1
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Tossavainen H, Pitkänen I, Antenucci L, Thapa C, Permi P. Chemical shift assignments of the catalytic domain of Staphylococcus aureus LytM. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:1-5. [PMID: 37914968 PMCID: PMC11082022 DOI: 10.1007/s12104-023-10161-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
S. aureus resistance to antibiotics has increased rapidly. MRSA strains can simultaneously be resistant to many different classes of antibiotics, including the so-called "last-resort" drugs. Resistance complicates treatment, increases mortality and substantially increases the cost of treatment. The need for new drugs against (multi)resistant S. aureus is high. M23B family peptidoglycan hydrolases, enzymes that can kill S. aureus by cleaving glycine-glycine peptide bonds in S. aureus cell wall are attractive targets for drug development because of their binding specificity and lytic activity. M23B enzymes lysostaphin, LytU and LytM have closely similar catalytic domain structures. They however differ in their lytic activities, which can arise from non-conserved residues in the catalytic groove and surrounding loops or differences in dynamics. We report here the near complete 1H/13C/15N resonance assignment of the catalytic domain of LytM, residues 185-316. The chemical shift data allow comparative structural and functional studies between the enzymes and is essential for understanding how these hydrolases degrade the cell wall.
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Affiliation(s)
- Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ilona Pitkänen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Lina Antenucci
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Chandan Thapa
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
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2
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Shestak NV, Grishin AV, Lyashchuk AM, Lunin VG, Anna SK. The choice of chromatographic resin for the purification of recombinant lysostaphin affects its activity. Protein Expr Purif 2023; 207:106274. [PMID: 37084838 DOI: 10.1016/j.pep.2023.106274] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 04/23/2023]
Abstract
Lysostaphin is a zinc-dependent endopeptidase that is effective against both antibiotic-sensitive and antibiotic-resistant strains of Staphylococcus aureus. Lysostaphin is typically purified on cation-exchange or metal-chelate affinity resins, and there are data indicating potential influence of the chromatographic resin on the lysostaphin activity. In this study, we systematically investigated the impact of the resin used to purify the recombinant lysostaphin on its activity. To this end, recombinant lysostaphin with an additional histidine tag at the C-terminus was purified using a cation-exchange resin, three types of nickel-chelate resins with different strength of metal ion binding, or a zinc-chelate resin. Lysostaphin samples purified on the cation-exchange resin (WorkBeads 40S), the nickel-chelate resin with the strong nickel ion binding (WorkBeads NiMAC), and the zinc-chelate resin (WorkBeads NTA with immobilized zinc ions) had equal activity. On the contrary, the activity of lysostaphin preparations purified on nickel-chelate resins with medium (WorkBeads Ni-NTA) and relatively weak (WorkBeads Ni-IDA) nickel ion binding was significantly reduced. The decrease in activity can be explained by the interaction of lysostaphin with the nickel ions leached from the resin and is caused by either the exchange of the zinc ion in the lysostaphin active center with a nickel ion from the resin, or binding of an additional ion that inhibits the enzymatic activity. Removal of metal ions from the active site of lysostaphin and subsequent incorporation of the native zinc ions lead to complete restoration of the activity of the enzyme.
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Affiliation(s)
- Nikita V Shestak
- N. F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, Moscow, Gamalei st., 18, Russian Federation; Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119991, Moscow, Leninskiye Gory, 1, Russian Federation.
| | - Alexander V Grishin
- N. F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, Moscow, Gamalei st., 18, Russian Federation; All-Russian Research Institute of Agricultural Biotechnology, 127550, Moscow, Timiryazevskaya st., 42, Russian Federation.
| | - Alexander M Lyashchuk
- N. F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, Moscow, Gamalei st., 18, Russian Federation
| | - Vladimir G Lunin
- N. F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, Moscow, Gamalei st., 18, Russian Federation; All-Russian Research Institute of Agricultural Biotechnology, 127550, Moscow, Timiryazevskaya st., 42, Russian Federation
| | - S Karyagina Anna
- N. F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, Moscow, Gamalei st., 18, Russian Federation; All-Russian Research Institute of Agricultural Biotechnology, 127550, Moscow, Timiryazevskaya st., 42, Russian Federation; A. N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Leninskiye Gory, 1, Russian Federation
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3
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Kwan JMC, Qiao Y. Mechanistic Insights into the Activities of Major Families of Enzymes in Bacterial Peptidoglycan Assembly and Breakdown. Chembiochem 2023; 24:e202200693. [PMID: 36715567 DOI: 10.1002/cbic.202200693] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 01/31/2023]
Abstract
Serving as an exoskeletal scaffold, peptidoglycan is a polymeric macromolecule that is essential and conserved across all bacteria, yet is absent in mammalian cells; this has made bacterial peptidoglycan a well-established excellent antibiotic target. In addition, soluble peptidoglycan fragments derived from bacteria are increasingly recognised as key signalling molecules in mediating diverse intra- and inter-species communication in nature, including in gut microbiota-host crosstalk. Each bacterial species encodes multiple redundant enzymes for key enzymatic activities involved in peptidoglycan assembly and breakdown. In this review, we discuss recent findings on the biochemical activities of major peptidoglycan enzymes, including peptidoglycan glycosyltransferases (PGT) and transpeptidases (TPs) in the final stage of peptidoglycan assembly, as well as peptidoglycan glycosidases, lytic transglycosylase (LTs), amidases, endopeptidases (EPs) and carboxypeptidases (CPs) in peptidoglycan turnover and metabolism. Biochemical characterisation of these enzymes provides valuable insights into their substrate specificity, regulation mechanisms and potential modes of inhibition.
