number of stem modifications by d,d- and l,d-carboxypeptidases.
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Affiliation(s)
- James D Chang
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Ashley G Wallace
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Erin E Foster
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
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18
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Chang JD, Foster EE, Wallace AG, Kim SJ. Peptidoglycan O-acetylation increases in response to vancomycin treatment in vancomycin-resistant Enterococcus faecalis. Sci Rep 2017; 7:46500. [PMID: 28406232 PMCID: PMC5390252 DOI: 10.1038/srep46500] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/15/2017] [Indexed: 01/30/2023] Open
Abstract
Vancomycin resistance is conferred upon vancomycin-resistant enterococci (VRE) through the replacement of peptidoglycan (PG) stem terminal d-Ala-d-Ala with d-Ala-d-Lac. The d-Ala-d-Lac incorporation can affect both the fitness and virulence of VRE. Here we comprehensively investigate the changes to PG composition in vancomycin-resistant Enterococcus faecalis following the growth in presence of vancomycin using liquid chromatography-mass spectrometry. Using high-resolution mass spectrometry, 104 unique muropeptides fragments were identified and the relative abundance of each fragment was accurately quantified by integrating the ion current of a selected ion using extracted-ion chromatogram. The analysis indicates reduced PG cross-linking, increased carboxypeptidase activities, increased N-deacetylation, and increased O-acetylation in VRE when grown in the presence of vancomycin. We found that O-acetylation preferentially occurred on muropeptides fragments with reduced cross-linking with a pentapeptide stem that terminated in d-Ala-d-Lac. These findings show that O-acetylation preferentially occurred in regions of the cell wall with reduced PG cross-linking on PG units that have stems terminating in d-Ala-d-Lac, serving as markers to prevent both the PG-stem modification by carboxypeptidases and the cell wall degradation by autolysins. Accurate quantitative PG composition analysis provided compositional insights into altered cell wall biosynthesis and modification processes in VRE that contribute to lysozyme resistance and enhanced virulence for VRE grown in the presence of vancomycin.
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Affiliation(s)
- James D Chang
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Erin E Foster
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Ashley G Wallace
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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19
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Li S, Cui S, Yin D, Zhu Q, Ma Y, Qian Z, Gu Y. Dual antibacterial activities of a chitosan-modified upconversion photodynamic therapy system against drug-resistant bacteria in deep tissue. NANOSCALE 2017; 9:3912-3924. [PMID: 28261736 DOI: 10.1039/c6nr07188k] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photodynamic therapy (PDT) has recently been proposed as an innovative approach to combat multi-drug resistant (MDR) bacteria. To improve the penetration depth of current PDT, a core-shell upconversion nanoparticle (UCNP) based PDT system, composed of a cationic N-octyl chitosan (OC) coated UCNP loaded with the photosensitizer zinc phthalocyanine (OC-UCNP-ZnPc), was constructed to enhance the antibacterial efficacy against MDR bacteria in deep tissue. The core-shell UCNPs displayed a higher upconversion fluorescence efficiency compared to the inner UCNP core. Dual antibacterial activities induced by chitosan and PDT-induced ROS were demonstrated, independent of the bacterial species. In particular, these nanoconstructs exhibited excellent antibacterial effects on the MDR bacteria including methicillin-resistant Staphylococcus aureus (MRSA) and β-lactamase-producing Escherichia coli. In vivo antibacterial therapy for murine MRSA-infected abscesses in the deep tissue (1 cm) strongly confirmed the outstanding anti-MRSA efficacy of OC-UCNP-ZnPc. Our results indicated that the OC-UCNP-ZnPc based PDT system triggered by deep-penetrating NIR light has a prominent antibacterial effect on MDR bacteria, which could be a promising strategy for deep-tissue infections.
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Affiliation(s)
- Siwen Li
- Department of Biomedical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China.
| | - Sisi Cui
- Department of Biomedical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China. and School of Life Science, Northeast Normal University, No. 5268 Renmin Street, Changchun, Jilin 130024, China
| | - Deyan Yin
- Department of Biomedical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China.
| | - Qiuyun Zhu
- Department of Biomedical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China.
| | - Yuxiang Ma
- Department of Biomedical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China.
| | - Zhiyu Qian
- Department of Biomedical Engineering, School of Automation, Nanjing University of Aeronautics and Astronautics, 29th JiangJun Street, Nanjing 211106, Jiangsu Province, China
| | - Yueqing Gu
- Department of Biomedical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China.