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Affiliation(s)
- Jeric Mun Chung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), 21 Nanyang Link, Singapore, 637371, Singapore.,LKC School of Medicine, Nanyang Technological University (NTU) Singapore, 11 Mandalay Road, Singapore, Singapore, 208232, Singapore
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), Singapore, 21 Nanyang Link, Singapore, 637371, Singapore
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4
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Comparison of the individual and combined actions of charged amino acids and glycine on the lysis of Escherichia coli cells by human and chicken lysozyme. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Guan S, Zhong L, Yu H, Wang L, Jin Y, Liu J, Xiang H, Yu H, Wang L, Wang D. Molecular docking and proteomics reveals the synergistic antibacterial mechanism of theaflavin with β-lactam antibiotics against MRSA. Front Microbiol 2022; 13:993430. [PMID: 36452924 PMCID: PMC9702817 DOI: 10.3389/fmicb.2022.993430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/11/2022] [Indexed: 04/09/2024] Open
Abstract
Recurrent epidemics of methicillin-resistant Staphylococcus aureus (S. aureus) (MRSA) have illustrated that the effectiveness of antibiotics in clinical application is rapidly fading. A feasible approach is to combine natural products with existing antibiotics to achieve an antibacterial effect. In this molecular docking study, we found that theaflavin (TF) preferentially binds the allosteric site of penicillin-binding protein 2a (PBP2a), inducing the PBP2a active site to open, which is convenient for β-lactam antibiotics to treat MRSA infection, instead of directly exerting antibacterial activity at the active site. Subsequent TMT-labeled proteomics analysis showed that TF treatment did not significantly change the landscape of the S. aureus USA300 proteome. Checkerboard dilution tests and kill curve assays were performed to validate the synergistic effect of TF and ceftiofur, and the fractional inhibitory concentration index (FICI) was 0.1875. The antibacterial effect of TF combined with ceftiofur was better than that of single-drug treatment in vitro. In addition, TF effectively enhanced the activity of ceftiofur in a mouse model of MRSA-induced pneumonia. Our findings provide a potential therapeutic strategy to combine existing antibiotics with natural products to resolve the prevalent infections of multidrug-resistant pathogens.
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Affiliation(s)
- Shuhan Guan
- College of Animal Science, Jilin University, Changchun, China
| | - Ling Zhong
- College of Animal Science, Jilin University, Changchun, China
| | - Hangqian Yu
- College of Animal Science, Jilin University, Changchun, China
| | - Li Wang
- Changchun University of Chinese Medicine, Changchun, China
| | - Yajing Jin
- College of Animal Science, Jilin University, Changchun, China
| | - Jingyu Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Hua Xiang
- College of Animal Medicine, Jilin Agricultural University, Changchun, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun, China
| | - Lin Wang
- State Key Laboratory for Zoonotic Diseases, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Dacheng Wang
- College of Animal Science, Jilin University, Changchun, China
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6
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Razew A, Schwarz JN, Mitkowski P, Sabala I, Kaus-Drobek M. One fold, many functions-M23 family of peptidoglycan hydrolases. Front Microbiol 2022; 13:1036964. [PMID: 36386627 PMCID: PMC9662197 DOI: 10.3389/fmicb.2022.1036964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/05/2022] [Indexed: 12/02/2023] Open
Abstract
Bacterial cell walls are the guards of cell integrity. They are composed of peptidoglycan that provides rigidity to sustain internal turgor and ensures isolation from the external environment. In addition, they harbor the enzymatic machinery to secure cell wall modulations needed throughout the bacterial lifespan. The main players in this process are peptidoglycan hydrolases, a large group of enzymes with diverse specificities and different mechanisms of action. They are commonly, but not exclusively, found in prokaryotes. Although in most cases, these enzymes share the same molecular function, namely peptidoglycan hydrolysis, they are leveraged to perform a variety of physiological roles. A well-investigated family of peptidoglycan hydrolases is M23 peptidases, which display a very conserved fold, but their spectrum of lytic action is broad and includes both Gram- positive and Gram- negative bacteria. In this review, we summarize the structural, biochemical, and functional studies concerning the M23 family of peptidases based on literature and complement this knowledge by performing large-scale analyses of available protein sequences. This review has led us to gain new insight into the role of surface charge in the activity of this group of enzymes. We present relevant conclusions drawn from the analysis of available structures and indicate the main structural features that play a crucial role in specificity determination and mechanisms of latency. Our work systematizes the knowledge of the M23 family enzymes in the context of their unique antimicrobial potential against drug-resistant pathogens and presents possibilities to modulate and engineer their features to develop perfect antibacterial weapons.