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Stogios PJ, Kuhn ML, Evdokimova E, Law M, Courvalin P, Savchenko A. Structural and Biochemical Characterization of Acinetobacter spp. Aminoglycoside Acetyltransferases Highlights Functional and Evolutionary Variation among Antibiotic Resistance Enzymes. ACS Infect Dis 2017; 3:132-143. [PMID: 27785912 DOI: 10.1021/acsinfecdis.6b00058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Modification of aminoglycosides by N-acetyltransferases (AACs) is one of the major mechanisms of resistance to these antibiotics in human bacterial pathogens. More than 50 enzymes belonging to the AAC(6') subfamily have been identified in Gram-negative and Gram-positive clinical isolates. Our understanding of the molecular function and evolutionary origin of these resistance enzymes remains incomplete. Here we report the structural and enzymatic characterization of AAC(6')-Ig and AAC(6')-Ih from Acinetobacter spp. The crystal structure of AAC(6')-Ig in complex with tobramycin revealed a large substrate-binding cleft remaining partially unoccupied by the substrate, which is in stark contrast with the previously characterized AAC(6')-Ib enzyme. Enzymatic analysis indicated that AAC(6')-Ig and -Ih possess a broad specificity against aminoglycosides but with significantly lower turnover rates as compared to other AAC(6') enzymes. Structure- and function-informed phylogenetic analysis of AAC(6') enzymes led to identification of at least three distinct subfamilies varying in oligomeric state, active site composition, and drug recognition mode. Our data support the concept of AAC(6') functionality originating through convergent evolution from diverse Gcn5-related-N-acetyltransferase (GNAT) ancestral enzymes, with AAC(6')-Ig and -Ih representing enzymes that may still retain ancestral nonresistance functions in the cell as provided by their particular active site properties.
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Affiliation(s)
- Peter J. Stogios
- Department of Chemical
Engineering and Applied Chemistry, University of Toronto, 200 College
Street, Toronto, Ontario M5G 1L6, Canada
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Elena Evdokimova
- Department of Chemical
Engineering and Applied Chemistry, University of Toronto, 200 College
Street, Toronto, Ontario M5G 1L6, Canada
| | - Melissa Law
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Patrice Courvalin
- Institut Pasteur, Unité des Agents Antibactériens, 25 rue du Docteur Roux, 75724 Cedex 15 Paris, France
| | - Alexei Savchenko
- Department of Chemical
Engineering and Applied Chemistry, University of Toronto, 200 College
Street, Toronto, Ontario M5G 1L6, Canada
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Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases. Curr Opin Struct Biol 2017; 44:87-100. [PMID: 28109980 DOI: 10.1016/j.sbi.2017.01.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/23/2016] [Accepted: 01/02/2017] [Indexed: 01/26/2023]
Abstract
The major component of bacterial cell wall is peptidoglycan (PG), a complex polymer formed by long glycan chains cross-linked by peptide stems. PG is in constant equilibrium requiring well-orchestrated coordination between synthesis and degradation. The resulting cell-wall fragments can be recycled, act as messengers for bacterial communication, as effector molecules in immune response or as signaling molecules triggering antibiotics resistance. Tailoring and recycling of PG requires the cleavage of different covalent bonds of the PG sacculi by a diverse set of specific enzymes whose activities are strictly regulated. Here, we review the molecular mechanisms that govern PG remodeling focusing on the structural information available for the bacterial lytic enzymes and the mechanisms by which they recognize their substrates.