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Affiliation(s)
| | | | | | - Izabela Sabala
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Kaus-Drobek
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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7
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Zha J, Li J, Su Z, Akimbekov N, Wu X. Lysostaphin: Engineering and Potentiation toward Better Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11441-11457. [PMID: 36082619 DOI: 10.1021/acs.jafc.2c03459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lysostaphin is a potent bacteriolytic enzyme with endopeptidase activity against the common pathogen Staphylococcus aureus. By digesting the pentaglycine crossbridge in the cell wall peptidoglycan of S. aureus including the methicillin-resistant strains, lysostaphin initiates rapid lysis of planktonic and sessile cells (biofilms) and has great potential for use in agriculture, food industries, and pharmaceutical industries. In the past few decades, there have been tremendous efforts in potentiating lysostaphin for better applications in these fields, including engineering of the enzyme for higher potency and lower immunogenicity with longer-lasting effects, formulation and immobilization of the enzyme for higher stability and better durability, and recombinant expression for low-cost industrial production and in situ biocontrol. These achievements are extensively reviewed in this article focusing on applications in disease control, food preservation, surface decontamination, and pathogen detection. In addition, some basic properties of lysostaphin that have been controversial and only elucidated recently are summarized, including the substrate-binding properties, the number of zinc-binding sites, the substrate range, and the cleavage site in the pentaglycine crossbridge. Resistance to lysostaphin is also highlighted with a focus on various mechanisms. This article is concluded with a discussion on the limitations and future perspectives for the actual applications of lysostaphin.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Jingyuan Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zheng Su
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Nuraly Akimbekov
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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8
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Influence of NaCl and pH on lysostaphin catalytic activity, cell binding, and bacteriolytic activity. Appl Microbiol Biotechnol 2022; 106:6519-6534. [DOI: 10.1007/s00253-022-12173-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/02/2022]
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9
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Guo Q, Ren CW, Cai JH, Zhang CY, Li YT, Xu B, Farooq MA. The synergistic inhibition and mechanism of epicatechin gallate and Chitosan against Methicillin-resistant Staphylococcus aureus and the application in pork preservation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Wysocka A, Jagielska E, Łężniak Ł, Sabała I. Two New M23 Peptidoglycan Hydrolases With Distinct Net Charge. Front Microbiol 2021; 12:719689. [PMID: 34630350 PMCID: PMC8498115 DOI: 10.3389/fmicb.2021.719689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial peptidoglycan hydrolases play an essential role in cell wall metabolism during bacterial growth, division, and elongation (autolysins) or in the elimination of closely related species from the same ecological niche (bacteriocins). Most studies concerning the peptidoglycan hydrolases present in Gram-positive bacteria have focused on clinically relevant Staphylococcus aureus or the model organism Bacillus subtilis, while knowledge relating to other species remains limited. Here, we report two new peptidoglycan hydrolases from the M23 family of metallopeptidases derived from the same staphylococcal species, Staphylococcus pettenkoferi. They share modular architecture, significant sequence identity (60%), catalytic and binding residue conservation, and similar modes of activation, but differ in gene distribution, putative biological role, and, strikingly, in their isoelectric points (pIs). One of the peptides has a high pI, similar to that reported for all M23 peptidases evaluated to date, whereas the other displays a low pI, a unique feature among M23 peptidases. Consequently, we named them SpM23_B (Staphylococcus pettenkoferi M23 "Basic") and SpM23_A (Staphylococcus pettenkoferi M23 "Acidic"). Using genetic and biochemical approaches, we have characterized these two novel lytic enzymes, both in vitro and in their physiological context. Our study presents a detailed characterization of two novel and clearly distinct peptidoglycan hydrolases to understand their role in bacterial physiology.
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Affiliation(s)
- Alicja Wysocka
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Jagielska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Łukasz Łężniak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Izabela Sabała
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
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11
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Structural Investigations on the SH3b Domains of Clostridium perfringens Autolysin through NMR Spectroscopy and Structure Simulation Enlighten the Cell Wall Binding Function. Molecules 2021; 26:molecules26185716. [PMID: 34577187 PMCID: PMC8470621 DOI: 10.3390/molecules26185716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Clostridium perfringens autolysin (CpAcp) is a peptidoglycan hydrolase associated with cell separation, division, and growth. It consists of a signal peptide, ten SH3b domains, and a catalytic domain. The structure and function mechanisms of the ten SH3bs related to cell wall peptidoglycan binding remain unclear. Here, the structures of CpAcp SH3bs were studied through NMR spectroscopy and structural simulation. The NMR structure of SH3b6 was determined at first, which adopts a typical β-barrel fold and has three potential ligand-binding pockets. The largest pocket containing eight conserved residues was suggested to bind with peptide ligand in a novel model. The structures of the other nine SH3bs were subsequently predicted to have a fold similar to SH3b6. Their ligand pockets are largely similar to those of SH3b6, although with varied size and morphology, except that SH3b1/2 display a third pocket markedly different from those in other SH3bs. Thus, it was supposed that SH3b3-10 possess similar ligand-binding ability, while SH3b1/2 have a different specificity and additional binding site for ligand. As an entirety, ten SH3bs confer a capacity for alternatively binding to various peptidoglycan sites in the cell wall. This study presents an initial insight into the structure and potential function of CpAcp SH3bs.
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12
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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: 3] [Impact Index Per Article: 1.0] [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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13
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Mitchell SJ, Verma D, Griswold KE, Bailey-Kellogg C. Building blocks and blueprints for bacterial autolysins. PLoS Comput Biol 2021; 17:e1008889. [PMID: 33793553 PMCID: PMC8051824 DOI: 10.1371/journal.pcbi.1008889] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/16/2021] [Accepted: 03/17/2021] [Indexed: 01/31/2023] Open
Abstract
Bacteria utilize a wide variety of endogenous cell wall hydrolases, or autolysins, to remodel their cell walls during processes including cell division, biofilm formation, and programmed death. We here systematically investigate the composition of these enzymes in order to gain insights into their associated biological processes, potential ways to disrupt them via chemotherapeutics, and strategies by which they might be leveraged as recombinant antibacterial biotherapies. To do so, we developed LEDGOs (lytic enzyme domains grouped by organism), a pipeline to create and analyze databases of autolytic enzyme sequences, constituent domain annotations, and architectural patterns of multi-domain enzymes that integrate peptidoglycan binding and degrading functions. We applied LEDGOs to eight pathogenic bacteria, gram negatives Acinetobacter baumannii, Klebsiella pneumoniae, Neisseria gonorrhoeae, and Pseudomonas aeruginosa; and gram positives Clostridioides difficile, Enterococcus faecium, Staphylococcus aureus, and Streptococcus pneumoniae. Our analysis of the autolytic enzyme repertoires of these pathogens reveals commonalities and differences in their key domain building blocks and architectures, including correlations and preferred orders among domains in multi-domain enzymes, repetitions of homologous binding domains with potentially complementarity recognition modalities, and sequence similarity patterns indicative of potential divergence of functional specificity among related domains. We have further identified a variety of unannotated sequence regions within the lytic enzymes that may themselves contain new domains with important functions.
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Affiliation(s)
- Spencer J. Mitchell
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
| | - Deeptak Verma
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America
- Lyticon LLC, Lebanon, New Hampshire, United States of America
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
- Lyticon LLC, Lebanon, New Hampshire, United States of America
- * E-mail:
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14
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Kang SJ, Jun JS, Moon JA, Hong KW. Surface display of p75, a Lactobacillus rhamnosus GG derived protein, on Bacillus subtilis spores and its antibacterial activity against Listeria monocytogenes. AMB Express 2020; 10:139. [PMID: 32770428 PMCID: PMC7415045 DOI: 10.1186/s13568-020-01073-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/25/2020] [Indexed: 01/05/2023] Open
Abstract
Lactobacillus rhamnosus p75 protein with peptidoglycan hydrolase (PGH) activity is one of the key molecules exhibiting anti-apoptotic and cell-protective activity for human intestinal epithelial cells. In this study, with the goal of developing new probiotics, the p75 protein was displayed on the surface of Bacillus subtilis spores using spore coat protein CotG as an anchoring motif. The PGH activity, stability, and the antibacterial activity of the spore-displayed p75 (CotG-p75) protein were also investigated. The PGH activity of the CotG-p75 against peptidoglycan extracted from B. subtilis was confirmed by the ninhydrin test. Under various harsh conditions, compared to the control groups, the PGH activities of CotG-p75 were very stable in the range of pH 3–7 and maintained at 70% at 50 °C. In addition, the antibacterial activity of CotG-p75 against Listeria monocytogenes was evaluated by a time-kill assay. After 6 h incubation in phosphate-buffered saline, CotG-p75 reduced the number of viable cells of L. monocytogenes by up to 2.0 log. Scanning electron microscopy analysis showed that the cell wall of L. monocytogenes was partially damaged by the treatment with CotG-p75. Our preliminary results show that CotG-p75 could be a good candidate for further research to develop new genetically engineered probiotics.
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15
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Taheri-Anganeh M, Khatami SH, Jamali Z, Movahedpour A, Ghasemi Y, Savardashtaki A, Mostafavi-Pour Z. LytU-SH3b fusion protein as a novel and efficient enzybiotic against methicillin-resistant Staphylococcus aureus. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2019; 8:151-158. [PMID: 32042832 PMCID: PMC6995334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a challenging infectious agent worldwide. The ever growing antibiotic resistance has made the researchers to look for new anti-staphylococcal agents. Autolysins are staphylococcal enzymes that lyse bacterial cell wall for cell division. Autolysins can be used as novel enzybiotics (enzymes have antibiotic effects) for staphylococcal infections. LytU is a newly explored autolysin. SH3b is a potent cell wall binding domain that can be fused to lytic enzymes to increase their activity. The aim of this study was to design a novel and efficient fusion enzybiotic that could lyse staphylococcal cell wall peptidoglycan by disrupting the bacteria. LytU-SH3b fusion construct was synthesized and LytU was amplified through the construct, using overhang PCR. The fusion and native forms that had his-tag were synthesized by recombinant technology in Escherichia coli BL21 (DE3) strain and purified utilizing Ni-NTA agarose beads. LytU and LytU-SH3b activity and potency were assessed using plate lysis assay, turbidity reduction assay and minimal inhibitory concentration (MIC) tests. All these tests showed that LytU-SH3b has more activity and potency than LytU. LytU-SH3b has MIC 421 fold lesser than LytU. Finally, LytU-SH3b is a novel and efficient recombinant enzybiotic that can lyse MRSA as an alternative to chemical small molecule antibiotics.
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Affiliation(s)
- Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Recombinant Protein Laboratory, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Jamali
- Cardiovascular Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zohreh Mostafavi-Pour
- Recombinant Protein Laboratory, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran,Maternal-Fetal Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran,Corresponding Author: Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, IR Iran. Tel: +98-713 2303029; Fax: +98-713 2303029
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16
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Kim D, Kwon SJ, Sauve J, Fraser K, Kemp L, Lee I, Nam J, Kim J, Dordick JS. Modular Assembly of Unique Chimeric Lytic Enzymes on a Protein Scaffold Possessing Anti-Staphylococcal Activity. Biomacromolecules 2019; 20:4035-4043. [PMID: 31524374 DOI: 10.1021/acs.biomac.9b01134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lytic enzymes have been considered as potential alternatives to antibiotics. These enzymes, particularly those that target Gram-positive bacteria, consist of modular cell wall-binding and catalytic domains, which can be shuffled with those of other lytic enzymes to produce unnatural chimeric enzymes. In this work, we report the in vitro shuffling of two different modular domains using a protein self-assembly methodology. Catalytic domains (CD) and cell wall-binding domains (BD) from the bacteriocin lysostaphin (Lst) and a putative autolysin from Staphylococcus aureus (SA1), respectively, were genetically site-specifically biotinylated and assembled with streptavidin to generate 23 permuted chimeras. The specific assembly of a CD (3 equiv) and a BD (1 equiv) from Lst and SA1, respectively [CDL-BDS (3:1)], on a streptavidin scaffold yielded high lytic activity against S. aureus (at least 5.6 log reduction), which was higher than that obtained with either native Lst or SA1 alone. Moreover, at 37 °C, the initial rate of cell lysis was over 3-fold higher than that with free Lst, thereby revealing the unique catalytic properties of the chimeric proteins. In vitro self-assembly of functional domains from modular lytic enzymes on a protein scaffold likely expands the repertoire of bactericidal enzymes with improved activities.