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Abstract
Vancomycin resistance in Gram-positive bacteria results from the replacement of the d-alanyl–d-alanine target of peptidoglycan precursors with d-alanyl–d-lactate or d-alanyl–d-serine (d-Ala-d-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of d-Ala-d-Ser-terminating precursors by converting l-Ser to d-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in l-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanTG from VanG-type resistant Enterococcus faecalis BM4518 was determined. The structure showed significant similarity to type III pyridoxal 5′-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanTG and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn696 which are responsible for the l-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanTG against l-Ser versus l-Ala implied that this enzyme relies on its membrane-bound domain for l-Ser transport to increase the overall rate of d-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria. Vancomycin is one of the drugs of last resort against Gram-positive antibiotic-resistant pathogens. However, bacteria have evolved a sophisticated mechanism which remodels the drug target, the d-alanine ending precursors in cell wall synthesis, into precursors terminating with d-lactate or d-serine, to which vancomycin has less affinity. d-Ser is synthesized by VanT serine racemase, which has two unusual characteristics: (i) it is one of the few serine racemases identified in bacteria and (ii) it contains a membrane-bound domain involved in l-Ser uptake. The structure of the catalytic domain of VanTG showed high similarity to alanine racemases, and we identified three specific active site substitutions responsible for l-Ser specificity. The data provide the molecular basis for VanT evolution to a bifunctional enzyme coordinating both transport and racemization. Our findings also illustrate the evolution of the essential alanine racemase into a vancomycin resistance enzyme in response to antibiotic pressure.
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Zhang J, Yang YH, Jiang YL, Zhou CZ, Chen Y. Structural and biochemical analyses of the Streptococcus pneumonia L,D-carboxypeptidase DacB. ACTA ACUST UNITED AC 2015; 71:283-92. [PMID: 25664738 DOI: 10.1107/s1399004714025371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022]
Abstract
The L,D-carboxypeptidase DacB plays a key role in the remodelling of Streptococcus pneumoniae peptidoglycan during cell division. In order to decipher its substrate-binding properties and catalytic mechanism, the 1.71 Å resolution crystal structure of DacB from S. pneumoniae TIGR4 is reported. Structural analyses in combination with comparisons with the recently reported structures of DacB from S. pneumoniae D39 and R6 clearly demonstrate that DacB adopts a zinc-dependent carboxypeptidase fold and belongs to the metallopeptidase M15B subfamily. In addition, enzymatic activity assays further confirm that DacB indeed acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem, with Km and kcat values of 2.84 ± 0.37 mM and 91.49 ± 0.05 s(-1), respectively. Subsequent molecular docking and site-directed mutagenesis enable the assignment of the key residues that bind to the tetrapeptide. Altogether, these findings provide structural insights into substrate recognition in the metallopeptidase M15B subfamily.
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Affiliation(s)
- Juan Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Yi-Hu Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
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24
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Binda E, Marinelli F, Marcone GL. Old and New Glycopeptide Antibiotics: Action and Resistance. Antibiotics (Basel) 2014; 3:572-94. [PMID: 27025757 PMCID: PMC4790382 DOI: 10.3390/antibiotics3040572] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/20/2014] [Accepted: 10/23/2014] [Indexed: 12/05/2022] Open
Abstract
Glycopeptides are considered antibiotics of last resort for the treatment of life-threatening infections caused by relevant Gram-positive human pathogens, such as Staphylococcus aureus, Enterococcus spp. and Clostridium difficile. The emergence of glycopeptide-resistant clinical isolates, first among enterococci and then in staphylococci, has prompted research for second generation glycopeptides and a flurry of activity aimed at understanding resistance mechanisms and their evolution. Glycopeptides are glycosylated non-ribosomal peptides produced by a diverse group of soil actinomycetes. They target Gram-positive bacteria by binding to the acyl-d-alanyl-d-alanine (d-Ala-d-Ala) terminus of the growing peptidoglycan on the outer surface of the cytoplasmatic membrane. Glycopeptide-resistant organisms avoid such a fate by replacing the d-Ala-d-Ala terminus with d-alanyl-d-lactate (d-Ala-d-Lac) or d-alanyl-d-serine (d-Ala-d-Ser), thus markedly reducing antibiotic affinity for the cellular target. Resistance has manifested itself in enterococci and staphylococci largely through the expression of genes (named van) encoding proteins that reprogram cell wall biosynthesis and, thus, evade the action of the antibiotic. These resistance mechanisms were most likely co-opted from the glycopeptide producing actinomycetes, which use them to avoid suicide during antibiotic production, rather than being orchestrated by pathogen bacteria upon continued treatment. van-like gene clusters, similar to those described in enterococci, were in fact identified in many glycopeptide-producing actinomycetes, such as Actinoplanes teichomyceticus, which produces teicoplanin, and Streptomyces toyocaensis, which produces the A47934 glycopeptide. In this paper, we describe the natural and semi-synthetic glycopeptide antibiotics currently used as last resort drugs for Gram-positive infections and compare the van gene-based strategies of glycopeptide resistance among the pathogens and the producing actinomycetes. Particular attention is given to the strategy of immunity recently described in Nonomuraea sp. ATCC 39727. Nonomuraea sp. ATCC 39727 is the producer of A40926, which is the natural precursor of the second generation semi-synthetic glycopeptide dalbavancin, very recently approved for acute bacterial skin and skin structure infections. A thorough understanding of glycopeptide immunity in this producing microorganism may be particularly relevant to predict and eventually control the evolution of resistance that might arise following introduction of dalbavancin and other second generation glycopeptides into clinics.