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Affiliation(s)
- Domyoung Kim
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Jessica Sauve
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Keith Fraser
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Leighann Kemp
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Inseon Lee
- Department of Chemical and Biological Engineering , Korea University , 145 Anam-ro , Seongbuk-gu, Seoul 02841 , Republic of Korea
| | - Jahyun Nam
- Department of Chemical and Biological Engineering , Korea University , 145 Anam-ro , Seongbuk-gu, Seoul 02841 , Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering , Korea University , 145 Anam-ro , Seongbuk-gu, Seoul 02841 , Republic of Korea
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
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17
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Cardoso CV, Barbosa EV, Liberal MHT, Chagas EFD. Transgenic technology: the strategy for the control and prevention of bovine staphylococcal mastitis? ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biori.2019.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Mitkowski P, Jagielska E, Nowak E, Bujnicki JM, Stefaniak F, Niedziałek D, Bochtler M, Sabała I. Structural bases of peptidoglycan recognition by lysostaphin SH3b domain. Sci Rep 2019; 9:5965. [PMID: 30979923 PMCID: PMC6461655 DOI: 10.1038/s41598-019-42435-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/29/2019] [Indexed: 11/09/2022] Open
Abstract
Staphylococcus simulans lysostaphin cleaves pentaglycine cross-bridges between stem peptides in the peptidoglycan of susceptible staphylococci, including S. aureus. This enzyme consists of an N-terminal catalytic domain and a cell wall binding domain (SH3b), which anchors the protein to peptidoglycan. Although structures of SH3bs from lysostaphin are available, the binding modes of peptidoglycan to these domains are still unclear. We have solved the crystal structure of the lysostaphin SH3b domain in complex with a pentaglycine peptide representing the peptidoglycan cross-bridge. The structure identifies a groove between β1 and β2 strands as the pentaglycine binding site. The structure suggests that pentaglycine specificity of the SH3b arises partially directly by steric exclusion of Cβ atoms in the ligand and partially indirectly due to the selection of main chain conformations that are easily accessible for glycine, but not other amino acid residues. We have revealed further interactions of SH3b with the stem peptides with the support of bioinformatics tools. Based on the structural data we have attempted engineering of the domain specificity and have investigated the relevance of the introduced substitutions on the domain binding and specificity, also in the contexts of the mature lysostaphin and of its bacteriolytic activity.
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Affiliation(s)
- Paweł Mitkowski
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Jagielska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Nowak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Filip Stefaniak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Dorota Niedziałek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Izabela Sabała
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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19
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ClyJ Is a Novel Pneumococcal Chimeric Lysin with a Cysteine- and Histidine-Dependent Amidohydrolase/Peptidase Catalytic Domain. Antimicrob Agents Chemother 2019; 63:AAC.02043-18. [PMID: 30642930 DOI: 10.1128/aac.02043-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/05/2019] [Indexed: 12/14/2022] Open
Abstract
Streptococcus pneumoniae is one of the leading pathogens that cause a variety of mucosal and invasive infections. With the increased emergence of multidrug-resistant S. pneumoniae, new antimicrobials with mechanisms of action different from conventional antibiotics are urgently needed. In this study, we identified a putative lysin (gp20) encoded by the Streptococcus phage SPSL1 using the LytA autolysin as a template. Molecular dissection of gp20 revealed a binding domain (GPB) containing choline-binding repeats (CBRs) that are high specificity for S. pneumoniae By fusing GPB to the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) catalytic domain of the PlyC lysin, we constructed a novel chimeric lysin, ClyJ, with improved activity to the pneumococcal Cpl-1 lysin. No resistance was observed in S. pneumoniae strains after exposure to incrementally doubling concentrations of ClyJ for 8 continuous days in vitro In a mouse bacteremia model using penicillin G as a control, a single intraperitoneal injection of ClyJ improved the survival rate of lethal S. pneumoniae-infected mice in a dose-dependent manner. Given its high lytic activity and safety profile, ClyJ may represent a promising alternative to combat pneumococcal infections.
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20
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Singh V, Phukan UJ. Interaction of host and Staphylococcus aureus protease-system regulates virulence and pathogenicity. Med Microbiol Immunol 2018; 208:585-607. [PMID: 30483863 DOI: 10.1007/s00430-018-0573-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023]
Abstract
Staphylococcus aureus causes various health care- and community-associated infections as well as certain chronic TH2 driven inflammatory diseases. It is a potent pathogen with serious virulence and associated high morbidity. Severe pathogenicity is accredited to the S. aureus secreted virulence factors such as proteases and host protease modulators. These virulence factors promote adhesion and invasion of bacteria through damage of tight junction barrier and keratinocytes. They inhibit activation and transmigration of various immune cells such as neutrophils (and neutrophil proteases) to evade opsono-phagocytosis and intracellular bacterial killing. Additionally, they protect the bacteria from extracellular killing by disrupting integrity of extracellular matrix. Platelet activation and agglutination is also impaired by these factors. They also block the classical as well as alternative pathways of complement activation and assist in spread of infection through blood and tissue. As these factors are exquisite factors of S. aureus mediated disease development, we have focused on review of diversification of various protease-system associated virulence factors, their structural building, diverse role in disease development and available therapeutic counter measures. This review summarises the role of protease-associated virulence factors during invasion and progression of disease.
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Affiliation(s)
- Vigyasa Singh
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Ujjal Jyoti Phukan
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India.
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21
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Kalali Y, Haghighat S, Mahdavi M. Passive immunotherapy with specific IgG fraction against autolysin: Analogous protectivity in the MRSA infection with antibiotic therapy. Immunol Lett 2018; 212:125-131. [PMID: 30496765 DOI: 10.1016/j.imlet.2018.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 11/16/2022]
Abstract
Staphylococcus aureus is a leading infectious cause of life-threatening diseases in human beings, with no effective vaccine available to date against this bacterium. Treatment of methicillin-resistant S. aureus (MRSA) infections has become increasingly difficult because of the emergence of multidrug-resistant isolates. Immunotherapy represents a potential approach to prevent S. aureus-related infections. Autolysin is one of the virulence factors, which controls the growth, cell lysis, daughter-cell separation, and biofilm formation. Our study focused on passive immunization against MRSA infection. Herein, rabbit polyclonal IgG was produced following the preparation of r-autolysin. Specificity of IgG against r-autolysin was investigated by ELISA and western blotting assays. IgG fraction was prepared using sulfate ammonium precipitation, and the ability of antiserum to promote phagocytosis of bacteria was assessed by opsonophagocytosis assay. Then, passive immunization of mice was carried out with polyclonal IgG fraction and, mice were sacrificed three days after challenge and their kidneys, liver, and spleen were collected. Results exhibited that the passive immunization with rabbit polyclonal anti-IgG fraction tremendously improved survival rates of mice challenged by S. aureus as well as vancomycin treatment compared with the negative control groups. In addition, a remarkable decrease in bacterial numbers was observed in mice treated with rabbit polyclonal anti-IgG. Importantly, our findings demonstrated that passive immunotherapy and antibiotic therapy lead to decreased histopathological damage in mice infected by S. aureus as compared with control groups. Our results suggested that the passive immunization may result in the introduction of excellent strategies to control infections caused by MRSA, like antibiotic therapy.
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Affiliation(s)
- Yasamin Kalali
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Setareh Haghighat
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehdi Mahdavi
- Recombinant Vaccine Research Center, Tehran University of Medical Sciences, Tehran, Iran
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22
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Tossavainen H, Raulinaitis V, Kauppinen L, Pentikäinen U, Maaheimo H, Permi P. Structural and Functional Insights Into Lysostaphin-Substrate Interaction. Front Mol Biosci 2018; 5:60. [PMID: 30018958 PMCID: PMC6038053 DOI: 10.3389/fmolb.2018.00060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Lysostaphin from Staphylococcus simulans and its family enzymes rapidly acquire prominence as the next generation agents in treatment of S. aureus infections. The specificity of lysostaphin is promoted by its C-terminal cell wall targeting domain selectivity toward pentaglycine bridges in S. aureus cell wall. Scission of these cross-links is carried out by its N-terminal catalytic domain, a zinc-dependent endopeptidase. Understanding the determinants affecting the efficiency of catalysis and strength and specificity of interactions lies at the heart of all lysostaphin family enzyme applications. To this end, we have used NMR, SAXS and molecular dynamics simulations to characterize lysostaphin structure and dynamics, to address the inter-domain interaction, the enzyme-substrate interaction as well as the catalytic properties of pentaglycine cleavage in solution. Our NMR structure confirms the recent crystal structure, yet, together with the molecular dynamics simulations, emphasizes the dynamic nature of the loops embracing the catalytic site. We found no evidence for inter-domain interaction, but, interestingly, the SAXS data delineate two preferred conformation subpopulations. Catalytic H329 and H360 were observed to bind a second zinc ion, which reduces lysostaphin pentaglycine cleaving activity. Binding of pentaglycine or its lysine derivatives to the targeting domain was found to be of very low affinity. The pentaglycine interaction site was located to the N-terminal groove of the domain. Notably, the targeting domain binds the peptidoglycan stem peptide Ala-d-γ-Glu-Lys-d-Ala-d-Ala with a much higher, micromolar affinity. Binding site mapping reveals two interaction sites of different affinities on the surface of the domain for this peptide.
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Affiliation(s)
- Helena Tossavainen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Vytas Raulinaitis
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Linda Kauppinen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku Centre for Biotechnology, Turku, Finland
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
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23
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Raulinaitis V, Tossavainen H, Aitio O, Juuti JT, Hiramatsu K, Kontinen V, Permi P. Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family. Sci Rep 2017; 7:6020. [PMID: 28729697 PMCID: PMC5519744 DOI: 10.1038/s41598-017-06135-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023] Open
Abstract
We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the overall structure common to the lysostaphin family. Purified LytU lyses S. aureus cells and cleaves pentaglycine, a reaction conveniently monitored by NMR spectroscopy. Substituting the cofactor zinc ion with a copper or cobalt ion remarkably increases the rate of pentaglycine cleavage. NMR and isothermal titration calorimetry further reveal that, uniquely for its family, LytU is able to bind a second zinc ion which is coordinated by catalytic histidines and is therefore inhibitory. The pH-dependence and high affinity of binding carry further physiological implications.