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Affiliation(s)
- Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
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25
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Abdullah MR, Gutiérrez-Fernández J, Pribyl T, Gisch N, Saleh M, Rohde M, Petruschka L, Burchhardt G, Schwudke D, Hermoso JA, Hammerschmidt S. Structure of the pneumococcal l,d-carboxypeptidase DacB and pathophysiological effects of disabled cell wall hydrolases DacA and DacB. Mol Microbiol 2014; 93:1183-206. [PMID: 25060741 DOI: 10.1111/mmi.12729] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2014] [Indexed: 12/19/2022]
Abstract
Bacterial cell wall hydrolases are essential for peptidoglycan turnover and crucial to preserve cell shape. The d,d-carboxypeptidase DacA and l,d-carboxypeptidase DacB of Streptococcus pneumoniae function in a sequential manner. Here, we determined the structure of the surface-exposed lipoprotein DacB. The crystal structure of DacB, radically different to that of DacA, contains a mononuclear Zn(2+) catalytic centre located in the middle of a large and fully exposed groove. Two different conformations were found presenting a different arrangement of the active site topology. The critical residues for catalysis and substrate specificity were identified. Loss-of-function of DacA and DacB altered the cell shape and this was consistent with a modified peptidoglycan peptide composition in dac mutants. Contrary, an lgt mutant lacking lipoprotein diacylglyceryl transferase activity required for proper lipoprotein maturation retained l,d-carboxypeptidase activity and showed an intact murein sacculus. In addition we demonstrated pathophysiological effects of disabled DacA or DacB activities. Real-time bioimaging of intranasal infected mice indicated a substantial attenuation of ΔdacB and ΔdacAΔdacB pneumococci, while ΔdacA had no significant effect. In addition, uptake of these mutants by professional phagocytes was enhanced, while the adherence to lung epithelial cells was decreased. Thus, structural and functional studies suggest DacA and DacB as optimal drug targets.
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Affiliation(s)
- Mohammed R Abdullah
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald, D-17487, Greifswald, Germany
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26
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Abstract
In this issue of Structure, Hoyland and colleagues describe the structure of a peptidoglycan L,D-carboxypeptidase in both substrate-bound and apoenzyme forms. These studies reveal the basis for enzyme specificity and assist greatly in a field where form and function overlap.
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Affiliation(s)
- Ian T Cadby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew L Lovering
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
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27
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Hoyland CN, Aldridge C, Cleverley RM, Duchêne MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ. Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition. Structure 2014; 22:949-60. [PMID: 24909784 PMCID: PMC4087270 DOI: 10.1016/j.str.2014.04.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/24/2014] [Accepted: 04/29/2014] [Indexed: 01/30/2023]
Abstract
Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.
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Affiliation(s)
- Christopher N Hoyland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christine Aldridge
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Robert M Cleverley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marie-Clémence Duchêne
- Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - George Minasov
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Olena Onopriyenko
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Karzan Sidiq
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Peter J Stogios
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Wayne F Anderson
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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