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Affiliation(s)
- Vytas Raulinaitis
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Olli Aitio
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Jarmo T Juuti
- Antimicrobial Resistance Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland
| | - Keiichi Hiramatsu
- Research Centre for Infection Control Science, Juntendo University, Bunkyo-ku, Tokyo, Japan
| | - Vesa Kontinen
- Antimicrobial Resistance Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland.,Research Centre for Infection Control Science, Juntendo University, Bunkyo-ku, Tokyo, Japan
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland. .,Department of Biological and Environmental Science, and Department of Chemistry, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014, Jyvaskyla, Finland.
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24
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Wu X, Kwon SJ, Kim J, Kane RS, Dordick JS. Biocatalytic Nanocomposites for Combating Bacterial Pathogens. Annu Rev Chem Biomol Eng 2017; 8:87-113. [DOI: 10.1146/annurev-chembioeng-060816-101612] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xia Wu
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ravi S. Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Jonathan S. Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180
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25
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Cao Y, Hao Y, Yang D, Pang B, Wang L. Fluorescent PCR detection of mecA in drug resistant MRSA: a methodological study. Br J Biomed Sci 2017; 74:152-155. [PMID: 28493763 DOI: 10.1080/09674845.2017.1297214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Y Cao
- a Clinical Laboratory , Liaocheng People's Hospital, Taishan Medical University , Shandong , China.,b School of Medicine , Shandong University , Shandong , P.R. China
| | - Y Hao
- a Clinical Laboratory , Liaocheng People's Hospital, Taishan Medical University , Shandong , China
| | - D Yang
- a Clinical Laboratory , Liaocheng People's Hospital, Taishan Medical University , Shandong , China
| | - B Pang
- a Clinical Laboratory , Liaocheng People's Hospital, Taishan Medical University , Shandong , China
| | - L Wang
- c School of Biomedical Sciences , Charles Sturt University , Wagga Wagga , Australia
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26
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Raulinaitis V, Tossavainen H, Aitio O, Seppala R, Permi P. 1H, 13C and 15N resonance assignments of the new lysostaphin family endopeptidase catalytic domain from Staphylococcus aureus. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:69-73. [PMID: 27943001 DOI: 10.1007/s12104-016-9722-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
Lysostaphin family endopeptidases, produced by Staphylococcus genus, are zinc-dependent enzymes that cleave pentaglycine bridges of cell wall peptidoglycan. They act as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Consequently, these enzymes are compelling targets for new drugs as well as are potential antimicrobial agents themselves against Staphylococcus pathogens, which depend on cell wall to retain their immunity against antibiotics. The rapid spread of methicillin and vancomycin-resistant Staphylococcus aureus strains draws demand for new therapeutic approaches. S. aureus gene sa0205 was found to be implicated in resistance to vancomycin and synthesis of the bacteria cell wall. The gene encodes for a catalytic domain of a lysostaphin-type endopeptidase. We aim to obtain the structure of the Sa0205 catalytic domain, the first solution structure of the catalytic domain of the lysostaphin family enzymes. In addition, we are to investigate the apparent binding of the second zinc ion, which has not been previously reported for the enzyme group. Herein, we present the backbone and side chain resonance assignments of Sa0205 endopeptidase catalytic domain in its one and two zinc-bound forms.
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Affiliation(s)
- Vytas Raulinaitis
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland
| | - Olli Aitio
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland
- Glykos Finland Ltd., Viikinkaari 6, 00790, Helsinki, Finland
| | - Raili Seppala
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, 00014, Helsinki, Finland.
- Departments of Biological and Environmental Science and Chemistry, Nanoscience Center, University of Jyvaskyla, 40014, Jyvaskyla, Finland.
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27
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Jagielska E, Chojnacka O, Sabała I. LytM Fusion with SH3b-Like Domain Expands Its Activity to Physiological Conditions. Microb Drug Resist 2016; 22:461-9. [PMID: 27351490 PMCID: PMC5036312 DOI: 10.1089/mdr.2016.0053] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus remains one of the most common and at the same time the most dangerous bacteria. The spreading antibiotic resistance calls for intensification of research on staphylococcal physiology and development of new strategies for combating this threatening pathogen. We have engineered new chimeric enzymes comprising the enzymatically active domain (EAD) of autolysin LytM from S. aureus and the cell wall binding domain (CBD) from bacteriocin lysostaphin. They display potent activity in extended environmental conditions. Our results exemplify the possibility of exploring autolytic enzymes in engineering lysins with desired features. Moreover, they suggest a possible mechanism of autolysin physiological activity regulation by local ionic environments in the cell wall.
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Affiliation(s)
- Elzbieta Jagielska
- International Institute of Molecular and Cell Biology in Warsaw , Warsaw, Poland
| | - Olga Chojnacka
- International Institute of Molecular and Cell Biology in Warsaw , Warsaw, Poland
| | - Izabela Sabała
- International Institute of Molecular and Cell Biology in Warsaw , Warsaw, Poland
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28
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Blazanovic K, Zhao H, Choi Y, Li W, Salvat RS, Osipovitch DC, Fields J, Moise L, Berwin BL, Fiering SN, Bailey-Kellogg C, Griswold KE. Structure-based redesign of lysostaphin yields potent antistaphylococcal enzymes that evade immune cell surveillance. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2015; 2:15021. [PMID: 26151066 PMCID: PMC4470366 DOI: 10.1038/mtm.2015.21] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 12/22/2022]
Abstract
Staphylococcus aureus infections exert a tremendous burden on the health-care system, and the threat of drug-resistant strains continues to grow. The bacteriolytic enzyme lysostaphin is a potent antistaphylococcal agent with proven efficacy against both drug-sensitive and drug-resistant strains; however, the enzyme's own bacterial origins cause undesirable immunogenicity and pose a barrier to clinical translation. Here, we deimmunized lysostaphin using a computationally guided process that optimizes sets of mutations to delete immunogenic T cell epitopes without disrupting protein function. In vitro analyses showed the methods to be both efficient and effective, producing seven different deimmunized designs exhibiting high function and reduced immunogenic potential. Two deimmunized candidates elicited greatly suppressed proliferative responses in splenocytes from humanized mice, while at the same time the variants maintained wild-type efficacy in a staphylococcal pneumonia model. Overall, the deimmunized enzymes represent promising leads in the battle against S. aureus.
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Affiliation(s)
| | - Hongliang Zhao
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA ; Laboratory of Microorganism Engineering, Beijing Institute of Biotechnology , Beijing, People's Republic of China
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth , Hanover, New Hampshire, USA
| | - Wen Li
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA
| | - Regina S Salvat
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA
| | - Daniel C Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth , Hanover, New Hampshire, USA
| | - Jennifer Fields
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA
| | - Leonard Moise
- Institute for Immunology and Informatics, University of Rhode Island , Providence, Rhode Island, USA
| | - Brent L Berwin
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA
| | - Steven N Fiering
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA
| | | | - Karl E Griswold
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA ; Department of Biological Sciences, Dartmouth , Hanover, New Hampshire, USA
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Dostal SM, Fang Y, Guerrette JC, Scanlon TC, Griswold KE. Genetically enhanced lysozyme evades a pathogen derived inhibitory protein. ACS Chem Biol 2015; 10:1110-7. [PMID: 25607237 DOI: 10.1021/cb500976y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The accelerating spread of drug-resistant bacteria is creating demand for novel antibiotics. Bactericidal enzymes, such as human lysozyme (hLYZ), are interesting drug candidates due to their inherent catalytic nature and lack of susceptibility to the resistance mechanisms typically directed toward chemotherapeutics. However, natural antibacterial enzymes have their own limitations. For example, hLYZ is susceptible to pathogen derived inhibitory proteins, such as Escherichia coli Ivy. Here, we describe proof of concept studies demonstrating that hLYZ can be effectively redesigned to evade this potent lysozyme inhibitor. Large combinatorial libraries of hLYZ were analyzed using an innovative screening platform based on microbial coculture in hydrogel microdroplets. Isolated hLYZ variants were orders of magnitude less susceptible to E. coli Ivy yet retained high catalytic proficiency and inherent antibacterial activity. Interestingly, the engineered escape variants showed a disadvantageous increase in susceptibility to the related Ivy ortholog from Pseudomonas aeruginosa as well as an unrelated E. coli inhibitory protein, MliC. Thus, while we have achieved our original objective with respect to escaping E. coli Ivy, engineering hLYZ for broad-spectrum evasion of proteinaceous inhibitors will require consideration of the complex and varied determinants that underlie molecular recognition by these emerging virulence factors.
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Affiliation(s)
- Sarah M. Dostal
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
| | - Yongliang Fang
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
| | - Jonathan C. Guerrette
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
| | - Thomas C. Scanlon
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
| | - Karl E. Griswold
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
- Program in Molecular and Cellular Biology, Dartmouth College, Hanover, New Hampshire 03755, United States
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Osipovitch DC, Therrien S, Griswold KE. Discovery of novel S. aureus autolysins and molecular engineering to enhance bacteriolytic activity. Appl Microbiol Biotechnol 2015; 99:6315-26. [PMID: 25690309 DOI: 10.1007/s00253-015-6443-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/24/2015] [Accepted: 01/26/2015] [Indexed: 01/21/2023]
Abstract
Staphylococcus aureus is a dangerous bacterial pathogen whose clinical impact has been amplified by the emergence and rapid spread of antibiotic resistance. In the search for more effective therapeutic strategies, great effort has been placed on the study and development of staphylolytic enzymes, which benefit from high potency activity toward drug-resistant strains, and a low inherent susceptibility to emergence of new resistance phenotypes. To date, the majority of therapeutic candidates have derived from either bacteriophage or environmental competitors of S. aureus. Little to no consideration has been given to cis-acting autolysins that represent key elements in the bacterium's endogenous cell wall maintenance and recycling machinery. In this study, five putative autolysins were cloned from the S. aureus genome, and their activities were evaluated. Four of these novel enzymes, or component domains thereof, demonstrated lytic activity toward live S. aureus cells, but their potencies were 10s to 1000s of times lower than that of the well-characterized therapeutic candidate lysostaphin. We hypothesized that their poor activities were due in part to suboptimal cell wall targeting associated with their native cell wall binding domains, and we sought to enhance their antibacterial potential via chimeragenesis with the peptidoglycan binding domain of lysostaphin. The most potent chimera exhibited a 140-fold increase in lytic rate, bringing it within 8-fold of lysostaphin. While this enzyme was sensitive to certain biologically relevant environmental factors and failed to exhibit a measurable minimal inhibitory concentration, it was able to kill lysostaphin-resistant S. aureus and ultimately proved active in lung surfactant. We conclude that the S. aureus proteome represents a rich and untapped reservoir of novel antibacterial enzymes, and we demonstrate enhanced bacteriolytic activity via improved cell wall targeting of autolysin catalytic domains.
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Affiliation(s)
- Daniel C Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth College, Hanover, NH, 03755, USA
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